def master_prepare(self,app,appconfig):
'''Prepare the master job'''
from pandatools import Client
from taskbuffer.JobSpec import JobSpec
from taskbuffer.FileSpec import FileSpec
job = app._getParent()
logger.debug('ExecutablePandaRTHandler master_prepare called for %s', job.getFQID('.'))
# set chirp variables
if configPanda['chirpconfig'] or configPanda['chirpserver']:
setChirpVariables()
# Pack inputsandbox
inputsandbox = 'sources.%s.tar' % commands.getoutput('uuidgen 2> /dev/null')
inpw = job.getInputWorkspace()
# add user script to inputsandbox
if hasattr(job.application.exe, "name"):
if not job.application.exe in job.inputsandbox:
job.inputsandbox.append(job.application.exe)
for fname in [f.name for f in job.inputsandbox]:
fname.rstrip(os.sep)
path = fname[:fname.rfind(os.sep)]
f = fname[fname.rfind(os.sep)+1:]
rc, output = commands.getstatusoutput('tar rf %s -C %s %s' % (inpw.getPath(inputsandbox), path, f))
if rc:
logger.error('Packing inputsandbox failed with status %d',rc)
logger.error(output)
raise ApplicationConfigurationError('Packing inputsandbox failed.')
if len(job.inputsandbox) > 0:
rc, output = commands.getstatusoutput('gzip %s' % (inpw.getPath(inputsandbox)))
if rc:
logger.error('Packing inputsandbox failed with status %d',rc)
logger.error(output)
raise ApplicationConfigurationError('Packing inputsandbox failed.')
inputsandbox += ".gz"
else:
inputsandbox = None
# Upload Inputsandbox
if inputsandbox:
logger.debug('Uploading source tarball ...')
uploadSources(inpw.getPath(),os.path.basename(inputsandbox))
self.inputsandbox = inputsandbox
else:
self.inputsandbox = None
# input dataset
if job.inputdata:
if job.inputdata._name != 'DQ2Dataset':
raise ApplicationConfigurationError('PANDA application supports only DQ2Datasets')
# run brokerage here if not splitting
if not job.splitter:
from GangaPanda.Lib.Panda.Panda import runPandaBrokerage
runPandaBrokerage(job)
elif job.splitter._name not in ['DQ2JobSplitter', 'ArgSplitter', 'ArgSplitterTask']:
raise ApplicationConfigurationError('Panda splitter must be DQ2JobSplitter or ArgSplitter')
if job.backend.site == 'AUTO':
raise ApplicationConfigurationError('site is still AUTO after brokerage!')
# 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()
job.outputdata.datasetname,outlfn = dq2outputdatasetname(job.outputdata.datasetname, job.id, job.outputdata.isGroupDS, job.outputdata.groupname)
self.outDsLocation = Client.PandaSites[job.backend.site]['ddm']
try:
Client.addDataset(job.outputdata.datasetname,False,location=self.outDsLocation)
logger.info('Output dataset %s registered at %s'%(job.outputdata.datasetname,self.outDsLocation))
dq2_set_dataset_lifetime(job.outputdata.datasetname, location=self.outDsLocation)
except exceptions.SystemExit:
raise BackendError('Panda','Exception in Client.addDataset %s: %s %s'%(job.outputdata.datasetname,sys.exc_info()[0],sys.exc_info()[1]))
# handle the libds
if job.backend.libds:
self.libDataset = job.backend.libds
self.fileBO = getLibFileSpecFromLibDS(self.libDataset)
self.library = self.fileBO.lfn
elif job.backend.bexec:
self.libDataset = job.outputdata.datasetname+'.lib'
self.library = '%s.tgz' % self.libDataset
try:
Client.addDataset(self.libDataset,False,location=self.outDsLocation)
dq2_set_dataset_lifetime(self.libDataset, location=self.outDsLocation)
logger.info('Lib dataset %s registered at %s'%(self.libDataset,self.outDsLocation))
except exceptions.SystemExit:
raise BackendError('Panda','Exception in Client.addDataset %s: %s %s'%(self.libDataset,sys.exc_info()[0],sys.exc_info()[1]))
# collect extOutFiles
self.extOutFile = []
for tmpName in job.outputdata.outputdata:
if tmpName != '':
self.extOutFile.append(tmpName)
for tmpName in job.outputsandbox:
if tmpName != '':
self.extOutFile.append(tmpName)
for tmpName in job.backend.extOutFile:
if tmpName != '':
self.extOutFile.append(tmpName)
# create build job
if job.backend.bexec != '':
jspec = JobSpec()
jspec.jobDefinitionID = job.id
jspec.jobName = commands.getoutput('uuidgen 2> /dev/null')
jspec.transformation = '%s/buildGen-00-00-01' % Client.baseURLSUB
if Client.isDQ2free(job.backend.site):
jspec.destinationDBlock = '%s/%s' % (job.outputdata.datasetname,self.libDataset)
jspec.destinationSE = 'local'
else:
jspec.destinationDBlock = self.libDataset
jspec.destinationSE = job.backend.site
jspec.prodSourceLabel = configPanda['prodSourceLabelBuild']
jspec.processingType = configPanda['processingType']
jspec.assignedPriority = configPanda['assignedPriorityBuild']
jspec.computingSite = job.backend.site
jspec.cloud = job.backend.requirements.cloud
jspec.jobParameters = '-o %s' % (self.library)
if self.inputsandbox:
jspec.jobParameters += ' -i %s' % (self.inputsandbox)
else:
raise ApplicationConfigurationError('Executable on Panda with build job defined, but inputsandbox is emtpy !')
matchURL = re.search('(http.*://[^/]+)/',Client.baseURLCSRVSSL)
if matchURL:
jspec.jobParameters += ' --sourceURL %s ' % matchURL.group(1)
if job.backend.bexec != '':
jspec.jobParameters += ' --bexec "%s" ' % urllib.quote(job.backend.bexec)
jspec.jobParameters += ' -r %s ' % '.'
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)
return jspec
else:
return None
def master_prepare(self, app, appconfig):
'''Prepare the master job'''
from pandatools import Client
from taskbuffer.JobSpec import JobSpec
from taskbuffer.FileSpec import FileSpec
job = app._getParent()
logger.debug('ExecutablePandaRTHandler master_prepare called for %s',
job.getFQID('.'))
# set chirp variables
if configPanda['chirpconfig'] or configPanda['chirpserver']:
setChirpVariables()
# Pack inputsandbox
inputsandbox = 'sources.%s.tar' % commands.getoutput(
'uuidgen 2> /dev/null')
inpw = job.getInputWorkspace()
# add user script to inputsandbox
if hasattr(job.application.exe, "name"):
if not job.application.exe in job.inputsandbox:
job.inputsandbox.append(job.application.exe)
for fname in [f.name for f in job.inputsandbox]:
fname.rstrip(os.sep)
path = fname[:fname.rfind(os.sep)]
f = fname[fname.rfind(os.sep) + 1:]
rc, output = commands.getstatusoutput(
'tar rf %s -C %s %s' % (inpw.getPath(inputsandbox), path, f))
if rc:
logger.error('Packing inputsandbox failed with status %d', rc)
logger.error(output)
raise ApplicationConfigurationError(
None, 'Packing inputsandbox failed.')
if len(job.inputsandbox) > 0:
rc, output = commands.getstatusoutput('gzip %s' %
(inpw.getPath(inputsandbox)))
if rc:
logger.error('Packing inputsandbox failed with status %d', rc)
logger.error(output)
raise ApplicationConfigurationError(
None, 'Packing inputsandbox failed.')
inputsandbox += ".gz"
else:
inputsandbox = None
# Upload Inputsandbox
if inputsandbox:
logger.debug('Uploading source tarball ...')
uploadSources(inpw.getPath(), os.path.basename(inputsandbox))
self.inputsandbox = inputsandbox
else:
self.inputsandbox = None
# input dataset
if job.inputdata:
if job.inputdata._name != 'DQ2Dataset':
raise ApplicationConfigurationError(
None, 'PANDA application supports only DQ2Datasets')
# run brokerage here if not splitting
if not job.splitter:
from GangaPanda.Lib.Panda.Panda import runPandaBrokerage
runPandaBrokerage(job)
elif job.splitter._name not in [
'DQ2JobSplitter', 'ArgSplitter', 'ArgSplitterTask'
]:
raise ApplicationConfigurationError(
None, 'Panda splitter must be DQ2JobSplitter or ArgSplitter')
if job.backend.site == 'AUTO':
raise ApplicationConfigurationError(
None, 'site is still AUTO after brokerage!')
# 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()
job.outputdata.datasetname, outlfn = dq2outputdatasetname(
job.outputdata.datasetname, job.id, job.outputdata.isGroupDS,
job.outputdata.groupname)
self.outDsLocation = Client.PandaSites[job.backend.site]['ddm']
try:
Client.addDataset(job.outputdata.datasetname,
False,
location=self.outDsLocation)
logger.info('Output dataset %s registered at %s' %
(job.outputdata.datasetname, self.outDsLocation))
dq2_set_dataset_lifetime(job.outputdata.datasetname,
location=self.outDsLocation)
except exceptions.SystemExit:
raise BackendError(
'Panda', 'Exception in Client.addDataset %s: %s %s' %
(job.outputdata.datasetname, sys.exc_info()[0],
sys.exc_info()[1]))
# handle the libds
if job.backend.libds:
self.libDataset = job.backend.libds
self.fileBO = getLibFileSpecFromLibDS(self.libDataset)
self.library = self.fileBO.lfn
elif job.backend.bexec:
self.libDataset = job.outputdata.datasetname + '.lib'
self.library = '%s.tgz' % self.libDataset
try:
Client.addDataset(self.libDataset,
False,
location=self.outDsLocation)
dq2_set_dataset_lifetime(self.libDataset,
location=self.outDsLocation)
logger.info('Lib dataset %s registered at %s' %
(self.libDataset, self.outDsLocation))
except exceptions.SystemExit:
raise BackendError(
'Panda', 'Exception in Client.addDataset %s: %s %s' %
(self.libDataset, sys.exc_info()[0], sys.exc_info()[1]))
# collect extOutFiles
self.extOutFile = []
for tmpName in job.outputdata.outputdata:
if tmpName != '':
self.extOutFile.append(tmpName)
for tmpName in job.outputsandbox:
if tmpName != '':
self.extOutFile.append(tmpName)
for tmpName in job.backend.extOutFile:
if tmpName != '':
self.extOutFile.append(tmpName)
# create build job
if job.backend.bexec != '':
jspec = JobSpec()
jspec.jobDefinitionID = job.id
jspec.jobName = commands.getoutput('uuidgen 2> /dev/null')
jspec.transformation = '%s/buildGen-00-00-01' % Client.baseURLSUB
if Client.isDQ2free(job.backend.site):
jspec.destinationDBlock = '%s/%s' % (
job.outputdata.datasetname, self.libDataset)
jspec.destinationSE = 'local'
else:
jspec.destinationDBlock = self.libDataset
jspec.destinationSE = job.backend.site
jspec.prodSourceLabel = configPanda['prodSourceLabelBuild']
jspec.processingType = configPanda['processingType']
jspec.assignedPriority = configPanda['assignedPriorityBuild']
jspec.computingSite = job.backend.site
jspec.cloud = job.backend.requirements.cloud
jspec.jobParameters = '-o %s' % (self.library)
if self.inputsandbox:
jspec.jobParameters += ' -i %s' % (self.inputsandbox)
else:
raise ApplicationConfigurationError(
None,
'Executable on Panda with build job defined, but inputsandbox is emtpy !'
)
matchURL = re.search('(http.*://[^/]+)/', Client.baseURLCSRVSSL)
if matchURL:
jspec.jobParameters += ' --sourceURL %s ' % matchURL.group(1)
if job.backend.bexec != '':
jspec.jobParameters += ' --bexec "%s" ' % urllib.quote(
job.backend.bexec)
jspec.jobParameters += ' -r %s ' % '.'
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)
return jspec
else:
return None
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
