Public Member Functions
def	__init__ (self)

def	CheckBatchScript (self, batchScript)

def	DefineOptions (self)

def	ManageOutputDir (self)

def	mkdir (self, dirname)

def	ParseOptions (self)

def	PrepareJob (self, value, dirname=None)

def	PrepareJobs (self, listOfValues, listOfDirNames=None)

def	PrepareJobUser (self, value)

def	RunningMode (self, batch)

def	SubmitJob (self, jobDir)

def	SubmitJobArray (self, numbOfJobs=1)

def	SubmitJobs (self, waitingTimeInSec=0)

Public Attributes
	listOfJobs_

	outputDir_

	parser_

	remoteOutputDir_

	remoteOutputFile_

Detailed Description

This class manages batch jobs
Used in batch scripts
Colin Bernet 2008

Definition at line 14 of file batchmanager.py.

Constructor & Destructor Documentation

def batchmanager.BatchManager.__init__ ( self )

Definition at line 24 of file batchmanager.py.

References batchmanager.BatchManager.DefineOptions().

     def __init__(self):
         self.DefineOptions()

Member Function Documentation

def batchmanager.BatchManager.CheckBatchScript	(	self,
		batchScript
	)

Definition at line 204 of file batchmanager.py.

References reco.if().

     def CheckBatchScript( self, batchScript ):
 
         if batchScript == '':
             return
 
         if( os.path.isfile(batchScript)== False ):
             print 'file ',batchScript,' does not exist'
             sys.exit(3)
 
         try:
             ifile = open(batchScript)
         except:
             print 'cannot open input %s' % batchScript
             sys.exit(3)
         else:
             for line in ifile:
                 p = re.compile("\s*cp.*\$jobdir\s+(\S+)$");
                 m=p.match(line)
                 if m:
                     if os.path.isdir( os.path.expandvars(m.group(1)) ):
                         print 'output directory ',  m.group(1), 'already exists!'
                         print 'exiting'
                         sys.exit(2)
                     else:
                         if self.options_.negate==False:
                             os.mkdir( os.path.expandvars(m.group(1)) )
                         else:
                             print 'not making dir', self.options_.negate
 

def batchmanager.BatchManager.DefineOptions ( self )

Definition at line 28 of file batchmanager.py.

Referenced by batchmanager.BatchManager.__init__().

     def DefineOptions(self):
         # define options and arguments ====================================
         # how to add more doc to the help?
         self.parser_ = OptionParser()
         self.parser_.add_option("-o", "--output-dir", dest="outputDir",
                                 help="Name of the local output directory for your jobs. This directory will be created automatically.",
                                 default=None)
         self.parser_.add_option("-r", "--remote-copy", dest="remoteCopy",
                                 help="remote output directory for your jobs. Example: /store/cmst3/user/cbern/CMG/HT/Run2011A-PromptReco-v1/AOD/PAT_CMG/RA2. This directory *must* be provided as a logical file name (LFN). When this option is used, all root files produced by a job are copied to the remote directory, and the job index is appended to the root file name. The Logger directory  will be sent back to the submision directory. For remote copy to PSI specify path like: '/pnfs/psi.ch/...'. Note: enviromental variable X509_USER_PROXY must point to home area before renewing proxy",
                                 default=None)
         self.parser_.add_option("-f", "--force", action="store_true",
                                 dest="force", default=False,
                                 help="Don't ask any questions, just over-write")
         # this opt can be removed
         self.parser_.add_option("-n", "--negate", action="store_true",
                                 dest="negate", default=False,
                                 help="create jobs, but does not submit the jobs.")
         self.parser_.add_option("-b", "--batch", dest="batch",
                                 help="batch command. default is: 'bsub -q 8nh < batchScript.sh'. You can also use 'nohup < ./batchScript.sh &' to run locally.",
                                 default="bsub -q 8nh < ./batchScript.sh")
         self.parser_.add_option( "--option",
                                 dest="extraOptions",
                                 type="string",
                                 action="append",
                                 default=[],
                                 help="Save one extra option (either a flag, or a key=value pair) that can be then accessed from the job config file")
 

def batchmanager.BatchManager.ManageOutputDir ( self )

Definition at line 126 of file batchmanager.py.

     def ManageOutputDir( self ):
 
         #if the output dir is not specified, generate a name
         #else
         #test if the directory exists
         #if yes, returns
 
         outputDir = self.options_.outputDir
 
         if outputDir==None:
             today = datetime.today()
             outputDir = 'OutCmsBatch_%s' % today.strftime("%d%h%y_%H%M%S")
             print 'output directory not specified, using %s' % outputDir
 
         self.outputDir_ = os.path.abspath(outputDir)
 
         if( os.path.isdir(self.outputDir_) == True ):
             input = ''
             if not self.options_.force:
                 while input != 'y' and input != 'n':
                     input = raw_input( 'The directory ' + self.outputDir_ + ' exists. Are you sure you want to continue? its contents will be overwritten [y/n] ' )
             if input == 'n':
                 sys.exit(1)
             else:
                 os.system( 'rm -rf ' + self.outputDir_)
 
         self.mkdir( self.outputDir_ )
 
 

def batchmanager.BatchManager.mkdir	(	self,
		dirname
	)

Definition at line 234 of file batchmanager.py.

References reco.if().

Referenced by batchmanager.BatchManager.PrepareJob().

     def mkdir( self, dirname ):
         # there is probably a command for this in python
         mkdir = 'mkdir -p %s' % dirname
         ret = os.system( mkdir )
         if( ret != 0 ):
             print 'please remove or rename directory: ', dirname
             sys.exit(4)
 
 

def batchmanager.BatchManager.ParseOptions ( self )

Definition at line 55 of file batchmanager.py.

References reco::parser::ExpressionQuaterOperator< Op >.args_, reco::parser::MethodInvoker.args_, ExternalLHEProducer.args_, cmdline::CmdLine.args_, Json::Path.args_, pftools::CalibCompare.options_, pftools::Exercises3.options_, tensorflow::TBBSession.options_, and tensorflow::NTSession.options_.

     def ParseOptions(self):
         (self.options_,self.args_) = self.parser_.parse_args()
         if self.options_.remoteCopy == None:
             self.remoteOutputDir_ = ""
         else:
             # removing possible trailing slash
             self.remoteOutputDir_ = self.options_.remoteCopy.rstrip('/')
             if "psi.ch" in self.remoteOutputDir_: # T3 @ PSI:
                 # overwriting protection to be improved
                 if self.remoteOutputDir_.startswith("/pnfs/psi.ch"):
                     ld_lib_path = os.environ.get('LD_LIBRARY_PATH')
                     if ld_lib_path != "None":
                         os.environ['LD_LIBRARY_PATH'] = "/usr/lib64/:"+ld_lib_path  # to solve gfal conflict with CMSSW
                     os.system("gfal-mkdir srm://t3se01.psi.ch/"+self.remoteOutputDir_)
                     outputDir = self.options_.outputDir
                     if outputDir==None:
                         today = datetime.today()
                         outputDir = 'OutCmsBatch_%s' % today.strftime("%d%h%y_%H%M")
                     self.remoteOutputDir_+="/"+outputDir
                     os.system("gfal-mkdir srm://t3se01.psi.ch/"+self.remoteOutputDir_)
                     if ld_lib_path != "None":
                         os.environ['LD_LIBRARY_PATH'] = ld_lib_path  # back to original to avoid conflicts
                 else:
                     print "remote directory must start with /pnfs/psi.ch to send to the tier3 at PSI"
                     print self.remoteOutputDir_, "not valid"
                     sys.exit(1)
             else: # assume EOS
                 if not castortools.isLFN( self.remoteOutputDir_ ):
                     print 'When providing an output directory, you must give its LFN, starting by /store. You gave:'
                     print self.remoteOutputDir_
                     sys.exit(1)
                 self.remoteOutputDir_ = castortools.lfnToEOS( self.remoteOutputDir_ )
                 dirExist = castortools.isDirectory( self.remoteOutputDir_ )
                 # nsls = 'nsls %s > /dev/null' % self.remoteOutputDir_
                 # dirExist = os.system( nsls )
                 if dirExist is False:
                     print 'creating ', self.remoteOutputDir_
                     if castortools.isEOSFile( self.remoteOutputDir_ ):
                         # the output directory is currently a file..
                         # need to remove it.
                         castortools.rm( self.remoteOutputDir_ )
                     castortools.createEOSDir( self.remoteOutputDir_ )
                 else:
                     # directory exists.
                     if self.options_.negate is False and self.options_.force is False:
                         #COLIN need to reimplement protectedRemove in eostools
                         raise ValueError(  ' '.join(['directory ', self.remoteOutputDir_, ' already exists.']))
                     # if not castortools.protectedRemove( self.remoteOutputDir_, '.*root'):
                     # the user does not want to delete the root files
 
         self.remoteOutputFile_ = ""
         self.ManageOutputDir()
         return (self.options_, self.args_)
 
 

def batchmanager.BatchManager.PrepareJob	(	self,
		value,
		dirname = `None`
	)

Prepare a job for a given value.

calls PrepareJobUser, which should be overloaded by the user.

Definition at line 155 of file batchmanager.py.

References join(), TFileService.mkdir(), TFileDirectory.mkdir(), batchHippy.MyBatchManager.mkdir(), batchmanager.BatchManager.mkdir(), dqmoffline::l1t::L1TDiffHarvesting::L1TDiffPlotHandler.outputDir_, MillePedeFileExtractor.outputDir_, L1GtVhdlWriter.outputDir_, dqmoffline::l1t::L1TEfficiencyPlotHandler.outputDir_, batchmanager.BatchManager.outputDir_, L1GtVhdlWriterCore.outputDir_, LaserSorter.outputDir_, cmsBatch.MyBatchManager.PrepareJobUser(), and batchmanager.BatchManager.PrepareJobUser().

     def PrepareJob( self, value, dirname=None):
         '''Prepare a job for a given value.
 
         calls PrepareJobUser, which should be overloaded by the user.
         '''
         print 'PrepareJob : %s' % value
         dname = dirname
         if dname  is None:
             dname = 'Job_{value}'.format( value=value )
         jobDir = '/'.join( [self.outputDir_, dname])
         print '\t',jobDir
         self.mkdir( jobDir )
         self.listOfJobs_.append( jobDir )
         self.PrepareJobUser( jobDir, value )
 

def batchmanager.BatchManager.PrepareJobs	(	self,
		listOfValues,
		listOfDirNames = `None`
	)

Definition at line 110 of file batchmanager.py.

     def PrepareJobs(self, listOfValues, listOfDirNames=None):
         print 'PREPARING JOBS ======== '
         self.listOfJobs_ = []
 
         if listOfDirNames is None:
             for value in listOfValues:
                 self.PrepareJob( value )
         else:
             for value, name in zip( listOfValues, listOfDirNames):
                 self.PrepareJob( value, name )
         print "list of jobs:"
         pp = pprint.PrettyPrinter(indent=4)
         pp.pprint( self.listOfJobs_)
 
 

def batchmanager.BatchManager.PrepareJobUser	(	self,
		value
	)

Hook allowing user to define how one of his jobs should be prepared.

Definition at line 170 of file batchmanager.py.

Referenced by batchmanager.BatchManager.PrepareJob().

     def PrepareJobUser(self, value ):
         '''Hook allowing user to define how one of his jobs should be prepared.'''
         print '\to be customized'
 
 

def batchmanager.BatchManager.RunningMode	(	self,
		batch
	)

Return "LXPUS", "PSI", "NAF", "LOCAL", or None,

"LXPLUS" : batch command is bsub, and logged on lxplus
"PSI"    : batch command is qsub, and logged to t3uiXX
"NAF"    : batch command is qsub, and logged on naf
"IC"     : batch command is qsub, and logged on hep.ph.ic.ac.uk
"LOCAL"  : batch command is nohup.

In all other cases, a CmsBatchException is raised

Definition at line 243 of file batchmanager.py.

Referenced by cmsBatch.MyBatchManager.PrepareJobUser(), and heppy_batch.MyBatchManager.PrepareJobUser().

     def RunningMode(self, batch):
 
         '''Return "LXPUS", "PSI", "NAF", "LOCAL", or None,
 
         "LXPLUS" : batch command is bsub, and logged on lxplus
         "PSI"    : batch command is qsub, and logged to t3uiXX
         "NAF"    : batch command is qsub, and logged on naf
         "IC"     : batch command is qsub, and logged on hep.ph.ic.ac.uk
         "LOCAL"  : batch command is nohup.
 
         In all other cases, a CmsBatchException is raised
         '''
 
         hostName = os.environ['HOSTNAME']
 
         onLxplus = hostName.startswith('lxplus')
         onPSI    = hostName.startswith('t3ui')
         onNAF =  hostName.startswith('naf')
 
         batchCmd = batch.split()[0]
 
         if batchCmd == 'bsub':
             if not onLxplus:
                 err = 'Cannot run %s on %s' % (batchCmd, hostName)
                 raise ValueError( err )
             else:
                 print 'running on LSF : %s from %s' % (batchCmd, hostName)
                 return 'LXPLUS'
 
         elif batchCmd == "qsub":
             if onPSI:
                 print 'running on SGE : %s from %s' % (batchCmd, hostName)
                 return 'PSI'
             elif onNAF:
                 print 'running on NAF : %s from %s' % (batchCmd, hostName)
                 return 'NAF'
             elif onIC:
                 print 'running on IC : %s from %s' % (batchCmd, hostName)
                 return 'IC'
             else:
                 err = 'Cannot run %s on %s' % (batchCmd, hostName)
                 raise ValueError( err )
 
         elif batchCmd == 'nohup' or batchCmd == './batchScript.sh':
             print 'running locally : %s on %s' % (batchCmd, hostName)
             return 'LOCAL'
         else:
             err = 'unknown batch command: X%sX' % batchCmd
             raise ValueError( err )

def batchmanager.BatchManager.SubmitJob	(	self,
		jobDir
	)

Hook for job submission.

Definition at line 194 of file batchmanager.py.

Referenced by batchmanager.BatchManager.SubmitJobs().

     def SubmitJob( self, jobDir ):
         '''Hook for job submission.'''
         print 'submitting (to be customized): ', jobDir
         os.system( self.options_.batch )
 
 

def batchmanager.BatchManager.SubmitJobArray	(	self,
		numbOfJobs = `1`
	)

Hook for array job submission.

Definition at line 200 of file batchmanager.py.

     def SubmitJobArray( self, numbOfJobs = 1 ):
         '''Hook for array job submission.'''
         print 'Submitting array with %s jobs'  % numbOfJobs
 

def batchmanager.BatchManager.SubmitJobs	(	self,
		waitingTimeInSec = `0`
	)

Submit all jobs. Possibly wait between each job

Definition at line 175 of file batchmanager.py.

References reco.if(), batchmanager.BatchManager.listOfJobs_, and batchmanager.BatchManager.SubmitJob().

     def SubmitJobs( self, waitingTimeInSec=0 ):
         '''Submit all jobs. Possibly wait between each job'''
 
         if(self.options_.negate):
             print '*NOT* SUBMITTING JOBS - exit '
             return
         print 'SUBMITTING JOBS ======== '
         for jobDir  in self.listOfJobs_:
             root = os.getcwd()
             # run it
             print 'processing ', jobDir
             os.chdir( jobDir )
             self.SubmitJob( jobDir )
             # and come back
             os.chdir(root)
             print 'waiting %s seconds...' % waitingTimeInSec
             time.sleep( waitingTimeInSec )
             print 'done.'
 