Tidy up master_openworm.py & make more cmd line options

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

@@ -28,6 +28,7 @@ jobs:
 
     - name: Run the Docker image
       run: |
+        sudo apt-get update && sudo apt-get install -y x11-xserver-utils # for xhost
         ./run.sh
 
     - name: Info on generated files

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

@@ -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 +4,9 @@ output/C2*
 /output/siminfo.py
 /output/wor*
 /output/Sibernetic_*
+/output/test*
+/output/box
+/output/swim*
+/output/alone*
+/output/cube*
+/output/master*

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!"
+

master_openworm.py

@@ -12,67 +12,20 @@
 import math
 
 print("*****************************")
-print("OpenWorm Master Script")
+print("  OpenWorm Master Script")
 print("*****************************")
 print("")
-print(
-    "This script attempts to run a full pass through the OpenWorm scientific libraries."
-)
+print("This script attempts to run a full pass through the OpenWorm software stack.")
 print(
     "This depends on several other repositories being loaded to work and presumes it is running in a preloaded Docker instance."
 )
 print("It will report out where steps are missing.")
 print("Eventually all the steps will be filled in.")
 print("")
 
-print("****************************")
-print("Step 1: Rebuild c302 from the latest owmeta")
-print("****************************")
-print("Not yet implemented. See https://github.com/openworm/c302/issues/10")
-
 
 print("****************************")
-print("Step 2: Execute unit tests via the c302 simulation framework")
-print("****************************")
-"""
-from runAndPlot import run_c302
-orig_display_var = None
-if os.environ.has_key('DISPLAY'):
-    orig_display_var = os.environ['DISPLAY']
-    del os.environ['DISPLAY'] # https://www.neuron.yale.edu/phpBB/viewtopic.php?f=6&t=1603
-
-run_c302(DEFAULTS['reference'],
-         DEFAULTS['c302params'],
-         '',
-         DEFAULTS['duration'],
-         DEFAULTS['dt'],
-         'jNeuroML_NEURON',
-         data_reader=DEFAULTS['datareader'],
-         save=True,
-         show_plot_already=False,
-         target_directory=os.path.join(os.environ['C302_HOME'], 'examples'),
-         save_fig_to='tmp_images')
-prev_dir = os.getcwd()
-os.chdir(DEFAULTS['outDir'])
-try:
-    os.mkdir('c302_out')
-except OSError as e:
-    if e.errno != errno.EEXIST:
-        raise
-src_files = os.listdir(os.path.join(os.environ['C302_HOME'], 'examples', 'tmp_images'))
-for file_name in src_files:
-    full_file_name = os.path.join(os.environ['C302_HOME'], 'examples', 'tmp_images', file_name)
-    print("COPY %s" % full_file_name)
-    if (os.path.isfile(full_file_name)):
-        shutil.copy2(full_file_name, 'c302_out')
-shutil.rmtree(os.path.join(os.environ['C302_HOME'], 'examples', 'tmp_images'))
-os.chdir(prev_dir)
-if orig_display_var:
-    os.environ['DISPLAY'] = orig_display_var
-"""
-
-print("****************************")
-print("Step 3: Run c302 + Sibernetic in the same loop.")
+print("  Step 1: Run c302 + Sibernetic in the same loop.")
 print("****************************")
 
 OW_OUT_DIR = os.environ["OW_OUT_DIR"]
@@ -112,8 +65,6 @@ def execute_with_realtime_output(command, directory, env=None):
 except Exception:
     print("Unexpected error: %s" % sys.exc_info()[0])
 
-OW_OUT_DIR = os.environ["OW_OUT_DIR"]
-
 
 try:
     if os.access(OW_OUT_DIR, os.W_OK) is not True:
@@ -130,20 +81,26 @@ def execute_with_realtime_output(command, directory, env=None):
 if "DURATION" in os.environ:
     sim_duration = float(os.environ["DURATION"])
 
-noc302 = False
+
+configuration = "worm_crawl_half_resolution"
+if "CONFIGURATION" in os.environ:
+    configuration = os.environ["CONFIGURATION"]
+
 if "NOC302" in os.environ:
-    noc302 = bool(os.environ["NOC302"])
+    noc302 = os.environ["NOC302"] == "1"
+else:
+    noc302 = "worm" not in configuration
 
-DEFAULTS = {
+PARAMETERS = {
     "duration": sim_duration,
     "dt": 0.005,
     "dtNrn": 0.05,
     "logstep": 100,
-    "reference": "FW",
+    "reference": "FW", # "TargetMuscle",
     "c302params": "C2",
     "verbose": False,
     "device": "CPU",
-    "configuration": "worm_crawl_half_resolution",
+    "configuration": configuration,
     "noc302": noc302,
     "datareader": "UpdatedSpreadsheetDataReader2",
     "outDir": OW_OUT_DIR,
@@ -161,6 +118,10 @@ def execute_with_realtime_output(command, directory, env=None):
 )  # TODO: terminate xvfb after recording
 
 try:
+    print("Starting Sibernetic simulation with parameters:")
+    for p in PARAMETERS:
+        print("  %s: %s" % (p, PARAMETERS[p]))
+
     command = """python3 sibernetic_c302.py
                 -duration %s
                 -dt %s
@@ -172,23 +133,24 @@ def execute_with_realtime_output(command, directory, env=None):
                 -c302params %s
                 -datareader %s
                 -outDir %s""" % (
-        DEFAULTS["duration"],
-        DEFAULTS["dt"],
-        DEFAULTS["dtNrn"],
-        DEFAULTS["logstep"],
-        DEFAULTS["device"],
-        DEFAULTS["configuration"],
-        DEFAULTS["reference"],
-        DEFAULTS["c302params"],
-        DEFAULTS["datareader"],
+        PARAMETERS["duration"],
+        PARAMETERS["dt"],
+        PARAMETERS["dtNrn"],
+        PARAMETERS["logstep"],
+        PARAMETERS["device"],
+        PARAMETERS["configuration"],
+        PARAMETERS["reference"],
+        PARAMETERS["c302params"],
+        PARAMETERS["datareader"],
         "simulations",
     )
-    # DEFAULTS['outDir'])
+    # PARAMETERS['outDir'])
 
     if noc302:
         command += " -noc302"
 
     execute_with_realtime_output(command, os.environ["SIBERNETIC_HOME"], env=my_env)
+
 except KeyboardInterrupt:
     pass
 
@@ -198,7 +160,7 @@ def execute_with_realtime_output(command, directory, env=None):
 for dirpath, dirnames, filenames in os.walk(sibernetic_sim_dir):
     for directory in dirnames:
         if directory.startswith(
-            "%s_%s" % (DEFAULTS["c302params"], DEFAULTS["reference"])
+            "%s_%s" % (PARAMETERS["c302params"], PARAMETERS["reference"])
         ):
             all_subdirs.append(os.path.join(dirpath, directory))
         if directory.startswith("Sibernetic"):
@@ -237,6 +199,16 @@ def execute_with_realtime_output(command, directory, env=None):
     print("Moving %s to %s" % (report, new_sim_out))
     shutil.move(report, new_sim_out)
 
+# Copy position files etc.
+txt_files = glob.glob("%s/*.txt" % latest_subdir)
+for txt_file in txt_files:
+    print("Moving %s to %s" % (txt_file, new_sim_out))
+    shutil.move(txt_file, new_sim_out)
+dat_files = glob.glob("%s/*.dat" % latest_subdir)
+for dat_file in dat_files:
+    print("Moving %s to %s" % (dat_file, new_sim_out))
+    shutil.move(dat_file, new_sim_out)
+
 # Copy WCON file(s)
 wcons = glob.glob("%s/*.wcon" % latest_subdir)
 for wcon in wcons:
@@ -267,7 +239,7 @@ def execute_with_realtime_output(command, directory, env=None):
 )
 
 command = "./Release/Sibernetic -f %s -l_from lpath=%s" % (
-    DEFAULTS["configuration"],
+    PARAMETERS["configuration"],
     latest_subdir,
 )
 execute_with_realtime_output(command, os.environ["SIBERNETIC_HOME"], env=my_env)
@@ -350,7 +322,7 @@ def execute_with_realtime_output(command, directory, env=None):
 
 
 print("****************************")
-print("Step 4: Run movement analysis")
+print("  Step 2: Run movement analysis")
 print("****************************")
 print("Not yet implemented.")
 print(
@@ -360,6 +332,6 @@ def execute_with_realtime_output(command, directory, env=None):
 
 
 print("****************************")
-print("Step 5: Report on movement analysis fit to real worm videos")
+print(" Step 3: Report on movement analysis fit to real worm videos")
 print("****************************")
 print("Not yet implemented.")

run-jl.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+version=$(<VERSION) # Read version of Dockerfile from file VERSION
+
+docker run -it --rm -p 8888:8888 "openworm/openworm:$version" jupyter lab --NotebookApp.default_url=/lab/ --ip=0.0.0.0 --port=8888 --allow-root

run-quick.sh

@@ -1,4 +1,5 @@
 #!/bin/bash
+set -ex
 
 #from: https://unix.stackexchange.com/a/129401
 while getopts ":d:p:" opt; do
@@ -16,7 +17,7 @@ OW_OUT_DIR=/home/ow/shared
 HOST_OUT_DIR=$PWD
 version=$(<VERSION) # Read version of Dockerfile from file VERSION
 
-xhost +
+xhost + || true # allow connections to X server, don't throw an error if it fails
 
 
 NOC302_PART="-e NOC302=1"
@@ -33,6 +34,6 @@ $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