Merge branch 'papeleux' into 'master'

parametricJob : fix kill scripts

See merge request am-dept/linuxbin!38

cfg/clifton/cmake.profile

+add2env PATH "/opt/cmake/bin" front

cfg/spring/gmsh.profile

+add2env PATH "/opt/gmsh/bin" front
+add2env LD_LIBRARY_PATH "/opt/gmsh/lib"
+add2env PYTHONPATH "/opt/gmsh/lib"

cfg/spring/matlab.profile

+add2env PATH "/opt/matlab/bin"

cfg/spring/mumps.profile

+add2env LD_LIBRARY_PATH "/opt/mumps/lib"
+add2env LIB "/opt/mumps/lib"
+add2env INCLUDE "/opt/mumps/include"

cfg/spring/oneApi.bashrc

+# Intel compiler and/or TBB/MKL 
+#
+# EXPLANATIONS [RB]: (see "cfg/garfield/compilers.*")
+
+if [ -d /opt/intel ] ; then
+     #. /opt/intel/oneapi/setvars.sh intel64
+     # since last update of one api latest -> 2022.2.0 (not complete)
+     . /opt/intel/oneapi/tbb/latest/env/vars.sh intel64
+     . /opt/intel/oneapi/mkl/latest/env/vars.sh intel64
+     . /opt/intel/oneapi/compiler/latest/env/vars.sh intel64
+     #. /opt/intel/oneapi/tbb/2021.6.0/env/vars.sh intel64     
+     #. /opt/intel/oneapi/mkl/2022.1.0/env/vars.sh intel64
+     #. /opt/intel/oneapi/compiler/2022.1.0/env/vars.sh intel64
+
+fi

cfg/spring/oneApi.profile

+# Intel compiler and/or TBB/MKL 
+#
+# EXPLANATIONS [RB]: (see "cfg/garfield/compilers.*")
+
+if [ -d /opt/intel ] ; then
+     #. /opt/intel/oneapi/setvars.sh intel64
+     . /opt/intel/oneapi/tbb/latest/env/vars.sh intel64     
+     . /opt/intel/oneapi/mkl/latest/env/vars.sh intel64
+     . /opt/intel/oneapi/compiler/latest/env/vars.sh intel64
+
+fi

cfg/spring/parasolid.profile

+# Parasolid
+
+add2env PATH "/opt/parasolid/shared_object"
+add2env INCLUDE "/opt/parasolid"
+export P_SCHEMA=/opt/parasolid/schema

cfg/spring/samcef.profile

+export SAM_ZONE=200000000
+add2env PATH "/opt/samcef"

cfg/vaillant/cmake.profile

+# 
+add2env PATH "/opt/cmake/bin" front

parametricJob.py

@@ -4,7 +4,7 @@
 #from future import standard_library
 #standard_library.install_aliases()
 import sys, os, os.path, shutil, socket, platform, glob, fnmatch
-import datetime, tarfile, subprocess, string
+import datetime, tarfile, subprocess, string, re
 from prmClasses import *
 
 # -- Base Class ----------------------------------------------------------------
@@ -35,7 +35,6 @@ class ParametricJob(PRMSet):
         return niceCmd
 
     def getMailData(self):
-        import re
         fromAddr = "%s@%s" % (os.path.basename(sys.argv[0]), socket.gethostbyaddr(socket.gethostname())[0])
         toAddr   = self.pars['MAIL_ADDR'].val
         if re.match('(.+)@(.+)',toAddr):
@@ -166,7 +165,6 @@ class ParametricJob(PRMSet):
         return cfgfile
 
     def hasSysCmd(self, cmd):
-        import subprocess
         status, result = subprocess.getstatusoutput("which %s" % cmd)
         return status==0
 
@@ -269,7 +267,6 @@ class ParametricJob(PRMSet):
         # get guess profile
         cfgfile = self.guessProfile()        
         cfgFileName, cfgFileExtension = os.path.splitext(self.cfgfile)
-        import re
         m = re.compile(cfgFileName+'([0-9]+)\\'+cfgFileExtension)
         #print (cfgFileName+'([0-9]+)\\'+cfgFileExtension)
         launchId = 0        
@@ -297,7 +294,7 @@ class ParametricJob(PRMSet):
         #file.write("echo \"at JobId = $jobId\"\n")
         #file.write('%s -x -i $jobId -d "%s"\n' % (sys.argv[0], os.getcwd()) )
         script =  re.sub(r'(.+)Gui.pyw',r'\1.py', sys.argv[0]) #if launched through a Gui => use the basic script instead in batch
-        file.write('%s -x -i %d -d "%s"\n' % (script, launchId, os.getcwd()) )
+        file.write('setsid %s -x -i %d -d "%s"\n' % (script, launchId, os.getcwd()) ) # setsid added to generate a new process group (used to easily kill process tree), else the process group is the same as atd daemon (=> killScript kill all at process running)
         file.close()
         os.chmod(scriptname,0o700)
         
@@ -312,14 +309,12 @@ class ParametricJob(PRMSet):
         #shcmd="at now + 1 minutes -f %s" % (scriptname)
         #shcmd="at now %s" % scriptname
         print("shcmd = ", shcmd)
-        import subprocess
         status, result = subprocess.getstatusoutput(shcmd)
         if status!=0:
             print("Job submission FAILED!")
         else:
             print("Submission SUCCESSFUL!")
             #print "result = ", result
-            import re
             m = re.search('job ([0-9]+)',result)
             batchId = m.group(1)
             #print m.group
@@ -402,14 +397,12 @@ class ParametricJob(PRMSet):
         # send to sge
         print("sending job '%s' to SGE" % jobname)
         shcmd="qsub ./%s" % scriptname
-        import subprocess
         status, result = subprocess.getstatusoutput(shcmd)
         print(result)
         if status!=0:
             print("Job submission FAILED!")
         else:
             print("Submission SUCCESSFUL!")
-            import re
             m = re.compile('Your job ([0-9]+)').match(result)
             sgeId = m.group(1)
             if m:
@@ -498,14 +491,12 @@ class ParametricJob(PRMSet):
         # send to slurm
         print("sending job '%s' to Slurm" % jobname)
         shcmd="sbatch ./%s" % scriptname
-        import subprocess
         status, result = subprocess.getstatusoutput(shcmd)
         print(result)
         if status!=0:
             print("Job submission FAILED!")
         else:
             print("Submission SUCCESSFUL!")
-            import re
             m = re.compile('Submitted batch job ([0-9]+)').match(result)
             slurmId = m.group(1)
             if m:
@@ -628,7 +619,6 @@ class ParametricJob(PRMSet):
         # send to PBS
         print('sending job "%s" to PBS' % jobname)
         shcmd='qsub ./%s' % scriptname
-        import subprocess
         status, result = subprocess.getstatusoutput(shcmd)
         print('command status = ', status)
         print('command result = ', result)
@@ -644,23 +634,6 @@ class ParametricJob(PRMSet):
             self.PBSCancelScript(PbsId)
             print("\tuse ' qstat -f %s ' to check the status of the PBS scheduling queue of your job" % PbsId)
             print("\tuse ' qdel %s ' to kill your job" % PbsId)
-            '''
-            #import re
-            #m = re.compile('waiting for job ([0-9]+) to start').match(result)            
-            #result : 3067709.frontal2
-            #m = re.compile('([0-9]+)\.(.+)').match(result)
-            #print "m = ", m
-            #PbsId = m.group(1)
-            if m:
-                cfgFileName, cfgFileExtension = os.path.splitext(self.cfgfile)
-                os.system("cp %s %s%s%s"%(self.cfgfile, cfgFileName, PbsId, cfgFileExtension))
-                self.PBSCancelScript(PbsId)
-                print "\tuse ' qstat -f %s ' to check the status of the PBS scheduling queue of your job" % PbsId
-                #print "\tuse ' sprio -l -j %s ' to check the factor priority of your job" % PbsId
-                #print "\tuse ' sstat  -a --format=JobID,NTasks,MaxRSS,MaxVMSize -j %s ' to get information about your running job (adapt format to your needs)" % PbsId
-                print "\tuse ' qdel %s ' to kill your job" % PbsId
-                #print "\tuse ' sacct --format=JobID,NTasks,NCPUS,CPUTime,Elapsed,MaxRSS,MaxVMSize -j %s ' to get information about your finished job (adapt format to your needs)" % PbsId
-             '''
         # to avoid closing the gui
         if not (re.match(r'(.+)Gui.pyw', sys.argv[0])): 
             sys.exit()