Gpu r

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 <dueo@zhaw.ch>
 
@@ -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"]

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'
 ```
+..
 
 

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
+}

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,

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

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