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Merge pull request #338 from openworm/dev_0.9.4
Release 0.9.4 - uses latest sibernetic and c302, tested with both Intel and AMD drivers
2 parents 86e7af4 + ad624d5 commit f47c43a

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‎.github/workflows/docker-image-intel.yml

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name: Docker Image Test Build - Intel drivers
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on:
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push:
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branches: [ master, dev* ]
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pull_request:
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branches: [ master, dev* ]
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jobs:
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build:
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runs-on: ubuntu-latest
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steps:
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- uses: actions/checkout@v3
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- name: Build the Docker image
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run: |
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chmod a+w output/
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ls -alt
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./build_intel.sh
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- name: Info on Docker images
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run: |
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docker -v
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docker images
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- name: Run the Docker image
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run: |
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./run.sh
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- name: Info on generated files
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run: |
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ls -alth
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ls -alth output
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ls -alth output/*
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more output/*/report.json

‎.github/workflows/docker-image-quickrun.yml

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./run-quick.sh
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- name: Info on generated files
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run: |
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ls -alt
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ls -alt output
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ls -alt output/*
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ls -alth
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ls -alth output
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ls -alth output/*

‎.github/workflows/docker-image.yml

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./run.sh
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- name: Info on generated files
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run: |
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ls -alt
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ls -alt output
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ls -alt output/*
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ls -alth
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ls -alth output
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ls -alth output/*

‎.github/workflows/docker-pull.yml

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on:
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push:
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branches: [ master, dev* ]
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branches: [ master ]
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pull_request:
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branches: [ master, dev* ]
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branches: [ master ]
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jobs:
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- name: Run the Docker image
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run: |
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# Don't build. Will be pulled when run below
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# Don't build. Will be pulled from Dockerhub when run below
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./run.sh
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- name: Info on Docker images
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- name: Info on generated files
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run: |
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ls -alt
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ls -alt output
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ls -alt output/*
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ls -alth
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ls -alth output
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ls -alth output/*
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more output/*

‎Dockerfile

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LABEL maintainer="David Lung ([email protected]); Padraig Gleeson ([email protected])"
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ARG INTEL_SDK_VERSION=2017_7.0.0.2511_x64
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#COPY ./silent-intel-sdk.cfg /tmp/silent-intel-sdk.cfg
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ARG USR=ow
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ENV USER=$USR
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chmod 0440 /etc/sudoers.d/$USER && \
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chown ${uid}:${gid} -R /home/$USER
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ENV DEBIAN_FRONTEND noninteractive # TODO: change
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#RUN useradd -ms /bin/bash $USER
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################################################################################
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######## Update/install essential libraries
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libxft-dev python3-matplotlib unzip ffmpeg xvfb tmux
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#RUN sudo pip install --upgrade pip
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#RUN sudo apt-get install nvidia-opencl-dev
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RUN sudo usermod -a -G video $USER
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RUN git clone https://github.com/openworm/c302.git && \
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cd c302 && \
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git checkout ow-0.9.3a && \
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git checkout ow-0.9.4 && \
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sudo pip install .
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# Note: pyNeuroML installed with the above library
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RUN git clone https://github.com/openworm/sibernetic.git && \
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cd sibernetic && \
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git checkout ow-0.9.3 # fixed to a specific branch
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git checkout ow-0.9.4 # fixed to a specific branch
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################################################################################
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################################################################################
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######## Install Intel OpenCL libraries needed for Sibernetic
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RUN mkdir intel-opencl-tmp && \
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cd intel-opencl-tmp && \
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mkdir intel-opencl && \
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wget https://github.com/openworm/OpenWorm/raw/dev_inte/SRB5.0_linux64.zip && \
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unzip SRB5.0_linux64.zip && \
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tar -C intel-opencl -Jxf intel-opencl-r5.0-63503.x86_64.tar.xz && \
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tar -C intel-opencl -Jxf intel-opencl-devel-r5.0-63503.x86_64.tar.xz && \
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tar -C intel-opencl -Jxf intel-opencl-cpu-r5.0-63503.x86_64.tar.xz && \
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sudo cp -R intel-opencl/* / && \
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sudo ldconfig && \
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cd .. && \
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sudo rm -r intel-opencl-tmp
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RUN sudo cp -R /opt/intel/opencl/include/CL /usr/include/ && \
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sudo apt install -y ocl-icd-opencl-dev vim
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#sudo ln -s /opt/intel/opencl/libOpenCL.so.1 /usr/lib/libOpenCL.so
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######## Install AMD's OpenCL Drivers (AMD-APP-SDK 3.0)
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RUN wget https://master.dl.sourceforge.net/project/nicehashsgminerv5viptools/APP%20SDK%20A%20Complete%20Development%20Platform/AMD%20APP%20SDK%203.0%20for%2064-bit%20Linux/AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
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RUN tar -xf AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2
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RUN printf 'Y\n\n' | sudo ./AMD-APP-SDK-v3.0.130.136-GA-linux64.sh
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RUN sudo ln -s /opt/AMDAPPSDK-3.0/lib/x86_64/sdk/libOpenCL.so.1 /usr/lib/libOpenCL.so.1
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RUN sudo ln -s /opt/AMDAPPSDK-3.0/lib/x86_64/sdk/libamdocl64.so /usr/lib/libamdocl64.so
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RUN sudo apt install -y ocl-icd-opencl-dev vim
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RUN echo "OpenCL Driver Installation Complete"
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RUN echo "CLINFO:"
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RUN clinfo
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################################################################################
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######## Build Sibernetic
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RUN cd sibernetic && \
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sed -i -e "s/n2.7/n3.10/g" makefile && \
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make clean && make all && ldd ./Release/Sibernetic # Use python 3 libs
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‎Dockerfile_intel

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FROM ubuntu:22.04
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LABEL maintainer="David Lung ([email protected]); Padraig Gleeson ([email protected])"
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ARG USR=ow
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ENV USER=$USR
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RUN apt-get update && \
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apt-get upgrade -y && \
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apt-get dist-upgrade -y
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RUN mkdir -p /etc/sudoers.d && \
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export uid=1000 gid=1000 && \
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mkdir -p /home/$USER && \
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echo "$USER:x:${uid}:${gid}:$USER,,,:/home/$USER:/bin/bash" >> /etc/passwd && \
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echo "$USER:x:${uid}:" >> /etc/group && \
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echo "$USER ALL=(ALL) NOPASSWD: ALL" > /etc/sudoers.d/$USER && \
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chmod 0440 /etc/sudoers.d/$USER && \
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chown ${uid}:${gid} -R /home/$USER
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ENV DEBIAN_FRONTEND noninteractive # TODO: change
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################################################################################
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######## Update/install essential libraries
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RUN apt-get update && apt-get install -y --no-install-recommends apt-utils \
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wget nano htop build-essential make git automake autoconf \
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g++ rpm libtool libncurses5-dev zlib1g-dev bison flex lsb-core \
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sudo xorg openbox x11-xserver-utils \
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libxext-dev libncurses-dev python3-dev mercurial \
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freeglut3-dev libglu1-mesa-dev libglew-dev python3-dev python3-pip python3-lxml python3-scipy python3-tk \
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kmod dkms linux-source linux-headers-generic \
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maven openjdk-8-jdk \
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python3-setuptools python3-yaml libnuma1 \
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openmpi-bin libopenmpi-dev \
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libgl1-mesa-glx libgl1-mesa-dri libfreetype6-dev \
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libxft-dev python3-matplotlib unzip ffmpeg xvfb tmux
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#RUN sudo pip install --upgrade pip
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RUN sudo usermod -a -G video $USER
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#USER $USER
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ENV HOME /home/$USER
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WORKDIR $HOME
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#### TODO: check that this is the best way to switch to py3...
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RUN sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 10
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RUN sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
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################################################################################
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######## Install NEURON simulator
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RUN pip3 install neuron==8.0.1
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################################################################################
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######## Install c302 for building neuronal network models
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RUN git clone https://github.com/openworm/c302.git && \
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cd c302 && \
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git checkout ow-0.9.4 && \
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sudo pip install .
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# Note: pyNeuroML installed with the above library
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RUN pip3 install owmeta-core==0.13.5
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RUN owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'
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################################################################################
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######## Install Sibernetic for the worm body model
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RUN git clone https://github.com/openworm/sibernetic.git && \
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cd sibernetic && \
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git checkout ow-0.9.4 # fixed to a specific branch
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################################################################################
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######## Set some paths//environment variables
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ENV C302_HOME=$HOME/c302/c302
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ENV SIBERNETIC_HOME=$HOME/sibernetic
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ENV PYTHONPATH=$PYTHONPATH:$HOME/c302:$SIBERNETIC_HOME
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################################################################################
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######## Install Intel OpenCL libraries needed for Sibernetic
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# Legacy install of Intel's OpenCL Drivers:
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RUN mkdir intel-opencl-tmp && \
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cd intel-opencl-tmp && \
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mkdir intel-opencl && \
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wget https://github.com/openworm/OpenWorm/raw/dev_inte/SRB5.0_linux64.zip && \
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unzip SRB5.0_linux64.zip && \
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tar -C intel-opencl -Jxf intel-opencl-r5.0-63503.x86_64.tar.xz && \
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tar -C intel-opencl -Jxf intel-opencl-devel-r5.0-63503.x86_64.tar.xz && \
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tar -C intel-opencl -Jxf intel-opencl-cpu-r5.0-63503.x86_64.tar.xz && \
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sudo cp -R intel-opencl/* / && \
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sudo ldconfig && \
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cd .. && \
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sudo rm -r intel-opencl-tmp
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RUN sudo cp -R /opt/intel/opencl/include/CL /usr/include/ && \
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sudo apt install -y ocl-icd-opencl-dev vim
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RUN echo "OpenCL Driver Installation Complete"
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################################################################################
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######## Build Sibernetic
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RUN cd sibernetic && \
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make clean && make all && ldd ./Release/Sibernetic # Use python 3 libs
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################################################################################
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######## Copy master python script
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# Not working with --chown=$USER:$USER
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COPY ./master_openworm.py $HOME/master_openworm.py
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RUN sudo chown $USER:$USER $HOME/master_openworm.py
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RUN echo '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alt"' >> ~/.bashrc
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RUN pip list
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RUN echo "Built the OpenWorm Docker image!"

‎VERSION

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0.9.3
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0.9.4

‎build_intel.sh

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#!/bin/bash
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# A version of the docker container using the Intel libraries for OpenCL
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version=$(<VERSION) # Read version of Dockerfile from file VERSION
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docker build --platform linux/amd64 "$@" -t "openworm/openworm:$version" -f Dockerfile_intel .

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