def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
"""prepare the subjob specific configuration"""
job = app._getParent() # Returns job or subjob object
logger.debug("AthenaLocalRTHandler prepare called, %s", job.id)
input_files = []
input_guids = []
input_tag_files = []
input_tag_guids = []
input_esd_files = []
input_esd_guids = []
# If job has inputdata
if job.inputdata:
# DQ2Dataset, ATLASLocalDataset and ATLASCastorDataset job splitting is done in AthenaSplitterJob
if job._getRoot().subjobs:
if job.inputdata._name == 'ATLASLocalDataset' or job.inputdata._name == 'ATLASCastorDataset':
if not job.inputdata.names:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
input_files = job.inputdata.names
elif job.inputdata._name == 'ATLASDataset':
if not job.inputdata.lfn:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
input_files = job.inputdata.lfn
elif job.inputdata._name == 'ATLASTier3Dataset':
if not job.inputdata.names:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
if job.inputdata.names:
input_files = job.inputdata.names
input_guids = input_files
elif job.inputdata._name == 'DQ2Dataset':
if not job.inputdata.names:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
input_guids = job.inputdata.guids
input_files = job.inputdata.names
if not job.inputdata.type in [
'DQ2_LOCAL', 'FILE_STAGER', 'LFC', 'TAG',
'TNT_LOCAL', 'TNT_DOWNLOAD'
]:
job.inputdata.type = 'DQ2_LOCAL'
else:
if job.inputdata._name == 'ATLASCastorDataset':
input_files = ATLASCastorDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASLocalDataset':
input_files = ATLASLocalDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASDataset':
input_files = ATLASDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASTier3Dataset':
if job.inputdata.names:
input_files = job.inputdata.names
input_guids = input_files
elif job.inputdata.pfnListFile:
logger.info('Loading file names from %s' %
job.inputdata.pfnListFile.name)
pfnListFile = open(job.inputdata.pfnListFile.name)
job.inputdata.names = [
line.strip() for line in pfnListFile
]
pfnListFile.close()
input_files = job.inputdata.names
input_guids = input_files
else:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
elif job.inputdata._name == 'DQ2Dataset':
if not job.inputdata.type in [
'DQ2_LOCAL', 'FILE_STAGER', 'LFC', 'TAG',
'TNT_LOCAL', 'TNT_DOWNLOAD'
]:
job.inputdata.type = 'DQ2_LOCAL'
contents = job.inputdata.get_contents()
input_files = [lfn for guid, lfn in contents]
input_guids = [guid for guid, lfn in contents]
if job.inputdata.tagdataset:
tag_contents = job.inputdata.get_tag_contents()
input_tag_files = [lfn for guid, lfn in tag_contents]
input_tag_guids = [guid for guid, lfn in tag_contents]
if job.inputdata.use_aodesd_backnav:
esd_contents = job.inputdata.get_contents(backnav=True)
input_esd_files = [lfn for guid, lfn in esd_contents]
input_esd_guids = [guid for guid, lfn in esd_contents]
job.inputdata.names = input_files
job.inputdata.guids = input_guids
# Outputdataset
output_location = ''
if job.outputdata:
if job.outputdata._name == 'DQ2OutputDataset':
if job.outputdata.location:
if isDQ2SRMSite(job.outputdata.location):
output_location = job.outputdata.location
else:
logger.warning('Unknown output location %s.',
job.outputdata.location)
elif job._getRoot().subjobs and job._getRoot(
).outputdata.location:
if isDQ2SRMSite(job._getRoot().outputdata.location):
output_location = job._getRoot().outputdata.location
else:
logger.warning('Unknown output location %s.',
job.getRoot().outputdata.location)
logger.debug('Output: %s,%s', output_location,
job.outputdata.location)
elif job.outputdata.location == '' and job.outputdata._name == 'DQ2OutputDataset':
output_location = ''
elif job.outputdata.location:
output_location = expandfilename(job.outputdata.location)
else:
try:
output_location = config['LocalOutputLocation']
if job.outputdata:
job.outputdata.location = expandfilename(
output_location)
except ConfigError:
logger.warning(
'No default output location specified in the configuration.'
)
else:
try:
output_location = config['LocalOutputLocation']
except ConfigError:
logger.warning(
'No default output location specified in the configuration.'
)
if job._getRoot().subjobs:
jid = "%d.%d" % (job._getRoot().id, job.id)
else:
jid = "%d" % job.id
if output_location and job.outputdata and job.outputdata._name != 'DQ2OutputDataset':
if job._getRoot().subjobs:
if config['NoSubDirsAtAllForLocalOutput']:
output_location = output_location
elif config['SingleDirForLocalOutput']:
output_location = os.path.join(output_location,
"%d" % (job._getRoot().id))
elif config['IndividualSubjobDirsForLocalOutput']:
output_location = os.path.join(
output_location, "%d/%d" % (job._getRoot().id, job.id))
else:
output_location = os.path.join(output_location, jid)
if job.outputdata:
# Remove trailing number if job is copied
pat = re.compile(r'\/[\d\.]+\/[\d\.]+$')
if re.findall(pat, output_location):
output_location = re.sub(pat, '', output_location)
if config['NoSubDirsAtAllForLocalOutput']:
output_location = output_location
elif config['SingleDirForLocalOutput']:
output_location = os.path.join(
output_location, "%d" % (job._getRoot().id))
elif config['IndividualSubjobDirsForLocalOutput']:
output_location = os.path.join(
output_location,
"%d/%d" % (job._getRoot().id, job.id))
else:
output_location = os.path.join(output_location, jid)
job.outputdata.location = output_location
if job.outputdata and job.outputdata._name == 'DQ2OutputDataset':
# output dataset name from master_prepare
output_datasetname = self.output_datasetname
output_lfn = self.output_lfn
output_jobid = jid
# Set subjob datasetname
job.outputdata.datasetname = output_datasetname
# Set master job datasetname
if job._getRoot().subjobs:
job._getRoot().outputdata.datasetname = output_datasetname
# Create output dataset -> moved to the worker node code !
if not job.outputdata.dataset_exists(output_datasetname):
if job._getRoot().subjobs:
if job.id == 0:
#job.outputdata.create_dataset(output_datasetname)
pass
else:
#job.outputdata.create_dataset(output_datasetname)
pass
else:
if (job._getRoot().subjobs
and job.id == 0) or not job._getRoot().subjobs:
logger.warning(
"Dataset %s already exists - appending new files to this dataset",
output_datasetname)
output_location = job.outputdata.get_locations(
datasetname=output_datasetname, quiet=True)
logger.debug('Output3: %s,%s', output_location,
job.outputdata.location)
if output_location:
output_location = output_location[0]
if job._getRoot().subjobs:
job._getRoot(
).outputdata.location = output_location
job.outputdata.location = output_location
else:
job.outputdata.location = output_location
logger.debug('Output4: %s,%s', output_location,
job.outputdata.location)
inputbox = [
File(os.path.join(os.path.dirname(__file__), 'athena-utility.sh'))
]
if input_guids:
inputbox += [
FileBuffer('input_guids', '\n'.join(input_guids) + '\n')
]
if input_files:
inputbox += [
FileBuffer('input_files', '\n'.join(input_files) + '\n')
]
if input_tag_guids:
inputbox += [
FileBuffer('input_tag_guids',
'\n'.join(input_tag_guids) + '\n')
]
if input_tag_files:
inputbox += [
FileBuffer('input_tag_files',
'\n'.join(input_tag_files) + '\n')
]
if input_esd_guids:
inputbox += [
FileBuffer('input_esd_guids',
'\n'.join(input_esd_guids) + '\n')
]
if input_esd_files:
inputbox += [
FileBuffer('input_esd_files',
'\n'.join(input_esd_files) + '\n')
]
# check for output data given in prepare info
if job.outputdata and job.application.atlas_exetype == "ATHENA":
for of in job.application.atlas_run_config['output']['alloutputs']:
if not of in job.outputdata.outputdata:
job.outputdata.outputdata.append(of)
if job.outputdata and job.outputdata.outputdata:
inputbox += [
FileBuffer('output_files',
'\n'.join(job.outputdata.outputdata) + '\n')
]
elif job.outputdata and not job.outputdata.outputdata:
raise ApplicationConfigurationError(
None,
'j.outputdata.outputdata is empty - Please specify output filename(s).'
)
exe = os.path.join(os.path.dirname(__file__), 'run-athena-local.sh')
outputbox = jobmasterconfig.outputbox
environment = jobmasterconfig.env.copy()
## create and add sample files for FileStager
if job.inputdata and job.inputdata._name == 'StagerDataset':
if not job.inputdata.dataset:
raise ApplicationConfigurationError(
None, 'dataset name not specified in job.inputdata')
## ship fs-copy.py with the job as it's going to be used as a copy command wrapper by FileStager
inputbox += [
File(os.path.join(os.path.dirname(__file__), 'fs-copy.py'))
]
(jo_path, ic_path) = job.inputdata.make_FileStager_jobOptions(
job=job, max_events=app.max_events)
inputbox += [File(jo_path), File(ic_path)]
## re-make the environment['ATHENA_OPTIONS']
athena_options = os.path.basename(File(jo_path).name)
for option_file in app.option_file:
athena_option = os.path.basename(option_file.name)
athena_options += ' ' + athena_option
if app.options:
athena_options = app.options + ' ' + athena_options
environment['ATHENA_OPTIONS'] = athena_options
environment['DATASETTYPE'] = 'FILE_STAGER'
## ask to send back the FileStager.out/err generated by fs-copy.py
outputbox += ['FileStager.out', 'FileStager.err']
# If ArgSplitter is used
try:
if job.application.args:
environment['ATHENA_OPTIONS'] = environment[
'ATHENA_OPTIONS'] + ' ' + ' '.join(job.application.args)
if job.application.options:
job.application.options = job.application.options + ' ' + job.application.args
else:
job.application.options = job.application.args
except AttributeError:
pass
if job.outputdata and job.outputdata._name=='DQ2OutputDataset' and output_location == [ ]:
raise ApplicationConfigurationError(
None,
'j.outputdata.outputdata is empty - Please specify output filename(s).'
)
# set EOS env setting
environment['EOS_COMMAND_PATH'] = config['PathToEOSBinary']
# flag for single output dir
if (config['SingleDirForLocalOutput'] or
config['NoSubDirsAtAllForLocalOutput']) and job._getParent():
environment['SINGLE_OUTPUT_DIR'] = jid
# change the filename
newoutput = []
for outf in job.outputdata.outputdata:
newfile, newfileExt = os.path.splitext(outf)
jid = "%d.%d" % (job._getParent().id, job.id)
newoutput.append("%s.%s%s" % (newfile, jid, newfileExt))
job.outputdata.outputdata = newoutput[:]
environment['OUTPUT_LOCATION'] = output_location
if job.outputdata and job.outputdata._name == 'DQ2OutputDataset':
environment['OUTPUT_DATASETNAME'] = output_datasetname
environment['OUTPUT_LFN'] = output_lfn
environment['OUTPUT_JOBID'] = output_jobid
environment['DQ2_URL_SERVER'] = configDQ2['DQ2_URL_SERVER']
environment['DQ2_URL_SERVER_SSL'] = configDQ2['DQ2_URL_SERVER_SSL']
environment['DQ2_OUTPUTFILE_NAMELENGTH'] = str(
configDQ2['OUTPUTFILE_NAMELENGTH'])
if job.outputdata.use_shortfilename:
environment['GANGA_SHORTFILENAME'] = '1'
else:
environment['GANGA_SHORTFILENAME'] = ''
try:
environment['GANGA_GLITE_UI'] = configLCG['GLITE_SETUP']
except:
pass
environment['DQ2_OUTPUT_SPACE_TOKENS'] = ':'.join(
configDQ2['DQ2_OUTPUT_SPACE_TOKENS'])
environment['DQ2_BACKUP_OUTPUT_LOCATIONS'] = ':'.join(
configDQ2['DQ2_BACKUP_OUTPUT_LOCATIONS'])
# CN: extra condition for TNTSplitter
if job._getRoot().splitter and job._getRoot(
).splitter._name == 'TNTJobSplitter':
# set up dq2 environment
datasetname = job.inputdata.dataset
environment['DATASETNAME'] = ':'.join(datasetname)
environment['DATASETLOCATION'] = ':'.join(
job.inputdata.get_locations())
environment['DQ2_URL_SERVER'] = configDQ2['DQ2_URL_SERVER']
environment['DQ2_URL_SERVER_SSL'] = configDQ2['DQ2_URL_SERVER_SSL']
#environment['DATASETTYPE']=job.inputdata.type
# At present, DQ2 download is the only thing that works
environment['DATASETTYPE'] = "DQ2_DOWNLOAD"
if job.inputdata.accessprotocol:
environment[
'DQ2_LOCAL_PROTOCOL'] = job.inputdata.accessprotocol
if job.inputsandbox: inputbox += job.inputsandbox
# Fix DATASETNAME env variable for DQ2_COPY mode
if job.inputdata and job.inputdata._name in [
'DQ2Dataset'
] and job.inputdata.type in ['DQ2_LOCAL', 'DQ2_COPY', 'FILE_STAGER']:
if job.inputdata.dataset:
from GangaAtlas.Lib.ATLASDataset.DQ2Dataset import resolve_container
datasets = resolve_container(job.inputdata.dataset)
environment['DATASETNAME'] = datasets[0]
try:
environment['DATASETLOCATION'] = ':'.join(
job.inputdata.get_locations(
overlap=False)[datasets[0]])
except:
printout = 'Job submission failed ! Dataset %s could not be found in DQ2 ! Maybe retry ?' % (
datasets[0])
raise ApplicationConfigurationError(None, printout)
if job.inputdata and job.inputdata._name == 'ATLASTier3Dataset':
environment['DATASETTYPE'] = 'TIER3'
# USE_POOLFILECATALOG_FAILOVER of Local/ATLASLocalDataset
if job.inputdata and job.inputdata._name == 'ATLASLocalDataset':
if job.inputdata.use_poolfilecatalog_failover:
environment['USE_POOLFILECATALOG_FAILOVER'] = '1'
# CREATE_POOLFILECATALOG of Local/ATLASLocalDataset
environment['CREATE_POOLFILECATALOG'] = '1'
if job.inputdata and job.inputdata._name == 'ATLASLocalDataset':
if not job.inputdata.create_poolfilecatalog:
environment['CREATE_POOLFILECATALOG'] = '0'
# Write trf parameters
trf_params = ' '
for key, value in job.application.trf_parameter.iteritems():
if key == 'dbrelease':
environment['DBDATASETNAME'] = value.split(':')[0]
environment['DBFILENAME'] = value.split(':')[1]
else:
trf_params = trf_params + key + '=' + str(value) + ' '
if trf_params != ' ' and job.application.atlas_exetype == 'TRF':
_append_file_buffer(inputbox, 'trf_params', [trf_params])
if not 'db_dq2localid.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox, 'db_dq2localid.py')
# set RecExCommon options
environment['RECEXTYPE'] = job.application.recex_type
# Athena run dir
if job.application.atlas_exetype == "ATHENA" and job.application.atlas_run_dir != "":
environment['ATLAS_RUN_DIR'] = job.application.atlas_run_dir
# Set DQ2_LOCAL_SITE_ID
if hasattr(job.backend, 'extraopts'):
if job.backend.extraopts.find('site=hh') > 0:
environment['DQ2_LOCAL_SITE_ID'] = 'DESY-HH_SCRATCHDISK'
environment[
'GANGA_LCG_CE'] = 'grid-ce5.desy.de:2119' # hack for FILE_STAGER at NAF
elif job.backend.extraopts.find('site=zn') > 0:
environment['DQ2_LOCAL_SITE_ID'] = 'DESY-ZN_SCRATCHDISK'
environment[
'GANGA_LCG_CE'] = 'lcg-ce0.ifh.de:2119' # hack for FILE_STAGER at NAF
else:
environment['DQ2_LOCAL_SITE_ID'] = configDQ2[
'DQ2_LOCAL_SITE_ID']
else:
environment['DQ2_LOCAL_SITE_ID'] = configDQ2['DQ2_LOCAL_SITE_ID']
return StandardJobConfig(File(exe), inputbox, [], outputbox,
environment)
def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig):
"""prepare the subjob specific configuration"""
job = app._getParent() # Returns job or subjob object
logger.debug("AthenaLocalRTHandler prepare called, %s", job.id )
input_files = []
input_guids = []
input_tag_files = []
input_tag_guids = []
input_esd_files = []
input_esd_guids = []
# If job has inputdata
if job.inputdata:
# DQ2Dataset, ATLASLocalDataset and ATLASCastorDataset job splitting is done in AthenaSplitterJob
if job._getRoot().subjobs:
if job.inputdata._name == 'ATLASLocalDataset' or job.inputdata._name == 'ATLASCastorDataset':
if not job.inputdata.names: raise ApplicationConfigurationError(None,'No inputdata has been specified.')
input_files = job.inputdata.names
elif job.inputdata._name == 'ATLASDataset':
if not job.inputdata.lfn: raise ApplicationConfigurationError(None,'No inputdata has been specified.')
input_files = job.inputdata.lfn
elif job.inputdata._name == 'ATLASTier3Dataset':
if not job.inputdata.names:
raise ApplicationConfigurationError(None,'No inputdata has been specified.')
if job.inputdata.names:
input_files = job.inputdata.names
input_guids = input_files
elif job.inputdata._name == 'DQ2Dataset':
if not job.inputdata.names: raise ApplicationConfigurationError(None,'No inputdata has been specified.')
input_guids = job.inputdata.guids
input_files = job.inputdata.names
if not job.inputdata.type in ['DQ2_LOCAL', 'FILE_STAGER', 'LFC', 'TAG', 'TNT_LOCAL', 'TNT_DOWNLOAD' ]:
job.inputdata.type ='DQ2_LOCAL'
else:
if job.inputdata._name == 'ATLASCastorDataset':
input_files = ATLASCastorDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASLocalDataset':
input_files = ATLASLocalDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASDataset':
input_files = ATLASDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASTier3Dataset':
if job.inputdata.names:
input_files = job.inputdata.names
input_guids = input_files
elif job.inputdata.pfnListFile:
logger.info('Loading file names from %s'%job.inputdata.pfnListFile.name)
pfnListFile = open(job.inputdata.pfnListFile.name)
job.inputdata.names = [ line.strip() for line in pfnListFile]
pfnListFile.close()
input_files = job.inputdata.names
input_guids = input_files
else:
raise ApplicationConfigurationError(None,'No inputdata has been specified.')
elif job.inputdata._name == 'DQ2Dataset':
if not job.inputdata.type in ['DQ2_LOCAL', 'FILE_STAGER', 'LFC', 'TAG', 'TNT_LOCAL', 'TNT_DOWNLOAD' ]:
job.inputdata.type ='DQ2_LOCAL'
contents = job.inputdata.get_contents()
input_files = [ lfn for guid, lfn in contents ]
input_guids = [ guid for guid, lfn in contents ]
if job.inputdata.tagdataset:
tag_contents = job.inputdata.get_tag_contents()
input_tag_files = [ lfn for guid, lfn in tag_contents ]
input_tag_guids = [ guid for guid, lfn in tag_contents ]
if job.inputdata.use_aodesd_backnav:
esd_contents = job.inputdata.get_contents(backnav=True)
input_esd_files = [ lfn for guid, lfn in esd_contents ]
input_esd_guids = [ guid for guid, lfn in esd_contents ]
job.inputdata.names = input_files
job.inputdata.guids = input_guids
# Outputdataset
output_location=''
if job.outputdata:
if job.outputdata._name=='DQ2OutputDataset':
if job.outputdata.location:
if isDQ2SRMSite(job.outputdata.location):
output_location = job.outputdata.location
else:
logger.warning('Unknown output location %s.',job.outputdata.location)
elif job._getRoot().subjobs and job._getRoot().outputdata.location:
if isDQ2SRMSite(job._getRoot().outputdata.location):
output_location = job._getRoot().outputdata.location
else:
logger.warning('Unknown output location %s.',job.getRoot().outputdata.location)
logger.debug('Output: %s,%s',output_location, job.outputdata.location)
elif job.outputdata.location=='' and job.outputdata._name=='DQ2OutputDataset':
output_location = ''
elif job.outputdata.location:
output_location = expandfilename(job.outputdata.location)
else:
try:
output_location=config['LocalOutputLocation']
if job.outputdata:
job.outputdata.location = expandfilename(output_location)
except ConfigError:
logger.warning('No default output location specified in the configuration.')
else:
try:
output_location=config['LocalOutputLocation']
except ConfigError:
logger.warning('No default output location specified in the configuration.')
if job._getRoot().subjobs:
jid = "%d.%d" % (job._getRoot().id, job.id)
else:
jid = "%d" % job.id
if output_location and job.outputdata and job.outputdata._name!='DQ2OutputDataset':
if job._getRoot().subjobs:
if config['NoSubDirsAtAllForLocalOutput']:
output_location = output_location
elif config['SingleDirForLocalOutput']:
output_location = os.path.join(output_location, "%d" % (job._getRoot().id))
elif config['IndividualSubjobDirsForLocalOutput']:
output_location = os.path.join(output_location, "%d/%d" % (job._getRoot().id, job.id))
else:
output_location = os.path.join(output_location, jid)
if job.outputdata:
# Remove trailing number if job is copied
pat = re.compile(r'\/[\d\.]+\/[\d\.]+$')
if re.findall(pat,output_location):
output_location = re.sub(pat, '', output_location)
if config['NoSubDirsAtAllForLocalOutput']:
output_location = output_location
elif config['SingleDirForLocalOutput']:
output_location = os.path.join(output_location, "%d" % (job._getRoot().id))
elif config['IndividualSubjobDirsForLocalOutput']:
output_location = os.path.join(output_location, "%d/%d" % (job._getRoot().id, job.id))
else:
output_location = os.path.join(output_location, jid)
job.outputdata.location = output_location
if job.outputdata and job.outputdata._name=='DQ2OutputDataset':
# output dataset name from master_prepare
output_datasetname = self.output_datasetname
output_lfn = self.output_lfn
output_jobid = jid
# Set subjob datasetname
job.outputdata.datasetname=output_datasetname
# Set master job datasetname
if job._getRoot().subjobs:
job._getRoot().outputdata.datasetname=output_datasetname
# Create output dataset -> moved to the worker node code !
if not job.outputdata.dataset_exists(output_datasetname):
if job._getRoot().subjobs:
if job.id==0:
#job.outputdata.create_dataset(output_datasetname)
pass
else:
#job.outputdata.create_dataset(output_datasetname)
pass
else:
if (job._getRoot().subjobs and job.id==0) or not job._getRoot().subjobs:
logger.warning("Dataset %s already exists - appending new files to this dataset", output_datasetname)
output_location = job.outputdata.get_locations(datasetname=output_datasetname, quiet=True)
logger.debug('Output3: %s,%s',output_location, job.outputdata.location)
if output_location:
output_location = output_location[0]
if job._getRoot().subjobs:
job._getRoot().outputdata.location=output_location
job.outputdata.location=output_location
else:
job.outputdata.location=output_location
logger.debug('Output4: %s,%s',output_location, job.outputdata.location)
inputbox = [File(os.path.join(os.path.dirname(__file__),'athena-utility.sh'))]
if input_guids:
inputbox += [ FileBuffer('input_guids','\n'.join(input_guids)+'\n') ]
if input_files:
inputbox += [ FileBuffer('input_files','\n'.join(input_files)+'\n') ]
if input_tag_guids:
inputbox += [ FileBuffer('input_tag_guids','\n'.join(input_tag_guids)+'\n') ]
if input_tag_files:
inputbox += [ FileBuffer('input_tag_files','\n'.join(input_tag_files)+'\n') ]
if input_esd_guids:
inputbox += [ FileBuffer('input_esd_guids','\n'.join(input_esd_guids)+'\n') ]
if input_esd_files:
inputbox += [ FileBuffer('input_esd_files','\n'.join(input_esd_files)+'\n') ]
# check for output data given in prepare info
if job.outputdata and job.application.atlas_exetype == "ATHENA":
for of in job.application.atlas_run_config['output']['alloutputs']:
if not of in job.outputdata.outputdata:
job.outputdata.outputdata.append(of)
if job.outputdata and job.outputdata.outputdata:
inputbox += [ FileBuffer('output_files','\n'.join(job.outputdata.outputdata)+'\n') ]
elif job.outputdata and not job.outputdata.outputdata:
raise ApplicationConfigurationError(None,'j.outputdata.outputdata is empty - Please specify output filename(s).')
exe = os.path.join(os.path.dirname(__file__),'run-athena-local.sh')
outputbox = jobmasterconfig.outputbox
environment = jobmasterconfig.env.copy()
## create and add sample files for FileStager
if job.inputdata and job.inputdata._name == 'StagerDataset':
if not job.inputdata.dataset:
raise ApplicationConfigurationError(None,'dataset name not specified in job.inputdata')
## ship fs-copy.py with the job as it's going to be used as a copy command wrapper by FileStager
inputbox += [ File( os.path.join( os.path.dirname(__file__), 'fs-copy.py') ) ]
(jo_path, ic_path) = job.inputdata.make_FileStager_jobOptions(job=job, max_events=app.max_events)
inputbox += [ File(jo_path), File(ic_path) ]
## re-make the environment['ATHENA_OPTIONS']
athena_options = os.path.basename( File(jo_path).name )
for option_file in app.option_file:
athena_option = os.path.basename(option_file.name)
athena_options += ' ' + athena_option
if app.options:
athena_options = app.options + ' ' + athena_options
environment['ATHENA_OPTIONS'] = athena_options
environment['DATASETTYPE'] = 'FILE_STAGER'
## ask to send back the FileStager.out/err generated by fs-copy.py
outputbox += ['FileStager.out', 'FileStager.err']
# If ArgSplitter is used
try:
if job.application.args:
environment['ATHENA_OPTIONS'] = environment['ATHENA_OPTIONS'] + ' ' + ' '.join(job.application.args)
if job.application.options:
job.application.options = job.application.options + ' ' + job.application.args
else:
job.application.options=job.application.args
except AttributeError:
pass
if job.outputdata and job.outputdata._name=='DQ2OutputDataset' and output_location == [ ]:
raise ApplicationConfigurationError(None,'j.outputdata.outputdata is empty - Please specify output filename(s).')
# set EOS env setting
environment['EOS_COMMAND_PATH'] = config['PathToEOSBinary']
# flag for single output dir
if (config['SingleDirForLocalOutput'] or config['NoSubDirsAtAllForLocalOutput']) and job._getParent():
environment['SINGLE_OUTPUT_DIR'] = jid
# change the filename
newoutput = []
for outf in job.outputdata.outputdata:
newfile, newfileExt = os.path.splitext(outf)
jid = "%d.%d" % (job._getParent().id, job.id)
newoutput.append("%s.%s%s" % (newfile, jid, newfileExt) )
job.outputdata.outputdata = newoutput[:]
environment['OUTPUT_LOCATION'] = output_location
if job.outputdata and job.outputdata._name == 'DQ2OutputDataset':
environment['OUTPUT_DATASETNAME'] = output_datasetname
environment['OUTPUT_LFN'] = output_lfn
environment['OUTPUT_JOBID'] = output_jobid
environment['DQ2_URL_SERVER']=configDQ2['DQ2_URL_SERVER']
environment['DQ2_URL_SERVER_SSL']=configDQ2['DQ2_URL_SERVER_SSL']
environment['DQ2_OUTPUTFILE_NAMELENGTH'] = str(configDQ2['OUTPUTFILE_NAMELENGTH'])
if job.outputdata.use_shortfilename:
environment['GANGA_SHORTFILENAME'] = '1'
else:
environment['GANGA_SHORTFILENAME'] = ''
try:
environment['GANGA_GLITE_UI']=configLCG['GLITE_SETUP']
except:
pass
environment['DQ2_OUTPUT_SPACE_TOKENS']= ':'.join(configDQ2['DQ2_OUTPUT_SPACE_TOKENS'])
environment['DQ2_BACKUP_OUTPUT_LOCATIONS']= ':'.join(configDQ2['DQ2_BACKUP_OUTPUT_LOCATIONS'])
# CN: extra condition for TNTSplitter
if job._getRoot().splitter and job._getRoot().splitter._name == 'TNTJobSplitter':
# set up dq2 environment
datasetname = job.inputdata.dataset
environment['DATASETNAME']= ':'.join(datasetname)
environment['DATASETLOCATION'] = ':'.join(job.inputdata.get_locations())
environment['DQ2_URL_SERVER']=configDQ2['DQ2_URL_SERVER']
environment['DQ2_URL_SERVER_SSL']=configDQ2['DQ2_URL_SERVER_SSL']
#environment['DATASETTYPE']=job.inputdata.type
# At present, DQ2 download is the only thing that works
environment['DATASETTYPE']="DQ2_DOWNLOAD"
if job.inputdata.accessprotocol:
environment['DQ2_LOCAL_PROTOCOL'] = job.inputdata.accessprotocol
if job.inputsandbox: inputbox += job.inputsandbox
# Fix DATASETNAME env variable for DQ2_COPY mode
if job.inputdata and job.inputdata._name in [ 'DQ2Dataset' ] and job.inputdata.type in [ 'DQ2_LOCAL', 'DQ2_COPY', 'FILE_STAGER' ]:
if job.inputdata.dataset:
from GangaAtlas.Lib.ATLASDataset.DQ2Dataset import resolve_container
datasets = resolve_container(job.inputdata.dataset)
environment['DATASETNAME'] = datasets[0]
try:
environment['DATASETLOCATION'] = ':'.join(job.inputdata.get_locations(overlap=False)[ datasets[0] ])
except:
printout = 'Job submission failed ! Dataset %s could not be found in DQ2 ! Maybe retry ?' %(datasets[0])
raise ApplicationConfigurationError(None,printout )
if job.inputdata and job.inputdata._name == 'ATLASTier3Dataset':
environment['DATASETTYPE'] = 'TIER3'
# USE_POOLFILECATALOG_FAILOVER of Local/ATLASLocalDataset
if job.inputdata and job.inputdata._name == 'ATLASLocalDataset':
if job.inputdata.use_poolfilecatalog_failover:
environment['USE_POOLFILECATALOG_FAILOVER'] = '1'
# CREATE_POOLFILECATALOG of Local/ATLASLocalDataset
environment['CREATE_POOLFILECATALOG'] = '1'
if job.inputdata and job.inputdata._name == 'ATLASLocalDataset':
if not job.inputdata.create_poolfilecatalog:
environment['CREATE_POOLFILECATALOG'] = '0'
# Write trf parameters
trf_params = ' '
for key, value in job.application.trf_parameter.iteritems():
if key == 'dbrelease':
environment['DBDATASETNAME'] = value.split(':')[0]
environment['DBFILENAME'] = value.split(':')[1]
else:
trf_params = trf_params + key + '=' + str(value) + ' '
if trf_params!=' ' and job.application.atlas_exetype=='TRF':
_append_file_buffer(inputbox,'trf_params', [ trf_params ])
if not 'db_dq2localid.py' in [ os.path.basename(file.name) for file in inputbox ]:
_append_files(inputbox, 'db_dq2localid.py')
# set RecExCommon options
environment['RECEXTYPE'] = job.application.recex_type
# Athena run dir
if job.application.atlas_exetype == "ATHENA" and job.application.atlas_run_dir != "":
environment['ATLAS_RUN_DIR'] = job.application.atlas_run_dir
# Set DQ2_LOCAL_SITE_ID
if hasattr(job.backend, 'extraopts'):
if job.backend.extraopts.find('site=hh')>0:
environment['DQ2_LOCAL_SITE_ID'] = 'DESY-HH_SCRATCHDISK'
environment['GANGA_LCG_CE'] = 'grid-ce5.desy.de:2119' # hack for FILE_STAGER at NAF
elif job.backend.extraopts.find('site=zn')>0:
environment['DQ2_LOCAL_SITE_ID'] = 'DESY-ZN_SCRATCHDISK'
environment['GANGA_LCG_CE'] = 'lcg-ce0.ifh.de:2119' # hack for FILE_STAGER at NAF
else:
environment['DQ2_LOCAL_SITE_ID'] = configDQ2['DQ2_LOCAL_SITE_ID']
else:
environment['DQ2_LOCAL_SITE_ID'] = configDQ2['DQ2_LOCAL_SITE_ID']
return StandardJobConfig(File(exe), inputbox, [], outputbox, environment)
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
"""prepare the subjob specific configuration"""
job = app._getParent() # Returns job or subjob object
logger.debug("AthenaLCGRTHandler prepare called, %s", job.id)
# prepare inputdata
input_files = []
input_guids = []
input_tag_files = []
input_tag_guids = []
input_esd_files = []
input_esd_guids = []
add_files = []
if job.inputdata:
# DQ2Dataset, ATLASLocalDataset and ATLASCastorDataset job splitting is done in AthenaSplitterJob
if job._getRoot().subjobs:
if job.inputdata._name == 'ATLASLocalDataset' or job.inputdata._name == 'ATLASCastorDataset':
if not job.inputdata.names:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
input_files = job.inputdata.names
elif job.inputdata._name == 'ATLASDataset':
if not job.inputdata.lfn:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
input_files = job.inputdata.lfn
elif job.inputdata._name == 'ATLASTier3Dataset':
if not job.inputdata.names:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
if job.inputdata.names:
input_files = job.inputdata.names
input_guids = input_files
elif job.inputdata._name in [
'DQ2Dataset', 'AMIDataset', 'EventPicking'
]:
if not job.inputdata.names:
raise ApplicationConfigurationError(
None,
'No inputdata has been specified. Failure in job %s.%s. Dataset %s'
%
(job._getRoot().id, job.id, job.inputdata.dataset))
input_guids = job.inputdata.guids
input_files = job.inputdata.names
if job.inputdata.tag_info:
# check for conflicts with TAG_LOCAL or TAG_COPY
if job.inputdata.type in ['TAG_LOCAL', 'TAG_COPY']:
raise ApplicationConfigurationError(
None,
"Cannot provide both tag_info and run as '%s'. Please use one or the other!"
% job.inputdata.type)
# check if FILE_STAGER is used
if job.inputdata.type == 'FILE_STAGER':
logger.warning(
"TAG jobs currently can't use the FILE_STAGER. Switching to DQ2_COPY instead."
)
job.inputdata.type = 'DQ2_COPY'
# add additional file info for tags
for tag_file in job.inputdata.tag_info:
for ref in job.inputdata.tag_info[tag_file][
'refs']:
add_files.append(ref[1] + ':' + ref[0] + ':' +
ref[2])
if not job.inputdata.type in [
'DQ2_LOCAL', 'LFC', 'TAG', 'TNT_LOCAL',
'TNT_DOWNLOAD', 'DQ2_COPY', 'FILE_STAGER',
'TAG_LOCAL', 'TAG_COPY'
]:
job.inputdata.type = 'DQ2_LOCAL'
if not job.inputdata.datatype in [
'DATA', 'MC', 'MuonCalibStream'
]:
job.inputdata.datatype = 'MC'
else:
if job.inputdata._name == 'ATLASCastorDataset':
input_files = ATLASCastorDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASLocalDataset':
input_files = ATLASLocalDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASDataset':
input_files = ATLASDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASTier3Dataset':
if job.inputdata.names:
input_files = job.inputdata.names
input_guids = input_files
elif job.inputdata.pfnListFile:
logger.info('Loading file names from %s' %
job.inputdata.pfnListFile.name)
pfnListFile = open(job.inputdata.pfnListFile.name)
job.inputdata.names = [
line.strip() for line in pfnListFile
]
pfnListFile.close()
input_files = job.inputdata.names
input_guids = input_files
else:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
elif job.inputdata._name in [
'DQ2Dataset', 'AMIDataset', 'EventPicking'
]:
if not job.inputdata.type in [
'DQ2_LOCAL', 'LFC', 'TAG', 'TNT_LOCAL',
'TNT_DOWNLOAD', 'DQ2_COPY', 'FILE_STAGER',
'TAG_LOCAL', 'TAG_COPY'
]:
job.inputdata.type = 'DQ2_LOCAL'
if not job.inputdata.datatype in [
'DATA', 'MC', 'MuonCalibStream'
]:
job.inputdata.datatype = 'MC'
input_guids, input_files = _splitlist(
job.inputdata.get_contents())
if job.inputdata.tagdataset:
input_tag_guids, input_tag_files = _splitlist(
job.inputdata.get_tag_contents())
if job.inputdata.use_aodesd_backnav:
input_esd_guids, input_esd_files = _splitlist(
job.inputdata.get_contents(backnav=True))
job.inputdata.names = input_files
job.inputdata.guids = input_guids
# prepare outputdata
output_location = ''
if job.outputdata:
if job.outputdata._name == 'DQ2OutputDataset':
if job.outputdata.location:
if type(job.outputdata.location) == str and isDQ2SRMSite(
job.outputdata.location):
output_location = job.outputdata.location
else:
logger.warning('Unknown output location %s.',
job.outputdata.location)
#if job.backend.requirements._name == 'AtlasLCGRequirements':
# if job.backend.requirements.cloud:
# if whichCloud(output_location) != job.backend.requirements.cloud:
# printout = 'Job submission failed ! j.outputdata.location=%s is not in the same cloud as j.backend.requirements.cloud=%s' %(job.outputdata.location, job.backend.requirements.cloud )
# raise ApplicationConfigurationError(None, printout)
# if job.backend.requirements.sites:
# if whichCloud(output_location) != whichCloud(job.backend.requirements.sites[0]):
# printout = 'Job submission failed ! j.outputdata.location=%s is not in the same cloud as j.backend.requirements.sites=%s'%(job.outputdata.location, job.backend.requirements.sites)
# raise ApplicationConfigurationError(None,printout )
elif job._getRoot().subjobs and job._getRoot(
).outputdata.location:
if isDQ2SRMSite(job._getRoot().outputdata.location):
output_location = job._getRoot().outputdata.location
else:
logger.warning('Unknown output location %s.',
job.getRoot().outputdata.location)
logger.debug('Output: %s,%s', output_location,
job.outputdata.location)
else:
if job.outputdata.location:
output_location = job.outputdata.location
else:
try:
output_location = config['LCGOutputLocation']
except ConfigError:
logger.warning(
'No default output location specified in the configuration.'
)
if job.outputdata.location:
job.outputdata.location = output_location
logger.debug('Output: %s,%s', output_location,
job.outputdata.location)
if job._getRoot().subjobs:
jid = "%d.%d" % (job._getRoot().id, job.id)
else:
jid = "%d" % job.id
if output_location and job.outputdata and job.outputdata._name != 'DQ2OutputDataset':
output_location = os.path.join(output_location, jid)
if job.outputdata:
# Remove trailing number if job is copied
pat = re.compile(r'\/[\d\.]+\/[\d\.]+$')
if re.findall(pat, output_location):
output_location = re.sub(pat, '', output_location)
output_location = os.path.join(output_location, jid)
job.outputdata.location = output_location
if job.outputdata and job.outputdata._name == 'DQ2OutputDataset':
# output dataset name from master_prepare
output_datasetname = self.output_datasetname
output_lfn = self.output_lfn
output_jobid = jid
# Set subjob datasetname
job.outputdata.datasetname = output_datasetname
# Set master job datasetname
if job._getRoot().subjobs:
job._getRoot().outputdata.datasetname = output_datasetname
# Create output dataset -> moved to the worker node code !
if not job.outputdata.dataset_exists(output_datasetname):
if job._getRoot().subjobs:
if job.id == 0:
#job.outputdata.create_dataset(output_datasetname)
pass
else:
#job.outputdata.create_dataset(output_datasetname)
pass
if output_location and configDQ2['USE_STAGEOUT_SUBSCRIPTION']:
job.outputdata.create_subscription(output_datasetname,
output_location)
else:
if (job._getRoot().subjobs
and job.id == 0) or not job._getRoot().subjobs:
logger.warning(
"Dataset %s already exists - appending new files to this dataset",
output_datasetname)
output_location = job.outputdata.get_locations(
datasetname=output_datasetname, quiet=True)
logger.debug('Output3: %s,%s', output_location,
job.outputdata.location)
if output_location:
output_location = output_location[0]
if job._getRoot().subjobs:
job._getRoot(
).outputdata.location = output_location
job.outputdata.location = output_location
else:
job.outputdata.location = output_location
logger.debug('Output4: %s,%s', output_location,
job.outputdata.location)
if getConfig('LCG')['JobLogHandler'] == 'DQ2' and (
not job.outputdata or
(job.outputdata and job.outputdata._name != 'DQ2OutputDataset')):
raise ApplicationConfigurationError(
None,
'Staging of log files in DQ2 requested, but DQ2 output dataset not specified.'
)
# prepare inputsandbox
inputbox = [File(os.path.join(__directory__, 'athena-utility.sh'))]
if input_guids:
_append_file_buffer(inputbox, 'input_guids', input_guids)
if input_files:
_append_file_buffer(inputbox, 'input_files', input_files)
if add_files: _append_file_buffer(inputbox, 'add_files', add_files)
if input_tag_guids:
_append_file_buffer(inputbox, 'input_tag_guids', input_tag_guids)
if input_tag_files:
_append_file_buffer(inputbox, 'input_tag_files', input_tag_files)
if input_esd_guids:
_append_file_buffer(inputbox, 'input_esd_guids', input_esd_guids)
if input_esd_files:
_append_file_buffer(inputbox, 'input_esd_files', input_esd_files)
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
for tag_file in job.inputdata.tag_info:
if job.inputdata.tag_info[tag_file]['path'] != '':
inputbox.append(
File(
os.path.join(
job.inputdata.tag_info[tag_file]['path'],
tag_file)))
# check for output data given in prepare info
if job.outputdata and job.application.atlas_exetype == "ATHENA":
for of in job.application.atlas_run_config['output']['alloutputs']:
if not of in job.outputdata.outputdata:
job.outputdata.outputdata.append(of)
if job.outputdata and job.outputdata.outputdata:
_append_file_buffer(inputbox, 'output_files',
job.outputdata.outputdata)
elif job.outputdata and not job.outputdata.outputdata:
raise ApplicationConfigurationError(
None,
'j.outputdata.outputdata is empty - Please specify output filename(s).'
)
exe = os.path.join(__directory__, 'run-athena-lcg.sh')
outputbox = jobmasterconfig.outputbox
requirements = jobmasterconfig.requirements.__copy__()
environment = jobmasterconfig.env.copy()
# If ArgSplitter is used
try:
if job.application.args:
environment['ATHENA_OPTIONS'] = environment[
'ATHENA_OPTIONS'] + ' ' + ' '.join(job.application.args)
if job.application.options:
job.application.options = job.application.options + ' ' + job.application.args
else:
job.application.options = job.application.args
except AttributeError:
pass
if output_location and output_location.find(
'/castor/cern.ch/grid/atlas/t0') >= 0:
raise ApplicationConfigurationError(
None,
'You are try to save the output to TIER0DISK - please use another area !'
)
if not output_location:
output_location = ''
if configDQ2['USE_STAGEOUT_SUBSCRIPTION']:
output_location = ''
environment['OUTPUT_LOCATION'] = output_location
environment['ATLASOutputDatasetLFC'] = config['ATLASOutputDatasetLFC']
if job.outputdata and job.outputdata._name == 'DQ2OutputDataset':
environment['OUTPUT_DATASETNAME'] = output_datasetname
environment['OUTPUT_LFN'] = output_lfn
environment['OUTPUT_JOBID'] = output_jobid
environment['DQ2_URL_SERVER'] = configDQ2['DQ2_URL_SERVER']
environment['DQ2_URL_SERVER_SSL'] = configDQ2['DQ2_URL_SERVER_SSL']
environment['DQ2_OUTPUTFILE_NAMELENGTH'] = configDQ2[
'OUTPUTFILE_NAMELENGTH']
if job.outputdata.use_shortfilename:
environment['GANGA_SHORTFILENAME'] = '1'
else:
environment['GANGA_SHORTFILENAME'] = ''
environment['DQ2_OUTPUT_SPACE_TOKENS'] = ':'.join(
configDQ2['DQ2_OUTPUT_SPACE_TOKENS'])
environment['DQ2_BACKUP_OUTPUT_LOCATIONS'] = ':'.join(
configDQ2['DQ2_BACKUP_OUTPUT_LOCATIONS'])
# CN: extra condition for TNTSplitter
if job._getRoot().splitter and job._getRoot(
).splitter._name == 'TNTJobSplitter':
# set up dq2 environment
datasetname = job.inputdata.dataset
environment['DATASETNAME'] = ':'.join(datasetname)
environment['DATASETLOCATION'] = ':'.join(
job.inputdata.get_locations())
environment['DQ2_URL_SERVER'] = configDQ2['DQ2_URL_SERVER']
environment['DQ2_URL_SERVER_SSL'] = configDQ2['DQ2_URL_SERVER_SSL']
environment['DATASETTYPE'] = job.inputdata.type
environment['DATASETDATATYPE'] = job.inputdata.datatype
if job.inputdata.accessprotocol:
environment[
'DQ2_LOCAL_PROTOCOL'] = job.inputdata.accessprotocol
if job.inputsandbox: inputbox += job.inputsandbox
if job.inputdata and job.inputdata._name == 'DQ2Dataset' and job.inputdata.tag_info:
if job.inputdata.tag_info[job.inputdata.tag_info.keys(
)[0]]['dataset'] != '' and job.inputdata.tag_info[tag_file][
'path'] == '':
environment['TAG_TYPE'] = 'DQ2'
else:
environment['TAG_TYPE'] = 'LOCAL'
# Fix DATASETNAME env variable for DQ2_COPY mode
if job.inputdata and (job.inputdata._name in [
'DQ2Dataset', 'AMIDataset', 'EventPicking'
]) and (job.inputdata.type in [
'DQ2_LOCAL', 'DQ2_COPY', 'FILE_STAGER', 'TAG_LOCAL', 'TAG_COPY'
]):
if job.inputdata.dataset:
from GangaAtlas.Lib.ATLASDataset.DQ2Dataset import resolve_container
datasets = resolve_container(job.inputdata.dataset)
environment['DATASETNAME'] = datasets[0]
try:
environment['DATASETLOCATION'] = ':'.join(
job.inputdata.get_locations(
overlap=False)[datasets[0]])
except:
printout = 'Job submission failed ! Dataset %s could not be found in DQ2 ! Maybe retry ?' % (
datasets[0])
raise ApplicationConfigurationError(None, printout)
if job.inputdata and job.inputdata._name == 'ATLASTier3Dataset':
environment['DATASETTYPE'] = 'TIER3'
# Work around for glite WMS spaced environement variable problem
inputbox.append(
FileBuffer('athena_options', environment['ATHENA_OPTIONS'] + '\n'))
# Write trf parameters
trf_params = ' '
for key, value in job.application.trf_parameter.iteritems():
if key == 'dbrelease':
environment['DBDATASETNAME'] = value.split(':')[0]
environment['DBFILENAME'] = value.split(':')[1]
else:
trf_params = trf_params + key + '=' + str(value) + ' '
if trf_params != ' ' and job.application.atlas_exetype == 'TRF':
_append_file_buffer(inputbox, 'trf_params', [trf_params])
# set RecExCommon options
environment['RECEXTYPE'] = job.application.recex_type
# event based splitting: set max_events and skip_events
if job._getRoot().splitter and hasattr(
job._getRoot().splitter,
'numevtsperjob') and job._getRoot().splitter.numevtsperjob > 0:
environment['ATHENA_MAX_EVENTS'] = str(job.application.max_events)
environment['ATHENA_SKIP_EVENTS'] = str(
job.application.skip_events)
# pick event
if job._getRoot().splitter and job._getRoot(
).inputdata and job._getRoot().inputdata._name == 'EventPicking':
#Replace blank space
environment['ATHENA_RUN_EVENTS'] = str(
job.application.run_event).replace(' ', '')
environment['ATHENA_FILTER_POLICY'] = str(
job.inputdata.pick_filter_policy)
# append a property for monitoring to the jobconfig of subjobs
lcg_config = LCGJobConfig(File(exe), inputbox, [], outputbox,
environment, [], requirements)
lcg_config.monitoring_svc = mc['Athena']
return lcg_config
def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig):
"""prepare the subjob specific configuration"""
job = app._getParent() # Returns job or subjob object
logger.debug("AthenaLCGRTHandler prepare called, %s", job.id)
# prepare inputdata
input_files = []
input_guids = []
input_tag_files = []
input_tag_guids = []
input_esd_files = []
input_esd_guids = []
add_files = []
if job.inputdata:
# DQ2Dataset, ATLASLocalDataset and ATLASCastorDataset job splitting is done in AthenaSplitterJob
if job._getRoot().subjobs:
if job.inputdata._name == 'ATLASLocalDataset':
if not job.inputdata.names: raise ApplicationConfigurationError('No inputdata has been specified.')
input_files = job.inputdata.names
elif job.inputdata._name == 'ATLASTier3Dataset':
if not job.inputdata.names:
raise ApplicationConfigurationError('No inputdata has been specified.')
if job.inputdata.names:
input_files = job.inputdata.names
input_guids = input_files
elif job.inputdata._name in [ 'DQ2Dataset', 'EventPicking']:
if not job.inputdata.names: raise ApplicationConfigurationError('No inputdata has been specified. Failure in job %s.%s. Dataset %s' %(job._getRoot().id, job.id, job.inputdata.dataset) )
input_guids = job.inputdata.guids
input_files = job.inputdata.names
if job.inputdata.tag_info:
# check for conflicts with TAG_LOCAL or TAG_COPY
if job.inputdata.type in ['TAG_LOCAL', 'TAG_COPY']:
raise ApplicationConfigurationError("Cannot provide both tag_info and run as '%s'. Please use one or the other!" % job.inputdata.type)
# check if FILE_STAGER is used
if job.inputdata.type == 'FILE_STAGER':
logger.warning("TAG jobs currently can't use the FILE_STAGER. Switching to DQ2_COPY instead.")
job.inputdata.type = 'DQ2_COPY'
# add additional file info for tags
for tag_file in job.inputdata.tag_info:
for ref in job.inputdata.tag_info[tag_file]['refs']:
add_files.append( ref[1] + ':' + ref[0] + ':' + ref[2] )
if not job.inputdata.type in ['DQ2_LOCAL', 'LFC', 'TAG', 'TNT_LOCAL', 'TNT_DOWNLOAD', 'DQ2_COPY', 'FILE_STAGER', 'TAG_LOCAL', 'TAG_COPY' ]:
job.inputdata.type ='DQ2_LOCAL'
if not job.inputdata.datatype in ['DATA', 'MC', 'MuonCalibStream']:
job.inputdata.datatype ='MC'
else:
if job.inputdata._name == 'ATLASLocalDataset':
input_files = ATLASLocalDataset.get_filenames(app)
elif job.inputdata._name == 'ATLASTier3Dataset':
if job.inputdata.names:
input_files = job.inputdata.names
input_guids = input_files
elif job.inputdata.pfnListFile:
logger.info('Loading file names from %s'%job.inputdata.pfnListFile.name)
pfnListFile = open(job.inputdata.pfnListFile.name)
job.inputdata.names = [ line.strip() for line in pfnListFile]
pfnListFile.close()
input_files = job.inputdata.names
input_guids = input_files
else:
raise ApplicationConfigurationError('No inputdata has been specified.')
elif job.inputdata._name in [ 'DQ2Dataset', 'EventPicking']:
if not job.inputdata.type in ['DQ2_LOCAL', 'LFC', 'TAG', 'TNT_LOCAL', 'TNT_DOWNLOAD', 'DQ2_COPY', 'FILE_STAGER', 'TAG_LOCAL', 'TAG_COPY' ]:
job.inputdata.type ='DQ2_LOCAL'
if not job.inputdata.datatype in ['DATA', 'MC', 'MuonCalibStream']:
job.inputdata.datatype ='MC'
input_guids, input_files = _splitlist(job.inputdata.get_contents())
if job.inputdata.use_aodesd_backnav:
input_esd_guids, input_esd_files = _splitlist(job.inputdata.get_contents(backnav=True))
job.inputdata.names = input_files
job.inputdata.guids = input_guids
# prepare outputdata
output_location = ''
if job.outputdata:
if job.outputdata._name=='DQ2OutputDataset':
if job.outputdata.location:
if type(job.outputdata.location) == str and isDQ2SRMSite(job.outputdata.location):
output_location = job.outputdata.location
else:
logger.warning('Unknown output location %s.',job.outputdata.location)
#if job.backend.requirements._name == 'AtlasLCGRequirements':
# if job.backend.requirements.cloud:
# if whichCloud(output_location) != job.backend.requirements.cloud:
# printout = 'Job submission failed ! j.outputdata.location=%s is not in the same cloud as j.backend.requirements.cloud=%s' %(job.outputdata.location, job.backend.requirements.cloud )
# raise ApplicationConfigurationError(None, printout)
# if job.backend.requirements.sites:
# if whichCloud(output_location) != whichCloud(job.backend.requirements.sites[0]):
# printout = 'Job submission failed ! j.outputdata.location=%s is not in the same cloud as j.backend.requirements.sites=%s'%(job.outputdata.location, job.backend.requirements.sites)
# raise ApplicationConfigurationError(None,printout )
elif job._getRoot().subjobs and job._getRoot().outputdata.location:
if isDQ2SRMSite(job._getRoot().outputdata.location):
output_location = job._getRoot().outputdata.location
else:
logger.warning('Unknown output location %s.',job.getRoot().outputdata.location)
logger.debug('Output: %s,%s',output_location, job.outputdata.location)
else:
if job.outputdata.location:
output_location = job.outputdata.location
else:
try:
output_location = config['LCGOutputLocation']
except ConfigError:
logger.warning('No default output location specified in the configuration.')
if job.outputdata.location:
job.outputdata.location = output_location
logger.debug('Output: %s,%s',output_location, job.outputdata.location)
if job._getRoot().subjobs:
jid = "%d.%d" % (job._getRoot().id, job.id)
else:
jid = "%d" % job.id
if output_location and job.outputdata and job.outputdata._name!='DQ2OutputDataset':
output_location = os.path.join(output_location, jid)
if job.outputdata:
# Remove trailing number if job is copied
pat = re.compile(r'\/[\d\.]+\/[\d\.]+$')
if re.findall(pat,output_location):
output_location = re.sub(pat, '', output_location)
output_location = os.path.join(output_location, jid)
job.outputdata.location = output_location
if job.outputdata and job.outputdata._name=='DQ2OutputDataset':
# output dataset name from master_prepare
output_datasetname = self.output_datasetname
output_lfn = self.output_lfn
output_jobid = jid
# Set subjob datasetname
job.outputdata.datasetname=output_datasetname
# Set master job datasetname
if job._getRoot().subjobs:
job._getRoot().outputdata.datasetname=output_datasetname
# Create output dataset -> moved to the worker node code !
if not job.outputdata.dataset_exists(output_datasetname):
if job._getRoot().subjobs:
if job.id==0:
#job.outputdata.create_dataset(output_datasetname)
pass
else:
#job.outputdata.create_dataset(output_datasetname)
pass
if output_location and configDQ2['USE_STAGEOUT_SUBSCRIPTION']:
job.outputdata.create_subscription(output_datasetname, output_location)
else:
if (job._getRoot().subjobs and job.id==0) or not job._getRoot().subjobs:
logger.warning("Dataset %s already exists - appending new files to this dataset", output_datasetname)
output_location = job.outputdata.get_locations(datasetname=output_datasetname, quiet=True)
logger.debug('Output3: %s,%s',output_location, job.outputdata.location)
if output_location:
output_location = output_location[0]
if job._getRoot().subjobs:
job._getRoot().outputdata.location=output_location
job.outputdata.location=output_location
else:
job.outputdata.location=output_location
logger.debug('Output4: %s,%s',output_location, job.outputdata.location)
if getConfig('LCG')['JobLogHandler'] == 'DQ2' and (not job.outputdata or (job.outputdata and job.outputdata._name != 'DQ2OutputDataset')):
raise ApplicationConfigurationError('Staging of log files in DQ2 requested, but DQ2 output dataset not specified.')
# prepare inputsandbox
inputbox = [File(os.path.join(__directory__,'athena-utility.sh')) ]
if input_guids: _append_file_buffer(inputbox,'input_guids',input_guids)
if input_files: _append_file_buffer(inputbox,'input_files',input_files)
if add_files: _append_file_buffer(inputbox,'add_files',add_files)
if input_tag_guids: _append_file_buffer(inputbox,'input_tag_guids',input_tag_guids)
if input_tag_files: _append_file_buffer(inputbox,'input_tag_files',input_tag_files)
if input_esd_guids: _append_file_buffer(inputbox,'input_esd_guids',input_esd_guids)
if input_esd_files: _append_file_buffer(inputbox,'input_esd_files',input_esd_files)
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
for tag_file in job.inputdata.tag_info:
if job.inputdata.tag_info[tag_file]['path'] != '':
inputbox.append( File( os.path.join( job.inputdata.tag_info[tag_file]['path'], tag_file) ) )
# check for output data given in prepare info
if job.outputdata and job.application.atlas_exetype == "ATHENA":
for of in job.application.atlas_run_config['output']['alloutputs']:
if not of in job.outputdata.outputdata:
job.outputdata.outputdata.append(of)
if job.outputdata and job.outputdata.outputdata:
_append_file_buffer(inputbox,'output_files',job.outputdata.outputdata)
elif job.outputdata and not job.outputdata.outputdata:
raise ApplicationConfigurationError('j.outputdata.outputdata is empty - Please specify output filename(s).')
exe = os.path.join(__directory__,'run-athena-lcg.sh')
outputbox = jobmasterconfig.outputbox
requirements = jobmasterconfig.requirements.__copy__()
environment = jobmasterconfig.env.copy()
# If ArgSplitter is used
try:
if job.application.args:
environment['ATHENA_OPTIONS'] = environment['ATHENA_OPTIONS'] + ' ' + ' '.join(job.application.args)
if job.application.options:
job.application.options = job.application.options + ' ' + job.application.args
else:
job.application.options = job.application.args
except AttributeError:
pass
if output_location and output_location.find('/castor/cern.ch/grid/atlas/t0')>=0:
raise ApplicationConfigurationError('You are try to save the output to TIER0DISK - please use another area !')
if not output_location:
output_location = ''
if configDQ2['USE_STAGEOUT_SUBSCRIPTION']:
output_location = ''
environment['OUTPUT_LOCATION'] = output_location
environment['ATLASOutputDatasetLFC'] = config['ATLASOutputDatasetLFC']
if job.outputdata and job.outputdata._name == 'DQ2OutputDataset':
environment['OUTPUT_DATASETNAME'] = output_datasetname
environment['OUTPUT_LFN'] = output_lfn
environment['OUTPUT_JOBID'] = output_jobid
environment['DQ2_URL_SERVER']= configDQ2['DQ2_URL_SERVER']
environment['DQ2_URL_SERVER_SSL'] = configDQ2['DQ2_URL_SERVER_SSL']
environment['DQ2_OUTPUTFILE_NAMELENGTH'] = configDQ2['OUTPUTFILE_NAMELENGTH']
if job.outputdata.use_shortfilename:
environment['GANGA_SHORTFILENAME'] = '1'
else:
environment['GANGA_SHORTFILENAME'] = ''
environment['DQ2_OUTPUT_SPACE_TOKENS']= ':'.join(configDQ2['DQ2_OUTPUT_SPACE_TOKENS'])
environment['DQ2_BACKUP_OUTPUT_LOCATIONS']= ':'.join(configDQ2['DQ2_BACKUP_OUTPUT_LOCATIONS'])
# CN: extra condition for TNTSplitter
if job._getRoot().splitter and job._getRoot().splitter._name == 'TNTJobSplitter':
# set up dq2 environment
datasetname = job.inputdata.dataset
environment['DATASETNAME']= ':'.join(datasetname)
environment['DATASETLOCATION'] = ':'.join(job.inputdata.get_locations())
environment['DQ2_URL_SERVER'] = configDQ2['DQ2_URL_SERVER']
environment['DQ2_URL_SERVER_SSL'] = configDQ2['DQ2_URL_SERVER_SSL']
environment['DATASETTYPE'] = job.inputdata.type
environment['DATASETDATATYPE'] = job.inputdata.datatype
if job.inputdata.accessprotocol:
environment['DQ2_LOCAL_PROTOCOL'] = job.inputdata.accessprotocol
if job.inputsandbox: inputbox += job.inputsandbox
if job.inputdata and job.inputdata._name == 'DQ2Dataset' and job.inputdata.tag_info:
if job.inputdata.tag_info[job.inputdata.tag_info.keys()[0] ]['dataset'] != '' and job.inputdata.tag_info[tag_file]['path'] == '':
environment['TAG_TYPE'] = 'DQ2'
else:
environment['TAG_TYPE'] = 'LOCAL'
# Fix DATASETNAME env variable for DQ2_COPY mode
if job.inputdata and ( job.inputdata._name in [ 'DQ2Dataset', 'EventPicking']) and (job.inputdata.type in ['DQ2_LOCAL', 'DQ2_COPY', 'FILE_STAGER', 'TAG_LOCAL', 'TAG_COPY' ]):
if job.inputdata.dataset:
from GangaAtlas.Lib.ATLASDataset.DQ2Dataset import resolve_container
datasets = resolve_container(job.inputdata.dataset)
environment['DATASETNAME'] = datasets[0]
try:
environment['DATASETLOCATION'] = ':'.join(job.inputdata.get_locations(overlap=False)[ datasets[0] ])
except:
printout = 'Job submission failed ! Dataset %s could not be found in DQ2 ! Maybe retry ?' %(datasets[0])
raise ApplicationConfigurationError(printout )
if job.inputdata and job.inputdata._name == 'ATLASTier3Dataset':
environment['DATASETTYPE'] = 'TIER3'
# Work around for glite WMS spaced environement variable problem
inputbox.append(FileBuffer('athena_options',environment['ATHENA_OPTIONS']+'\n'))
# Write trf parameters
trf_params = ' '
for key, value in job.application.trf_parameter.iteritems():
if key == 'dbrelease':
environment['DBDATASETNAME'] = value.split(':')[0]
environment['DBFILENAME'] = value.split(':')[1]
else:
trf_params = trf_params + key + '=' + str(value) + ' '
if trf_params!=' ' and job.application.atlas_exetype=='TRF':
_append_file_buffer(inputbox,'trf_params', [ trf_params ] )
# set RecExCommon options
environment['RECEXTYPE'] = job.application.recex_type
# event based splitting: set max_events and skip_events
if job._getRoot().splitter and hasattr(job._getRoot().splitter, 'numevtsperjob') and job._getRoot().splitter.numevtsperjob > 0 :
environment['ATHENA_MAX_EVENTS'] = str(job.application.max_events)
environment['ATHENA_SKIP_EVENTS'] = str(job.application.skip_events)
# pick event
if job._getRoot().splitter and job._getRoot().inputdata and job._getRoot().inputdata._name == 'EventPicking' :
#Replace blank space
environment['ATHENA_RUN_EVENTS'] = str(job.application.run_event).replace(' ', '')
environment['ATHENA_FILTER_POLICY'] = str(job.inputdata.pick_filter_policy)
# append a property for monitoring to the jobconfig of subjobs
lcg_config = LCGJobConfig(File(exe), inputbox, [], outputbox, environment, [], requirements)
lcg_config.monitoring_svc = mc['Athena']
return lcg_config
