Tidy up master_openworm.py & make more cmd line options

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

@@ -2,9 +2,9 @@ name: Docker Image Build - Intel drivers
 
 on:
   push:
-    branches: [ master, dev*, test* ]
+    branches: [ master, dev*, test*, experimental ]
   pull_request:
-    branches: [ master, dev*, test* ]
+    branches: [ master, dev*, test*, experimental ]
 
 jobs:
 
@@ -28,11 +28,10 @@ jobs:
 
     - name: Run the Docker image
       run: |
-        ./run.sh
+        echo "Skipping actual run of Intel Docker image, due to segfaults observed on GitHub runners"
+        #sudo apt-get update && sudo apt-get install -y x11-xserver-utils # for xhost
+        #./run.sh
 
     - name: Info on generated files
       run: |
         ls -alth
-        ls -alth output
-        ls -alth output/*
-        more output/*/report.json

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

@@ -2,9 +2,9 @@ name: Docker Image Quick Run
 
 on:
   push:
-    branches: [ master, dev*, test* ]
+    branches: [ master, dev*, test*, experimental ]
   pull_request:
-    branches: [ master, dev*, test* ]
+    branches: [ master, dev*, test*, experimental ]
 
 jobs:
 
@@ -25,6 +25,7 @@ jobs:
         docker images
     - name: Run the Docker image
       run: |
+        sudo apt-get update && sudo apt-get install -y x11-xserver-utils # for xhost
         ./run-quick.sh
     - name: Info on generated files
       run: |

.github/workflows/docker-image.yml

@@ -2,9 +2,9 @@ name: Docker Image Build and Run
 
 on:
   push:
-    branches: [ master, dev*, test* ]
+    branches: [ master, dev*, experimental, test* ]
   pull_request:
-    branches: [ master, dev*, test* ]
+    branches: [ master, dev*, experimental, test* ]
 
 jobs:
 
@@ -14,18 +14,33 @@ jobs:
 
     steps:
     - uses: actions/checkout@v4
+
     - name: Build the Docker image
       run: |
         chmod a+w output/
         ls -alth
         ./build.sh
+
     - name: Info on Docker images
       run: |
         docker -v
         docker images
-    - name: Run the Docker image
+
+    - name: Run the Docker image with the default falling cube demo from sibernetic 
+      run: |
+        sudo apt-get update && sudo apt-get install -y x11-xserver-utils # for xhost
+        ./run.sh -d 20 -c demo1
+
+    - name: Run the Docker image with a worm simulation - no c302
+      run: |
+        ./stop.sh
+        ./run.sh -d 10 -n 
+
+    - name: Run the Docker image with a worm simulation
       run: |
-        ./run.sh
+        ./stop.sh
+        ./run.sh -d 150 # temp longer simulation for testing
+
     - name: Info on generated files
       run: |
         ls -alth

.gitignore

@@ -4,3 +4,10 @@ output/C2*
 /output/siminfo.py
 /output/wor*
 /output/Sibernetic_*
+/output/test*
+/output/box
+/output/swim*
+/output/alone*
+/output/cube*
+/output/master*
+/output/deep_swim*

Dockerfile

@@ -29,12 +29,11 @@ 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 \
+  libxext-dev libncurses-dev \
   freeglut3-dev libglu1-mesa-dev libglew-dev python3-dev python3-pip \
   kmod dkms linux-source linux-headers-generic \
-  maven openjdk-8-jdk \
+  openjdk-21-jdk \
   libnuma1 \
-  openmpi-bin  libopenmpi-dev \
   libgl1 libglx-mesa0  libgl1-mesa-dri libfreetype6-dev \
   libxft-dev  unzip ffmpeg xvfb tmux
 
@@ -96,7 +95,8 @@ ENV NEURON_MODULE_OPTIONS=-nogui
 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
+    rm AMD-APP-SDKInstaller-v3.0.130.136-GA-linux64.tar.bz2 && \
+    rm AMD-APP-SDK-v3.0.130.136-GA-linux64.sh 
 
 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
@@ -116,6 +116,12 @@ RUN cd sibernetic && \
     make clean && make all && ldd ./Release/Sibernetic  # Use python 3 libs
 
 
+################################################################################
+########     Set up JupyterLab
+
+RUN sudo pip install notebook jupyterlab --break-system-packages
+
+
 ################################################################################
 ########     Copy master python script
 
@@ -125,6 +131,9 @@ 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!"
+

Dockerfile_intel

@@ -1,4 +1,9 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
+
+################################################################################
+########     Note: main Dockerfile using AMD libraries should be used unless
+########     there is a specific reason to use Intel OpenCL libraries
+################################################################################
 
 LABEL maintainer="David Lung ([email protected]); Padraig Gleeson ([email protected])"
 
@@ -18,72 +23,76 @@ RUN mkdir -p /etc/sudoers.d && \
   chmod 0440 /etc/sudoers.d/$USER && \
   chown ${uid}:${gid} -R /home/$USER
 
-ENV DEBIAN_FRONTEND noninteractive # TODO: change
+ENV DEBIAN_FRONTEND=noninteractive
 
 
 ################################################################################
 ########     Update/install essential libraries
 
-RUN apt-get update && apt-get install -y --no-install-recommends apt-utils \
+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 lsb-core \
+  g++ rpm libtool libncurses5-dev zlib1g-dev bison flex \
   sudo xorg openbox x11-xserver-utils \
-  libxext-dev libncurses-dev python3-dev mercurial \
-  freeglut3-dev libglu1-mesa-dev libglew-dev python3-dev python3-pip python3-lxml  python3-scipy python3-tk \
+  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 \
-  python3-setuptools python3-yaml libnuma1 \
+  libnuma1 \
   openmpi-bin  libopenmpi-dev \
-  libgl1-mesa-glx libgl1-mesa-dri libfreetype6-dev \
-  libxft-dev python3-matplotlib unzip ffmpeg xvfb tmux
+  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
+ENV HOME=/home/$USER
 WORKDIR $HOME
 
-#### 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  sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
 
 
 ################################################################################
 ########     Install NEURON simulator
 
-RUN pip3 install neuron==8.2.6
+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-0.9.5 && \
-  sudo pip install .
+  git checkout ow-0.9.7 && \
+  sudo pip install .  --break-system-packages
 
 # Note: pyNeuroML installed with the above library
 
-RUN pip3 install owmeta-core==0.13.5
-RUN owm bundle remote --user add ow 'https://raw.githubusercontent.com/openworm/owmeta-bundles/master/index.json'
 
 
 ################################################################################
 ########     Install Sibernetic for the worm body model
 
 RUN git clone https://github.com/openworm/sibernetic.git && \
   cd sibernetic && \
-  git checkout ow-0.9.5  # fixed to a specific branch
+  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=$PYTHONPATH:$HOME/c302:$SIBERNETIC_HOME
+ENV PYTHONPATH=$HOME/c302:$SIBERNETIC_HOME
+
+ENV NEURON_MODULE_OPTIONS=-nogui
 
 
 ################################################################################
@@ -124,7 +133,7 @@ RUN cd sibernetic && \
 COPY ./master_openworm.py $HOME/master_openworm.py
 RUN sudo chown $USER:$USER $HOME/master_openworm.py
 
-RUN echo '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alt"' >> ~/.bashrc
+RUN printf '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alth"\n' >> ~/.bashrc
 
 RUN pip list
 

build_intel.sh

@@ -3,4 +3,14 @@
 # A version of the docker container using the Intel libraries for OpenCL
 
 version=$(<VERSION) # Read version of Dockerfile from file VERSION
-docker build --platform linux/amd64  "$@" -t "openworm/openworm:$version" -f Dockerfile_intel .
+
+# Set the platform flag if we're on ARM
+arch=$(uname -m)
+if [[ "$arch" == "arm64" || "$arch" == "aarch64" ]]; then
+    platform_flag="--platform linux/amd64"
+else
+    platform_flag=""
+fi
+
+# Build the Docker image
+docker build $platform_flag "$@" -t "openworm/openworm:$version" -f Dockerfile_intel .