rem stringlengths 0 322k | add stringlengths 0 2.05M | context stringlengths 8 228k |
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self.read(*args, **kwargs) | if len(args) + len(kwargs) > 0: self.read(*args, **kwargs) | def __init__(self, *args, **kwargs): ''' Create a table set instance |
s += PrettyStrings.formatDatum("compute element", str(job.backend.actualCE)) | try: s += PrettyStrings.formatDatum("compute element", str(job.backend.actualCE)) except: pass | def getStatus(self): """ This method prints basic information about the running job, like its job-id and the worker node the job is running on. """ if self.__checkStatus(): s = PrettyStrings.makeHeader("current job status") job = self.getJobObject() |
if j.backend.__class__.__name__ == 'Panda' and j.backend.url is not None: j.info.monitoring_links = [(task_mon_link,'dashboard'), (j.backend.url, 'panda')] | if j.backend.__class__.__name__ == 'Panda' and len(j.backend.buildjobs) > 0 and j.backend.buildjobs[0].url is not None: j.info.monitoring_links = [(task_mon_link,'dashboard'), (j.backend.buildjobs[0].url, 'panda')] | def submit(self, **opts): """Log submit event on client.""" j = self.job_info # called on client, so job_info is Job object self._log('debug', 'submit %s' % j.fqid) # ignore master wrapper jobs if j.subjobs: self._log('debug', 'Not sending unwanted message on submit for master wrapper job %s.' % j.fqid) return # send G... |
raise ApplicationConfigurationError(None,"job.outputdata.outputdata must be empty if atlas_exetype='ATHENA' (outputs are auto-detected)") | raise ApplicationConfigurationError(None,"job.outputdata.outputdata must be empty if atlas_exetype='ATHENA' and Panda backend is used (outputs are auto-detected)") | def master_prepare(self,app,appconfig): '''Prepare the master job''' |
raise ApplicationConfigurationError(None,"job.outputdata.outputdata is required for atlas_exetype in ['PYARA','ARES','TRF','ROOT']") | raise ApplicationConfigurationError(None,"job.outputdata.outputdata is required for atlas_exetype in ['PYARA','ARES','TRF','ROOT'] and Panda backend") | def master_prepare(self,app,appconfig): '''Prepare the master job''' |
logger.warning('Job %s has disappeared from the batch system.', str(j.id)) | logger.warning('Job %s has disappeared from the batch system.', str(j.getFQID('.'))) | def get_status(f): """Give (pid,queue,actualCE,exit code) for job""" |
print report | def fill_report(uuid = None, eventVersion = None, remoteSite=None, localSite=None, timeStart=None, catStart=None, relativeStart=None, transferStart=None, validateStart=None, timeEnd=None, duid=None,version=None, dataset=None, protocol=None, filename=None, filesize=None, guid=None, usr=None, hostname=None, ip=None, susp... | |
raise RegistryKeyError('Job id=%d not found'%id) | if self.name == 'templates': raise RegistryKeyError('Template %d not found'%id) else: raise RegistryKeyError('Job %d not found'%id) | def __call__(self,id): """ Retrieve a job by id. """ t = type(id) if t is int: try: return self.objects[id] except KeyError: raise RegistryKeyError('Job id=%d not found'%id) elif t is tuple: ids = id elif t is str: ids = id.split(".") else: raise RegistryAccessError('Expected a job id: int, (int,int), or "int.int"') |
raise RegistryKeyError('Job %d not found'%ids[0]) | if self.name == 'templates': raise RegistryKeyError('Template %d not found'%ids[0]) else: raise RegistryKeyError('Job %d not found'%ids[0]) | def __call__(self,id): """ Retrieve a job by id. """ t = type(id) if t is int: try: return self.objects[id] except KeyError: raise RegistryKeyError('Job id=%d not found'%id) elif t is tuple: ids = id elif t is str: ids = id.split(".") else: raise RegistryAccessError('Expected a job id: int, (int,int), or "int.int"') |
logger.info('Compressing to %s ...', archiveFullName ) | def prepare(self, **options): """Extract Athena job configuration and prepare job for submission""" | |
archiveName, archiveFullName = AthenaUtils.archiveSourceFiles(self.userarea, runDir, currentDir, tmpDir, verbose, self.glue_packages) | archiveName, archiveFullName = AthenaUtils.archiveSourceFiles(self.userarea, runDir, currentDir, archiveDir, verbose, self.glue_packages) | def prepare(self, **options): """Extract Athena job configuration and prepare job for submission""" |
AthenaUtils.archiveInstallArea(self.userarea, self.grouparea, archiveName, archiveFullName, tmpDir, nobuild, verbose) | AthenaUtils.archiveInstallArea(self.userarea, self.grouparea, archiveName, archiveFullName, archiveDir, nobuild, verbose) | def prepare(self, **options): """Extract Athena job configuration and prepare job for submission""" |
out = commands.getoutput('pushd . && cd %s && tar -f %s -rh %s && popd' % (tmpDir, archiveFullName, filename)) | out = commands.getoutput('pushd . && cd %s && tar -f %s -rh %s && popd' % (archiveDir, archiveFullName, filename)) | def prepare(self, **options): """Extract Athena job configuration and prepare job for submission""" |
self.atlas_environment=['DBRELEASE_OVERRIDE=%s'%dbvers] | self.atlas_environment+=['DBRELEASE_OVERRIDE=%s'%dbvers] | def master_configure(self): |
if not cmtconfig in [ 'i686-slc4-gcc34-opt', 'i686-slc5-gcc43-opt' ] | if not cmtconfig in [ 'i686-slc4-gcc34-opt', 'i686-slc5-gcc43-opt' ]: | def master_prepare( self, app, appconfig): """Prepare the master job""" |
c = StandardJobConfig(app.exe,app._getParent().inputsandbox,app.args,app._getParent().outputsandbox,app.env) | c = StandardJobConfig(app.exe,app._getParent().inputsandbox,convertIntToStringArgs(app.args),app._getParent().outputsandbox,app.env) | def prepare(self,app,appconfig,appmasterconfig,jobmasterconfig): from Ganga.GPIDev.Adapters.StandardJobConfig import StandardJobConfig |
return LCGJobConfig(app.exe,app._getParent().inputsandbox,app.args,app._getParent().outputsandbox,app.env) | return LCGJobConfig(app.exe,app._getParent().inputsandbox,convertIntToStringArgs(app.args),app._getParent().outputsandbox,app.env) | def prepare(self,app,appconfig,appmasterconfig,jobmasterconfig): from Ganga.Lib.LCG import LCGJobConfig |
return gLiteJobConfig(app.exe,app._getParent().inputsandbox,app.args,app._getParent().outputsandbox,app.env) | return gLiteJobConfig(app.exe,app._getParent().inputsandbox,convertIntToStringArgs(app.args),app._getParent().outputsandbox,app.env) | def prepare(self,app,appconfig,appmasterconfig,jobmasterconfig): from Ganga.Lib.gLite import gLiteJobConfig |
if cmtconfig != 'i686-slc4-gcc34-opt': | if not cmtconfig in [ 'i686-slc4-gcc34-opt', 'i686-slc5-gcc43-opt' ] | def master_prepare( self, app, appconfig): """Prepare the master job""" |
if app.options: self.job_options += ' %s ' % app.options | def master_prepare(self,app,appconfig): '''Prepare the master job''' | |
uploadFileServer= "http://127.0.0.1:8000/errorreports" | uploadFileServer= "http://gangamon.cern.ch/django/errorreports/" | def report_inner(job=None): userInfoDirName = "userreport" tempDirName = "reportsRepository" #job relevant info inputDirName = "inputdir" outputDirName = "outputdir" jobSummaryFileName = "jobsummary.txt" jobFullPrintFileName = "jobfullprint.txt" #non job relevant info - user's info environFileName = "environ.txt" user... |
else: break | def split(self,job): | |
athena_options = ' '.join([os.path.basename(opt_file.name) for opt_file in app.option_file])2 | athena_options = ' '.join([os.path.basename(opt_file.name) for opt_file in app.option_file]) | def master_prepare( self, app, appconfig): """Prepare the master job""" |
mydelid = self.credential.identity() | mydelid = '%s_%s' % (self.credential.identity(), get_uuid()) | def cream_proxy_delegation(self, ce): '''CREAM CE proxy delegation''' |
infos = [] for odat in j.outputdata.outputdata: info = [f for f in j.outputdata.output if odat in f][0].split(",") info[0] = datasetname infos.append(",".join(info)) outputdata.register_datasets_details(None, infos) | try: infos = [] for odat in j.outputdata.outputdata: info = [f for f in j.outputdata.output if odat in f][0].split(",") info[0] = datasetname infos.append(",".join(info)) outputdata.register_datasets_details(None, infos) except DQFileExistsInDatasetException: pass | def checkCompletedApp(self, app): j = app._getParent() for odat in j.outputdata.outputdata: if 0==len([f for f in j.outputdata.output if ".".join(odat.split(".")[:-1]) in f]): logger.error("Job %s has not produced %s file, only: %s" % (j.id, odat, j.outputdata.output)) return False # if this is the first app to complet... |
m=md5.new() m.update(usrDN) | md.update(usrDN) | def fill_report(uuid = None, eventVersion = None, remoteSite=None, localSite=None, timeStart=None, catStart=None, relativeStart=None, transferStart=None, validateStart=None, timeEnd=None, duid=None,version=None, dataset=None, protocol=None, filename=None, filesize=None, guid=None, usr=None, hostname=None, ip=None, susp... |
jspec.destinationSE = job.backend.site | if Client.isDQ2free(job.backend.site): jspec.destinationSE = 'local' else: jspec.destinationSE = job.backend.site | def master_prepare(self,app,appconfig): '''Prepare the master job''' |
jspec.destinationSE = site | if Client.isDQ2free(job.backend.site): jspec.destinationSE = 'local' else: jspec.destinationSE = site | def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig): '''prepare the subjob specific configuration''' |
def cmd(self,cmd,soutfile=None,allowed_exit=[0], capture_stderr=False,timeout=None): | def cmd(self,cmd,soutfile=None,allowed_exit=[0], capture_stderr=False,timeout=None, mention_outputfile_on_errors=True): | def cmd(self,cmd,soutfile=None,allowed_exit=[0], capture_stderr=False,timeout=None): "Execute an OS command and captures the stderr and stdout which are returned in a file" |
logger.warning('full output is in file: %s',soutfile) | if mention_outputfile_on_errors: logger.warning('full output is in file: %s',soutfile) | def cmd(self,cmd,soutfile=None,allowed_exit=[0], capture_stderr=False,timeout=None): "Execute an OS command and captures the stderr and stdout which are returned in a file" |
rc,outfile,m = self.cmd(cmd,None,allowed_exit,capture_stderr,timeout) | rc,outfile,m = self.cmd(cmd,None,allowed_exit,capture_stderr,timeout,mention_outputfile_on_errors=False) | def cmd1(self,cmd,allowed_exit=[0],capture_stderr=False,timeout=None): "Executes an OS command and captures the stderr and stdout which are returned as a string" rc,outfile,m = self.cmd(cmd,None,allowed_exit,capture_stderr,timeout) output=file(outfile).read() os.unlink(outfile) return rc,output, m |
logger.warning("Filling provenance info for dataset %s...", d ) | logger.info("Filling provenance info for dataset %s...", d ) | def fill_provenance(self,extraargs = []): |
logger.warning("Good Run List '%s' file selected" % self.goodRunListXML.name) | logger.info("Good Run List '%s' file selected" % self.goodRunListXML.name) | def search(self, pattern='', maxresults = config['MaxNumOfDatasets'], extraargs = []): argument=[] dsetList = [] if self.goodRunListXML.name != '': |
raise TypeError("keep_going must be a boolean. Probably you wanted to do %s(%s).%s()" % (keep_going,self.name,keep_going,method)) | raise GangaException("The variable 'keep_going' must be a boolean. Probably you wanted to do %s(%s).%s()" % (self.name,keep_going,method)) | def do_collective_operation(self,keep_going,method,*args,**kwds): """ """ if not type(keep_going) is bool: raise TypeError("keep_going must be a boolean. Probably you wanted to do %s(%s).%s()" % (keep_going,self.name,keep_going,method)) result = [] for id,obj in self.objects.iteritems(): try: if type(method) is str: do... |
spacetokens.append(queueToAllowedSites(s)) | spacetokens.append(convertQueueNameToDQ2Names(s)) | def list_sites(self): from pandatools import Client refreshPandaSpecs() |
tokens = queueToAllowedSites(s) | tokens = convertQueueNameToDQ2Names(s) | def list_ddm_sites(self,allowTape=False): from pandatools import Client refreshPandaSpecs() |
tokens = queueToAllowedSites(self.site) | tokens = convertQueueNameToDQ2Names(self.site) | def list_ddm_sites(self,allowTape=False): from pandatools import Client refreshPandaSpecs() |
if 'ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET' in config and config['ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET']: nickname = getNickname(allowMissingNickname=True) else: nickname = getNickname(allowMissingNickname=False) if nickname and 'USE_NICKNAME_DQ2OUTPUTDATASET' in config and config['USE_NICKNAME_DQ2OUTPUTDATASET']:... | def __init__(self): super( AthenaMCInputDatasets, self ).__init__() # Extract username from certificate proxy = GridProxy() username = proxy.identity() | |
assert _usertag and _usertag!="users" | assert _usertag | def get_dataset(self, app,backend): '''seek dataset informations and returns (hopefully) a formatted set of information for all processing jobs (turls, catalog servers, dataset location for each lfn). Called by master_submit''' |
assert _usertag and _usertag!="users" | assert _usertag | def prep_data(self,app): ''' generate output paths and file prefixes based on app and outputdata information. Generate corresponding entries in DQ2. ''' fileprefixes,outputpaths=self.outrootfiles.copy(),{} # first of all, check that _usertag is set properly: try: assert _usertag and _usertag!="users" except: logger.err... |
assert _usertag and _usertag!="users" | assert _usertag | def getDQ2Locations(self,se_name): ''' Provides the triplet: LFC, site and srm path from input se''' lfcstrings=getLFCmap() outputlocation={} default_site="CERN-PROD_SCRATCHDISK" job=self._getParent() app=job.application # first of all, check that _usertag is set properly: try: assert _usertag and _usertag!="users" ex... |
def runMonitoring( self, steps=1, timeout=60 ): | def runMonitoring( self, steps=1, timeout=60, jobs=None ): | def runMonitoring( self, steps=1, timeout=60 ): """ Enable/Run the monitoring loop and wait for the monitoring steps completion. Parameters: steps: number of monitoring steps to run timeout: how long to wait for monitor steps termination (seconds) Return: False, if the loop cannot be started or the timeout occured wh... |
try: statusfile=file(statusfilename,'w') except IOError,x: print 'ERROR: not able to write a status file: ', statusfilename print 'ERROR: ',x raise | heartbeatfilename = os.path.join(sharedoutputpath,'__heartbeat__') statusfile=open_file(statusfilename) heartbeatfile=open_file(heartbeatfilename) | def flush_file(f): f.flush() os.fsync(f.fileno()) #this forces a global flush (cache synchronization on AFS) |
os.utime(statusfilename,None) | heartbeatfile.write('.') flush_file(heartbeatfile) | def flush_file(f): f.flush() os.fsync(f.fileno()) #this forces a global flush (cache synchronization on AFS) |
time = get_last_alive(statusfile) | time = get_last_alive(heartbeatfile) | def get_status(f): """Give (pid,queue,exit code) for job""" |
config.addOption('timeout',300,'Timeout in seconds after which a job is declared killed if it has not touched its heartbeat file. Heartbeat is touched every 30s so do not set this below 120 or so.') | config.addOption('timeout',600,'Timeout in seconds after which a job is declared killed if it has not touched its heartbeat file. Heartbeat is touched every 30s so do not set this below 120 or so.') | def filefilter(fn): # FILTER OUT Batch INTERNAL INPUT/OUTPUT FILES: # 10 digits . any number of digits . err or out import re internals = re.compile(r'\d{10}\.\d+.(out|err)') return internals.match(fn) or fn == '.Batch.start' |
config.addOption('timeout',300,'Timeout in seconds after which a job is declared killed if it has not touched its heartbeat file. Heartbeat is touched every 30s so do not set this below 120 or so.') | config.addOption('timeout',600,'Timeout in seconds after which a job is declared killed if it has not touched its heartbeat file. Heartbeat is touched every 30s so do not set this below 120 or so.') | def __init__(self): super(LSF,self).__init__() |
config.addOption('timeout',300,'Timeout in seconds after which a job is declared killed if it has not touched its heartbeat file. Heartbeat is touched every 30s so do not set this below 120 or so.') | config.addOption('timeout',600,'Timeout in seconds after which a job is declared killed if it has not touched its heartbeat file. Heartbeat is touched every 30s so do not set this below 120 or so.') | def __init__(self): super(PBS,self).__init__() |
self.status_colours = { 'new' : fx.normal, 'submitted' : fg.orange, 'running' : fg.green, 'completed' : fg.blue, 'failed' : fg.red } | try: status_colours = config['jobs_status_colours'] self.status_colours = dict( [ (k, eval(v)) for k,v in status_colours.iteritems() ] ) except Exception,x: logger.warning('configuration problem with colour specification: "%s"', str(x)) status_colours = config.options['jobs_status_colours'].default_value self.status_co... | def __init__(self,name): super(JobRegistrySlice,self).__init__(name,display_prefix="jobs") from Ganga.Utility.ColourText import Foreground, Background, Effects fg = Foreground() fx = Effects() bg = Background() self.status_colours = { 'new' : fx.normal, 'submitted' : fg.orange, 'running' : fg.green, 'complet... |
if 'ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET' in config and config['ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET']: | if 'ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET' in configDQ2 and configDQ2['ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET']: | def __init__(self): super( AthenaMCInputDatasets, self ).__init__() # Extract username from certificate proxy = GridProxy() username = proxy.identity() if 'ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET' in config and config['ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET']: nickname = getNickname(allowMissingNickname=True) else: ni... |
if nickname and 'USE_NICKNAME_DQ2OUTPUTDATASET' in config and config['USE_NICKNAME_DQ2OUTPUTDATASET']: | if nickname and 'USE_NICKNAME_DQ2OUTPUTDATASET' in configDQ2 and configDQ2['USE_NICKNAME_DQ2OUTPUTDATASET']: | def __init__(self): super( AthenaMCInputDatasets, self ).__init__() # Extract username from certificate proxy = GridProxy() username = proxy.identity() if 'ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET' in config and config['ALLOW_MISSING_NICKNAME_DQ2OUTPUTDATASET']: nickname = getNickname(allowMissingNickname=True) else: ni... |
datasets = resolve_container(self.dataset) | datasets = resolve_container([self.datasetname]) | def check_content_consistency(self, numsubjobs, **options ): """Check outputdataset consistency""" # Resolve container into datasets datasets = resolve_container(self.dataset) |
numrequestedoutputfiles = len(self.outputdata.outputdata)*numsubjobs | numrequestedoutputfiles = len(self.outputdata)*numsubjobs | def check_content_consistency(self, numsubjobs, **options ): """Check outputdataset consistency""" # Resolve container into datasets datasets = resolve_container(self.dataset) |
logger.warning('Number of output files %s in outputdataset %s is not consistent with number of subjobs and requested outputfiles %s - Please carefully check output !', numoutputfiles, dataset, numrequestedoutputfiles) | logger.warning('%s output files in outputdataset %s is not consistent with %s subjobs and %s requested outputfiles - Please carefully check output !', numoutputfiles, dataset,numsubjobs, numrequestedoutputfiles) | def check_content_consistency(self, numsubjobs, **options ): """Check outputdataset consistency""" # Resolve container into datasets datasets = resolve_container(self.dataset) |
numrequestedoutputfiles = len(self.outputdata.outputdata) if not numrequestedoutputfiles == numoutputfiles: logger.warning('Number of output files %s in outputdataset %s is not consistent with number of subjobs and requested outputfiles %s - Please carefully check output !', numoutputfiles, dataset, numrequestedoutputf... | for outputinfo in self.output: filename = outputinfo.split(',')[1] if not filename in contents_files: logger.warning('output file %s is not in outputdataset %s - Please carefully check output !', filename, dataset) | def check_content_consistency(self, numsubjobs, **options ): """Check outputdataset consistency""" # Resolve container into datasets datasets = resolve_container(self.dataset) |
def wn_dest_ce(): | def wn_dest_ce(ji): | def cl_unique_job_id(job): """Build unique_job_id. Only run on client.""" return job.info.uuid |
dest_ce = CommonUtil.env('GLOBUS_CE') if not dest_ce: dest_ce = CommonUtil.stdout('edg-brokerinfo getCE') if not dest_ce: dest_ce = CommonUtil.stdout('glite-brokerinfo getCE') return CommonUtil.strip_to_none(dest_ce) | return '%s_localbatch_%s' % (ji['GANGA_HOSTNAME'], ji['Batch']) | def wn_dest_ce(): """Build dest_ce. Only run on worker node.""" dest_ce = CommonUtil.env('GLOBUS_CE') if not dest_ce: dest_ce = CommonUtil.stdout('edg-brokerinfo getCE') if not dest_ce: dest_ce = CommonUtil.stdout('glite-brokerinfo getCE') return CommonUtil.strip_to_none(dest_ce) |
def wn_dest_site(): | def wn_dest_site(ji): | def wn_dest_site(): """Build dest_site. Only run on worker node.""" return CommonUtil.env('SITE_NAME') |
return CommonUtil.env('SITE_NAME') | return ji['GANGA_HOSTNAME'] | def wn_dest_site(): """Build dest_site. Only run on worker node.""" return CommonUtil.env('SITE_NAME') |
supports_keep_going = 'keep_going' in inspect.getargspec(self.backend.master_submit).args | supports_keep_going = 'keep_going' in inspect.getargspec(self.backend.master_submit)[0] | def submit(self,keep_going=None,keep_on_fail=None): '''Submits a job. Return true on success. |
supports_master_resubmit = len(inspect.getargspec(self.backend.master_resubmit).args)>1 | supports_master_resubmit = len(inspect.getargspec(self.backend.master_resubmit)[0])>1 | def resubmit(self,backend=None): """Resubmit a failed or completed job. A backend object may be specified to change some submission parameters (which parameters may be effectively changed depends on a particular backend implementation). |
new_file_handler = handlers.RotatingFileHandler(logfile,maxBytes=logfile_size) | new_file_handler = handlers.RotatingFileHandler(logfile,maxBytes=logfile_size,backupCount=1) | def _make_file_handler(logfile,logfile_size): import traceback import os.path logfile = os.path.expanduser(logfile) global file_handler if logfile: try: new_file_handler = handlers.RotatingFileHandler(logfile,maxBytes=logfile_size) except IOError,x: private_logger.error('Cannot open the log file: %s',str(x)) return # r... |
cmd += ' -e %s' % ce | cmd += ' -e %s' % ce.split('/cream')[0] | def cream_proxy_delegation(self, ce): '''CREAM CE proxy delegation''' |
for f in input_sandbox: getPackedInputSandbox(f) | def preparejob(self,jobconfig,master_input_sandbox): | |
if app.max_events > 0: | if app.atlas_exetype == 'ATHENA' and app.max_events > 0: | def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig): '''prepare the subjob specific configuration''' |
if not orig_numfiles>0: | if not orig_numsubjobs>0 and not orig_numfiles>0: | def split(self,job): |
if job.backend._name == 'LCG': | if job.backend._name in [ 'LCG' ]: | def retrieve(self, type=None, name=None, **options ): """Retrieve files listed in outputdata and registered in output from remote SE to local filesystem in background thread""" from Ganga.GPIDev.Lib.Job import Job from GangaAtlas.Lib.ATLASDataset import Download import os, threading |
if (job.outputdata.outputdata and job.backend._name == 'LCG' and job.outputdata.output) or (job.backend._name == 'Panda' and job.outputdata.output): | if (job.outputdata.outputdata and job.backend._name in [ 'LCG', 'CREAM'] and job.outputdata.output) or (job.backend._name == 'Panda' and job.outputdata.output): | def retrieve(self, type=None, name=None, **options ): """Retrieve files listed in outputdata and registered in output from remote SE to local filesystem in background thread""" from Ganga.GPIDev.Lib.Job import Job from GangaAtlas.Lib.ATLASDataset import Download import os, threading |
break | def split(self,job): | |
sites = [site for site in complete_sites[cloud] if site in allowed_sites[backend]] | if backend == "Panda": sites = [site for site in complete_sites[cloud] if Client.convertDQ2toPandaID(site) in allowed_sites["Panda"]] else: sites = [site for site in complete_sites[cloud] if site in allowed_sites[backend]] | def findCompleteCloudBackend(self,db_sites,allowed_sites,replicas): # Sort complete replicas into clouds # returns sorted list of tuples (cloud, backend) clouds = config["cloudPreference"] + TiersOfATLAS.ToACache.dbcloud.keys() complete_sites = {} for c in clouds: complete_sites[c] = [] for s in replicas[1]: try: cloud... |
sites = [site for site in incomplete_sites[cloud] if site in allowed_sites[backend]] | if backend == "Panda": sites = [site for site in incomplete_sites[cloud] if Client.convertDQ2toPandaID(site) in allowed_sites["Panda"]] else: sites = [site for site in incomplete_sites[cloud] if site in allowed_sites[backend]] | def findIncompleteCloudBackend(self,db_sites,allowed_sites,replicas): # If no cloud/backend combination is found for complete replicas, # find cloud/backend with maximal number of replicas # returns list of tuples sorted by number of sites with replicas: (cloud, backend) clouds = config["cloudPreference"] + TiersOfATLA... |
allowed_sites["Panda"] = [site["ddm"] for site in Client.getSiteSpecs()[1].values()] | allowed_sites["Panda"] = Client.PandaSites.keys() | def check(self): super(AnaTransform,self).check() if not self.inputdata.dataset: return if not self.backend: logger.warning("Determining backend and cloud...") |
dest_ce = CommonUtil.env('GLOBUS_CE') if not dest_ce: dest_ce = CommonUtil.stdout('edg-brokerinfo getCE') if not dest_ce: dest_ce = CommonUtil.stdout('glite-brokerinfo getCE') | dest_ce = CommonUtil.env('CE_ID') | def wn_dest_ce(): """Build dest_ce. Only run on worker node.""" dest_ce = CommonUtil.env('GLOBUS_CE') if not dest_ce: dest_ce = CommonUtil.stdout('edg-brokerinfo getCE') if not dest_ce: dest_ce = CommonUtil.stdout('glite-brokerinfo getCE') return CommonUtil.strip_to_none(dest_ce) |
logger.warning('The job %d has reached unexpected the Cleared state and Ganga cannot retrieve the output.',job.id) | logger.warning('The job %d has reached unexpected the Cleared state and Ganga cannot retrieve the output.',job.getFQID('.')) | def updateGangaJobStatus(job,status): '''map backend job status to Ganga job status''' |
print param | def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig): '''prepare the subjob specific configuration''' | |
mo = self.__job.info.monitor | def complete(self, cause): if not JEMloader.INITIALIZED: logger.debug("Job Execution Monitor is disabled or failed to initialize") return | |
elif not self.__job.info.monitor or self.__job.info.monitor.__class__.__name__ != "JobExecutionMonitor": | elif not isinstance(mo, JobExecutionMonitor.JobExecutionMonitor): return elif mo.enabled == False: | def complete(self, cause): if not JEMloader.INITIALIZED: logger.debug("Job Execution Monitor is disabled or failed to initialize") return |
if job.inputdata.pfnListFile: | if job.inputdata.pfnListFile.name: | def split(self,job): from Ganga.GPIDev.Lib.Job import Job subjobs = [] logger.debug("ATLASTier3Splitter split called") if not job.inputdata: raise ApplicationConfigurationError(None, "ATLASTier3Splitter requires ATLASTier3Dataset") if job.inputdata._name != 'ATLASTier3Dataset': raise ApplicationConfigurationError(None... |
logger.debug("setting %s to '%s'" % (k, str(v))) | def getPath(executable): """ If the given file is found as-is (because the path is included), return None. Else, search the exe in $PATH, and return the path to it if found. """ if os.path.isfile(executable): return None else: paths = os.environ['PATH'].split(os.pathsep) for p in paths: f = os.path.join(p, executable) ... | |
fpaths = list_castor_files(dirs=self.dataset, pattern='.*\.root.*') | fpaths = list_castor_files(dirs=self.dataset, pattern='.*') | def get_surls(self, ddmSiteName=None, guidRefill=True): '''Gets a list of physical files located at certain site. Using DQ2_LOCAL_SITE_ID if site name is not specified explicitely. |
fpaths = find(dirs=self.dataset, pattern='.*\.root.*') | fpaths = find(dirs=self.dataset, pattern='.*') | def get_surls(self, ddmSiteName=None, guidRefill=True): '''Gets a list of physical files located at certain site. Using DQ2_LOCAL_SITE_ID if site name is not specified explicitely. |
list.append(sjs.time.timestamps[status]) | if type(sjs.time.timestamps[status]) == datetime.datetime: list.append(sjs.time.timestamps[status]) else: logger.debug('Attempt to add a non datetime object in the timestamp, job=%d, subjob=%d',j.id,sjs.id) | def sjStatList_return(self, status): list = [] final = ['backend_final', 'final'] j = self.getJobObject() for sjs in j.subjobs: try: list.append(sjs.time.timestamps[status]) except KeyError: logger.debug("Status '%s' not found in timestamps of job %d.%d.", status, sjs.master.id, sjs.id) list.sort() try: if status in fi... |
self.indivOutDsList = [tmpDSName] | self.indivOutDsList.append(tmpDSName) | def master_prepare(self,app,appconfig): '''Prepare the master job''' |
AthenaUtils.convertConfToOutput(self.runConfig,jspec,outMap,job.backend.individualOutDS,self.extOutFile) | AthenaUtils.convertConfToOutput(self.runConfig,jspec,outMap,job.backend.individualOutDS,self.extOutFile,masterjob.outputdata.datasetname) | def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig): '''prepare the subjob specific configuration''' |
subjobOutputLocation = Client.PandaSites[job.backend.site]['ddm'] | def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig): '''prepare the subjob specific configuration''' | |
if not f.dataset in self.indivOutDsList: | if not f.dataset in self.indivOutContList: | def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig): '''prepare the subjob specific configuration''' |
logger.info('Creating individualOutDS %s'%f.dataset) Client.addDataset(f.dataset,False,location=self.outDsLocation) dq2_set_dataset_lifetime(f.dataset, self.outDsLocation) self.indivOutDsList.append(f.dataset) | logger.info('Creating output container %s'%f.dataset) Client.createContainer(f.dataset,False) self.indivOutContList.append(f.dataset) except exceptions.SystemExit: raise BackendError('Panda','Exception in Client.createContainer %s: %s %s'%(f.dataset,sys.exc_info()[0],sys.exc_info()[1])) if not f.destinationDBlock in se... | def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig): '''prepare the subjob specific configuration''' |
splitter.update_siteindex = False | def check(self): super(AnaTransform,self).check() if not self.inputdata.dataset: return if not self.backend: logger.warning("Determining backend and cloud...") | |
self.partitions_sites = None | self.partitions_sites = [sj.backend.site for sj in sjl] | def check(self): super(AnaTransform,self).check() if not self.inputdata.dataset: return if not self.backend: logger.warning("Determining backend and cloud...") |
j.backend.requirements.sites = self.partitions_sites[partitions[0]-1] | if stripProxy(j.backend)._name == "Panda": j.backend.site = self.partitions_sites[partitions[0]-1] else: j.backend.requirements.sites = self.partitions_sites[partitions[0]-1] | def getJobsForPartitions(self, partitions): j = self.createNewJob(partitions[0]) if len(partitions) >= 1: j.splitter = AnaTaskSplitterJob() j.splitter.subjobs = partitions j.inputdata = self.partitions_data[partitions[0]-1] if self.partitions_sites: j.backend.requirements.sites = self.partitions_sites[partitions[0]-1] ... |
if job.inputdata.tag_info: | if self.inputdatatype == 'DQ2' and job.inputdata.tag_info: | def prepare(self,app,appsubconfig,appmasterconfig,jobmasterconfig): '''prepare the subjob specific configuration''' |
print t_total, critical_thread_ids, non_critical_thread_ids | def should_wait_batch_cb(t_total, critical_thread_ids, non_critical_thread_ids): print t_total, critical_thread_ids, non_critical_thread_ids # if there are critical threads then wait or shutdown depending on configuration if critical_thread_ids: if t_total < config['forced_shutdown_timeout']: return True else: logger.w... | |
exec self.importDynamicUtil() | def _cl_task_meta_message(self): j = self.job_info # called on client, so job_info is Job object exec self.importDynamicUtil() msg = { 'APPLICATION': LCGAthenaUtil.cl_application(j), # e.g. ATHENA 'APPLICATIONVERSION': LCGAthenaUtil.cl_application_version(j), # e.g. 15.5.1 'INPUTDATASET': LCGAthenaUtil.cl_input_dataset... | |
'OWNERDN': dynamic_util.cl_ownerdn(), | 'OWNERDN': self.dynamic_util.cl_ownerdn(), | def _cl_task_meta_message(self): j = self.job_info # called on client, so job_info is Job object exec self.importDynamicUtil() msg = { 'APPLICATION': LCGAthenaUtil.cl_application(j), # e.g. ATHENA 'APPLICATIONVERSION': LCGAthenaUtil.cl_application_version(j), # e.g. 15.5.1 'INPUTDATASET': LCGAthenaUtil.cl_input_dataset... |
'TASKNAME': dynamic_util.cl_task_name(j), | 'TASKNAME': self.dynamic_util.cl_task_name(j), | def _cl_task_meta_message(self): j = self.job_info # called on client, so job_info is Job object exec self.importDynamicUtil() msg = { 'APPLICATION': LCGAthenaUtil.cl_application(j), # e.g. ATHENA 'APPLICATIONVERSION': LCGAthenaUtil.cl_application_version(j), # e.g. 15.5.1 'INPUTDATASET': LCGAthenaUtil.cl_input_dataset... |
exec self.importDynamicUtil() | def _cl_job_meta_message(self): j = self.job_info # called on client, so job_info is Job object exec self.importDynamicUtil() msg = { 'GRIDJOBID': dynamic_util.cl_grid_job_id(j), # e.g. https://grid-lb0.desy.de:9000/moqY5njFGurEuoDkkJmtBA 'INPUTDATASET': LCGAthenaUtil.cl_input_dataset(j), # e.g. fdr08_run2.0052283.phys... | |
'GRIDJOBID': dynamic_util.cl_grid_job_id(j), | 'GRIDJOBID': self.dynamic_util.cl_grid_job_id(j), | def _cl_job_meta_message(self): j = self.job_info # called on client, so job_info is Job object exec self.importDynamicUtil() msg = { 'GRIDJOBID': dynamic_util.cl_grid_job_id(j), # e.g. https://grid-lb0.desy.de:9000/moqY5njFGurEuoDkkJmtBA 'INPUTDATASET': LCGAthenaUtil.cl_input_dataset(j), # e.g. fdr08_run2.0052283.phys... |
'JOB_ID_INSIDE_THE_TASK': dynamic_util.cl_job_id_inside_the_task(j), | 'JOB_ID_INSIDE_THE_TASK': self.dynamic_util.cl_job_id_inside_the_task(j), | def _cl_job_meta_message(self): j = self.job_info # called on client, so job_info is Job object exec self.importDynamicUtil() msg = { 'GRIDJOBID': dynamic_util.cl_grid_job_id(j), # e.g. https://grid-lb0.desy.de:9000/moqY5njFGurEuoDkkJmtBA 'INPUTDATASET': LCGAthenaUtil.cl_input_dataset(j), # e.g. fdr08_run2.0052283.phys... |
'TASKNAME': dynamic_util.cl_task_name(j), 'UNIQUEJOBID': dynamic_util.cl_unique_job_id(j), | 'TASKNAME': self.dynamic_util.cl_task_name(j), 'UNIQUEJOBID': self.dynamic_util.cl_unique_job_id(j), | def _cl_job_meta_message(self): j = self.job_info # called on client, so job_info is Job object exec self.importDynamicUtil() msg = { 'GRIDJOBID': dynamic_util.cl_grid_job_id(j), # e.g. https://grid-lb0.desy.de:9000/moqY5njFGurEuoDkkJmtBA 'INPUTDATASET': LCGAthenaUtil.cl_input_dataset(j), # e.g. fdr08_run2.0052283.phys... |
self.job_options += '-c %s ' % app.options | if app.options.startswith('-c'): self.job_options += ' %s ' % app.options else: self.job_options += ' -c %s ' % app.options | def master_prepare(self,app,appconfig): '''Prepare the master job''' |
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