Back to dockerfile & master_openworm.py from master; to v0.9.2

Author: pgleeson

Dockerfile

@@ -1,4 +1,4 @@
-FROM ubuntu:22.04
+FROM ubuntu:18.04
 
 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 python3-dev mercurial \
+  libxext-dev libncurses-dev python-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
 
@@ -62,7 +62,8 @@ RUN  sudo update-alternatives --install /usr/bin/pip pip /usr/bin/pip3 10
 ################################################################################
 ########     Install NEURON simulator
 
-RUN pip3 install neuron==8.0.1
+RUN sudo pip install neuron==7.8.1
+
 
 ################################################################################
 ########     Install pyNeuroML for handling NeuroML network model
@@ -149,7 +150,8 @@ sudo apt install -y ocl-icd-opencl-dev vim
 ########     Build Sibernetic
 
 RUN cd sibernetic && \
-    sed -i -e "s/n2.7/n3.10/g" makefile && \
+    sed -i -e "s/lpython2.7/lpython3.6m/g" makefile && \
+    sed -i -e "s/n2.7/n3.6/g" makefile && \
     make clean && make all  # Use python 3 libs
 
 # intel i5, hd 5500, linux 4.15.0-39-generic

VERSION

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

master_openworm.py

@@ -2,7 +2,7 @@
 import matplotlib
 matplotlib.use('Agg')
 import shutil
-from subprocess import Popen, PIPE, check_output, STDOUT
+from subprocess import Popen, PIPE, check_output
 import os
 import pwd
 import shlex
@@ -12,7 +12,7 @@
 import math
 
 print("*****************************")
-print("OpenWorm Master Script v0.9.3")
+print("OpenWorm Master Script v0.9.2")
 print("*****************************")
 print("")
 print("This script attempts to run a full pass through the OpenWorm scientific libraries.")
@@ -76,28 +76,16 @@
 def execute_with_realtime_output(command, directory, env=None):
     p = None
     try:
-
-        print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>')
-        print('>> Executing command: %s'%command)
-        print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>')
-        p = Popen(shlex.split(command),
-                  stdout=PIPE,
-                  stderr=STDOUT,
-                  cwd=directory,
-                  env=env)
+        p = Popen(shlex.split(command), stdout=PIPE, bufsize=1, cwd=directory, env=env)
         with p.stdout:
             for line in iter(p.stdout.readline, b''):
-                 print('>> %s'%line.decode('utf-8'), end='')
+                 print(line.decode('utf-8'), end='')     
         p.wait() # wait for the subprocess to exit
     except KeyboardInterrupt as e:
         print("Caught CTRL+C")
         if p:
             p.kill()
         raise e
-    print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>')
-    print('>> Command exited with %i: %s'%(p.returncode,command))
-    print('>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>\n')
-
 
 
 sys.path.append(os.environ['C302_HOME'])
@@ -122,10 +110,6 @@ def execute_with_realtime_output(command, directory, env=None):
 if 'DURATION' in os.environ:
     sim_duration = float(os.environ['DURATION'])
 
-noc302 = False
-if 'NOC302' in os.environ:
-    noc302 = bool(os.environ['NOC302'])
-
 DEFAULTS = {'duration': sim_duration,
             'dt': 0.005,
             'dtNrn': 0.05,
@@ -135,7 +119,7 @@ def execute_with_realtime_output(command, directory, env=None):
             'verbose': False,
             'device': 'GPU',
             'configuration': 'worm_crawl_half_resolution',
-            'noc302': noc302,
+            'noc302': False,
             'datareader': 'UpdatedSpreadsheetDataReader2',
             'outDir': OW_OUT_DIR}
 
@@ -167,9 +151,6 @@ def execute_with_realtime_output(command, directory, env=None):
                 DEFAULTS['datareader'],
                 'simulations')
                 #DEFAULTS['outDir'])
-
-    if noc302: command += ' -noc302'
-
     execute_with_realtime_output(command, os.environ['SIBERNETIC_HOME'], env=my_env)
 except KeyboardInterrupt as e:
     pass
@@ -181,13 +162,9 @@ def execute_with_realtime_output(command, directory, env=None):
     for directory in dirnames:
         if directory.startswith('%s_%s' % (DEFAULTS['c302params'], DEFAULTS['reference'])):
             all_subdirs.append(os.path.join(dirpath, directory))
-        if directory.startswith('Sibernetic'):
-            all_subdirs.append(os.path.join(dirpath, directory))
 
 latest_subdir = max(all_subdirs, key=os.path.getmtime)
-print('\n========================================================================\n')
-print('Finished main simulation, data saved in: %s'%latest_subdir)
-execute_with_realtime_output('ls -alt %s'%latest_subdir, os.environ['SIBERNETIC_HOME'], env=my_env)
+
 
 try:
     os.mkdir('%s/output' % OW_OUT_DIR)
@@ -221,9 +198,6 @@ def execute_with_realtime_output(command, directory, env=None):
     print("Moving %s to %s"%(wcon, new_sim_out))
     shutil.move(wcon, new_sim_out)
 
-time.sleep(2)
-
-
 
 # Rerun and record simulation
 os.system('export DISPLAY=:44')
@@ -236,9 +210,7 @@ def execute_with_realtime_output(command, directory, env=None):
 os.system('tmux send-keys -t SiberneticRecording q')
 os.system('tmux send-keys -t SiberneticRecording "exit" C-m')
 
-time.sleep(5)
-
-execute_with_realtime_output('ls -alt %s'%latest_subdir, os.environ['SIBERNETIC_HOME'], env=my_env)
+time.sleep(3)
 
 # Remove black frames at the beginning of the recorded video
 command = "ffmpeg -i %s/%s -vf blackdetect=d=0:pic_th=0.70:pix_th=0.10 -an -f null - 2>&1 | grep blackdetect" % (new_sim_out, sibernetic_movie_name)
@@ -275,7 +247,7 @@ def execute_with_realtime_output(command, directory, env=None):
 os.system('ffmpeg -ss 1 -i %s/cut_%s -vf "select=gt(scene\,0.1)" -vsync vfr -vf fps=fps=1/1 %s' % (new_sim_out, sibernetic_movie_name, 'tmp/out%06d.jpg'))
 os.system('ffmpeg -r 100 -i %s -r 100 -vb 60M %s/speeded_%s' % ('tmp/out%06d.jpg', new_sim_out, sibernetic_movie_name))
 
-os.system('rm -r tmp/*')
+os.system('sudo rm -r tmp/*')