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FROM ubuntu:18.04
LABEL maintainer="David Lung ([email protected]); Padraig Gleeson ([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
################################################################################
######## Update/install essential libraries
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 python3-dev python3-pip python3-lxml python3-scipy python3-tk \
kmod dkms linux-source linux-headers-generic \
maven openjdk-8-jdk \
python3-setuptools python3-yaml libnuma1 \
openmpi-bin libopenmpi-dev \
libgl1-mesa-glx libgl1-mesa-dri libfreetype6-dev \
libxft-dev python3-matplotlib unzip ffmpeg xvfb tmux
#RUN sudo pip install --upgrade pip
#RUN sudo apt-get install nvidia-opencl-dev
RUN sudo usermod -a -G video $USER
USER $USER
ENV HOME /home/$USER
WORKDIR $HOME
################################################################################
######## Install NEURON simulator
RUN mkdir neuron && \
cd neuron && \
git clone https://github.com/nrnhines/iv.git && \
git clone https://github.com/nrnhines/nrn.git && \
cd iv && \
git checkout 76c123b && \
./build.sh && \
./configure --prefix=`pwd` && \
make -j3 && \
sudo make install && \
cd ../nrn && \
git checkout e0950a1 && \
./build.sh && \
./configure --prefix=`pwd` --with-iv=$HOME/neuron/iv --with-nrnpython=/usr/bin/python3 --with-paranrn && \
make -j3 && \
sudo make install && \
cd src/nrnpython && \
sudo python3 setup.py install
################################################################################
######## Install pyNeuroML for handling NeuroML network model
RUN git clone https://github.com/NeuroML/pyNeuroML.git && \
cd pyNeuroML && \
git checkout master && \
sudo python3 setup.py install
################################################################################
######## Install PyOpenWorm
RUN git clone https://github.com/openworm/PyOpenWorm.git && \
cd PyOpenWorm && \
git checkout ow-0.9 && \
sudo apt-get install -y python3-cffi && \
sudo python3 setup.py install && \
pow clone https://github.com/openworm/OpenWormData.git
################################################################################
######## Install c302 for building neuronal network models
RUN git clone https://github.com/openworm/c302.git && \
cd c302 && \
git checkout ow-0.9.1 && \
sudo python3 setup.py install
################################################################################
######## Install Sibernetic for the worm body model
RUN git clone https://github.com/openworm/sibernetic.git && \
cd sibernetic && \
git checkout ow-0.9.1 # fixed to a specific branch
RUN cp c302/pyopenworm.conf sibernetic/ # Temp step until PyOpenWorm can be run from any dir...
################################################################################
######## Set some paths//environment variables
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=$HOME/c302/c302
ENV SIBERNETIC_HOME=$HOME/sibernetic
ENV PYTHONPATH=$PYTHONPATH:$HOME/c302:$SIBERNETIC_HOME
# Not working with --chown=$USER:$USER
COPY ./master_openworm.py $HOME/master_openworm.py
RUN sudo chown $USER:$USER $HOME/master_openworm.py
################################################################################
######## Install Intel OpenCL libraries needed for Sibernetic
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 sudo cp -R /opt/intel/opencl/include/CL /usr/include/ && \
sudo apt install -y ocl-icd-opencl-dev vim
#sudo ln -s /opt/intel/opencl/libOpenCL.so.1 /usr/lib/libOpenCL.so
################################################################################
######## Build Sibernetic
RUN cd sibernetic && \
sed -i -e "s/lpython2.7/lpython3.6m/g" makefile && \
sed -i -e "s/n2.7/n3.6/g" makefile && \
make clean && make all # Use python 3 libs
# intel i5, hd 5500, linux 4.15.0-39-generic
# ./Release/Sibernetic -f worm -no_g device=CPU 190ms
# ./Release/Sibernetic -f worm -no_g device=GPU 150ms (initialization takes some time)
# Intel(R) Xeon(R) CPU E5-1650 v4 @ 3.60GHz, linux 4.4.0-139-generic
# ./Release/Sibernetic -f worm -no_g device=CPU 60ms
#
# after installing the nvidia driver used in host:
## wget http://us.download.nvidia.com/tesla/390.30/nvidia-diag-driver-local-repo-ubuntu1604-390.30_1.0-1_amd64.deb
## sudo dpkg -i nvidia-diag-driver-local-repo-ubuntu1604-390.30_1.0-1_amd64.deb
## sudo apt-key add /var/nvidia-diag-driver-local-repo-390.30/7fa2af80.pub
## sudo apt-get update
## sudo apt-get install -y cuda-drivers
# ./Release/Sibernetic -f worm -no_g device=GPU 37ms
#### TODO: check that this is the best way to switch to py3...
RUN sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 10
RUN echo '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alt"' >> ~/.bashrc
RUN echo "Built the OpenWorm Docker image!"