batchmanager.BatchManager Class Reference

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 16 of file batchmanager.py.

Constructor & Destructor Documentation

__init__()

def batchmanager.BatchManager.__init__

(

self

)

Definition at line 26 of file batchmanager.py.

    def __init__(self):
        self.DefineOptions()
 
 

References batchmanager.BatchManager.DefineOptions().

Member Function Documentation

CheckBatchScript()

def batchmanager.BatchManager.CheckBatchScript	(		self,
			batchScript
	)

Definition at line 206 of file batchmanager.py.

    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)
 

References edm.print().

DefineOptions()

def batchmanager.BatchManager.DefineOptions

(

self

)

Definition at line 30 of file batchmanager.py.

    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")
 

Referenced by batchmanager.BatchManager.__init__().

ManageOutputDir()

def batchmanager.BatchManager.ManageOutputDir

(

self

)

Definition at line 128 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_ )
 
 

References edm.print().

mkdir()

def batchmanager.BatchManager.mkdir	(		self,
			dirname
	)

Definition at line 236 of file batchmanager.py.

    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)
 
 

References edm.print().

Referenced by batchmanager.BatchManager.PrepareJob().

ParseOptions()

def batchmanager.BatchManager.ParseOptions

(

self

)

Definition at line 57 of file batchmanager.py.

    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_)
 
 

References reco::parser::MethodInvoker.args_, reco::parser::ExpressionQuaterOperator< Op >.args_, ExternalLHEProducer.args_, cmdline::CmdLine.args_, Json::Path.args_, main.parse_args(), batchmanager.BatchManager.parser_, MonitorElementsDb.parser_, l1t::XmlConfigParser.parser_, DCCTBBlockPrototype.parser_, DCCTBDataMapper.parser_, and MonitorXMLParser.parser_.

PrepareJob()

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 157 of file batchmanager.py.

    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 )
 

References mps_setup.append, join(), batchmanager.BatchManager.listOfJobs_, TFileDirectory.mkdir(), TFileService.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(), batchmanager.BatchManager.PrepareJobUser(), and edm.print().

PrepareJobs()

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

Definition at line 112 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_)
 
 

References edm.print().

PrepareJobUser()

def batchmanager.BatchManager.PrepareJobUser	(		self,
			value
	)

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

Definition at line 172 of file batchmanager.py.

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

References edm.print().

Referenced by batchmanager.BatchManager.PrepareJob().

RunningMode()

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 245 of file batchmanager.py.

    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 )

References edm.print().

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

SubmitJob()

def batchmanager.BatchManager.SubmitJob	(		self,
			jobDir
	)

Hook for job submission.

Definition at line 196 of file batchmanager.py.

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

References edm.print().

Referenced by batchmanager.BatchManager.SubmitJobs().

SubmitJobArray()

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

Hook for array job submission.

Definition at line 202 of file batchmanager.py.

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

References edm.print().

SubmitJobs()

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

Submit all jobs. Possibly wait between each job

Definition at line 177 of file batchmanager.py.

    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.')
 

References batchmanager.BatchManager.listOfJobs_, edm.print(), and batchmanager.BatchManager.SubmitJob().

Member Data Documentation

listOfJobs_

batchmanager.BatchManager.listOfJobs_

Definition at line 114 of file batchmanager.py.

Referenced by batchmanager.BatchManager.PrepareJob(), and batchmanager.BatchManager.SubmitJobs().

outputDir_

batchmanager.BatchManager.outputDir_

Definition at line 142 of file batchmanager.py.

Referenced by batchmanager.BatchManager.PrepareJob(), and valtools.webpage.readCaptions().

parser_

batchmanager.BatchManager.parser_

Definition at line 33 of file batchmanager.py.

Referenced by valtools.webpage.parseArgs(), and batchmanager.BatchManager.ParseOptions().

remoteOutputDir_

batchmanager.BatchManager.remoteOutputDir_

Definition at line 60 of file batchmanager.py.

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

remoteOutputFile_

batchmanager.BatchManager.remoteOutputFile_

Definition at line 107 of file batchmanager.py.