Merge pull request #363 from openworm/test_versions

To v0.9.6; Use ubnutu 24.04 as base

Author: pgleeson

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:24.04
 
 LABEL maintainer="David Lung ([email protected]); Padraig Gleeson ([email protected])"
 
@@ -24,18 +24,19 @@ 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
 
@@ -45,37 +46,32 @@ RUN sudo usermod -a -G video $USER
 ENV HOME=/home/$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 sudo pip3 install neuron==8.1.0
+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 development && \
+  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-0.9.6  # fixed to a specific branch
 
 
 ################################################################################
@@ -85,6 +81,8 @@ 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)

Dockerfile_intel

@@ -53,7 +53,7 @@ RUN  sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
 ################################################################################
 ########     Install NEURON simulator
 
-RUN pip3 install neuron==8.0.1
+RUN pip3 install neuron==8.2.6
 
 
 ################################################################################

VERSION

@@ -1 +1 @@
-0.9.5
+0.9.6

master_openworm.py

@@ -12,7 +12,7 @@
 import math
 
 print("*****************************")
-print("OpenWorm Master Script v0.9.3")
+print("OpenWorm Master Script")
 print("*****************************")
 print("")
 print("This script attempts to run a full pass through the OpenWorm scientific libraries.")
@@ -152,7 +152,7 @@ def execute_with_realtime_output(command, directory, env=None):
 os.system('echo Starting xvfb && Xvfb %s -listen tcp -ac -screen 0 1920x1080x24+32 &'%DISPLAY) # TODO: terminate xvfb after recording
 
 try:
-    command = """python sibernetic_c302.py
+    command = """python3 sibernetic_c302.py
                 -duration %s
                 -dt %s
                 -dtNrn %s

run.sh

@@ -36,6 +36,6 @@ $DURATION_PART \
 --privileged \
 -v $HOST_OUT_DIR:$OW_OUT_DIR:rw \
 openworm/openworm:$version \
-bash -c "DISPLAY=:44 python master_openworm.py"
+bash -c "DISPLAY=:44 python3 master_openworm.py"
 
 docker logs -f openworm_$version