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RunJobUtilities.py
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944 lines (792 loc) · 36.1 KB
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import commands
import json
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)
msgdic["dbTime"] = job.dbTime
msgdic["dbData"] = job.dbData
if job.external_stageout_time:
msgdic['external_stageout_time'] = job.external_stageout_time
if job.outputZipName and job.outputZipBucketID:
msgdic['outputZipName'] = job.outputZipName
msgdic['outputZipBucketID'] = job.outputZipBucketID
# hpc job status
if job.mode:
msgdic["mode"] = job.mode
if job.hpcStatus:
msgdic['hpcStatus'] = job.hpcStatus
if job.yodaJobMetrics:
msgdic["yodaJobMetrics"] = json.dumps(job.yodaJobMetrics)
if job.HPCJobId:
msgdic['HPCJobId'] = job.HPCJobId
# corrupted files
if job.corruptedFiles:
msgdic['corruptedFiles'] = job.corruptedFiles
if job.outputZipName and job.outputZipBucketID:
msgdic['outputZipName'] = job.outputZipName
msgdic['outputZipBucketID'] = job.outputZipBucketID
if job.refreshNow:
msgdic['refreshNow'] = job.refreshNow
if job.coreCount or job.coreCount == 0:
msgdic['coreCount'] = job.coreCount
# 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 and job.pilotErrorDiag != "None" and len(job.pilotErrorDiag.strip()) != 0:
# 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:
if job.subStatus:
msgdic['subStatus'] = job.subStatus
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 at %s (Trial %d/%d)" % (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' and inf not in ins: # 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 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
path = os.path.join(workdir, outf)
if (not os.path.isfile(path) and not fullpath) or (not os.path.isfile(outf) and fullpath):
pilotErrorDiag = "Expected output file %s does not exist" % (path)
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 addFullPathsAsInput(jobPars, full_paths_dictionary):
""" Replace LFNs with full root paths """
# jobPars = .. --inputEVNTFile=EVNT.01416937._000003.pool.root,EVNT.01416937._000004.pool.root ..
# ->
# jobPars = .. --inputEVNTFile=root://../EVNT.01416937._000003.pool.root,root://../EVNT.01416937._000004.pool.root
# FORMAT: full_paths_dictionary = { 'LFN1':'protocol://fullpath/LFN1', .. }
# Extract the inputEVNTFile from the jobPars
if "--inputEVNTFile" in jobPars:
found_items = re.findall(r'\S+', jobPars)
pattern = r"\'?\-\-inputEVNTFile\=(.+)\'?"
for item in found_items:
found = re.findall(pattern, item)
if len(found) > 0:
input_files = found[0]
if input_files.endswith("\'"):
input_files = input_files[:-1]
if len(input_files) > 0:
for lfn in input_files.split(','):
if lfn in full_paths_dictionary.keys():
full_path = full_paths_dictionary[lfn]['pfn']
if full_path not in jobPars:
jobPars = jobPars.replace(lfn, full_path)
else:
tolog("!!WARNING!!3435!! Did not find LFN=%s" % lfn)
else:
tolog(
"!!WARNING!!3434!! Zero length list, cannot update LFN:s with full paths (remote I/O will not work)")
return jobPars
def updateRunCommandList(runCommandList, pworkdir, jobId, statusPFCTurl, analysisJob, usedFAXandDirectIO, hasInput, prodDBlockToken, full_paths_dictionary=None):
""" update the run command list if --directIn is no longer needed """
# the method is using the file state dictionary
# remove later
dumpFileStates(pworkdir, jobId, ftype="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 or 'local' in prodDBlockToken:
# if hasOnlyCopyToScratch(pworkdir, jobId): # python bug? does not work, have to use previous two lines?
_runCommandList = []
if only_copy_to_scratch:
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", "")
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 == True:
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 --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 and analysisJob:
cmd += " --usePFCTurl"
tolog("(Added --usePFCTurl)")
tolog("Updated run command: %s" % (cmd))
_runCommandList2.append(cmd)
_runCommandList = _runCommandList2
### new movers quick integration: reuse usedFAXandDirectIO variable with special meaning
### to avoid any LFC and prefixes lookups in transformation scripts
### since new movers already form proper pfn values
### proper workflow is required: to be reimplemented later
if usedFAXandDirectIO == 'newmover' or usedFAXandDirectIO == 'newmover-directaccess':
_runCommandList2 = []
for cmd in _runCommandList:
# remove --oldPrefix, --newPrefix
# add --usePFCTurl
if "--oldPrefix" in cmd:
pattern = "(\-\-oldPrefix\ \S+)"
cmd = removePattern(cmd, pattern)
tolog("(Removed --oldPrefix pattern)")
if "--newPrefix" in cmd:
pattern = "(\-\-newPrefix\ \S+)"
cmd = removePattern(cmd, pattern)
tolog("(Removed --newPrefix pattern)")
if "--usePFCTurl" not in cmd and analysisJob:
cmd += " --usePFCTurl"
tolog("(Added --usePFCTurl)")
# add --directIn if need
if usedFAXandDirectIO == 'newmover-directaccess':
if "--directIn" not in cmd and analysisJob:
cmd += " --directIn"
tolog("(Added --directIn)")
tolog("Updated run command: %s" % cmd)
_runCommandList2.append(cmd)
_runCommandList = _runCommandList2
# for remote i/o in production jobs, we need to update the jobPars
if full_paths_dictionary:
_runCommandList3 = []
for cmd in _runCommandList:
if full_paths_dictionary and full_paths_dictionary != {}:
cmd = addFullPathsAsInput(cmd, full_paths_dictionary)
tolog("Updated input file list with full paths: %s" % cmd)
else:
tolog("!!WARNING!!5555!! Empty full paths dictionary (direct I/O will not work)")
_runCommandList3.append(cmd)
_runCommandList = _runCommandList3
tolog("Dumping final input file states")
dumpFileStates(pworkdir, jobId, ftype="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)
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