def master_prepare(self,app,appmasterconfig):
# PandaTools
from pandatools import Client
from pandatools import AthenaUtils
from taskbuffer.JobSpec import JobSpec
from taskbuffer.FileSpec import FileSpec
job = app._getParent()
logger.debug('AthenaMCPandaRTHandler master_prepare called for %s', job.getFQID('.'))
usertag = configDQ2['usertag']
#usertag='user09'
nickname = getNickname(allowMissingNickname=True)
self.libDataset = '%s.%s.ganga.%s_%d.lib._%06d' % (usertag,nickname,commands.getoutput('hostname').split('.')[0],int(time.time()),job.id)
# self.userprefix='%s.%s.ganga' % (usertag,gridProxy.identity())
sources = 'sources.%s.tar.gz' % commands.getoutput('uuidgen 2> /dev/null')
self.library = '%s.lib.tgz' % self.libDataset
# check DBRelease
# if job.backend.dbRelease != '' and job.backend.dbRelease.find(':') == -1:
# raise ApplicationConfigurationError(None,"ERROR : invalid argument for backend.dbRelease. Must be 'DatasetName:FileName'")
# unpack library
logger.debug('Creating source tarball ...')
tmpdir = '/tmp/%s' % commands.getoutput('uuidgen 2> /dev/null')
os.mkdir(tmpdir)
inputbox=[]
if os.path.exists(app.transform_archive):
# must add a condition on size.
inputbox += [ File(app.transform_archive) ]
if app.evgen_job_option:
self.evgen_job_option=app.evgen_job_option
if os.path.exists(app.evgen_job_option):
# locally modified job option file to add to the input sand box
inputbox += [ File(app.evgen_job_option) ]
self.evgen_job_option=app.evgen_job_option.split("/")[-1]
# add input sandbox files
if (job.inputsandbox):
for file in job.inputsandbox:
inputbox += [ file ]
# add option files
for extFile in job.backend.extOutFile:
try:
shutil.copy(extFile,tmpdir)
except IOError:
os.makedirs(tmpdir)
shutil.copy(extFile,tmpdir)
# fill the archive
for opt_file in inputbox:
try:
shutil.copy(opt_file.name,tmpdir)
except IOError:
os.makedirs(tmpdir)
shutil.copy(opt_file.name,tmpdir)
# now tar it up again
inpw = job.getInputWorkspace()
rc, output = commands.getstatusoutput('tar czf %s -C %s .' % (inpw.getPath(sources),tmpdir))
if rc:
logger.error('Packing sources failed with status %d',rc)
logger.error(output)
raise ApplicationConfigurationError(None,'Packing sources failed.')
shutil.rmtree(tmpdir)
# upload sources
logger.debug('Uploading source tarball ...')
try:
cwd = os.getcwd()
os.chdir(inpw.getPath())
rc, output = Client.putFile(sources)
if output != 'True':
logger.error('Uploading sources %s failed. Status = %d', sources, rc)
logger.error(output)
raise ApplicationConfigurationError(None,'Uploading archive failed')
finally:
os.chdir(cwd)
# Use Panda's brokerage
## if job.inputdata and len(app.sites)>0:
## # update cloud, use inputdata's
## from dq2.info.TiersOfATLAS import whichCloud,ToACache
## inclouds=[]
## for site in app.sites:
## cloudSite=whichCloud(app.sites[0])
## if cloudSite not in inclouds:
## inclouds.append(cloudSite)
## # now converting inclouds content into proper brokering stuff.
## outclouds=[]
## for cloudSite in inclouds:
## for cloudID, eachCloud in ToACache.dbcloud.iteritems():
## if cloudSite==eachCloud:
## cloud=cloudID
## outclouds.append(cloud)
## break
## print outclouds
## # finally, matching with user's wishes
## if len(outclouds)>0:
## if not job.backend.requirements.cloud: # no user wish, update
## job.backend.requirements.cloud=outclouds[0]
## else:
## try:
## assert job.backend.requirements.cloud in outclouds
## except:
## raise ApplicationConfigurationError(None,'Input dataset not available in target cloud %s. Please try any of the following %s' % (job.backend.requirements.cloud, str(outclouds)))
from GangaPanda.Lib.Panda.Panda import runPandaBrokerage
runPandaBrokerage(job)
if job.backend.site == 'AUTO':
raise ApplicationConfigurationError(None,'site is still AUTO after brokerage!')
# output dataset preparation and registration
try:
outDsLocation = Client.PandaSites[job.backend.site]['ddm']
except:
raise ApplicationConfigurationError(None,"Could not extract output dataset location from job.backend.site value: %s. Aborting" % job.backend.site)
if not app.dryrun:
for outtype in app.outputpaths.keys():
dset=string.replace(app.outputpaths[outtype],"/",".")
dset=dset[1:]
# dataset registration must be done only once.
print "registering output dataset %s at %s" % (dset,outDsLocation)
try:
Client.addDataset(dset,False,location=outDsLocation)
dq2_set_dataset_lifetime(dset, location=outDsLocation)
except:
raise ApplicationConfigurationError(None,"Fail to create output dataset %s. Aborting" % dset)
# extend registration to build job lib dataset:
print "registering output dataset %s at %s" % (self.libDataset,outDsLocation)
try:
Client.addDataset(self.libDataset,False,location=outDsLocation)
dq2_set_dataset_lifetime(self.libDataset, outDsLocation)
except:
raise ApplicationConfigurationError(None,"Fail to create output dataset %s. Aborting" % self.libDataset)
###
cacheVer = "-AtlasProduction_" + str(app.prod_release)
logger.debug("master job submit?")
self.outsite=job.backend.site
if app.se_name and app.se_name != "none" and not self.outsite:
self.outsite=app.se_name
# create build job
jspec = JobSpec()
jspec.jobDefinitionID = job.id
jspec.jobName = commands.getoutput('uuidgen 2> /dev/null')
jspec.AtlasRelease = 'Atlas-%s' % app.atlas_rel
jspec.homepackage = 'AnalysisTransforms'+cacheVer#+nightVer
jspec.transformation = '%s/buildJob-00-00-03' % Client.baseURLSUB # common base to Athena and AthenaMC jobs: buildJob is a pilot job which takes care of all inputs for the real jobs (in prepare()
jspec.destinationDBlock = self.libDataset
jspec.destinationSE = job.backend.site
jspec.prodSourceLabel = 'panda'
jspec.assignedPriority = 2000
jspec.computingSite = job.backend.site
jspec.cloud = job.backend.requirements.cloud
# jspec.jobParameters = self.args not known yet
jspec.jobParameters = '-o %s' % (self.library)
if app.userarea:
print app.userarea
jspec.jobParameters += ' -i %s' % (os.path.basename(app.userarea))
else:
jspec.jobParameters += ' -i %s' % (sources)
jspec.cmtConfig = AthenaUtils.getCmtConfig(athenaVer=app.atlas_rel)
matchURL = re.search('(http.*://[^/]+)/',Client.baseURLSSL)
if matchURL:
jspec.jobParameters += ' --sourceURL %s' % matchURL.group(1)
fout = FileSpec()
fout.lfn = self.library
fout.type = 'output'
fout.dataset = self.libDataset
fout.destinationDBlock = self.libDataset
jspec.addFile(fout)
flog = FileSpec()
flog.lfn = '%s.log.tgz' % self.libDataset
flog.type = 'log'
flog.dataset = self.libDataset
flog.destinationDBlock = self.libDataset
jspec.addFile(flog)
#print "MASTER JOB DETAILS:",jspec.jobParameters
return jspec
def master_prepare(self,app,appconfig):
'''Prepare the master job'''
from pandatools import Client
from pandatools import MiscUtils
from pandatools import AthenaUtils
from pandatools import PsubUtils
# create a random number for this submission to allow multiple use of containers
self.rndSubNum = random.randint(1111,9999)
job = app._getParent()
logger.debug('AthenaJediRTHandler master_prepare called for %s', job.getFQID('.'))
if app.useRootCoreNoBuild:
logger.info('Athena.useRootCoreNoBuild is True, setting Panda.nobuild=True.')
job.backend.nobuild = True
if job.backend.bexec and job.backend.nobuild:
raise ApplicationConfigurationError("Contradicting options: job.backend.bexec and job.backend.nobuild are both enabled.")
if job.backend.requirements.rootver != '' and job.backend.nobuild:
raise ApplicationConfigurationError("Contradicting options: job.backend.requirements.rootver given and job.backend.nobuild are enabled.")
# Switch on compilation flag if bexec is set or libds is empty
if job.backend.bexec != '' or not job.backend.nobuild:
app.athena_compile = True
for sj in job.subjobs:
sj.application.athena_compile = True
logger.info('"job.backend.nobuild=False" or "job.backend.bexec" is set - Panda build job is enabled.')
if job.backend.nobuild:
app.athena_compile = False
for sj in job.subjobs:
sj.application.athena_compile = False
logger.info('"job.backend.nobuild=True" or "--nobuild" chosen - Panda build job is switched off.')
# check for auto datri
if job.outputdata.location != '':
if not PsubUtils.checkDestSE(job.outputdata.location,job.outputdata.datasetname,False):
raise ApplicationConfigurationError("Problems with outputdata.location setting '%s'" % job.outputdata.location)
# validate application
if not app.atlas_release and not job.backend.requirements.rootver and not app.atlas_exetype in [ 'EXE' ]:
raise ApplicationConfigurationError("application.atlas_release is not set. Did you run application.prepare()")
self.dbrelease = app.atlas_dbrelease
if self.dbrelease != '' and self.dbrelease != 'LATEST' and self.dbrelease.find(':') == -1:
raise ApplicationConfigurationError("ERROR : invalid argument for DB Release. Must be 'LATEST' or 'DatasetName:FileName'")
self.runConfig = AthenaUtils.ConfigAttr(app.atlas_run_config)
for k in self.runConfig.keys():
self.runConfig[k]=AthenaUtils.ConfigAttr(self.runConfig[k])
if not app.atlas_run_dir:
raise ApplicationConfigurationError("application.atlas_run_dir is not set. Did you run application.prepare()")
self.rundirectory = app.atlas_run_dir
self.cacheVer = ''
if app.atlas_project and app.atlas_production:
self.cacheVer = "-" + app.atlas_project + "_" + app.atlas_production
# handle different atlas_exetypes
self.job_options = ''
if app.atlas_exetype == 'TRF':
self.job_options += ' '.join([os.path.basename(fopt.name) for fopt in app.option_file])
#if not job.outputdata.outputdata:
# raise ApplicationConfigurationError("job.outputdata.outputdata is required for atlas_exetype in ['PYARA','ARES','TRF','ROOT','EXE' ] and Panda backend")
#raise ApplicationConfigurationError("Sorry TRF on Panda backend not yet supported")
if app.options:
self.job_options += ' %s ' % app.options
elif app.atlas_exetype == 'ATHENA':
if len(app.atlas_environment) > 0 and app.atlas_environment[0].find('DBRELEASE_OVERRIDE')==-1:
logger.warning("Passing of environment variables to Athena using Panda not supported. Ignoring atlas_environment setting.")
if job.outputdata.outputdata:
raise ApplicationConfigurationError("job.outputdata.outputdata must be empty if atlas_exetype='ATHENA' and Panda backend is used (outputs are auto-detected)")
if app.options:
if app.options.startswith('-c'):
self.job_options += ' %s ' % app.options
else:
self.job_options += ' -c %s ' % app.options
logger.warning('The value of j.application.options has been prepended with " -c " ')
logger.warning('Please make sure to use proper quotes for the values of j.application.options !')
self.job_options += ' '.join([os.path.basename(fopt.name) for fopt in app.option_file])
# check for TAG compression
if 'subcoll.tar.gz' in app.append_to_user_area:
self.job_options = ' uncompress.py ' + self.job_options
elif app.atlas_exetype in ['PYARA','ARES','ROOT','EXE']:
#if not job.outputdata.outputdata:
# raise ApplicationConfigurationError("job.outputdata.outputdata is required for atlas_exetype in ['PYARA','ARES','TRF','ROOT','EXE' ] and Panda backend")
self.job_options += ' '.join([os.path.basename(fopt.name) for fopt in app.option_file])
# sort out environment variables
env_str = ""
if len(app.atlas_environment) > 0:
for env_var in app.atlas_environment:
env_str += "export %s ; " % env_var
else:
env_str = ""
# below fixes issue with runGen -- job_options are executed by os.system when dbrelease is used, and by the shell otherwise
## - REMOVED FIX DUE TO CHANGE IN PILOT - MWS 8/11/11
if job.backend.requirements.usecommainputtxt:
input_str = '/bin/echo %IN > input.txt; cat input.txt; '
else:
input_str = '/bin/echo %IN | sed \'s/,/\\\n/g\' > input.txt; cat input.txt; '
if app.atlas_exetype == 'PYARA':
self.job_options = env_str + input_str + ' python ' + self.job_options
elif app.atlas_exetype == 'ARES':
self.job_options = env_str + input_str + ' athena.py ' + self.job_options
elif app.atlas_exetype == 'ROOT':
self.job_options = env_str + input_str + ' root -b -q ' + self.job_options
elif app.atlas_exetype == 'EXE':
self.job_options = env_str + input_str + self.job_options
if app.options:
self.job_options += ' %s ' % app.options
if self.job_options == '':
raise ApplicationConfigurationError("No Job Options found!")
logger.info('Running job options: %s'%self.job_options)
# validate dbrelease
if self.dbrelease != "LATEST":
self.dbrFiles,self.dbrDsList = getDBDatasets(self.job_options,'',self.dbrelease)
# handle the output dataset
if job.outputdata:
if job.outputdata._name != 'DQ2OutputDataset':
raise ApplicationConfigurationError('Panda backend supports only DQ2OutputDataset')
else:
logger.info('Adding missing DQ2OutputDataset')
job.outputdata = DQ2OutputDataset()
# validate the output dataset name (and make it a container)
job.outputdata.datasetname,outlfn = dq2outputdatasetname(job.outputdata.datasetname, job.id, job.outputdata.isGroupDS, job.outputdata.groupname)
if not job.outputdata.datasetname.endswith('/'):
job.outputdata.datasetname+='/'
# add extOutFiles
self.extOutFile = []
for tmpName in job.outputdata.outputdata:
if tmpName != '':
self.extOutFile.append(tmpName)
for tmpName in job.backend.extOutFile:
if tmpName != '':
self.extOutFile.append(tmpName)
# use the shared area if possible
tmp_user_area_name = app.user_area.name
if app.is_prepared is not True:
from Ganga.Utility.files import expandfilename
shared_path = os.path.join(expandfilename(getConfig('Configuration')['gangadir']),'shared',getConfig('Configuration')['user'])
tmp_user_area_name = os.path.join(os.path.join(shared_path,app.is_prepared.name),os.path.basename(app.user_area.name))
# Add inputsandbox to user_area
if job.inputsandbox:
logger.warning("Submitting Panda job with inputsandbox. This may slow the submission slightly.")
if tmp_user_area_name:
inpw = os.path.dirname(tmp_user_area_name)
self.inputsandbox = os.path.join(inpw, 'sources.%s.tar' % commands.getoutput('uuidgen 2> /dev/null'))
else:
inpw = job.getInputWorkspace()
self.inputsandbox = inpw.getPath('sources.%s.tar' % commands.getoutput('uuidgen 2> /dev/null'))
if tmp_user_area_name:
rc, output = commands.getstatusoutput('cp %s %s.gz' % (tmp_user_area_name, self.inputsandbox))
if rc:
logger.error('Copying user_area failed with status %d',rc)
logger.error(output)
raise ApplicationConfigurationError('Packing inputsandbox failed.')
rc, output = commands.getstatusoutput('gunzip %s.gz' % (self.inputsandbox))
if rc:
logger.error('Unzipping user_area failed with status %d',rc)
logger.error(output)
raise ApplicationConfigurationError('Packing inputsandbox failed.')
for fname in [os.path.abspath(f.name) for f in job.inputsandbox]:
fname.rstrip(os.sep)
path = os.path.dirname(fname)
fn = os.path.basename(fname)
#app.atlas_run_dir
# get Athena versions
rc, out = AthenaUtils.getAthenaVer()
# failed
if not rc:
#raise ApplicationConfigurationError('CMT could not parse correct environment ! \n Did you start/setup ganga in the run/ or cmt/ subdirectory of your athena analysis package ?')
logger.warning("CMT could not parse correct environment for inputsandbox - will use the atlas_run_dir as default")
# as we don't have to be in the run dir now, create a copy of the run_dir directory structure and use that
input_dir = os.path.dirname(self.inputsandbox)
run_path = "%s/sbx_tree/%s" % (input_dir, app.atlas_run_dir)
rc, output = commands.getstatusoutput("mkdir -p %s" % run_path)
if not rc:
# copy this sandbox file
rc, output = commands.getstatusoutput("cp %s %s" % (fname, run_path))
if not rc:
path = os.path.join(input_dir, 'sbx_tree')
fn = os.path.join(app.atlas_run_dir, fn)
else:
raise ApplicationConfigurationError("Couldn't copy file %s to recreate run_dir for input sandbox" % fname)
else:
raise ApplicationConfigurationError("Couldn't create directory structure to match run_dir %s for input sandbox" % run_path)
else:
userarea = out['workArea']
# strip the path from the filename if present in the userarea
ua = os.path.abspath(userarea)
if ua in path:
fn = fname[len(ua)+1:]
path = ua
rc, output = commands.getstatusoutput('tar -h -r -f %s -C %s %s' % (self.inputsandbox, path, fn))
if rc:
logger.error('Packing inputsandbox failed with status %d',rc)
logger.error(output)
raise ApplicationConfigurationError('Packing inputsandbox failed.')
# remove sandbox tree if created
if "sbx_tree" in os.listdir(os.path.dirname(self.inputsandbox)):
rc, output = commands.getstatusoutput("rm -r %s/sbx_tree" % os.path.dirname(self.inputsandbox))
if rc:
raise ApplicationConfigurationError("Couldn't remove directory structure used for input sandbox")
rc, output = commands.getstatusoutput('gzip %s' % (self.inputsandbox))
if rc:
logger.error('Packing inputsandbox failed with status %d',rc)
logger.error(output)
raise ApplicationConfigurationError('Packing inputsandbox failed.')
self.inputsandbox += ".gz"
else:
self.inputsandbox = tmp_user_area_name
# job name
jobName = 'ganga.%s' % MiscUtils.wrappedUuidGen()
# make task
taskParamMap = {}
# Enforce that outputdataset name ends with / for container
if not job.outputdata.datasetname.endswith('/'):
job.outputdata.datasetname = job.outputdata.datasetname + '/'
taskParamMap['taskName'] = job.outputdata.datasetname
taskParamMap['uniqueTaskName'] = True
taskParamMap['vo'] = 'atlas'
taskParamMap['architecture'] = AthenaUtils.getCmtConfig(athenaVer=app.atlas_release, cmtConfig=app.atlas_cmtconfig)
if app.atlas_release:
taskParamMap['transUses'] = 'Atlas-%s' % app.atlas_release
else:
taskParamMap['transUses'] = ''
taskParamMap['transHome'] = 'AnalysisTransforms'+self.cacheVer#+nightVer
configSys = getConfig('System')
gangaver = configSys['GANGA_VERSION'].lower()
if not gangaver:
gangaver = "ganga"
if app.atlas_exetype in ["ATHENA", "TRF"]:
taskParamMap['processingType'] = '{0}-jedi-athena'.format(gangaver)
else:
taskParamMap['processingType'] = '{0}-jedi-run'.format(gangaver)
#if options.eventPickEvtList != '':
# taskParamMap['processingType'] += '-evp'
taskParamMap['prodSourceLabel'] = 'user'
if job.backend.site != 'AUTO':
taskParamMap['cloud'] = Client.PandaSites[job.backend.site]['cloud']
taskParamMap['site'] = job.backend.site
elif job.backend.requirements.cloud != None and not job.backend.requirements.anyCloud:
taskParamMap['cloud'] = job.backend.requirements.cloud
if job.backend.requirements.excluded_sites != []:
taskParamMap['excludedSite'] = expandExcludedSiteList( job )
# if only a single site specifed, don't set includedSite
#if job.backend.site != 'AUTO':
# taskParamMap['includedSite'] = job.backend.site
#taskParamMap['cliParams'] = fullExecString
if job.backend.requirements.noEmail:
taskParamMap['noEmail'] = True
if job.backend.requirements.skipScout:
taskParamMap['skipScout'] = True
if not app.atlas_exetype in ["ATHENA", "TRF"]:
taskParamMap['nMaxFilesPerJob'] = job.backend.requirements.maxNFilesPerJob
if job.backend.requirements.disableAutoRetry:
taskParamMap['disableAutoRetry'] = 1
# source URL
matchURL = re.search("(http.*://[^/]+)/",Client.baseURLCSRVSSL)
if matchURL != None:
taskParamMap['sourceURL'] = matchURL.group(1)
# dataset names
outDatasetName = job.outputdata.datasetname
logDatasetName = re.sub('/$','.log/',job.outputdata.datasetname)
# log
taskParamMap['log'] = {'dataset': logDatasetName,
'container': logDatasetName,
'type':'template',
'param_type':'log',
'value':'{0}.${{SN}}.log.tgz'.format(logDatasetName[:-1])
}
# job parameters
if app.atlas_exetype in ["ATHENA", "TRF"]:
taskParamMap['jobParameters'] = [
{'type':'constant',
'value': ' --sourceURL ${SURL}',
},
]
else:
taskParamMap['jobParameters'] = [
{'type':'constant',
'value': '-j "" --sourceURL ${SURL}',
},
]
taskParamMap['jobParameters'] += [
{'type':'constant',
'value': '-r {0}'.format(self.rundirectory),
},
]
# Add the --trf option to jobParameters if required
if app.atlas_exetype == "TRF":
taskParamMap['jobParameters'] += [{'type': 'constant', 'value': '--trf'}]
# output
# output files
outMap = {}
if app.atlas_exetype in ["ATHENA", "TRF"]:
outMap, tmpParamList = AthenaUtils.convertConfToOutput(self.runConfig, self.extOutFile, job.outputdata.datasetname, destination=job.outputdata.location)
taskParamMap['jobParameters'] += [
{'type':'constant',
'value': '-o "%s" ' % outMap
},
]
taskParamMap['jobParameters'] += tmpParamList
else:
if job.outputdata.outputdata:
for tmpLFN in job.outputdata.outputdata:
if len(job.outputdata.datasetname.split('.')) > 2:
lfn = '{0}.{1}'.format(*job.outputdata.datasetname.split('.')[:2])
else:
lfn = job.outputdata.datasetname[:-1]
lfn += '.$JOBSETID._${{SN/P}}.{0}'.format(tmpLFN)
dataset = '{0}_{1}/'.format(job.outputdata.datasetname[:-1],tmpLFN)
taskParamMap['jobParameters'] += MiscUtils.makeJediJobParam(lfn,dataset,'output',hidden=True, destination=job.outputdata.location)
outMap[tmpLFN] = lfn
taskParamMap['jobParameters'] += [
{'type':'constant',
'value': '-o "{0}"'.format(str(outMap)),
},
]
if app.atlas_exetype in ["ATHENA"]:
# jobO parameter
tmpJobO = self.job_options
# replace full-path jobOs
for tmpFullName,tmpLocalName in AthenaUtils.fullPathJobOs.iteritems():
tmpJobO = re.sub(tmpFullName,tmpLocalName,tmpJobO)
# modify one-liner for G4 random seeds
if self.runConfig.other.G4RandomSeeds > 0:
if app.options != '':
tmpJobO = re.sub('-c "%s" ' % app.options,
'-c "%s;from G4AtlasApps.SimFlags import SimFlags;SimFlags.SeedsG4=${RNDMSEED}" ' \
% app.options,tmpJobO)
else:
tmpJobO = '-c "from G4AtlasApps.SimFlags import SimFlags;SimFlags.SeedsG4=${RNDMSEED}" '
dictItem = {'type':'template',
'param_type':'number',
'value':'${RNDMSEED}',
'hidden':True,
'offset':self.runConfig.other.G4RandomSeeds,
}
taskParamMap['jobParameters'] += [dictItem]
elif app.atlas_exetype in ["TRF"]:
# replace parameters for TRF
tmpJobO = self.job_options
# output : basenames are in outMap['IROOT'] trough extOutFile
tmpOutMap = []
for tmpName,tmpLFN in outMap['IROOT']:
tmpJobO = tmpJobO.replace('%OUT.' + tmpName,tmpName)
# replace DBR
tmpJobO = re.sub('%DB=[^ \'\";]+','${DBR}',tmpJobO)
if app.atlas_exetype in ["TRF"]:
taskParamMap['useLocalIO'] = 1
# build
if job.backend.nobuild:
taskParamMap['jobParameters'] += [
{'type':'constant',
'value': '-a {0}'.format(os.path.basename(self.inputsandbox)),
},
]
else:
taskParamMap['jobParameters'] += [
{'type':'constant',
'value': '-l ${LIB}',
},
]
#
# input
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
if job.backend.requirements.nFilesPerJob > 0 and job.inputdata.number_of_files == 0 and job.backend.requirements.split > 0:
job.inputdata.number_of_files = job.backend.requirements.nFilesPerJob * job.backend.requirements.split
if job.inputdata and job.inputdata._name == 'DQ2Dataset' and job.inputdata.number_of_files != 0:
taskParamMap['nFiles'] = job.inputdata.number_of_files
elif job.backend.requirements.nFilesPerJob > 0 and job.backend.requirements.split > 0:
# pathena does this for some reason even if there is no input files
taskParamMap['nFiles'] = job.backend.requirements.nFilesPerJob * job.backend.requirements.split
if job.backend.requirements.nFilesPerJob > 0:
taskParamMap['nFilesPerJob'] = job.backend.requirements.nFilesPerJob
if job.backend.requirements.nEventsPerFile > 0:
taskParamMap['nEventsPerFile'] = job.backend.requirements.nEventsPerFile
if not job.backend.requirements.nGBPerJob in [ 0,'MAX']:
try:
if job.backend.requirements.nGBPerJob != 'MAX':
job.backend.requirments.nGBPerJob = int(job.backend.requirements.nGBPerJob)
except:
logger.error("nGBPerJob must be an integer or MAX")
# check negative
if job.backend.requirements.nGBPerJob <= 0:
logger.error("nGBPerJob must be positive")
# don't set MAX since it is the defalt on the server side
if not job.backend.requirements.nGBPerJob in [-1,'MAX']:
taskParamMap['nGBPerJob'] = job.backend.requirements.nGBPerJob
if app.atlas_exetype in ["ATHENA", "TRF"]:
inputMap = {}
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
tmpDict = {'type':'template',
'param_type':'input',
'value':'-i "${IN/T}"',
'dataset': ','.join(job.inputdata.dataset),
'expand':True,
'exclude':'\.log\.tgz(\.\d+)*$',
}
#if options.inputType != '':
# tmpDict['include'] = options.inputType
taskParamMap['jobParameters'].append(tmpDict)
taskParamMap['dsForIN'] = ','.join(job.inputdata.dataset)
inputMap['IN'] = ','.join(job.inputdata.dataset)
else:
# no input
taskParamMap['noInput'] = True
if job.backend.requirements.split > 0:
taskParamMap['nEvents'] = job.backend.requirements.split
else:
taskParamMap['nEvents'] = 1
taskParamMap['nEventsPerJob'] = 1
taskParamMap['jobParameters'] += [
{'type':'constant',
'value': '-i "[]"',
},
]
else:
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
tmpDict = {'type':'template',
'param_type':'input',
'value':'-i "${IN/T}"',
'dataset': ','.join(job.inputdata.dataset),
'expand':True,
'exclude':'\.log\.tgz(\.\d+)*$',
}
#if options.nSkipFiles != 0:
# tmpDict['offset'] = options.nSkipFiles
taskParamMap['jobParameters'].append(tmpDict)
taskParamMap['dsForIN'] = ','.join(job.inputdata.dataset)
else:
# no input
taskParamMap['noInput'] = True
if job.backend.requirements.split > 0:
taskParamMap['nEvents'] = job.backend.requirements.split
else:
taskParamMap['nEvents'] = 1
taskParamMap['nEventsPerJob'] = 1
# param for DBR
if self.dbrelease != '':
dbrDS = self.dbrelease.split(':')[0]
# change LATEST to DBR_LATEST
if dbrDS == 'LATEST':
dbrDS = 'DBR_LATEST'
dictItem = {'type':'template',
'param_type':'input',
'value':'--dbrFile=${DBR}',
'dataset':dbrDS,
}
taskParamMap['jobParameters'] += [dictItem]
# no expansion
#if options.notExpandDBR:
#dictItem = {'type':'constant',
# 'value':'--noExpandDBR',
# }
#taskParamMap['jobParameters'] += [dictItem]
# secondary FIXME disabled
self.secondaryDSs = {}
if self.secondaryDSs != {}:
inMap = {}
streamNames = []
for tmpDsName,tmpMap in self.secondaryDSs.iteritems():
# make template item
streamName = tmpMap['streamName']
dictItem = MiscUtils.makeJediJobParam('${'+streamName+'}',tmpDsName,'input',hidden=True,
expand=True,include=tmpMap['pattern'],offset=tmpMap['nSkip'],
nFilesPerJob=tmpMap['nFiles'])
taskParamMap['jobParameters'] += dictItem
inMap[streamName] = 'tmp_'+streamName
streamNames.append(streamName)
# make constant item
strInMap = str(inMap)
# set placeholders
for streamName in streamNames:
strInMap = strInMap.replace("'tmp_"+streamName+"'",'${'+streamName+'/T}')
dictItem = {'type':'constant',
'value':'--inMap "%s"' % strInMap,
}
taskParamMap['jobParameters'] += [dictItem]
# misc
jobParameters = ''
# use Athena packages
if app.atlas_exetype == 'ARES' or (app.atlas_exetype in ['PYARA','ROOT','EXE'] and app.useAthenaPackages):
jobParameters += "--useAthenaPackages "
# use RootCore
if app.useRootCore or app.useRootCoreNoBuild:
jobParameters += "--useRootCore "
# use mana
if app.useMana:
jobParameters += "--useMana "
if app.atlas_release != "":
jobParameters += "--manaVer %s " % app.atlas_release
# root
if app.atlas_exetype in ['PYARA','ROOT','EXE'] and job.backend.requirements.rootver != '':
rootver = re.sub('/','.', job.backend.requirements.rootver)
jobParameters += "--rootVer %s " % rootver
# write input to txt
#if options.writeInputToTxt != '':
# jobParameters += "--writeInputToTxt %s " % options.writeInputToTxt
# debug parameters
#if options.queueData != '':
# jobParameters += "--overwriteQueuedata=%s " % options.queueData
# JEM
#if options.enableJEM:
# jobParameters += "--enable-jem "
# if options.configJEM != '':
# jobParameters += "--jem-config %s " % options.configJEM
# set task param
if jobParameters != '':
taskParamMap['jobParameters'] += [
{'type':'constant',
'value': jobParameters,
},
]
# force stage-in
if job.backend.accessmode == "LocalIO":
taskParamMap['useLocalIO'] = 1
# set jobO parameter
if app.atlas_exetype in ["ATHENA", "TRF"]:
taskParamMap['jobParameters'] += [
{'type':'constant',
'value': '-j "',
'padding':False,
},
]
taskParamMap['jobParameters'] += PsubUtils.convertParamStrToJediParam(tmpJobO,inputMap,job.outputdata.datasetname[:-1], True,False)
taskParamMap['jobParameters'] += [
{'type':'constant',
'value': '"',
},
]
else:
taskParamMap['jobParameters'] += [ {'type':'constant',
'value': '-p "{0}"'.format(urllib.quote(self.job_options)),
},
]
# build step
if not job.backend.nobuild:
jobParameters = '-i ${IN} -o ${OUT} --sourceURL ${SURL} '
if job.backend.bexec != '':
jobParameters += ' --bexec "%s" ' % urllib.quote(job.backend.bexec)
if app.atlas_exetype == 'ARES' or (app.atlas_exetype in ['PYARA','ROOT','EXE'] and app.useAthenaPackages):
# use Athena packages
jobParameters += "--useAthenaPackages "
# use RootCore
if app.useRootCore or app.useRootCoreNoBuild:
jobParameters += "--useRootCore "
# run directory
if app.atlas_exetype in ['PYARA','ARES','ROOT','EXE']:
jobParameters += '-r {0} '.format(self.rundirectory)
# no compile
#if options.noCompile:
# jobParameters += "--noCompile "
# use mana
if app.useMana:
jobParameters += "--useMana "
if app.atlas_release != "":
jobParameters += "--manaVer %s " % app.atlas_release
# root
if app.atlas_exetype in ['PYARA','ROOT','EXE'] and job.backend.requirements.rootver != '':
rootver = re.sub('/','.', job.backend.requirements.rootver)
jobParameters += "--rootVer %s " % rootver
# cmt config
if app.atlas_exetype in ['PYARA','ARES','ROOT','EXE']:
if not app.atlas_cmtconfig in ['','NULL',None]:
jobParameters += " --cmtConfig %s " % app.atlas_cmtconfig
#cmtConfig = AthenaUtils.getCmtConfig(athenaVer=app.atlas_release, cmtConfig=app.atlas_cmtconfig)
#if cmtConfig:
# jobParameters += "--cmtConfig %s " % cmtConfig
# debug parameters
#if options.queueData != '':
# jobParameters += "--overwriteQueuedata=%s " % options.queueData
# set task param
taskParamMap['buildSpec'] = {
'prodSourceLabel':'panda',
'archiveName':os.path.basename(self.inputsandbox),
'jobParameters':jobParameters,
}
# enable merging
if job.backend.requirements.enableMerge:
jobParameters = '-r {0} '.format(self.rundirectory)
if 'exec' in job.backend.requirements.configMerge and job.backend.requirements.configMerge['exec'] != '':
jobParameters += '-j "{0}" '.format(job.backend.requirements.configMerge['exec'])
if not job.backend.nobuild:
jobParameters += '-l ${LIB} '
else:
jobParameters += '-a {0} '.format(os.path.basename(self.inputsandbox))
jobParameters += "--sourceURL ${SURL} "
jobParameters += '${TRN_OUTPUT:OUTPUT} ${TRN_LOG:LOG}'
taskParamMap['mergeSpec'] = {}
taskParamMap['mergeSpec']['useLocalIO'] = 1
taskParamMap['mergeSpec']['jobParameters'] = jobParameters
taskParamMap['mergeOutput'] = True
# Selected by Jedi
#if not app.atlas_exetype in ['PYARA','ROOT','EXE']:
# taskParamMap['transPath'] = 'http://atlpan.web.cern.ch/atlpan/runAthena-00-00-12'
logger.debug(taskParamMap)
# upload sources
if self.inputsandbox and not job.backend.libds:
uploadSources(os.path.dirname(self.inputsandbox),os.path.basename(self.inputsandbox))
if not self.inputsandbox == tmp_user_area_name:
logger.info('Removing source tarball %s ...' % self.inputsandbox )
os.remove(self.inputsandbox)
return taskParamMap
def prepare(self,app,appconfig,appmasterconfig,jobmasterconfig):
'''prepare the subjob specific configuration'''
# PandaTools
from pandatools import Client
from pandatools import AthenaUtils
from taskbuffer.JobSpec import JobSpec
from taskbuffer.FileSpec import FileSpec
job = app._getParent()
logger.debug('AthenaMCPandaRTHandler prepare called for %s', job.getFQID('.'))
try:
assert self.outsite
except:
logger.error("outsite not set. Aborting")
raise Exception()
job.backend.site = self.outsite
job.backend.actualCE = self.outsite
cloud = job._getRoot().backend.requirements.cloud
job.backend.requirements.cloud = cloud
# now just filling the job from AthenaMC data
jspec = JobSpec()
jspec.jobDefinitionID = job._getRoot().id
jspec.jobName = commands.getoutput('uuidgen 2> /dev/null')
jspec.AtlasRelease = 'Atlas-%s' % app.atlas_rel
if app.transform_archive:
jspec.homepackage = 'AnalysisTransforms'+app.transform_archive
elif app.prod_release:
jspec.homepackage = 'AnalysisTransforms-AtlasProduction_'+str(app.prod_release)
jspec.transformation = '%s/runAthena-00-00-11' % Client.baseURLSUB
#---->???? prodDBlock and destinationDBlock when facing several input / output datasets?
jspec.prodDBlock = 'NULL'
if job.inputdata and len(app.inputfiles)>0 and app.inputfiles[0] in app.dsetmap:
jspec.prodDBlock = app.dsetmap[app.inputfiles[0]]
# How to specify jspec.destinationDBlock when more than one type of output is available? Panda prod jobs seem to specify only the last output dataset
outdset=""
for type in ["EVNT","RDO","HITS","AOD","ESD","NTUP"]:
if type in app.outputpaths.keys():
outdset=string.replace(app.outputpaths[type],"/",".")
outdset=outdset[1:-1]
break
if not outdset:
try:
assert len(app.outputpaths.keys())>0
except:
logger.error("app.outputpaths is empty: check your output datasets")
raise
type=app.outputpaths.keys()[0]
outdset=string.replace(app.outputpaths[type],"/",".")
outdset=outdset[1:-1]
jspec.destinationDBlock = outdset
jspec.destinationSE = self.outsite
jspec.prodSourceLabel = 'user'
jspec.assignedPriority = 1000
jspec.cloud = cloud
# memory
if job.backend.requirements.memory != -1:
jspec.minRamCount = job.backend.requirements.memory
jspec.computingSite = self.outsite
jspec.cmtConfig = AthenaUtils.getCmtConfig(athenaVer=app.atlas_rel)
# library (source files)
flib = FileSpec()
flib.lfn = self.library
# flib.GUID =
flib.type = 'input'
# flib.status =
flib.dataset = self.libDataset
flib.dispatchDBlock = self.libDataset
jspec.addFile(flib)
# input files FIXME: many more input types
for lfn in app.inputfiles:
useguid=app.turls[lfn].replace("guid:","")
finp = FileSpec()
finp.lfn = lfn
finp.GUID = useguid
finp.dataset = app.dsetmap[lfn]
finp.prodDBlock = app.dsetmap[lfn]
finp.prodDBlockToken = 'local'
finp.dispatchDBlock = app.dsetmap[lfn]
finp.type = 'input'
finp.status = 'ready'
jspec.addFile(finp)
# add dbfiles if any:
for lfn in app.dbfiles:
useguid=app.dbturls[lfn].replace("guid:","")
finp = FileSpec()
finp.lfn = lfn
finp.GUID = useguid
finp.dataset = app.dsetmap[lfn]
finp.prodDBlock = app.dsetmap[lfn]
finp.prodDBlockToken = 'local'
finp.dispatchDBlock = app.dsetmap[lfn]
finp.type = 'input'
finp.status = 'ready'
jspec.addFile(finp)
# then minbias files
for lfn in app.mbfiles:
useguid=app.minbias_turls[lfn].replace("guid:","")
finp = FileSpec()
finp.lfn = lfn
finp.GUID = useguid
finp.dataset = app.dsetmap[lfn]
finp.prodDBlock = app.dsetmap[lfn]
finp.prodDBlockToken = 'local'
finp.dispatchDBlock = app.dsetmap[lfn]
finp.type = 'input'
finp.status = 'ready'
jspec.addFile(finp)
# then cavern files
for lfn in app.cavernfiles:
useguid=app.cavern_turls[lfn].replace("guid:","")
finp = FileSpec()
finp.lfn = lfn
finp.GUID = useguid
finp.dataset = app.dsetmap[lfn]
finp.prodDBlock = app.dsetmap[lfn]
finp.prodDBlockToken = 'local'
finp.dispatchDBlock = app.dsetmap[lfn]
finp.type = 'input'
finp.status = 'ready'
jspec.addFile(finp)
# output files( this includes the logfiles)
# Output files
jidtag=""
job = app._getParent() # Returns job or subjob object
if job._getRoot().subjobs:
jidtag = job._getRoot().id
else:
jidtag = "%d" % job.id
outfiles=app.subjobsOutfiles[job.id]
pandaOutfiles={}
for type in outfiles.keys():
pandaOutfiles[type]=outfiles[type]+"."+str(jidtag)
if type=="LOG":
pandaOutfiles[type]+=".tgz"
#print pandaOutfiles
for outtype in pandaOutfiles.keys():
fout = FileSpec()
dset=string.replace(app.outputpaths[outtype],"/",".")
dset=dset[1:-1]
fout.dataset=dset
fout.lfn=pandaOutfiles[outtype]
fout.type = 'output'
# fout.destinationDBlock = jspec.destinationDBlock
fout.destinationDBlock = fout.dataset
fout.destinationSE = jspec.destinationSE
if outtype=='LOG':
fout.type='log'
fout.destinationDBlock = fout.dataset
fout.destinationSE = job.backend.site
jspec.addFile(fout)
# job parameters
param = '-l %s ' % self.library # user tarball.
# use corruption checker
if job.backend.requirements.corCheck:
param += '--corCheck '
# disable to skip missing files
if job.backend.requirements.notSkipMissing:
param += '--notSkipMissing '
# transform parameters
# need to update arglist with final output file name...
newArgs=[]
if app.mode == "evgen":
app.args[3]=app.args[3]+" -t "
if app.verbosity:
app.args[3]=app.args[3]+" -l %s " % app.verbosity
for arg in app.args[3:]:
for type in outfiles.keys():
if arg.find(outfiles[type])>-1:
arg=arg.replace(outfiles[type],pandaOutfiles[type])
newArgs.append(arg)
arglist=string.join(newArgs," ")
# print "Arglist:",arglist
param += ' -r ./ '
param += ' -j "%s"' % urllib.quote(arglist)
allinfiles=app.inputfiles+app.dbfiles
# Input files.
param += ' -i "%s" ' % allinfiles
if len(app.mbfiles)>0:
param+= ' -m "%s" ' % app.mbfiles
if len(app.cavernfiles)>0:
param+= ' -n "%s" ' % app.cavernfiles
# param += '-m "[]" ' #%minList FIXME
# param += '-n "[]" ' #%cavList FIXME
del pandaOutfiles["LOG"] # logfiles do not appear in IROOT block, and this one is not needed anymore...
param += ' -o "{\'IROOT\':%s }"' % str(pandaOutfiles.items())
# source URL
matchURL = re.search("(http.*://[^/]+)/",Client.baseURLSSL)
if matchURL != None:
param += " --sourceURL %s " % matchURL.group(1)
param += " --trf"
jspec.jobParameters = param
jspec.metadata="--trf \"%s\"" % arglist
#print "SUBJOB DETAILS:",jspec.values()
if app.dryrun:
print "job.application.dryrun activated, printing out job parameters"
print jspec.values()
return
return jspec
def retry(self,JobsetID,newSite=False,newOpts={},noSubmit=False,ignoreDuplication=False,useJobsetID=False,retryBuild=False,reproduceFiles=[],unsetRetryID=False):
# get logger
tmpLog = PLogger.getPandaLogger()
# check proxy
self.gridPassPhrase,self.vomsFQAN = PsubUtils.checkGridProxy(
self.gridPassPhrase,
False,
self.verbose,
useCache=True)
# force update just in case
self.status(JobsetID,True)
# set an empty map since mutable default value is used
if newOpts == {}:
newOpts = {}
# get jobset
newJobsetID = -1
jobList = self.getJobIDsWithSetID(JobsetID)
if jobList == None:
# works only for jobsetID
if useJobsetID:
return
# works with jobID
isJobset = False
jobList = [JobsetID]
else:
isJobset = True
tmpMsg = "ID=%s is composed of JobID=" % JobsetID
for tmpJobID in jobList:
tmpMsg += '%s,' % tmpJobID
tmpMsg = tmpMsg[:-1]
tmpLog.info(tmpMsg)
for JobID in jobList:
# get job info from local repository
localJob = self.getJobInfo(JobID)
if localJob == None:
tmpLog.warning("JobID=%s not found in local repository. Synchronization may be needed" % JobID)
return None
# for JEDI
if localJob.isJEDI():
status,out = Client.retryTask(
localJob.jediTaskID,
verbose=self.verbose,
properErrorCode=True,
newParams=newOpts)
if status != 0:
tmpLog.error(status)
tmpLog.error(out)
tmpLog.error("Failed to retry TaskID=%s" % localJob.jediTaskID)
return False
tmpStat,tmpDiag = out
if (not tmpStat in [0,True] and newOpts == {}) or (newOpts != {} and tmpStat != 3):
tmpLog.error(tmpDiag)
tmpLog.error("Failed to retry TaskID=%s" % localJob.jediTaskID)
return False
tmpLog.info(tmpDiag)
continue
# skip running job
if localJob.dbStatus != 'frozen':
tmpLog.info('Retry failed subjobs in running jobId=%s' % JobID)
status,out = Client.retryFailedJobsInActive(JobID,verbose=self.verbose)
if status != 0:
tmpLog.error(status)
tmpLog.error(out)
tmpLog.error("Failed to retry JobID=%s" % JobID)
else:
job = self.status(JobID)
if isJobset:
continue
else:
return
# skip already retried
if localJob.retryID != '0':
if isJobset:
tmpLog.info('Skip JobID=%s since already retried by JobID=%s JobsetID=%s' % \
(JobID,localJob.retryID,localJob.retryJobsetID))
continue
else:
tmpLog.warning('This job was already retried by JobID=%s' % localJob.retryID)
return
# check status of buildJob
if not retryBuild and not localJob.buildStatus in ['','finished']:
tmpMsgStr = 'Cannot retry since status of buildJob %s is %s (!= finished). ' \
% (localJob.PandaID.split(',')[0],localJob.buildStatus)
tmpMsgStr += 'Please execute %s with the same input/output datasets (or containers). ' % localJob.jobType
tmpMsgStr += 'It will run only on failed/cancelled/unused input files '
tmpMsgStr += 'and append output files to the output dataset container. '
tmpMsgStr += 'Or you may set retryBuild=True in pbook.retry() '
tmpLog.warning(tmpMsgStr)
if isJobset:
continue
else:
return
# check opts for newSite
if newSite or newOpts != {}:
if not localJob.outDS.endswith('/') and not newOpts.has_key('outDS') and not newOpts.has_key('--outDS'):
tmpLog.warning('You need to specify --outDS in newOpts to retry at new site unless container is used as output')
return
# get list of failed jobs
pandaIDs = localJob.PandaID.split(',')
statusList= localJob.jobStatus.split(',')
jobList = []
for idx in range(len(pandaIDs)):
# check status unless reproduce files
if reproduceFiles == [] and not statusList[idx] in ['failed','cancelled']:
continue
jobList.append(pandaIDs[idx])
# no failed job
if jobList == []:
if isJobset:
tmpLog.info('Skip JobID=%s since no failed jobs' % JobID)
continue
else:
tmpLog.info('No failed jobs to be retried for JobID=%s' % JobID)
return
# get full job spec
tmpLog.info("Retrying JobID=%s ..." % JobID)
tmpLog.info("Getting job info")
idxJL = 0
nQuery = 500
pandaJobs = []
while idxJL < len(jobList):
# avoid burst query
tmpLog.info(" %5s/%s" % (idxJL,len(jobList)))
status,oTmp = Client.getFullJobStatus(
jobList[idxJL:idxJL+nQuery],
verbose=self.verbose)
if status != 0:
tmpLog.error(status)
tmpLog.error(oTmp)
tmpLog.error("Cannot get job info from Panda server")
return
pandaJobs += oTmp
idxJL += nQuery
time.sleep(1)
tmpLog.info(" %5s/%s" % (len(jobList),len(jobList)))
# get PandaIDs to reproduce files
if reproduceFiles != []:
# change wildcard to .* for regexp
reproduceFilePatt = []
for tmpReproduceFile in reproduceFiles:
if '*' in tmpReproduceFile:
tmpReproduceFile = tmpReproduceFile.replace('*','.*')
reproduceFilePatt.append(tmpReproduceFile)
# get list of jobs which produced interesting files
tmpJobList = []
tmpPandaJobs = []
for tmpPandaJob in pandaJobs:
# check names
tmpMatchFlag = False
for tmpFile in tmpPandaJob.Files:
if tmpFile.type == 'output' and tmpFile.status == 'ready':
for tmpReproduceFile in reproduceFilePatt:
# normal matching
if tmpReproduceFile == tmpFile.lfn:
tmpMatchFlag = True
break
# wild card
if '*' in tmpReproduceFile and \
re.search('^'+tmpReproduceFile,tmpFile.lfn) != None:
tmpMatchFlag = True
break
if tmpMatchFlag:
break
# append
if tmpMatchFlag:
tmpJobList.append(tmpPandaJob.PandaID)
tmpPandaJobs.append(tmpPandaJob)
# use new list
jobList = tmpJobList
pandaJobs = tmpPandaJobs
if jobList == []:
tmpLog.info("No jobs to reproduce files : Jobs in JobID=%s didn't produce lost files" % JobID)
continue
# jobdefID
newJobdefID = PsubUtils.readJobDefID()
# reset some parameters
retryJobs = []
retrySite = None
retryElement = None
retryDestSE = None
outDsName = None
shadowList = []
oldLibDS = None
newLibDS = None
newLibTgz = None
rebroMap = {}
for idx in range(len(jobList)):
job = pandaJobs[idx]
# skip exired
if job == None:
tmpLog.warning("Could not retry jobs older than 30 days : JobID=%s (PandaID=%s) expired" \
% (JobID,jobList[idxJob]))
return
# skip jobs reassigned by rebrokerage
if (job.jobStatus == 'cancelled' and job.taskBufferErrorCode in [105,'105']) or \
(job.jobStatus == 'failed' and job.taskBufferErrorCode in [106,'106']):
# extract JobIDs of reassigned jobs
tmpM = re.search('JobsetID=(\d+) JobID=(\d+)',job.taskBufferErrorDiag)
if tmpM != None:
tmpRebKey = (tmpM.group(1),tmpM.group(2))
if not rebroMap.has_key(tmpRebKey):
rebroMap[tmpRebKey] = 0
# count # of reassigned jobs
rebroMap[tmpRebKey] += 1
continue
# get shadow list
if (not ignoreDuplication) and outDsName == None and job.prodSourceLabel == 'user':
# look for dataset for log since it doesn't have suffix even when --individualOutDS is used
for tmpFile in job.Files:
if tmpFile.type == 'log':
outDsName = tmpFile.dataset
break
# output dataset was not found
if outDsName == None:
tmpLog.error("Could not get output dataset name for JobID=%s (PandaID=%s)" \
% (JobID,job.PandaID))
return
# get files in shadow
if outDsName.endswith('/'):
shadowList = Client.getFilesInShadowDataset(
outDsName,
Client.suffixShadow,
self.verbose)
else:
# disable duplication check mainly for old overlay jobs since non-signal files are wrongly skipped
#shadowList = Client.getFilesInShadowDatasetOld(outDsName,Client.suffixShadow,self.verbose)
pass
# unify sitename
if retrySite == None:
retrySite = job.computingSite
retryElement = job.computingElement
retryDestSE = job.destinationSE
# reset
job.jobStatus = None
job.commandToPilot = None
job.startTime = None
job.endTime = None
job.attemptNr = 1+job.attemptNr
for attr in job._attributes:
if attr.endswith('ErrorCode') or attr.endswith('ErrorDiag'):
setattr(job,attr,None)
job.transExitCode = None
job.computingSite = retrySite
job.computingElement = retryElement
job.destinationSE = retryDestSE
job.dispatchDBlock = None
if not unsetRetryID:
job.jobExecutionID = JobID
job.jobDefinitionID = newJobdefID
job.parentID = job.PandaID
if job.jobsetID != ['NULL',None,-1]:
if not unsetRetryID:
job.sourceSite = job.jobsetID
job.jobsetID = newJobsetID
skipInputList = []
numUsedFiles = 0
# loop over all files
for file in job.Files:
file.rowID = None
if file.type == 'input':
# protection against wrong sync which doesn't update buildStatus correctly
if not retryBuild and file.lfn.endswith('.lib.tgz') and file.GUID == 'NULL':
tmpLog.warning('GUID for %s is unknown. Cannot retry when corresponding buildJob failed' \
% file.lfn)
return
if not retryBuild or not file.lfn.endswith('.lib.tgz'):
file.status = 'ready'
# set new lib dataset
if retryBuild and file.lfn.endswith('.lib.tgz'):
if newLibTgz != None:
file.lfn = newLibTgz
file.dataset = newLibDS
file.dispatchDBlock = newLibDS
# check with shadow for non lib.tgz/DBR
tmpDbrMatch = re.search('^DBRelease-.*\.tar\.gz$',file.lfn)
if tmpDbrMatch == None and not file.lfn.endswith('.lib.tgz'):
if file.lfn in shadowList:
skipInputList.append(file)
else:
numUsedFiles += 1
elif file.type in ('output','log'):
file.destinationSE = retryDestSE
file.destinationDBlock = re.sub('_sub\d+$','',file.destinationDBlock)
# add retry num
if file.dataset.endswith('/') or job.prodSourceLabel == 'panda':
oldOutDsName = file.destinationDBlock
retryDsPatt = '_r'
if reproduceFiles != []:
retryDsPatt = '_rp'
retryMatch = re.search(retryDsPatt+'(\d+)$',file.destinationDBlock)
if retryMatch == None:
file.destinationDBlock += (retryDsPatt+'1')
else:
tmpDestinationDBlock = re.sub(retryDsPatt+'(\d+)$','',file.destinationDBlock)
file.destinationDBlock = tmpDestinationDBlock + retryDsPatt + '%d' % (1+int(retryMatch.group(1)))
if job.processingType == 'usermerge':
job.jobParameters = job.jobParameters.replace(' %s ' % oldOutDsName,
' %s ' % file.destinationDBlock)
# use new dataset name for buildXYZ
if job.prodSourceLabel == 'panda':
if file.lfn.endswith('.lib.tgz'):
# get new libDS and lib.tgz names
oldLibDS = file.dataset
file.dataset = file.destinationDBlock
newLibDS = file.dataset
file.lfn = re.sub(oldLibDS,newLibDS,file.lfn)
newLibTgz = file.lfn
else:
file.dataset = file.destinationDBlock
# add attempt nr
oldName = file.lfn
if job.prodSourceLabel == 'panda' and file.lfn.endswith('.lib.tgz'):
continue
else:
# append attempt number at the tail
file.lfn = re.sub("\.\d+$","",file.lfn)
file.lfn = "%s.%d" % (file.lfn,job.attemptNr)
newName = file.lfn
# modify jobParameters
job.jobParameters = re.sub("'%s'" % oldName ,"'%s'" % newName,
job.jobParameters)
# look for output in trf
oldGenelicName = re.sub('\.\d+$','',oldName)
match = re.search(oldGenelicName+'(\.\d+)*(%20|")',job.jobParameters)
if match != None:
job.jobParameters = job.jobParameters.replace(match.group(0),newName+match.group(2))
# change lib.tgz name
if retryBuild and newLibDS != None:
job.jobParameters = re.sub(oldLibDS,newLibDS,job.jobParameters)
# change destinationDBlock
if job.prodSourceLabel == 'panda':
job.destinationDBlock = newLibDS
# all files are used by others
if numUsedFiles == 0 and skipInputList != []:
continue
# remove skipped files
strSkipped = ''
for tmpFile in skipInputList:
strSkipped += '%s,' % tmpFile.lfn
job.Files.remove(tmpFile)
strSkipped = strSkipped[:-1]
# modify jobpar
if strSkipped != '':
optionToSkipFiles = '--skipInputByRetry'
if not optionToSkipFiles in job.jobParameters:
# just append
job.jobParameters += "%s=%s " % (optionToSkipFiles,strSkipped)
else:
# extract already skipped files
tmpMatch = re.search("(%s=[^ ]+)",job.jobParameters)
if tmpMatch == None:
tmpLog.error("Failed to extract arg of %s for PandaID=%s" \
% (optionToSkipFiles,job.PandaID))
return
# replace
job.jobParameters = re.sub(tmpMatch.group(1),"%s,%s" % (tmpMatch.group(1),optionToSkipFiles),
job.jobParameters)
if self.verbose:
tmpLog.debug(job.jobParameters)
# append
retryJobs.append(job)
# info on rebrokeage
if rebroMap != {}:
for tmpRebKey,tmpRebNumJobs in rebroMap.iteritems():
tmpRebSetID,tmpRebJobID = tmpRebKey
tmpLog.info('Skip %s jobs since JobID=%s JobsetID=%s already reassigned them to another site' % \
(tmpRebNumJobs,tmpRebJobID,tmpRebSetID))
if retryJobs == []:
tmpLog.info("No more jobs to be retried for JobID=%s" % JobID)
if isJobset:
continue
else:
return
# all input files were or are being used by other jobs
if retryJobs == []:
tmpLog.info('All input files were or are being used by other jobs for the same output. No jobs to be retried. If you need to ignore duplication check (e.g., using the same EVNT file for multiple simulation subjobs), set ignoreDuplication=True. i.e. retry(123,ignoreDuplication=True)')
if isJobset:
continue
else:
return
# check voms role
if not retryJobs[0].workingGroup in ['NULL',None,'']:
# VOMS role was used
if not "--workingGroup" in job.metadata:
# extract voms roles from metadata
match = re.search("--voms( |=)[ \"]*([^ \"]+)",job.metadata)
if match != None:
vomsRoles = match.group(2)
else:
vomsRoles = "atlas:/atlas/%s/Role=production" % retryJobs[0].workingGroup
# regenerate proxy with VOMS roles
try:
tmpLog.info("Checking proxy role to resubmit %s jobs" % retryJobs[0].workingGroup)
self.gridPassPhrase,self.vomsFQAN = PsubUtils.checkGridProxy(
self.gridPassPhrase,
False,
self.verbose,vomsRoles,
useCache=True)
except:
tmpLog.error("Failed to generate a proxy with %s" % vomsRoles)
return
# check runtime env for new site submission
if (newSite or newOpts != {}):
if retryJobs[0].processingType == 'pathena' or '--useAthenaPackages' in retryJobs[0].metadata:
from pandatools import AthenaUtils
stA,retA = AthenaUtils.getAthenaVer()
if not stA:
tmpLog.error("Failed to get Athena rel/cache version in current runtime env")
return
athenaVer = retA['athenaVer']
cacheVer = retA['cacheVer']
nightVer = retA['nightVer']
wrongSetup = False
if retryJobs[0].AtlasRelease != 'Atlas-%s' % athenaVer:
wrongSetup = True
errMsg = "Current Athena version Atlas-%s is inconsitent with the previous submission %s. " % (athenaVer,retryJobs[0].AtlasRelease)
elif retryJobs[0].homepackage != 'AnalysisTransforms'+cacheVer+nightVer:
wrongSetup = True
errMsg = "Current cache version %s is inconsitent with the previous submission. " % cacheVer.replace('-','').replace('_','-')
if wrongSetup:
errMsg += 'You need to have the same runtime env as before since all job spec need to be re-created to send jobs to a new site. '
errMsg += 'Please setup Athena correctly and restart pbook'
tmpLog.error(errMsg)
return
# test mode
if noSubmit:
continue
# invoke pathena/prun to send job to new site
if (newSite or newOpts != {}) and retryJobs[0].processingType != 'usermerge':
# set parent jobID and jobsetID
newOpts['provenanceID'] = retryJobs[0].jobExecutionID
newOpts['panda_parentJobsetID'] = retryJobs[0].sourceSite
tmpLog.info("Constructing job spec again to be sent to another site ...")
comStat= PsubUtils.execWithModifiedParams(retryJobs,newOpts,self.verbose,newSite)
if comStat == 0:
# update database
time.sleep(2)
self.sync()
else:
tmpLog.error("Failed to submit jobs to Panda server")
return
# register datasets
tmpOutDsLocation = Client.PandaSites[retryJobs[-1].computingSite]['ddm']
addedDataset = []
shadowDSname = None
for tmpFile in retryJobs[-1].Files:
if tmpFile.type in ['output','log'] and tmpFile.dataset.endswith('/'):
# add shadow
"""
removed shadow
if shadowDSname == None and tmpFile.type == 'log':
shadowDSname = "%s%s" % (tmpFile.destinationDBlock,Client.suffixShadow)
Client.addDataset(shadowDSname,self.verbose)
"""
# add datasets
if not tmpFile.destinationDBlock in addedDataset:
# create dataset
Client.addDataset(
tmpFile.destinationDBlock,
self.verbose,
location=tmpOutDsLocation,
dsCheck=False)
# add to container
Client.addDatasetsToContainer(
tmpFile.dataset,
[tmpFile.destinationDBlock],
self.verbose)
# append
addedDataset.append(tmpFile.destinationDBlock)
# register libDS
if retryBuild and newLibDS != None:
Client.addDataset(
newLibDS,
self.verbose,
location=tmpOutDsLocation,
dsCheck=False)
# submit
tmpLog.info("Submitting job ...")
status,out = Client.submitJobs(retryJobs,verbose=self.verbose)
if out == None or status != 0:
tmpLog.error(status)
tmpLog.error(out)
tmpLog.error("Failed to submit jobs to Panda server")
return
# update database
pandaIDstatus = {}
newJobID = None
for items in out:
# get newJobID
if newJobID == None:
newJobID = items[1]
# check PandaID
PandaID = items[0]
if PandaID == 'NULL':
tmpLog.error("Panda server returned wrong IDs. It may have a temporary problem")
return
# set newJobsetID
if newJobsetID in [None,-1]:
newJobsetID = items[2]['jobsetID']
# dummy statuso
pandaIDstatus[PandaID] = ('defined','NULL')
# set retry ID
if not unsetRetryID:
localJob.retryID = newJobID
if not newJobsetID in [None,-1,'NULL']:
localJob.retryJobsetID = newJobsetID
try:
PdbUtils.updateJobDB(localJob,self.verbose)
except:
tmpLog.error("Failed to set retryID for JobID=%s" % JobID)
return
# set new paramers
newLocalJob = PdbUtils.convertPtoD(retryJobs,pandaIDstatus)
newLocalJob.JobID = newJobID
if not newJobsetID in [None,-1,'NULL']:
newLocalJob.groupID = newJobsetID
newLocalJob.creationTime = datetime.datetime.utcnow()
# insert to DB
try:
PdbUtils.insertJobDB(newLocalJob,self.verbose)
except:
tmpLog.error("Failed to insert JobID=%s to local repository" % newJobID)
return
# write new jobdefID
PsubUtils.writeJobDefID(newJobID)
# done
tmpMsg = 'Done. New JobID=%s' % newJobID
if not newJobsetID in [None,-1,'NULL']:
tmpMsg += " JobsetID=%s" % newJobsetID
tmpLog.info(tmpMsg)
def master_prepare(self, app, appconfig):
'''Prepare the master job'''
from pandatools import Client
from pandatools import MiscUtils
from pandatools import AthenaUtils
from pandatools import PsubUtils
from taskbuffer.JobSpec import JobSpec
from taskbuffer.FileSpec import FileSpec
from pandatools import PandaToolsPkgInfo
# create a random number for this submission to allow multiple use of containers
self.rndSubNum = random.randint(1111, 9999)
job = app._getParent()
logger.debug('AthenaJediRTHandler master_prepare called for %s',
job.getFQID('.'))
if app.useRootCoreNoBuild:
logger.info(
'Athena.useRootCoreNoBuild is True, setting Panda.nobuild=True.'
)
job.backend.nobuild = True
if job.backend.bexec and job.backend.nobuild:
raise ApplicationConfigurationError(
None,
"Contradicting options: job.backend.bexec and job.backend.nobuild are both enabled."
)
if job.backend.requirements.rootver != '' and job.backend.nobuild:
raise ApplicationConfigurationError(
None,
"Contradicting options: job.backend.requirements.rootver given and job.backend.nobuild are enabled."
)
# Switch on compilation flag if bexec is set or libds is empty
if job.backend.bexec != '' or not job.backend.nobuild:
app.athena_compile = True
for sj in job.subjobs:
sj.application.athena_compile = True
logger.info(
'"job.backend.nobuild=False" or "job.backend.bexec" is set - Panda build job is enabled.'
)
if job.backend.nobuild:
app.athena_compile = False
for sj in job.subjobs:
sj.application.athena_compile = False
logger.info(
'"job.backend.nobuild=True" or "--nobuild" chosen - Panda build job is switched off.'
)
# check for auto datri
if job.outputdata.location != '':
if not PsubUtils.checkDestSE(job.outputdata.location,
job.outputdata.datasetname, False):
raise ApplicationConfigurationError(
None, "Problems with outputdata.location setting '%s'" %
job.outputdata.location)
# validate application
if not app.atlas_release and not job.backend.requirements.rootver and not app.atlas_exetype in [
'EXE'
]:
raise ApplicationConfigurationError(
None,
"application.atlas_release is not set. Did you run application.prepare()"
)
self.dbrelease = app.atlas_dbrelease
if self.dbrelease != '' and self.dbrelease != 'LATEST' and self.dbrelease.find(
':') == -1:
raise ApplicationConfigurationError(
None,
"ERROR : invalid argument for DB Release. Must be 'LATEST' or 'DatasetName:FileName'"
)
self.runConfig = AthenaUtils.ConfigAttr(app.atlas_run_config)
for k in self.runConfig.keys():
self.runConfig[k] = AthenaUtils.ConfigAttr(self.runConfig[k])
if not app.atlas_run_dir:
raise ApplicationConfigurationError(
None,
"application.atlas_run_dir is not set. Did you run application.prepare()"
)
self.rundirectory = app.atlas_run_dir
self.cacheVer = ''
if app.atlas_project and app.atlas_production:
self.cacheVer = "-" + app.atlas_project + "_" + app.atlas_production
# handle different atlas_exetypes
self.job_options = ''
if app.atlas_exetype == 'TRF':
self.job_options += ' '.join(
[os.path.basename(fopt.name) for fopt in app.option_file])
#if not job.outputdata.outputdata:
# raise ApplicationConfigurationError(None,"job.outputdata.outputdata is required for atlas_exetype in ['PYARA','ARES','TRF','ROOT','EXE' ] and Panda backend")
#raise ApplicationConfigurationError(None,"Sorry TRF on Panda backend not yet supported")
if app.options:
self.job_options += ' %s ' % app.options
elif app.atlas_exetype == 'ATHENA':
if len(app.atlas_environment) > 0 and app.atlas_environment[
0].find('DBRELEASE_OVERRIDE') == -1:
logger.warning(
"Passing of environment variables to Athena using Panda not supported. Ignoring atlas_environment setting."
)
if job.outputdata.outputdata:
raise ApplicationConfigurationError(
None,
"job.outputdata.outputdata must be empty if atlas_exetype='ATHENA' and Panda backend is used (outputs are auto-detected)"
)
if app.options:
if app.options.startswith('-c'):
self.job_options += ' %s ' % app.options
else:
self.job_options += ' -c %s ' % app.options
logger.warning(
'The value of j.application.options has been prepended with " -c " '
)
logger.warning(
'Please make sure to use proper quotes for the values of j.application.options !'
)
self.job_options += ' '.join(
[os.path.basename(fopt.name) for fopt in app.option_file])
# check for TAG compression
if 'subcoll.tar.gz' in app.append_to_user_area:
self.job_options = ' uncompress.py ' + self.job_options
elif app.atlas_exetype in ['PYARA', 'ARES', 'ROOT', 'EXE']:
#if not job.outputdata.outputdata:
# raise ApplicationConfigurationError(None,"job.outputdata.outputdata is required for atlas_exetype in ['PYARA','ARES','TRF','ROOT','EXE' ] and Panda backend")
self.job_options += ' '.join(
[os.path.basename(fopt.name) for fopt in app.option_file])
# sort out environment variables
env_str = ""
if len(app.atlas_environment) > 0:
for env_var in app.atlas_environment:
env_str += "export %s ; " % env_var
else:
env_str = ""
# below fixes issue with runGen -- job_options are executed by os.system when dbrelease is used, and by the shell otherwise
## - REMOVED FIX DUE TO CHANGE IN PILOT - MWS 8/11/11
if job.backend.requirements.usecommainputtxt:
input_str = '/bin/echo %IN > input.txt; cat input.txt; '
else:
input_str = '/bin/echo %IN | sed \'s/,/\\\n/g\' > input.txt; cat input.txt; '
if app.atlas_exetype == 'PYARA':
self.job_options = env_str + input_str + ' python ' + self.job_options
elif app.atlas_exetype == 'ARES':
self.job_options = env_str + input_str + ' athena.py ' + self.job_options
elif app.atlas_exetype == 'ROOT':
self.job_options = env_str + input_str + ' root -b -q ' + self.job_options
elif app.atlas_exetype == 'EXE':
self.job_options = env_str + input_str + self.job_options
if app.options:
self.job_options += ' %s ' % app.options
if self.job_options == '':
raise ApplicationConfigurationError(None, "No Job Options found!")
logger.info('Running job options: %s' % self.job_options)
# validate dbrelease
if self.dbrelease != "LATEST":
self.dbrFiles, self.dbrDsList = getDBDatasets(
self.job_options, '', self.dbrelease)
# handle the output dataset
if job.outputdata:
if job.outputdata._name != 'DQ2OutputDataset':
raise ApplicationConfigurationError(
None, 'Panda backend supports only DQ2OutputDataset')
else:
logger.info('Adding missing DQ2OutputDataset')
job.outputdata = DQ2OutputDataset()
# validate the output dataset name (and make it a container)
job.outputdata.datasetname, outlfn = dq2outputdatasetname(
job.outputdata.datasetname, job.id, job.outputdata.isGroupDS,
job.outputdata.groupname)
if not job.outputdata.datasetname.endswith('/'):
job.outputdata.datasetname += '/'
# add extOutFiles
self.extOutFile = []
for tmpName in job.outputdata.outputdata:
if tmpName != '':
self.extOutFile.append(tmpName)
for tmpName in job.backend.extOutFile:
if tmpName != '':
self.extOutFile.append(tmpName)
# use the shared area if possible
tmp_user_area_name = app.user_area.name
if app.is_prepared is not True:
from Ganga.Utility.files import expandfilename
shared_path = os.path.join(
expandfilename(getConfig('Configuration')['gangadir']),
'shared',
getConfig('Configuration')['user'])
tmp_user_area_name = os.path.join(
os.path.join(shared_path, app.is_prepared.name),
os.path.basename(app.user_area.name))
# Add inputsandbox to user_area
if job.inputsandbox:
logger.warning(
"Submitting Panda job with inputsandbox. This may slow the submission slightly."
)
if tmp_user_area_name:
inpw = os.path.dirname(tmp_user_area_name)
self.inputsandbox = os.path.join(
inpw, 'sources.%s.tar' %
commands.getoutput('uuidgen 2> /dev/null'))
else:
inpw = job.getInputWorkspace()
self.inputsandbox = inpw.getPath(
'sources.%s.tar' %
commands.getoutput('uuidgen 2> /dev/null'))
if tmp_user_area_name:
rc, output = commands.getstatusoutput(
'cp %s %s.gz' % (tmp_user_area_name, self.inputsandbox))
if rc:
logger.error('Copying user_area failed with status %d', rc)
logger.error(output)
raise ApplicationConfigurationError(
None, 'Packing inputsandbox failed.')
rc, output = commands.getstatusoutput('gunzip %s.gz' %
(self.inputsandbox))
if rc:
logger.error('Unzipping user_area failed with status %d',
rc)
logger.error(output)
raise ApplicationConfigurationError(
None, 'Packing inputsandbox failed.')
for fname in [os.path.abspath(f.name) for f in job.inputsandbox]:
fname.rstrip(os.sep)
path = os.path.dirname(fname)
fn = os.path.basename(fname)
#app.atlas_run_dir
# get Athena versions
rc, out = AthenaUtils.getAthenaVer()
# failed
if not rc:
#raise ApplicationConfigurationError(None, 'CMT could not parse correct environment ! \n Did you start/setup ganga in the run/ or cmt/ subdirectory of your athena analysis package ?')
logger.warning(
"CMT could not parse correct environment for inputsandbox - will use the atlas_run_dir as default"
)
# as we don't have to be in the run dir now, create a copy of the run_dir directory structure and use that
input_dir = os.path.dirname(self.inputsandbox)
run_path = "%s/sbx_tree/%s" % (input_dir,
app.atlas_run_dir)
rc, output = commands.getstatusoutput("mkdir -p %s" %
run_path)
if not rc:
# copy this sandbox file
rc, output = commands.getstatusoutput(
"cp %s %s" % (fname, run_path))
if not rc:
path = os.path.join(input_dir, 'sbx_tree')
fn = os.path.join(app.atlas_run_dir, fn)
else:
raise ApplicationConfigurationError(
None,
"Couldn't copy file %s to recreate run_dir for input sandbox"
% fname)
else:
raise ApplicationConfigurationError(
None,
"Couldn't create directory structure to match run_dir %s for input sandbox"
% run_path)
else:
userarea = out['workArea']
# strip the path from the filename if present in the userarea
ua = os.path.abspath(userarea)
if ua in path:
fn = fname[len(ua) + 1:]
path = ua
rc, output = commands.getstatusoutput(
'tar -h -r -f %s -C %s %s' % (self.inputsandbox, path, fn))
if rc:
logger.error('Packing inputsandbox failed with status %d',
rc)
logger.error(output)
raise ApplicationConfigurationError(
None, 'Packing inputsandbox failed.')
# remove sandbox tree if created
if "sbx_tree" in os.listdir(os.path.dirname(self.inputsandbox)):
rc, output = commands.getstatusoutput(
"rm -r %s/sbx_tree" % os.path.dirname(self.inputsandbox))
if rc:
raise ApplicationConfigurationError(
None,
"Couldn't remove directory structure used for input sandbox"
)
rc, output = commands.getstatusoutput('gzip %s' %
(self.inputsandbox))
if rc:
logger.error('Packing inputsandbox failed with status %d', rc)
logger.error(output)
raise ApplicationConfigurationError(
None, 'Packing inputsandbox failed.')
self.inputsandbox += ".gz"
else:
self.inputsandbox = tmp_user_area_name
# job name
jobName = 'ganga.%s' % MiscUtils.wrappedUuidGen()
# make task
taskParamMap = {}
# Enforce that outputdataset name ends with / for container
if not job.outputdata.datasetname.endswith('/'):
job.outputdata.datasetname = job.outputdata.datasetname + '/'
taskParamMap['taskName'] = job.outputdata.datasetname
taskParamMap['uniqueTaskName'] = True
taskParamMap['vo'] = 'atlas'
taskParamMap['architecture'] = AthenaUtils.getCmtConfig(
athenaVer=app.atlas_release, cmtConfig=app.atlas_cmtconfig)
if app.atlas_release:
taskParamMap['transUses'] = 'Atlas-%s' % app.atlas_release
else:
taskParamMap['transUses'] = ''
taskParamMap[
'transHome'] = 'AnalysisTransforms' + self.cacheVer #+nightVer
configSys = getConfig('System')
gangaver = configSys['GANGA_VERSION'].lower()
if not gangaver:
gangaver = "ganga"
if app.atlas_exetype in ["ATHENA", "TRF"]:
taskParamMap['processingType'] = '{0}-jedi-athena'.format(gangaver)
else:
taskParamMap['processingType'] = '{0}-jedi-run'.format(gangaver)
#if options.eventPickEvtList != '':
# taskParamMap['processingType'] += '-evp'
taskParamMap['prodSourceLabel'] = 'user'
if job.backend.site != 'AUTO':
taskParamMap['cloud'] = Client.PandaSites[
job.backend.site]['cloud']
taskParamMap['site'] = job.backend.site
elif job.backend.requirements.cloud != None and not job.backend.requirements.anyCloud:
taskParamMap['cloud'] = job.backend.requirements.cloud
if job.backend.requirements.excluded_sites != []:
taskParamMap['excludedSite'] = expandExcludedSiteList(job)
# if only a single site specifed, don't set includedSite
#if job.backend.site != 'AUTO':
# taskParamMap['includedSite'] = job.backend.site
#taskParamMap['cliParams'] = fullExecString
if job.backend.requirements.noEmail:
taskParamMap['noEmail'] = True
if job.backend.requirements.skipScout:
taskParamMap['skipScout'] = True
if not app.atlas_exetype in ["ATHENA", "TRF"]:
taskParamMap[
'nMaxFilesPerJob'] = job.backend.requirements.maxNFilesPerJob
if job.backend.requirements.disableAutoRetry:
taskParamMap['disableAutoRetry'] = 1
# source URL
matchURL = re.search("(http.*://[^/]+)/", Client.baseURLCSRVSSL)
if matchURL != None:
taskParamMap['sourceURL'] = matchURL.group(1)
# dataset names
outDatasetName = job.outputdata.datasetname
logDatasetName = re.sub('/$', '.log/', job.outputdata.datasetname)
# log
taskParamMap['log'] = {
'dataset': logDatasetName,
'container': logDatasetName,
'type': 'template',
'param_type': 'log',
'value': '{0}.${{SN}}.log.tgz'.format(logDatasetName[:-1])
}
# job parameters
if app.atlas_exetype in ["ATHENA", "TRF"]:
taskParamMap['jobParameters'] = [
{
'type': 'constant',
'value': ' --sourceURL ${SURL}',
},
]
else:
taskParamMap['jobParameters'] = [
{
'type': 'constant',
'value': '-j "" --sourceURL ${SURL}',
},
]
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value': '-r {0}'.format(self.rundirectory),
},
]
# output
# output files
outMap = {}
if app.atlas_exetype in ["ATHENA", "TRF"]:
outMap, tmpParamList = AthenaUtils.convertConfToOutput(
self.runConfig,
self.extOutFile,
job.outputdata.datasetname,
destination=job.outputdata.location)
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value': '-o "%s" ' % outMap
},
]
taskParamMap['jobParameters'] += tmpParamList
else:
if job.outputdata.outputdata:
for tmpLFN in job.outputdata.outputdata:
if len(job.outputdata.datasetname.split('.')) > 2:
lfn = '{0}.{1}'.format(
*job.outputdata.datasetname.split('.')[:2])
else:
lfn = job.outputdata.datasetname[:-1]
lfn += '.$JOBSETID._${{SN/P}}.{0}'.format(tmpLFN)
dataset = '{0}_{1}/'.format(
job.outputdata.datasetname[:-1], tmpLFN)
taskParamMap[
'jobParameters'] += MiscUtils.makeJediJobParam(
lfn,
dataset,
'output',
hidden=True,
destination=job.outputdata.location)
outMap[tmpLFN] = lfn
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value': '-o "{0}"'.format(str(outMap)),
},
]
if app.atlas_exetype in ["ATHENA"]:
# jobO parameter
tmpJobO = self.job_options
# replace full-path jobOs
for tmpFullName, tmpLocalName in AthenaUtils.fullPathJobOs.iteritems(
):
tmpJobO = re.sub(tmpFullName, tmpLocalName, tmpJobO)
# modify one-liner for G4 random seeds
if self.runConfig.other.G4RandomSeeds > 0:
if app.options != '':
tmpJobO = re.sub('-c "%s" ' % app.options,
'-c "%s;from G4AtlasApps.SimFlags import SimFlags;SimFlags.SeedsG4=${RNDMSEED}" ' \
% app.options,tmpJobO)
else:
tmpJobO = '-c "from G4AtlasApps.SimFlags import SimFlags;SimFlags.SeedsG4=${RNDMSEED}" '
dictItem = {
'type': 'template',
'param_type': 'number',
'value': '${RNDMSEED}',
'hidden': True,
'offset': self.runConfig.other.G4RandomSeeds,
}
taskParamMap['jobParameters'] += [dictItem]
elif app.atlas_exetype in ["TRF"]:
# replace parameters for TRF
tmpJobO = self.job_options
# output : basenames are in outMap['IROOT'] trough extOutFile
tmpOutMap = []
for tmpName, tmpLFN in outMap['IROOT']:
tmpJobO = tmpJobO.replace('%OUT.' + tmpName, tmpName)
# replace DBR
tmpJobO = re.sub('%DB=[^ \'\";]+', '${DBR}', tmpJobO)
if app.atlas_exetype in ["TRF"]:
taskParamMap['useLocalIO'] = 1
# build
if job.backend.nobuild:
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value':
'-a {0}'.format(os.path.basename(self.inputsandbox)),
},
]
else:
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value': '-l ${LIB}',
},
]
#
# input
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
if job.backend.requirements.nFilesPerJob > 0 and job.inputdata.number_of_files == 0 and job.backend.requirements.split > 0:
job.inputdata.number_of_files = job.backend.requirements.nFilesPerJob * job.backend.requirements.split
if job.inputdata and job.inputdata._name == 'DQ2Dataset' and job.inputdata.number_of_files != 0:
taskParamMap['nFiles'] = job.inputdata.number_of_files
elif job.backend.requirements.nFilesPerJob > 0 and job.backend.requirements.split > 0:
# pathena does this for some reason even if there is no input files
taskParamMap[
'nFiles'] = job.backend.requirements.nFilesPerJob * job.backend.requirements.split
if job.backend.requirements.nFilesPerJob > 0:
taskParamMap[
'nFilesPerJob'] = job.backend.requirements.nFilesPerJob
if job.backend.requirements.nEventsPerFile > 0:
taskParamMap[
'nEventsPerFile'] = job.backend.requirements.nEventsPerFile
if not job.backend.requirements.nGBPerJob in [0, 'MAX']:
try:
if job.backend.requirements.nGBPerJob != 'MAX':
job.backend.requirments.nGBPerJob = int(
job.backend.requirements.nGBPerJob)
except:
logger.error("nGBPerJob must be an integer or MAX")
# check negative
if job.backend.requirements.nGBPerJob <= 0:
logger.error("nGBPerJob must be positive")
# don't set MAX since it is the defalt on the server side
if not job.backend.requirements.nGBPerJob in [-1, 'MAX']:
taskParamMap['nGBPerJob'] = job.backend.requirements.nGBPerJob
if app.atlas_exetype in ["ATHENA", "TRF"]:
inputMap = {}
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
tmpDict = {
'type': 'template',
'param_type': 'input',
'value': '-i "${IN/T}"',
'dataset': ','.join(job.inputdata.dataset),
'expand': True,
'exclude': '\.log\.tgz(\.\d+)*$',
}
#if options.inputType != '':
# tmpDict['include'] = options.inputType
taskParamMap['jobParameters'].append(tmpDict)
taskParamMap['dsForIN'] = ','.join(job.inputdata.dataset)
inputMap['IN'] = ','.join(job.inputdata.dataset)
else:
# no input
taskParamMap['noInput'] = True
if job.backend.requirements.split > 0:
taskParamMap['nEvents'] = job.backend.requirements.split
else:
taskParamMap['nEvents'] = 1
taskParamMap['nEventsPerJob'] = 1
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value': '-i "[]"',
},
]
else:
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
tmpDict = {
'type': 'template',
'param_type': 'input',
'value': '-i "${IN/T}"',
'dataset': ','.join(job.inputdata.dataset),
'expand': True,
'exclude': '\.log\.tgz(\.\d+)*$',
}
#if options.nSkipFiles != 0:
# tmpDict['offset'] = options.nSkipFiles
taskParamMap['jobParameters'].append(tmpDict)
taskParamMap['dsForIN'] = ','.join(job.inputdata.dataset)
else:
# no input
taskParamMap['noInput'] = True
if job.backend.requirements.split > 0:
taskParamMap['nEvents'] = job.backend.requirements.split
else:
taskParamMap['nEvents'] = 1
taskParamMap['nEventsPerJob'] = 1
# param for DBR
if self.dbrelease != '':
dbrDS = self.dbrelease.split(':')[0]
# change LATEST to DBR_LATEST
if dbrDS == 'LATEST':
dbrDS = 'DBR_LATEST'
dictItem = {
'type': 'template',
'param_type': 'input',
'value': '--dbrFile=${DBR}',
'dataset': dbrDS,
}
taskParamMap['jobParameters'] += [dictItem]
# no expansion
#if options.notExpandDBR:
#dictItem = {'type':'constant',
# 'value':'--noExpandDBR',
# }
#taskParamMap['jobParameters'] += [dictItem]
# secondary FIXME disabled
self.secondaryDSs = {}
if self.secondaryDSs != {}:
inMap = {}
streamNames = []
for tmpDsName, tmpMap in self.secondaryDSs.iteritems():
# make template item
streamName = tmpMap['streamName']
dictItem = MiscUtils.makeJediJobParam(
'${' + streamName + '}',
tmpDsName,
'input',
hidden=True,
expand=True,
include=tmpMap['pattern'],
offset=tmpMap['nSkip'],
nFilesPerJob=tmpMap['nFiles'])
taskParamMap['jobParameters'] += dictItem
inMap[streamName] = 'tmp_' + streamName
streamNames.append(streamName)
# make constant item
strInMap = str(inMap)
# set placeholders
for streamName in streamNames:
strInMap = strInMap.replace("'tmp_" + streamName + "'",
'${' + streamName + '/T}')
dictItem = {
'type': 'constant',
'value': '--inMap "%s"' % strInMap,
}
taskParamMap['jobParameters'] += [dictItem]
# misc
jobParameters = ''
# use Athena packages
if app.atlas_exetype == 'ARES' or (app.atlas_exetype
in ['PYARA', 'ROOT', 'EXE']
and app.useAthenaPackages):
jobParameters += "--useAthenaPackages "
# use RootCore
if app.useRootCore or app.useRootCoreNoBuild:
jobParameters += "--useRootCore "
# use mana
if app.useMana:
jobParameters += "--useMana "
if app.atlas_release != "":
jobParameters += "--manaVer %s " % app.atlas_release
# root
if app.atlas_exetype in ['PYARA', 'ROOT', 'EXE'
] and job.backend.requirements.rootver != '':
rootver = re.sub('/', '.', job.backend.requirements.rootver)
jobParameters += "--rootVer %s " % rootver
# write input to txt
#if options.writeInputToTxt != '':
# jobParameters += "--writeInputToTxt %s " % options.writeInputToTxt
# debug parameters
#if options.queueData != '':
# jobParameters += "--overwriteQueuedata=%s " % options.queueData
# JEM
#if options.enableJEM:
# jobParameters += "--enable-jem "
# if options.configJEM != '':
# jobParameters += "--jem-config %s " % options.configJEM
# set task param
if jobParameters != '':
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value': jobParameters,
},
]
# force stage-in
if job.backend.accessmode == "LocalIO":
taskParamMap['useLocalIO'] = 1
# set jobO parameter
if app.atlas_exetype in ["ATHENA", "TRF"]:
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value': '-j "',
'padding': False,
},
]
taskParamMap[
'jobParameters'] += PsubUtils.convertParamStrToJediParam(
tmpJobO, inputMap, job.outputdata.datasetname[:-1], True,
False)
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value': '"',
},
]
else:
taskParamMap['jobParameters'] += [
{
'type': 'constant',
'value': '-p "{0}"'.format(urllib.quote(self.job_options)),
},
]
# build step
if not job.backend.nobuild:
jobParameters = '-i ${IN} -o ${OUT} --sourceURL ${SURL} '
if job.backend.bexec != '':
jobParameters += ' --bexec "%s" ' % urllib.quote(
job.backend.bexec)
if app.atlas_exetype == 'ARES' or (app.atlas_exetype
in ['PYARA', 'ROOT', 'EXE']
and app.useAthenaPackages):
# use Athena packages
jobParameters += "--useAthenaPackages "
# use RootCore
if app.useRootCore or app.useRootCoreNoBuild:
jobParameters += "--useRootCore "
# run directory
if app.atlas_exetype in ['PYARA', 'ARES', 'ROOT', 'EXE']:
jobParameters += '-r {0} '.format(self.rundirectory)
# no compile
#if options.noCompile:
# jobParameters += "--noCompile "
# use mana
if app.useMana:
jobParameters += "--useMana "
if app.atlas_release != "":
jobParameters += "--manaVer %s " % app.atlas_release
# root
if app.atlas_exetype in [
'PYARA', 'ROOT', 'EXE'
] and job.backend.requirements.rootver != '':
rootver = re.sub('/', '.', job.backend.requirements.rootver)
jobParameters += "--rootVer %s " % rootver
# cmt config
if app.atlas_exetype in ['PYARA', 'ARES', 'ROOT', 'EXE']:
if not app.atlas_cmtconfig in ['', 'NULL', None]:
jobParameters += " --cmtConfig %s " % app.atlas_cmtconfig
#cmtConfig = AthenaUtils.getCmtConfig(athenaVer=app.atlas_release, cmtConfig=app.atlas_cmtconfig)
#if cmtConfig:
# jobParameters += "--cmtConfig %s " % cmtConfig
# debug parameters
#if options.queueData != '':
# jobParameters += "--overwriteQueuedata=%s " % options.queueData
# set task param
taskParamMap['buildSpec'] = {
'prodSourceLabel': 'panda',
'archiveName': os.path.basename(self.inputsandbox),
'jobParameters': jobParameters,
}
# enable merging
if job.backend.requirements.enableMerge:
jobParameters = '-r {0} '.format(self.rundirectory)
if 'exec' in job.backend.requirements.configMerge and job.backend.requirements.configMerge[
'exec'] != '':
jobParameters += '-j "{0}" '.format(
job.backend.requirements.configMerge['exec'])
if not job.backend.nobuild:
jobParameters += '-l ${LIB} '
else:
jobParameters += '-a {0} '.format(
os.path.basename(self.inputsandbox))
jobParameters += "--sourceURL ${SURL} "
jobParameters += '${TRN_OUTPUT:OUTPUT} ${TRN_LOG:LOG}'
taskParamMap['mergeSpec'] = {}
taskParamMap['mergeSpec']['useLocalIO'] = 1
taskParamMap['mergeSpec']['jobParameters'] = jobParameters
taskParamMap['mergeOutput'] = True
# Selected by Jedi
#if not app.atlas_exetype in ['PYARA','ROOT','EXE']:
# taskParamMap['transPath'] = 'http://atlpan.web.cern.ch/atlpan/runAthena-00-00-12'
logger.debug(taskParamMap)
# upload sources
if self.inputsandbox and not job.backend.libds:
uploadSources(os.path.dirname(self.inputsandbox),
os.path.basename(self.inputsandbox))
if not self.inputsandbox == tmp_user_area_name:
logger.info('Removing source tarball %s ...' %
self.inputsandbox)
os.remove(self.inputsandbox)
return taskParamMap
def retry(self,
JobsetID,
newSite=False,
newOpts={},
noSubmit=False,
ignoreDuplication=True):
# get logger
tmpLog = PLogger.getPandaLogger()
# check proxy
self.gridPassPhrase, self.vomsFQAN = PsubUtils.checkGridProxy(
self.gridPassPhrase, False, self.verbose)
# get jobset
newJobsetID = -1
jobList = self.getJobIDsWithSetID(JobsetID)
if jobList == None:
isJobset = False
jobList = [JobsetID]
else:
isJobset = True
tmpMsg = "JobsetID=%s is composed of JobID=" % JobsetID
for tmpJobID in jobList:
tmpMsg += '%s,' % tmpJobID
tmpMsg = tmpMsg[:-1]
tmpLog.info(tmpMsg)
for JobID in jobList:
# get job info from local repository
localJob = self.getJobInfo(JobID)
if localJob == None:
tmpLog.warning(
"JobID=%s not found in local repository. Synchronization may be needed"
% JobID)
return None
# skip running job
if localJob.dbStatus != 'frozen':
tmpLog.warning('Cannot retry running jobs')
if isJobset:
continue
else:
return
# skip already retried
if localJob.retryID != '0':
if isJobset:
tmpLog.info('Skip JobID=%s since already retried by JobID=%s JobsetID=%s' % \
(JobID,localJob.retryID,localJob.retryJobsetID))
continue
else:
tmpLog.warning('This job was already retried by JobID=%s' %
localJob.retryID)
return
# check status of buildJob
if not localJob.buildStatus in ['', 'finished']:
tmpMsgStr = 'Cannot retry since status of buildJob %s is %s (!= finished). ' \
% (localJob.PandaID.split(',')[0],localJob.buildStatus)
tmpMsgStr += 'Please execute %s with the same input/output datasets (or containers). ' % localJob.jobType
tmpMsgStr += 'It will run only on failed/cancelled/unused input files '
tmpMsgStr += 'and append output files to the output dataset container'
tmpLog.warning(tmpMsgStr)
if isJobset:
continue
else:
return
# check opts for newSite
if newSite:
if not localJob.outDS.endswith('/') and not newOpts.has_key(
'outDS') and not newOpts.has_key('--outDS'):
tmpLog.warning(
'You need to specify --outDS in newOpts to retry at new site unless container is used as output'
)
return
# get list of failed jobs
pandaIDs = localJob.PandaID.split(',')
statusList = localJob.jobStatus.split(',')
jobList = []
for idx in range(len(pandaIDs)):
# check status
if not statusList[idx] in ['failed', 'cancelled']:
continue
jobList.append(pandaIDs[idx])
# no failed job
if jobList == []:
if isJobset:
tmpLog.info('Skip JobID=%s since no failed jobs' % JobID)
continue
else:
tmpLog.info('No failed jobs to be retried for JobID=%s' %
JobID)
return
# get full job spec
tmpLog.info("Retrying JobID=%s ..." % JobID)
tmpLog.info("Getting job info")
idxJL = 0
nQuery = 500
pandaJobs = []
while idxJL < len(jobList):
# avoid burst query
tmpLog.info(" %5s/%s" % (idxJL, len(jobList)))
status, oTmp = Client.getFullJobStatus(jobList[idxJL:idxJL +
nQuery],
verbose=self.verbose)
if status != 0:
tmpLog.error(status)
tmpLog.error(oTmp)
tmpLog.error("Cannot get job info from Panda server")
return
pandaJobs += oTmp
idxJL += nQuery
time.sleep(1)
tmpLog.info(" %5s/%s" % (len(jobList), len(jobList)))
# jobdefID
newJobdefID = PsubUtils.readJobDefID()
# reset some parameters
retryJobs = []
retrySite = None
retryElement = None
retryDestSE = None
outDsName = None
shadowList = []
for idx in range(len(jobList)):
job = pandaJobs[idx]
# skip exired
if job == None:
tmpLog.warning("Could not retry jobs older than 30 days : JobID=%s (PandaID=%s) expired" \
% (JobID,jobList[idxJob]))
return
# get shadow list
if (not ignoreDuplication
) and outDsName == None and job.prodSourceLabel == 'user':
# look for dataset for log since it doesn't have suffix even when --individualOutDS is used
for tmpFile in job.Files:
if tmpFile.type == 'log':
outDsName = tmpFile.dataset
break
# output dataset was not found
if outDsName == None:
tmpLog.error("Could not get output dataset name for JobID=%s (PandaID=%s)" \
% (JobID,job.PandaID))
return
# get files in shadow
if outDsName.endswith('/'):
shadowList = Client.getFilesInShadowDataset(
outDsName, Client.suffixShadow, self.verbose)
else:
# disable duplication check mainly for old overlay jobs since non-signal files are wrongly skipped
#shadowList = Client.getFilesInShadowDatasetOld(outDsName,Client.suffixShadow,self.verbose)
pass
# unify sitename
if retrySite == None:
retrySite = job.computingSite
retryElement = job.computingElement
retryDestSE = job.destinationSE
# reset
job.jobStatus = None
job.commandToPilot = None
job.startTime = None
job.endTime = None
job.attemptNr = 1 + job.attemptNr
for attr in job._attributes:
if attr.endswith('ErrorCode') or attr.endswith(
'ErrorDiag'):
setattr(job, attr, None)
job.transExitCode = None
job.computingSite = retrySite
job.computingElement = retryElement
job.destinationSE = retryDestSE
job.dispatchDBlock = None
job.jobExecutionID = JobID
job.jobDefinitionID = newJobdefID
job.parentID = job.PandaID
if job.jobsetID != ['NULL', None, -1]:
job.sourceSite = job.jobsetID
job.jobsetID = newJobsetID
skipInputList = []
numUsedFiles = 0
for file in job.Files:
file.rowID = None
if file.type == 'input':
# protection against wrong sync which doesn't update buildStatus correctly
if file.lfn.endswith(
'.lib.tgz') and file.GUID == 'NULL':
tmpLog.warning('GUID for %s is unknown. Cannot retry when corresponding buildJob failed' \
% file.lfn)
return
file.status = 'ready'
# check with shadow for non lib.tgz/DBR
tmpDbrMatch = re.search('^DBRelease-.*\.tar\.gz$',
file.lfn)
if tmpDbrMatch == None and not file.lfn.endswith(
'.lib.tgz'):
if file.lfn in shadowList:
skipInputList.append(file)
else:
numUsedFiles += 1
elif file.type in ('output', 'log'):
file.destinationSE = retryDestSE
file.destinationDBlock = re.sub(
'_sub\d+$', '', file.destinationDBlock)
# add retry num
if file.dataset.endswith('/'):
retryMatch = re.search('_r(\d+)$',
file.destinationDBlock)
if retryMatch == None:
file.destinationDBlock += '_r1'
else:
tmpDestinationDBlock = re.sub(
'_r(\d+)$', '', file.destinationDBlock)
file.destinationDBlock = tmpDestinationDBlock + '_r%d' % (
1 + int(retryMatch.group(1)))
# add attempt nr
oldName = file.lfn
file.lfn = re.sub("\.\d+$", "", file.lfn)
file.lfn = "%s.%d" % (file.lfn, job.attemptNr)
newName = file.lfn
# modify jobParameters
job.jobParameters = re.sub("'%s'" % oldName,
"'%s'" % newName,
job.jobParameters)
# look for output in trf
oldGenelicName = re.sub('\.\d+$', '', oldName)
match = re.search(oldGenelicName + '(\.\d+)*(%20|")',
job.jobParameters)
if match != None:
job.jobParameters = job.jobParameters.replace(
match.group(0), newName + match.group(2))
# all files are used by others
if numUsedFiles == 0 and skipInputList != []:
continue
# remove skipped files
strSkipped = ''
for tmpFile in skipInputList:
strSkipped += '%s,' % tmpFile.lfn
job.Files.remove(tmpFile)
strSkipped = strSkipped[:-1]
# modify jobpar
if strSkipped != '':
optionToSkipFiles = '--skipInputByRetry'
if not optionToSkipFiles in job.jobParameters:
# just append
job.jobParameters += "%s=%s " % (optionToSkipFiles,
strSkipped)
else:
# extract already skipped files
tmpMatch = re.search("(%s=[^ ]+)", job.jobParameters)
if tmpMatch == None:
tmpLog.error("Failed to extract arg of %s for PandaID=%s" \
% (optionToSkipFiles,job.PandaID))
return
# replace
job.jobParameters = re.sub(
tmpMatch.group(1),
"%s,%s" % (tmpMatch.group(1), optionToSkipFiles),
job.jobParameters)
if self.verbose:
tmpLog.debug(job.jobParameters)
# append
retryJobs.append(job)
# all input files were or are being used by other jobs
if retryJobs == []:
tmpLog.info(
'All input files were or are being used by other jobs for the same output. No jobs to be retried. If you need to ignore duplication check (e.g., using the same EVNT file for multiple simulation subjobs), set ignoreDuplication=True. i.e. retry(123,ignoreDuplication=True)'
)
return
# check voms role
if not retryJobs[0].workingGroup in ['NULL', None, '']:
# VOMS role was used
if not "--workingGroup" in job.metadata:
# extract voms roles from metadata
match = re.search("--voms( |=)[ \"]*([^ \"]+)",
job.metadata)
if match != None:
vomsRoles = match.group(2)
else:
vomsRoles = "atlas:/atlas/%s/Role=production" % retryJobs[
0].workingGroup
# regenerate proxy with VOMS roles
try:
tmpLog.info("Checking proxy role to resubmit %s jobs" %
retryJobs[0].workingGroup)
self.gridPassPhrase, self.vomsFQAN = PsubUtils.checkGridProxy(
self.gridPassPhrase, False, self.verbose,
vomsRoles)
except:
tmpLog.error("Failed to generate a proxy with %s" %
vomsRoles)
return
# check runtime env for new site submission
if newSite:
if retryJobs[
0].processingType == 'pathena' or '--useAthenaPackages' in retryJobs[
0].metadata:
from pandatools import AthenaUtils
stA, retA = AthenaUtils.getAthenaVer()
if not stA:
tmpLog.error(
"Failed to get Athena rel/cache version in current runtime env"
)
return
athenaVer = retA['athenaVer']
cacheVer = retA['cacheVer']
nightVer = retA['nightVer']
wrongSetup = False
if retryJobs[0].AtlasRelease != 'Atlas-%s' % athenaVer:
wrongSetup = True
errMsg = "Current Athena version Atlas-%s is inconsitent with the previous submission %s. " % (
athenaVer, retryJobs[0].AtlasRelease)
elif retryJobs[
0].homepackage != 'AnalysisTransforms' + cacheVer + nightVer:
wrongSetup = True
errMsg = "Current cache version %s is inconsitent with the previous submission. " % cacheVer.replace(
'-', '').replace('_', '-')
if wrongSetup:
errMsg += 'You need to have the same runtime env as before since all job spec need to be re-created to send jobs to a new site. '
errMsg += 'Please setup Athena correctly and restart pbook'
tmpLog.error(errMsg)
return
# test mode
if noSubmit:
continue
# invoke pathena/prun to send job to new site
if newSite:
tmpLog.info(
"Constrcuting job spec again to be sent to another site ..."
)
comStat = PsubUtils.execWithModifiedParams(
retryJobs, newOpts, self.verbose)
if comStat == 0:
# update database
time.sleep(2)
self.sync()
else:
tmpLog.error("Failed to submit jobs to Panda server")
return
# register datasets
tmpOutDsLocation = Client.PandaSites[
retryJobs[-1].computingSite]['ddm']
addedDataset = []
shadowDSname = None
for tmpFile in retryJobs[-1].Files:
if tmpFile.type in ['output', 'log'
] and tmpFile.dataset.endswith('/'):
# add shadow
if shadowDSname == None and tmpFile.type == 'log':
shadowDSname = "%s%s" % (tmpFile.destinationDBlock,
Client.suffixShadow)
Client.addDataset(shadowDSname, self.verbose)
# add datasets
if not tmpFile.destinationDBlock in addedDataset:
# create dataset
Client.addDataset(tmpFile.destinationDBlock,
self.verbose,
location=tmpOutDsLocation)
# add to container
Client.addDatasetsToContainer(
tmpFile.dataset, [tmpFile.destinationDBlock],
self.verbose)
# append
addedDataset.append(tmpFile.destinationDBlock)
# submit
tmpLog.info("Submitting job ...")
status, out = Client.submitJobs(retryJobs, verbose=self.verbose)
if out == None or status != 0:
tmpLog.error(status)
tmpLog.error(out)
tmpLog.error("Failed to submit jobs to Panda server")
return
# update database
pandaIDstatus = {}
newJobID = None
for items in out:
# get newJobID
if newJobID == None:
newJobID = items[1]
# check PandaID
PandaID = items[0]
if PandaID == 'NULL':
tmpLog.error(
"Panda server returned wrong IDs. It may have a temporary problem"
)
return
# set newJobsetID
if newJobsetID in [None, -1]:
newJobsetID = items[2]['jobsetID']
# dummy statuso
pandaIDstatus[PandaID] = ('defined', 'NULL')
# set retry ID
localJob.retryID = newJobID
if not newJobsetID in [None, -1, 'NULL']:
localJob.retryJobsetID = newJobsetID
try:
PdbUtils.updateJobDB(localJob, self.verbose)
except:
tmpLog.error("Failed to set retryID for JobID=%s" % JobID)
return
# set new paramers
newLocalJob = PdbUtils.convertPtoD(retryJobs, pandaIDstatus)
newLocalJob.JobID = newJobID
if not newJobsetID in [None, -1, 'NULL']:
newLocalJob.groupID = newJobsetID
newLocalJob.creationTime = datetime.datetime.utcnow()
# insert to DB
try:
PdbUtils.insertJobDB(newLocalJob, self.verbose)
except:
tmpLog.error("Failed to insert JobID=%s to local repository" %
newJobID)
return
# write new jobdefID
PsubUtils.writeJobDefID(newJobID)
# done
tmpMsg = 'Done. New JobID=%s' % newJobID
if not newJobsetID in [None, -1, 'NULL']:
tmpMsg += " JobsetID=%s" % newJobsetID
tmpLog.info(tmpMsg)
def master_prepare(self, app, appmasterconfig):
# PandaTools
from pandatools import Client
from pandatools import AthenaUtils
from taskbuffer.JobSpec import JobSpec
from taskbuffer.FileSpec import FileSpec
job = app._getParent()
logger.debug('AthenaMCPandaRTHandler master_prepare called for %s',
job.getFQID('.'))
usertag = configDQ2['usertag']
#usertag='user09'
nickname = getNickname(allowMissingNickname=True)
self.libDataset = '%s.%s.ganga.%s_%d.lib._%06d' % (
usertag, nickname, commands.getoutput('hostname').split('.')[0],
int(time.time()), job.id)
# self.userprefix='%s.%s.ganga' % (usertag,gridProxy.identity())
sources = 'sources.%s.tar.gz' % commands.getoutput(
'uuidgen 2> /dev/null')
self.library = '%s.lib.tgz' % self.libDataset
# check DBRelease
# if job.backend.dbRelease != '' and job.backend.dbRelease.find(':') == -1:
# raise ApplicationConfigurationError(None,"ERROR : invalid argument for backend.dbRelease. Must be 'DatasetName:FileName'")
# unpack library
logger.debug('Creating source tarball ...')
tmpdir = '/tmp/%s' % commands.getoutput('uuidgen 2> /dev/null')
os.mkdir(tmpdir)
inputbox = []
if os.path.exists(app.transform_archive):
# must add a condition on size.
inputbox += [File(app.transform_archive)]
if app.evgen_job_option:
self.evgen_job_option = app.evgen_job_option
if os.path.exists(app.evgen_job_option):
# locally modified job option file to add to the input sand box
inputbox += [File(app.evgen_job_option)]
self.evgen_job_option = app.evgen_job_option.split("/")[-1]
# add input sandbox files
if (job.inputsandbox):
for file in job.inputsandbox:
inputbox += [file]
# add option files
for extFile in job.backend.extOutFile:
try:
shutil.copy(extFile, tmpdir)
except IOError:
os.makedirs(tmpdir)
shutil.copy(extFile, tmpdir)
# fill the archive
for opt_file in inputbox:
try:
shutil.copy(opt_file.name, tmpdir)
except IOError:
os.makedirs(tmpdir)
shutil.copy(opt_file.name, tmpdir)
# now tar it up again
inpw = job.getInputWorkspace()
rc, output = commands.getstatusoutput('tar czf %s -C %s .' %
(inpw.getPath(sources), tmpdir))
if rc:
logger.error('Packing sources failed with status %d', rc)
logger.error(output)
raise ApplicationConfigurationError(None,
'Packing sources failed.')
shutil.rmtree(tmpdir)
# upload sources
logger.debug('Uploading source tarball ...')
try:
cwd = os.getcwd()
os.chdir(inpw.getPath())
rc, output = Client.putFile(sources)
if output != 'True':
logger.error('Uploading sources %s failed. Status = %d',
sources, rc)
logger.error(output)
raise ApplicationConfigurationError(
None, 'Uploading archive failed')
finally:
os.chdir(cwd)
# Use Panda's brokerage
## if job.inputdata and len(app.sites)>0:
## # update cloud, use inputdata's
## from dq2.info.TiersOfATLAS import whichCloud,ToACache
## inclouds=[]
## for site in app.sites:
## cloudSite=whichCloud(app.sites[0])
## if cloudSite not in inclouds:
## inclouds.append(cloudSite)
## # now converting inclouds content into proper brokering stuff.
## outclouds=[]
## for cloudSite in inclouds:
## for cloudID, eachCloud in ToACache.dbcloud.iteritems():
## if cloudSite==eachCloud:
## cloud=cloudID
## outclouds.append(cloud)
## break
## print outclouds
## # finally, matching with user's wishes
## if len(outclouds)>0:
## if not job.backend.requirements.cloud: # no user wish, update
## job.backend.requirements.cloud=outclouds[0]
## else:
## try:
## assert job.backend.requirements.cloud in outclouds
## except:
## raise ApplicationConfigurationError(None,'Input dataset not available in target cloud %s. Please try any of the following %s' % (job.backend.requirements.cloud, str(outclouds)))
from GangaPanda.Lib.Panda.Panda import runPandaBrokerage
runPandaBrokerage(job)
if job.backend.site == 'AUTO':
raise ApplicationConfigurationError(
None, 'site is still AUTO after brokerage!')
# output dataset preparation and registration
try:
outDsLocation = Client.PandaSites[job.backend.site]['ddm']
except:
raise ApplicationConfigurationError(
None,
"Could not extract output dataset location from job.backend.site value: %s. Aborting"
% job.backend.site)
if not app.dryrun:
for outtype in app.outputpaths.keys():
dset = string.replace(app.outputpaths[outtype], "/", ".")
dset = dset[1:]
# dataset registration must be done only once.
print "registering output dataset %s at %s" % (dset,
outDsLocation)
try:
Client.addDataset(dset, False, location=outDsLocation)
dq2_set_dataset_lifetime(dset, location=outDsLocation)
except:
raise ApplicationConfigurationError(
None,
"Fail to create output dataset %s. Aborting" % dset)
# extend registration to build job lib dataset:
print "registering output dataset %s at %s" % (self.libDataset,
outDsLocation)
try:
Client.addDataset(self.libDataset,
False,
location=outDsLocation)
dq2_set_dataset_lifetime(self.libDataset, outDsLocation)
except:
raise ApplicationConfigurationError(
None, "Fail to create output dataset %s. Aborting" %
self.libDataset)
###
cacheVer = "-AtlasProduction_" + str(app.prod_release)
logger.debug("master job submit?")
self.outsite = job.backend.site
if app.se_name and app.se_name != "none" and not self.outsite:
self.outsite = app.se_name
# create build job
jspec = JobSpec()
jspec.jobDefinitionID = job.id
jspec.jobName = commands.getoutput('uuidgen 2> /dev/null')
jspec.AtlasRelease = 'Atlas-%s' % app.atlas_rel
jspec.homepackage = 'AnalysisTransforms' + cacheVer #+nightVer
jspec.transformation = '%s/buildJob-00-00-03' % Client.baseURLSUB # common base to Athena and AthenaMC jobs: buildJob is a pilot job which takes care of all inputs for the real jobs (in prepare()
jspec.destinationDBlock = self.libDataset
jspec.destinationSE = job.backend.site
jspec.prodSourceLabel = 'panda'
jspec.assignedPriority = 2000
jspec.computingSite = job.backend.site
jspec.cloud = job.backend.requirements.cloud
# jspec.jobParameters = self.args not known yet
jspec.jobParameters = '-o %s' % (self.library)
if app.userarea:
print app.userarea
jspec.jobParameters += ' -i %s' % (os.path.basename(app.userarea))
else:
jspec.jobParameters += ' -i %s' % (sources)
jspec.cmtConfig = AthenaUtils.getCmtConfig(athenaVer=app.atlas_rel)
matchURL = re.search('(http.*://[^/]+)/', Client.baseURLSSL)
if matchURL:
jspec.jobParameters += ' --sourceURL %s' % matchURL.group(1)
fout = FileSpec()
fout.lfn = self.library
fout.type = 'output'
fout.dataset = self.libDataset
fout.destinationDBlock = self.libDataset
jspec.addFile(fout)
flog = FileSpec()
flog.lfn = '%s.log.tgz' % self.libDataset
flog.type = 'log'
flog.dataset = self.libDataset
flog.destinationDBlock = self.libDataset
jspec.addFile(flog)
#print "MASTER JOB DETAILS:",jspec.jobParameters
return jspec
def prepare(self, app, appconfig, appmasterconfig, jobmasterconfig):
'''prepare the subjob specific configuration'''
# PandaTools
from pandatools import Client
from pandatools import AthenaUtils
from taskbuffer.JobSpec import JobSpec
from taskbuffer.FileSpec import FileSpec
job = app._getParent()
logger.debug('AthenaMCPandaRTHandler prepare called for %s',
job.getFQID('.'))
try:
assert self.outsite
except:
logger.error("outsite not set. Aborting")
raise Exception()
job.backend.site = self.outsite
job.backend.actualCE = self.outsite
cloud = job._getRoot().backend.requirements.cloud
job.backend.requirements.cloud = cloud
# now just filling the job from AthenaMC data
jspec = JobSpec()
jspec.jobDefinitionID = job._getRoot().id
jspec.jobName = commands.getoutput('uuidgen 2> /dev/null')
jspec.AtlasRelease = 'Atlas-%s' % app.atlas_rel
if app.transform_archive:
jspec.homepackage = 'AnalysisTransforms' + app.transform_archive
elif app.prod_release:
jspec.homepackage = 'AnalysisTransforms-AtlasProduction_' + str(
app.prod_release)
jspec.transformation = '%s/runAthena-00-00-11' % Client.baseURLSUB
#---->???? prodDBlock and destinationDBlock when facing several input / output datasets?
jspec.prodDBlock = 'NULL'
if job.inputdata and len(
app.inputfiles) > 0 and app.inputfiles[0] in app.dsetmap:
jspec.prodDBlock = app.dsetmap[app.inputfiles[0]]
# How to specify jspec.destinationDBlock when more than one type of output is available? Panda prod jobs seem to specify only the last output dataset
outdset = ""
for type in ["EVNT", "RDO", "HITS", "AOD", "ESD", "NTUP"]:
if type in app.outputpaths.keys():
outdset = string.replace(app.outputpaths[type], "/", ".")
outdset = outdset[1:-1]
break
if not outdset:
try:
assert len(app.outputpaths.keys()) > 0
except:
logger.error(
"app.outputpaths is empty: check your output datasets")
raise
type = app.outputpaths.keys()[0]
outdset = string.replace(app.outputpaths[type], "/", ".")
outdset = outdset[1:-1]
jspec.destinationDBlock = outdset
jspec.destinationSE = self.outsite
jspec.prodSourceLabel = 'user'
jspec.assignedPriority = 1000
jspec.cloud = cloud
# memory
if job.backend.requirements.memory != -1:
jspec.minRamCount = job.backend.requirements.memory
jspec.computingSite = self.outsite
jspec.cmtConfig = AthenaUtils.getCmtConfig(athenaVer=app.atlas_rel)
# library (source files)
flib = FileSpec()
flib.lfn = self.library
# flib.GUID =
flib.type = 'input'
# flib.status =
flib.dataset = self.libDataset
flib.dispatchDBlock = self.libDataset
jspec.addFile(flib)
# input files FIXME: many more input types
for lfn in app.inputfiles:
useguid = app.turls[lfn].replace("guid:", "")
finp = FileSpec()
finp.lfn = lfn
finp.GUID = useguid
finp.dataset = app.dsetmap[lfn]
finp.prodDBlock = app.dsetmap[lfn]
finp.prodDBlockToken = 'local'
finp.dispatchDBlock = app.dsetmap[lfn]
finp.type = 'input'
finp.status = 'ready'
jspec.addFile(finp)
# add dbfiles if any:
for lfn in app.dbfiles:
useguid = app.dbturls[lfn].replace("guid:", "")
finp = FileSpec()
finp.lfn = lfn
finp.GUID = useguid
finp.dataset = app.dsetmap[lfn]
finp.prodDBlock = app.dsetmap[lfn]
finp.prodDBlockToken = 'local'
finp.dispatchDBlock = app.dsetmap[lfn]
finp.type = 'input'
finp.status = 'ready'
jspec.addFile(finp)
# then minbias files
for lfn in app.mbfiles:
useguid = app.minbias_turls[lfn].replace("guid:", "")
finp = FileSpec()
finp.lfn = lfn
finp.GUID = useguid
finp.dataset = app.dsetmap[lfn]
finp.prodDBlock = app.dsetmap[lfn]
finp.prodDBlockToken = 'local'
finp.dispatchDBlock = app.dsetmap[lfn]
finp.type = 'input'
finp.status = 'ready'
jspec.addFile(finp)
# then cavern files
for lfn in app.cavernfiles:
useguid = app.cavern_turls[lfn].replace("guid:", "")
finp = FileSpec()
finp.lfn = lfn
finp.GUID = useguid
finp.dataset = app.dsetmap[lfn]
finp.prodDBlock = app.dsetmap[lfn]
finp.prodDBlockToken = 'local'
finp.dispatchDBlock = app.dsetmap[lfn]
finp.type = 'input'
finp.status = 'ready'
jspec.addFile(finp)
# output files( this includes the logfiles)
# Output files
jidtag = ""
job = app._getParent() # Returns job or subjob object
if job._getRoot().subjobs:
jidtag = job._getRoot().id
else:
jidtag = "%d" % job.id
outfiles = app.subjobsOutfiles[job.id]
pandaOutfiles = {}
for type in outfiles.keys():
pandaOutfiles[type] = outfiles[type] + "." + str(jidtag)
if type == "LOG":
pandaOutfiles[type] += ".tgz"
#print pandaOutfiles
for outtype in pandaOutfiles.keys():
fout = FileSpec()
dset = string.replace(app.outputpaths[outtype], "/", ".")
dset = dset[1:-1]
fout.dataset = dset
fout.lfn = pandaOutfiles[outtype]
fout.type = 'output'
# fout.destinationDBlock = jspec.destinationDBlock
fout.destinationDBlock = fout.dataset
fout.destinationSE = jspec.destinationSE
if outtype == 'LOG':
fout.type = 'log'
fout.destinationDBlock = fout.dataset
fout.destinationSE = job.backend.site
jspec.addFile(fout)
# job parameters
param = '-l %s ' % self.library # user tarball.
# use corruption checker
if job.backend.requirements.corCheck:
param += '--corCheck '
# disable to skip missing files
if job.backend.requirements.notSkipMissing:
param += '--notSkipMissing '
# transform parameters
# need to update arglist with final output file name...
newArgs = []
if app.mode == "evgen":
app.args[3] = app.args[3] + " -t "
if app.verbosity:
app.args[3] = app.args[3] + " -l %s " % app.verbosity
for arg in app.args[3:]:
for type in outfiles.keys():
if arg.find(outfiles[type]) > -1:
arg = arg.replace(outfiles[type], pandaOutfiles[type])
newArgs.append(arg)
arglist = string.join(newArgs, " ")
# print "Arglist:",arglist
param += ' -r ./ '
param += ' -j "%s"' % urllib.quote(arglist)
allinfiles = app.inputfiles + app.dbfiles
# Input files.
param += ' -i "%s" ' % allinfiles
if len(app.mbfiles) > 0:
param += ' -m "%s" ' % app.mbfiles
if len(app.cavernfiles) > 0:
param += ' -n "%s" ' % app.cavernfiles
# param += '-m "[]" ' #%minList FIXME
# param += '-n "[]" ' #%cavList FIXME
del pandaOutfiles[
"LOG"] # logfiles do not appear in IROOT block, and this one is not needed anymore...
param += ' -o "{\'IROOT\':%s }"' % str(pandaOutfiles.items())
# source URL
matchURL = re.search("(http.*://[^/]+)/", Client.baseURLSSL)
if matchURL != None:
param += " --sourceURL %s " % matchURL.group(1)
param += " --trf"
jspec.jobParameters = param
jspec.metadata = "--trf \"%s\"" % arglist
#print "SUBJOB DETAILS:",jspec.values()
if app.dryrun:
print "job.application.dryrun activated, printing out job parameters"
print jspec.values()
return
return jspec
