Merge pull request #4 from yairomer/dev

Ver 0.5

Dockerfile

@@ -1,10 +1,9 @@
-FROM nvidia/cuda:9.0-cudnn7-devel-ubuntu16.04
-# FROM nvidia/cuda:9.2-cudnn7-devel-ubuntu18.04
+FROM nvidia/cuda:10.0-cudnn7-devel-ubuntu18.04
 
 ## Install basic packages and useful utilities
 ## ===========================================
 ENV DEBIAN_FRONTEND noninteractive
-RUN apt-get update -y && \
+RUN apt-get update -y  && \
     apt-get upgrade -y && \
     apt-get install -y software-properties-common && \
     add-apt-repository ppa:neovim-ppa/stable && \
@@ -25,6 +24,7 @@ RUN apt-get update -y && \
         python \
         python-dev \
         python-pip \
+        pylint \
         sshfs \
         wget \
         curl \
@@ -69,13 +69,26 @@ RUN apt-get update -y && \
         texlive-latex-extra \
         texlive-xetex \
         graphviz \
+        libncurses5-dev \
+        libncursesw5-dev \
         && \
     apt-get install -y neovim && \
     pip install pynvim==0.3.2 && \
     apt-get clean
 
     ## ToDo: increase memory limit to 10GB in: /etc/ImageMagick-6/policy.xml
 
+## Install nvtop
+## =============
+RUN git clone https://github.com/Syllo/nvtop.git /tmp/nvtop && \
+    mkdir /tmp/nvtop/build && \
+    cd /tmp/nvtop/build && \
+    cmake .. || : && \
+    make || : && \
+    make install || : && \
+    cd / && \
+    rm -r /tmp/nvtop
+
 ## Set locale
 ## ==========
 RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
@@ -85,7 +98,7 @@ RUN echo "en_US.UTF-8 UTF-8" > /etc/locale.gen && \
 ## ==========
 RUN mkdir /var/run/sshd && \
     sed 's/^#\?PasswordAuthentication .*$/PasswordAuthentication yes/g' -i /etc/ssh/sshd_config && \
-    sed 's/^Port .*$/Port 9022/g' -i /etc/ssh/sshd_config && \
+    sed 's/^#\?Port .*$/Port 9022/g' -i /etc/ssh/sshd_config && \
     sed 's@session\s*required\s*pam_loginuid.so@session optional pam_loginuid.so@g' -i /etc/pam.d/sshd
 
 ## VSCode
@@ -118,42 +131,49 @@ RUN mkdir /app && \
 
 ## Setup python environment
 ## ========================
-RUN pip3 install pip==18.1 && \
+RUN pip3 install pip==20.0.2 && \
     hash -r pip && \
     pip3 install -U \
-        virtualenv==16.2.0 \
-        ipython==7.0.1 \
-        numpy==1.15.2 \
-        scipy==1.1.0 \
-        matplotlib==3.0.0 \
-        PyQt5==5.11.3 \
-        seaborn==0.9.0 \
-        plotly==3.5.0 \
-        bokeh==1.0.4 \
+        virtualenv==20.0.10 \
+        ipython==7.13.0 \
+        numpy==1.18.1 \
+        scipy==1.4.0 \
+        cvxpy==1.0.28 \
+        matplotlib==3.2.0 \
+        PyQt5==5.14.1 \
+        seaborn==0.10.0 \
+        plotly==4.5.3 \
+        dash==1.9.1 \
+        bokeh==2.0.0 \
         ggplot==0.11.5 \
-        altair==2.3.0 \
-        pandas==0.23.4 \
-        pyyaml==3.13 \
-        protobuf==3.6.1 \
-        ipdb==0.11 \
-        flake8==3.5.0 \
-        cython==0.28.5 \
-        sympy==1.3 \
+        altair==4.0.1 \
+        pandas==1.0.1 \
+        pyyaml==5.3 \
+        protobuf==3.11.3 \
+        ipdb==0.13.2 \
+        flake8==3.7.9 \
+        cython==0.29.15 \
+        sympy==1.5.1 \
         nose==1.3.7 \
         sphinx==1.8.1 \
-        tqdm==4.27.0 \
-        opencv-contrib-python==3.4.3.18 \
-        scikit-image==0.14.1 \
-        scikit-learn==0.20.0 \
-        imageio==2.4.1 \
-        torchvision==0.2.1 \
-        tensorflow-gpu==1.12.0 \
-        tensorboardX==1.4 \
+        tqdm==4.43.0 \
+        opencv-contrib-python==4.2.0.32 \
+        scikit-image==0.16.2 \
+        scikit-learn==0.22.2 \
+        imageio==2.8.0 \
+        torchvision==0.4.0 \
+        torchviz==0.0.1 \
+        Pillow==6.1 \
+        torchsummary==1.5.1 \
+        tensorflow-gpu==2.0.0 \
+        tensorboardX==2.0 \
         jupyter==1.0.0 \
-        jupyterthemes==0.19.6 \
-        jupyter_contrib_nbextensions==0.5.0 \
-        jupyterlab==0.4.0 \
-        ipywidgets==7.4.2 \
+        jupyterthemes==0.20.0 \
+        jupyter_contrib_nbextensions==0.5.1 \
+        jupyterlab==2.0.1 \
+        ipywidgets==7.5.1 \
+        visdom==0.1.8.9 \
+        line_profiler==3.0.2 \
         && \
         rm -r /root/.cache/pip
 ENV MPLBACKEND=Agg
@@ -174,18 +194,31 @@ RUN pip install six==1.11 && \
     jupyter-nbextension install rise --py --sys-prefix --system && \
     cp -r /root/.jupyter /etc/skel/
 
+## Install Orca (for exporting Plotly figures to images)
+## =====================================================
+RUN apt install -y xvfb libgconf2-4 && \
+    wget https://github.com/plotly/orca/releases/download/v1.1.1/orca-1.1.1-x86_64.AppImage -P /tmp && \
+    chmod 777 /tmp/orca-1.1.1-x86_64.AppImage && \
+    cd /tmp && \
+    ./orca-1.1.1-x86_64.AppImage --appimage-extract && \
+    mv /tmp/squashfs-root /opt/squashfs-root && \
+    chmod -R 777 /opt/squashfs-root && \
+    printf '#!/bin/bash \nxvfb-run --auto-servernum --server-args "-screen 0 640x480x24" /opt/squashfs-root/app/orca "$@"' > /usr/bin/orca && \
+    chmod 777 /usr/bin/orca && \
+    rm -r /tmp/orca-1.1.1-x86_64.AppImage
+
 ## Create virtual environment
 ## ==========================
 RUN cd /app/ && \
     virtualenv --system-site-packages dockvenv && \
-    virtualenv --relocatable dockvenv && \
     grep -rlnw --null /usr/local/bin/ -e '#!/usr/bin/python3' | xargs -0r cp -t /app/dockvenv/bin/ && \
     sed -i "s/#"'!'"\/usr\/bin\/python3/#"'!'"\/usr\/bin\/env python/g" /app/dockvenv/bin/* && \
     mv /app/dockvenv /root/ && \
     ln -sfT /root/dockvenv /app/dockvenv && \
     cp -rp /root/dockvenv /etc/skel/ && \
     sed -i "s/^\(PATH=\"\)\(.*\)$/\1\/app\/dockvenv\/bin\/:\2/g" /etc/environment
 ENV PATH=/app/dockvenv/bin:$PATH
+    # virtualenv dockvenv && \
 
 ## Node.js
 ## =======
@@ -200,16 +233,22 @@ RUN cd /tmp && \
     dpkg -i dumb-init.deb && \
     rm dumb-init.deb
 
+## Create container config file
+## ============================
+RUN mkdir /tmp/dock_config && \
+    chmod a+wrx /tmp/dock_config
+
 ## Copy scripts
 ## ============
 RUN mkdir /app/bin && \
     chmod a=u -R /app/bin && \
     sed -i "s/^\(PATH=\"\)\(.*\)$/\1\/app\/bin\/:\2/g" /etc/environment
 ENV PATH="/app/bin:$PATH"
-COPY /resources/entrypoint.sh /app/bin/run
+COPY /resources/switch_user_run.sh /app/bin/switch_user_run
 COPY /resources/default_notebook.sh /app/bin/default_notebook
 COPY /resources/default_jupyterlab.sh /app/bin/default_jupyterlab
 COPY /resources/run_server.sh /app/bin/run_server
+COPY /resources/run_in_detached_tmux.sh /app/bin/run_in_detached_tmux
 
 RUN touch /etc/skel/.sudo_as_admin_successful
 
@@ -228,4 +267,4 @@ ENV LANGUAGE en_US:en
 ENV LC_ALL en_US.UTF-8  
 
 WORKDIR /root
-ENTRYPOINT ["/usr/bin/dumb-init", "--", "run"]
+ENTRYPOINT ["/usr/bin/dumb-init", "--", "switch_user_run"]

README.md

@@ -151,5 +151,4 @@ For convenient the docker image comes with a few preconfigured scripts (which ar
 - *default-jupyterlab*: Opens Jupyter Lab at the root directory using port 9901 (without a password nor token)
 - *run_server*: Starts Jupyter Notebook and Lab using a tmux session.
 
-
-The Enjoy ;)
+Enjoy ;)

docs/installing_dpendencies.md

@@ -1,24 +1,28 @@
 # Installing dependencies
 
 ## NVIDIA dirvers
+
 This docker image uses CUDA 9.0 which requires NVIDIA drivers of version 384.81 or later.
 (To fine the list of NVIDIA drivers version and CUDA version supported be your graphic card
 go to: https://www.geforce.com/drivers)
 
 For some reason installing NVIDIA drivers on Linux tend to cause problems, but in many cases the following
 In some cases the following line would simply to the tick:
+
 ``` bash
 sudo apt -y install nvidia-driver-{driver_version}
 ```
 
 In the case where apt is not able to fine the desired driver try the following method:
+
 1. Go to https://developer.download.nvidia.com/compute/cuda/repos/ and find the the link to the repository
 installation file which fits the desired CUDA version and your system. It should be of the format of:
 *https://developer.download.nvidia.com/compute/cuda/repos/{os_version}/{arch}/cuda-repo-{os_version}_{cuda_version}_{arch}.deb*
 In addition find in the same folder the link to the repository keys, it should be a file of the format:
 *https://developer.download.nvidia.com/compute/cuda/repos/{os_version}/{arch}/{some_number}.pub*
 
 2. Run the following commands to install the NVIDIA drivers + CUDA
+
 ``` bash
 cd /tmp
 curl -L {link_to_the_repo_file_from_stage_1} -o cuda_installation.deb
@@ -28,7 +32,9 @@ sudo apt-get update
 sudo apt-get install -y cuda
 rm cuda_installation.deb
 ```
+
 Example, installing CUDA 10.0 on Ubnutnu 18.04
+
 ``` bash
 cd /tmp
 curl -L wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/cuda-repo-ubuntu1804_10.0.130-1_amd64.deb -o cuda_installation.deb
@@ -39,19 +45,24 @@ apt-get install cuda -y
 ```
 
 For more information you can look at the guides from NVIDIA website:
+
 - CUDA installation guide: https://docs.nvidia.com/cuda/cuda-installation-guide-linux/index.html
 - The quick start guide: https://docs.nvidia.com/cuda/cuda-quick-start-guide/index.html
 
 ## Docker
+
 Install he latest docker version by following the instructions here:
 https://docs.docker.com/install/linux/docker-ce/ubuntu/#set-up-the-repository
 
 To enable a user to run docker without the need to use *sudo* run the following command:
-```
+
+``` bash
 sudo usermod -aG docker {username}
 ```
+
 Replace {username} with the name of the desired user. To apply this change you will need the user to logout
 and back in again.
 
 ## NVIDIA docker
+
 Install nvidia-docker by following the instructions here: https://github.com/NVIDIA/nvidia-docker