diff --git a/.gitignore b/.gitignore index 548b6fe..5aaa7db 100644 --- a/.gitignore +++ b/.gitignore @@ -23,3 +23,4 @@ simulations izhikevich15jun19 MATLAB/results/*.dat NeuroML2/results/*.dat +*.npy diff --git a/AIBS.ipynb b/AIBS.ipynb new file mode 100644 index 0000000..0aec4c7 --- /dev/null +++ b/AIBS.ipynb @@ -0,0 +1,25145 @@ +{ + "cells": [ + { + "cell_type": "code", + "execution_count": 1, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Using local development versions of packages\n" + ] + } + ], + "source": [ + "try:\n", + " import rickpy\n", + " rickpy.use_dev_packages(['rickpy','scidash/sciunit','scidash/neuronunit','neuroml/pyNeuroML'])\n", + " import imp\n", + " imp.reload(rickpy)\n", + " print(\"Using local development versions of packages\")\n", + "except ImportError:\n", + " print(\"Using packages from system path\")" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "%matplotlib notebook\n", + "import os,sys\n", + "import numpy as np\n", + "import matplotlib.pyplot as plt\n", + "import quantities as pq\n", + "import sciunit\n", + "import neuronunit\n", + "from neuronunit import aibs\n", + "from neuronunit.models.reduced import ReducedModel" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": { + "collapsed": false + }, + "outputs": [], + "source": [ + "# This example is from https://github.com/OpenSourceBrain/IzhikevichModel.\n", + "IZHIKEVICH_PATH = os.path.join('/home/mnt/osb/IzhikevichModel') # Replace this the path to your \n", + " # working copy of \n", + " # github.com/OpenSourceBrain/IzhikevichModel. \n", + "IZHIKEVICH_PATH = os.getcwd()\n", + "LEMS_MODEL_PATH = os.path.join(IZHIKEVICH_PATH,'NeuroML2/LEMS_2007One.xml')" + ] + }, + { + "cell_type": "code", + "execution_count": 6, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "name": "stderr", + "output_type": "stream", + "text": [ + "INFO:allensdk.api.api:Downloading URL: http://api.brain-map.org/api/v2/data/query.json?q=model::Specimen,rma::criteria,[id$eq'354190013'],rma::include,structure,donor(transgenic_lines),specimen_tags,cell_soma_locations,ephys_features,data_sets,neuron_reconstructions,cell_reporter,rma::options[num_rows$eq'all']\n", + "INFO:allensdk.api.api:Downloading URL: http://api.brain-map.org/api/v2/data/query.json?q=model::EphysSweep,rma::criteria,[specimen_id$eq354190013],rma::options[num_rows$eq'all']\n" + ] + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "Getting data values from neuroelectro.org\n", + "http://www.neuroelectro.org/api/1/nes/?nlex=nifext_50&e__name=Input+Resistance\n", + "Getting data values from neuroelectro.org\n", + "http://www.neuroelectro.org/api/1/nes/?nlex=nifext_50&e__name=Membrane+Time+Constant\n", + "Getting data values from neuroelectro.org\n", + "http://www.neuroelectro.org/api/1/nes/?nlex=nifext_50&e__name=Cell+Capacitance\n", + "Getting data values from neuroelectro.org\n", + "http://www.neuroelectro.org/api/1/nes/?nlex=nifext_50&e__name=Resting+membrane+potential\n", + "Getting data values from neuroelectro.org\n", + "http://www.neuroelectro.org/api/1/nes/?nlex=nifext_50&e__name=Spike+Half-Width\n", + "Getting data values from neuroelectro.org\n", + "http://www.neuroelectro.org/api/1/nes/?nlex=nifext_50&e__name=Spike+Amplitude\n", + "Getting data values from neuroelectro.org\n", + "http://www.neuroelectro.org/api/1/nes/?nlex=nifext_50&e__name=Spike+Threshold\n" + ] + } + ], + "source": [ + "import quantities as pq\n", + "from neuronunit import tests as nu_tests, neuroelectro\n", + "neuron = {'nlex_id': 'nifext_50'} # Layer V pyramidal cell\n", + "tests = []\n", + "\n", + "dataset_id = 354190013 # Internal ID that AIBS uses for a particular Scnn1a-Tg2-Cre \n", + " # Primary visual area, layer 5 neuron.\n", + "observation = aibs.get_observation(dataset_id,'rheobase')\n", + "tests += [nu_tests.RheobaseTest(observation=observation)]\n", + " \n", + "test_class_params = [(nu_tests.InputResistanceTest,None),\n", + " (nu_tests.TimeConstantTest,None),\n", + " (nu_tests.CapacitanceTest,None),\n", + " (nu_tests.RestingPotentialTest,None),\n", + " (nu_tests.InjectedCurrentAPWidthTest,None),\n", + " (nu_tests.InjectedCurrentAPAmplitudeTest,None),\n", + " (nu_tests.InjectedCurrentAPThresholdTest,None)]\n", + "\n", + "for cls,params in test_class_params:\n", + " observation = cls.neuroelectro_summary_observation(neuron)\n", + " tests += [cls(observation,params=params)]\n", + " \n", + "def update_amplitude(test,tests,score):\n", + " rheobase = score.prediction['value']\n", + " for i in [5,6,7]:\n", + " print(tests[i])\n", + " # Set current injection to just suprathreshold\n", + " tests[i].params['injected_square_current']['amplitude'] = rheobase*1.01 \n", + " \n", + "hooks = {tests[0]:{'f':update_amplitude}}\n", + "suite = sciunit.TestSuite(\"vm_suite\",tests,hooks=hooks)" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/html": [ + "Executing test RheobaseTest on model vanilla... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.815835 seconds (0.013597 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.652456 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 0.0 pA current and got 0 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:13:54 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (November 30, 2016 10:01:28 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.829494 seconds (0.013825 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.651127 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 260.0 pA current and got 47 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:04 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:13:54 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.833404 seconds (0.013890 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.680917 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 130.0 pA current and got 20 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:09 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:05 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.848445 seconds (0.014141 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.674069 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 65.0 pA current and got 6 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:14 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:10 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.816149 seconds (0.013602 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.720760 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 32.5 pA current and got 0 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:19 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:15 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.805721 seconds (0.013429 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.604095 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 48.75 pA current and got 0 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:24 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:20 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.814585 seconds (0.013576 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.599450 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 56.875 pA current and got 3 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:29 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:25 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.816873 seconds (0.013615 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.639743 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 52.8125 pA current and got 1 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:34 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:30 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.826332 seconds (0.013772 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.610910 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 50.78125 pA current and got 0 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:39 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:34 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.830969 seconds (0.013849 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.617808 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 51.796875 pA current and got 1 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:44 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:40 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.820571 seconds (0.013676 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.739909 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 51.2890625 pA current and got 0 spikes\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:14:56 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:44 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.809306 seconds (0.013488 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.716303 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "Injected 51.54296875 pA current and got 0 spikes\n", + "Highest subthreshold current is 51.54 pA\n", + "Lowest suprathreshold current is 51.8 pA\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.818744 seconds (0.013646 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.681394 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Ratio = 0.40\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "InjectedCurrentAPWidthTest\n", + "InjectedCurrentAPAmplitudeTest\n", + "InjectedCurrentAPThresholdTest\n" + ] + }, + { + "data": { + "text/html": [ + "Executing test InputResistanceTest on model vanilla... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:15:17 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:14:56 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.806645 seconds (0.013444 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.585301 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.807863 seconds (0.013464 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.605871 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.53\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test TimeConstantTest on model vanilla... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.831683 seconds (0.013861 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.599699 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.836295 seconds (0.013938 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.583224 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.28\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test CapacitanceTest on model vanilla... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.828940 seconds (0.013816 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 2.621487 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.802957 seconds (0.013383 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.628311 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.52\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RestingPotentialTest on model vanilla... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:15:53 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:15:18 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.806557 seconds (0.013443 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.623433 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.807593 seconds (0.013460 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.588382 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 1.26\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPWidthTest on model vanilla... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 9:16:03 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:15:54 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.816175 seconds (0.013603 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.631770 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "[ 351.] 1 1\n", + "[ 0.0008775] s 2.5e-06 s [ 2.19375000e-09] s**2\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.824206 seconds (0.013737 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.602030 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.62\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPAmplitudeTest on model vanilla... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.831461 seconds (0.013858 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 2.781849 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.821558 seconds (0.013693 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.678545 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -1.72\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPThresholdTest on model vanilla... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.814804 seconds (0.013580 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.737844 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/vanilla.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/vanilla.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/vanilla_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.817045 seconds (0.013617 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.698220 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 2.39\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
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RheobaseTestInputResistanceTestTimeConstantTestCapacitanceTestRestingPotentialTestInjectedCurrentAPWidthTestInjectedCurrentAPAmplitudeTestInjectedCurrentAPThresholdTest
vanillaRatio = 0.40Z = -0.53Z = 0.28Z = 0.52Z = 1.26Z = -0.62Z = -1.72Z = 2.39
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" + ], + "text/plain": [ + " RheobaseTest InputResistanceTest TimeConstantTest CapacitanceTest \\\n", + "vanilla Ratio = 0.40 Z = -0.53 Z = 0.28 Z = 0.52 \n", + "\n", + " RestingPotentialTest InjectedCurrentAPWidthTest \\\n", + "vanilla Z = 1.26 Z = -0.62 \n", + "\n", + " InjectedCurrentAPAmplitudeTest InjectedCurrentAPThresholdTest \n", + "vanilla Z = -1.72 Z = 2.39 " + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "model = ReducedModel(LEMS_MODEL_PATH,name='vanilla')\n", + "suite.judge(model)" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "text/html": [ + "Executing test RheobaseTest on model V_rest=-75mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod (December 1, 2016 10:34:30 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:16:04 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:34:30 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 9:16:04 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS.mod into RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS.lo `test -f 'RS.c' || echo '/'`RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS.c -fPIC -DPIC -o .libs/RS.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.830420 seconds (0.013840 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.807503 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:34:35 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:34:31 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.826532 seconds (0.013776 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.689491 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:34:41 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:34:36 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.856759 seconds (0.014279 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 2.283657 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:34:47 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:34:41 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.912406 seconds (0.015207 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.642350 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:34:52 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:34:47 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.832590 seconds (0.013876 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.674462 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:34:57 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:34:52 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.824593 seconds (0.013743 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.681657 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:35:02 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:34:57 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.835752 seconds (0.013929 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.654219 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:35:07 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:35:03 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.871634 seconds (0.014527 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.662799 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:35:12 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:35:08 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.856167 seconds (0.014269 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.631095 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:35:17 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:35:13 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.831826 seconds (0.013864 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.623146 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:35:22 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:35:18 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.811821 seconds (0.013530 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.632580 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:35:27 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:35:23 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.839355 seconds (0.013989 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.651592 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.821613 seconds (0.013694 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.619508 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Ratio = 1.39\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "InjectedCurrentAPWidthTest\n", + "InjectedCurrentAPAmplitudeTest\n", + "InjectedCurrentAPThresholdTest\n" + ] + }, + { + "data": { + "text/html": [ + "Executing test InputResistanceTest on model V_rest=-75mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:35:37 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:35:28 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.827760 seconds (0.013796 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.749963 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.852457 seconds (0.014208 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.648277 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.96\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test TimeConstantTest on model V_rest=-75mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.840547 seconds (0.014009 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.607325 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.837133 seconds (0.013952 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.698658 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.23\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test CapacitanceTest on model V_rest=-75mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.841652 seconds (0.014028 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.675763 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.825156 seconds (0.013753 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.638637 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 1.12\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RestingPotentialTest on model V_rest=-75mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:36:14 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:35:37 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.802727 seconds (0.013379 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.670581 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.850641 seconds (0.014177 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.703752 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -1.03\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPWidthTest on model V_rest=-75mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:36:23 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:36:14 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.802277 seconds (0.013371 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.640827 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "[ 323. 323.] 2 2\n", + "[ 0.0008075 0.0008075] s 2.5e-06 s [ 2.01875000e-09 2.01875000e-09] s**2\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.833167 seconds (0.013886 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.694358 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.75\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPAmplitudeTest on model V_rest=-75mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.857885 seconds (0.014298 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.758094 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.849485 seconds (0.014158 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.714686 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -1.32\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPThresholdTest on model V_rest=-75mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.817941 seconds (0.013632 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.651649 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-75mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-75mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-75mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.853300 seconds (0.014222 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.639774 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 1.76\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RheobaseTest on model V_rest=-70mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod (December 1, 2016 10:36:52 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:36:24 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:36:52 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:36:24 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS.mod into RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS.lo `test -f 'RS.c' || echo '/'`RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS.c -fPIC -DPIC -o .libs/RS.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.825665 seconds (0.013761 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.711815 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:36:58 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:36:53 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.855141 seconds (0.014252 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.704188 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:03 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:36:58 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.841260 seconds (0.014021 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.691741 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:11 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:03 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.847926 seconds (0.014132 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.642158 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:20 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:11 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.829885 seconds (0.013831 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.645271 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:25 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:20 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.836843 seconds (0.013947 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.735789 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:30 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:25 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.848311 seconds (0.014139 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.686793 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:35 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:30 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.831372 seconds (0.013856 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.637850 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:40 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:35 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.818120 seconds (0.013635 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.663571 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:45 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:40 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.834008 seconds (0.013900 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.695783 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:50 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:46 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.828431 seconds (0.013807 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.681819 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:37:55 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:51 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.854970 seconds (0.014249 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.689457 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.837839 seconds (0.013964 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.696857 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Ratio = 1.00\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "InjectedCurrentAPWidthTest\n", + "InjectedCurrentAPAmplitudeTest\n", + "InjectedCurrentAPThresholdTest\n" + ] + }, + { + "data": { + "text/html": [ + "Executing test InputResistanceTest on model V_rest=-70mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:38:05 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:37:56 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.820561 seconds (0.013676 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.685264 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.834400 seconds (0.013907 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.659900 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.87\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test TimeConstantTest on model V_rest=-70mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.828446 seconds (0.013807 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.593597 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.833736 seconds (0.013896 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.620918 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.12\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test CapacitanceTest on model V_rest=-70mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.832720 seconds (0.013879 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.673250 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.827284 seconds (0.013788 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.697271 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.92\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RestingPotentialTest on model V_rest=-70mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:38:35 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:38:06 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.836915 seconds (0.013949 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.683078 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.846938 seconds (0.014116 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.694792 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.27\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPWidthTest on model V_rest=-70mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:38:46 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:38:36 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.857248 seconds (0.014287 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.722089 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "[ 332. 331.] 2 2\n", + "[ 0.00083 0.0008275] s 2.5e-06 s [ 2.07500000e-09 2.06875000e-09] s**2\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.831581 seconds (0.013860 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.688497 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.71\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPAmplitudeTest on model V_rest=-70mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.805691 seconds (0.013428 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.674314 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.829219 seconds (0.013820 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.706300 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -1.45\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPThresholdTest on model V_rest=-70mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.817915 seconds (0.013632 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.717960 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-70mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-70mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-70mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.829280 seconds (0.013821 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.622028 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 1.97\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RheobaseTest on model V_rest=-65mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod (December 1, 2016 10:39:14 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:38:46 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:39:14 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:38:46 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS.mod into RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS.lo `test -f 'RS.c' || echo '/'`RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS.c -fPIC -DPIC -o .libs/RS.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.806455 seconds (0.013441 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.615551 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:39:20 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:39:15 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.827321 seconds (0.013789 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.668851 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:39:25 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:39:20 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.853523 seconds (0.014225 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.680095 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:39:30 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:39:25 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.851808 seconds (0.014197 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.699681 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:39:35 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:39:31 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.860448 seconds (0.014341 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.682627 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:39:40 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:39:36 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.871588 seconds (0.014526 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.732547 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:39:46 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:39:41 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.822241 seconds (0.013704 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.727622 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:39:51 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:39:46 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.856076 seconds (0.014268 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.713542 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:39:56 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:39:51 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.812593 seconds (0.013543 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.698343 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:40:06 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:39:56 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.842837 seconds (0.014047 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.725142 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:40:18 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:40:07 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.818645 seconds (0.013644 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.685185 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:40:25 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:40:19 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.809114 seconds (0.013485 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.603905 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.809953 seconds (0.013499 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.616636 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Ratio = 0.66\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "InjectedCurrentAPWidthTest\n", + "InjectedCurrentAPAmplitudeTest\n", + "InjectedCurrentAPThresholdTest\n" + ] + }, + { + "data": { + "text/html": [ + "Executing test InputResistanceTest on model V_rest=-65mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:40:42 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:40:26 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.822090 seconds (0.013702 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.579540 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.809182 seconds (0.013486 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.618213 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.73\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test TimeConstantTest on model V_rest=-65mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.811552 seconds (0.013526 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 2.875657 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.838886 seconds (0.013981 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.626163 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.04\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test CapacitanceTest on model V_rest=-65mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.821473 seconds (0.013691 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.619010 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.823447 seconds (0.013724 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.660545 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.71\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RestingPotentialTest on model V_rest=-65mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:41:18 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:40:43 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.869039 seconds (0.014484 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.709637 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.852673 seconds (0.014211 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.716362 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.50\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPWidthTest on model V_rest=-65mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:41:28 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:41:18 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.838848 seconds (0.013981 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.736824 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "[ 341.] 1 1\n", + "[ 0.0008525] s 2.5e-06 s [ 2.13125000e-09] s**2\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.821839 seconds (0.013697 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.738500 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.66\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPAmplitudeTest on model V_rest=-65mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.805333 seconds (0.013422 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.756842 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.814727 seconds (0.013579 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.715076 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -1.58\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPThresholdTest on model V_rest=-65mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.810484 seconds (0.013508 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.641320 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-65mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-65mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-65mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.826176 seconds (0.013770 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.692129 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 2.18\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RheobaseTest on model V_rest=-60mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod (December 1, 2016 10:41:57 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:41:29 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:41:57 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:41:29 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS.mod into RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS.lo `test -f 'RS.c' || echo '/'`RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS.c -fPIC -DPIC -o .libs/RS.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.835998 seconds (0.013933 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.621297 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:03 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:41:58 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.820548 seconds (0.013676 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.712287 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:08 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:03 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.813412 seconds (0.013557 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.680584 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:13 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:08 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.800723 seconds (0.013345 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.610324 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:18 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:13 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.817076 seconds (0.013618 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.645832 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:23 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:18 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.842912 seconds (0.014049 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.674533 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:28 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:23 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.824463 seconds (0.013741 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.688573 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:33 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:29 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.873182 seconds (0.014553 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.671777 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:38 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:34 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.836247 seconds (0.013937 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.613989 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:43 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:39 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.847800 seconds (0.014130 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.660125 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:49 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:44 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.830581 seconds (0.013843 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.672943 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:42:54 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:49 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.820478 seconds (0.013675 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.622213 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.857759 seconds (0.014296 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.633386 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Ratio = 0.40\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "InjectedCurrentAPWidthTest\n", + "InjectedCurrentAPAmplitudeTest\n", + "InjectedCurrentAPThresholdTest\n" + ] + }, + { + "data": { + "text/html": [ + "Executing test InputResistanceTest on model V_rest=-60mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:43:04 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:42:54 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.820540 seconds (0.013676 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.658497 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.850864 seconds (0.014181 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.642825 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.53\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test TimeConstantTest on model V_rest=-60mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.848254 seconds (0.014138 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.657357 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.942525 seconds (0.015709 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.741913 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.28\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test CapacitanceTest on model V_rest=-60mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.856143 seconds (0.014269 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.710412 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.887938 seconds (0.014799 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.842880 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.52\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RestingPotentialTest on model V_rest=-60mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:43:35 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:43:04 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.806259 seconds (0.013438 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.721348 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.825805 seconds (0.013763 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.695508 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 1.26\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPWidthTest on model V_rest=-60mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:43:45 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:43:35 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.838105 seconds (0.013968 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.698000 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "[ 351.] 1 1\n", + "[ 0.0008775] s 2.5e-06 s [ 2.19375000e-09] s**2\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.852700 seconds (0.014212 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.674652 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.62\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPAmplitudeTest on model V_rest=-60mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.841347 seconds (0.014022 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.666860 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.846842 seconds (0.014114 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.712051 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -1.72\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPThresholdTest on model V_rest=-60mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.839206 seconds (0.013987 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.717056 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-60mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-60mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-60mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.816417 seconds (0.013607 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 2.050834 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 2.39\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RheobaseTest on model V_rest=-55mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod (December 1, 2016 10:44:14 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:43:45 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:44:14 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:43:45 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS.mod into RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS.lo `test -f 'RS.c' || echo '/'`RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS.c -fPIC -DPIC -o .libs/RS.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.812988 seconds (0.013550 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.662666 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:44:19 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:44:15 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.836336 seconds (0.013939 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 4.217875 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:44:27 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:44:20 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.797172 seconds (0.013286 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.647515 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:44:32 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:44:28 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.831473 seconds (0.013858 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.676419 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:44:38 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:44:33 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.821317 seconds (0.013689 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.597482 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:44:42 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:44:38 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.937090 seconds (0.015618 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.640515 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:44:48 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:44:43 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.819905 seconds (0.013665 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.636467 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:44:53 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:44:48 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.835755 seconds (0.013929 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.659061 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:44:58 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:44:53 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.809030 seconds (0.013484 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.640133 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:45:03 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:44:58 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.833218 seconds (0.013887 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.643763 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:45:08 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:45:03 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.819459 seconds (0.013658 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.635326 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:45:13 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:45:08 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.847224 seconds (0.014120 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.660111 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.831771 seconds (0.013863 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.616762 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Ratio = 0.20\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "InjectedCurrentAPWidthTest\n", + "InjectedCurrentAPAmplitudeTest\n", + "InjectedCurrentAPThresholdTest\n" + ] + }, + { + "data": { + "text/html": [ + "Executing test InputResistanceTest on model V_rest=-55mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:45:28 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:45:14 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.825562 seconds (0.013759 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.600795 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.859236 seconds (0.014321 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.692856 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.21\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test TimeConstantTest on model V_rest=-55mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.852697 seconds (0.014212 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.619453 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.827561 seconds (0.013793 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.672300 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.69\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test CapacitanceTest on model V_rest=-55mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.837206 seconds (0.013953 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.619719 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.830197 seconds (0.013837 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.631517 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.35\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RestingPotentialTest on model V_rest=-55mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:45:58 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:45:28 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.848245 seconds (0.014137 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.649017 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.833565 seconds (0.013893 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.582515 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 2.03\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPWidthTest on model V_rest=-55mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:46:07 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:45:58 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.877148 seconds (0.014619 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.779695 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "[ 361.] 1 1\n", + "[ 0.0009025] s 2.5e-06 s [ 2.25625000e-09] s**2\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.829924 seconds (0.013832 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.739138 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.57\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPAmplitudeTest on model V_rest=-55mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.850386 seconds (0.014173 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.818804 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.816065 seconds (0.013601 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.718221 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -1.85\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPThresholdTest on model V_rest=-55mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.825108 seconds (0.013752 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.673377 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-55mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-55mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-55mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.820695 seconds (0.013678 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.615632 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 2.61\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RheobaseTest on model V_rest=-50mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod (December 1, 2016 10:46:37 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:46:08 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:46:37 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:46:08 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS.mod into RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS.lo `test -f 'RS.c' || echo '/'`RS.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS.c -fPIC -DPIC -o .libs/RS.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.839783 seconds (0.013996 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.619435 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:46:42 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:46:37 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.831006 seconds (0.013850 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 4.327914 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:46:50 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:46:43 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.809170 seconds (0.013486 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.591583 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:46:55 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:46:50 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.807806 seconds (0.013463 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.606167 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:47:00 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:46:55 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.828831 seconds (0.013814 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.690646 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:47:06 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:47:01 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.802681 seconds (0.013378 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.594066 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:47:11 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:47:06 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.836120 seconds (0.013935 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.647394 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:47:16 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:47:11 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.824937 seconds (0.013749 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.605680 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:47:21 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:47:16 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.849820 seconds (0.014164 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.632060 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:47:26 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:47:21 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.840709 seconds (0.014012 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.649805 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:47:31 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:47:26 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.815111 seconds (0.013585 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.681899 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:47:36 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:47:31 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.816086 seconds (0.013601 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.611383 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.821496 seconds (0.013692 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.612829 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Ratio = 0.07\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "InjectedCurrentAPWidthTest\n", + "InjectedCurrentAPAmplitudeTest\n", + "InjectedCurrentAPThresholdTest\n" + ] + }, + { + "data": { + "text/html": [ + "Executing test InputResistanceTest on model V_rest=-50mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:47:46 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:47:36 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.837723 seconds (0.013962 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.811383 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.809163 seconds (0.013486 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.742558 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.29\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test TimeConstantTest on model V_rest=-50mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.908080 seconds (0.015135 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.777480 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.892702 seconds (0.014878 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.755115 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 1.42\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test CapacitanceTest on model V_rest=-50mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.833021 seconds (0.013884 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.672933 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.837605 seconds (0.013960 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.659185 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 0.23\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test RestingPotentialTest on model V_rest=-50mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:48:17 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:47:46 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.855068 seconds (0.014251 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.627197 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.895723 seconds (0.014929 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.628869 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 2.79\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPWidthTest on model V_rest=-50mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists but is different\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod (December 1, 2016 10:48:27 PM UTC) was modified later than /tmp/x86_64/libnrnmech.la (December 1, 2016 10:48:17 PM UTC)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Newer mod files exist!\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to delete any previous: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Deleted.\n", + "pyNeuroML >>> jNeuroML >> (INFO) directoryToExecuteIn: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/x86_64/bin/nocmodl\" RS_Iext\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Translating RS_Iext.mod into RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Error >> > Thread Safe\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o RS_Iext.lo `test -f 'RS_Iext.c' || echo '/'`RS_Iext.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c RS_Iext.c -fPIC -DPIC -o .libs/RS_Iext.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=compile gcc -DHAVE_CONFIG_H -I. -I.. -I\"/home/jovyan/nrn-7.4/include/nrn\" -I\"/home/jovyan/nrn-7.4/x86_64/lib\" -g -O2 -c -o mod_func.lo mod_func.c\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: compile: gcc -DHAVE_CONFIG_H -I. -I.. -I/home/jovyan/nrn-7.4/include/nrn -I/home/jovyan/nrn-7.4/x86_64/lib -g -O2 -c mod_func.c -fPIC -DPIC -o .libs/mod_func.o\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > \"/home/jovyan/nrn-7.4/share/nrn/libtool\" --mode=link gcc -module -g -O2 -o libnrnmech.la -rpath \"/home/jovyan/nrn-7.4/x86_64/lib\" RS.lo RS_Iext.lo mod_func.lo -L\"/home/jovyan/nrn-7.4/x86_64/lib\" -lnrnoc -loc -lmemacs -lnrnmpi -lscopmath -lsparse13 -lreadline -lncurses -L\"/home/jovyan/nrn-7.4/x86_64/lib\" \"/home/jovyan/nrn-7.4/x86_64/lib/libnrniv.la\" -livoc -lneuron_gnu -lmeschach -lsundials -livos -lm -ldl\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: rm -fr .libs/libnrnmech.la .libs/libnrnmech.lai .libs/libnrnmech.so .libs/libnrnmech.so.0 .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: gcc -shared -fPIC -DPIC .libs/RS.o .libs/RS_Iext.o .libs/mod_func.o -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -Wl,-rpath -Wl,/home/jovyan/nrn-7.4/x86_64/lib -L/home/jovyan/nrn-7.4/x86_64/lib /home/jovyan/nrn-7.4/x86_64/lib/libnrnoc.so /home/jovyan/nrn-7.4/x86_64/lib/liboc.so /home/jovyan/nrn-7.4/x86_64/lib/libmemacs.so /home/jovyan/nrn-7.4/x86_64/lib/libnrnmpi.so /home/jovyan/nrn-7.4/x86_64/lib/libscopmath.so /home/jovyan/nrn-7.4/x86_64/lib/libsparse13.so -lreadline -lncurses /home/jovyan/nrn-7.4/x86_64/lib/libnrniv.so /home/jovyan/nrn-7.4/x86_64/lib/libivoc.so /home/jovyan/nrn-7.4/x86_64/lib/libneuron_gnu.so /home/jovyan/nrn-7.4/x86_64/lib/libmeschach.so /home/jovyan/nrn-7.4/x86_64/lib/libsundials.so /home/jovyan/nrn-7.4/x86_64/lib/libivos.so -lm -ldl -O2 -pthread -Wl,-soname -Wl,libnrnmech.so.0 -o .libs/libnrnmech.so.0.0.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so.0\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so.0\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: (cd \".libs\" && rm -f \"libnrnmech.so\" && ln -s \"libnrnmech.so.0.0.0\" \"libnrnmech.so\")\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > libtool: link: ( cd \".libs\" && rm -f \"libnrnmech.la\" && ln -s \"../libnrnmech.la\" \"libnrnmech.la\" )\n", + "pyNeuroML >>> jNeuroML >> (INFO) NMODL Compile >> > Successfully created x86_64/special\n", + "pyNeuroML >>> jNeuroML >> (INFO) Successful compilation\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.801193 seconds (0.013353 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.695358 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "[ 373.] 1 1\n", + "[ 0.0009325] s 2.5e-06 s [ 2.33125000e-09] s**2\n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.888337 seconds (0.014806 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.677613 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -0.52\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPAmplitudeTest on model V_rest=-50mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.830848 seconds (0.013847 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 2.390985 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.840153 seconds (0.014003 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.755049 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = -1.99\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "Executing test InjectedCurrentAPThresholdTest on model V_rest=-50mV... " + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "name": "stdout", + "output_type": "stream", + "text": [ + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.839212 seconds (0.013987 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.649035 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n", + "pyNeuroML >>> Executing: (java -Xmx400M -Djava.awt.headless=true -jar \"/opt/conda/lib/python3.5/site-packages/pyneuroml/lib/jNeuroML-0.8.0-jar-with-dependencies.jar\" \"/tmp/V_rest=-50mV.xml\" -neuron -run -nogui) in directory: .\n", + "pyNeuroML >>> Command completed. Output: \n", + "pyNeuroML >>> jNeuroML >> jNeuroML v0.8.0\n", + "pyNeuroML >>> jNeuroML >> (INFO) Reading from: /tmp/V_rest=-50mV.xml\n", + "pyNeuroML >>> jNeuroML >> (INFO) Creating NeuronWriter for V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding simulation Component(id=sim1 type=Simulation) of network/component: net1 (Type: network)\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding population: RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Adding projections/connections...\n", + "pyNeuroML >>> jNeuroML >> (INFO) -- Writing to mod: /tmp/RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) File /tmp/RS_Iext.mod exists and is identical\n", + "pyNeuroML >>> jNeuroML >> (INFO) Trying to compile mods in: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to compile the mod files in: /tmp, forcing recompile: false\n", + "pyNeuroML >>> jNeuroML >> (INFO) Parent dir: /tmp\n", + "pyNeuroML >>> jNeuroML >> (INFO) Assuming *nix environment...\n", + "pyNeuroML >>> jNeuroML >> (INFO) Name of file to be created: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Backup file to check for success: /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) commandToExecute: /home/jovyan/nrn-7.4/x86_64/bin/nrnivmodl\n", + "pyNeuroML >>> jNeuroML >> (INFO) Going to check if mods in /tmp are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Not being asked to recompile, and no mod files exist in /tmp which are newer than /tmp/x86_64/libnrnmech.la\n", + "pyNeuroML >>> jNeuroML >> (INFO) Success: true\n", + "pyNeuroML >>> jNeuroML >> (INFO) Have successfully executed command: /home/jovyan/nrn-7.4/x86_64/bin/nrniv -python /tmp/V_rest=-50mV_nrn.py\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> NEURON -- Release 7.4 (1370:16a7055d4a86) 2015-11-09\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Duke, Yale, and the BlueBrain Project -- Copyright 1984-2015\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> See http://www.neuron.yale.edu/neuron/credits\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> Additional mechanisms from files\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Error >>> RS.mod RS_Iext.mod\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Starting simulation in NEURON generated from NeuroML2 model...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> \n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Population RS_pop contains 1 instance(s) of component: RS of type: izhikevich2007Cell\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Running a simulation of 1600.0ms (dt = 0.0025ms)\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished NEURON simulation in 0.833867 seconds (0.013898 mins)...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saving results at t=1600.0000000291218...\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: time.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Saved data to: RS_One.dat\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Finished saving results in 1.638675 seconds\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> Done\n", + "pyNeuroML >>> jNeuroML >> (INFO) NRN Output >>> first instance of n_RS_pop\n", + "pyNeuroML >>> jNeuroML >> (INFO) Exit value for running NEURON: 0\n", + "pyNeuroML >>> jNeuroML >> \n" + ] + }, + { + "data": { + "text/html": [ + "Score is Z = 2.82\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "application/javascript": [ + "$(\"head\").append($(\"\").attr({\n", + " rel: \"stylesheet\",\n", + " type: \"text/css\",\n", + " href: \"//ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.0/css/jquery.dataTables.css\"\n", + "}));\n", + "$.getScript(\"//ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.0/jquery.dataTables.min.js\", function () {\n", + "$('#4951085247241278928').dataTable();});\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "
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MeanRheobaseTestInputResistanceTestTimeConstantTestCapacitanceTestRestingPotentialTestInjectedCurrentAPWidthTestInjectedCurrentAPAmplitudeTestInjectedCurrentAPThresholdTest
V_rest=-75mV0.412Ratio = 1.39Z = -0.96Z = -0.23Z = 1.12Z = -1.03Z = -0.75Z = -1.32Z = 1.76
V_rest=-70mV0.514Ratio = 1.00Z = -0.87Z = -0.12Z = 0.92Z = -0.27Z = -0.71Z = -1.45Z = 1.97
V_rest=-65mV0.500Ratio = 0.66Z = -0.73Z = 0.04Z = 0.71Z = 0.50Z = -0.66Z = -1.58Z = 2.18
V_rest=-60mV0.427Ratio = 0.40Z = -0.53Z = 0.28Z = 0.52Z = 1.26Z = -0.62Z = -1.72Z = 2.39
V_rest=-55mV0.379Ratio = 0.20Z = -0.21Z = 0.69Z = 0.35Z = 2.03Z = -0.57Z = -1.85Z = 2.61
V_rest=-50mV0.301Ratio = 0.07Z = 0.29Z = 1.42Z = 0.23Z = 2.79Z = -0.52Z = -1.99Z = 2.82
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" + ], + "text/plain": [ + " RheobaseTest InputResistanceTest TimeConstantTest \\\n", + "V_rest=-75mV Ratio = 1.39 Z = -0.96 Z = -0.23 \n", + "V_rest=-70mV Ratio = 1.00 Z = -0.87 Z = -0.12 \n", + "V_rest=-65mV Ratio = 0.66 Z = -0.73 Z = 0.04 \n", + "V_rest=-60mV Ratio = 0.40 Z = -0.53 Z = 0.28 \n", + "V_rest=-55mV Ratio = 0.20 Z = -0.21 Z = 0.69 \n", + "V_rest=-50mV Ratio = 0.07 Z = 0.29 Z = 1.42 \n", + "\n", + " CapacitanceTest RestingPotentialTest InjectedCurrentAPWidthTest \\\n", + "V_rest=-75mV Z = 1.12 Z = -1.03 Z = -0.75 \n", + "V_rest=-70mV Z = 0.92 Z = -0.27 Z = -0.71 \n", + "V_rest=-65mV Z = 0.71 Z = 0.50 Z = -0.66 \n", + "V_rest=-60mV Z = 0.52 Z = 1.26 Z = -0.62 \n", + "V_rest=-55mV Z = 0.35 Z = 2.03 Z = -0.57 \n", + "V_rest=-50mV Z = 0.23 Z = 2.79 Z = -0.52 \n", + "\n", + " InjectedCurrentAPAmplitudeTest InjectedCurrentAPThresholdTest \n", + "V_rest=-75mV Z = -1.32 Z = 1.76 \n", + "V_rest=-70mV Z = -1.45 Z = 1.97 \n", + "V_rest=-65mV Z = -1.58 Z = 2.18 \n", + "V_rest=-60mV Z = -1.72 Z = 2.39 \n", + "V_rest=-55mV Z = -1.85 Z = 2.61 \n", + "V_rest=-50mV Z = -1.99 Z = 2.82 " + ] + }, + "execution_count": 8, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "models = []\n", + "for vr in np.linspace(-75,-50,6):\n", + " model = ReducedModel(LEMS_MODEL_PATH, \n", + " name='V_rest=%dmV' % vr, \n", + " attrs={'//izhikevich2007Cell':\n", + " {'vr':'%d mV' % vr}\n", + " })\n", + " #model.skip_run = True\n", + " models.append(model)\n", + "suite.set_verbose(False) # Turn off most print statements. \n", + "score_matrix = suite.judge(models)\n", + "score_matrix.show_mean = True\n", + "score_matrix.sortable = True\n", + "score_matrix" + ] + }, + { + "cell_type": "code", + "execution_count": 9, + "metadata": { + "collapsed": false + }, + "outputs": [ + { + "data": { + "application/javascript": [ + "$(\"head\").append($(\"\").attr({\n", + " rel: \"stylesheet\",\n", + " type: \"text/css\",\n", + " href: \"//ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.0/css/jquery.dataTables.css\"\n", + "}));\n", + "$.getScript(\"//ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.0/jquery.dataTables.min.js\", function () {\n", + "$('#8177426948237355811').dataTable();});\n" + ], + "text/plain": [ + "" + ] + }, + "metadata": {}, + "output_type": "display_data" + }, + { + "data": { + "text/html": [ + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "\n", + "
MeanRheobaseTestInputResistanceTestTimeConstantTestCapacitanceTestRestingPotentialTestInjectedCurrentAPWidthTestInjectedCurrentAPAmplitudeTestInjectedCurrentAPThresholdTest
V_rest=-75mV0.412Ratio = 1.39Z = -0.96Z = -0.23Z = 1.12Z = -1.03Z = -0.75Z = -1.32Z = 1.76
V_rest=-70mV0.514Ratio = 1.00Z = -0.87Z = -0.12Z = 0.92Z = -0.27Z = -0.71Z = -1.45Z = 1.97
V_rest=-65mV0.500Ratio = 0.66Z = -0.73Z = 0.04Z = 0.71Z = 0.50Z = -0.66Z = -1.58Z = 2.18
V_rest=-60mV0.427Ratio = 0.40Z = -0.53Z = 0.28Z = 0.52Z = 1.26Z = -0.62Z = -1.72Z = 2.39
V_rest=-55mV0.379Ratio = 0.20Z = -0.21Z = 0.69Z = 0.35Z = 2.03Z = -0.57Z = -1.85Z = 2.61
V_rest=-50mV0.301Ratio = 0.07Z = 0.29Z = 1.42Z = 0.23Z = 2.79Z = -0.52Z = -1.99Z = 2.82
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');\n", + " var titletext = $(\n", + " '
');\n", + " titlebar.append(titletext)\n", + " this.root.append(titlebar);\n", + " this.header = titletext[0];\n", + "}\n", + "\n", + "\n", + "\n", + "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "\n", + "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", + "\n", + "}\n", + "\n", + "mpl.figure.prototype._init_canvas = function() {\n", + " var fig = this;\n", + "\n", + " var canvas_div = $('
');\n", + "\n", + " canvas_div.attr('style', 'position: relative; clear: both; outline: 0');\n", + "\n", + " function canvas_keyboard_event(event) {\n", + " return fig.key_event(event, event['data']);\n", + " }\n", + "\n", + " canvas_div.keydown('key_press', canvas_keyboard_event);\n", + " canvas_div.keyup('key_release', canvas_keyboard_event);\n", + " this.canvas_div = canvas_div\n", + " this._canvas_extra_style(canvas_div)\n", + " this.root.append(canvas_div);\n", + "\n", + " var canvas = $('');\n", + " canvas.addClass('mpl-canvas');\n", + " canvas.attr('style', \"left: 0; top: 0; z-index: 0; outline: 0\")\n", + "\n", + " this.canvas = canvas[0];\n", + " this.context = canvas[0].getContext(\"2d\");\n", + "\n", + " var rubberband = $('');\n", + " rubberband.attr('style', \"position: absolute; left: 0; top: 0; z-index: 1;\")\n", + "\n", + " var pass_mouse_events = true;\n", + "\n", + " canvas_div.resizable({\n", + " start: function(event, ui) {\n", + " pass_mouse_events = false;\n", + " },\n", + " resize: function(event, ui) {\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " stop: function(event, ui) {\n", + " pass_mouse_events = true;\n", + " fig.request_resize(ui.size.width, ui.size.height);\n", + " },\n", + " });\n", + "\n", + " function mouse_event_fn(event) {\n", + " if (pass_mouse_events)\n", + " return fig.mouse_event(event, event['data']);\n", + " }\n", + "\n", + " rubberband.mousedown('button_press', mouse_event_fn);\n", + " rubberband.mouseup('button_release', mouse_event_fn);\n", + " // Throttle sequential mouse events to 1 every 20ms.\n", + " rubberband.mousemove('motion_notify', mouse_event_fn);\n", + "\n", + " rubberband.mouseenter('figure_enter', mouse_event_fn);\n", + " rubberband.mouseleave('figure_leave', mouse_event_fn);\n", + "\n", + " canvas_div.on(\"wheel\", function (event) {\n", + " event = event.originalEvent;\n", + " event['data'] = 'scroll'\n", + " if (event.deltaY < 0) {\n", + " event.step = 1;\n", + " } else {\n", + " event.step = -1;\n", + " }\n", + " mouse_event_fn(event);\n", + " });\n", + "\n", + " canvas_div.append(canvas);\n", + " canvas_div.append(rubberband);\n", + "\n", + " this.rubberband = rubberband;\n", + " this.rubberband_canvas = rubberband[0];\n", + " this.rubberband_context = rubberband[0].getContext(\"2d\");\n", + " this.rubberband_context.strokeStyle = \"#000000\";\n", + "\n", + " this._resize_canvas = function(width, height) {\n", + " // Keep the size of the canvas, canvas container, and rubber band\n", + " // canvas in synch.\n", + " canvas_div.css('width', width)\n", + " canvas_div.css('height', height)\n", + "\n", + " canvas.attr('width', width);\n", + " canvas.attr('height', height);\n", + "\n", + " rubberband.attr('width', width);\n", + " rubberband.attr('height', height);\n", + " }\n", + "\n", + " // Set the figure to an initial 600x600px, this will subsequently be updated\n", + " // upon first draw.\n", + " this._resize_canvas(600, 600);\n", + "\n", + " // Disable right mouse context menu.\n", + " $(this.rubberband_canvas).bind(\"contextmenu\",function(e){\n", + " return false;\n", + " });\n", + "\n", + " function set_focus () {\n", + " canvas.focus();\n", + " canvas_div.focus();\n", + " }\n", + "\n", + " window.setTimeout(set_focus, 100);\n", + "}\n", + "\n", + "mpl.figure.prototype._init_toolbar = function() {\n", + " var fig = this;\n", + "\n", + " var nav_element = $('
')\n", + " nav_element.attr('style', 'width: 100%');\n", + " this.root.append(nav_element);\n", + "\n", + " // Define a callback function for later on.\n", + " function toolbar_event(event) {\n", + " return fig.toolbar_button_onclick(event['data']);\n", + " }\n", + " function toolbar_mouse_event(event) {\n", + " return fig.toolbar_button_onmouseover(event['data']);\n", + " }\n", + "\n", + " for(var toolbar_ind in mpl.toolbar_items) {\n", + " var name = mpl.toolbar_items[toolbar_ind][0];\n", + " var tooltip = mpl.toolbar_items[toolbar_ind][1];\n", + " var image = mpl.toolbar_items[toolbar_ind][2];\n", + " var method_name = mpl.toolbar_items[toolbar_ind][3];\n", + "\n", + " if (!name) {\n", + " // put a spacer in here.\n", + " continue;\n", + " }\n", + " var button = $('