OpenWorm/Dockerfile at master · Color-Of-Code/OpenWorm · GitHub

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FROM ubuntu:24.04

LABEL maintainer="David Lung (lungdm@gmail.com); Padraig Gleeson (p.gleeson@gmail.com)"

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


################################################################################
########     Update/install essential libraries

RUN apt-get update
RUN 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 \
  sudo xorg openbox x11-xserver-utils \
  libxext-dev libncurses-dev mercurial \
  freeglut3-dev libglu1-mesa-dev libglew-dev python3-dev python3-pip \
  kmod dkms linux-source linux-headers-generic \
  maven openjdk-8-jdk \
  libnuma1 \
  openmpi-bin  libopenmpi-dev \
  libgl1 libglx-mesa0  libgl1-mesa-dri libfreetype6-dev \
  libxft-dev  unzip ffmpeg xvfb tmux

#RUN  sudo pip install --upgrade pip

RUN sudo usermod -a -G video $USER

#USER $USER
ENV HOME=/home/$USER
WORKDIR $HOME


################################################################################
########     Install NEURON simulator

RUN sudo pip install neuron==8.2.6  --break-system-packages


################################################################################
########     Install c302 for building neuronal network models

RUN git clone https://github.com/openworm/c302.git && \
  cd c302 && \
  git checkout ow-0.9.7 && \
  sudo pip install .  --break-system-packages

# Note: pyNeuroML installed with the above library


################################################################################
########     Install Sibernetic for the worm body model

RUN git clone https://github.com/openworm/sibernetic.git && \
  cd sibernetic && \
  git checkout ow-0.9.7  # fixed to a specific branch


################################################################################
########     Install extra Python dependencies

RUN sudo pip install ruff  --break-system-packages


################################################################################
########     Set some paths//environment variables

ENV C302_HOME=$HOME/c302/c302
ENV SIBERNETIC_HOME=$HOME/sibernetic
ENV PYTHONPATH=$HOME/c302:$SIBERNETIC_HOME

ENV NEURON_MODULE_OPTIONS=-nogui


################################################################################
########     Install AMD's OpenCL Drivers (AMD-APP-SDK 3.0)

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 && \
    tar -xf AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2 && \
    printf 'Y\n\n' | sudo ./AMD-APP-SDK-v3.0.130.136-GA-linux64.sh && \
    rm AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2

RUN sudo ln -s /opt/AMDAPPSDK-3.0/lib/x86_64/sdk/libOpenCL.so.1 /usr/lib/libOpenCL.so.1
RUN sudo ln -s /opt/AMDAPPSDK-3.0/lib/x86_64/sdk/libamdocl64.so /usr/lib/libamdocl64.so

RUN sudo apt install -y ocl-icd-opencl-dev vim

RUN echo "OpenCL Driver Installation Complete"

RUN echo "CLINFO:"
RUN clinfo


################################################################################
########     Build Sibernetic

RUN cd sibernetic && \
    make clean && make all && ldd ./Release/Sibernetic  # Use python 3 libs


################################################################################
########     Copy master python script

# Not working with --chown=$USER:$USER
COPY ./master_openworm.py $HOME/master_openworm.py
RUN sudo chown $USER:$USER $HOME/master_openworm.py

RUN printf '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alth"\n' >> ~/.bashrc

RUN pip list

RUN echo "Built the OpenWorm Docker image!"