Merge pull request #327 from openworm/dev_0.9.3

Release 0.9.3

Author: pgleeson

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

@@ -10,7 +10,8 @@ jobs:
 
   build:
 
-    runs-on: [ ubuntu-18.04, ubuntu-20.04, ubuntu-22.04 ]
+    runs-on: ubuntu-latest
+
     steps:
     - uses: actions/checkout@v2
     - name: Build the Docker image

.github/workflows/docker-image.yml

@@ -21,6 +21,7 @@ jobs:
         ./build.sh
     - name: Info on Docker images
       run: |
+        docker -v
         docker images
     - name: Run the Docker image
       run: |
@@ -30,4 +31,4 @@ jobs:
         ls -alt
         ls -alt output
         ls -alt output/C2*
-        cat output/C2_*/report.json
+        cat output/C2*/report.json

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:18.04
+FROM ubuntu:22.04
 
 LABEL maintainer="David Lung ([email protected]); Padraig Gleeson ([email protected])"
 
@@ -36,7 +36,7 @@ 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 \
+  libxext-dev libncurses-dev python3-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 \
@@ -50,7 +50,7 @@ RUN apt-get update && apt-get install -y --no-install-recommends apt-utils \
 
 RUN sudo usermod -a -G video $USER
 
-USER $USER
+#USER $USER
 ENV HOME /home/$USER
 WORKDIR $HOME
 
@@ -62,50 +62,29 @@ RUN  sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
 ################################################################################
 ########     Install NEURON simulator
 
-RUN sudo pip install neuron==7.8.1
-
-
-################################################################################
-########     Install pyNeuroML for handling NeuroML network model
-
-# Pin version of pymongo required for py3.6... TODO remove...
-RUN sudo pip install pymongo==4.1.1
-
-RUN git clone https://github.com/NeuroML/pyNeuroML.git && \
-  cd pyNeuroML && \
-  git checkout master  && \
-  sudo python3 setup.py install
-
-# TODO remove this line after we have better dependency management.  The
-# current version of gitpython requires python >= 3.7, which is newer than the
-# python included in the base image. Therefore, we manually install an older
-# gitpython to be used with OpenWormData.
-# See https://github.com/openworm/OpenWorm/pull/316
-RUN sudo pip install 'gitpython==2.1.15' markupsafe
-
-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
+RUN pip3 install neuron==8.0.1
 
 
 ################################################################################
 ########     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
+  git checkout ow-0.9.3 && \
+  sudo pip install .
+
+# 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-0.9.1 # fixed to a specific branch
+  git checkout ow-0.9.3  # fixed to a specific branch
 
 RUN cp c302/pyopenworm.conf sibernetic/   # Temp step until PyOpenWorm can be run from any dir...
 
@@ -120,10 +99,6 @@ 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
@@ -150,25 +125,16 @@ sudo apt install -y ocl-icd-opencl-dev vim
 ########     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 && \
+    sed -i -e "s/n2.7/n3.10/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
 
+################################################################################
+########     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 echo '\n\nalias cd..="cd .."\nalias h=history\nalias ll="ls -alt"' >> ~/.bashrc
 

VERSION

@@ -1 +1 @@
-0.9.2
+0.9.3

build.cmd

@@ -1 +1 @@
-docker build -t "openworm/openworm:0.9.2" .
+docker build -t "openworm/openworm:0.9.3" .

master_openworm.py

@@ -107,7 +107,7 @@ def execute_with_realtime_output(command, directory, env=None):
 sys.path.append(os.environ['C302_HOME'])
 
 try:
-    os.system('xhost +')
+    os.system('echo Granting permissions for xhost && xhost +')
 except:
     print("Unexpected error: %s" % sys.exc_info()[0])
 
@@ -137,18 +137,19 @@ def execute_with_realtime_output(command, directory, env=None):
             'reference': 'FW',
             'c302params': 'C2',
             'verbose': False,
-            'device': 'GPU',
+            'device': 'CPU',
             'configuration': 'worm_crawl_half_resolution',
             'noc302': noc302,
             'datareader': 'UpdatedSpreadsheetDataReader2',
             'outDir': OW_OUT_DIR}
 
 my_env = os.environ.copy()
-my_env["DISPLAY"] = ":44"
+DISPLAY = ':44'
+my_env["DISPLAY"] = DISPLAY
 
 # Xvfb or X virtual framebuffer is a display server implementing the X11 display server protocol.
 # In contrast to other display servers, Xvfb performs all graphical operations in virtual memory without showing any screen output.
-os.system('Xvfb :44 -listen tcp -ac -screen 0 1920x1080x24+32 &') # TODO: terminate xvfb after recording
+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
@@ -230,9 +231,11 @@ def execute_with_realtime_output(command, directory, env=None):
 time.sleep(2)
 
 # Rerun and record simulation
-os.system('export DISPLAY=:44')
+execute_with_realtime_output('ls -alt /tmp/.X11-unix', os.environ['SIBERNETIC_HOME'], env=my_env)
+os.system('export DISPLAY=%s'%DISPLAY)
+execute_with_realtime_output('ls -alt /tmp/.X11-unix', os.environ['SIBERNETIC_HOME'], env=my_env)
 sibernetic_movie_name = '%s.mp4' % os.path.split(latest_subdir)[-1]
-command = 'tmux new-session -d -s SiberneticRecording "DISPLAY=:44 ffmpeg -r 30 -f x11grab -draw_mouse 0 -s 1920x1080 -i :44 -filter:v "crop=1200:800:100:100" -cpu-used 0 -b:v 384k -qmin 10 -qmax 42 -maxrate 384k -bufsize 1000k -an %s/%s"' % (new_sim_out, sibernetic_movie_name)
+command = 'tmux new-session -d -P -s SiberneticRecording "DISPLAY=%s ffmpeg -r 30 -f x11grab -draw_mouse 0 -s 1920x1080 -i %s -filter:v "crop=1200:800:100:100" -cpu-used 0 -b:v 384k -qmin 10 -qmax 42 -maxrate 384k -bufsize 1000k -an %s/%s"' % (DISPLAY, DISPLAY, new_sim_out, sibernetic_movie_name)
 execute_with_realtime_output(command, os.environ['SIBERNETIC_HOME'], env=my_env)
 
 time.sleep(3)

run-shell-only.cmd

@@ -6,5 +6,5 @@ docker run -it ^
     -e OW_OUT_DIR=%OW_OUT_DIR% ^
     --privileged ^
     -v %HOST_OUT_DIR%:%OW_OUT_DIR%:rw ^
-    openworm/openworm:0.9.2 ^
+    openworm/openworm:0.9.3 ^
     /bin/bash

run.cmd

@@ -20,7 +20,7 @@ docker run -d ^
   -e DURATION=%DURATION% ^
   --privileged ^
   -v %HOST_OUT_DIR%:%OW_OUT_DIR%:rw ^
-  openworm/openworm:0.9.2 ^
+  openworm/openworm:0.9.3 ^
   /bin/bash -c "python master_openworm.py"
 
 docker logs -f openworm