def prepare(self,app,appconfig,appmasterconfig,jobmasterconfig):
from Ganga.Lib.LCG import LCGJobConfig
c = LCGJobConfig(app.exe,app.inputs,app.args,app.outputs,app.envs)
c.monitoring_svc = mc['GangaTutorial']
return c
def prepare(self, app, appconfig, appmasterconfig, jobmasterconfig):
from Ganga.Lib.LCG import LCGJobConfig
c = LCGJobConfig(app.exe, app.inputs, app.args, app.outputs, app.envs)
c.monitoring_svc = mc['GangaTutorial']
return c
def prepare(self, app, appconfig, appmasterconfig, jobmasterconfig):
from Ganga.Lib.LCG import LCGJobConfig
prepared_exe = app.exe
if app.is_prepared is not None:
shared_path = os.path.join(expandfilename(getConfig('Configuration')['gangadir']),
'shared', getConfig('Configuration')['user'])
if isinstance(app.exe, str):
# we have a file. is it an absolute path?
if os.path.abspath(app.exe) == app.exe:
logger.info("Submitting a prepared application; taking any input files from %s" % (
app.is_prepared.name))
prepared_exe = File(os.path.join(os.path.join(
shared_path, app.is_prepared.name), os.path.basename(File(app.exe).name)))
# else assume it's a system binary, so we don't need to
# transport anything to the sharedir
else:
prepared_exe = app.exe
elif isinstance(app.exe, File):
logger.info("Submitting a prepared application; taking any input files from %s" % (
app.is_prepared.name))
prepared_exe = File(os.path.join(
os.path.join(shared_path, app.is_prepared.name), os.path.basename(app.exe.name)))
return LCGJobConfig(prepared_exe, app._getParent().inputsandbox, convertIntToStringArgs(app.args), app._getParent().outputsandbox, app.env)
def prepare(self,app,appconfig,appmasterconfig,jobmasterconfig):
from Ganga.Lib.LCG import LCGJobConfig
prepared_exe = File(os.path.join( os.path.dirname(__file__), "runNA62MC.sh"))
#if app.is_prepared is not None:
# logger.info("Submitting a prepared application; taking any input files from %s" %(app.is_prepared.name))
# prepared_exe = File(os.path.join(os.path.join(shared_path,app.is_prepared.name),os.path.basename(prepared_exe.name)))
#outputbox = [ 'na62run%d.stderr.err' % app.run_number, 'na62run%d.stdout.out' % app.run_number ]
outputbox = []
outputbox += app._getParent().outputsandbox
inputbox = [ File(os.path.join(os.path.join(shared_path,app.is_prepared.name), app.getMACFileName())) ]
inputbox.append( File(os.path.join(shared_path,app.is_prepared.name, app.script_name)) )
inputbox.append( File(os.path.join(shared_path,app.is_prepared.name, "input_files.tgz")) )
inputbox += app._getParent().inputsandbox
env = {'NA62SCRIPT':app.script_name,
'NA62STDOUT':'na62run%d.out' % app.run_number,
'NA62STDERR':'na62run%d.err' % app.run_number}
args = [app.getMACFileName(), "%s/r%d/%s" % (app.job_type, app.getRevision(), app.getDecayString())]
# add the output files
app._getParent().outputfiles = [SandboxFile('na62run%d.out' % app.run_number), SandboxFile('na62run%d.err' % app.run_number),
SandboxFile('__jdlfile__'), SandboxFile(app.getMACFileName()) ]
return LCGJobConfig(prepared_exe,inputbox,args,outputbox,env)
def prepare(self, app, appconfig, appmasterconfig, jobmasterconfig):
from Ganga.Lib.LCG import LCGJobConfig
runScript, inputsandbox, rootenv = downloadWrapper(app)
# propage command line args
argList = [str(s) for s in app.args]
return LCGJobConfig(runScript, inputsandbox, argList,
app._getParent().outputsandbox, rootenv)
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
local = PDF_Local.prepare\
( self, app, appsubconfig, appmasterconfig, jobmasterconfig )
inbox = []
inbox.extend(local.inputbox)
requirements = LCGRequirements()
tag = "VO-camont-Camtology-%s" % appsubconfig["version"]
requirements.software = [tag]
lcg = LCGJobConfig( exe = local.exe, inputbox = inbox,\
outputbox = local.outputbox, requirements = requirements )
return lcg
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
local = VansegLocal.prepare\
( self, app, appsubconfig, appmasterconfig, jobmasterconfig )
inbox = []
inbox.extend(local.inputbox)
exeFile = File(fullpath(app.exe))
if not exeFile in inbox:
inbox.append(exeFile)
requirements = LCGRequirements()
lcg = LCGJobConfig( exe = local.exe, inputbox = inbox,\
outputbox = local.outputbox, requirements = requirements )
return lcg
def prepare(self, app, appconfig, appmasterconfig, jobmasterconfig):
logger.debug('LCGRTHandler prepare called.')
job = app._getParent()
masterjob = job._getParent()
job.backend.requirements.other = masterjob.backend.requirements.other
job.backend.requirements.walltime = masterjob.backend.requirements.walltime
from Ganga.Lib.LCG import LCGJobConfig
return LCGJobConfig(app.exe,
app._getParent().inputsandbox,
convertIntToStringArgs(app.args),
app._getParent().outputsandbox, app.env)
def prepare(self, app, appconfig, appmasterconfig, jobmasterconfig):
from Ganga.Lib.LCG import LCGJobConfig
if not app.queue:
raise ApplicationConfigurationError(
None, 'queue not specified for PandaPilot')
args = app.arg_pattern.replace('%%QUEUE%%', app.queue)
job = app._getParent()
if not job.backend.requirements.sites:
job.backend.requirements.sites = [queueToDDM(app.queue)]
if not job.backend.requirements.sites:
raise ApplicationConfigurationError(
None, 'Could not map queue name to LCG site')
logger.info('Sending pilot for %s to %s' %
(app.queue, job.backend.requirements.sites))
return LCGJobConfig(app.exe,
app._getParent().inputsandbox, [args],
app._getParent().outputsandbox, None)
def master_prepare(self, app, appconfig):
"""Prepare the master job"""
job = app._getParent() # Returns job or subjob object
logger.debug('AthenaLCGRTHandler master_prepare called: %s', job.id)
if job._getRoot().subjobs:
jobid = "%d" % (job._getRoot().id)
else:
jobid = "%d" % job.id
# Generate output dataset name
if job.outputdata:
if job.outputdata._name == 'DQ2OutputDataset':
dq2_datasetname = job.outputdata.datasetname
dq2_isGroupDS = job.outputdata.isGroupDS
dq2_groupname = job.outputdata.groupname
else:
dq2_datasetname = ''
dq2_isGroupDS = False
dq2_groupname = ''
self.output_datasetname, self.output_lfn = dq2outputdatasetname(
dq2_datasetname, jobid, dq2_isGroupDS, dq2_groupname)
# Check if all sites are in the same cloud
if job.backend.requirements.sites:
firstCloud = whichCloud(job.backend.requirements.sites[0])
for site in job.backend.requirements.sites:
cloud = whichCloud(site)
if cloud != firstCloud:
printout = 'Job submission failed ! Site specified with j.backend.requirements.sites=%s are not in the same cloud !' % (
job.backend.requirements.sites)
raise ApplicationConfigurationError(None, printout)
#this next for loop instructs ganga to use option_files that live in the appropriate shared directory (the job
#will already have been prepared
#(if is_prepared is True, then we've most likely submitted a job via GangaRobot. We know what we're doing.
#if app.is_prepared is not True:
# for position in xrange(len(app.option_file)):
# app.option_file[position]=File(os.path.join(app.is_prepared.name,os.path.basename(app.option_file[position].name)))
# Expand Athena jobOptions
if not app.atlas_exetype in ['EXE']:
athena_options = ' '.join([
os.path.basename(opt_file.name) for opt_file in app.option_file
])
#if app.options: athena_options = ' -c ' + app.options + ' ' + athena_options
if app.options:
athena_options = app.options + ' ' + athena_options
inputbox = [File(opt_file.name) for opt_file in app.option_file]
else:
athena_options = ' '.join([
os.path.basename(opt_file.name) for opt_file in app.option_file
])
inputbox = []
athena_usersetupfile = os.path.basename(app.user_setupfile.name)
# prepare input sandbox
inputbox.append(File(os.path.join(__directory__, 'athena-utility.sh')))
if job.inputdata and job.inputdata._name == "AMIDataset" and job.inputdata.goodRunListXML.name != '':
inputbox.append(File(job.inputdata.goodRunListXML.name))
if job.inputdata and job.inputdata._name == 'ATLASDataset':
if job.inputdata.lfc:
_append_files(inputbox, 'ganga-stagein-lfc.py')
else:
_append_files(inputbox, 'ganga-stagein.py')
if app.user_area.name:
#we will now use the user_area that's stored in the users shared directory
if app.is_prepared is not True:
tmp_user_name = os.path.join(
os.path.join(shared_path, app.is_prepared.name),
os.path.basename(app.user_area.name))
inputbox.append(File(tmp_user_name))
else:
inputbox.append(File(app.user_area.name))
#if app.group_area.name: inputbox += [ File(app.group_area.name) ]
if app.group_area.name and str(app.group_area.name).find('http') < 0:
#we will now use the group_area that's stored in the users shared directory
if app.is_prepared is not True:
tmp_group_name = os.path.join(
os.path.join(shared_path, app.is_prepared.name),
os.path.basename(app.group_area.name))
inputbox.append(File(tmp_group_name))
else:
inputbox.append(File(app.group_area.name))
if app.user_setupfile.name:
inputbox.append(File(app.user_setupfile.name))
# CN: added TNTJobSplitter clause
if job.inputdata and (job.inputdata._name in [
'DQ2Dataset', 'AMIDataset', 'EventPicking'
]) or (job._getRoot().splitter
and job._getRoot().splitter._name == 'TNTJobSplitter'):
_append_files(inputbox, 'ganga-stage-in-out-dq2.py', 'dq2_get',
'dq2info.tar.gz')
if job.inputdata and job.inputdata.type == 'LFC' and not (
job._getRoot().splitter
and job._getRoot().splitter._name == 'TNTJobSplitter'):
_append_files(inputbox, 'dq2_get_old')
if job.inputdata and job.inputdata._name == 'ATLASTier3Dataset':
_append_files(inputbox, 'ganga-stage-in-out-dq2.py',
'dq2info.tar.gz')
## insert more scripts to inputsandbox for FileStager
if job.inputdata and (job.inputdata._name in [
'DQ2Dataset', 'AMIDataset', 'EventPicking'
]) and job.inputdata.type in ['FILE_STAGER']:
_append_files(inputbox, 'make_filestager_joption.py', 'dm_util.py',
'fs-copy.py')
#_append_files(inputbox,'make_filestager_joption.py','dm_util.py')
if job.outputdata and job.outputdata._name == 'DQ2OutputDataset':
#if not job.outputdata.location:
# raise ApplicationConfigurationError(None,'j.outputdata.location is empty - Please specify a DQ2 output location - job not submitted !')
if not 'ganga-stage-in-out-dq2.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox, 'ganga-stage-in-out-dq2.py')
_append_files(inputbox, 'ganga-joboption-parse.py')
if not 'dq2info.tar.gz' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox, 'dq2info.tar.gz')
# add libDCache.so and libRFIO.so to fix broken access in athena 12.0.x
if not 'ganga-stage-in-out-dq2.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox, 'ganga-stage-in-out-dq2.py')
if not 'dq2tracerreport.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox, 'dq2tracerreport.py')
if not 'db_dq2localid.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox, 'db_dq2localid.py')
if not 'getstats.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox, 'getstats.py')
if str(app.atlas_release).find('12.') >= 0:
_append_files(inputbox, 'libDCache.so', 'libRFIO.so', 'libdcap.so')
elif str(app.atlas_release).find('13.') >= 0:
_append_files(inputbox, 'libdcap.so')
else:
_append_files(inputbox, 'libdcap.so')
if job.inputsandbox: inputbox += job.inputsandbox
# prepare environment
if not app.atlas_release:
raise ApplicationConfigurationError(
None,
'j.application.atlas_release is empty - No ATLAS release version found. Run prepare() or specify a version explictly.'
)
environment = {
'ATLAS_RELEASE': app.atlas_release,
'ATHENA_OPTIONS': athena_options,
'ATHENA_USERSETUPFILE': athena_usersetupfile,
'ATLAS_PROJECT': app.atlas_project,
'ATLAS_EXETYPE': app.atlas_exetype,
'GANGA_VERSION': configSystem['GANGA_VERSION']
}
environment['DCACHE_RA_BUFFER'] = config['DCACHE_RA_BUFFER']
if app.atlas_environment:
for var in app.atlas_environment:
try:
vars = re.match("^(\w+)=(.*)", var).group(1)
value = re.match("^(\w+)=(.*)", var).group(2)
environment[vars] = value
except:
logger.warning(
'Athena.atlas_environment variable not correctly configured: %s',
var)
pass
if app.atlas_production and app.atlas_release.find(
'12.') >= 0 and app.atlas_project != 'AtlasPoint1':
temp_atlas_production = re.sub('\.', '_', app.atlas_production)
prod_url = config[
'PRODUCTION_ARCHIVE_BASEURL'] + '/AtlasProduction_' + temp_atlas_production + '_noarch.tar.gz'
logger.info('Using Production cache from: %s', prod_url)
environment['ATLAS_PRODUCTION_ARCHIVE'] = prod_url
if app.atlas_production and (app.atlas_project == 'AtlasPoint1'
or app.atlas_release.find('12.') <= 0):
environment['ATLAS_PRODUCTION'] = app.atlas_production
if app.user_area.name:
environment['USER_AREA'] = os.path.basename(app.user_area.name)
#if app.group_area.name: environment['GROUP_AREA']=os.path.basename(app.group_area.name)
if app.group_area.name:
if str(app.group_area.name).find('http') >= 0:
environment['GROUP_AREA_REMOTE'] = str(app.group_area.name)
else:
environment['GROUP_AREA'] = os.path.basename(
app.group_area.name)
if app.max_events:
if (app.max_events != -999) and (app.max_events > -2):
environment['ATHENA_MAX_EVENTS'] = str(app.max_events)
if job.backend.requirements._name == 'AtlasLCGRequirements':
requirements = AtlasLCGRequirements()
elif job.backend.requirements._name == 'AtlasCREAMRequirements':
requirements = AtlasCREAMRequirements()
else:
requirements = AtlasLCGRequirements()
if job.inputdata and job.inputdata._name == 'ATLASDataset':
if job.inputdata.lfc:
environment['GANGA_LFC_HOST'] = job.inputdata.lfc
if 'ganga-stage-in-out-dq2.py' in [
os.path.basename(file.name) for file in inputbox
]:
environment['DQ2_URL_SERVER'] = configDQ2['DQ2_URL_SERVER']
environment['DQ2_URL_SERVER_SSL'] = configDQ2['DQ2_URL_SERVER_SSL']
if job.inputdata and (job.inputdata._name
in ['DQ2Dataset', 'AMIDataset', 'EventPicking']):
if job.inputdata.dataset:
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
if job.inputdata.failover:
environment['DATASETFAILOVER'] = 1
environment['DATASETDATATYPE'] = job.inputdata.datatype
if job.inputdata.accessprotocol:
environment[
'DQ2_LOCAL_PROTOCOL'] = job.inputdata.accessprotocol
if job.inputdata.check_md5sum:
environment['GANGA_CHECKMD5SUM'] = 1
else:
raise ApplicationConfigurationError(
None,
'j.inputdata.dataset is empty - DQ2 dataset name needs to be specified.'
)
# Raise submission exception
if (not job.backend.CE and not (job.backend.requirements._name in [
'AtlasLCGRequirements', 'AtlasCREAMRequirements'
] and job.backend.requirements.sites)
and not (job.splitter
and job.splitter._name == 'DQ2JobSplitter')
and not (job.splitter
and job.splitter._name == 'TNTJobSplitter')
and not (job.splitter
and job.splitter._name == 'AnaTaskSplitterJob')
and not (job.splitter
and job.splitter._name == 'ATLASTier3Splitter')):
raise ApplicationConfigurationError(
None,
'Job submission failed ! Please use DQ2JobSplitter or specify j.backend.requirements.sites or j.backend.requirements.CE !'
)
if job.inputdata.match_ce_all or job.inputdata.min_num_files > 0:
raise ApplicationConfigurationError(
None,
'Job submission failed ! Usage of j.inputdata.match_ce_all or min_num_files is obsolete ! Please use DQ2JobSplitter or specify j.backend.requirements.sites or j.backend.requirements.CE !'
)
#if job.inputdata.number_of_files and (job.splitter and job.splitter._name == 'DQ2JobSplitter'):
# allLoc = job.inputdata.get_locations(complete=0)
# completeLoc = job.inputdata.get_locations(complete=1)
# incompleteLoc = []
# for loc in allLoc:
# if loc not in completeLoc:
# incompleteLoc.append(loc)
# if incompleteLoc:
# raise ApplicationConfigurationError(None,'Job submission failed ! Dataset is incomplete ! Usage of j.inputdata.number_of_files and DQ2JobSplitter is not allowed for incomplete datasets !')
# Add TAG datasetname
if job.inputdata.tagdataset:
environment['TAGDATASETNAME'] = ':'.join(
job.inputdata.tagdataset)
# prepare job requirements
requirementsSoftware = getLCGReleaseTag(app)
releaseBlacklist = job.backend.requirements.list_release_blacklist()
if requirementsSoftware and requirementsSoftware[0] in releaseBlacklist:
logger.error(
'The athena release %s you are using is not recommended for distributed analysis !',
requirementsSoftware[0])
logger.error(
'For details, please have a look at https://twiki.cern.ch/twiki/bin/view/Atlas/DAGangaFAQ#Athena_Versions_Issues or ask for help and advice on the distributed analysis help list !'
)
requirements.software = requirementsSoftware
else:
requirements.software = requirementsSoftware
# Set athena architecture: 32 or 64 bit
environment['ATLAS_ARCH'] = '32'
if requirementsSoftware and requirementsSoftware[0].find(
'x86_64') >= 0:
environment['ATLAS_ARCH'] = '64'
# add software requirement of dq2clients
if job.inputdata and job.inputdata._name in [
'DQ2Dataset', 'AMIDataset', 'EventPicking'
] and job.inputdata.type in [
'TNT_DOWNLOAD', 'DQ2_COPY', 'FILE_STAGER'
] or app.atlas_dbrelease or configDQ2['USE_ACCESS_INFO']:
try:
# override the default one if the dq2client_version is presented
# in the job backend's requirements object
dq2client_version = job.backend.requirements.dq2client_version
except AttributeError:
pass
if dq2client_version:
#requirements.software += ['VO-atlas-dq2clients-%s' % dq2client_version]
environment['DQ2_CLIENT_VERSION'] = dq2client_version
if app.atlas_dbrelease:
if not app._name == "AthenaTask" and not (
job.splitter and
(job.splitter._name == 'DQ2JobSplitter'
or job.splitter._name == 'ATLASTier3Splitter')):
raise ApplicationConfigurationError(
None,
'Job submission failed ! Please use DQ2JobSplitter if you are using j.application.atlas_dbrelease !'
)
try:
environment['ATLAS_DBRELEASE'] = app.atlas_dbrelease.split(
':')[0]
environment['ATLAS_DBFILE'] = app.atlas_dbrelease.split(':')[1]
except:
logger.warning(
'Problems with the atlas_dbrelease configuration')
# Fill AtlasLCGRequirements access mode
if configDQ2['USE_ACCESS_INFO']:
logger.warning(
"config['DQ2']['USE_ACCESS_INFO']=True - You are using the improved worker node input access method - make sure you are using at least athena version 15.0.0 or the latest FileStager tag !"
)
import pickle, StringIO
#if job.backend.requirements.sites:
info = job.backend.requirements.list_access_info()
fileHandle = StringIO.StringIO()
pickle.dump(info, fileHandle)
fileHandle.seek(-1)
lines = fileHandle.read()
inputbox.append(FileBuffer('access_info.pickle', lines))
_append_files(inputbox, 'access_info.py')
if not 'make_filestager_joption.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox, 'make_filestager_joption.py',
'dm_util.py', 'fs-copy.py')
# jobscript
exe = os.path.join(__directory__, 'run-athena-lcg.sh')
# output sandbox
outputbox = [
'output_guids', 'output_location', 'output_data', 'stats.pickle'
]
## retrieve the FileStager log
if configDQ2['USE_ACCESS_INFO'] or (
job.inputdata and
(job.inputdata._name
in ['DQ2Dataset', 'AMIDataset', 'EventPicking'])
and job.inputdata.type in ['FILE_STAGER']):
outputbox += ['FileStager.out', 'FileStager.err']
if job.outputsandbox: outputbox += job.outputsandbox
# Switch for DEBUG print-out in logfiles
if app.useNoDebugLogs:
environment['GANGA_LOG_DEBUG'] = '0'
else:
environment['GANGA_LOG_DEBUG'] = '1'
return LCGJobConfig(File(exe), inputbox, [], outputbox, environment,
[], requirements)
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, appconfig, appmasterconfig, jobmasterconfig):
"""Prepare the job"""
inputbox = []
# prepare environment
environment = {}
environment = jobmasterconfig.env.copy()
environment["INPUTDATASETS"] = ""
environment["INPUTFILES"] = ""
environment["INPUTTURLS"] = ""
alllfns = app.inputfiles + app.cavernfiles + app.mbfiles + app.dbfiles
guids = app.turls
guids.update(app.cavern_turls)
guids.update(app.minbias_turls)
guids.update(app.dbturls)
infilenr = 0
for infile in alllfns:
environment["INPUTFILES"] += "lfn[%d]='%s';" % (infilenr, infile)
environment["INPUTDATASETS"] += "dset[%d]='%s';" % (
infilenr, app.dsetmap[infile])
## insites=app.sitemap[infile]
## # compare with environment["OUTSITE"] and reorder if needed.
## newinsites=self.sortSites(insites,environment["OUTSITE"])
## environment["INPUTSITES"]+="site[%d]='%s';"%(infilenr,newinsites)
environment["INPUTTURLS"] += "turl[%d]='%s';" % (infilenr,
guids[infile])
infilenr += 1
logger.debug(
"%s %s %s" %
(str(environment["INPUTDATASETS"]), str(
environment["INPUTTURLS"]), str(environment["INPUTFILES"])))
if environment["INPUTDATASETS"]:
# Work around for glite WMS spaced environement variable problem
inputbox += [
FileBuffer('inputdsets.conf',
environment['INPUTDATASETS'] + '\n')
]
if environment["INPUTTURLS"]:
# Work around for glite WMS spaced environement variable problem
inputbox += [
FileBuffer('inputturls.conf', environment['INPUTTURLS'] + '\n')
]
if environment["INPUTFILES"]:
# Work around for glite WMS spaced environement variable problem
inputbox += [
FileBuffer('inputfiles.conf', environment['INPUTFILES'] + '\n')
]
# now doing output files....
job = app._getParent() # Returns job or subjob object
outfilelist = ""
for type in app.outputpaths.keys():
if type == "LOG" and "LOG" not in job.outputdata.outrootfiles:
# logfiles are no longer saved in DQ2 datasets unless they are explicitly named in the outrootfiles dictionnary
continue
outfilelist += app.outputpaths[type] + app.subjobsOutfiles[
job.id][type] + " "
environment["OUTPUTFILES"] = outfilelist
# Work around for glite WMS spaced environement variable problem
inputbox += [
FileBuffer('outputfiles.conf', environment['OUTPUTFILES'] + '\n')
]
# setting up job wrapper arguments.
args = app.args
trfargs = ' '.join(app.args[4:])
inputbox += [FileBuffer('trfargs.conf', trfargs + '\n')]
jid = ""
if job._getRoot().subjobs:
jid = job._getRoot().id
else:
jid = "%d" % job.id
environment["OUTPUT_JOBID"] = str(jid) # used for versionning
if app.dryrun:
environment["DRYRUN"] = "TRUE"
if app.dbrelease:
environment["ATLASDBREL"] = app.dbrelease
inputdata = []
filename = "wrapper.sh"
exe = os.path.join(os.path.dirname(__file__), filename)
# output sandbox
outputbox = jobmasterconfig.outputbox
if job.backend._name == "LCG" or job.backend._name == "Cronus" or job.backend._name == "Condor" or job.backend._name == "NG" or job.backend._name == "SGE":
logger.debug("submission to %s" % job.backend._name)
# prepare job requirements
requirements = jobmasterconfig.requirements
if "INPUTTURLS" in environment:
logger.debug(environment["INPUTTURLS"])
if string.find(environment["INPUTTURLS"], "file:") >= 0:
raise ApplicationConfigurationError(
None,
"Input file was found to be local, and LCG backend does not support replication of local files to the GRID yet. Please register your input dataset in DQ2 before resubmitting this job. Aborting"
)
if string.lower(app.se_name) == "local":
raise ApplicationConfigurationError(
None,
"Output file cannot be committed to local filesystem on a grid job. Please change se_name"
)
lcg_job_config = LCGJobConfig(File(exe), inputbox, args, outputbox,
environment, inputdata, requirements)
lcg_job_config.monitoring_svc = mc['AthenaMC/LCG']
return lcg_job_config
else:
logger.debug(
"Backend %s not fully supported , will try our best anyway..."
% job.backend._name)
# if there are input data files and they are on the grid, prestage them on local area (use either app.datasets.input_dataset or /tmp/$login/data (and update environment["INPUTFILE"] accordingly inf the later is used...)
# later development....
return StandardJobConfig(File(exe), inputbox, args, outputbox,
environment)
def prepare(self, app, appconfig, appmasterconfig, jobmasterconfig):
logger.debug('RAT::LCGRTHandler prepare ...')
from Ganga.Lib.LCG import LCGJobConfig
#create the backend wrapper script
job = app.getJobObject()
# Check the current worker node permissions
grid_config = RATUtil.GridConfig.get_instance()
for ce in grid_config.get_excluded_worker_nodes():
ganga_job.backend.requirements.excludedCEs += '%s ' % ce
#Check whether we're looking for a non-default sw dir
if app.softwareEnvironment is None:
# The relative path for CVMFS, SNOPLUS_CVMFS_DIR will be set at the backend
# Note the extra \ to escape the dollar in the initial python wrapper
app.softwareEnvironment = '\$SNOPLUS_CVMFS_DIR/sw/%s/env_rat-%s.sh' % (
app.ratVersion, app.ratVersion)
#we need to know the name of the file to run
macroFile = None
prodFile = None
if app.ratMacro != '':
decimated = app.ratMacro.split('/')
macroFile = decimated[len(decimated) - 1]
else:
decimated = app.prodScript.split('/')
prodFile = decimated[len(decimated) - 1]
foutList = '['
finList = '['
for i, var in enumerate(app.outputFiles):
foutList += '%s,' % var
for i, var in enumerate(app.inputFiles):
finList += '%s,' % var
if len(foutList) != 1:
foutList = '%s]' % foutList[:
-1] #remove final comma, add close bracket
if len(finList) != 1:
finList = '%s]' % finList[:
-1] #remove final comma, add close bracket
args = ''
args += '-g lcg '
args += '-v %s ' % (app.ratVersion)
args += '-e %s ' % (app.softwareEnvironment)
args += '-d %s ' % (app.outputDir)
args += '-o %s ' % (foutList)
args += '-x %s ' % (app.inputDir)
args += '-i %s ' % (finList)
if app.ratMacro != '':
args += '-m %s ' % (macroFile)
else:
args += '-k -m %s ' % (prodFile)
if app.useDB:
args += '--dbuser %s ' % (app.config['rat_db_user'])
args += '--dbpassword %s ' % (app.config['rat_db_pswd'])
args += '--dbname %s ' % (app.config['rat_db_name'])
args += '--dbprotocol %s ' % (app.config['rat_db_protocol'])
args += '--dburl %s ' % (app.config['rat_db_url'])
if app.discardOutput:
args += '--nostore '
wrapperArgs = ['-a', '"%s"' % (args)]
wrapperArgs += ['ratProdRunner.py', 'lcg']
app._getParent().inputsandbox.append('%s/ratProdRunner.py' %
_app_directory)
return LCGJobConfig(File('%s/sillyPythonWrapper.py' % _app_directory),
inputbox=app._getParent().inputsandbox,
outputbox=app._getParent().outputsandbox,
args=wrapperArgs)
def prepare(self, app, appconfig, appmasterconfig, jobmasterconfig):
'''Prepare method: called to configure the job for the specified backend.
'''
logger.debug('RAT::LCGRTHandler prepare ...')
from Ganga.Lib.LCG import LCGJobConfig
job = app.getJobObject()
#remove the leading directory path of the macro (on the grid node we'll just
#have the macro file)
decimated = app.ratMacro.split('/')
ratMacro = decimated[len(decimated) - 1]
#Set the output directory
if app.outputDir == None:
if app.config['grid_outputDir'] == None:
logger.error('Output directory not defined')
raise Exception
else:
app.outputDir = app.config['grid_outputDir']
outputDir = app.outputDir
lfcDir = os.path.join('lfn:/grid/snoplus.snolab.ca', outputDir)
# Check the current worker node permissions
grid_config = RATUtil.GridConfig.get_instance()
for ce in grid_config.get_excluded_worker_nodes():
ganga_job.backend.requirements.excludedCEs += '%s ' % ce
# By default require 1500 MB of RAM
memory_set = False
if len(job.backend.requirements.other) != 0:
for r in job.backend.requirements.other:
if "GlueHostMainMemoryRAMSize" in r:
memory_set = True
if not memory_set:
job.backend.requirements.other += [
'other.GlueHostMainMemoryRAMSize >= 1500'
]
#on the grid, we need to use our own version of python
#so have to send a python script to setup the correct environment
#AND then run the correct python script!
rrArgs = '' #args to send to ratRunner
spArgs = [] #args to send to sillyPythonWrapper
#ensure the rrArgs are space separated
rrArgs += '-g lcg ' #always at lcg
rrArgs += '-b %s ' % app.ratBaseVersion
rrArgs += '-m %s ' % ratMacro
rrArgs += '-d %s ' % outputDir
if app.softwareEnvironment is None:
# The relative path for CVMFS, SNOPLUS_CVMFS_DIR will be set at the backend
# Note the extra \ to escape the dollar in the initial python wrapper
rrArgs += '-e \$SNOPLUS_CVMFS_DIR/sw/%s/env_rat-%s.sh ' % (
app.ratBaseVersion, app.ratBaseVersion)
else:
rrArgs += '-e %s ' % app.softwareEnvironment
if app.ratVersion != None:
rrArgs += '-v %s ' % app.ratVersion
#ship code to backend
zipFileName = app.zipFileName
decimated = zipFileName.split('/')
zipFileName = decimated[len(decimated) - 1]
rrArgs += '-f %s ' % zipFileName
if app.outputFile:
rrArgs += '-o %s ' % app.outputFile
if app.inputFile:
rrArgs += '-i %s ' % app.inputFile
if app.nEvents:
rrArgs += '-N %s ' % app.nEvents
elif app.tRun:
rrArgs += '-T %s ' % app.tRun
if app.useDB:
rrArgs += '--dbuser %s ' % (app.config['rat_db_user'])
rrArgs += '--dbpassword %s ' % (app.config['rat_db_pswd'])
rrArgs += '--dbname %s ' % (app.config['rat_db_name'])
rrArgs += '--dbprotocol %s ' % (app.config['rat_db_protocol'])
rrArgs += '--dburl %s ' % (app.config['rat_db_url'])
if app.discardOutput:
rrArgs += '--nostore '
spArgs += ['-a', '"%s"' % rrArgs] #appends ratRunner args
spArgs += ['ratRunner.py', 'lcg']
app._getParent().inputsandbox.append('%s/ratRunner.py' %
_app_directory)
app._getParent().inputsandbox.append('%s/job_tools.py' %
_app_directory)
app._getParent().inputsandbox.append('%s/check_root_output.py' %
_app_directory)
return LCGJobConfig(File('%s/sillyPythonWrapper.py' % _app_directory),
inputbox=app._getParent().inputsandbox,
outputbox=app._getParent().outputsandbox,
args=spArgs)
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
def master_prepare(self, app, appmasterconfig):
if app.siteroot:
os.environ["SITEROOT"] = app.siteroot
os.environ["CMTSITE"] = app.cmtsite
job = app._getParent()
if job.backend._name in ["Local", "PBS"]:
if app.dryrun:
os.environ["SITEROOT"] = "NONE"
os.environ["CMTSITE"] = "NONE"
try:
assert "SITEROOT" in os.environ
except:
raise ApplicationConfigurationError(
None, " ATLAS environment not defined")
try:
assert "CMTSITE" in os.environ
except:
raise ApplicationConfigurationError(
None,
"cmt not setup properly. Please check your ATLAS setup or run on the grid"
)
if os.environ["CMTSITE"] == "CERN" and "AtlasVersion" in os.environ:
logger.debug(
"Checking AtlasVersion: %s and selected atlas release %s" %
(os.environ["AtlasVersion"], app.atlas_rel))
try:
assert app.atlas_rel == os.environ["AtlasVersion"]
except:
logger.error(
"Mismatching atlas release. Local setup is %s, resetting requested atlas release to local value."
% os.environ["AtlasVersion"])
app.atlas_release = os.environ["AtlasVersion"]
app.atlas_rel == os.environ["AtlasVersion"]
elif "ATLAS_RELEASE" in os.environ:
logger.debug(
"Checking ATLAS_RELEASE: %s and selected atlas release %s"
% (os.environ["ATLAS_RELEASE"], app.atlas_rel))
try:
assert app.atlas_rel == os.environ["ATLAS_RELASE"]
except:
logger.error(
"Mismatching atlas release. Local setup is %s, resetting requested atlas release to local value."
% os.environ["ATLAS_RELEASE"])
app.atlas_rel = os.environ["ATLAS_RELEASE"]
else:
logger.warning(
"Could not compare requested release and local setup. Hope you are doing something sensible..."
)
if job.backend._name == "LSF":
try:
assert "CMTSITE" in os.environ and os.environ[
"CMTSITE"] == "CERN"
except:
raise ApplicationConfigurationError(
None,
"Error, CERN ATLAS AFS environment not defined. Needed by LSF backend"
)
environment = {'T_LCG_GFAL_INFOSYS': 'atlas-bdii.cern.ch:2170'}
trfopts = app.transflags
# need to parse them to be able to pass them in an environment variable
trfopts = trfopts.replace(" ", "/W")
trfopts = trfopts.replace("-", "/F")
trflags = trfopts
if app.mode == "evgen":
trflags = "/Ft"
if app.verbosity:
trflags += "/W/Fl/W%s" % app.verbosity
if trflags:
environment["TRFLAGS"] = trflags
# setting output site from input data if any.
outsite, backup, outputlocation, backuplocation = "", "", "", ""
logger.info("checking sites from input data: %s" % str(app.sites))
# must distinguish running site (backend.requirements.sites) and output storage site (app.se_name)
# matching with user's wishes (app.se_name or backend.requirements.sites)
usersites = []
if len(job.backend.requirements.sites) > 0:
usersites = job.backend.requirements.sites
## elif job.application.se_name and job.application.se_name != "none":
## usersites=job.application.se_name.split(" ")
logger.info("user selection: %s" % str(usersites))
# select sites which are matching user's wishes, if any.
selectedSites = app.sites
if len(selectedSites) == 0:
selectedSites = usersites
if len(usersites) > 0 and len(app.sites) > 0:
selectedSites = job.inputdata.trimSites(usersites, app.sites)
# evgen case (no input data-> app.sites=[])
if len(app.sites) == 0 and app.se_name and app.se_name != "none":
selectedSites = app.se_name.split(" ")
# This comes last: using surviving sites from matching process.
if len(selectedSites) == 0:
try:
assert len(usersites) == 0
except:
raise ApplicationConfigurationError(
None,
"Could not find a match between input dataset locations: %s and your requested sites: %s. Please use a space token compatible with one of the input dataset locations (replace _XXXDISK or _XXXTAPE by _LOCALGROUPDISK or _SCRATCHDISK if necessary)"
% (str(app.sites), str(usersites)))
logger.warning(
"Failed to obtain processing site from input data, will use default value: CERN-PROD_SCRATCHDISK and submit production to CERN"
)
selectedSites.append(_defaultSite)
[outlfc, outsite,
outputlocation] = job.outputdata.getDQ2Locations(selectedSites[0])
if len(selectedSites) > 1:
[outlfc2, backup,
backuplocation] = job.outputdata.getDQ2Locations(selectedSites[1])
# app.se_name set: users wishes to get the output data written to another site than the one hosting the input.
# One needs to ensure that this location is at least in the same cloud as the targetted processing site. This is done by insuring that the lfcs are the same.
userSEs = []
outse = ""
if job.application.se_name and job.application.se_name != "none":
userSEs = job.application.se_name.split(" ")
# loop through userSEs until up to 2 valid sites are found...
outse = ""
for SE in userSEs:
[lfc, se, location] = job.outputdata.getDQ2Locations(SE)
if lfc == outlfc:
if not outse:
outse = se # important to use outse and not outsite here, as outsite is used for selection of processing site.
# userSEs overrides outlfc,outputlocation, but not outsite as outsite is unfortunately used for choice of the processing site.
outputlocation = location
else:
outlfc2 = lfc
backup = se
backuplocation = location
break
# finally: if no backup location is defined at this point, enforce CERN-PROD_SCRATCHDISK as backup location
if backup == "":
[outlfc2, backup,
backuplocation] = job.outputdata.getDQ2Locations(_defaultSite)
logger.info("Final selection of output sites: %s , backup: %s" %
(outsite, backup))
try:
assert outsite
except:
raise ApplicationConfigurationError(
None,
"Could not find suitable location for your output. Please subscribe your input dataset (if any) to a suitable location or change application.se_name to a suitable space token"
)
# srmv2 sites special treatment: the space token has been prefixed to the outputlocation and must be removed now:
imin = string.find(outputlocation, "token:")
imax = string.find(outputlocation, "srm:")
spacetoken = ""
if imin > -1 and imax > -1:
spacetoken = outputlocation[imin + 6:imax - 1]
outputlocation = outputlocation[imax:]
# same treatment for backup location if any
imin = string.find(backuplocation, "token:")
imax = string.find(backuplocation, "srm:")
bst = ""
if imin > -1 and imax > -1:
bst = backuplocation[imin + 6:imax - 1]
backuplocation = backuplocation[imax:]
environment["OUTLFC"] = outlfc
environment["OUTSITE"] = outsite
if outse:
environment[
"OUTSITE"] = outse # user's choice for output storage location overriding AthenaMC's.
environment["OUTPUT_LOCATION"] = outputlocation
if spacetoken:
environment["SPACETOKEN"] = spacetoken
if backup:
environment["OUTLFC2"] = outlfc2
environment["OUTSITE2"] = backup
environment["OUTPUT_LOCATION2"] = backuplocation
environment["PROD_RELEASE"] = app.prod_release
# setting environment["BACKEND"]
# Local, Condor become "batch". LSF becomes "batch" unless the inputdata is on castor (in this case, it becomes "castor")
environment["BACKEND"] = job.backend._name
environment["BACKEND_DATA"] = app.backend_inputdata
if job.backend._name == "LSF" and len(app.turls.values()) > 0:
turl = app.turls.values()[0]
if string.find(turl, "castor") > -1:
environment["BACKEND_DATA"] = "castor"
else:
environment["BACKEND_DATA"] = "batch"
if job.backend._name in ["Local", "Condor", "PBS"]:
environment["BACKEND_DATA"] = "batch"
environment["SITEROOT"] = os.environ["SITEROOT"]
environment["CMTSITE"] = os.environ["CMTSITE"]
# finalise environment
# preparing input sandbox, output sandbox , environment vars and job requirements
inputbox = [
File(os.path.join(os.path.dirname(__file__), 'setup-release.sh')),
File(os.path.join(os.path.dirname(__file__), 'stage-in.sh')),
File(os.path.join(os.path.dirname(__file__), 'stage-out.sh')),
File(os.path.join(os.path.dirname(__file__), 'adler32.py'))
]
if os.path.exists(app.transform_archive):
# must add a condition on size.
inputbox += [File(app.transform_archive)]
elif app.transform_archive:
# tarball in local or remote web area.
if string.find(app.transform_archive, "http") >= 0:
environment['TRANSFORM_ARCHIVE'] = "%s" % (
app.transform_archive)
else:
myfile = os.path.basename(app.transform_archive)
myfile = "http://cern.ch/atlas-computing/links/kitsDirectory/Production/kits/" + myfile
environment['TRANSFORM_ARCHIVE'] = "%s" % (myfile)
if app.evgen_job_option and os.path.exists(app.evgen_job_option):
# locally modified job option file to add to the input sand box
inputbox += [File(app.evgen_job_option)]
# need to strip the path away.
self.evgen_job_option = app.evgen_job_option.split("/")[-1]
environment['CUSTOM_JOB_OPTION'] = "%s" % (self.evgen_job_option)
elif app.evgen_job_option:
self.evgen_job_option = app.evgen_job_option
# user area:
if app.userarea:
inputbox.append(File(app.userarea))
environment['USER_AREA'] = os.path.basename(app.userarea)
if (job.inputsandbox):
for file in job.inputsandbox:
inputbox += [file]
outputbox = []
outputGUIDs = 'output_guids'
outputLOCATION = 'output_location'
outputbox.append(outputGUIDs)
outputbox.append(outputLOCATION)
outputbox.append('output_data')
if (job.outputsandbox):
for file in job.outputsandbox:
outputbox += [file]
# switch JobTransforms/AtlasProduction package.
self.isJT = string.find(app.transform_archive, "JobTransform")
if self.isJT > -1 and app.mode == "evgen":
environment['T_CONTEXT'] = str(
self.number_events_job
) # needed to avoid prodsys failure mechanism based on a hardcoded minimum number of event of 5000 per job
# prepare job requirements
if hasattr(job.backend, 'requirements') and hasattr(
job.backend.requirements, 'sites') and hasattr(
job.backend.requirements, 'software') and hasattr(
job.backend.requirements, 'other'):
requirements = job.backend.requirements
else:
requirements = AtlasLCGRequirements()
# requirements.other.append('other.GlueCEStateStatus=="Production"') # missing production
imax = string.rfind(app.atlas_rel, ".")
rel = string.atof(
app.atlas_rel[:imax]
) # to deal with string comparisons: [2-9].0.0 > 11.0.0.
if app.atlas_rel <= "11.4.0" or rel <= 11.4:
requirements.software = ['VO-atlas-release-%s' % app.atlas_rel]
elif app.atlas_rel < "12.0.3":
requirements.software = ['VO-atlas-offline-%s' % app.atlas_rel]
elif app.atlas_rel >= "14.0.0" and app.atlas_rel <= "15.6.1":
requirements.software = [
'VO-atlas-offline-%s-i686-slc4-gcc34-opt' % app.atlas_rel
]
elif app.atlas_rel > "15.6.1":
requirements.software = [
'VO-atlas-offline-%s-i686-slc5-gcc43-opt' % app.atlas_rel
]
else:
requirements.software = ['VO-atlas-production-%s' % app.atlas_rel]
# case of prod_release set
if app.prod_release:
# no prod release tag before 13.0.X
if app.atlas_rel < "14.0.0" and app.atlas_rel > "13.0.0":
requirements.software = [
'VO-atlas-production-%s' % app.prod_release
]
elif app.atlas_rel >= "14.0.0" and app.atlas_rel <= "15.6.1":
requirements.software = [
'VO-atlas-production-%s-i686-slc4-gcc34-opt' %
app.prod_release
]
elif app.atlas_rel > "15.6.1":
requirements.software = [
'VO-atlas-production-%s-i686-slc5-gcc43-opt' %
app.prod_release
]
if app.transform_archive and string.find(app.transform_archive,
"AtlasTier0") > -1:
requirements.software = ['VO-atlas-tier0-%s' % app.prod_release]
## extraConfig=getConfig('defaults_AtlasLCGRequirements')
## if 'dq2client_version' in extraConfig:
## dq2client_version = extraConfig['dq2client_version']
## if job.backend.requirements.dq2client_version:
## dq2client_version = job.backend.requirements.dq2client_version
## try:
## assert dq2client_version!=""
## except:
## raise ApplicationConfigurationError(None,"Please give a value to dq2client_version in job.backend.requirements.")
# requirements.software += ['VO-atlas-dq2clients-%s' % dq2client_version]
# requirements.other+=['RegExp("VO-atlas-dq2clients",other.GlueHostApplicationSoftwareRunTimeEnvironment)']
# controlled relaxation for simple cases: one single input dataset, less than 200 subjobs. In this case, the subjobs can be submitted to the whole cloud.
loosematch = "true"
if job.splitter and job.splitter.numsubjobs > 200:
loosematch = "false"
if job.inputdata and (job.inputdata.cavern or job.inputdata.minbias):
loosematch = "false"
# commented the nex block out as stage-in.sh can now ensure that the local copy is downloaded in the first attempt. However, as a safety net, we maintain the veto on complex jobs with pileup and or minbias, because they are heavy weight anyway and should not be run everywhere.
# if app.dbrelease:
# loosematch="false"
if len(job.backend.requirements.sites) > 0:
loosematch = "false" # specified sites take precedence over cloud.
userCloud = job.backend.requirements.cloud
if userCloud == 'ALL':
userCloud = '' # not supporting the AthenaLCGRequirements catch-all
# By default: job to data, strict: target outsite and nothing else.
requirements.sites = outsite
if loosematch == "true" and userCloud:
logger.debug(
"Your job qualifies for controlled relaxation of the current job-to-data policy. Now checking that requested cloud matches with input data"
)
from dq2.info.TiersOfATLAS import whichCloud, ToACache
targetSites = whichCloud(outsite)
cloud = ""
for cloudID, sites in ToACache.dbcloud.iteritems():
if sites == targetSites:
cloud = cloudID
try:
assert cloud == userCloud
except:
raise ApplicationConfigurationError(
None,
"Requested cloud: %s did not match selected processing cloud: %s. Reverting to submission to site %s"
% (userCloud, cloud, outsite))
requirements.cloud = cloud
# looks like cloud has to be converted in a list of sites anyway, and this is not done in AtlasLCGRequirements.convert()...
allsites = requirements.list_sites_cloud()
try:
assert len(allsites) > 0
except:
raise ApplicationConfigurationError(
None,
"Could not get any sites from the specified cloud: %s. You will have to specify a target site in job.backend.requirements.sites"
% cloud)
# need to weed out unwanted sites from excluded list
excludedSites = requirements.excluded_sites
goodsites = []
for checksite in allsites:
selsite = True
for site in excludedSites:
imax = site.find("_")
shortSite = site[:imax]
if shortSite in checksite:
# print "site is excluded, skipping ", checksite
selsite = False
break
if selsite and checksite not in goodsites:
goodsites.append(checksite)
# print len(allsites),len(goodsites)
if len(goodsites) > 0:
allsites = goodsites
job.backend.requirements.sites = allsites
logger.debug(
"Relaxing job to data policy to job to cloud. Selected cloud is %s"
% cloud)
logger.debug("master job submit?")
if job.backend._name == "LCG" or job.backend._name == "Cronus" or job.backend._name == "Condor" or job.backend._name == "NG":
return LCGJobConfig("", inputbox, [], outputbox, environment, [],
requirements)
else:
return StandardJobConfig("", 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("TagPrepareLCGRTHandler prepare called, %s", job.id)
# prepare inputdata
input_files = []
input_guids = []
if job.inputdata:
# check for subjobs
if job._getRoot().subjobs:
if job.inputdata._name == 'ATLASLocalDataset':
if not job.inputdata.names:
raise ApplicationConfigurationError(
None, 'No inputdata has been specified.')
input_files = job.inputdata.names
elif job.inputdata._name == 'DQ2Dataset':
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
job.inputdata.type = 'DQ2_COPY'
else:
if job.inputdata._name == 'ATLASLocalDataset':
input_files = ATLASLocalDataset.get_filenames(app)
elif job.inputdata._name == 'DQ2Dataset':
job.inputdata.type = 'DQ2_COPY'
input_guids, input_files = _splitlist(
job.inputdata.get_contents())
job.inputdata.names = input_files
job.inputdata.guids = input_guids
if job.outputdata:
raise ApplicationConfigurationError(
None, 'No outputdata required for TagPrepare job.')
if job._getRoot().subjobs:
jid = "%d.%d" % (job._getRoot().id, job.id)
else:
jid = "%d" % job.id
if getConfig('LCG')['JobLogHandler'] == 'DQ2':
raise ApplicationConfigurationError(
None,
'Staging of log files in DQ2 requested but not possible for TagPrepare.'
)
# prepare inputsandbox
inputbox = [
File(os.path.join(__athdirectory__, 'athena-utility.sh')),
File(os.path.join(__directory__, 'get_tag_info.py'))
]
if input_guids:
_append_file_buffer(inputbox, 'input_guids', input_guids)
if input_files:
_append_file_buffer(inputbox, 'input_files', input_files)
exe = os.path.join(__directory__, 'run-tagprepare-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
output_location = ''
environment['OUTPUT_LOCATION'] = output_location
environment['ATLASOutputDatasetLFC'] = config['ATLASOutputDatasetLFC']
# Fix DATASETNAME env variable for DQ2_COPY mode
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
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)
# Work around for glite WMS spaced environement variable problem
inputbox.append(
FileBuffer('athena_options', environment['ATHENA_OPTIONS'] + '\n'))
# append a property for monitoring to the jobconfig of subjobs
lcg_config = LCGJobConfig(File(exe), inputbox, [], outputbox,
environment, [], requirements)
return lcg_config
def master_prepare(self, app, appconfig):
"""Prepare the master job"""
job = app._getParent() # Returns job or subjob object
logger.debug('TagPrepareLCGRTHandler master_prepare called: %s',
job.id)
self.username = gridProxy.identity(safe=True)
# Check if all sites are in the same cloud
if job.backend.requirements.sites:
firstCloud = whichCloud(job.backend.requirements.sites[0])
for site in job.backend.requirements.sites:
cloud = whichCloud(site)
if cloud != firstCloud:
printout = 'Job submission failed ! Site specified with j.backend.requirements.sites=%s are not in the same cloud !' % (
job.backend.requirements.sites)
raise ApplicationConfigurationError(None, printout)
# prepare input sandbox
inputbox = [(File(os.path.join(__athdirectory__,
'athena-utility.sh'))),
(File(os.path.join(__directory__, 'get_tag_info.py')))]
# CN: added TNTJobSplitter clause
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
_append_files(
inputbox,
os.path.join(__athdirectory__, 'ganga-stage-in-out-dq2.py'),
os.path.join(__athdirectory__, 'dq2_get'),
os.path.join(__athdirectory__, 'dq2info.tar.gz'))
## insert more scripts to inputsandbox for FileStager
if job.inputdata and job.inputdata._name == 'DQ2Dataset' and job.inputdata.type in [
'FILE_STAGER'
]:
_append_files(inputbox, 'make_filestager_joption.py', 'dm_util.py',
'fs-copy.py')
#_append_files(inputbox,'make_filestager_joption.py','dm_util.py')
# add libDCache.so and libRFIO.so to fix broken access in athena 12.0.x
if not 'ganga-stage-in-out-dq2.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(
inputbox,
os.path.join(__athdirectory__, 'ganga-stage-in-out-dq2.py'))
if not 'dq2tracerreport.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox,
os.path.join(__athdirectory__, 'dq2tracerreport.py'))
if not 'db_dq2localid.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox,
os.path.join(__athdirectory__, 'db_dq2localid.py'))
if not 'getstats.py' in [
os.path.basename(file.name) for file in inputbox
]:
_append_files(inputbox,
os.path.join(__athdirectory__, 'getstats.py'))
_append_files(inputbox, os.path.join(__athdirectory__, 'libdcap.so'))
if job.inputsandbox: inputbox += job.inputsandbox
# prepare environment
environment = {
'MAXNUMREFS': str(app.max_num_refs),
'STREAM_REF': app.stream_ref,
'ATLAS_RELEASE': app.atlas_release,
'ATHENA_OPTIONS': '',
'ATHENA_USERSETUPFILE': '',
'ATLAS_PROJECT': '',
'ATLAS_EXETYPE': 'ATHENA',
'GANGA_VERSION': configSystem['GANGA_VERSION']
}
environment['DCACHE_RA_BUFFER'] = config['DCACHE_RA_BUFFER']
requirements = AtlasLCGRequirements()
if job.inputdata and job.inputdata._name == 'DQ2Dataset':
if job.inputdata.dataset:
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
if job.inputdata.failover:
environment['DATASETFAILOVER'] = 1
environment['DATASETDATATYPE'] = job.inputdata.datatype
if job.inputdata.accessprotocol:
environment[
'DQ2_LOCAL_PROTOCOL'] = job.inputdata.accessprotocol
if job.inputdata.check_md5sum:
environment['GANGA_CHECKMD5SUM'] = 1
else:
raise ApplicationConfigurationError(
None,
'j.inputdata.dataset is empty - DQ2 dataset name needs to be specified.'
)
# Raise submission exception
if (not job.backend.CE and not (job.backend.requirements._name
== 'AtlasLCGRequirements'
and job.backend.requirements.sites)
and not (job.splitter
and job.splitter._name == 'DQ2JobSplitter')
and not (job.splitter
and job.splitter._name == 'TNTJobSplitter')
and not (job.splitter
and job.splitter._name == 'AnaTaskSplitterJob')):
raise ApplicationConfigurationError(
None,
'Job submission failed ! Please use DQ2JobSplitter or specify j.backend.requirements.sites or j.backend.requirements.CE !'
)
if job.inputdata.match_ce_all or job.inputdata.min_num_files > 0:
raise ApplicationConfigurationError(
None,
'Job submission failed ! Usage of j.inputdata.match_ce_all or min_num_files is obsolete ! Please use DQ2JobSplitter or specify j.backend.requirements.sites or j.backend.requirements.CE !'
)
#if job.inputdata.number_of_files and (job.splitter and job.splitter._name == 'DQ2JobSplitter'):
# allLoc = job.inputdata.get_locations(complete=0)
# completeLoc = job.inputdata.get_locations(complete=1)
# incompleteLoc = []
# for loc in allLoc:
# if loc not in completeLoc:
# incompleteLoc.append(loc)
# if incompleteLoc:
# raise ApplicationConfigurationError(None,'Job submission failed ! Dataset is incomplete ! Usage of j.inputdata.number_of_files and DQ2JobSplitter is not allowed for incomplete datasets !')
# prepare job requirements
cmtconfig = app.atlas_cmtconfig
if not cmtconfig in ['i686-slc4-gcc34-opt', 'i686-slc5-gcc43-opt']:
cmtconfig = 'i686-slc4-gcc34-opt'
requirements.software = [
'VO-atlas-offline-%s-%s' % (app.atlas_release, cmtconfig)
]
# add software requirement of dq2clients
if job.inputdata and job.inputdata.type in [
'DQ2_DOWNLOAD', 'TNT_DOWNLOAD', 'DQ2_COPY', 'FILE_STAGER'
]:
try:
# override the default one if the dq2client_version is presented
# in the job backend's requirements object
dq2client_version = job.backend.requirements.dq2client_version
except AttributeError:
pass
if dq2client_version:
requirements.software += [
'VO-atlas-dq2clients-%s' % dq2client_version
]
environment['DQ2_CLIENT_VERSION'] = dq2client_version
# jobscript
exe = os.path.join(__directory__, 'run-tagprepare-lcg.sh')
#exe = os.path.join(__directory__,'get_tag_info.py')
# output sandbox
outputbox = ['taginfo.pkl']
if job.outputsandbox: outputbox += job.outputsandbox
return LCGJobConfig(File(exe), inputbox, [], outputbox, environment,
[], requirements)
def prepare(self, app, appconfig, appmasterconfig, jobmasterconfig):
from Ganga.Lib.LCG import LCGJobConfig
return LCGJobConfig(app._scriptname,
app._getParent().inputsandbox, [],
app._getParent().outputsandbox, app.env)
def prepare(self,app,appconfig,appmasterconfig,jobmasterconfig):
"""Prepare the job"""
inputbox=[ ]
# prepare environment
environment={}
environment=jobmasterconfig.env.copy()
environment["INPUTDATASETS"]=""
environment["INPUTFILES"]=""
environment["INPUTTURLS"]=""
alllfns=app.inputfiles+app.cavernfiles+app.mbfiles+app.dbfiles
guids=app.turls
guids.update(app.cavern_turls)
guids.update(app.minbias_turls)
guids.update(app.dbturls)
infilenr=0
for infile in alllfns:
environment["INPUTFILES"]+="lfn[%d]='%s';" %(infilenr,infile)
environment["INPUTDATASETS"]+="dset[%d]='%s';"%(infilenr,app.dsetmap[infile])
## insites=app.sitemap[infile]
## # compare with environment["OUTSITE"] and reorder if needed.
## newinsites=self.sortSites(insites,environment["OUTSITE"])
## environment["INPUTSITES"]+="site[%d]='%s';"%(infilenr,newinsites)
environment["INPUTTURLS"]+="turl[%d]='%s';"%(infilenr,guids[infile])
infilenr += 1
logger.debug("%s %s %s" % (str(environment["INPUTDATASETS"]),str(environment["INPUTTURLS"]),str(environment["INPUTFILES"])))
if environment["INPUTDATASETS"] :
# Work around for glite WMS spaced environement variable problem
inputbox += [ FileBuffer('inputdsets.conf',environment['INPUTDATASETS']+'\n') ]
if environment["INPUTTURLS"] :
# Work around for glite WMS spaced environement variable problem
inputbox += [ FileBuffer('inputturls.conf',environment['INPUTTURLS']+'\n') ]
if environment["INPUTFILES"] :
# Work around for glite WMS spaced environement variable problem
inputbox += [ FileBuffer('inputfiles.conf',environment['INPUTFILES']+'\n') ]
# now doing output files....
job = app._getParent() # Returns job or subjob object
outfilelist=""
for type in app.outputpaths.keys():
if type=="LOG" and "LOG" not in job.outputdata.outrootfiles:
# logfiles are no longer saved in DQ2 datasets unless they are explicitly named in the outrootfiles dictionnary
continue
outfilelist+=app.outputpaths[type]+app.subjobsOutfiles[job.id][type]+" "
environment["OUTPUTFILES"]=outfilelist
# Work around for glite WMS spaced environement variable problem
inputbox += [ FileBuffer('outputfiles.conf',environment['OUTPUTFILES']+'\n') ]
# setting up job wrapper arguments.
args=app.args
trfargs=' '.join(app.args[4:])
inputbox += [ FileBuffer('trfargs.conf',trfargs+'\n') ]
jid=""
if job._getRoot().subjobs:
jid = job._getRoot().id
else:
jid = "%d" % job.id
environment["OUTPUT_JOBID"]=str(jid) # used for versionning
if app.dryrun:
environment["DRYRUN"] = "TRUE"
if app.dbrelease:
environment["ATLASDBREL"]=app.dbrelease
inputdata = []
filename="wrapper.sh"
exe = os.path.join(os.path.dirname(__file__),filename)
# output sandbox
outputbox =jobmasterconfig.outputbox
if job.backend._name=="LCG" or job.backend._name=="Cronus" or job.backend._name=="Condor" or job.backend._name=="NG" or job.backend._name=="SGE":
logger.debug("submission to %s" % job.backend._name)
# prepare job requirements
requirements = jobmasterconfig.requirements
if "INPUTTURLS" in environment:
logger.debug(environment["INPUTTURLS"])
if string.find(environment["INPUTTURLS"],"file:")>=0:
raise ApplicationConfigurationError(None,"Input file was found to be local, and LCG backend does not support replication of local files to the GRID yet. Please register your input dataset in DQ2 before resubmitting this job. Aborting")
if string.lower(app.se_name)=="local":
raise ApplicationConfigurationError(None,"Output file cannot be committed to local filesystem on a grid job. Please change se_name")
lcg_job_config = LCGJobConfig(File(exe),inputbox,args,outputbox,environment,inputdata,requirements)
lcg_job_config.monitoring_svc = mc['AthenaMC/LCG']
return lcg_job_config
else:
logger.debug("Backend %s not fully supported , will try our best anyway..." % job.backend._name)
# if there are input data files and they are on the grid, prestage them on local area (use either app.datasets.input_dataset or /tmp/$login/data (and update environment["INPUTFILE"] accordingly inf the later is used...)
# later development....
return StandardJobConfig(File(exe),inputbox,args,outputbox,environment)
