sherpaTarCreator.sge_grace.batchJob Class Reference

Inheritance diagram for sherpaTarCreator.sge_grace.batchJob:

Collaboration diagram for sherpaTarCreator.sge_grace.batchJob:

Public Member Functions
def	submit (self, dryRun=False)
def	write (self, useSingularity=True, extraDirs=[])

Public Attributes
	id
	name
	cmds
	hours
	nCores
	memMB
	env
	basedir
	dependsOnOk
	dependsOnAny

Detailed Description

Definition at line 14 of file sge_grace.py.

Member Function Documentation

submit()

def sherpaTarCreator.sge_grace.batchJob.submit	(		self,
			dryRun = False
	)

Definition at line 16 of file sge_grace.py.

    def submit(self, dryRun=False):
 
        cmd = "qsub -e "+self.basedir+"/"+self.name+".log -o "+self.basedir+"/"+self.name+".log"
 
        if len(self.dependsOnOk)>0 or len(self.dependsOnAny)>0:
            cmd += " -hold_jid "
            if len(self.dependsOnOk)>0:
                #okdeps = "afterok:"+",afterok:".join(self.dependsOnOk)
                #cmd += okdeps+","
                cmd += str(self.dependsOnOk[-1])
            if len(self.dependsOnAny)>0:
                #anydeps = "afterany:"+",afterany:".join(self.dependsOnAny)
                #cmd += anydeps+","
                cmd += str(self.dependsOnAny[-1])
 
        if "ecm" in self.basedir:
            jobname = os.path.basename(os.path.normpath(self.basedir+"/../"))+"_"+self.name
        else:
            jobname = os.path.basename(os.path.normpath(self.basedir))+"_"+self.name
        #cmd += " -J "+jobname+" "+self.basedir+"/"+self.name+".sh" # >> qsub.log \n"
 
        user = os.environ.get('USER')
        cmd += " >> qsub.log <<EOF \n"
        cmd += "#!/bin/bash -l\n"
        cmd += "set -e;\n"
        cmd += "#$ -S /bin/bash\n"
        cmd += "#$ -l h_rt=%i:0:0\n" % self.hours
        cmd += "#$ -l mem=%iG\n" % int(round(0.001*self.memMB))
        cmd += "#$ -N j%s\n" % jobname
        cmd += "#$ -pe mpi %i\n" % self.nCores
        cmd += "#$ -wd %s\n" % self.basedir
        cmd += "cd %s;\n" % self.basedir
        cmd += "ulimit -f 3000000;\n"
        cmd += "export PARROT_CVMFS_ALIEN_CACHE=/lustre/scratch/scratch/%s/cvmfs_cache/\n" % user
        cmd += 'export PARROT_CVMFS_REPO="<default-repositories> url=http://cvmfs-atlas-nightlies.cern.ch/cvmfs/atlas-nightlies.cern.ch"\n'
        cmd += "module unload compilers mpi\n"
        cmd += "module load compilers/gnu/4.9.2\n"
        cmd += "module load cctools/7.0.11/gnu-4.9.2\n"
        cmd += "module load mpi/openmpi/1.8.4/gnu-4.9.2\n"
        cmd += "module load python/2.7.12\n"
        cmd += "module load python2/recommended\n"
        cmd += "module load scons/2.3.4\n"
        cmd += "module load texinfo/6.6\n"
        mpiwrap = 'gerun ' if self.nCores > 4 else ''
        cmd += "(parrot_run bash -c \'"+mpiwrap+self.basedir+"/"+self.name+".sh\') >> "+self.basedir+"/"+self.name+".log;\n"
        cmd += "exit 0;\n"
        cmd += "EOF\n"
 
        if dryRun:
            print (cmd+"\n")
            self.id = -1
        else:
            print (cmd)
            p = subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE,stderr=subprocess.PIPE)
            retcode = p.communicate()
            if len(retcode[0]):
                print (retcode[0])
            if len(retcode[1]):
                print (retcode[1])
            if p.returncode:
                print ("ERROR: error while submitting job")
                print ("return code: " + str(p.returncode))
                sys.exit(11)
 
            p.wait()
            self.id = getJobIDfromlastJob()
 
        print("Submitted "+str(self.id)+" ("+self.name+")")
 
 

write()

def sherpaTarCreator.batchJobBase.batchJobBase.write (   self,   useSingularity = True,   extraDirs = []  )

inherited

Definition at line 24 of file batchJobBase.py.

  def write(self, useSingularity=True, extraDirs=[]):
    executable =  "#!/bin/sh -\n"
 
    # COMPILER_PATH
    if useSingularity:
      platform = str(os.environ['COMPILER_PATH']).split('/')[-1].replace('el9', 'almalinux9')
      executable += 'if [ "$1" != "--really" ]; then \n'
      executable += '  exec singularity exec -e --no-home'
      for dir in ["/cvmfs", "/var", self.basedir, "$(pwd | cut -d '/' -f 1-2)"] + extraDirs:
        executable += ' -B '+dir
      executable += ' /cvmfs/atlas.cern.ch/repo/containers/fs/singularity/'
      executable += platform + ' /bin/bash -- "$0" --really "$@";\n'
      executable += 'fi\n'
      executable += "shift;\n\n"
      executable += "export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase\n"
      executable += "source ${ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh\n"
 
    executable += "ulimit -f 1000000;\n"
    executable += "cd "+self.basedir+"\n\n"
    executable += "echo 'ncores="+str(self.nCores)+" nhours="+str(self.hours)+" "+self.basedir+"/"+self.name+".sh';\n"
    for cmd in self.cmds:
      executable += cmd+"\n"
    executable += "exit 0\n"
 
 
    filename = self.basedir+"/"+self.name+".sh"
    with open(filename, 'w') as f:
        f.write(executable)
 
    #make shell-files executable
    st = os.stat(filename)
    os.chmod(filename, st.st_mode | stat.S_IEXEC)
 
 

Member Data Documentation

basedir

sherpaTarCreator.batchJobBase.batchJobBase.basedir

inherited

Definition at line 19 of file batchJobBase.py.

cmds

sherpaTarCreator.batchJobBase.batchJobBase.cmds

inherited

Definition at line 10 of file batchJobBase.py.

dependsOnAny

sherpaTarCreator.batchJobBase.batchJobBase.dependsOnAny

inherited

Definition at line 22 of file batchJobBase.py.

dependsOnOk

sherpaTarCreator.batchJobBase.batchJobBase.dependsOnOk

inherited

Definition at line 21 of file batchJobBase.py.

env

sherpaTarCreator.batchJobBase.batchJobBase.env

inherited

Definition at line 18 of file batchJobBase.py.

hours

sherpaTarCreator.batchJobBase.batchJobBase.hours

inherited

Definition at line 11 of file batchJobBase.py.

id

sherpaTarCreator.sge_grace.batchJob.id

Definition at line 66 of file sge_grace.py.

memMB

sherpaTarCreator.batchJobBase.batchJobBase.memMB

inherited

Definition at line 13 of file batchJobBase.py.

name

sherpaTarCreator.batchJobBase.batchJobBase.name

inherited

Definition at line 9 of file batchJobBase.py.

nCores

sherpaTarCreator.batchJobBase.batchJobBase.nCores

inherited

Definition at line 12 of file batchJobBase.py.

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The documentation for this class was generated from the following file:

• sge_grace.py