def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiExec): This application is only expected to handle GaudiExec Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
if not isinstance(app.uploadedInput, DiracFile):
generateDiracInput(app)
assert isinstance(app.uploadedInput, DiracFile), "Failed to upload needed file, aborting submit"
rep_data = app.uploadedInput.getReplicas()
assert rep_data != {}, "Failed to find a replica, aborting submit"
if isinstance(app.jobScriptArchive, (DiracFile, LocalFile)):
app.jobScriptArchive = None
generateDiracScripts(app)
assert isinstance(app.jobScriptArchive, DiracFile), "Failed to upload needed file, aborting submit"
rep_data = app.jobScriptArchive.getReplicas()
assert rep_data != {}, "Failed to find a replica, aborting submit"
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiExec): This application is only expected to handle GaudiExec Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
if not isinstance(app.uploadedInput, DiracFile):
generateDiracInput(app)
assert isinstance(app.uploadedInput, DiracFile), "Failed to upload needed file, aborting submit. Tried to upload to: %s\nIf your Ganga installation is not at CERN your username may be trying to create a non-existent LFN. Try setting the 'DIRAC' configuration 'DiracLFNBase' to your grid user path.\n" % DiracFile.diracLFNBase()
rep_data = app.uploadedInput.getReplicas()
assert rep_data != {}, "Failed to find a replica, aborting submit"
if isinstance(app.jobScriptArchive, (DiracFile, LocalFile)):
app.jobScriptArchive = None
generateDiracScripts(app)
assert isinstance(app.jobScriptArchive, DiracFile), "Failed to upload needed file, aborting submit"
rep_data = app.jobScriptArchive.getReplicas()
assert rep_data != {}, "Failed to find a replica, aborting submit"
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def configure(self, master_appconfig):
## strip leading and trailing blanks from arguments
self.arguments = [ a.strip() for a in self.arguments ]
## strip leading and trailing blanks from the command
self.commands = [ a.strip() for a in self.commands ]
## the script layout
the_script = layout.format (
scripts = [ os.path.join ( f.subdir , os.path.basename ( f.name ) ) for f in self.scripts ] ,
arguments = self.arguments ,
command = self.commands
)
# add summary.xml
outputsandbox_temp = XMLPostProcessor._XMLJobFiles()
outputsandbox_temp += unique(self.getJobObject().outputsandbox)
outputsandbox = unique(outputsandbox_temp)
input_files = []
input_files += [ FileBuffer('gaudipython-wrapper.py', the_script ) ]
logger.debug("Returning StandardJobConfig")
return (None, StandardJobConfig(inputbox=input_files,
outputbox=outputsandbox))
def sandbox_prepare(app, appsubconfig, appmasterconfig, jobmasterconfig):
logger.debug("RTUTils sandbox_prepare")
job = stripProxy(app).getJobObject()
# Add the job.in/outputsandbox as splitters create subjobs that are
# seperate Job objects and therefore have their own job.in/outputsandbox
# which is NOT in general copied from the master in/outputsandbox
# inputsandbox = job.inputsandbox[:] # copied in splitter
#outputsandbox = job.outputsandbox[:]
inputsandbox = []
outputsandbox = []
# Here add any sandbox files coming from the appsubconfig
# currently none. masterjobconfig inputsandbox added automatically
if appsubconfig:
inputsandbox += appsubconfig.getSandboxFiles()
# Strangly NEITHER the master outputsandbox OR job.outputsandbox
# are added automatically.
if jobmasterconfig:
outputsandbox += jobmasterconfig.getOutputSandboxFiles()
if appsubconfig:
outputsandbox += appsubconfig.getOutputSandboxFiles()
return unique(inputsandbox), unique(outputsandbox)
def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiExec): This application is only expected to handle GaudiExec Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
inputsandbox, outputsandbox = master_sandbox_prepare(
app, appmasterconfig)
if isinstance(app.jobScriptArchive, LocalFile):
app.jobScriptArchive = None
generateJobScripts(app, appendJobScripts=True)
scriptArchive = os.path.join(app.jobScriptArchive.localDir,
app.jobScriptArchive.namePattern)
inputsandbox.append(File(name=scriptArchive))
if app.getMetadata:
logger.info("Adding options to make the summary.xml")
inputsandbox.append(
FileBuffer(
'summary.py',
"\nfrom Gaudi.Configuration import *\nfrom Configurables import LHCbApp\nLHCbApp().XMLSummary='summary.xml'"
))
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def configure(self, master_appconfig):
# self._configure()
modulename = split(self.module.name)[-1].split('.')[0]
script = """
from copy import deepcopy
from Gaudi.Configuration import *
importOptions('data.py')
import %s as USERMODULE
EventSelectorInput = deepcopy(EventSelector().Input)
FileCatalogCatalogs = deepcopy(FileCatalog().Catalogs)
EventSelector().Input=[]
FileCatalog().Catalogs=[]\n""" % modulename
script_configure = "USERMODULE.configure(EventSelectorInput,FileCatalogCatalogs%s)\n"
if self.params:
param_string = ",params=%s" % self.params
else:
param_string = ""
script_configure = script_configure % param_string
script += script_configure
script += "USERMODULE.run(%d)\n" % self.events
script += getXMLSummaryScript()
# add summary.xml
outputsandbox_temp = XMLPostProcessor._XMLJobFiles()
outputsandbox_temp += unique(self.getJobObject().outputsandbox)
outputsandbox = unique(outputsandbox_temp)
input_files = []
input_files += [FileBuffer('gaudipython-wrapper.py', script)]
logger.debug("Returning StandardJobConfig")
return (None, StandardJobConfig(inputbox=input_files,
outputbox=outputsandbox))
def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiExec): This application is only expected to handle GaudiExec Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
# If we are getting the metadata we need to make sure the summary.xml is added to the output sandbox if not there already.
if app.getMetadata and not 'summary.xml' in outputsandbox:
outputsandbox += ['summary.xml']
if not isinstance(app.uploadedInput, DiracFile):
generateDiracInput(app)
assert isinstance(app.uploadedInput, DiracFile), "Failed to upload needed file, aborting submit. Tried to upload to: %s\nIf your Ganga installation is not at CERN your username may be trying to create a non-existent LFN. Try setting the 'DIRAC' configuration 'DiracLFNBase' to your grid user path.\n" % DiracFile.diracLFNBase()
rep_data = app.uploadedInput.getReplicas()
assert rep_data != {}, "Failed to find a replica, aborting submit"
if isinstance(app.jobScriptArchive, (DiracFile, LocalFile)):
app.jobScriptArchive = None
generateDiracScripts(app)
assert isinstance(app.jobScriptArchive, DiracFile), "Failed to upload needed file, aborting submit"
rep_data = app.jobScriptArchive.getReplicas()
assert rep_data != {}, "Failed to find a replica, aborting submit"
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def sandbox_prepare(app, appsubconfig, appmasterconfig, jobmasterconfig):
logger.debug("RTUTils sandbox_prepare")
job = app.getJobObject()
# Add the job.in/outputsandbox as splitters create subjobs that are
# seperate Job objects and therefore have their own job.in/outputsandbox
# which is NOT in general copied from the master in/outputsandbox
# inputsandbox = job.inputsandbox[:] # copied in splitter
# outputsandbox = job.outputsandbox[:]
inputsandbox = []
outputsandbox = []
# Here add any sandbox files coming from the appsubconfig
# currently none. masterjobconfig inputsandbox added automatically
if appsubconfig:
inputsandbox += appsubconfig.getSandboxFiles()
# Strangly NEITHER the master outputsandbox OR job.outputsandbox
# are added automatically.
if jobmasterconfig:
outputsandbox += jobmasterconfig.getOutputSandboxFiles()
if appsubconfig:
outputsandbox += appsubconfig.getOutputSandboxFiles()
return unique(inputsandbox), unique(outputsandbox)
def configure(self, master_appconfig):
## strip leading and trailing blanks from arguments
self.arguments = [ a.strip() for a in self.arguments ]
## strip leading and trailing blanks from the command
self.commands = [ a.strip() for a in self.commands ]
## the script layout
the_script = layout.format (
scripts = [ os.path.join ( f.subdir , os.path.basename ( f.name ) ) for f in self.scripts ] ,
imports = [ os.path.join ( f.subdir , os.path.basename ( f.name ) ) for f in self.imports ] ,
arguments = self.arguments ,
command = self.commands
)
print 'SCRIPT:\n', the_script
# add summary.xml
outputsandbox_temp = XMLPostProcessor._XMLJobFiles()
outputsandbox_temp += unique(self.getJobObject().outputsandbox)
outputsandbox = unique(outputsandbox_temp)
input_files = []
input_files += [ FileBuffer('gaudipython-wrapper.py', the_script ) ]
logger.debug("Returning StandardJobConfig")
return (None, StandardJobConfig(inputbox=input_files,
outputbox=outputsandbox))
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig, ['inputsandbox'])
# add summary.xml
outputsandbox += ['summary.xml', '__parsedxmlsummary__']
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig, ['inputsandbox'])
# add summary.xml
outputsandbox += ['summary.xml', '__parsedxmlsummary__']
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
"""
This function prepares the application of a master job during submit. A priori we aren't doing anything with this in Im3ShapeApp but until this is understood I'd rather not remove it
Args:
app (IApplication): This is the application given in the master job
appasterconfig (tuple): This is the configuration which is to prepare the app in the master job # TODO check type and this interface
"""
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiExec): This application is only expected to handle GaudiExec Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
cred_req = app.getJobObject().backend.credential_requirements
check_creds(cred_req)
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
# If we are getting the metadata we need to make sure the summary.xml is added to the output sandbox if not there already.
if app.getMetadata and not 'summary.xml' in outputsandbox:
outputsandbox += ['summary.xml']
# Check a previously uploaded input is there in case of a job copy
if isinstance(app.uploadedInput, DiracFile):
if app.uploadedInput.getReplicas() == {}:
app.uploadedInput = None
logger.info("Previously uploaded cmake target missing from Dirac. Uploading it again.")
if not isinstance(app.uploadedInput, DiracFile):
generateDiracInput(app)
try:
assert isinstance(app.uploadedInput, DiracFile)
except AssertionError:
raise ApplicationPrepareError("Failed to upload needed file, aborting submit. Tried to upload to: %s\nIf your Ganga installation is not at CERN your username may be trying to create a non-existent LFN. Try setting the 'DIRAC' configuration 'DiracLFNBase' to your grid user path.\n" % DiracFile.diracLFNBase(cred_req))
rep_data = app.uploadedInput.getReplicas()
try:
assert rep_data != {}
except AssertionError:
raise ApplicationPrepareError("Failed to find a replica of uploaded file, aborting submit")
if isinstance(app.jobScriptArchive, (DiracFile, LocalFile)):
app.jobScriptArchive = None
generateDiracScripts(app)
try:
assert isinstance(app.jobScriptArchive, DiracFile)
except AssertionError:
raise ApplicationPrepareError("Failed to upload needed file, aborting submit")
rep_data = app.jobScriptArchive.getReplicas()
try:
assert rep_data != {}
except AssertionError:
raise ApplicationPrepareError("Failed to find a replica, aborting submit")
#Create a replica of the job and scripts files
replicateJobFile(app.jobScriptArchive)
replicateJobFile(app.uploadedInput)
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
"""
This function prepares the application of a master job during submit. A priori we aren't doing anything with this in Im3ShapeApp but until this is understood I'd rather not remove it
Args:
app (IApplication): This is the application given in the master job
appasterconfig (tuple): This is the configuration which is to prepare the app in the master job # TODO check type and this interface
"""
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig, ["inputsandbox"])
# add summary.xml
outputsandbox += ["summary.xml", "__parsedxmlsummary__"]
logger.debug("Master Prepare LHCbGaudiDiracRunTimeHandler")
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
if type(app.exe) == File:
input_dir = app.getJobObject().getInputWorkspace().getPath()
exefile = os.path.join(input_dir, os.path.basename(app.exe.name))
if not os.path.exists(exefile):
msg = 'Executable: "%s" must exist!' % str(exefile)
raise ApplicationConfigurationError(None, msg)
os.system('chmod +x %s' % exefile)
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiRun): This application is only expected to handle GaudiRun Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
WarnUsers()
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig, appmasterconfig, jobmasterconfig)
run_script = self.__create_run_script(
app, appsubconfig, appmasterconfig, jobmasterconfig, inputsandbox, outputsandbox
)
return StandardJobConfig(
FileBuffer("gaudi-script.py", run_script, executable=1),
inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox),
)
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(
app, appmasterconfig)
if type(app.exe) == File:
exefile = os.path.join(get_share_path(app),
os.path.basename(app.exe.name))
if not os.path.exists(exefile):
msg = 'Executable must exist!'
raise ApplicationConfigurationError(None, msg)
os.system('chmod +x %s' % exefile)
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(
app, appmasterconfig)
if type(app.exe) == File:
input_dir = app.getJobObject().getInputWorkspace().getPath()
exefile = os.path.join(input_dir, os.path.basename(app.exe.name))
if not os.path.exists(exefile):
msg = 'Executable: "%s" must exist!' % str(exefile)
raise ApplicationConfigurationError(None, msg)
os.system('chmod +x %s' % exefile)
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
logger.debug("Master Prepare")
inputsandbox, outputsandbox = master_sandbox_prepare(
app, appmasterconfig, ['inputsandbox'])
# add summary.xml
outputsandbox += ['summary.xml', '__parsedxmlsummary__']
logger.debug("Master Prepare LHCbGaudiDiracRunTimeHandler")
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_sandbox_prepare(app, appmasterconfig, sharedir_roots=None):
if sharedir_roots is None:
sharedir_roots = ['']
logger.debug("RTUTils master_sandbox_prepare")
# catch errors from not preparing properly
if not hasattr(stripProxy(app), 'is_prepared') or app.is_prepared is None:
logger.warning('Application is not prepared properly')
if hasattr(stripProxy(app), 'is_prepared'):
logger.warning("app.is_prepared: %s" % str(app.is_prepared))
import traceback
traceback.print_stack()
raise GangaException(None, 'Application not prepared properly')
# Note EITHER the master inputsandbox OR the job.inputsandbox is added to
# the subjob inputsandbox depending if the jobmasterconfig object is present
# or not... Therefore combine the job.inputsandbox with appmasterconfig.
job = stripProxy(app).getJobObject()
# user added items from the interactive GPI
from Ganga.Utility.Config import getConfig
if not getConfig('Output')['ForbidLegacyInput']:
inputsandbox = job.inputsandbox[:]
else:
if len(job.inputsandbox) > 0:
from Ganga.GPIDev.Lib.Job import JobError
raise JobError(
"InputFiles have been requested but there are objects in the inputSandBox... Aborting Job Prepare!"
)
inputsandbox = []
for filepattern in getInputFilesPatterns(job)[0]:
inputsandbox.append(File(filepattern))
if len(inputsandbox) > 100:
logger.warning(
'InputSandbox exceeds maximum size (100) supported by the Dirac backend'
)
raise GangaException(None, 'InputSandbox exceed maximum size')
outputsandbox = getOutputSandboxPatterns(job) # job.outputsandbox[:]
# inputsandbox files stored in share_dir from prepare method
sharedir_handler(app, sharedir_roots, inputsandbox)
# Here add any sandbox files/data coming from the appmasterconfig
# from master_configure. Catch the case where None is passed (as in tests)
if appmasterconfig:
inputsandbox += appmasterconfig.getSandboxFiles()
outputsandbox += appmasterconfig.getOutputSandboxFiles()
return unique(inputsandbox), unique(outputsandbox)
def get_output(self, job):
'''Builds lists of output files and output data.'''
outputdata = [
f.namePattern for f in job.outputfiles
if outputFilePostProcessingOnWN(job, getName(f))
]
outsandbox = [
f.namePattern for f in job.outputfiles
if not outputFilePostProcessingOnWN(job, getName(f))
]
# if user put any files in both, remove them from the sandbox
for f in outsandbox:
if outputdata.count(f) != 0:
outsandbox.remove(f)
msg = 'User placed the file %s in both the outputsandbox and '
msg += 'outputdata. It will be removed from the sandbox.'
logger.warning(msg, f)
gaudi_outsandbox, gaudi_outputdata = self.get_output_files()
# handle (as best we can) any user supplied wildcards
datalist = [] # files in sandbox that match pattern in data
for f in outputdata:
datalist += fnmatch.filter(gaudi_outsandbox, f)
sandlist = [] # files in data that match sandbox pattern
for f in outsandbox:
sandlist += fnmatch.filter(gaudi_outputdata, f)
datadatalist = [] # files in data that match patterns in data
for f in outputdata:
datadatalist += fnmatch.filter(gaudi_outputdata, f)
# files in sandbox which match patterns in data -> data
for f in datalist:
gaudi_outputdata.append(f)
if f in gaudi_outsandbox:
gaudi_outsandbox.remove(f)
# files in data which match patterns in sandbox but not data -> sandbox
for f in sandlist:
if datalist.count(f) == 0 and datadatalist.count(f) == 0:
gaudi_outsandbox.append(f)
if f in gaudi_outputdata:
gaudi_outputdata.remove(f)
outsandbox += gaudi_outsandbox
outputdata += gaudi_outputdata
return unique(outsandbox), unique(outputdata)
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig,
appmasterconfig,
jobmasterconfig)
run_script = self.__create_run_script(app, appsubconfig,
appmasterconfig, jobmasterconfig,
inputsandbox, outputsandbox)
return StandardJobConfig(FileBuffer('gaudi-script.py',
run_script,
executable=1),
inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
inputsandbox, outputsandbox = sandbox_prepare(
app, appsubconfig, appmasterconfig, jobmasterconfig)
input_data, parametricinput_data = dirac_inputdata(app)
job = app.getJobObject()
outputfiles = [this_file.namePattern for this_file in job.outputfiles if isinstance(this_file, DiracFile)]
gaudi_script_path = os.path.join(
job.getInputWorkspace().getPath(), "gaudi-script.py")
script_generator(gaudi_script_template(),
#remove_unreplaced = False,
outputfile_path=gaudi_script_path,
PLATFORM=app.platform,
COMMAND='gaudirun.py' # ,
#OUTPUTFILESINJECTEDCODE = getWNCodeForOutputPostprocessing(job, ' ')
)
dirac_script = script_generator(diracAPI_script_template(),
DIRAC_IMPORT='from DIRAC.Interfaces.API.Dirac import Dirac',
DIRAC_JOB_IMPORT='from DIRAC.Interfaces.API.Job import Job',
DIRAC_OBJECT='Dirac()',
JOB_OBJECT='Job()',
NAME=mangle_job_name(app),
EXE=gaudi_script_path,
EXE_ARG_STR=' '.join(
[str(arg) for arg in app.args]),
EXE_LOG_FILE='Ganga_%s_%s.log' % (
app.appname, app.version),
INPUTDATA=input_data,
PARAMETRIC_INPUTDATA=parametricinput_data,
OUTPUT_SANDBOX=outputsandbox,
OUTPUTDATA=list(outputfiles),
OUTPUT_PATH="", # job.fqid,
OUTPUT_SE=getConfig(
'DIRAC')['DiracOutputDataSE'],
SETTINGS=diracAPI_script_settings(app),
DIRAC_OPTS=job.backend.diracOpts,
PLATFORM=app.platform,
# leave the sandbox for altering later as needs
# to be done in backend.submit to combine master.
# Note only using 2 #s as auto-remove 3
INPUT_SANDBOX='##INPUT_SANDBOX##'
)
return StandardJobConfig(dirac_script,
inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_sandbox_prepare(app, appmasterconfig, sharedir_roots=None):
if sharedir_roots is None:
sharedir_roots = ['']
logger.debug("RTUTils master_sandbox_prepare")
# catch errors from not preparing properly
if not hasattr(stripProxy(app), 'is_prepared') or app.is_prepared is None:
logger.warning('Application is not prepared properly')
if hasattr(stripProxy(app), 'is_prepared'):
logger.warning("app.is_prepared: %s" % str(app.is_prepared))
import traceback
traceback.print_stack()
raise GangaException(None, 'Application not prepared properly')
# Note EITHER the master inputsandbox OR the job.inputsandbox is added to
# the subjob inputsandbox depending if the jobmasterconfig object is present
# or not... Therefore combine the job.inputsandbox with appmasterconfig.
job = stripProxy(app).getJobObject()
# user added items from the interactive GPI
from Ganga.Utility.Config import getConfig
if not getConfig('Output')['ForbidLegacyInput']:
inputsandbox = job.inputsandbox[:]
else:
if len(job.inputsandbox) > 0:
from Ganga.GPIDev.Lib.Job import JobError
raise JobError("InputFiles have been requested but there are objects in the inputSandBox... Aborting Job Prepare!")
inputsandbox = []
for filepattern in getInputFilesPatterns(job)[0]:
inputsandbox.append(File(filepattern))
if len(inputsandbox) > 100:
logger.warning('InputSandbox exceeds maximum size (100) supported by the Dirac backend')
raise GangaException(None, 'InputSandbox exceed maximum size')
outputsandbox = getOutputSandboxPatterns(job) # job.outputsandbox[:]
# inputsandbox files stored in share_dir from prepare method
sharedir_handler(app, sharedir_roots, inputsandbox)
# Here add any sandbox files/data coming from the appmasterconfig
# from master_configure. Catch the case where None is passed (as in tests)
if appmasterconfig:
inputsandbox += appmasterconfig.getSandboxFiles()
outputsandbox += appmasterconfig.getOutputSandboxFiles()
return unique(inputsandbox), unique(outputsandbox)
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(
app, appmasterconfig)
# check file is set OK
if not app.script.name:
msg = 'Root.script.name must be set.'
raise ApplicationConfigurationError(msg)
sharedir_scriptpath = os.path.join(get_share_path(app),
os.path.basename(app.script.name))
if not os.path.exists(sharedir_scriptpath):
msg = 'Script must exist!'
raise ApplicationConfigurationError(msg)
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(
app, appmasterconfig)
# check file is set OK
if not app.script.name:
msg = 'Root.script.name must be set.'
raise ApplicationConfigurationError(None, msg)
sharedir_scriptpath = os.path.join(get_share_path(app),
os.path.basename(app.script.name))
if not os.path.exists(sharedir_scriptpath):
msg = 'Script must exist!'
raise ApplicationConfigurationError(None, msg)
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def dirac_inputdata(app, hasOtherInputData=False):
""" Construct the JDL component which requests the inputdata for a job
Args:
app (IApplication): app which belongs to the job of interest
hasOtherInputData (bool): This is used to stop BannedSites being added to the JDL structure through backend.settings
"""
job = app.getJobObject()
input_data = None
parametricinput_data = None
inputLFNs = []
input_data = None
parametricinput_data = None
if not job.inputdata and (not job.master or not job.master.inputdata):
return input_data, parametricinput_data
wanted_job = job
if not job.inputdata and job.master and job.master.inputdata is not None and job.master.inputdata:
wanted_job = job.master
inputLFNs = [
'LFN:' + this_file.lfn for this_file in wanted_job.inputdata
if isinstance(this_file, DiracFile)
]
# master job with a splitter reaching prepare, hence bulk submit
if not job.master and job.splitter:
parametricinput_data = dirac_parametric_split(app)
if parametricinput_data is not None and len(
parametricinput_data) > getConfig('DIRAC')['MaxDiracBulkJobs']:
raise BackendError(
'Dirac',
'Number of bulk submission jobs \'%s\' exceeds the maximum allowed \'%s\' if more are needed please modify your config. Note there is a hard limit in Dirac of currently 1000.'
% (len(parametricinput_data),
getConfig('DIRAC')['MaxDiracBulkJobs']))
# master job with no splitter or subjob already split proceed as normal
else:
input_data = inputLFNs
if 'Destination' not in job.backend.settings and not inputLFNs and not hasOtherInputData:
t1_sites = getConfig('DIRAC')['noInputDataBannedSites']
logger.info(
'Job has no inputdata (T1 sites will be banned to help avoid overloading them).'
)
if 'BannedSites' in job.backend.settings:
job.backend.settings['BannedSites'].extend(t1_sites)
job.backend.settings['BannedSites'] = unique(
job.backend.settings['BannedSites'])
else:
if t1_sites:
job.backend.settings['BannedSites'] = t1_sites[:]
if not input_data and not parametricinput_data:
input_data = inputLFNs
return input_data, parametricinput_data
def get_output(self, job):
'''Builds lists of output files and output data.'''
outputdata = [f.namePattern for f in job.outputfiles if outputFilePostProcessingOnWN(job, getName(f)) ]
outsandbox = [f.namePattern for f in job.outputfiles if not outputFilePostProcessingOnWN(job, getName(f)) ]
# if user put any files in both, remove them from the sandbox
for f in outsandbox:
if outputdata.count(f) != 0:
outsandbox.remove(f)
msg = 'User placed the file %s in both the outputsandbox and '
msg += 'outputdata. It will be removed from the sandbox.'
logger.warning(msg, f)
gaudi_outsandbox, gaudi_outputdata = self.get_output_files()
# handle (as best we can) any user supplied wildcards
datalist = [] # files in sandbox that match pattern in data
for f in outputdata:
datalist += fnmatch.filter(gaudi_outsandbox, f)
sandlist = [] # files in data that match sandbox pattern
for f in outsandbox:
sandlist += fnmatch.filter(gaudi_outputdata, f)
datadatalist = [] # files in data that match patterns in data
for f in outputdata:
datadatalist += fnmatch.filter(gaudi_outputdata, f)
# files in sandbox which match patterns in data -> data
for f in datalist:
gaudi_outputdata.append(f)
if f in gaudi_outsandbox:
gaudi_outsandbox.remove(f)
# files in data which match patterns in sandbox but not data -> sandbox
for f in sandlist:
if datalist.count(f) == 0 and datadatalist.count(f) == 0:
gaudi_outsandbox.append(f)
if f in gaudi_outputdata:
gaudi_outputdata.remove(f)
outsandbox += gaudi_outsandbox
outputdata += gaudi_outputdata
return unique(outsandbox), unique(outputdata)
def dirac_inputdata(app):
job = stripProxy(app).getJobObject()
input_data = None
parametricinput_data = None
inputLFNs = []
if hasattr(job.inputdata, "getLFNs"):
inputLFNs = job.inputdata.getLFNs()
if job.master:
logger.debug("job.master.inputdata: %s " % str(job.master.inputdata))
logger.debug("job.inputdata: %s" % str(job.inputdata))
if hasattr(job.inputdata, "getLFNs"):
logger.debug("getLFNs(): %s" % job.inputdata.getLFNs())
has_input_DiracFile = False
for this_file in job.inputfiles:
if isType(this_file, DiracFile):
has_input_DiracFile = True
break
if job.master and not has_input_DiracFile:
for this_file in job.master.inputfiles:
if isType(this_file, DiracFile):
has_input_DiracFile = True
break
if len(inputLFNs) > 0:
# master job with a splitter reaching prepare, hence bulk submit
if not job.master and job.splitter:
parametricinput_data = dirac_parametric_split(app)
if parametricinput_data is not None and len(parametricinput_data) > getConfig("DIRAC")["MaxDiracBulkJobs"]:
raise BackendError(
"Dirac",
"Number of bulk submission jobs '%s' exceeds the maximum allowed '%s' if more are needed please modify your config. Note there is a hard limit in Dirac of currently 1000."
% (len(parametricinput_data), getConfig("DIRAC")["MaxDiracBulkJobs"]),
)
# master job with no splitter or subjob already split proceed as normal
else:
input_data = job.inputdata.getLFNs()
elif "Destination" not in job.backend.settings and not has_input_DiracFile:
##THIS IS NOT VERY DIRAC CENTRIC
##PLEASE WHEN TIME MOVE TO LHCBDIRAC where T1 is more applicable rcurrie
##Also editing the settings on the fly is asking for potential problems, should avoid
t1_sites = getConfig("DIRAC")["noInputDataBannedSites"]
logger.info("Job has no inputdata (T1 sites will be banned to help avoid overloading them).")
if "BannedSites" in job.backend.settings:
job.backend.settings["BannedSites"].extend(t1_sites)
job.backend.settings["BannedSites"] = unique(job.backend.settings["BannedSites"])
else:
job.backend.settings["BannedSites"] = t1_sites[:]
# import traceback
# traceback.print_stack()
return input_data, parametricinput_data
def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiExec): This application is only expected to handle GaudiExec Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
if isinstance(app.jobScriptArchive, LocalFile):
app.jobScriptArchive = None
generateJobScripts(app, appendJobScripts=True)
scriptArchive = os.path.join(app.jobScriptArchive.localDir, app.jobScriptArchive.namePattern)
inputsandbox.append(File(name=scriptArchive))
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def configure(self, master_appconfig):
# self._configure()
name = join('.', self.script[0].subdir, split(self.script[0].name)[-1])
script = "from Gaudi.Configuration import *\n"
if self.args:
script += 'import sys\nsys.argv += %s\n' % str(self.args)
script += "importOptions('data.py')\n"
script += "execfile(\'%s\')\n" % name
# add summary.xml
outputsandbox_temp = XMLPostProcessor._XMLJobFiles()
outputsandbox_temp += unique(self.getJobObject().outputsandbox)
outputsandbox = unique(outputsandbox_temp)
input_files = []
input_files += [FileBuffer('gaudipython-wrapper.py', script)]
logger.debug("Returning Job Configuration")
return (None, StandardJobConfig(inputbox=input_files,
outputbox=outputsandbox))
def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiExec): This application is only expected to handle GaudiExec Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
if isinstance(app.jobScriptArchive, LocalFile):
app.jobScriptArchive = None
generateJobScripts(app, appendJobScripts=True)
scriptArchive = os.path.join(app.jobScriptArchive.localDir, app.jobScriptArchive.namePattern)
inputsandbox.append(File(name=scriptArchive))
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def configure(self, master_appconfig):
# self._configure()
name = join('.', self.script[0].subdir, split(self.script[0].name)[-1])
script = "from Gaudi.Configuration import *\n"
if self.args:
script += 'import sys\nsys.argv += %s\n' % str(self.args)
script += "importOptions('data.py')\n"
script += "execfile(\'%s\')\n" % name
# add summary.xml
outputsandbox_temp = XMLPostProcessor._XMLJobFiles()
outputsandbox_temp += unique(self.getJobObject().outputsandbox)
outputsandbox = unique(outputsandbox_temp)
input_files = []
input_files += [FileBuffer('gaudipython-wrapper.py', script)]
logger.debug("Returning Job Configuration")
return (None,
StandardJobConfig(inputbox=input_files,
outputbox=outputsandbox))
def sandbox_prepare(app, appsubconfig, appmasterconfig, jobmasterconfig):
logger.debug("RTUTils sandbox_prepare")
inputsandbox = []
outputsandbox = []
# Here add any sandbox files coming from the appsubconfig
# currently none. masterjobconfig inputsandbox added automatically
if appsubconfig:
inputsandbox += appsubconfig.getSandboxFiles()
# Strangly NEITHER the master outputsandbox OR job.outputsandbox
# are added automatically.
if jobmasterconfig:
outputsandbox += jobmasterconfig.getOutputSandboxFiles()
if appsubconfig:
outputsandbox += appsubconfig.getOutputSandboxFiles()
return unique(inputsandbox), unique(outputsandbox)
def configure(self, master_appconfig):
self._configure()
name = join('.', self.script[0].subdir, split(self.script[0].name)[-1])
script = "from Gaudi.Configuration import *\n"
if self.args:
script += 'import sys\nsys.argv += %s\n' % str(self.args)
script += "importOptions('data.py')\n"
script += "execfile(\'%s\')\n" % name
self.extra.input_buffers['gaudipython-wrapper.py'] = script
outsb = self.getJobObject().outputsandbox
self.extra.outputsandbox = unique(outsb)
return (None, self.extra)
def configure(self,master_appconfig):
self._configure()
name = join('.',self.script[0].subdir,split(self.script[0].name)[-1])
script = "from Gaudi.Configuration import *\n"
if self.args:
script += 'import sys\nsys.argv += %s\n' % str(self.args)
script += "importOptions('data.py')\n"
script += "execfile(\'%s\')\n" % name
self.extra.input_buffers['gaudipython-wrapper.py'] = script
outsb = self.getJobObject().outputsandbox
self.extra.outputsandbox = unique(outsb)
return (None,self.extra)
def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiExec): This application is only expected to handle GaudiExec Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig)
if isinstance(app.jobScriptArchive, LocalFile):
app.jobScriptArchive = None
generateJobScripts(app, appendJobScripts=True)
scriptArchive = os.path.join(app.jobScriptArchive.localDir, app.jobScriptArchive.namePattern)
inputsandbox.append(File(name=scriptArchive))
if app.getMetadata:
logger.info("Adding options to make the summary.xml")
inputsandbox.append(FileBuffer('summary.py', "\nfrom Gaudi.Configuration import *\nfrom Configurables import LHCbApp\nLHCbApp().XMLSummary='summary.xml'"))
return StandardJobConfig(inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def configure(self, master_appconfig):
# self._configure()
modulename = split(self.module.name)[-1].split('.')[0]
script = """
from copy import deepcopy
from Gaudi.Configuration import *
importOptions('data.py')
import %s as USERMODULE
EventSelectorInput = deepcopy(EventSelector().Input)
FileCatalogCatalogs = deepcopy(FileCatalog().Catalogs)
EventSelector().Input=[]
FileCatalog().Catalogs=[]\n""" % modulename
script_configure = "USERMODULE.configure(EventSelectorInput,FileCatalogCatalogs%s)\n"
if self.params:
param_string = ",params=%s" % self.params
else:
param_string = ""
script_configure = script_configure % param_string
script += script_configure
script += "USERMODULE.run(%d)\n" % self.events
script += getXMLSummaryScript()
# add summary.xml
outputsandbox_temp = XMLPostProcessor._XMLJobFiles()
outputsandbox_temp += unique(self.getJobObject().outputsandbox)
outputsandbox = unique(outputsandbox_temp)
input_files = []
input_files += [FileBuffer('gaudipython-wrapper.py', script)]
logger.debug("Returning StandardJobConfig")
return (None,
StandardJobConfig(inputbox=input_files,
outputbox=outputsandbox))
def dirac_inputdata(app, hasOtherInputData=False):
""" Construct the JDL component which requests the inputdata for a job
Args:
app (IApplication): app which belongs to the job of interest
hasOtherInputData (bool): This is used to stop BannedSites being added to the JDL structure through backend.settings
"""
job = app.getJobObject()
input_data = None
parametricinput_data = None
inputLFNs = []
input_data = None
parametricinput_data = None
if not job.inputdata and (not job.master or not job.master.inputdata):
return input_data, parametricinput_data
wanted_job = job
if not job.inputdata and job.master and job.master.inputdata is not None and job.master.inputdata:
wanted_job = job.master
inputLFNs = ['LFN:'+this_file.lfn for this_file in wanted_job.inputdata if isinstance(this_file, DiracFile)]
# master job with a splitter reaching prepare, hence bulk submit
if not job.master and job.splitter:
parametricinput_data = dirac_parametric_split(app)
if parametricinput_data is not None and len(parametricinput_data) > getConfig('DIRAC')['MaxDiracBulkJobs']:
raise BackendError('Dirac', 'Number of bulk submission jobs \'%s\' exceeds the maximum allowed \'%s\' if more are needed please modify your config. Note there is a hard limit in Dirac of currently 1000.' % (
len(parametricinput_data), getConfig('DIRAC')['MaxDiracBulkJobs']))
# master job with no splitter or subjob already split proceed as normal
else:
input_data = inputLFNs
if 'Destination' not in job.backend.settings and not inputLFNs and not hasOtherInputData:
t1_sites = getConfig('DIRAC')['noInputDataBannedSites']
logger.info('Job has no inputdata (T1 sites will be banned to help avoid overloading them).')
if 'BannedSites' in job.backend.settings:
job.backend.settings['BannedSites'].extend(t1_sites)
job.backend.settings['BannedSites'] = unique(job.backend.settings['BannedSites'])
else:
if t1_sites:
job.backend.settings['BannedSites'] = t1_sites[:]
if not input_data and not parametricinput_data:
input_data = inputLFNs
return input_data, parametricinput_data
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig,
appmasterconfig,
jobmasterconfig)
input_data, parametricinput_data = dirac_inputdata(app)
logger.debug("input_data: " + str(input_data))
job = app.getJobObject()
outputfiles = [
this_file for this_file in job.outputfiles
if isType(this_file, DiracFile)
]
lhcb_dirac_outputfiles = lhcbdirac_outputfile_jdl(outputfiles)
# NOTE special case for replicas: replicate string must be empty for no
# replication
params = {
'DIRAC_IMPORT':
'from LHCbDIRAC.Interfaces.API.DiracLHCb import DiracLHCb',
'DIRAC_JOB_IMPORT':
'from LHCbDIRAC.Interfaces.API.LHCbJob import LHCbJob',
'DIRAC_OBJECT': 'DiracLHCb()',
'JOB_OBJECT': 'LHCbJob()',
'NAME': mangle_job_name(app),
'INPUTDATA': input_data,
'PARAMETRIC_INPUTDATA': parametricinput_data,
'OUTPUT_SANDBOX': API_nullifier(outputsandbox),
'OUTPUTFILESSCRIPT': lhcb_dirac_outputfiles,
'OUTPUT_PATH': "", # job.fqid,
'SETTINGS': diracAPI_script_settings(app),
'DIRAC_OPTS': job.backend.diracOpts,
'PLATFORM': getConfig('ROOT')['arch'],
'REPLICATE':
'True' if getConfig('DIRAC')['ReplicateOutputData'] else '',
# leave the sandbox for altering later as needs
# to be done in backend.submit to combine master.
# Note only using 2 #s as auto-remove 3
'INPUT_SANDBOX': '##INPUT_SANDBOX##'
}
scriptpath = os.path.join(get_share_path(app),
os.path.basename(app.script.name))
wrapper_path = os.path.join(
job.getInputWorkspace(create=True).getPath(), 'script_wrapper.py')
python_wrapper =\
"""#!/usr/bin/env python
import os, sys
def formatVar(var):
try:
float(var)
return str(var)
except ValueError as v:
return '\\\"%s\\\"' % str(var)
script_args = '###SCRIPT_ARGS###'
del sys.argv[sys.argv.index('script_wrapper.py')]
###FIXARGS###
if script_args == []: script_args = ''
os.system('###COMMAND###' % script_args)
###INJECTEDCODE###
"""
python_wrapper = python_wrapper.replace(
'###SCRIPT_ARGS###',
str('###JOINER###'.join([str(a) for a in app.args])))
params.update({
'APP_NAME': 'Root',
'APP_VERSION': app.version,
'APP_SCRIPT': wrapper_path,
'APP_LOG_FILE': 'Ganga_Root.log'
})
#params.update({'ROOTPY_SCRIPT': wrapper_path,
# 'ROOTPY_VERSION': app.version,
# 'ROOTPY_LOG_FILE': 'Ganga_Root.log',
# 'ROOTPY_ARGS': [str(a) for a in app.args]})
f = open(wrapper_path, 'w')
if app.usepython:
python_wrapper = script_generator(
python_wrapper,
remove_unreplaced=False,
FIXARGS='',
COMMAND='/usr/bin/env python %s %s' %
(os.path.basename(app.script.name), '%s'),
JOINER=' ',
#INJECTEDCODE = getWNCodeForOutputPostprocessing(job,'')
)
else:
python_wrapper = script_generator(
python_wrapper,
remove_unreplaced=False,
FIXARGS='script_args=[formatVar(v) for v in script_args]',
COMMAND=
'export DISPLAY=\"localhoast:0.0\" && root -l -q \"%s(%s)\"' %
(os.path.basename(app.script.name), '%s'),
JOINER=',',
#INJECTEDCODE = getWNCodeForOutputPostprocessing(job,'')
)
f.write(python_wrapper)
f.close()
dirac_script = script_generator(lhcbdiracAPI_script_template(),
**params)
return StandardJobConfig(dirac_script,
inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig,
appmasterconfig,
jobmasterconfig)
input_data, parametricinput_data = dirac_inputdata(app)
# outputdata, outputdata_path = dirac_ouputdata(app)
job = stripProxy(app).getJobObject()
outputfiles = [
this_file for this_file in job.outputfiles
if isType(this_file, DiracFile)
]
commandline = []
commandline.append(app.exe)
if isType(app.exe, File):
#logger.info("app: %s" % str(app.exe.name))
#fileName = os.path.join(get_share_path(app), os.path.basename(app.exe.name))
#logger.info("EXE: %s" % str(fileName))
#inputsandbox.append(File(name=fileName))
inputsandbox.append(app.exe)
commandline[0] = os.path.join('.', os.path.basename(app.exe.name))
commandline.extend([str(arg) for arg in app.args])
logger.debug('Command line: %s: ', commandline)
#exe_script_path = os.path.join(job.getInputWorkspace().getPath(), "exe-script.py")
exe_script_name = 'exe-script.py'
logger.info("Setting Command to be: '%s'" % repr(commandline))
inputsandbox.append(
FileBuffer(
name=exe_script_name,
contents=script_generator(
exe_script_template(),
#remove_unreplaced = False,
# ,
COMMAND=repr(commandline),
OUTPUTFILESINJECTEDCODE=getWNCodeForOutputPostprocessing(
job, ' ')),
executable=True))
contents = script_generator(
exe_script_template(),
COMMAND=repr(commandline),
OUTPUTFILESINJECTEDCODE=getWNCodeForOutputPostprocessing(
job, ' '))
#logger.info("Script is: %s" % str(contents))
from os.path import abspath, expanduser
for this_file in job.inputfiles:
if isinstance(this_file, LocalFile):
for name in this_file.getFilenameList():
inputsandbox.append(File(abspath(expanduser(name))))
elif isinstance(this_file, DiracFile):
name = this_file.lfn
if isinstance(input_data, list):
input_data.append(name)
else:
input_data = [name]
dirac_outputfiles = dirac_outputfile_jdl(outputfiles,
config['RequireDefaultSE'])
# NOTE special case for replicas: replicate string must be empty for no
# replication
dirac_script = script_generator(
diracAPI_script_template(),
DIRAC_IMPORT='from DIRAC.Interfaces.API.Dirac import Dirac',
DIRAC_JOB_IMPORT='from DIRAC.Interfaces.API.Job import Job',
DIRAC_OBJECT='Dirac()',
JOB_OBJECT='Job()',
NAME=mangle_job_name(app),
# os.path.basename(exe_script_path),
EXE=exe_script_name,
# ' '.join([str(arg) for arg in app.args]),
EXE_ARG_STR='',
EXE_LOG_FILE='Ganga_Executable.log',
ENVIRONMENT=None, # app.env,
INPUTDATA=input_data,
PARAMETRIC_INPUTDATA=parametricinput_data,
OUTPUT_SANDBOX=API_nullifier(outputsandbox),
OUTPUTFILESSCRIPT=dirac_outputfiles,
OUTPUT_PATH="", # job.fqid,
SETTINGS=diracAPI_script_settings(app),
DIRAC_OPTS=job.backend.diracOpts,
REPLICATE='True' if config['ReplicateOutputData'] else '',
# leave the sandbox for altering later as needs
# to be done in backend.submit to combine master.
# Note only using 2 #s as auto-remove 3
INPUT_SANDBOX='##INPUT_SANDBOX##')
#logger.info("dirac_script: %s" % dirac_script)
#logger.info("inbox: %s" % str(unique(inputsandbox)))
#logger.info("outbox: %s" % str(unique(outputsandbox)))
return StandardJobConfig(dirac_script,
inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def get_user_dlls(appname, version, user_release_area, platform, env):
user_ra = user_release_area
update_project_path(user_release_area)
from Ganga.Utility.files import fullpath
full_user_ra = fullpath(user_ra) # expand any symbolic links
# Work our way through the CMTPROJECTPATH until we find a cmt directory
if 'CMTPROJECTPATH' not in env:
return [], [], []
projectdirs = env['CMTPROJECTPATH'].split(os.pathsep)
appveruser = os.path.join(appname + '_' + version, 'cmt')
appverrelease = os.path.join(
appname.upper(), appname.upper() + '_' + version, 'cmt')
for projectdir in projectdirs:
projectDir = fullpath(os.path.join(projectdir, appveruser))
logger.debug('Looking for projectdir %s' % projectDir)
if os.path.exists(projectDir):
break
projectDir = fullpath(os.path.join(projectdir, appverrelease))
logger.debug('Looking for projectdir %s' % projectDir)
if os.path.exists(projectDir):
break
logger.debug('Using the CMT directory %s for identifying projects' % projectDir)
# rc, showProj, m = shell.cmd1('cd ' + projectDir +';cmt show projects',
# capture_stderr=True)
from GangaGaudi.Lib.Applications.GaudiUtils import shellEnv_cmd
rc, showProj, m = shellEnv_cmd('cmt show projects', env, projectDir)
logger.debug(showProj)
libs = []
merged_pys = []
subdir_pys = {}
project_areas = []
py_project_areas = []
for line in showProj.split('\n'):
for entry in line.split():
if entry.startswith(user_ra) or entry.startswith(full_user_ra):
tmp = entry.rstrip('\)')
libpath = fullpath(os.path.join(tmp, 'InstallArea', platform, 'lib'))
logger.debug(libpath)
project_areas.append(libpath)
pypath = fullpath(os.path.join(tmp, 'InstallArea', 'python'))
logger.debug(pypath)
py_project_areas.append(pypath)
pypath = fullpath(os.path.join(tmp, 'InstallArea', platform, 'python'))
logger.debug(pypath)
py_project_areas.append(pypath)
# savannah 47793 (remove multiple copies of the same areas)
from Ganga.Utility.util import unique
project_areas = unique(project_areas)
py_project_areas = unique(py_project_areas)
ld_lib_path = []
if 'LD_LIBRARY_PATH' in env:
ld_lib_path = env['LD_LIBRARY_PATH'].split(':')
project_areas_dict = {}
for area in project_areas:
if area in ld_lib_path:
project_areas_dict[area] = ld_lib_path.index(area)
else:
project_areas_dict[area] = 666
from operator import itemgetter
sorted_project_areas = []
for item in sorted(project_areas_dict.items(), key=itemgetter(1)):
sorted_project_areas.append(item[0])
lib_names = []
for libpath in sorted_project_areas:
if os.path.exists(libpath):
for f in os.listdir(libpath):
if lib_names.count(f) > 0:
continue
fpath = os.path.join(libpath, f)
if os.path.exists(fpath):
lib_names.append(f)
libs.append(fpath)
else:
logger.warning("File %s in %s does not exist. Skipping...", str(f), str(libpath))
for pypath in py_project_areas:
if os.path.exists(pypath):
from GangaGaudi.Lib.Applications.GaudiUtils import pyFileCollector
from Ganga.Utility.Config import getConfig
configGaudi = getConfig('GAUDI')
pyFileCollector(
pypath, merged_pys, subdir_pys, configGaudi['pyFileCollectionDepth'])
import pprint
logger.debug("%s", pprint.pformat(libs))
logger.debug("%s", pprint.pformat(merged_pys))
logger.debug("%s", pprint.pformat(subdir_pys))
return libs, merged_pys, subdir_pys
def getOutputSandboxFiles(self):
"""Get all output sandbox files. The duplicates are removed. """
from Ganga.Utility.util import unique
return unique(self.outputbox)
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig, appmasterconfig, jobmasterconfig)
input_data, parametricinput_data = dirac_inputdata(app)
logger.debug("input_data: " + str(input_data))
job = app.getJobObject()
outputfiles = [this_file for this_file in job.outputfiles if isType(this_file, DiracFile)]
lhcb_dirac_outputfiles = lhcbdirac_outputfile_jdl(outputfiles)
# NOTE special case for replicas: replicate string must be empty for no
# replication
params = {'DIRAC_IMPORT': 'from LHCbDIRAC.Interfaces.API.DiracLHCb import DiracLHCb',
'DIRAC_JOB_IMPORT': 'from LHCbDIRAC.Interfaces.API.LHCbJob import LHCbJob',
'DIRAC_OBJECT': 'DiracLHCb()',
'JOB_OBJECT': 'LHCbJob()',
'NAME': mangle_job_name(app),
'INPUTDATA': input_data,
'PARAMETRIC_INPUTDATA': parametricinput_data,
'OUTPUT_SANDBOX': API_nullifier(outputsandbox),
'OUTPUTFILESSCRIPT' : lhcb_dirac_outputfiles,
'OUTPUT_PATH': "", # job.fqid,
'OUTPUT_SE': getConfig('DIRAC')['DiracOutputDataSE'],
'SETTINGS': diracAPI_script_settings(app),
'DIRAC_OPTS': job.backend.diracOpts,
'PLATFORM': getConfig('ROOT')['arch'],
'REPLICATE': 'True' if getConfig('DIRAC')['ReplicateOutputData'] else '',
# leave the sandbox for altering later as needs
# to be done in backend.submit to combine master.
# Note only using 2 #s as auto-remove 3
'INPUT_SANDBOX': '##INPUT_SANDBOX##'
}
scriptpath = os.path.join(get_share_path(app),
os.path.basename(app.script.name))
wrapper_path = os.path.join(job.getInputWorkspace(create=True).getPath(),
'script_wrapper.py')
python_wrapper =\
"""#!/usr/bin/env python
import os, sys
def formatVar(var):
try:
float(var)
return str(var)
except ValueError as v:
return '\\\"%s\\\"' % str(var)
script_args = '###SCRIPT_ARGS###'
del sys.argv[sys.argv.index('script_wrapper.py')]
###FIXARGS###
if script_args == []: script_args = ''
os.system('###COMMAND###' % script_args)
###INJECTEDCODE###
"""
python_wrapper = python_wrapper.replace('###SCRIPT_ARGS###', str('###JOINER###'.join([str(a) for a in app.args])))
params.update({ 'APP_NAME' : 'Root',
'APP_VERSION' : app.version,
'APP_SCRIPT' : wrapper_path,
'APP_LOG_FILE' : 'Ganga_Root.log' })
#params.update({'ROOTPY_SCRIPT': wrapper_path,
# 'ROOTPY_VERSION': app.version,
# 'ROOTPY_LOG_FILE': 'Ganga_Root.log',
# 'ROOTPY_ARGS': [str(a) for a in app.args]})
f = open(wrapper_path, 'w')
if app.usepython:
python_wrapper = script_generator(python_wrapper,
remove_unreplaced=False,
FIXARGS='',
COMMAND='/usr/bin/env python %s %s' % (os.path.basename(app.script.name), '%s'),
JOINER=' ',
#INJECTEDCODE = getWNCodeForOutputPostprocessing(job,'')
)
else:
python_wrapper = script_generator(python_wrapper,
remove_unreplaced=False,
FIXARGS='script_args=[formatVar(v) for v in script_args]',
COMMAND='export DISPLAY=\"localhoast:0.0\" && root -l -q \"%s(%s)\"' % (os.path.basename(app.script.name), '%s'),
JOINER=',',
#INJECTEDCODE = getWNCodeForOutputPostprocessing(job,'')
)
f.write(python_wrapper)
f.close()
dirac_script = script_generator(lhcbdiracAPI_script_template(), **params)
return StandardJobConfig(dirac_script,
inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
"""
This function prepares the application of the actual job being submitted, master or not
Args:
app (IApplication): This is the application actually being submitted belonging to the master or sub job being configured
appsubconfig (tuple): This is used to prepare the inputsandbox according to the configuration for each subjob if it varies
appmasterconfig (tuple): This is also used to prepare the inputsandbox but contains the config of the app for the master job
jobmasterconfig (StandardJobConfig): This is the configuration of the master job which may or may not be the same job as owning the app
"""
# Construct some common objects used in job submission here
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig, appmasterconfig, jobmasterconfig)
input_data, parametricinput_data = dirac_inputdata(app, hasOtherInputData=True)
job = app.getJobObject()
# Construct the im3shape-script which is used by this job. i.e. the script and full command line to be used in this job
exe_script_name = "im3shape-script.py"
output_filename = os.path.basename(job.inputdata[0].lfn) + "." + str(app.rank) + "." + str(app.size)
im3shape_args = " ".join(
[
os.path.basename(job.inputdata[0].lfn),
os.path.basename(app.ini_location.namePattern), # input.fz, config.ini
app.catalog,
output_filename, # catalog, output
str(app.rank),
str(app.size),
]
)
full_cmd = app.exe_name + " " + im3shape_args
outputfiles = [this_file for this_file in job.outputfiles if isinstance(this_file, DiracFile)]
inputsandbox.append(
FileBuffer(
name=exe_script_name,
contents=script_generator(
Im3Shape_script_template(),
## ARGS for app from job.app
RUN_DIR=app.run_dir,
BLACKLIST=os.path.basename(app.blacklist.namePattern),
COMMAND=full_cmd,
## Stuff for Ganga
OUTPUTFILES=repr([this_file.namePattern for this_file in job.outputfiles]),
OUTPUTFILESINJECTEDCODE=getWNCodeForOutputPostprocessing(job, " "),
),
executable=True,
)
)
# TODO once there is a common, IApplication.getMeFilesForThisApp function replace this list with a getter ad it shouldn't really be hard-coded
app_file_list = [app.im3_location, app.ini_location, app.blacklist]
app_file_list = [this_file for this_file in app_file_list if isinstance(this_file, DiracFile)]
job.inputfiles.extend(app_file_list)
# Slightly mis-using this here but it would be nice to have these files
# job.inputfiles.extend(job.inputdata)
# NOTE special case for replicas: replicate string must be empty for no
# replication
dirac_script = script_generator(
diracAPI_script_template(),
DIRAC_IMPORT="from DIRAC.Interfaces.API.Dirac import Dirac",
DIRAC_JOB_IMPORT="from DIRAC.Interfaces.API.Job import Job",
DIRAC_OBJECT="Dirac()",
JOB_OBJECT="Job()",
NAME=mangle_job_name(app),
EXE=exe_script_name,
EXE_ARG_STR="",
EXE_LOG_FILE="Ganga_Executable.log",
ENVIRONMENT=None,
INPUTDATA=input_data,
PARAMETRIC_INPUTDATA=parametricinput_data,
OUTPUT_SANDBOX=API_nullifier(outputsandbox),
OUTPUTFILESSCRIPT=dirac_outputfile_jdl(outputfiles, False),
OUTPUT_PATH="", # job.fqid,
SETTINGS=diracAPI_script_settings(app),
DIRAC_OPTS=job.backend.diracOpts,
REPLICATE="True" if getConfig("DIRAC")["ReplicateOutputData"] else "",
# leave the sandbox for altering later as needs
# to be done in backend.submit to combine master.
# Note only using 2 #s as auto-remove 3
INPUT_SANDBOX="##INPUT_SANDBOX##",
)
return StandardJobConfig(dirac_script, inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
logger.debug("Prepare")
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig,
appmasterconfig,
jobmasterconfig)
job = stripProxy(app).getJobObject()
if job.inputdata:
if not job.splitter:
if len(job.inputdata) > 100:
raise BackendError(
"You're submitting a job to Dirac with no splitter and more than 100 files, please add a splitter and try again!"
)
outputfiles = [
this_file for this_file in job.outputfiles
if isType(this_file, DiracFile)
]
data_str = 'import os\n'
data_str += 'execfile(\'data.py\')\n'
if hasattr(job, '_splitter_data'):
data_str += job._splitter_data
inputsandbox.append(FileBuffer('data-wrapper.py', data_str))
input_data = []
# Cant wait to get rid of this when people no-longer specify
# inputdata in options file
#######################################################################
# splitters ensure that subjobs pick up inputdata from job over that in
# optsfiles but need to take care of unsplit jobs
if not job.master:
share_path = os.path.join(get_share_path(app), 'inputdata',
'options_data.pkl')
if not job.inputdata:
if os.path.exists(share_path):
f = open(share_path, 'r+b')
job.inputdata = pickle.load(f)
f.close()
#######################################################################
# Cant wait to get rid of this when people no-longer specify
# outputsandbox or outputdata in options file
#######################################################################
share_path = os.path.join(get_share_path(app), 'output',
'options_parser.pkl')
if os.path.exists(share_path):
# if not os.path.exists(share_path):
# raise GangaException('could not find the parser')
f = open(share_path, 'r+b')
parser = pickle.load(f)
f.close()
outbox, outdata = parser.get_output(job)
from Ganga.GPIDev.Lib.File import FileUtils
from Ganga.GPIDev.Base.Filters import allComponentFilters
fileTransform = allComponentFilters['gangafiles']
outdata_files = [
fileTransform(this_file, None) for this_file in outdata
if not FileUtils.doesFileExist(this_file, job.outputfiles)
]
job.non_copyable_outputfiles.extend([
output_file for output_file in outdata_files
if not isType(output_file, DiracFile)
])
outbox_files = [
fileTransform(this_file, None) for this_file in outbox
if not FileUtils.doesFileExist(this_file, job.outputfiles)
]
job.non_copyable_outputfiles.extend([
outbox_file for outbox_file in outbox_files
if not isType(outbox_file, DiracFile)
])
outputsandbox = [
f.namePattern for f in job.non_copyable_outputfiles
]
outputsandbox.extend([
f.namePattern for f in job.outputfiles
if not isType(f, DiracFile)
])
outputsandbox = unique(outputsandbox) # + outbox[:])
#######################################################################
input_data_dirac, parametricinput_data = dirac_inputdata(
job.application)
if input_data_dirac is not None:
for f in input_data_dirac:
if isType(f, DiracFile):
input_data.append(f.lfn)
elif isType(f, str):
input_data.append(f)
else:
raise ApplicationConfigurationError(
"Don't know How to handle anythig other than DiracFiles or strings to LFNs!"
)
commandline = "python ./gaudipython-wrapper.py"
if is_gaudi_child(app):
commandline = 'gaudirun.py '
commandline += ' '.join([str(arg) for arg in app.args])
commandline += ' options.pkl data-wrapper.py'
logger.debug('Command line: %s: ', commandline)
gaudi_script_path = os.path.join(job.getInputWorkspace().getPath(),
"gaudi-script.py")
script_generator(
gaudi_script_template(),
#remove_unreplaced = False,
outputfile_path=gaudi_script_path,
PLATFORM=app.platform,
COMMAND=commandline,
XMLSUMMARYPARSING=getXMLSummaryScript() # ,
#OUTPUTFILESINJECTEDCODE = getWNCodeForOutputPostprocessing(job, ' ')
)
#logger.debug( "input_data %s" % str( input_data ) )
# We want to propogate the ancestor depth to DIRAC when we have
# inputdata set
if job.inputdata is not None and isType(job.inputdata, LHCbDataset):
# As the RT Handler we already know we have a Dirac backend
if type(job.backend.settings) is not dict:
raise ApplicationConfigurationError(
None, 'backend.settings should be a dict')
if 'AncestorDepth' in job.backend.settings:
ancestor_depth = job.backend.settings['AncestorDepth']
else:
ancestor_depth = job.inputdata.depth
else:
ancestor_depth = 0
lhcbdirac_script_template = lhcbdiracAPI_script_template()
lhcb_dirac_outputfiles = lhcbdirac_outputfile_jdl(outputfiles)
# not necessary to use lhcbdiracAPI_script_template any more as doing our own uploads to Dirac
# remove after Ganga6 release
# NOTE special case for replicas: replicate string must be empty for no
# replication
dirac_script = script_generator(
lhcbdirac_script_template,
DIRAC_IMPORT=
'from LHCbDIRAC.Interfaces.API.DiracLHCb import DiracLHCb',
DIRAC_JOB_IMPORT=
'from LHCbDIRAC.Interfaces.API.LHCbJob import LHCbJob',
DIRAC_OBJECT='DiracLHCb()',
JOB_OBJECT='LHCbJob()',
NAME=mangle_job_name(app),
APP_NAME=stripProxy(app).appname,
APP_VERSION=app.version,
APP_SCRIPT=gaudi_script_path,
APP_LOG_FILE='Ganga_%s_%s.log' %
(stripProxy(app).appname, app.version),
INPUTDATA=input_data,
PARAMETRIC_INPUTDATA=parametricinput_data,
OUTPUT_SANDBOX=API_nullifier(outputsandbox),
OUTPUTFILESSCRIPT=lhcb_dirac_outputfiles,
# job.fqid,#outputdata_path,
OUTPUT_PATH="",
OUTPUT_SE=getConfig('DIRAC')['DiracOutputDataSE'],
SETTINGS=diracAPI_script_settings(job.application),
DIRAC_OPTS=job.backend.diracOpts,
PLATFORM=app.platform,
REPLICATE='True'
if getConfig('DIRAC')['ReplicateOutputData'] else '',
ANCESTOR_DEPTH=ancestor_depth,
## This is to be modified in the final 'submit' function in the backend
## The backend also handles the inputfiles DiracFiles ass appropriate
INPUT_SANDBOX='##INPUT_SANDBOX##')
logger.debug("prepare: LHCbGaudiDiracRunTimeHandler")
return StandardJobConfig(dirac_script,
inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def dirac_inputdata(app):
job = stripProxy(app).getJobObject()
input_data = None
parametricinput_data = None
inputLFNs = []
if hasattr(job.inputdata, 'getLFNs'):
inputLFNs = job.inputdata.getLFNs()
if job.master:
logger.debug("job.master.inputdata: %s " % str(job.master.inputdata))
logger.debug("job.inputdata: %s" % str(job.inputdata))
if hasattr(job.inputdata, 'getLFNs'):
logger.debug("getLFNs(): %s" % job.inputdata.getLFNs())
has_input_DiracFile = False
for this_file in job.inputfiles:
if isType(this_file, DiracFile):
has_input_DiracFile = True
break
if job.master and not has_input_DiracFile:
for this_file in job.master.inputfiles:
if isType(this_file, DiracFile):
has_input_DiracFile = True
break
if len(inputLFNs) > 0:
# master job with a splitter reaching prepare, hence bulk submit
if not job.master and job.splitter:
parametricinput_data = dirac_parametric_split(app)
if parametricinput_data is not None and len(
parametricinput_data) > getConfig(
'DIRAC')['MaxDiracBulkJobs']:
raise BackendError(
'Dirac',
'Number of bulk submission jobs \'%s\' exceeds the maximum allowed \'%s\' if more are needed please modify your config. Note there is a hard limit in Dirac of currently 1000.'
% (len(parametricinput_data),
getConfig('DIRAC')['MaxDiracBulkJobs']))
# master job with no splitter or subjob already split proceed as normal
else:
input_data = job.inputdata.getLFNs()
elif 'Destination' not in job.backend.settings and not has_input_DiracFile:
##THIS IS NOT VERY DIRAC CENTRIC
##PLEASE WHEN TIME MOVE TO LHCBDIRAC where T1 is more applicable rcurrie
##Also editing the settings on the fly is asking for potential problems, should avoid
t1_sites = getConfig('DIRAC')['noInputDataBannedSites']
logger.info(
'Job has no inputdata (T1 sites will be banned to help avoid overloading them).'
)
if 'BannedSites' in job.backend.settings:
job.backend.settings['BannedSites'].extend(t1_sites)
job.backend.settings['BannedSites'] = unique(
job.backend.settings['BannedSites'])
else:
job.backend.settings['BannedSites'] = t1_sites[:]
#import traceback
# traceback.print_stack()
return input_data, parametricinput_data
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
"""
This function prepares the application of the actual job being submitted, master or not
Args:
app (IApplication): This is the application actually being submitted belonging to the master or sub job being configured
appsubconfig (tuple): This is used to prepare the inputsandbox according to the configuration for each subjob if it varies
appmasterconfig (tuple): This is also used to prepare the inputsandbox but contains the config of the app for the master job
jobmasterconfig (StandardJobConfig): This is the configuration of the master job which may or may not be the same job as owning the app
"""
# Construct some common objects used in job submission here
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig, appmasterconfig, jobmasterconfig)
input_data, parametricinput_data = dirac_inputdata(app, hasOtherInputData=True)
job = app.getJobObject()
# Construct the im3shape-script which is used by this job. i.e. the script and full command line to be used in this job
exe_script_name = 'im3shape-script.py'
output_filename = os.path.basename(job.inputdata[0].lfn) + '.' + str(app.rank) + '.' + str(app.size)
im3shape_args = ' '.join([ os.path.basename(job.inputdata[0].lfn), os.path.basename(app.ini_location.namePattern), # input.fz, config.ini
app.catalog, output_filename, # catalog, output
str(app.rank), str(app.size) ])
full_cmd = app.exe_name + ' ' + im3shape_args
outputfiles = [this_file for this_file in job.outputfiles if isinstance(this_file, DiracFile)]
inputsandbox.append(FileBuffer( name=exe_script_name,
contents=script_generator(Im3Shape_script_template(),
## ARGS for app from job.app
RUN_DIR = app.run_dir,
BLACKLIST = os.path.basename(app.blacklist.namePattern),
COMMAND = full_cmd,
## Stuff for Ganga
OUTPUTFILES = repr([this_file.namePattern for this_file in job.outputfiles]),
OUTPUTFILESINJECTEDCODE = getWNCodeForOutputPostprocessing(job, ' '),
),
executable=True)
)
# TODO once there is a common, IApplication.getMeFilesForThisApp function replace this list with a getter ad it shouldn't really be hard-coded
app_file_list = [app.im3_location, app.ini_location, app.blacklist]
app_file_list = [this_file for this_file in app_file_list if isinstance(this_file, DiracFile)]
job.inputfiles.extend(app_file_list)
# Slightly mis-using this here but it would be nice to have these files
#job.inputfiles.extend(job.inputdata)
# NOTE special case for replicas: replicate string must be empty for no
# replication
dirac_script = script_generator(diracAPI_script_template(),
DIRAC_IMPORT = 'from DIRAC.Interfaces.API.Dirac import Dirac',
DIRAC_JOB_IMPORT = 'from DIRAC.Interfaces.API.Job import Job',
DIRAC_OBJECT = 'Dirac()',
JOB_OBJECT = 'Job()',
NAME = mangle_job_name(app),
EXE = exe_script_name,
EXE_ARG_STR = '',
EXE_LOG_FILE = 'Ganga_Executable.log',
ENVIRONMENT = None,
INPUTDATA = input_data,
PARAMETRIC_INPUTDATA = parametricinput_data,
OUTPUT_SANDBOX = API_nullifier(outputsandbox),
OUTPUTFILESSCRIPT = dirac_outputfile_jdl(outputfiles, False),
OUTPUT_PATH = "", # job.fqid,
SETTINGS = diracAPI_script_settings(app),
DIRAC_OPTS = job.backend.diracOpts,
REPLICATE = 'True' if getConfig('DIRAC')['ReplicateOutputData'] else '',
# leave the sandbox for altering later as needs
# to be done in backend.submit to combine master.
# Note only using 2 #s as auto-remove 3
INPUT_SANDBOX = '##INPUT_SANDBOX##'
)
return StandardJobConfig(dirac_script,
inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
logger.debug("Prepare")
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig,
appmasterconfig,
jobmasterconfig)
job = app.getJobObject()
logger.debug("Loading pickle files")
#outputfiles=set([file.namePattern for file in job.outputfiles]).difference(set(getOutputSandboxPatterns(job)))
# Cant wait to get rid of this when people no-longer specify
# inputdata in options file
#######################################################################
# splitters ensure that subjobs pick up inputdata from job over that in
# optsfiles but need to take sare of unsplit jobs
if not job.master:
share_path = os.path.join(get_share_path(app), 'inputdata',
'options_data.pkl')
if not job.inputdata:
if os.path.exists(share_path):
f = open(share_path, 'r+b')
job.inputdata = pickle.load(f)
f.close()
#######################################################################
# Cant wait to get rid of this when people no-longer specify
# outputsandbox or outputdata in options file
#######################################################################
share_path = os.path.join(get_share_path(app), 'output',
'options_parser.pkl')
logger.debug("Adding info from pickle files")
if os.path.exists(share_path):
f = open(share_path, 'r+b')
parser = pickle.load(f)
f.close()
outbox, outdata = parser.get_output(job)
from Ganga.GPIDev.Lib.File import FileUtils
from Ganga.GPIDev.Base.Filters import allComponentFilters
fileTransform = allComponentFilters['gangafiles']
job.non_copyable_outputfiles.extend([
fileTransform(this_file, None) for this_file in outdata
if not FileUtils.doesFileExist(this_file, job.outputfiles)
])
job.non_copyable_outputfiles.extend([
fileTransform(this_file, None) for this_file in outbox
if not FileUtils.doesFileExist(this_file, job.outputfiles)
])
outputsandbox.extend(
[f.namePattern for f in job.non_copyable_outputfiles])
outputsandbox.extend([f.namePattern for f in job.outputfiles])
outputsandbox = unique(outputsandbox)
#######################################################################
logger.debug("Doing XML Catalog stuff")
data = job.inputdata
data_str = ''
if data:
logger.debug("Returning options String")
data_str = data.optionsString()
if data.hasLFNs():
logger.debug("Returning Catalogue")
inputsandbox.append(
FileBuffer('catalog.xml', data.getCatalog()))
cat_opts = '\nfrom Gaudi.Configuration import FileCatalog\nFileCatalog().Catalogs = ["xmlcatalog_file:catalog.xml"]\n'
data_str += cat_opts
logger.debug("Doing splitter_data stuff")
if hasattr(job, '_splitter_data'):
data_str += job._splitter_data
inputsandbox.append(FileBuffer('data.py', data_str))
logger.debug("Doing GaudiPython stuff")
cmd = 'python ./gaudipython-wrapper.py'
opts = ''
if is_gaudi_child(job.application):
opts = 'options.pkl'
cmd = 'gaudirun.py ' + \
' '.join(job.application.args) + ' %s data.py' % opts
logger.debug("Setting up script")
script = script_generator(
create_runscript(job.application.newStyleApp),
remove_unreplaced=False,
OPTS=opts,
PROJECT_OPTS=job.application.setupProjectOptions,
APP_NAME=job.application.appname,
APP_VERSION=job.application.version,
APP_PACKAGE=job.application.package,
PLATFORM=job.application.platform,
CMDLINE=cmd,
XMLSUMMARYPARSING=getXMLSummaryScript()) # ,
# OUTPUTFILESINJECTEDCODE = getWNCodeForOutputPostprocessing(job, ''))
logger.debug("Returning StandardJobConfig")
return StandardJobConfig(FileBuffer('gaudi-script.py',
script,
executable=1),
inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
"""
Prepare the RTHandler for the master job so that applications to be submitted
Args:
app (GaudiExec): This application is only expected to handle GaudiExec Applications here
appmasterconfig (unknown): Output passed from the application master configuration call
"""
cred_req = app.getJobObject().backend.credential_requirements
check_creds(cred_req)
inputsandbox, outputsandbox = master_sandbox_prepare(
app, appmasterconfig)
# If we are getting the metadata we need to make sure the summary.xml is added to the output sandbox if not there already.
if app.getMetadata and not 'summary.xml' in outputsandbox:
outputsandbox += ['summary.xml']
# Check a previously uploaded input is there in case of a job copy
if isinstance(app.uploadedInput, DiracFile):
if app.uploadedInput.getReplicas() == {}:
app.uploadedInput = None
logger.info(
"Previously uploaded cmake target missing from Dirac. Uploading it again."
)
if not isinstance(app.uploadedInput, DiracFile):
generateDiracInput(app)
try:
assert isinstance(app.uploadedInput, DiracFile)
except AssertionError:
raise ApplicationPrepareError(
"Failed to upload needed file, aborting submit. Tried to upload to: %s\nIf your Ganga installation is not at CERN your username may be trying to create a non-existent LFN. Try setting the 'DIRAC' configuration 'DiracLFNBase' to your grid user path.\n"
% DiracFile.diracLFNBase(cred_req))
rep_data = app.uploadedInput.getReplicas()
try:
assert rep_data != {}
except AssertionError:
raise ApplicationPrepareError(
"Failed to find a replica of uploaded file, aborting submit")
if isinstance(app.jobScriptArchive, (DiracFile, LocalFile)):
app.jobScriptArchive = None
generateDiracScripts(app)
try:
assert isinstance(app.jobScriptArchive, DiracFile)
except AssertionError:
raise ApplicationPrepareError(
"Failed to upload needed file, aborting submit")
rep_data = app.jobScriptArchive.getReplicas()
try:
assert rep_data != {}
except AssertionError:
raise ApplicationPrepareError(
"Failed to find a replica, aborting submit")
#Create a replica of the job and scripts files
replicateJobFile(app.jobScriptArchive)
replicateJobFile(app.uploadedInput)
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def get_user_dlls(appname,version,user_release_area,platform,shell):
user_ra = user_release_area
update_cmtproject_path(user_release_area)
full_user_ra = fullpath(user_ra) # expand any symbolic links
# Work our way through the CMTPATH until we find a cmt directory
if not shell.env.has_key('CMTPATH'): return [], [], []
projectdirs = shell.env['CMTPATH'].split(os.pathsep)
#appveruser = os.path.join(appname + '_' + version,'cmt')
appveruser = os.path.join(version,'cmt')
#appverrelease = os.path.join(appname.upper(),appname.upper() + '_' + version,
appverrelease = os.path.join('cmt')
for projectdir in projectdirs:
dir = fullpath(os.path.join(projectdir,appveruser))
logger.error('Looking for projectdir %s' % dir)
if os.path.exists(dir):
break
dir = fullpath(os.path.join(projectdir,appverrelease))
logger.error('Looking for projectdir %s' % dir)
if os.path.exists(dir):
break
logger.error('Using the CMT directory %s for identifying projects' % dir)
rc, showProj, m = shell.cmd1('cd ' + dir +';cmt show projects',
capture_stderr=True)
logger.error(showProj)
libs=[]
merged_pys = []
subdir_pys = {}
project_areas = []
py_project_areas = []
for line in showProj.split('\n'):
for entry in line.split():
if entry.startswith(user_ra) or entry.startswith(full_user_ra):
tmp = entry.rstrip('\)')
libpath = fullpath(os.path.join(tmp,'InstallArea',platform,'lib'))
logger.debug(libpath)
project_areas.append(libpath)
pypath = fullpath(os.path.join(tmp,'InstallArea','python'))
logger.debug(pypath)
py_project_areas.append(pypath)
pypath = fullpath(os.path.join(tmp,'InstallArea',platform,'python'))
logger.debug(pypath)
py_project_areas.append(pypath)
# savannah 47793 (remove multiple copies of the same areas)
project_areas = unique(project_areas)
py_project_areas = unique(py_project_areas)
ld_lib_path = []
if shell.env.has_key('LD_LIBRARY_PATH'):
ld_lib_path = shell.env['LD_LIBRARY_PATH'].split(':')
project_areas_dict = {}
for area in project_areas:
if area in ld_lib_path:
project_areas_dict[area] = ld_lib_path.index(area)
else:
project_areas_dict[area] = 666
from operator import itemgetter
sorted_project_areas = []
for item in sorted(project_areas_dict.items(),key=itemgetter(1)):
sorted_project_areas.append(item[0])
lib_names = []
for libpath in sorted_project_areas:
if os.path.exists(libpath):
for f in os.listdir(libpath):
if lib_names.count(f) > 0: continue
fpath = os.path.join(libpath,f)
if os.path.exists(fpath):
lib_names.append(f)
libs.append(fpath)
else:
logger.warning("File %s in %s does not exist. Skipping...",
str(f),str(libpath))
for pypath in py_project_areas:
if os.path.exists( pypath):
for f in os.listdir( pypath):
confDB_path = os.path.join( pypath, f)
if confDB_path.endswith( '.py'):
if os.path.exists( confDB_path):
merged_pys.append( confDB_path)
else:
logger.warning("File %s in %s does not exist. Skipping...",
str(f),str(confDB_path))
elif os.path.isdir(confDB_path):
pyfiles = []
for g in os.listdir(confDB_path):
file_path = os.path.join(confDB_path, g)
if (file_path.endswith('.py')):
if os.path.exists(file_path):
pyfiles.append(file_path)
else:
logger.warning("File %s in %s does not exist. Skipping...",
str(g),str(f))
subdir_pys[ f] = pyfiles
logger.debug("%s",pprint.pformat( libs))
logger.debug("%s",pprint.pformat( merged_pys))
logger.debug("%s",pprint.pformat( subdir_pys))
return libs, merged_pys, subdir_pys
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(
app, appmasterconfig, ['inputsandbox'])
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def master_prepare(self, app, appmasterconfig):
inputsandbox, outputsandbox = master_sandbox_prepare(app, appmasterconfig, ['inputsandbox'])
return StandardJobConfig(inputbox=unique(inputsandbox),
outputbox=unique(outputsandbox))
def getOutputSandboxFiles(self):
"""Get all output sandbox files. The duplicates are removed. """
from Ganga.Utility.util import unique
return unique(self.outputbox)
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
inputsandbox, outputsandbox = sandbox_prepare(app, appsubconfig, appmasterconfig, jobmasterconfig)
job = app.getJobObject()
if job.inputdata:
if not job.splitter:
if len(job.inputdata) > 100:
raise BackendError(
"You're submitting a job to Dirac with no splitter and more than 100 files, please add a splitter and try again!"
)
outputfiles = [this_file for this_file in job.outputfiles if isType(this_file, DiracFile)]
data_str = "import os\n"
data_str += "execfile('data.py')\n"
if hasattr(job, "_splitter_data"):
data_str += job._splitter_data
inputsandbox.append(FileBuffer("data-wrapper.py", data_str))
input_data = []
# Cant wait to get rid of this when people no-longer specify
# inputdata in options file
#######################################################################
# splitters ensure that subjobs pick up inputdata from job over that in
# optsfiles but need to take care of unsplit jobs
if not job.master:
share_path = os.path.join(get_share_path(app), "inputdata", "options_data.pkl")
if not job.inputdata:
if os.path.exists(share_path):
f = open(share_path, "r+b")
job.inputdata = pickle.load(f)
f.close()
#######################################################################
# Cant wait to get rid of this when people no-longer specify
# outputsandbox or outputdata in options file
#######################################################################
share_path = os.path.join(get_share_path(app), "output", "options_parser.pkl")
if os.path.exists(share_path):
# if not os.path.exists(share_path):
# raise GangaException('could not find the parser')
f = open(share_path, "r+b")
parser = pickle.load(f)
f.close()
outbox, outdata = parser.get_output(job)
from Ganga.GPIDev.Lib.File import FileUtils
from Ganga.GPIDev.Base.Filters import allComponentFilters
fileTransform = allComponentFilters["gangafiles"]
outdata_files = [
fileTransform(this_file, None)
for this_file in outdata
if not FileUtils.doesFileExist(this_file, job.outputfiles)
]
job.non_copyable_outputfiles.extend(
[output_file for output_file in outdata_files if not isType(output_file, DiracFile)]
)
outbox_files = [
fileTransform(this_file, None)
for this_file in outbox
if not FileUtils.doesFileExist(this_file, job.outputfiles)
]
job.non_copyable_outputfiles.extend(
[outbox_file for outbox_file in outbox_files if not isType(outbox_file, DiracFile)]
)
outputsandbox = [f.namePattern for f in job.non_copyable_outputfiles]
outputsandbox.extend([f.namePattern for f in job.outputfiles if not isType(f, DiracFile)])
outputsandbox = unique(outputsandbox) # + outbox[:])
#######################################################################
input_data_dirac, parametricinput_data = dirac_inputdata(job.application)
if input_data_dirac is not None:
for f in input_data_dirac:
if isType(f, DiracFile):
input_data.append(f.lfn)
elif isType(f, str):
input_data.append(f)
else:
raise ApplicationConfigurationError(
"Don't know How to handle anythig other than DiracFiles or strings to LFNs!"
)
commandline = "python ./gaudipython-wrapper.py"
if is_gaudi_child(app):
commandline = "gaudirun.py "
commandline += " ".join([str(arg) for arg in app.args])
commandline += " options.pkl data-wrapper.py"
logger.debug("Command line: %s: ", commandline)
gaudi_script_path = os.path.join(job.getInputWorkspace().getPath(), "gaudi-script.py")
script_generator(
gaudi_script_template(),
# remove_unreplaced = False,
outputfile_path=gaudi_script_path,
PLATFORM=app.platform,
COMMAND=commandline,
XMLSUMMARYPARSING=getXMLSummaryScript() # ,
# OUTPUTFILESINJECTEDCODE = getWNCodeForOutputPostprocessing(job, ' ')
)
# logger.debug( "input_data %s" % str( input_data ) )
# We want to propogate the ancestor depth to DIRAC when we have
# inputdata set
if job.inputdata is not None and isType(job.inputdata, LHCbDataset):
# As the RT Handler we already know we have a Dirac backend
if type(job.backend.settings) is not dict:
raise ApplicationConfigurationError(None, "backend.settings should be a dict")
if "AncestorDepth" in job.backend.settings:
ancestor_depth = job.backend.settings["AncestorDepth"]
else:
ancestor_depth = job.inputdata.depth
else:
ancestor_depth = 0
lhcbdirac_script_template = lhcbdiracAPI_script_template()
lhcb_dirac_outputfiles = lhcbdirac_outputfile_jdl(outputfiles)
# not necessary to use lhcbdiracAPI_script_template any more as doing our own uploads to Dirac
# remove after Ganga6 release
# NOTE special case for replicas: replicate string must be empty for no
# replication
dirac_script = script_generator(
lhcbdirac_script_template,
DIRAC_IMPORT="from LHCbDIRAC.Interfaces.API.DiracLHCb import DiracLHCb",
DIRAC_JOB_IMPORT="from LHCbDIRAC.Interfaces.API.LHCbJob import LHCbJob",
DIRAC_OBJECT="DiracLHCb()",
JOB_OBJECT="LHCbJob()",
NAME=mangle_job_name(app),
APP_NAME=app.appname,
APP_VERSION=app.version,
APP_SCRIPT=gaudi_script_path,
APP_LOG_FILE="Ganga_%s_%s.log" % (app.appname, app.version),
INPUTDATA=input_data,
PARAMETRIC_INPUTDATA=parametricinput_data,
OUTPUT_SANDBOX=API_nullifier(outputsandbox),
OUTPUTFILESSCRIPT=lhcb_dirac_outputfiles,
# job.fqid,#outputdata_path,
OUTPUT_PATH="",
OUTPUT_SE=getConfig("DIRAC")["DiracOutputDataSE"],
SETTINGS=diracAPI_script_settings(job.application),
DIRAC_OPTS=job.backend.diracOpts,
PLATFORM=app.platform,
REPLICATE="True" if getConfig("DIRAC")["ReplicateOutputData"] else "",
ANCESTOR_DEPTH=ancestor_depth,
## This is to be modified in the final 'submit' function in the backend
## The backend also handles the inputfiles DiracFiles ass appropriate
INPUT_SANDBOX="##INPUT_SANDBOX##",
)
logger.debug("prepare: LHCbGaudiDiracRunTimeHandler")
return StandardJobConfig(dirac_script, inputbox=unique(inputsandbox), outputbox=unique(outputsandbox))
class Gaudi(Francesc):
_name = 'Gaudi'
__doc__ = GaudiDocString(_name)
_category = 'applications'
_exportmethods = ['getenv','getpack', 'make', 'cmt', 'register', 'add_output_dir', 'get_output_dir', 'add_dataset_name', 'get_dataset_name']
schema = get_common_gaudi_schema()
docstr = 'The name of the optionsfile. Import statements in the file ' \
'will be expanded at submission time and a full copy made'
schema['optsfile'] = FileItem(sequence=1,strict_sequence=0,defvalue=[],
doc=docstr)
docstr = 'The name of the rec optionsfile. '
schema['recoptsfile'] = FileItem(sequence=1,strict_sequence=0,defvalue=[],
doc=docstr)
docstr = 'The name of the ana optionsfile. '
schema['anaoptsfile'] = FileItem(sequence=1,strict_sequence=0,defvalue=[],
doc=docstr)
docstr = 'The name of the Gaudi application (e.g. "DaVinci", "Gauss"...)'
schema['appname'] = SimpleItem(defvalue=None,typelist=['str','type(None)'],
hidden=1,doc=docstr)
schema['configured'] = SimpleItem(defvalue=None,hidden=0,copyable=0,
typelist=['str','type(None)'])
docstr = 'A python configurable string that will be appended to the ' \
'end of the options file. Can be multiline by using a ' \
'notation like \nHistogramPersistencySvc().OutputFile = ' \
'\"myPlots.root"\\nEventSelector().PrintFreq = 100\n or by ' \
'using triple quotes around a multiline string.'
schema['extraopts'] = SimpleItem(defvalue=None,
typelist=['str','type(None)'],doc=docstr)
docstr = 'User metadata'
schema['metadata'] = SimpleItem(defvalue={},doc=docstr)
docstr = 'Task name'
schema['taskname'] = SimpleItem(defvalue='',doc=docstr)
docstr = 'Long idle job'
schema['long_idle'] = SimpleItem(defvalue=False,doc=docstr)
docstr = 'Create dataset'
schema['create_dataset'] = SimpleItem(defvalue=True,doc=docstr)
docstr = 'Auto add stream number'
schema['auto_stream'] = SimpleItem(defvalue=False,doc=docstr)
docstr = 'Use local random trigger files'
schema['local_rantrg'] = SimpleItem(defvalue=True,doc=docstr)
docstr = 'Patch files'
schema['patch'] = SimpleItem(defvalue=[],doc=docstr)
docstr = 'Use patch for BOSS'
schema['use_boss_patch'] = SimpleItem(defvalue=True,doc=docstr)
docstr = 'Auto upload files'
schema['auto_upload'] = SimpleItem(defvalue=[],doc=docstr)
docstr = 'User workarea'
schema['user_workarea'] = SimpleItem(defvalue='',doc=docstr)
docstr = 'Use custom packages'
schema['use_custom_package'] = SimpleItem(defvalue=False,doc=docstr)
docstr = 'Output directory'
schema['output_dir'] = SimpleItem(defvalue='GangaBoss',doc=docstr)
docstr = 'Output root directory'
schema['output_rootdir'] = SimpleItem(defvalue='',doc=docstr)
docstr = 'Output data type'
schema['output_step'] = SimpleItem(defvalue=[],doc=docstr)
_schema = Schema(Version(2, 1), schema)
def _auto__init__(self):
"""bootstrap Gaudi applications. If called via a subclass
set up some basic structure like version platform..."""
if not self.appname: return
self._init(self.appname,True)
def master_configure(self):
self._validate_version()
job = self.getJobObject()
self._master_configure()
inputs = self._check_inputs()
optsfiles = [fileitem.name for fileitem in self.optsfile]
recoptsfiles = [fileitem.name for fileitem in self.recoptsfile]
anaoptsfiles = [fileitem.name for fileitem in self.anaoptsfile]
try:
parser = PythonOptionsParser(optsfiles,self.extraopts,self.shell)
if recoptsfiles:
recparser = PythonOptionsParser(recoptsfiles,self.extraopts,self.shell)
if anaoptsfiles:
anaparser = PythonOptionsParser(anaoptsfiles,self.extraopts,self.shell)
except ApplicationConfigurationError, e:
debug_dir = job.getDebugWorkspace().getPath()
f = open(debug_dir + '/gaudirun.stdout','w')
f.write(e.message)
f.close()
msg = 'Unable to parse job options! Please check options ' \
'files and extraopts. The output from gaudyrun.py can be ' \
'found in %s. You can also view this from within ganga '\
'by doing job.peek(\'../debug/gaudirun.stdout\').' % f.name
#logger.error(msg)
raise ApplicationConfigurationError(None,msg)
self.extra.master_input_buffers['options.opts'] = parser.opts_str
if recoptsfiles:
self.extra.master_input_buffers['recoptions.opts'] = recparser.opts_str
if anaoptsfiles:
self.extra.master_input_buffers['anaoptions.opts'] = anaparser.opts_str
inputdata = parser.get_input_data()
# If user specified a dataset, ignore optsfile data but warn the user.
if len(inputdata.files) > 0:
if job.inputdata:
msg = 'A dataset was specified for this job but one was ' \
'also defined in the options file. Data in the options '\
'file will be ignored...hopefully this is OK.'
logger.warning(msg)
else:
logger.info('Using the inputdata defined in the options file.')
self.extra.inputdata = inputdata
# only output the last step
if not self.output_step:
if anaoptsfiles:
self.output_step.append('ana')
elif recoptsfiles:
self.output_step.append('rec')
else:
self.output_step.append('sim')
# data type for each step
simoutputsandbox,simoutputdata = parser.get_output(job)
for temp_output in simoutputdata:
temp_data_type = os.path.splitext(temp_output)[-1][1:]
temp_data_type = temp_data_type.strip()
if temp_data_type in ['rtraw']:
self.extra.data_type['sim'] = temp_data_type
if recoptsfiles:
recoutputsandbox,recoutputdata = recparser.get_output(job)
for temp_output in recoutputdata:
temp_data_type = os.path.splitext(temp_output)[-1][1:]
temp_data_type = temp_data_type.strip()
if temp_data_type in ['dst', 'rec']:
self.extra.data_type['rec'] = temp_data_type
if anaoptsfiles:
anaoutputsandbox,anaoutputdata = anaparser.get_output(job)
self.extra.ana_file_nos = anaparser.get_ana_file_nos()
for temp_output in anaoutputdata:
temp_data_type = os.path.splitext(temp_output)[-1][1:]
temp_data_type = temp_data_type.strip()
if temp_data_type in ['root']:
self.extra.data_type['ana'] = temp_data_type
logger.debug('The output step : %s' % self.output_step)
logger.debug('The data_type : %s' % self.extra.data_type)
# get output file name
if anaoptsfiles:
self.extra.outputsandbox,outputdata = anaoutputsandbox,anaoutputdata
elif recoptsfiles:
self.extra.outputsandbox,outputdata = recoutputsandbox,recoutputdata
else:
self.extra.outputsandbox,outputdata = simoutputsandbox,simoutputdata
self.extra.outputdata.files += outputdata
self.extra.outputdata.files = unique(self.extra.outputdata.files)
self._validate_input()
self._custom_package()
self._auto_upload_workarea()
if self.output_rootdir:
bdr = BDRegister(self.extra.metadata)
bdr.setRootDir(self.output_rootdir)
self._prepare_metadata(parser)
self._task_info()
# write env into input dir
input_dir = job.getInputWorkspace().getPath()
file = gzip.GzipFile(input_dir + '/gaudi-env.py.gz','wb')
file.write('gaudi_env = %s' % str(self.shell.env))
file.close()
return (inputs, self.extra) # return (changed, extra)