Update submission script for opengate

Link data instead of copy for ccIn2p3
lint

Author: tbaudier

gatetools/clustertools/opengate_job_ccin2p3.slurm

@@ -59,7 +59,7 @@ cd $TMPDIR
 LOCALMACRODIR=$(mktemp -d -p .)
 trap "wait ; transferJobData ; exit 1" 1 2 3 15
 cd ${LOCALMACRODIR}
-cp -r -L "${MACRODIR}"/* .
+ln -s "${MACRODIR}"/* .
 rm -rf output
 mkdir output
 

gatetools/clustertools/opengate_run.py

@@ -1,139 +1,215 @@
 #!/pbs/throng/creatis/cl7/opengate/venv/bin/python
 
 import os
-import tempfile
 import shutil
-import click
 import socket
-import subprocess
-import colorama
-import numpy as np
-import sys
+import tempfile
 import time
+
+import click
+import colorama
+
 import gatetools
 
+
 def get_dns_domain():
-    domain = socket.getfqdn().split('.', 1)
+    domain = socket.getfqdn().split(".", 1)
     if len(domain) >= 2:
         return domain[1]
     else:
         return domain[0]
 
-CONTEXT_SETTINGS = dict(help_option_names=['-h', '--help'])
+
+CONTEXT_SETTINGS = dict(help_option_names=["-h", "--help"])
+
+
 @click.command(context_settings=CONTEXT_SETTINGS)
-@click.argument('script', nargs=1)
-@click.option('-j', '--jobs', default=1, help='Number of jobs/core')
-@click.option('-o', '--output', default='', help='Output folder path (default: run.XXX)')
-@click.option('-p', '--param', default='', help='click parameter to pass to the python script (-p " --angle 10 --nbParticles 1e8"')
-@click.option('--copydata', is_flag=True, help='Hard copy data into run.XXX folder (default: symbolic link)')
-@click.option('-d', '--dry', is_flag=True, help='If dry is set, copy all files, write the submission command lines but do not execute them')
-@click.option('--env', default='', help='Bash script to set environment variables during job. This file is source at the beginning.')
-@click.option('--jobfile', default='', help='Job file for the cluster allowing to modify submission parameters (--jobfile="current" display the path of the current job file and exit)')
-def runJobs_click(script, jobs, env, output, param, copydata, dry, jobfile):
+@click.argument("script", nargs=1)
+@click.option("-j", "--jobs", default=1, help="Number of jobs/core")
+@click.option(
+    "-o", "--output", default="", help="Output folder path (default: run.XXX)"
+)
+@click.option(
+    "-p",
+    "--param",
+    default="",
+    help='click parameter to pass to the python script (-p " --angle 10 --nbParticles 1e8"',
+)
+@click.option(
+    "-d",
+    "--dry",
+    is_flag=True,
+    help="If dry is set, write the submission command lines but do not execute them",
+)
+@click.option(
+    "--env",
+    default="",
+    help="Bash script to set environment variables during job. This file is source at the beginning.",
+)
+@click.option(
+    "--jobfile",
+    default="",
+    help='Job file for the cluster allowing to modify submission parameters (--jobfile="current" display the path of the current job file and exit)',
+)
+def runJobs_click(script, jobs, env, output, param, dry, jobfile):
     """
     \b
-    Run python Gate jobs
+    Run python opengate jobs
 
-    script: input python script filename
+    !!! Your python script must write all the outputs inside the folder called output !!!
 
-    """
-    runJobs_opengate(script, jobs, env, output, param, copydata, dry, jobfile)
+    example to run 10 jobs with the script script.py:
+    opengate_run -j 10 script.py
+
+    example in bash to run 1 job with different angles with the script script.py and write outputs in different folders:
+    for angle in 10 20 30; do
+      opengate_run -j 1 -p " --angle $angle --nbParticles 1e8" -o output_angle_$angle script.py
 
+    Then you can merge the results with the command opengate_power_merge
+    """
+    runJobs_opengate(script, jobs, env, output, param, dry, jobfile)
 
 
-def runJobs_opengate(script, jobs=1, env='', output='', param='', copydata=False, dry=False, jobfile=''):
-    directoryJobFiles = os.path.join(os.path.dirname(os.path.realpath(gatetools.__file__)), "clustertools")
+def runJobs_opengate(
+    script, jobs=1, env="", output="", param="", dry=False, jobfile=""
+):
+    directoryJobFiles = os.path.join(
+        os.path.dirname(os.path.realpath(gatetools.__file__)), "clustertools"
+    )
 
     # Source env file
-    envCommand = ''
-    if not env == '':
+    envCommand = ""
+    if not env == "":
         if not os.path.isabs(env):
-          env = os.path.join(os.getcwd(), env)
+            env = os.path.join(os.getcwd(), env)
         if not os.path.isfile(env):
-            print(colorama.Fore.RED + 'ERROR: No env found : ' + env + colorama.Style.RESET_ALL)
+            print(
+                colorama.Fore.RED
+                + "ERROR: No env found : "
+                + env
+                + colorama.Style.RESET_ALL
+            )
             exit(1)
         else:
             envCommand = env
     else:
-        envCommand = 'NONE'
+        envCommand = "NONE"
 
     jobFile = ""
     # Take the correct job file according to the cluster name and jobfile option
-    if jobfile == '' or jobfile == "current":
-        if get_dns_domain() == 'in2p3.fr':
-            jobFile = os.path.join(directoryJobFiles, 'opengate_job_ccin2p3.slurm')
+    if jobfile == "" or jobfile == "current":
+        if get_dns_domain() == "in2p3.fr":
+            jobFile = os.path.join(directoryJobFiles, "opengate_job_ccin2p3.slurm")
         if jobfile == "current":
-            print(colorama.Fore.GREEN + 'Path to the job file: ' + colorama.Style.RESET_ALL)
+            print(
+                colorama.Fore.GREEN
+                + "Path to the job file: "
+                + colorama.Style.RESET_ALL
+            )
             print(jobFile)
             exit(1)
     else:
         jobFile = jobfile
         if not os.path.isabs(jobFile):
-          jobFile = os.path.join(os.getcwd(), jobFile)
+            jobFile = os.path.join(os.getcwd(), jobFile)
         if not os.path.isfile(jobFile):
-            print(colorama.Fore.RED + 'ERROR: The job file does not exist: ' + jobFile + colorama.Style.RESET_ALL)
+            print(
+                colorama.Fore.RED
+                + "ERROR: The job file does not exist: "
+                + jobFile
+                + colorama.Style.RESET_ALL
+            )
             exit(1)
 
     # Get python folder and files
     fullMacroDir = os.path.join(os.getcwd(), os.path.dirname(os.path.dirname(script)))
     fullScriptFile = os.path.join(fullMacroDir, os.path.basename(script))
     if not os.path.isfile(script):
-        print(colorama.Fore.RED + 'ERROR: The python file does not exist: ' + script + colorama.Style.RESET_ALL)
+        print(
+            colorama.Fore.RED
+            + "ERROR: The python file does not exist: "
+            + script
+            + colorama.Style.RESET_ALL
+        )
         exit(1)
 
     # Check output path is absolute or relative
     outputDir = output
-    if not outputDir == '' and not os.path.isabs(outputDir):
-      outputDir = os.path.join(os.getcwd(), outputDir)
+    if not outputDir == "" and not os.path.isabs(outputDir):
+        outputDir = os.path.join(os.getcwd(), outputDir)
     # Create output directory
-    if not outputDir == '' and os.path.isdir(outputDir):
-        print(colorama.Fore.YELLOW + 'WARNING: The output folder already exist: ' + outputDir + colorama.Style.RESET_ALL)
-        print(colorama.Fore.YELLOW + 'Evereything will be overwritten' + colorama.Style.RESET_ALL)
-    if outputDir == '':
-        outputDir = tempfile.mkdtemp(prefix='run.', dir=fullMacroDir)
+    if not outputDir == "" and os.path.isdir(outputDir):
+        print(
+            colorama.Fore.YELLOW
+            + "WARNING: The output folder already exist: "
+            + outputDir
+            + colorama.Style.RESET_ALL
+        )
+        print(
+            colorama.Fore.YELLOW
+            + "Evereything will be overwritten"
+            + colorama.Style.RESET_ALL
+        )
+    if outputDir == "":
+        outputDir = tempfile.mkdtemp(prefix="run.", dir=fullMacroDir)
     elif not os.path.isdir(outputDir):
         os.makedirs(outputDir)
-    runId = os.path.basename(outputDir)[os.path.basename(outputDir).find('.') +1:]
-    if runId == '':
+    runId = os.path.basename(outputDir)[os.path.basename(outputDir).find(".") + 1 :]
+    if runId == "":
         runId == os.path.basename(outputDir)
-    print('Run Id is: ' + runId)
+    print("Run Id is: " + runId)
 
     # Find qsub
-    qsub = shutil.which('qsub')
+    qsub = shutil.which("qsub")
     if qsub is None:
-        qsub = shutil.which('sbatch')
+        qsub = shutil.which("sbatch")
         if qsub is None:
-            print('No qsub, run Gate on multiple cores.')
+            print("No qsub, run Gate on multiple cores.")
 
     # Parameter files
-    paramFileName = os.path.join(outputDir, 'run.log')
+    paramFileName = os.path.join(outputDir, "run.log")
     paramFile = open(paramFileName, "w")
-    paramFile.write('number of jobs = ' + str(jobs) + '\n')
-    paramFile.write('script = ' + script + '\n')
-    paramFile.write('runId = ' + runId + '\n')
+    paramFile.write("number of jobs = " + str(jobs) + "\n")
+    paramFile.write("script = " + script + "\n")
+    paramFile.write("runId = " + runId + "\n")
 
-    #Create file to write commands in it
-    paramFile.write('\ncommands: \n')
+    # Create file to write commands in it
+    paramFile.write("\ncommands: \n")
 
     # Run jobs
     for i in range(0, jobs):
-        #Set paramtogate with param for each job
+        # Set paramtogate with param for each job
         paramtogateJob = param
 
-        if get_dns_domain() == 'in2p3.fr':
-            tempParamFile = tempfile.NamedTemporaryFile(mode='w+t', delete=False, prefix='var.', dir=outputDir)
+        command = ""
+        if get_dns_domain() == "in2p3.fr":
+            tempParamFile = tempfile.NamedTemporaryFile(
+                mode="w+t", delete=False, prefix="var.", dir=outputDir
+            )
             tempParamFile.write(paramtogateJob)
             tempParamFile.close()
-            command = 'sbatch -L sps -J gate.' + runId + \
-                      ' -D ' + outputDir + \
-                      ' --export=ALL,PARAM=\"' + tempParamFile.name + \
-                      '\",INDEX=' + str(i) + \
-                      ',INDEXMAX=' + str(jobs) + \
-                      ',OUTPUTDIR=' + outputDir + \
-                      ',MACROFILE=' + fullScriptFile + \
-                      ',MACRODIR=' + os.path.dirname(fullScriptFile) + \
-                      ',ENVCOMMAND=' + envCommand + \
-                      ' ' + jobFile
+            command = (
+                "sbatch -L sps -J gate."
+                + runId
+                + " -D "
+                + outputDir
+                + ' --export=ALL,PARAM="'
+                + tempParamFile.name
+                + '",INDEX='
+                + str(i)
+                + ",INDEXMAX="
+                + str(jobs)
+                + ",OUTPUTDIR="
+                + outputDir
+                + ",MACROFILE="
+                + fullScriptFile
+                + ",MACRODIR="
+                + os.path.dirname(fullScriptFile)
+                + ",ENVCOMMAND="
+                + envCommand
+                + " "
+                + jobFile
+            )
         paramFile.write(command)
         paramFile.write("\n")
         if dry:
@@ -144,8 +220,8 @@ def runJobs_opengate(script, jobs=1, env='', output='', param='', copydata=False
                 time.sleep(1)
 
     paramFile.close()
-    print(str(jobs) + ' jobs running')
-    print('Run folder is: ' + outputDir)
+    print(str(jobs) + " jobs running")
+    print("Run folder is: " + outputDir)
 
 
 if __name__ == "__main__":