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RunJobUtilities.py
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RunJobUtilities.py
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import commands
import os
import socket
import time
import re
import sys
from pUtil import timeStamp, debugInfo, tolog, readpar, verifyReleaseString,\
isAnalysisJob, dumpOrderedItems, grep, getExperiment, getGUID,\
getCmtconfig, timedCommand, getProperTimeout, removePattern, encode_string
from PilotErrors import PilotErrors
from FileStateClient import dumpFileStates, hasOnlyCopyToScratch
from SiteInformation import SiteInformation
# global variables
#siteroot = ""
def filterTCPString(TCPMessage):
""" Remove any unwanted characters from the TCP message string and truncate if necessary """
# sometimes a failed command will return html which end up in (e.g.) pilotErrorDiag, remove it
if TCPMessage.upper().find("<HTML>") >= 0:
# reset here. the error diag will be set in pilot.updatePandaServer()
tolog("Found html in TCP message string (will be reset): %s" % (TCPMessage))
TCPMessage = ""
# remove any ;-signs which will cause the TCP message to become corrupt (see use of ; below)
# and cause an exception in the TCP server (job will fail with no subprocesses error)
TCPMessage = TCPMessage.replace(";"," ")
# also remove any =-signs since they are interpreted as well
TCPMessage = TCPMessage.replace("!=","ne")
TCPMessage = TCPMessage.replace("="," ")
# also remove any "-signs
TCPMessage = TCPMessage.replace('"','')
# truncate if necessary
if len(TCPMessage) > 250:
tolog("TCP message string will be truncated to size 250")
tolog("Original TCP message string: %s" % (TCPMessage))
TCPMessage = TCPMessage[:250]
return TCPMessage
def updateJobInfo(job, server, port, logfile=None, final=False, latereg=False):
""" send job status updates to local pilot TCP server, in the format
of status=running;pid=2343; logfile is the file that contains
some debug information, usually used in failure case """
try:
s = socket.socket(socket.AF_INET, socket.SOCK_STREAM)
s.settimeout(120)
s.connect((server, port))
except Exception, e:
tolog("!!WARNING!!2999!! updateJobInfo caught a socket/connect exception: %s" % str(e))
return "NOTOK"
msgdic = {}
msgdic["pid"] = os.getpid()
msgdic["pgrp"] = os.getpgrp()
msgdic["jobid"] = job.jobId
msgdic["status"] = job.result[0]
msgdic["jobState"] = job.jobState
msgdic["transecode"] = job.result[1]
msgdic["pilotecode"] = job.result[2]
msgdic["timeStageIn"] = job.timeStageIn
msgdic["timeStageOut"] = job.timeStageOut
msgdic["timeSetup"] = job.timeSetup
msgdic["timeExe"] = job.timeExe
msgdic["cpuTime"] = job.cpuConsumptionTime
msgdic["cpuUnit"] = job.cpuConsumptionUnit
msgdic["cpuConversionFactor"] = job.cpuConversionFactor
msgdic["nEvents"] = job.nEvents
msgdic["nEventsW"] = job.nEventsW
msgdic["vmPeakMax"] = job.vmPeakMax
msgdic["vmPeakMean"] = job.vmPeakMean
msgdic["RSSMean"] = job.RSSMean
msgdic["JEM"] = job.JEM
msgdic["cmtconfig"] = getCmtconfig(job.cmtconfig)
# hpc job status
if job.mode:
msgdic["mode"] = job.mode
if job.hpcStatus:
msgdic['hpcStatus'] = job.hpcStatus
if job.refreshNow:
msgdic['refreshNow'] = job.refreshNow
if job.coreCount or job.coreCount == 0:
msgdic['coreCount'] = job.coreCount
if job.startTime:
msgdic['startTime'] = job.startTime
tolog('Job start time(UTC): %s' % msgdic['startTime'])
if job.endTime:
msgdic['endTime'] = job.endTime
tolog("Job end time(UTC): %s" % msgdic['endTime'])
if job.HPCJobId:
msgdic['HPCJobId'] = job.HPCJobId
# report FAX usage if at least one successful FAX transfer
if job.filesWithFAX > 0:
msgdic["filesWithFAX"] = job.filesWithFAX
if job.filesWithoutFAX > 0:
msgdic["filesWithoutFAX"] = job.filesWithoutFAX
if job.bytesWithFAX > 0:
msgdic["bytesWithFAX"] = job.bytesWithFAX
if job.bytesWithoutFAX > 0:
msgdic["bytesWithoutFAX"] = job.bytesWithoutFAX
# report alternative stage-out usage if at least one successful stage-out to an alternative SE
if job.filesAltStageOut > 0:
msgdic["filesAltStageOut"] = job.filesAltStageOut
tolog("filesAltStageOut=%d" % (job.filesAltStageOut))
else:
tolog("filesAltStageOut not set")
if job.filesNormalStageOut > 0:
msgdic["filesNormalStageOut"] = job.filesNormalStageOut
tolog("filesNormalStageOut=%d" % (job.filesNormalStageOut))
else:
tolog("filesNormalStageOut not set")
# truncate already now if necesary so not too much junk is sent back to the local pilot TCP server
if job.pilotErrorDiag != None:
# remove any unwanted characters from the string
job.pilotErrorDiag = encode_string(job.pilotErrorDiag)
msgdic["pilotErrorDiag"] = job.pilotErrorDiag
# report trf error message if set
if job.exeErrorDiag != "":
# remove any unwanted characters from the string
msgdic["exeErrorDiag"] = encode_string(job.exeErrorDiag)
msgdic["exeErrorCode"] = job.exeErrorCode
if logfile:
msgdic["logfile"] = logfile
# send the special setup string for the log transfer (on xrdcp systems)
if job.spsetup:
# temporarily remove = and ;-signs not to disrupt the TCP message (see ;-handling below)
msgdic["spsetup"] = job.spsetup.replace(";", "^").replace("=", "!")
tolog("Updated spsetup: %s" % (msgdic["spsetup"]))
# set final job state (will be propagated to the job state file)
if final:
job.finalstate = getFinalState(job.result)
tolog("Final payload state set to: %s" % (job.finalstate))
msgdic["finalstate"] = job.finalstate
if job.result[0] == "holding" and job.finalstate == "finished":
if readpar('retry').upper() == "TRUE":
tolog("This job is recoverable")
else:
tolog("This job is not recoverable since job recovery is switched off")
# variables needed for later registration of output files
# (log will be handled by the pilot)
if latereg:
latereg_str = "True"
else:
latereg_str = "False"
msgdic["output_latereg"] = latereg_str
msg = ''
for k in msgdic.keys():
msg += "%s=%s;" % (k, msgdic[k])
tolog("About to send TCP message to main pilot thread of length = %d" % len(msg))
if len(msg) > 4096:
tolog("!!WARNING!!1234!! TCP message too long (cannot truncate easily without harming encoded message)")
try:
s.send(msg)
tolog("(Sent)")
tm = s.recv(1024)
tolog("(Received)")
except Exception, e:
tolog("!!WARNING!!2999!! updateJobInfo caught a send/receive exception: %s" % str(e))
return "NOTOK"
else:
s.settimeout(None)
s.close()
tolog("Successfully sent and received TCP message")
return tm # =OK or NOTOK
def getFinalState(result):
"""
Figure out the final job state (finished or failed)
Simplies job recovery
"""
state = "failed"
# job has failed if transExitCode != 0
if result[1] != 0:
state = "failed"
else:
error = PilotErrors()
# job has finished if pilotErrorCode is in the allowed list or recoverable jobs
if ((error.isRecoverableErrorCode(result[2])) or (result[2] == error.ERR_KILLSIGNAL and result[0] == "holding")):
state = "finished"
return state
def updatePilotServer(job, server, port, logfile=None, final=False, latereg=False):
""" handle the local pilot TCP server updates """
if not final:
max_trials = 2
else:
max_trials = 10
status = False
trial = 1
while trial <= max_trials:
rt = updateJobInfo(job, server, port, logfile=logfile, final=final, latereg=latereg)
if rt == "OK":
tolog("Successfully updated local pilot TCP server for JobID %s at %s (Trial %d/%d)" % (job.jobId, timeStamp(), trial, max_trials))
status = True
break
else:
tolog("[Trial %d/%d] Failed to communicate with local pilot TCP server: %s" % (trial, max_trials, rt))
time.sleep(5)
trial += 1
if not status:
tolog("updatePilotServer failed")
if final:
tolog("!!FAILED!!3000!! Local pilot TCP server down, expecting pilot to fail job (cannot communicate final update back to main pilot thread)")
return status
def getFileNamesFromString(s=""):
"""
Return a list from the input string
Ex. s = "a+b+c+", return: [a,b,c]
"""
list = []
if len(s) > 0:
# remove any trailing + sign
if s[-1] == "+":
s = s[:-1]
# create the list
list = s.split("+")
# remove the path from the file names
for i in range(len(list)):
list[i] = os.path.basename(list[i])
return list
def getRemainingFiles(movedFileList, allFiles):
""" Make a diff between the moved files and all files """
# loop over all entries and remove those that are in the movedFileList
for file in movedFileList:
for i in range(len(allFiles)):
if file == allFiles[i]:
del allFiles[i]
break
return allFiles
def dumpOutput(filename):
""" dump an extract from an ascii file """
ret = ""
if os.path.exists(filename):
fsize = os.path.getsize(filename)
tolog("Filename : %s" % (filename))
tolog("File size: %s" % str(fsize))
if fsize > 2**14: # 16k
tolog("Begin output (first and last 8k)............................................")
ret = commands.getoutput("head --bytes=8192 %s" % filename)
if ret == "":
tolog("[no output?]")
else:
# protect against corrupted files containing illegal chars
try:
tolog(str(ret))
except Exception, e:
tolog("!!WARNING!!3000!! Could not dump file: %s" % str(e))
tolog("\n.... [snip] ....\n")
ret = commands.getoutput("tail --bytes=8192 %s" % filename)
if ret == "":
tolog("[no output?]")
else:
# protect against corrupted files containing illegal chars
try:
tolog(str(ret))
except Exception, e:
tolog("!!WARNING!!3000!! Could not dump file: %s" % str(e))
else:
tolog("Begin output (all)..........................................................")
ret = commands.getoutput("cat %s" % filename)
if ret == "":
tolog("[no output?]")
else:
# protect against corrupted files containing illegal chars
try:
tolog(ret)
except Exception, e:
tolog("!!WARNING!!3000!! Could not dump file: %s" % str(e))
tolog("End output..................................................................")
else:
tolog("!!WARNING!!3000!! file %s does not exist" % (filename))
return ret
def isCommandOk(cmd):
""" return True if the command is returning exit code 0 """
status = True
tolog("Executing command: %s" % (cmd))
a, b = commands.getstatusoutput(cmd)
if a != 0:
tolog("!!WARNING!!3000!! Command test failed with exit code %d: %s" % (a, b))
status = False
return status
def prepareInFiles(inFiles, filesizeIn, checksumIn):
""" prepare the input files (remove non-valid names) """
# if the file name list is modified, make sure that the file size and checksum lists are modified as well
ins = []
fIn = []
cIn = []
file_nr = -1
if inFiles: # non empty list
for inf in inFiles:
file_nr += 1
if inf and inf != 'NULL': # non-empty string and not NULL
ins.append(inf)
fIn.append(filesizeIn[file_nr])
cIn.append(checksumIn[file_nr])
if inFiles[0] != '':
tolog("Input file(s): (%d in total)" % (len(inFiles)))
dumpOrderedItems(inFiles)
else:
tolog("No input files for this job")
return ins, fIn, cIn
def prepareOutFiles(outFiles, logFile, workdir, fullpath=False):
""" verify and prepare and the output files for transfer """
# fullpath = True means that the file in outFiles already has a full path, adding it to workdir is then not needed
ec = 0
pilotErrorDiag = ""
outs = []
modt = []
from SiteMover import SiteMover
for outf in outFiles:
if outf and outf != 'NULL': # non-empty string and not NULL
if (not os.path.isfile("%s/%s" % (workdir, outf)) and not fullpath) or (not os.path.isfile(outf) and fullpath): # expected output file is missing
pilotErrorDiag = "Expected output file %s does not exist" % (outf)
tolog("!!FAILED!!3000!! %s" % (pilotErrorDiag))
error = PilotErrors()
ec = error.ERR_MISSINGOUTPUTFILE
break
else:
tolog("outf = %s" % (outf))
if fullpath:
# remove the full path here from outf
workdir = os.path.dirname(outf)
outf = os.path.basename(outf)
outs.append(outf)
# get the modification time for the file (needed by NG)
modt.append(SiteMover.getModTime(workdir, outf))
tolog("Output file(s):")
try:
_ec, _rs = commands.getstatusoutput("ls -l %s/%s" % (workdir, outf))
except Exception, e:
tolog(str(e))
else:
tolog(_rs)
if ec == 0:
# create a dictionary of the output files with matched modification times (needed to create the NG OutputFiles.xml)
outsDict = dict(zip(outs, modt))
# add the log file with a fictious date since it has not been created yet
outsDict[logFile] = ''
else:
outsDict = {}
return ec, pilotErrorDiag, outs, outsDict
def convertMetadata4NG(filenameOUT, filenameIN, outsDict, dataset, datasetDict):
""" convert the metadata-<jobId>.xml to NG format """
# note: 'dataset' will only be used if datasetDict is None
status = True
# xml tags and conversion dictionaries
_header = '<?xml version="1.0" encoding="UTF-8" standalone="no" ?>\n<!-- ATLAS file meta-data catalog -->\n<!DOCTYPE POOLFILECATALOG SYSTEM "InMemory">\n'
_tagsBEGIN_END = '<%s>%s</%s>\n'
_tagBEGIN = '<%s>\n'
_tagEND = '</%s>\n'
_tagDICT = { 'ID':'guid', 'fsize':'size', 'md5sum':'md5sum', 'adler32':'ad32', 'name':'lfn', 'csumtypetobeset':'ad32', 'surl':'surl' }
dic = {}
dic['md5sum'] = '' # to avoid KeyError's with older python
dic['adler32'] = ''
dic['fsize'] = ''
if os.path.exists(filenameIN):
try:
f = open(filenameIN, 'r')
except Exception, e:
tolog("!!WARNING!!1999!! Could not open file: %s, %s" % (filenameIN, str(e)))
status = False
else:
# get the metadata
xmlIN = f.read()
f.close()
xmlOUT = _header
xmlOUT += _tagBEGIN % 'outputfiles'
from xml.dom import minidom
xmldoc = minidom.parseString(xmlIN)
fileList = xmldoc.getElementsByTagName("File")
# convert the metadata to NG format
for _file in fileList:
xmlOUT += _tagBEGIN % 'file'
lfn = str(_file.getElementsByTagName("lfn")[0].getAttribute("name"))
guid = str(_file.getAttribute("ID"))
lrc_metadata_dom = _file.getElementsByTagName("metadata")
for i in range(len(lrc_metadata_dom)):
_key = str(_file.getElementsByTagName("metadata")[i].getAttribute("att_name"))
_value = str(_file.getElementsByTagName("metadata")[i].getAttribute("att_value"))
# e.g. key = 'fsize', get the corresponding NG name ('size')
_keyNG = _tagDICT[_key]
xmlOUT += ' ' + _tagsBEGIN_END % (_keyNG, _value, _keyNG)
xmlOUT += ' ' + _tagsBEGIN_END % ('guid', guid, 'guid')
xmlOUT += ' ' + _tagsBEGIN_END % ('lfn', lfn, 'lfn')
if datasetDict:
try:
xmlOUT += ' ' + _tagsBEGIN_END % ('dataset', datasetDict[lfn], 'dataset')
except Exception, e:
tolog("!!WARNING!!2999!! datasetDict could not be used: %s (using default dataset instead)" % str(e))
xmlOUT += ' ' + _tagsBEGIN_END % ('dataset', dataset, 'dataset')
else:
xmlOUT += ' ' + _tagsBEGIN_END % ('dataset', dataset, 'dataset')
xmlOUT += ' ' + _tagsBEGIN_END % ('date', outsDict[lfn], 'date')
xmlOUT += _tagEND % 'file'
xmlOUT += _tagEND % 'outputfiles'
tolog("Converted xml for NorduGrid / CERNVM")
# write the new metadata to the OutputFiles.xml
try:
f = open(filenameOUT, 'w')
except Exception, e:
tolog("!!WARNING!!1999!! Could not create output file: %s, %s" % (filenameOUT, str(e)))
status = False
else:
f.write(xmlOUT)
f.close()
else:
status = False
return status
def getOutFilesGuids(outFiles, workdir, experiment, TURL=False):
""" get the outFilesGuids from the PFC """
ec = 0
pilotErrorDiag = ""
outFilesGuids = []
# Get the experiment object and the GUID source filename
thisExperiment = getExperiment(experiment)
filename = thisExperiment.getGUIDSourceFilename()
# If a source file should not be used (ie empty filename string), then generate the GUIDs here
if filename == "":
tolog("Pilot will generate GUIDs for the output files")
for i in range (0, len(outFiles)):
guid = getGUID()
if guid == "":
guid = "- GUID generation failed -"
outFilesGuids.append(guid)
return ec, pilotErrorDiag, outFilesGuids
else:
tolog("Pilot will get GUIDs for the output files from source: %s" % (filename))
pfcFile = os.path.join(workdir, filename) #"%s/PoolFileCatalog.xml" % (workdir)
# The PFC used for Event Service will be TURL based, use the corresponding file
if TURL:
pfcFile = pfcFile.replace(".xml", "TURL.xml")
# Initialization: make sure the guid list has the same length as the file list
for i in range (0, len(outFiles)):
outFilesGuids.append(None)
# make sure the PFC exists
if os.path.isfile(pfcFile):
from xml.dom import minidom
xmldoc = minidom.parse(pfcFile)
fileList = xmldoc.getElementsByTagName("File")
for thisfile in fileList:
gpfn = str(thisfile.getElementsByTagName("pfn")[0].getAttribute("name"))
guid = str(thisfile.getAttribute("ID"))
for i in range(0, len(outFiles)):
if outFiles[i] == gpfn:
outFilesGuids[i] = guid
else:
pilotErrorDiag = "PFC file does not exist: %s" % (pfcFile)
tolog("!!FAILED!!3000!! %s" % (pilotErrorDiag))
error = PilotErrors()
ec = error.ERR_MISSINGPFC
return ec, pilotErrorDiag, outFilesGuids
def verifyMultiTrf(jobParameterList, jobHomePackageList, jobTrfList, jobAtlasRelease):
""" make sure that a multi-trf (or single trf) job is properly setup """
error = PilotErrors()
ec = 0
pilotErrorDiag = ""
N_jobParameterList = len(jobParameterList)
N_jobHomePackageList = len(jobHomePackageList)
N_jobTrfList = len(jobTrfList)
N_jobAtlasRelease = len(jobAtlasRelease)
# test jobs have multiple atlas releases defined, but not real tasks
if N_jobTrfList > N_jobAtlasRelease and N_jobAtlasRelease == 1:
# jobAtlasRelease = ['14.0.0'] -> ['14.0.0', '14.0.0']
jobAtlasRelease = jobAtlasRelease*N_jobTrfList
N_jobAtlasRelease = len(jobAtlasRelease)
if (N_jobParameterList == N_jobHomePackageList) and \
(N_jobHomePackageList == N_jobTrfList) and \
(N_jobTrfList == N_jobAtlasRelease):
if N_jobAtlasRelease == 1:
tolog("Multi-trf verification succeeded (single job)")
else:
tolog("Multi-trf verification succeeded")
else:
pilotErrorDiag = "Multi-trf verification failed: N(jobPars) eq %d, but N(homepackage,transformation,AtlasRelease) eq (%d,%d,%d)" %\
(N_jobParameterList, N_jobHomePackageList, N_jobTrfList, N_jobAtlasRelease)
tolog("!!FAILED!!2999!! %s" % (pilotErrorDiag))
ec = error.ERR_SETUPFAILURE
return ec, pilotErrorDiag, jobAtlasRelease
def updateCopysetups(cmd3, transferType=None, useCT=None, directIn=None, useFileStager=None):
""" Update the relevant copysetup fields for remote I/O or file stager """
si = SiteInformation()
_copysetupin = readpar('copysetupin')
_copysetup = readpar('copysetup')
if _copysetupin != "":
si.updateCopysetup(cmd3, 'copysetupin', _copysetupin, transferType=transferType, useCT=useCT, directIn=directIn, useFileStager=useFileStager)
else:
si.updateCopysetup(cmd3, 'copysetup', _copysetup, transferType=transferType, useCT=useCT, directIn=directIn, useFileStager=useFileStager)
def addSPSetupToCmd(special_setup_cmd, cmd):
""" Add the special command setup if it exists to the main run command """
if special_setup_cmd != "":
if not special_setup_cmd.endswith(";"):
special_setup_cmd += ";"
# the special command must be squeezed in before the trf but after the setup scripts
# find the last ; and add the special setup there
# in case of -f options, there's a possibility that the command can contain extra ;-signs, remove that part
pos_f = cmd.rfind("-f ")
if pos_f != -1:
_cmd0 = cmd[:pos_f]
_cmd1 = cmd[pos_f:]
else:
_cmd0 = cmd
_cmd1 = ""
last_semicolon = _cmd0.rfind(";")
cmd = _cmd0[:last_semicolon] + ";" + special_setup_cmd[:-1] + _cmd0[last_semicolon:] + _cmd1
tolog("Special setup command added to main run command")
return cmd
def removeSkippedFromJobPars(fname, jobPars):
""" remove skipped input files from jobPars """
# get the skipped file names from the xml
skipped = getLFNsFromSkippedXML(fname)
if skipped == []:
tolog("Did not find any skipped LFNs in: %s" % (fname))
else:
tolog("Removing skipped input files from jobPars")
tolog("..skipped: %s" % str(skipped))
tolog("..jobPars:\n%s" % (jobPars))
for skip in skipped:
tolog("..Removing: %s" % (skip))
# try difference styles
_skip = "\'%s\'," % (skip)
if _skip in jobPars:
jobPars = jobPars.replace(_skip,'')
tolog('..Removed %s from jobPars' % (_skip))
else:
_skip = "\'%s\'" % (skip)
if _skip in jobPars:
jobPars = jobPars.replace(_skip,'')
tolog('..Removed %s from jobPars' % (_skip))
else:
_skip = "%s," % (skip)
if _skip in jobPars:
jobPars = jobPars.replace(skip,'')
tolog('..Removed %s from jobPars' % (skip))
else:
if skip in jobPars:
jobPars = jobPars.replace(skip,'')
print '..Removed %s from jobPars' % (skip)
else:
# nothing to remove
tolog("..Found nothing to remove from jobPars: %s" % (jobPars))
return jobPars
def getLFNsFromSkippedXML(fname):
""" extract the list of skipped files from the skipped xml """
lfns = []
try:
f = open(fname, "r")
except Exception, e:
tolog("Warning: could not open skipped xml file: %s" % str(e))
else:
pre_xml = f.read()
f.close()
# add an XML header etc since the skipped xml is just an XML fragment
# so that it can be processed
xmlstr = '<?xml version="1.0" encoding="UTF-8" standalone="no" ?>\n'
xmlstr += "<!-- Edited By POOL -->\n"
xmlstr += '<!DOCTYPE POOLFILECATALOG SYSTEM "InMemory">\n'
xmlstr += "<POOLFILECATALOG>\n"
xmlstr += pre_xml
xmlstr += "</POOLFILECATALOG>\n"
from xml.dom import minidom
xmldoc = minidom.parseString(xmlstr)
fileList = xmldoc.getElementsByTagName("File")
for thisfile in fileList:
lfns.append(str(thisfile.getElementsByTagName("lfn")[0].getAttribute("name")))
return lfns
def setEnvVars(sitename):
""" Set ATLAS_CONDDB if necessary """
if not os.environ.has_key('ATLAS_CONDDB'):
atlas_conddb = readpar('gatekeeper')
if atlas_conddb != "to.be.set":
os.environ["ATLAS_CONDDB"] = atlas_conddb
tolog("Note: ATLAS_CONDDB was not set by the pilot wrapper script")
tolog("The pilot has set ATLAS_CONDDB to: %s" % (atlas_conddb))
else:
tolog("Warning: ATLAS_CONDDB was not set by the pilot wrapper and schedconfig.gatekeeper value is to.be.set (pilot will take no action)")
# set specially requested env vars
os.environ["PANDA_SITE_NAME"] = sitename
tolog("Set PANDA_SITE_NAME = %s" % (sitename))
copytool = readpar("copytoolin")
if copytool == "":
copytool = readpar("copytool")
if "^" in copytool:
copytool = copytool.split("^")[0]
os.environ["COPY_TOOL"] = copytool
tolog("Set COPY_TOOL = %s" % (copytool))
def updateRunCommandList(runCommandList, pworkdir, jobId, statusPFCTurl, analysisJob, usedFAXandDirectIO, hasInput):
""" update the run command list if --directIn is no longer needed """
# the method is using the file state dictionary
# remove later
dumpFileStates(pworkdir, jobId, type="input")
# remove any instruction regarding tag file creation for event service jobs
_runCommandList = []
for cmd in runCommandList:
if "--createTAGFileForES" in cmd:
cmd = cmd.replace("--createTAGFileForES","")
_runCommandList.append(cmd)
runCommandList = _runCommandList
# no need to continue if no input files
if not hasInput:
return runCommandList
# are there only copy_to_scratch transfer modes in the file state dictionary?
# if so, remove any lingering --directIn instruction
only_copy_to_scratch = hasOnlyCopyToScratch(pworkdir, jobId)
if only_copy_to_scratch:
# if hasOnlyCopyToScratch(pworkdir, jobId): # python bug? does not work, have to use previous two lines?
_runCommandList = []
tolog("There are only copy_to_scratch transfer modes in file state dictionary")
for cmd in runCommandList:
# remove the --directIn string if present
if "--directIn" in cmd:
tolog("(Removing --directIn instruction from run command since it is not needed)")
cmd = cmd.replace("--directIn", "")
# remove the --useFileStager string if present
if "--useFileStager" in cmd:
tolog("(Removing --useFileStager instruction from run command since it is not needed)")
cmd = cmd.replace("--useFileStager", "")
# remove additional run options if creation of TURL based PFC failed
if statusPFCTurl == False: # (note: can also be None, so do not use 'if not statusPFCTurl')
if "--usePFCTurl" in cmd:
tolog("(Removing --usePFCTurl instruction from run command since it is not needed)")
cmd = cmd.replace(" --usePFCTurl", "")
if not "--lfcHost" in cmd and analysisJob:
tolog("Adding lfcHost to run command")
cmd += ' --lfcHost %s' % (readpar('lfchost'))
tolog("Updated run command: %s" % (cmd))
_runCommandList.append(cmd)
else:
tolog("Nothing to update in run command list related to copy-to-scratch")
_runCommandList = runCommandList
# was FAX used as primary site mover in combination with direct I/O?
if usedFAXandDirectIO:
tolog("Since FAX was used as primary site mover in combination with direct I/O, the run command list need to be updated")
_runCommandList2 = []
for cmd in _runCommandList:
# remove the --lfcHost
if "--lfcHost" in cmd:
_lfcHost = ' --lfcHost %s' % (readpar('lfchost'))
cmd = cmd.replace(_lfcHost, '')
tolog("(Removed the LFC host:%s)" % (_lfcHost))
# remove the --oldPrefix
if "--oldPrefix" in cmd:
pattern = "(\-\-oldPrefix\ \S+)"
cmd = removePattern(cmd, pattern)
tolog("(Removed --oldPrefix pattern)")
# remove the --newPrefix
if "--newPrefix" in cmd:
pattern = "(\-\-newPrefix\ \S+)"
cmd = removePattern(cmd, pattern)
tolog("(Removed --newPrefix pattern)")
# add the --usePFCTurl if not there already
if not "--usePFCTurl" in cmd:
cmd += " --usePFCTurl"
tolog("(Added --usePFCTurl)")
tolog("Updated run command: %s" % (cmd))
_runCommandList2.append(cmd)
_runCommandList = _runCommandList2
tolog("Dumping final input file states")
dumpFileStates(pworkdir, jobId, type="input")
return _runCommandList
def updateRunCommandListMJ(runCommandList, pworkdir, jobId, statusPFCTurl, analysisJob, usedFAXandDirectIO, hasInput):
"""!!! Should be merged with updateRunCommandList !!!"""
""" update the run command list if --directIn is no longer needed """
# the method is using the file state dictionary
# remove later
dumpFileStates(pworkdir, jobId, type="input")
# remove any instruction regarding tag file creation for event service jobs
#_runCommandList = []
# for cmd in runCommandList:
cmd = runCommandList['parameters']
if "--createTAGFileForES" in cmd:
cmd = cmd.replace("--createTAGFileForES","")
runCommandList['parameters'] = cmd
# no need to continue if no input files
if not hasInput:
return runCommandList
# are there only copy_to_scratch transfer modes in the file state dictionary?
# if so, remove any lingering --directIn instruction
only_copy_to_scratch = hasOnlyCopyToScratch(pworkdir, jobId)
if only_copy_to_scratch:
# if hasOnlyCopyToScratch(pworkdir, jobId): # python bug? does not work, have to use previous two lines?
_runCommandList = []
tolog("There are only copy_to_scratch transfer modes in file state dictionary")
#for cmd in runCommandList:
# remove the --directIn string if present
cmd = runCommandList['parameters']
if "--directIn" in cmd:
tolog("(Removing --directIn instruction from run command since it is not needed)")
cmd = cmd.replace("--directIn", "")
# remove the --useFileStager string if present
if "--useFileStager" in cmd:
tolog("(Removing --useFileStager instruction from run command since it is not needed)")
cmd = cmd.replace("--useFileStager", "")
# remove additional run options if creation of TURL based PFC failed
if statusPFCTurl == False: # (note: can also be None, so do not use 'if not statusPFCTurl')
if "--usePFCTurl" in cmd:
tolog("(Removing --usePFCTurl instruction from run command since it is not needed)")
cmd = cmd.replace(" --usePFCTurl", "")
if not "--lfcHost" in cmd and analysisJob:
tolog("Adding lfcHost to run command")
cmd += ' --lfcHost %s' % (readpar('lfchost'))
tolog("Updated run command: %s" % (cmd))
runCommandList['parameters'] = cmd
else:
tolog("Nothing to update in run command list related to copy-to-scratch")
# was FAX used as primary site mover in combination with direct I/O?
if usedFAXandDirectIO:
tolog("Since FAX was used as primary site mover in combination with direct I/O, the run command list need to be updated")
# remove the --lfcHost
if "--lfcHost" in cmd:
_lfcHost = ' --lfcHost %s' % (readpar('lfchost'))
cmd = cmd.replace(_lfcHost, '')
tolog("(Removed the LFC host:%s)" % (_lfcHost))
# remove the --oldPrefix
if "--oldPrefix" in cmd:
pattern = "(\-\-oldPrefix\ \S+)"
cmd = removePattern(cmd, pattern)
tolog("(Removed --oldPrefix pattern)")
# remove the --newPrefix
if "--newPrefix" in cmd:
pattern = "(\-\-newPrefix\ \S+)"
cmd = removePattern(cmd, pattern)
tolog("(Removed --newPrefix pattern)")
# add the --usePFCTurl if not there already
if not "--usePFCTurl" in cmd:
cmd += " --usePFCTurl"
tolog("(Added --usePFCTurl)")
tolog("Updated run command: %s" % (cmd))
runCommandList['parameters'] = cmd
tolog("Dumping final input file states")
dumpFileStates(pworkdir, jobId, type="input")
return runCommandList
def getStdoutFilename(workdir, _stdout, current_job_number, number_of_jobs):
""" Return a proper stdout filename """
if number_of_jobs > 1:
_stdout = _stdout.replace(".txt", "_%d.txt" % (current_job_number))
return os.path.join(workdir, _stdout)
def findVmPeaks(setup):
""" Find the VmPeak values """
vmPeakMax = 0
vmPeakMean = 0
RSSMean = 0
# matched_lines = grep(["Py\:PerfMonSvc\s*INFO\s*VmPeak:\s*[0-9]"], stdout_filename)
# pattern = "([0-9]+)"
# # now extract the digits from the found lines
# N = 0
# vmPeaks = 0
# for line in matched_lines:
# _vmPeak = re.search(pattern, line)
# if _vmPeak:
# N += 1
# vmPeak = _vmPeak.group(1)
# if vmPeak > vmPeakMax:
# vmPeakMax = vmPeak
# vmPeaks += vmPeak
# use the VmPeak script to get all values
cmd = "%s python VmPeak.py >Pilot_VmPeak.txt" % (setup)
tolog("findVmPeaks: About to launch:\n %s " % cmd)
try:
ec, output = timedCommand(cmd, timeout=getProperTimeout(setup))
except Exception, e:
tolog("!!WARNING!!1111!! Failed to execute VmPeak script: %s" % (e))
else:
# now get the values from the deault file
file_name = os.path.join(os.getcwd(), "VmPeak_values.txt")
if ec == 0:
if os.path.exists(file_name):
try:
f = open(file_name, "r")
except Exception, e:
tolog("!!WARNING!!1111!! Failed to open VmPeak values file: %s" % (e))
else:
_values = f.read()
f.close()
values = _values.split(",")
try:
vmPeakMax = int(values[0])
vmPeakMean = int(values[1])
RSSMean = int(values[2])
except Exception, e:
tolog("!!WARNING!!1111!! VmPeak exception: %s" % (e))
else:
tolog("Note: File %s does not exist" % (file_name))
else:
tolog("!!WARNING!!1111!! VmPeak script returned: %d, %s" % (ec, output))
tolog("[VmPeak] vmPeakMax=%d" % (vmPeakMax))
tolog("[VmPeak] vmPeakMean=%d" % (vmPeakMean))
tolog("[VmPeak] RSSMean=%d" % (RSSMean))
return vmPeakMax, vmPeakMean, RSSMean
def getSourceSetup(runCommand):
""" Extract the source setup command from the run command """
if type(runCommand) is dict:
to_str = " ".join(runCommand['environment'])
to_str = "%s %s %s %s" % (to_str, runCommand["interpreter"], runCommand["payload"], runCommand["parameters"])
runCommand = to_str
setup = ""
pattern = re.compile(r"(source /.+?;)")
s = re.findall(pattern, runCommand)
if s != []:
setup = s[0]
return setup