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
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 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 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
