def get_master_input_sandbox(job, extra):
sandbox = job.inputsandbox[:]
sandbox += extra.master_input_files[:]
buffers = extra.master_input_buffers
sandbox += [FileBuffer(n, s) for (n, s) in buffers.items()]
logger.debug("Master input sandbox: %s", str(sandbox))
return sandbox
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
job = app.getJobObject()
version = appsubconfig["version"]
outDir = appsubconfig["outDir"]
docDir = appsubconfig["docDir"]
elementList = docDir.split(os.sep)
docList = appsubconfig["docList"]
softwareDir = appsubconfig["softwareDir"]
lineList = []
inbox = []
outbox = []
headList, headBox = self.head( job = job, version = version, \
softwareDir = softwareDir )
lineList.extend(headList)
outbox.extend(headBox)
bodyList, bodyBox = self.body( job = job, docDir = docDir, \
docList = docList )
lineList.extend(bodyList)
inbox.extend(bodyBox)
tailList, tailBox = self.tail(job=job)
lineList.extend(tailList)
outbox.extend(tailBox)
jobScript = "\n".join(lineList)
jobWrapper = FileBuffer("PDF.sh", jobScript, executable=1)
outbox.extend(job.outputsandbox)
return StandardJobConfig\
( exe = jobWrapper, inputbox = inbox, outputbox = outbox )
def configure(self, masterappconfig):
self.args = convertIntToStringArgs(self.args)
job = self.getJobObject()
if self.cmtsetup == None:
raise ApplicationConfigurationError(None,
'No cmt setup script given.')
# Need to handle the possibility of multiple output files !
# setup the output file
for arg in self.args:
if arg == '-o':
raise ApplicationConfigurationError(
None,
'Option "-o" given in args. You must use the outputfile variable instead, even if you have multiple output files.'
)
if self.outputfile == None:
raise ApplicationConfigurationError(
None, 'No output file given. Fill the outputfile variable.')
else:
if type(self.outputfile) == type([]):
for OutFi in self.outputfile:
self.args.append('-o')
self.args.append(OutFi)
else:
self.args.append('-o')
self.args.append(self.outputfile)
# So get the list of filenames get_dataset_filenames() and create a file containing the list of files and put it in the sandbox
if job.inputdata == None:
raise ApplicationConfigurationError(
None, 'The inputdata variable is not defined.')
fileList = job.inputdata.get_dataset_filenames()
if len(fileList) < 1:
raise ApplicationConfigurationError(None,
'No input data file given.')
self.args.extend(fileList)
argsStr = ' '.join(self.args)
# Create the bash script and put it in input dir.
script = '#!/bin/bash\n'
script += 'source ' + self.cmtsetup + '\n'
script += self.exe + ' ' + argsStr + '\n'
from Ganga.GPIDev.Lib.File import FileBuffer
if self.exe.find('.exe') > -1:
scriptname = self.exe.replace('.exe', '.sh')
else:
scriptname = self.exe + '.sh'
job.getInputWorkspace().writefile(FileBuffer(scriptname, script),
executable=1)
self._scriptname = job.inputdir + scriptname
return (None, None)
def preparejob(self, jobconfig, master_input_sandbox):
job = self.getJobObject()
# print str(job.backend_output_postprocess)
mon = job.getMonitoringService()
import Ganga.Core.Sandbox as Sandbox
subjob_input_sandbox = job.createPackedInputSandbox(jobconfig.getSandboxFiles() + Sandbox.getGangaModulesAsSandboxFiles(Sandbox.getDefaultModules()))
appscriptpath = [jobconfig.getExeString()] + jobconfig.getArgStrings()
if self.nice:
appscriptpath = ['nice', '-n %d' % self.nice] + appscriptpath
if self.nice < 0:
logger.warning('increasing process priority is often not allowed, your job may fail due to this')
sharedoutputpath = job.getOutputWorkspace().getPath()
## FIXME DON'T just use the blind list here, request the list of files to be in the output from a method.
outputpatterns = jobconfig.outputbox
environment = dict() if jobconfig.env is None else jobconfig.env
import tempfile
workdir = tempfile.mkdtemp(dir=config['location'])
import inspect
script_location = os.path.join(os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))),
'LocalHostExec.py')
from Ganga.GPIDev.Lib.File import FileUtils
script = FileUtils.loadScript(script_location, '')
script = script.replace('###INLINEMODULES###', inspect.getsource(Sandbox.WNSandbox))
from Ganga.GPIDev.Lib.File.OutputFileManager import getWNCodeForOutputSandbox, getWNCodeForOutputPostprocessing, getWNCodeForDownloadingInputFiles, getWNCodeForInputdataListCreation
from Ganga.Utility.Config import getConfig
jobidRepr = repr(job.getFQID('.'))
script = script.replace('###OUTPUTSANDBOXPOSTPROCESSING###', getWNCodeForOutputSandbox(job, ['stdout', 'stderr', '__syslog__'], jobidRepr))
script = script.replace('###OUTPUTUPLOADSPOSTPROCESSING###', getWNCodeForOutputPostprocessing(job, ''))
script = script.replace('###DOWNLOADINPUTFILES###', getWNCodeForDownloadingInputFiles(job, ''))
script = script.replace('###CREATEINPUTDATALIST###', getWNCodeForInputdataListCreation(job, ''))
script = script.replace('###APPLICATION_NAME###', repr(getName(job.application)))
script = script.replace('###INPUT_SANDBOX###', repr(subjob_input_sandbox + master_input_sandbox))
script = script.replace('###SHAREDOUTPUTPATH###', repr(sharedoutputpath))
script = script.replace('###APPSCRIPTPATH###', repr(appscriptpath))
script = script.replace('###OUTPUTPATTERNS###', str(outputpatterns))
script = script.replace('###JOBID###', jobidRepr)
script = script.replace('###ENVIRONMENT###', repr(environment))
script = script.replace('###WORKDIR###', repr(workdir))
script = script.replace('###INPUT_DIR###', repr(job.getStringInputDir()))
self.workdir = workdir
script = script.replace('###GANGADIR###', repr(getConfig('System')['GANGA_PYTHONPATH']))
wrkspace = job.getInputWorkspace()
scriptPath = wrkspace.writefile(FileBuffer('__jobscript__', script), executable=1)
return scriptPath
def downloadWrapper(app):
from os.path import join, split
from Ganga.GPIDev.Lib.File import FileBuffer
import string
from Ganga.GPIDev.Lib.File import getSharedPath
rootsys = join('.', 'root')
rootenv = {'ROOTSYS': rootsys}
script = app.script
if script == File():
if not app.usepython:
script = File(defaultScript())
else:
script = File(defaultPyRootScript())
else:
script = File(os.path.join(os.path.join(Ganga.GPIDev.Lib.File.getSharedPath(), app.is_prepared.name), os.path.basename(app.script.name)))
commandline = ''
scriptPath = join('.', script.subdir, split(script.name)[1])
if not app.usepython:
# Arguments to the ROOT script needs to be a comma separated list
# enclosed in (). Strings should be enclosed in escaped double quotes.
arglist = []
for arg in app.args:
if isinstance(arg, str):
arglist.append('\\\'' + arg + '\\\'')
else:
arglist.append(arg)
rootarg = '\(\"' + string.join([str(s) for s in arglist], ',') + '\"\)'
# use root
commandline = 'root.exe -b -q ' + scriptPath + rootarg + ''
else:
# use python
pyarg = string.join([str(s) for s in app.args], ' ')
commandline = '\'%(PYTHONCMD)s ' + scriptPath + ' ' + pyarg + ' -b \''
logger.debug("Command line: %s: ", commandline)
# Write a wrapper script that installs ROOT and runs script
script_location = os.path.join(os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))),
'wrapperScriptTemplate.py')
from Ganga.GPIDev.Lib.File import FileUtils
wrapperscript = FileUtils.loadScript(script_location, '')
wrapperscript = wrapperscript.replace('###COMMANDLINE###', commandline)
wrapperscript = wrapperscript.replace('###ROOTVERSION###', app.version)
wrapperscript = wrapperscript.replace('###SCRIPTPATH###', scriptPath)
wrapperscript = wrapperscript.replace('###USEPYTHON###', str(app.usepython))
logger.debug('Script to run on worker node\n' + wrapperscript)
scriptName = "rootwrapper_generated_%s.py" % randomString()
runScript = FileBuffer(scriptName, wrapperscript, executable=1)
inputsandbox = app._getParent().inputsandbox + [script]
return runScript, inputsandbox, rootenv
def configure(self, masterappconfig):
self.args = convertIntToStringArgs(self.args)
job = self.getJobObject()
if self.cmtsetup == None:
raise ApplicationConfigurationError(None,
'No cmt setup script given.')
# setup the output file
for arg in self.args:
if arg == '-o':
raise ApplicationConfigurationError(
None,
'Option "-o" given in args. You must use the outputfile variable instead.'
)
if self.outputfile == None:
raise ApplicationConfigurationError(
None, 'No output file given. Fill the outputfile variable.')
else:
self.args.append('-o')
self.args.append(self.outputfile)
# So get the list of filenames get_dataset_filenames() and create a file containing the list of files and put it in the sandbox
fileList = job.inputdir + 'FileList'
if not job.inputdata.set_dataset_into_list(fileList):
raise ApplicationConfigurationError(
None,
'Problem with the preparation of the list of input files')
self.args.append(fileList)
argsStr = ' '.join(self.args)
# ANT: Create the bash script here and put it in input dir.
script = '#!/bin/bash\n'
script += 'source ' + self.cmtsetup + '\n'
script += self.exe + ' ' + argsStr + '\n'
from Ganga.GPIDev.Lib.File import FileBuffer
if self.exe.find('.exe') > -1:
scriptname = self.exe.replace('.exe', '.sh')
else:
scriptname = self.exe + '.sh'
job.getInputWorkspace().writefile(FileBuffer(scriptname, script),
executable=1)
self._scriptname = job.inputdir + scriptname
return (None, None)
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 writefile(self, fileobj, executable=None):
from Ganga.GPIDev.Lib.File import FileBuffer
if not isType(fileobj, FileBuffer):
try:
name, contents = fileobj
except TypeError as err:
import traceback
traceback.print_stack()
logger.debug("TypeError: %s" % str(err))
pass
else:
fileobj = FileBuffer(name, contents)
logger.warning('file "%s": usage of tuples is deprecated, use FileBuffer instead', name)
# output file name
# Added a subdir to files, (see Ganga/GPIDev/Lib/File/File.py) This allows
# to copy files into the a subdirectory of the workspace
# FIXME: make a helper method for os.makedirs
path_to_build = os.path.join(self.getPath(), fileobj.subdir)
if not os.path.isdir(path_to_build):
os.makedirs(path_to_build)
logger.debug('created %s', self.getPath())
else:
logger.debug('already exists: %s', self.getPath())
outname = expandfilename(self.getPath(fileobj.getPathInSandbox()))
fileobj.create(outname)
if executable:
chmod_executable(outname)
return outname
def createNewJob(self):
"""Create any jobs required for this unit"""
j = GPI.Job()
j._impl.backend = self._getParent().backend.clone()
j._impl.application = self._getParent().application.clone()
j.inputdata = self.inputdata.clone()
trf = self._getParent()
task = trf._getParent()
# copy across the outputfiles
for f in trf.outputfiles:
j.outputfiles += [f.clone()]
j.inputsandbox = trf.inputsandbox
if type(self.eventswanted) == type(''):
subLines = self.eventswanted
else:
subLines = '\n'.join(self.eventswanted)
# Base for the naming of each subjob's CSV file
incsvfile = j._impl.application.csvfile
tmpname = os.path.basename(incsvfile)
if len(tmpname.split('.')) > 1:
patterncsv = '.'.join(tmpname.split('.')[0:-1])+"_sub%d."+ tmpname.split('.')[-1]
else:
patterncsv = tmpname+"_sub%d"
from Ganga.GPIDev.Lib.File import FileBuffer
thiscsv = patterncsv % self.subpartid
# Create the CSV file for this Unit
j._impl.getInputWorkspace().writefile(FileBuffer(thiscsv,subLines),executable=0)
j._impl.application.csvfile = j._impl.getInputWorkspace().getPath()+thiscsv
j.inputsandbox.append(j._impl.getInputWorkspace().getPath()+thiscsv)
# Base for the naming of each subjob's output file
tmpname = os.path.basename(j._impl.application.outputfile)
if len(tmpname.split('.')) > 1:
patternout = '.'.join(tmpname.split('.')[0:-1])+"_sub%d."+ tmpname.split('.')[-1]
else:
patternout = tmpname+"_sub%d"
j._impl.application.outputfile = patternout % self.subpartid
# Sort out the splitter
if trf.splitter:
j.splitter = trf.splitter.clone()
return j
def wrapper(self, regexp, version, timeout, kernel):
"""Write a wrapper Python script that executes the notebooks"""
wrapperscript = FileUtils.loadScript(self.templatelocation(), '')
wrapperscript = wrapperscript.replace('###NBFILES###', str(regexp))
wrapperscript = wrapperscript.replace('###VERSION###', str(version))
wrapperscript = wrapperscript.replace('###TIMEOUT###', str(timeout))
wrapperscript = wrapperscript.replace('###KERNEL###', str(kernel))
wrapperscript = wrapperscript.replace('###UUID###', str(uuid.uuid4()))
logger.debug('Script to run on worker node\n' + wrapperscript)
scriptName = "notebook_wrapper_generated.py"
runScript = FileBuffer(scriptName, wrapperscript, executable=1)
return runScript
def writefile(self, fileobj, executable=None):
from Ganga.GPIDev.Lib.File import FileBuffer
try:
name, contents = fileobj
except TypeError:
pass
else:
fileobj = FileBuffer(name, contents)
logger.warning(
'file "%s": usage of tuples is deprecated, use FileBuffer instead', name)
# output file name
# Added a subdir to files, (see Ganga/GPIDev/Lib/File/File.py) This allows
# to copy files into the a subdirectory of the workspace
# FIXME: make a helper method for os.makedirs
try:
os.makedirs(self.getPath() + fileobj.subdir)
logger.debug('created %s', self.getPath())
except OSError as x:
import errno
if x.errno == errno.EEXIST:
logger.debug('EEXIT: %s', self.getPath())
else:
raise
outname = expandfilename(self.getPath(fileobj.getPathInSandbox()))
fileobj.create(outname)
if executable:
chmod_executable(outname)
return outname
def split(self, job):
import os
subjobs = []
subsets = splitCSVFile(job.application.csvfile, self.nbevents)
# Less files than number of jobs wanted => easy
logger.info('Creating %d subjobs ...', len(allLines))
# Base for the naming of each subjob's CSV file
tmpname = os.path.basename(incsvfile)
if len(tmpname.split('.')) > 1:
patterncsv = '.'.join(
tmpname.split('.')[0:-1]) + "_sub%d." + tmpname.split('.')[-1]
else:
patterncsv = tmpname + "_sub%d"
# Base for the naming of each subjob's output file
tmpname = os.path.basename(job.application.outputfile)
if len(tmpname.split('.')) > 1:
patternout = '.'.join(
tmpname.split('.')[0:-1]) + "_sub%d." + tmpname.split('.')[-1]
else:
patternout = tmpname + "_sub%d"
for s, sub in enumerate(subsets):
j = addProxy(self.createSubjob(job))
j.inputdata = job.inputdata
subLines = '\n'.join(sub)
from Ganga.GPIDev.Lib.File import FileBuffer
thiscsv = patterncsv % s
# Save in the main job's inputdir now, then the file will be moved to
# the inputdir of each subjobs.
job.getInputWorkspace().writefile(FileBuffer(thiscsv, subLines),
executable=0)
j.application.csvfile = os.path.join(job.inputdir, thiscsv)
j.application.outputfile = patternout % s
# Prepare the output filenames which must be unique
subjobs.append(stripProxy(j))
return subjobs
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
job = app.getJobObject()
version = appsubconfig["version"]
libList = appsubconfig["libList"]
classifierDir = appsubconfig["classifierDir"]
outDir = appsubconfig["outDir"]
imageDir = appsubconfig["imageDir"]
elementList = imageDir.split(os.sep)
imageList = appsubconfig["imageList"]
tagFile = appsubconfig["tagFile"]
lineList = []
inbox = []
outbox = []
headList, headBox = self.head( job = job, version = version, \
libList = libList, classifierDir = classifierDir )
lineList.extend(headList)
outbox.extend(headBox)
bodyList, bodyBox = self.body( job = job, imageDir = imageDir, \
imageList = imageList, tagFile = tagFile )
lineList.extend(bodyList)
inbox.extend(bodyBox)
tailList, tailBox = self.tail(job=job)
lineList.extend(tailList)
outbox.extend(tailBox)
jobScript = "\n".join(lineList)
jobWrapper = FileBuffer("Classify.sh", jobScript, executable=1)
outbox.extend(job.outputsandbox)
return StandardJobConfig\
( exe = jobWrapper, inputbox = inbox, outputbox = outbox )
def prepare(self, app, appsubconfig, appmasterconfig, jobmasterconfig):
job = app.getJobObject()
exePath = appsubconfig["exePath"]
outDir = appsubconfig["outDir"]
imageDir = appsubconfig["imageDir"]
elementList = imageDir.split(os.sep)
imageSubdir = \
os.sep.join( elementList[ elementList.index( "images" ) : ] )
urlRoot = \
os.path.join( "http://hovercraft.hep.phy.cam.ac.uk", imageSubdir )
imageList = appsubconfig["imageList"]
lineList = []
outbox = []
headList, headBox = self.head(job=job, exePath=exePath)
lineList.extend(headList)
outbox.extend(headBox)
bodyList, bodyBox = self.body( job = job, imageDir = imageDir, \
urlRoot = urlRoot, imageList = imageList )
lineList.extend(bodyList)
outbox.extend(bodyBox)
tailList, tailBox = self.tail(job=job)
lineList.extend(tailList)
outbox.extend(tailBox)
jobScript = "\n".join(lineList)
jobWrapper = FileBuffer("VansegLocal.sh", jobScript, executable=1)
outbox.extend(job.outputsandbox)
return StandardJobConfig\
( exe = jobWrapper, outputbox = outbox )
def preparejob(self, jobconfig, master_job_sandbox):
'''Prepare the JDL'''
script = self.__jobWrapperTemplate__()
job = self.getJobObject()
inpw = job.getInputWorkspace()
wrapperlog = '__jobscript__.log'
import Ganga.Core.Sandbox as Sandbox
# FIXME: check what happens if 'stdout','stderr' are specified here
script = script.replace('###OUTPUTSANDBOX###',
repr(jobconfig.outputbox))
script = script.replace('###APPLICATION_NAME###',
getName(job.application))
script = script.replace('###APPLICATIONEXEC###',
repr(jobconfig.getExeString()))
script = script.replace('###APPLICATIONARGS###',
repr(jobconfig.getArguments()))
from Ganga.GPIDev.Lib.File.OutputFileManager import getWNCodeForOutputPostprocessing, getWNCodeForDownloadingInputFiles
script = script.replace('###OUTPUTUPLOADSPOSTPROCESSING###',
getWNCodeForOutputPostprocessing(job, ' '))
script = script.replace('###DOWNLOADINPUTFILES###',
getWNCodeForDownloadingInputFiles(job, ' '))
if jobconfig.env:
script = script.replace('###APPLICATIONENVS###',
repr(jobconfig.env))
else:
script = script.replace('###APPLICATIONENVS###', repr({}))
script = script.replace('###WRAPPERLOG###', repr(wrapperlog))
import inspect
script = script.replace('###INLINEMODULES###',
inspect.getsource(Sandbox.WNSandbox))
mon = job.getMonitoringService()
self.monInfo = None
# set the monitoring file by default to the stdout
if isinstance(self.monInfo, dict):
self.monInfo['remotefile'] = 'stdout'
# try to print out the monitoring service information in debug mode
try:
logger.debug('job info of monitoring service: %s' %
str(self.monInfo))
except:
pass
# prepare input/output sandboxes
import Ganga.Utility.files
from Ganga.GPIDev.Lib.File import File
from Ganga.Core.Sandbox.WNSandbox import PYTHON_DIR
import inspect
fileutils = File(inspect.getsourcefile(Ganga.Utility.files),
subdir=PYTHON_DIR)
packed_files = jobconfig.getSandboxFiles() + [fileutils]
sandbox_files = job.createPackedInputSandbox(packed_files)
# sandbox of child jobs should include master's sandbox
sandbox_files.extend(master_job_sandbox)
# check the input file size and pre-upload larger inputs to the iocache
lfc_host = ''
input_sandbox_uris = []
input_sandbox_names = []
ick = True
max_prestaged_fsize = 0
for f in sandbox_files:
idx = self.__check_and_prestage_inputfile__(f)
if not idx:
logger.error('input sandbox preparation failed: %s' % f)
ick = False
break
else:
if idx['lfc_host']:
lfc_host = idx['lfc_host']
if idx['remote']:
abspath = os.path.abspath(f)
fsize = os.path.getsize(abspath)
if fsize > max_prestaged_fsize:
max_prestaged_fsize = fsize
input_sandbox_uris.append(
idx['remote'][os.path.basename(f)])
input_sandbox_names.append(os.path.basename(
urlparse(f)[2]))
if idx['local']:
input_sandbox_uris += idx['local']
input_sandbox_names.append(os.path.basename(f))
if not ick:
logger.error('stop job submission')
return None
# determin the lcg-cp timeout according to the max_prestaged_fsize
# - using the assumption of 1 MB/sec.
max_prestaged_fsize = 0
lfc_host = ''
transfer_timeout = config['SandboxTransferTimeout']
predict_timeout = int(math.ceil(max_prestaged_fsize / 1000000.0))
if predict_timeout > transfer_timeout:
transfer_timeout = predict_timeout
if transfer_timeout < 60:
transfer_timeout = 60
script = script.replace('###TRANSFERTIMEOUT###',
'%d' % transfer_timeout)
# update the job wrapper with the inputsandbox list
script = script.replace(
'###INPUTSANDBOX###',
repr({
'remote': {},
'local': input_sandbox_names
}))
# write out the job wrapper and put job wrapper into job's inputsandbox
scriptPath = inpw.writefile(FileBuffer(
'__jobscript_%s__' % job.getFQID('.'), script),
executable=1)
input_sandbox = input_sandbox_uris + [scriptPath]
for isb in input_sandbox:
logger.debug('ISB URI: %s' % isb)
# compose output sandbox to include by default the following files:
# - gzipped stdout (transferred only when the JobLogHandler is WMS)
# - gzipped stderr (transferred only when the JobLogHandler is WMS)
# - __jobscript__.log (job wrapper's log)
output_sandbox = [wrapperlog]
from Ganga.GPIDev.Lib.File.OutputFileManager import getOutputSandboxPatterns
for outputSandboxPattern in getOutputSandboxPatterns(job):
output_sandbox.append(outputSandboxPattern)
if config['JobLogHandler'] in ['WMS']:
output_sandbox += ['stdout.gz', 'stderr.gz']
if len(jobconfig.outputbox):
output_sandbox += [Sandbox.OUTPUT_TARBALL_NAME]
# compose ARC XRSL
xrsl = {
#'VirtualOrganisation' : config['VirtualOrganisation'],
'executable': os.path.basename(scriptPath),
'environment': {
'GANGA_LCG_VO': config['VirtualOrganisation'],
'GANGA_LOG_HANDLER': config['JobLogHandler'],
'LFC_HOST': lfc_host
},
#'stdout' : 'stdout',
#'stderr' : 'stderr',
'inputFiles': input_sandbox,
'outputFiles': output_sandbox,
#'OutputSandboxBaseDestURI': 'gsiftp://localhost'
}
xrsl['environment'].update({'GANGA_LCG_CE': self.CE})
#xrsl['Requirements'] = self.requirements.merge(jobconfig.requirements).convert()
# if self.jobtype.upper() in ['NORMAL','MPICH']:
#xrsl['JobType'] = self.jobtype.upper()
# if self.jobtype.upper() == 'MPICH':
#xrsl['Requirements'].append('(other.GlueCEInfoTotalCPUs >= NodeNumber)')
# xrsl['Requirements'].append('Member("MPICH",other.GlueHostApplicationSoftwareRunTimeEnvironment)')
#xrsl['NodeNumber'] = self.requirements.nodenumber
# else:
# logger.warning('JobType "%s" not supported' % self.jobtype)
# return
# additional settings from the job
if jobconfig.env:
xrsl['environment'].update(jobconfig.env)
xrslText = Grid.expandxrsl(xrsl)
# append any additional requirements from the requirements object
xrslText += '\n'.join(self.requirements.other)
logger.debug('subjob XRSL: %s' % xrslText)
return inpw.writefile(FileBuffer('__xrslfile__', xrslText))
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 configure(self, masterappconfig):
if self.cmtsetup == None:
raise ApplicationConfigurationError(None,
'No cmt setup script given.')
# __________ TREx first ____________
trex_args = convertIntToStringArgs(self.trex_args)
job = self.getJobObject()
# Need to handle the possibility of multiple output files !
# setup the output file
for arg in trex_args:
if arg == '-o':
raise ApplicationConfigurationError(
None,
'Option "-o" given in trex_args. The module will define the output filename.'
)
# So get the list of filenames get_dataset_filenames() and create a file containing the list of files and put it in the sandbox
if job.inputdata == None:
raise ApplicationConfigurationError(
None, 'The inputdata variable is not defined.')
fileList = job.inputdata.get_dataset_filenames()
if len(fileList) < 1:
raise ApplicationConfigurationError(None,
'No input data file given.')
trex_args.extend(fileList)
firstFile = fileList[0].split('/')[-1]
# Define the output
trex_args.append('-o')
if self.filenamesubstr == None:
trex_outputfile = 'recoOutput.root'
else:
trex_outputfile = firstFile.replace(self.filenamesubstr, "trex")
trex_args.append(trex_outputfile)
# __________ Now oaAnalysis ____________
oaana_args = convertIntToStringArgs(self.oaana_args)
job = self.getJobObject()
# Need to handle the possibility of multiple output files !
# setup the output file
for arg in oaana_args:
if arg == '-o':
raise ApplicationConfigurationError(
None,
'Option "-o" given in oaana_args. You must use the oaana_outputfile variable instead.'
)
oaana_args.append('-o')
if self.filenamesubstr == None:
oaana_outputfile = 'recoOutput.root'
else:
oaana_outputfile = firstFile.replace(self.filenamesubstr, "anal")
# protection against failed substitution
if oaana_outputfile == trex_outputfile:
oaana_outputfile = oaana_outputfile.replace(
".root", "_anal.root")
oaana_args.append(oaana_outputfile)
# Use the reco output as an input for the VFT processing.
if self.oaana_only:
oaana_args.extend(fileList)
else:
oaana_args.append(trex_outputfile)
trex_argsStr = ' '.join(trex_args)
oaana_argsStr = ' '.join(oaana_args)
# Create the bash script and put it in input dir.
script = '#!/bin/bash\n'
script += 'source ' + self.cmtsetup + '\n'
if not self.oaana_only:
script += 'RunTREx.exe ' + trex_argsStr + '\n'
script += 'RunOAAnalysis.exe ' + oaana_argsStr + '\n'
from Ganga.GPIDev.Lib.File import FileBuffer
scriptname = 'TRExPlusOAAnalysis.sh'
job.getInputWorkspace().writefile(FileBuffer(scriptname, script),
executable=1)
self._scriptname = job.inputdir + scriptname
return (None, None)
def preparejob(self, jobconfig, master_input_sandbox):
"""Method for preparing job script"""
job = self.getJobObject()
from Ganga.GPIDev.Lib.File import File
from Ganga.Core.Sandbox.WNSandbox import PYTHON_DIR
import Ganga.Utility.files
import inspect
fileutils = File(inspect.getsourcefile(Ganga.Utility.files),
subdir=PYTHON_DIR)
inputfiles = jobconfig.getSandboxFiles() + [fileutils]
inbox = job.createPackedInputSandbox(inputfiles)
inbox.extend(master_input_sandbox)
inpDir = job.getInputWorkspace(create=True).getPath()
outDir = job.getOutputWorkspace(create=True).getPath()
workdir = tempfile.mkdtemp()
self.workdir = workdir
exeString = jobconfig.getExeString()
argList = jobconfig.getArgStrings()
argString = " ".join(map(lambda x: " %s " % x, argList))
outputSandboxPatterns = jobconfig.outputbox
patternsToZip = []
wnCodeForPostprocessing = ''
wnCodeToDownloadInputFiles = ''
if (len(job.outputfiles) > 0):
from Ganga.GPIDev.Lib.File.OutputFileManager import getOutputSandboxPatternsForInteractive, getWNCodeForOutputPostprocessing
(outputSandboxPatterns,
patternsToZip) = getOutputSandboxPatternsForInteractive(job)
wnCodeForPostprocessing = 'def printError(message):pass\ndef printInfo(message):pass' + \
getWNCodeForOutputPostprocessing(job, '')
all_inputfiles = [this_file for this_file in job.inputfiles]
if job.master is not None:
all_inputfiles.extend(
[this_file for this_file in job.master.inputfiles])
wnCodeToDownloadInputFiles = ''
if (len(all_inputfiles) > 0):
from Ganga.GPIDev.Lib.File.OutputFileManager import outputFilePostProcessingOnWN
for inputFile in all_inputfiles:
inputfileClassName = getName(inputFile)
logger.debug("name: %s" % inputfileClassName)
logger.debug(
"result: %s" %
str(outputFilePostProcessingOnWN(job, inputfileClassName)))
if outputFilePostProcessingOnWN(job, inputfileClassName):
inputFile.processWildcardMatches()
if inputFile.subfiles:
getfromFile = False
for subfile in inputFile.subfiles:
wnCodeToDownloadInputFiles += subfile.getWNScriptDownloadCommand(
'')
else:
getfromFile = True
else:
getFromFile = True
if getFromFile:
wnCodeToDownloadInputFiles += inputFile.getWNScriptDownloadCommand(
'')
wnCodeToDownloadInputData = ''
if job.inputdata and (len(job.inputdata) > 0):
from Ganga.GPIDev.Lib.File.OutputFileManager import getWNCodeForDownloadingInputFiles
wnCodeToDownloadInputData = getWNCodeForDownloadingInputFiles(
job, '')
import inspect
replace_dict = {
'###CONSTRUCT_TIME###': (time.strftime("%c")),
'###WNSANDBOX_SOURCE###':
inspect.getsource(Sandbox.WNSandbox),
'###GANGA_PYTHONPATH###':
getConfig("System")["GANGA_PYTHONPATH"],
'###OUTPUTDIR###':
outDir,
'###WORKDIR###':
workdir,
'###IN_BOX###':
inbox,
'###WN_INPUTFILES###':
wnCodeToDownloadInputFiles,
'###WN_INPUTDATA###':
wnCodeToDownloadInputData,
'###JOBCONFIG_ENV###':
jobconfig.env if jobconfig.env is not None else dict(),
'###EXE_STRING###':
exeString,
'###ARG_STRING###':
argString,
'###WN_POSTPROCESSING###':
wnCodeForPostprocessing,
'###PATTERNS_TO_ZIP###':
patternsToZip,
'###OUTPUT_SANDBOX_PATTERNS###':
outputSandboxPatterns
}
script_location = os.path.join(
os.path.dirname(
os.path.abspath(inspect.getfile(inspect.currentframe()))),
'InteractiveScriptTemplate.py.template')
from Ganga.GPIDev.Lib.File import FileUtils
commandString = FileUtils.loadScript(script_location, '')
for k, v in replace_dict.iteritems():
commandString = commandString.replace(str(k), str(v))
return job.getInputWorkspace().writefile(FileBuffer(
"__jobscript__", commandString),
executable=1)
def configure(self, masterappconfig):
if self.cmtsetup == None:
raise ApplicationConfigurationError(None,
'No cmt setup script given.')
# __________ Reco first ____________
reco_args = convertIntToStringArgs(self.reco_args)
job = self.getJobObject()
# Need to handle the possibility of multiple output files !
# setup the output file
for arg in reco_args:
if arg == '-o':
raise ApplicationConfigurationError(
None,
'Option "-o" given in reco_args. You must use the filenamesubstr and reconewstr variables instead to define an output.'
)
# So get the list of filenames get_dataset_filenames() and create a file containing the list of files and put it in the sandbox
if job.inputdata == None:
raise ApplicationConfigurationError(
None, 'The inputdata variable is not defined.')
fileList = job.inputdata.get_dataset_filenames()
if len(fileList) < 1:
raise ApplicationConfigurationError(None,
'No input data file given.')
firstFile = fileList[0].split('/')[-1]
# Define the output
reco_args.append('-o')
if self.filenamesubstr == None:
reco_outputfile = 'recoOutput.root'
else:
reco_outputfile = firstFile.replace(self.filenamesubstr,
self.reconewstr)
reco_args.append(reco_outputfile)
# Just to define the output before the potentially long list of input files
reco_args.extend(fileList)
# __________ Now VFT ____________
vft_args = convertIntToStringArgs(self.vft_args)
job = self.getJobObject()
# Need to handle the possibility of multiple output files !
# setup the output file
for arg in vft_args:
if arg == '-o':
raise ApplicationConfigurationError(
None,
'Option "-o" given in vft_args. You must use the filenamesubstr and reconewstr variables instead to define an output.'
)
# Define the output
vft_args.append('-o')
if self.filenamesubstr == None:
vft_outputfile = 'vftOutput.root'
else:
vft_outputfile = firstFile.replace(self.filenamesubstr,
self.vftnewstr)
vft_args.append(vft_outputfile)
# Use the reco output as an input for the VFT processing
# or use the input file list if running in VFT only mode.
if self.vft_only:
vft_args.extend(fileList)
else:
vft_args.append(reco_outputfile)
reco_argsStr = ' '.join(reco_args)
vft_argsStr = ' '.join(vft_args)
# Create the bash script and put it in input dir.
script = '#!/bin/bash\n'
script += 'source ' + self.cmtsetup + '\n'
if not self.vft_only:
script += self.reco_exe + ' ' + reco_argsStr + '\n'
script += self.vft_exe + ' ' + vft_argsStr + '\n'
from Ganga.GPIDev.Lib.File import FileBuffer
scriptname = 'RecoPlusVFT.sh'
job.getInputWorkspace().writefile(FileBuffer(scriptname, script),
executable=1)
self._scriptname = job.inputdir + scriptname
return (None, None)
def preparejob(self, jobconfig, master_input_sandbox):
job = self.getJobObject()
mon = job.getMonitoringService()
import Ganga.Core.Sandbox as Sandbox
from Ganga.GPIDev.Lib.File import File
from Ganga.Core.Sandbox.WNSandbox import PYTHON_DIR
import inspect
fileutils = File( inspect.getsourcefile(Ganga.Utility.files), subdir=PYTHON_DIR )
subjob_input_sandbox = job.createPackedInputSandbox(jobconfig.getSandboxFiles() + [ fileutils ] )
appscriptpath = [jobconfig.getExeString()] + jobconfig.getArgStrings()
sharedoutputpath = job.getOutputWorkspace().getPath()
## FIXME Check this isn't a GangaList
outputpatterns = jobconfig.outputbox
environment = jobconfig.env if not jobconfig.env is None else {}
import inspect
script_location = os.path.join(os.path.dirname(os.path.abspath(inspect.getfile(inspect.currentframe()))),
'BatchScriptTemplate.py')
from Ganga.GPIDev.Lib.File import FileUtils
text = FileUtils.loadScript(script_location, '')
import Ganga.Core.Sandbox as Sandbox
import Ganga.Utility as Utility
from Ganga.Utility.Config import getConfig
from Ganga.GPIDev.Lib.File.OutputFileManager import getWNCodeForOutputSandbox, getWNCodeForOutputPostprocessing, getWNCodeForDownloadingInputFiles
jobidRepr = repr(self.getJobObject().getFQID('.'))
replace_dict = {
'###OUTPUTSANDBOXPOSTPROCESSING###' : getWNCodeForOutputSandbox(job, ['__syslog__'], jobidRepr),
'###OUTPUTUPLOADSPOSTPROCESSING###' : getWNCodeForOutputPostprocessing(job, ''),
'###DOWNLOADINPUTFILES###' : getWNCodeForDownloadingInputFiles(job, ''),
'###INLINEMODULES###' : inspect.getsource(Sandbox.WNSandbox),
'###INLINEHOSTNAMEFUNCTION###' : inspect.getsource(Utility.util.hostname),
'###APPSCRIPTPATH###' : repr(appscriptpath),
#'###SHAREDINPUTPATH###' : repr(sharedinputpath)),
'###INPUT_SANDBOX###' : repr(subjob_input_sandbox + master_input_sandbox),
'###SHAREDOUTPUTPATH###' : repr(sharedoutputpath),
'###OUTPUTPATTERNS###' : repr(outputpatterns),
'###JOBID###' : jobidRepr,
'###ENVIRONMENT###' : repr(environment),
'###PREEXECUTE###' : self.config['preexecute'],
'###POSTEXECUTE###' : self.config['postexecute'],
'###JOBIDNAME###' : self.config['jobid_name'],
'###QUEUENAME###' : self.config['queue_name'],
'###HEARTBEATFREQUENCE###' : self.config['heartbeat_frequency'],
'###INPUT_DIR###' : repr(job.getStringInputDir()),
'###GANGADIR###' : repr(getConfig('System')['GANGA_PYTHONPATH'])
}
for k, v in replace_dict.iteritems():
text = text.replace(str(k), str(v))
logger.debug('subjob input sandbox %s ', subjob_input_sandbox)
logger.debug('master input sandbox %s ', master_input_sandbox)
from Ganga.GPIDev.Lib.File import FileBuffer
return job.getInputWorkspace().writefile(FileBuffer('__jobscript__', text), executable=1)
def configure(self, masterappconfig):
exefile = 'skimFromCSV.exe'
exe = 'skimFromCSV.exe'
# exe = '/'.join([os.getenv("RECONUTILSROOT"),os.getenv("CMTCONFIG"),exefile])
# if not isfile(exe):
# raise ApplicationConfigurationError(None,'Cannot find executable '+exe)
job = self.getJobObject()
if self.cmtsetup == None:
raise ApplicationConfigurationError('No cmt setup script given.')
if not isfile(self.cmtsetup):
raise ApplicationConfigurationError(
'Cannot find cmt setup script ' + self.cmtsetup)
# Copy CSV file to inputdir. Done in splitter for subjobs.
if not isfile(self.csvfile):
raise ApplicationConfigurationError('Cannot find CSV file ' +
self.csvfile)
from shutil import copy
tmpcsv = os.path.join(job.inputdir, os.path.basename(self.csvfile))
if not os.path.exists(tmpcsv):
copy(self.csvfile, job.inputdir)
self.csvfile = tmpcsv
args = []
args.append('-O')
args.append('file=' + self.csvfile)
if self.outputfile == None:
raise ApplicationConfigurationError(
'No output file given. Fill the outputfile variable.')
args.append('-o')
args.append(self.outputfile)
# Read the CSV file
csvfile = open(self.csvfile, 'rb')
run_subrun = []
for line in csvfile:
if line[0] == '#':
continue
row = line.split(",")
if len(row) < 3:
print "Ignoring badly-formatted line:", ",".join(row)
continue
r_sr = "%(run)08d-%(subrun)04d" % {
"run": int(row[0]),
"subrun": int(row[1])
}
if r_sr not in run_subrun:
run_subrun.append(r_sr)
# So get the list of filenames get_dataset_filenames() and create a file containing the list of files and put it in the sandbox
if job.inputdata == None:
raise ApplicationConfigurationError(
'The inputdata variable is not defined.')
rawFileList = job.inputdata.get_dataset_filenames()
if len(rawFileList) < 1:
raise ApplicationConfigurationError('No input data file given.')
fileList = []
for r_sr in run_subrun:
for rfile in rawFileList:
if rfile.find(r_sr) > -1:
fileList.append(rfile)
continue
if not len(fileList):
raise ApplicationConfigurationError(
'No file matching the run_subrun in the CSV file %s.' %
self.csvfile)
args.extend(fileList)
argsStr = ' '.join(args)
# Create the bash script and put it in input dir.
script = '#!/bin/bash\n'
script += 'source ' + self.cmtsetup + '\n'
script += '${RECONUTILSROOT}/${CMTCONFIG}/' + exe + ' ' + argsStr + '\n'
# Little trick to be able to control the final destination
# of the subjob's CSV file with SandboxFile or MassStorageFile
if job.master is not None:
script += 'cp %s .' % self.csvfile
from Ganga.GPIDev.Lib.File import FileBuffer
if exefile.find('.exe') > -1:
scriptname = exefile.replace('.exe', '.sh')
else:
scriptname = exefile + '.sh'
job.getInputWorkspace().writefile(FileBuffer(scriptname, script),
executable=1)
self._scriptname = job.inputdir + scriptname
return (None, None)
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 get_input_sandbox(extra):
sandbox = []
sandbox += extra.input_files[:]
sandbox += [FileBuffer(n, s) for (n, s) in extra.input_buffers.items()]
logger.debug("Input sandbox: %s", str(sandbox))
return sandbox
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 makesagajobdesc(self, job, jobconfig):
## We need a unique subdirectory per job to avoid input/output file clashes
## The easiest way to do this is with a UUID-style directory name
wd_uuid = "ganga-job-"
#if job.name == '':
# wd_uuid += "noname-"
#else:
# wd_uuid += job.name + "-"
import uuid
wd_uuid += str(uuid.uuid4())
job.backend.workdir_uuid = wd_uuid
## Now we need to create a wrapper script on the fly. The wrapper
## script will be be transfered to the execution host and takes care
## of the archive unpacking as well as job monitoring / reporting.
ws = SAGAWrapperScript()
import inspect
import Ganga.Core.Sandbox as Sandbox
import Ganga.Utility as Utility
ws.setInlineModules(inspect.getsource(Sandbox.WNSandbox))
ws.setExecutable(jobconfig.getExeString())
ws.setArguments(jobconfig.getArgStrings())
ws.setOutputPatterns(jobconfig.outputbox)
ws.setInputSandbox("_input_sandbox_" + str(job.id) + ".tgz")
text = ws.getScript()
jd = saga.job.description()
logger.debug("setting up new saga job with id: %s", job.id)
# create jobscript in input sandbox
from Ganga.GPIDev.Lib.File import FileBuffer
jobscript = job.getInputWorkspace().writefile(FileBuffer(
'__jobscript__', text),
executable=1)
logger.debug(" * created new jobscript wrapper: %s", jobscript)
# workdir
if len(job.backend.workdir) != 0:
jd.working_directory = job.backend.workdir
logger.debug(" * backend.workdir -> saga.workdir: %s",
jd.working_directory)
else: #default to the remote filesystem path component
jd.working_directory = saga.url(self.filesystem_url + "/" +
self.workdir_uuid + "/").path
logger.debug(
" * saga.workdir: %s (not given - extracted from 'filesystem_url')",
jd.working_directory)
# executable
exe = jd.working_directory + '__jobscript__'
jd.executable = exe #jobconfig.getExeString()
logger.debug(" * application.exe -> saga.executable: %s",
jd.executable)
# arguments
argList = jobconfig.getArgStrings()
#for arg in job.application.args:
# argList.append( arg ) #"\\'%s\\'" % arg )
if len(argList) != 0:
jd.arguments = argList
logger.debug(" * application.args -> saga.arguments: %s",
jd.arguments)
# environment
envList = []
for k, v in job.application.env.items():
envList.append(k + "=" + v) #"\\'%s\\'" % arg )
if len(envList) != 0:
jd.environment = envList
logger.debug(" * application.env -> saga.environment: %s",
jd.environment)
# queue
if len(job.backend.queue) != 0:
jd.queue = job.backend.queue
logger.debug(" * backend.queue -> saga.queue: %s", jd.queue)
# allocation
if len(job.backend.allocation) != 0:
jd.job_project = [job.backend.allocation]
logger.debug(" * backend.allocation -> saga.job_project: %s",
jd.job_project)
# spmd_variation
if len(job.backend.spmd_variation) != 0:
jd.spmd_variation = job.backend.spmd_variation
logger.debug(
" * backend.spmd_variation -> saga.spmd_variation: %s",
jd.spmd_variation)
# number_of_processes
if len(job.backend.number_of_processes) != 0:
jd.number_of_processes = job.backend.number_of_processes
logger.debug(
" * backend.number_of_processes -> saga.number_of_processes: %s",
jd.number_of_processes)
## We have to create special filenames for stdout/stderr redirection
## To avoid name clashes, we append a UUID to the filename.
path_component = saga.url(self.filesystem_url + "/" +
self.workdir_uuid + "/")
try:
d = saga.filesystem.directory(path_component,
saga.filesystem.Create)
logger.debug(
" * created output/working directory on the remote system: %s",
path_component)
except saga.exception as e:
logger.error(
'exception caught while creating output/working directory: %s',
e.get_all_messages())
self.getJobObject().updateStatus("failed")
## STDOUT
self.saga_job_out = path_component.url + "/out.log"
#jd.output = saga.url(self.saga_job_out).path
logger.debug(" * stdout should become available here: %s",
saga.url(self.saga_job_out).url)
## STDERR
self.saga_job_err = path_component.url + "/err.log"
#jd.error = saga.url(self.saga_job_err).path
logger.debug(" * stderr should become available here: %s",
saga.url(self.saga_job_err).url)
return jd
def configure(self, masterappconfig):
self.ana_useropt = convertIntToStringArgs(self.ana_useropt)
args = []
args.append('$RECONUTILSROOT/macros/grtf_VFT/make_ana.py')
job = self.getJobObject()
if self.cmtsetup == None:
raise ApplicationConfigurationError('No cmt setup script given.')
if not self.tree == None:
args.append('-t')
args.append(self.tree)
if not self.ana_custom == None:
args.append('-c')
args.append(self.ana_custom)
if not self.ana_useropt == None:
for UsrOpt in self.ana_useropt:
args.append('-O')
args.append(UsrOpt)
if self.ana_output == None:
raise ApplicationConfigurationError(
'No output file given. Fill the ana_output variable.')
else:
args.append('-o')
args.append(self.ana_output)
# So get the list of filenames get_dataset_filenames() and create a file containing the list of files and put it in the sandbox
if job.inputdata == None:
raise ApplicationConfigurationError(
'The inputdata variable is not defined.')
fileList = job.inputdata.get_dataset_filenames()
if len(fileList) < 1:
raise ApplicationConfigurationError('No input data file given.')
args.extend(fileList)
if self.run_pdf:
args.append('&&')
args.append(
'$ND280ANALYSISTOOLSROOT/macros/grtf/pdfgen/make_pdf.py')
if not 'ana_output' in [
self.pdf_rdp, self.pdf_mcp, self.pdf_oldrdp,
self.pdf_oldmcp
]:
raise ApplicationConfigurationError(
'None of the pdf inputs is set to use the make_ana.py output. Please set "pdf_rdp", "pdf_mcp", "pdf_oldrdp", or "pdf_oldmcp" to the value "ana_output"'
)
for key in ['pdf_rdp', 'pdf_mcp', 'pdf_oldrdp', 'pdf_oldmcp']:
if getattr(self, key) == 'ana_output':
setattr(self, key, self.ana_output)
argDict = {
'--custom': 'pdf_custom',
'--title': 'pdf_title',
'--rdp': 'pdf_rdp',
'--mcp': 'pdf_mcp',
'--oldrdp': 'pdf_oldrdp',
'--oldmcp': 'pdf_oldmcp',
'--rdptitle': 'pdf_rdptitle',
'--mcptitle': 'pdf_mcptitle',
'--oldrdptitle': 'pdf_oldrdptitle',
'--oldmcptitle': 'pdf_oldmcptitle',
'--out': 'pdf_output'
}
# argDict = { '--custom': self.pdf_custom, '--title': self.pdf_title, '--rdp': self.pdf_rdp, '--mcp': self.pdf_mcp, '--oldrdp': self.pdf_oldrdp, '--oldmcp': self.pdf_oldmcp, '--rdptitle': self.pdf_rdptitle, '--mcptitle': self.pdf_mcptitle, '--oldrdptitle': self.pdf_oldrdptitle, '--oldmcptitle': self.pdf_oldmcptitle, '--out': self.pdf_output }
for key in argDict:
if not getattr(self, argDict[key]) == None:
args.append(key + '=' + getattr(self, argDict[key]))
for opt in self.pdf_options:
for key in argDict:
if opt.find(key) > -1 and not getattr(
self, argDict[key]) == None:
raise ApplicationConfigurationError(
'The make_pdf.py command line argument %s was set through both the ganga application variable "%s" and pdf_options "%s". Use only one of them.'
% (key, argDict[key], opt))
args.append(opt)
# Create the bash script and put it in input dir.
script = '#!/bin/bash\n'
script += 'source ' + self.cmtsetup + '\n'
script += ' '.join(args) + '\n'
from Ganga.GPIDev.Lib.File import FileBuffer
scriptname = 'make_ana.sh'
job.getInputWorkspace().writefile(FileBuffer(scriptname, script),
executable=1)
self._scriptname = job.inputdir + scriptname
return (None, None)
def configure(self, masterappconfig):
if self.cmtsetup == None:
raise ApplicationConfigurationError('No cmt setup script given.')
# __________ Reco first ____________
reco_args = convertIntToStringArgs(self.reco_args)
job = self.getJobObject()
# Need to handle the possibility of multiple output files !
# setup the output file
for arg in reco_args:
if arg == '-o':
raise ApplicationConfigurationError(
'Option "-o" given in reco_args. You must use the filenamesubstr and reconewstr variables instead to define an output.'
)
# So get the list of filenames get_dataset_filenames() and create a file containing the list of files and put it in the sandbox
if job.inputdata == None:
raise ApplicationConfigurationError(
'The inputdata variable is not defined.')
fileList = job.inputdata.get_dataset_filenames()
if len(fileList) < 1:
raise ApplicationConfigurationError('No input data file given.')
firstFile = fileList[0].split('/')[-1]
# Define the output
reco_args.append('-o')
if self.filenamesubstr == None:
reco_outputfile = 'recoOutput.root'
else:
reco_outputfile = firstFile.replace(self.filenamesubstr,
self.reconewstr)
reco_args.append(reco_outputfile)
# Just to define the output before the potentially long list of input files
reco_args.extend(fileList)
# __________ Now oaAnalysis ____________
anal_args = convertIntToStringArgs(self.anal_args)
job = self.getJobObject()
# Need to handle the possibility of multiple output files !
# setup the output file
for arg in anal_args:
if arg == '-o':
raise ApplicationConfigurationError(
'Option "-o" given in anal_args. You must use the filenamesubstr and reconewstr variables instead to define an output.'
)
# Define the output
anal_args.append('-o')
if self.filenamesubstr == None:
anal_outputfile = 'analOutput.root'
else:
anal_outputfile = firstFile.replace(self.filenamesubstr,
self.analnewstr)
anal_args.append(anal_outputfile)
# Now add the input file
anal_args.append(reco_outputfile)
reco_argsStr = ' '.join(reco_args)
anal_argsStr = ' '.join(anal_args)
# Create the bash script and put it in input dir.
script = '#!/bin/bash\n'
script += 'source ' + self.cmtsetup + '\n'
script += 'RunOARecon.exe ' + reco_argsStr + '\n'
script += 'RunOAAnalysis.exe ' + anal_argsStr + '\n'
from Ganga.GPIDev.Lib.File import FileBuffer
scriptname = 'oaReconPlusoaAnalysis.sh'
job.getInputWorkspace().writefile(FileBuffer(scriptname, script),
executable=1)
self._scriptname = job.inputdir + scriptname
return (None, None)
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))
