Merge pull request #252 from openworm/development

Update main repo to have project wide dockerfile

.openworm.yml

@@ -1,6 +1,5 @@
 repo: openworm/OpenWorm
-shortDescription: "Project Home repo for OpenWorm Wiki and Project-wide issues"
+shortDescription: "Project Home repo for Central Dockerfile and Project-wide issues"
 contributor-guide: "http://docs.openworm.org/en/latest/community/#contribution-best-practices"
 coordinator: [email protected]
-documentation: "http://docs.openworm.org/en/latest/"
-gitter: "http://gitter.im/openworm/OpenWorm"
+documentation: "http://docs.openworm.org/en/latest/"

Dockerfile

@@ -0,0 +1,155 @@
+FROM ubuntu:16.04
+
+MAINTAINER David Lung "[email protected]"
+
+
+ARG INTEL_SDK_VERSION=2017_7.0.0.2511_x64
+
+COPY ./silent-intel-sdk.cfg /tmp/silent-intel-sdk.cfg
+
+
+ARG USR=ow
+ENV USER=$USR
+
+
+RUN apt-get update && \
+  apt-get upgrade -y && \
+  apt-get dist-upgrade -y
+
+
+
+RUN mkdir -p /etc/sudoers.d && \
+  export uid=1000 gid=1000 && \
+  mkdir -p /home/$USER && \
+  echo "$USER:x:${uid}:${gid}:$USER,,,:/home/$USER:/bin/bash" >> /etc/passwd && \
+  echo "$USER:x:${uid}:" >> /etc/group && \
+  echo "$USER ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$USER && \
+  chmod 0440 /etc/sudoers.d/$USER && \
+  chown ${uid}:${gid} -R /home/$USER
+
+
+ENV DEBIAN_FRONTEND noninteractive # TODO: change
+
+
+#RUN useradd -ms /bin/bash $USER
+
+
+RUN apt-get update && apt-get install -y --no-install-recommends apt-utils \
+  wget \
+  nano \
+  htop \
+  build-essential \
+  make \
+  git \
+  automake \
+  autoconf \
+  g++ \
+  rpm \
+  libtool \
+  libncurses5-dev \
+  zlib1g-dev \
+  bison \
+  flex \
+  lsb-core \
+  sudo \
+  xorg \
+  openbox \
+  x11-xserver-utils \
+  libxext-dev libncurses-dev python-dev mercurial \
+  freeglut3-dev libglu1-mesa-dev libglew-dev python-dev python-pip python-lxml python-numpy python-scipy python-tk \
+  kmod dkms \
+  linux-source linux-headers-generic \
+  maven openjdk-8-jdk \
+  python-setuptools python-yaml libnuma1 \
+  openmpi-bin  libopenmpi-dev \
+  libgl1-mesa-glx libgl1-mesa-dri libfreetype6-dev \ 
+  libpng12-dev libxft-dev python-matplotlib xubuntu-desktop ffmpeg xvfb tmux
+
+#RUN  sudo pip install --upgrade matplotlib 
+
+#RUN sudo apt-get install nvidia-opencl-dev
+
+RUN sudo usermod -a -G video $USER
+
+USER $USER
+ENV HOME /home/$USER
+WORKDIR $HOME
+
+RUN mkdir neuron && \
+  cd neuron && \
+  git clone https://github.com/lungd/iv.git && \
+  git clone https://github.com/lungd/nrn.git && \
+  cd iv && \
+  git checkout ow-0.1 && \
+  ./build.sh && \
+  ./configure --prefix=`pwd` && \
+  make && \
+  sudo make install && \
+  cd ../nrn && \
+  git checkout ow-0.1 && \
+  ./build.sh && \
+  ./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-nrnpython=/usr/bin/python --with-paranrn && \
+  make && \
+  sudo make install && \
+  cd src/nrnpython && \
+  sudo python setup.py install
+
+RUN mkdir intel-opencl-tmp && \
+  cd intel-opencl-tmp && \
+  mkdir intel-opencl && \
+  wget http://registrationcenter-download.intel.com/akdlm/irc_nas/11396/SRB5.0_linux64.zip && \
+  unzip SRB5.0_linux64.zip && \
+  tar -C intel-opencl -Jxf intel-opencl-r5.0-63503.x86_64.tar.xz && \
+  tar -C intel-opencl -Jxf intel-opencl-devel-r5.0-63503.x86_64.tar.xz && \
+  tar -C intel-opencl -Jxf intel-opencl-cpu-r5.0-63503.x86_64.tar.xz && \
+  sudo cp -R intel-opencl/* / && \
+  sudo ldconfig && \
+  cd .. && \
+  sudo rm -r intel-opencl-tmp
+
+RUN wget http://registrationcenter-download.intel.com/akdlm/irc_nas/vcp/11705/intel_sdk_for_opencl_$INTEL_SDK_VERSION.tgz && \
+  tar xvf intel_sdk_for_opencl_$INTEL_SDK_VERSION.tgz && \
+  cd intel_sdk_for_opencl_$INTEL_SDK_VERSION && \
+  sudo ./install.sh --silent /tmp/silent-intel-sdk.cfg && \
+  cd $HOME && \
+  rm intel_sdk_for_opencl_$INTEL_SDK_VERSION.tgz && \
+  sudo rm /tmp/silent-intel-sdk.cfg
+
+RUN git clone https://github.com/lungd/jNeuroML.git && \
+  cd jNeuroML && \
+  git checkout ow-0.1 && \
+  python getNeuroML.py ow-0.1
+
+RUN git clone https://github.com/lungd/pyNeuroML.git && \
+  cd pyNeuroML && \
+  git checkout ow-0.1 && \
+  sudo python setup.py install
+
+RUN git clone https://github.com/lungd/PyOpenWorm.git && \
+  cd PyOpenWorm && \
+  git checkout ow-0.1 && \
+  sudo python setup.py install
+
+RUN git clone https://github.com/lungd/CElegansNeuroML.git && \
+  cd CElegansNeuroML && \
+  git checkout ow-0.1
+
+RUN git clone https://github.com/lungd/sibernetic.git && \
+  cd sibernetic && \
+  git checkout ow-0.1 && \
+  make clean && make all
+
+ENV JNML_HOME=$HOME/jNeuroML
+ENV PATH=$PATH:$JNML_HOME
+ENV IV=$HOME/neuron/iv
+ENV N=$HOME/neuron/nrn
+ENV CPU=x86_64
+ENV PATH=$PATH:$IV/$CPU/bin:$N/$CPU/bin
+ENV NEURON_HOME=$N/$CPU
+ENV C302_HOME=$HOME/CElegansNeuroML/CElegans/pythonScripts/c302
+ENV SIBERNETIC_HOME=$HOME/sibernetic
+ENV PYTHONPATH=$PYTHONPATH:$C302_HOME:$SIBERNETIC_HOME
+
+# Not working with --chown=$USER:$USER
+COPY ./master_openworm.py $HOME/master_openworm.py
+RUN sudo chown $USER:$USER $HOME/master_openworm.py