diff --git a/Dockerfile b/Dockerfile index 23bc0da..7e0b311 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,9 +1,11 @@ -FROM tensorflow/tensorflow:latest-gpu-py3 +#FROM tensorflow/tensorflow:latest-gpu-py3 +# Added . to force rebuild +FROM tensorflow/tensorflow:latest-gpu-py3-jupyter #FROM tensorflow/tensorflow:1.0.0-gpu-py3 # Removing some notebook which caused confusion -RUN rm /notebooks/1_hello_tensorflow.ipynb -RUN rm /notebooks/2_getting_started.ipynb -RUN rm /notebooks/3_mnist_from_scratch.ipynb +#RUN rm /notebooks/1_hello_tensorflow.ipynb +#RUN rm /notebooks/2_getting_started.ipynb +#RUN rm /notebooks/3_mnist_from_scratch.ipynb MAINTAINER oliver duerr @@ -13,8 +15,9 @@ RUN pip --no-cache-dir install \ matplotlib \ pandas \ h5py \ -# keras \ + keras \ tflearn \ + scikit-image \ ggplot # RUN pip --no-cache-dir install tflearn @@ -27,13 +30,29 @@ RUN gpg -a --export E084DAB9 | apt-key add - RUN apt-get update && apt-get install -y git RUN apt-get -y install r-base +# Pydot for Keras for Beate +RUN apt-get -y install python-pydot python-pydot-ng graphviz #For Keras model visualization +RUN pip3 install pydot +RUN pip3 install graphviz + #RUN apt-get install libzmq3-de RUN pip3 install rpy2 +# jupyterlab +RUN pip install jupyterlab + +# For toc in notebook +RUN pip install jupyter_contrib_nbextensions +RUN jupyter contrib nbextension install --user +RUN pip install jupyter_nbextensions_configurator + # Clean RUN apt-get clean && \ rm -rf /var/lib/apt/lists/* +# Some nice stuff for R +RUN R -e "install.packages('tidyverse', repos = 'https://cloud.r-project.org')" + # Default directory that will be saved by htcondor #RUN mkdir /tmp/results #RUN nvidia-smi -f /tmp/temp.txt @@ -51,4 +70,6 @@ COPY notebooks /notebooks COPY run_jupyter_2.sh / +COPY run_jlab.sh / + CMD ["/run_jupyter_2.sh"] diff --git a/README.md b/README.md index f182faf..fb3dfc7 100644 --- a/README.md +++ b/README.md @@ -1,4 +1,5 @@ -# tf_docker +# tf_docker gpu_r + ## Docker container for tutorials on tensorflow. Based on https://github.com/tensorflow/tensorflow/tree/master/tensorflow/tools/docker @@ -48,5 +49,6 @@ docker run --net=host -d -e CONFIGPROXY_AUTH_TOKEN=$TOKEN \ -v /var/run/docker.sock:/docker.sock \ jupyter/tmpnb python orchestrate.py --image='oduerr/tf_docker' ``` +.. diff --git a/notebooks/UseR.ipynb b/notebooks/UseR.ipynb new file mode 100644 index 0000000..71619d4 --- /dev/null +++ b/notebooks/UseR.ipynb @@ -0,0 +1,91 @@ +{ + "cells": [ + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "### How to call R code " + ] + }, + { + "cell_type": "code", + "execution_count": 1, + "metadata": {}, + "outputs": [], + "source": [ + "import numpy as np" + ] + }, + { + "cell_type": "code", + "execution_count": 2, + "metadata": {}, + "outputs": [], + "source": [ + "x = np.linspace(0,2*3.14,100)\n", + "y = np.sin(x)" + ] + }, + { + "cell_type": "code", + "execution_count": 3, + "metadata": {}, + "outputs": [], + "source": [ + "%load_ext rpy2.ipython" + ] + }, + { + "cell_type": "code", + "execution_count": 4, + "metadata": {}, + "outputs": [], + "source": [ + "%Rpush x\n", + "%Rpush y" + ] + }, + { + "cell_type": "code", + "execution_count": 5, + "metadata": {}, + "outputs": [ + { + "data": { + "image/png": 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\n" + }, + "metadata": {}, + "output_type": "display_data" + } + ], + "source": [ + "%%R\n", + "#install.packages('tidyverse', repos=\"https://cloud.r-project.org\")\n", + "library(ggplot2)\n", + "df = data.frame(x=x,y=y)\n", + "ggplot(df,aes(x=x,y=y)) + geom_point() " + ] + } + ], + "metadata": { + "kernelspec": { + "display_name": "Python 3", + "language": "python", + "name": "python3" + }, + "language_info": { + "codemirror_mode": { + "name": "ipython", + "version": 3 + }, + "file_extension": ".py", + "mimetype": "text/x-python", + "name": "python", + "nbconvert_exporter": "python", + "pygments_lexer": "ipython3", + "version": "3.5.2" + } + }, + "nbformat": 4, + "nbformat_minor": 2 +} diff --git a/notebooks/infos.ipynb b/notebooks/infos.ipynb index 233ae26..0056181 100644 --- a/notebooks/infos.ipynb +++ b/notebooks/infos.ipynb @@ -2,29 +2,26 @@ "cells": [ { "cell_type": "code", - "execution_count": 1, - "metadata": { - "collapsed": false, - "deletable": true, - "editable": true - }, + "execution_count": 2, + "metadata": {}, "outputs": [ - { - "name": "stderr", - "output_type": "stream", - "text": [ - "Using TensorFlow backend.\n" - ] - }, { "name": "stdout", "output_type": "stream", "text": [ - "Tensorflow : 1.0.0\n", - "Keras : 2.0.0\n", - "tflearn : 0.3\n", - "Python : sys.version_info(major=3, minor=4, micro=3, releaselevel='final', serial=0)\n", - "Date : 2017-03-14 19:41:46\n" + "Tensorflow : 1.5.0\n", + "Keras : 2.1.3\n", + "tflearn : 0.3.2\n", + "Python : sys.version_info(major=3, minor=5, micro=2, releaselevel='final', serial=0)\n", + "Date : 2018-02-09 18:00:42\n", + "\n", + "root\n", + "/notebooks\n", + "No LSB modules are available.\n", + "Distributor ID:\tUbuntu\n", + "Description:\tUbuntu 16.04.3 LTS\n", + "Release:\t16.04\n", + "Codename:\txenial\n" ] } ], @@ -37,19 +34,22 @@ "import pkg_resources\n", "import datetime\n", "\n", + "\n", "print(\"Tensorflow : \", tf.__version__)\n", "print(\"Keras : \", keras.__version__)\n", "print(\"tflearn : \", pkg_resources.get_distribution(\"tflearn\").version) #Likes to hide a bit\n", "print(\"Python : \", sys.version_info)\n", - "print(\"Date : \", time.strftime(\"%Y-%m-%d %H:%M:%S\"))" + "print(\"Date : \", time.strftime(\"%Y-%m-%d %H:%M:%S\"))\n", + "\n", + "!echo \"\"\n", + "!whoami\n", + "!pwd\n", + "!lsb_release -a" ] }, { "cell_type": "markdown", - "metadata": { - "deletable": true, - "editable": true - }, + "metadata": {}, "source": [ "### More infos: \n", "\n", @@ -64,10 +64,7 @@ }, { "cell_type": "markdown", - "metadata": { - "deletable": true, - "editable": true - }, + "metadata": {}, "source": [ "### Cloning a course\n", "\n", @@ -77,11 +74,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "collapsed": false, - "deletable": true, - "editable": true - }, + "metadata": {}, "outputs": [], "source": [ "!git clone https://github.com/tensorchiefs/dl_course.git\n", @@ -91,11 +84,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "collapsed": false, - "deletable": true, - "editable": true - }, + "metadata": {}, "outputs": [], "source": [ "!pwd" @@ -104,11 +93,7 @@ { "cell_type": "code", "execution_count": null, - "metadata": { - "collapsed": false, - "deletable": true, - "editable": true - }, + "metadata": {}, "outputs": [], "source": [ "!ls" @@ -131,7 +116,7 @@ "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", - "version": "3.4.3" + "version": "3.5.2" } }, "nbformat": 4, diff --git a/run_jlab.sh b/run_jlab.sh new file mode 100755 index 0000000..c539738 --- /dev/null +++ b/run_jlab.sh @@ -0,0 +1,5 @@ +To enable widget such as sliders +jupyter nbextension enable --py --sys-prefix widgetsnbextension +jupyter-nbextensions_configurator enable #Allows the user to config notebooks +jupyter serverextension enable --py jupyterlab --sys-prefix +jupyter lab "$@" --ip=0.0.0.0 --allow-root --NotebookApp.token=tensorchiefs diff --git a/run_jupyter_2.sh b/run_jupyter_2.sh index 54fcd32..afd81dc 100755 --- a/run_jupyter_2.sh +++ b/run_jupyter_2.sh @@ -16,5 +16,6 @@ # To enable widget such as sliders jupyter nbextension enable --py --sys-prefix widgetsnbextension -jupyter notebook "$@" --allow-root --NotebookApp.token=tensorchiefs +jupyter-nbextensions_configurator enable #Allows the user to config notebooks +jupyter notebook --ip=0.0.0.0 --port=8888 --allow-root --NotebookApp.token=tensorchiefs