def TransferFiles(job_state, datadir, files, **kwargs):
"""
Transfers files from list 'files'
May change CWD with pUtil.chdir (several times)
:param job_state:
:param datadir: job data dir
:param files: list of filenames
:param kwargs: specific arguments for other purposes
:return:
"""
job = job_state.job
pUtil.chdir(datadir)
XMLMetadata = pUtil.getMetadata(job_state.site.workdir, job.jobId)
thisSite = DorE(kwargs, 'thisSite')
if not setGuids(job_state, files, **kwargs):
job.result[2] = PilotErrors().ERR_LOSTJOBPFC
return ReturnCode.FailedJob
outPFC = updateOutPFC(job, **kwargs)
if not outPFC:
return ReturnCode.FailedJob
dsname = defaultDSname(job.destinationDblock)
datasetDict = pUtil.getDatasetDict(job.outFiles, job.destinationDblock, job.logFile, job.logDblock)
if not datasetDict:
log("Output files will go to default dataset: %s" % (dsname))
# the cmtconfig is needed by at least the xrdcp site mover
cmtconfig = pUtil.getCmtconfig(job.cmtconfig)
tin_0 = os.times()
rf = None
_state = ReturnCode.OK
_msg = ""
ec = -1
try:
# Note: alt stage-out numbers are not saved in recovery mode (job object not returned from this function)
rc, pilotErrorDiag, rf, rs, job.filesNormalStageOut, job.filesAltStageOut, os_bucket_id = Mover.mover_put_data(
"xmlcatalog_file:%s" % outPFC, dsname,
thisSite.sitename, thisSite.computingElement, analysisJob=pUtil.isAnalysisJob(job.trf.split(",")[0]),
proxycheck=DorE(kwargs, 'proxycheckFlag'),
pinitdir=DorE(kwargs, 'pilot_initdir'),
datasetDict=datasetDict,
stageoutTries=DorE(kwargs, 'stageoutretry'),
cmtconfig=cmtconfig, recoveryWorkDir=thisSite.workdir,
job=job)
except Exception, e:
pilotErrorDiag = "Put function can not be called for staging out: %s" % str(e)
log("!!%s!!1105!! %s" % (env['errorLabel'], pilotErrorDiag))
ec = PilotErrors().ERR_PUTFUNCNOCALL
_state = ReturnCode.Holding
_msg = env['errorLabel']
def CreateTransferFileList(job_state, **kwargs):
"""
Function prepares job for staging out
:param job_state: (JobState) decoded job state file
mandatory
Other params can be passed into functions:
1. To overwrite environment variables:
Unused parameters are ommited.
:return:
1. (integer) return code
2. (string) logfile path
3. (string) dir with files
2. (list) list of files to be transferred
"""
currentDir = os.getcwd()
pUtil.chdir(job_state.site.workdir)
logfile = "%s/%s" % (job_state.site.workdir, job_state.job.logFile)
logfile = (
os.path.abspath(logfile)
if os.path.isfile(logfile) and not pUtil.isLogfileCopied(job_state.site.workdir)
else ""
)
remaining_files = []
filesDir = ""
if os.path.isdir(job_state.job.datadir):
pUtil.chdir(job_state.job.datadir)
remaining_files = pUtil.getRemainingOutputFiles(job_state.job.outFiles)
if not remaining_files:
remaining_files = []
filesDir = os.path.abspath(job_state.job.datadir)
pUtil.chdir(currentDir)
return ReturnCode.OK, logfile, filesDir, remaining_files
def CreateTransferFileList(job_state, **kwargs):
"""
Function prepares job for staging out
:param job_state: (JobState) decoded job state file
mandatory
Other params can be passed into functions:
1. To overwrite environment variables:
Unused parameters are ommited.
:return:
1. (integer) return code
2. (string) logfile path
3. (string) dir with files
2. (list) list of files to be transferred
"""
currentDir = os.getcwd()
pUtil.chdir(job_state.site.workdir)
logfile = "%s/%s" % (job_state.site.workdir, job_state.job.logFile)
logfile = os.path.abspath(logfile)\
if os.path.isfile(logfile) and not pUtil.isLogfileCopied(job_state.site.workdir) else ""
remaining_files = []
filesDir = ''
if os.path.isdir(job_state.job.datadir):
pUtil.chdir(job_state.job.datadir)
remaining_files = pUtil.getRemainingOutputFiles(job_state.job.outFiles)
if not remaining_files:
remaining_files = []
filesDir = os.path.abspath(job_state.job.datadir)
pUtil.chdir(currentDir)
return ReturnCode.OK, logfile, filesDir, remaining_files
def DeferredStageoutJob(job_dir, job_state_file="", deferred_stageout_logfile=False, **kwargs):
"""
Performs stageing out preparation and stages out the job in specified directory.
:param job_dir: (string) directory with a job.
mandatory parameter
:param job_state_file: (string) path to job state file or other file containing job state. If empty, job
state file is located as job_dir+'/jobState-*.*'.
defaults to ""
:param deferred_stageout_logfile: (string|False) template name for deferred log stageout
Replaces "{job_id}" with current job id like
"log-{job_id}.txt" -> "log-124124.txt"
Default False
Other parameters are passed into other functions
:return: (bool) the fact of stageout being performed
"""
log('Deferred stageout from job directory "%s"' % job_dir)
job_state = JobState()
if job_state_file == "":
try:
job_state_file = glob(job_dir + "/" + jobState_file_wildcart)[0]
except:
log("There is no job state file in the provided directory, exiting")
return False
log("Job state file is %s" % job_state_file)
# lockfd, lockfn = createAtomicLockFile(job_dir)
with LockFileWrapper(job_dir):
if not TestJobDirForDeferredStageoutNecessity(job_dir, job_state_file, **kwargs):
log('Job "%s" does not need deferred stageout procedure (yet)' % job_dir)
# releaseAtomicLockFile(lockfd, lockfn)
return False
if not job_state.get(job_state_file):
log("Job state file reading failed, exiting")
# releaseAtomicLockFile(lockfd, lockfn)
return False
log('Working with job in "%s"' % job_dir)
_job, _site, _node, _recoveryAttempt = job_state.decode()
if not (_job and _site and _node):
log("Can not decode jobState file, exiting")
# releaseAtomicLockFile(lockfd, lockfn)
return False
with LogWrapper(deferred_stageout_logfile, _job.jobId) as logger:
rc = PrepareJobForDeferredStageout(job_state, **kwargs)
if rc == ReturnCode.PostJobOnly:
pUtil.postJobTask(
job_state.job,
job_state.site,
DorE(kwargs, "workerNode"),
DorE(kwargs, "experiment"),
jr=True,
ra=job_state.recoveryAttempt,
)
# releaseAtomicLockFile(lockfd, lockfn)
return True
if rc > 0:
log("Job is not prepared for stageout, exiting")
if rc == ReturnCode.Cleanup:
cleanup(job_state)
# releaseAtomicLockFile(lockfd, lockfn)
return False
rc, logfile, datadir, filelist = CreateTransferFileList(job_state, **kwargs)
XMLStr = ""
if datadir == "":
try:
XMLStr = job_state.node["xml"]
except:
pass
if XMLStr == "":
XMLStr = pUtil.getMetadata(job_state.site.workdir, job_state.job.jobId)
currentdir = os.getcwd()
pUtil.chdir(job_state.site.workdir)
if len(filelist):
log("Stageout will now transfer the files")
rc = TransferFiles(job_state, datadir, filelist, **kwargs)
if rc == ReturnCode.Holding:
job_state.job.result[0] = "holding"
if rc == ReturnCode.FailedJob:
job_state.job.result[0] = "failed"
job_state.job.setState(job_state.job.result)
pUtil.chdir(job_state.site.workdir)
ret = True
if logfile != "" and not pUtil.isLogfileCopied(job_state.site.workdir):
log("Stageout will now transfer the log")
_log = JobLog()
ret, _ = _log.transferLogFile(
job_state.job, job_state.site, DorE(kwargs, "experiment"), dest=None, jr=True
)
if not ret:
rc = ReturnCode.Holding # We need to transfer log file regardless the files
if rc == ReturnCode.OK:
if pUtil.verifyTransfer(job_state.site.workdir):
job_state.job.result[0] = "finished"
else:
job_state.job.result[0] = "failed"
job_state.job.setState(job_state.job.result)
if job_state.job.result[0] in finalJobStates:
job_state.job.final_state = job_state.job.result[0]
log("Stageout will now update the server with new status")
rt, retNode = updatePandaServer(job_state, xmlstr=XMLStr, **kwargs)
if rt == 0:
log("Job %s updated (exit code %d)" % (job_state.job.jobId, job_state.job.result[2]))
# did the server send back a command?
if "tobekilled" in job_state.job.action:
log("!!WARNING!!1120!! Panda server returned a 'tobekilled' command")
job_state.job.result[0] = "failed"
# further recovery attempt unnecessary, but keep the work dir for debugging
if job_state.job.result[0] == "failed":
log("Further recovery attempts will be prevented for failed job (will leave work dir)")
if not job_state.rename(job_state.site, job_state.job):
log("(Fate of job state file left for next pilot)")
else:
log("!!WARNING!!1120!! Panda server returned a %d" % (rt))
# store the final state so that the next pilot will know
# store the metadata xml
retNode["xml"] = XMLStr
# update the job state file with the new state information
_retjs = pUtil.updateJobState(job_state.job, job_state.site, retNode, job_state.recoveryAttempt)
log("Stageout will now proceed to post-job actions")
if job_state.job.result[0] in finalJobStates:
pUtil.postJobTask(
job_state.job,
job_state.site,
DorE(kwargs, "workerNode"),
DorE(kwargs, "experiment"),
jr=True,
ra=job_state.recoveryAttempt,
)
pUtil.chdir(currentdir)
# releaseAtomicLockFile(lockfd, lockfn)
if job_state.job.result[0] == "finished":
log("Stageout will now remove the job, it is in finished state and can be removed")
cleanup(job_state)
return True
def DeferredStageoutHPCJob(job_dir, deferred_stageout_logfile=False, **kwargs):
"""
Performs stageing out preparation for the HPC job in specified directory.
:param job_dir: (string) directory with a job.
mandatory parameter
:param deferred_stageout_logfile: (string|False) template name for deferred log stageout
Replaces "{job_id}" with current job id like
"log-{job_id}.txt" -> "log-124124.txt"
Default False
Other parameters are passed into other functions
:return: (bool) the fact of stageout being performed
"""
log('Deferred stageout from HPC job directory "%s"' % job_dir)
file_path = job_dir + "/" + hpc_jobState_file_wildcart
current_dir = os.getcwd()
log("Working on %s" % file_path)
log("Chdir from current dir %s to %s" % (current_dir, job_dir))
pUtil.chdir(job_dir)
try:
with LockFileWrapper(file_path) as is_locked:
if not is_locked:
return False
from json import load
with open(file_path) as data_file:
HPC_state = load(data_file)
job_state_file = HPC_state["JobStateFile"]
job_command = HPC_state["JobCommand"]
# global_work_dir = HPC_state['GlobalWorkingDir']
JS = JobState()
JS.get(job_state_file)
_job, _site, _node, _recoveryAttempt = JS.decode()
with LogWrapper(deferred_stageout_logfile, _job.jobId) as logger:
jobStatus, jobAttemptNr, jobStatusCode = pUtil.getJobStatus(
_job.jobId, DorE(kwargs, "pshttpurl"), DorE(kwargs, "psport"), DorE(kwargs, "pilot_initdir")
)
# recover this job?
if jobStatusCode == 20:
log("Received general error code from dispatcher call (leave job for later pilot)")
# release the atomic lockfile and go to the next directory
# releaseAtomicLockFile(fd, lockfile_name)
return False
elif jobStatus in finalJobStates or "tobekilled" in _job.action:
log(
"Job %s is currently in state '%s' with attemptNr = %d (according to server - will not"
" perform staging out)" % (_job.jobId, jobStatus, jobAttemptNr)
)
# releaseAtomicLockFile(fd, lockfile_name)
return False
# update job state file at this point to prevent a parallel pilot from doing a simultaneous recovery
_retjs = pUtil.updateJobState(_job, _site, _node, _recoveryAttempt)
# releaseAtomicLockFile(fd, lockfile_name)
monitor = Monitor(env)
monitor.monitor_recovery_job(_job, _site, _node, job_command, job_state_file, recover_dir=job_dir)
log("Chdir back to %s" % current_dir)
pUtil.chdir(current_dir)
panda_jobs = glob(job_dir + "/PandaJob_*_*")
panda_logs = glob(job_dir + "/*.log.tgz.*")
if panda_jobs or panda_logs:
log(
"Number of founded panda jobs: %d, number of panda log tar file %d, will not remove job dir"
% (len(panda_jobs), len(panda_logs))
)
else:
log(
"Number of founded panda jobs: %d, number of panda log tar file %d, will remove job dir"
% (len(panda_jobs), len(panda_logs))
)
log("Remove job dir %s" % job_dir)
os.system("rm -rf %s" % job_dir)
return True
except:
log("Failed to start deferred stage out for HPC job: %s" % traceback.format_exc())
return False
log(
"!!WARNING!!1100!! Attempt number mismatch for job %s (according to server - will not be"
" recovered)" % job_state.job.jobId
)
log("....Initial attempt number: %d" % attemptNr)
log("....Current attempt number: %d" % jobAttemptNr)
log("....Job status (server) : %s" % jobStatus)
log("....Job status (state) : %s" % job_state.job.result[0])
return lognret(ReturnCode.Cleanup, "Further recovery attempts will be prevented for this job")
else:
log("Attempt numbers from server and job state file agree: %d" % attemptNr)
job_state.recoveryAttempt += 1
currentDir = os.getcwd()
pUtil.chdir(job_state.site.workdir)
# Update state to prevent another pilot to try to recover this job
# This was at the main logic, but I don't see, why should we do that while lockfile is present
pUtil.updateJobState(job_state.job, job_state.site, job_state.node, job_state.recoveryAttempt)
pUtil.chdir(currentDir)
ec = job_state.job.result[2]
logfile = "%s/%s" % (job_state.site.workdir, job_state.job.logFile)
if not ec:
if (
(not os.path.isfile(logfile))
and os.path.isdir(job_state.job.newDirNM)
and os.path.isfile(os.path.join(job_state.job.newDirNM, pilotLogFileInNewWD))
):
ec = pUtil.getExitCode(job_state.job.newDirNM, "pilotlog.txt")
def DeferredStageoutJob(job_dir, job_state_file="", deferred_stageout_logfile=False,
**kwargs):
"""
Performs stageing out preparation and stages out the job in specified directory.
:param job_dir: (string) directory with a job.
mandatory parameter
:param job_state_file: (string) path to job state file or other file containing job state. If empty, job
state file is located as job_dir+'/jobState-*.*'.
defaults to ""
:param deferred_stageout_logfile: (string|False) template name for deferred log stageout
Replaces "{job_id}" with current job id like
"log-{job_id}.txt" -> "log-124124.txt"
Default False
Other parameters are passed into other functions
:return: (bool) the fact of stageout being performed
"""
log("Deferred stageout from job directory \"%s\"" % job_dir)
job_state = JobState()
if job_state_file == "":
try:
job_state_file = glob(job_dir + "/" + jobState_file_wildcart)[0]
except:
log("There is no job state file in the provided directory, exiting")
return False
log("Job state file is %s"%job_state_file)
# lockfd, lockfn = createAtomicLockFile(job_dir)
with LockFileWrapper(job_dir):
if not TestJobDirForDeferredStageoutNecessity(job_dir, job_state_file, **kwargs):
log("Job \"%s\" does not need deferred stageout procedure (yet)" % job_dir)
# releaseAtomicLockFile(lockfd, lockfn)
return False
if not job_state.get(job_state_file):
log("Job state file reading failed, exiting")
# releaseAtomicLockFile(lockfd, lockfn)
return False
log("Working with job in \"%s\"" % job_dir)
_job, _site, _node, _recoveryAttempt = job_state.decode()
if not (_job and _site and _node):
log("Can not decode jobState file, exiting")
# releaseAtomicLockFile(lockfd, lockfn)
return False
with LogWrapper(deferred_stageout_logfile, _job.jobId) as logger:
rc = PrepareJobForDeferredStageout(job_state, **kwargs)
if rc == ReturnCode.PostJobOnly:
pUtil.postJobTask(job_state.job, job_state.site, DorE(kwargs, 'workerNode'), DorE(kwargs, 'experiment'),
jr=True, ra=job_state.recoveryAttempt)
# releaseAtomicLockFile(lockfd, lockfn)
return True
if rc > 0:
log("Job is not prepared for stageout, exiting")
if rc == ReturnCode.Cleanup:
cleanup(job_state)
# releaseAtomicLockFile(lockfd, lockfn)
return False
rc, logfile, datadir, filelist = CreateTransferFileList(job_state, **kwargs)
XMLStr = ''
if datadir == "":
try:
XMLStr = job_state.node['xml']
except:
pass
if XMLStr == '':
XMLStr = pUtil.getMetadata(job_state.site.workdir, job_state.job.jobId)
currentdir = os.getcwd()
pUtil.chdir(job_state.site.workdir)
if len(filelist):
log("Stageout will now transfer the files")
rc = TransferFiles(job_state, datadir, filelist, **kwargs)
if rc == ReturnCode.Holding:
job_state.job.result[0] = "holding"
if rc == ReturnCode.FailedJob:
job_state.job.result[0] = "failed"
job_state.job.setState(job_state.job.result)
pUtil.chdir(job_state.site.workdir)
ret = True
if logfile != "" and not pUtil.isLogfileCopied(job_state.site.workdir):
log("Stageout will now transfer the log")
_log = JobLog()
ret, _ = _log.transferLogFile(job_state.job, job_state.site, DorE(kwargs, 'experiment'), dest=None,
jr=True)
if not ret:
rc = ReturnCode.Holding # We need to transfer log file regardless the files
if rc == ReturnCode.OK:
if pUtil.verifyTransfer(job_state.site.workdir):
job_state.job.result[0] = "finished"
else:
job_state.job.result[0] = "failed"
job_state.job.setState(job_state.job.result)
if job_state.job.result[0] in finalJobStates:
job_state.job.final_state = job_state.job.result[0]
log("Stageout will now update the server with new status")
rt, retNode = updatePandaServer(job_state, xmlstr=XMLStr, **kwargs)
if rt == 0:
log("Job %s updated (exit code %d)" % (job_state.job.jobId, job_state.job.result[2]))
# did the server send back a command?
if "tobekilled" in job_state.job.action:
log("!!WARNING!!1120!! Panda server returned a \'tobekilled\' command")
job_state.job.result[0] = "failed"
# further recovery attempt unnecessary, but keep the work dir for debugging
if job_state.job.result[0] == "failed":
log("Further recovery attempts will be prevented for failed job (will leave work dir)")
if not job_state.rename(job_state.site, job_state.job):
log("(Fate of job state file left for next pilot)")
else:
log("!!WARNING!!1120!! Panda server returned a %d" % (rt))
# store the final state so that the next pilot will know
# store the metadata xml
retNode['xml'] = XMLStr
# update the job state file with the new state information
_retjs = pUtil.updateJobState(job_state.job, job_state.site, retNode, job_state.recoveryAttempt)
log("Stageout will now proceed to post-job actions")
if job_state.job.result[0] in finalJobStates:
pUtil.postJobTask(job_state.job, job_state.site,
DorE(kwargs, 'workerNode'), DorE(kwargs, 'experiment'), jr=True,
ra=job_state.recoveryAttempt)
pUtil.chdir(currentdir)
# releaseAtomicLockFile(lockfd, lockfn)
if job_state.job.result[0] == "finished":
log("Stageout will now remove the job, it is in finished state and can be removed")
cleanup(job_state)
return True
def DeferredStageoutHPCJob(job_dir, deferred_stageout_logfile=False, **kwargs):
"""
Performs stageing out preparation for the HPC job in specified directory.
:param job_dir: (string) directory with a job.
mandatory parameter
:param deferred_stageout_logfile: (string|False) template name for deferred log stageout
Replaces "{job_id}" with current job id like
"log-{job_id}.txt" -> "log-124124.txt"
Default False
Other parameters are passed into other functions
:return: (bool) the fact of stageout being performed
"""
log("Deferred stageout from HPC job directory \"%s\"" % job_dir)
file_path = job_dir+"/"+hpc_jobState_file_wildcart
current_dir = os.getcwd()
log("Working on %s" % file_path)
log("Chdir from current dir %s to %s" % (current_dir, job_dir))
pUtil.chdir(job_dir)
try:
with LockFileWrapper(file_path) as is_locked:
if not is_locked:
return False
from json import load
with open(file_path) as data_file:
HPC_state = load(data_file)
job_state_file = HPC_state['JobStateFile']
job_command = HPC_state['JobCommand']
# global_work_dir = HPC_state['GlobalWorkingDir']
JS = JobState()
JS.get(job_state_file)
_job, _site, _node, _recoveryAttempt = JS.decode()
with LogWrapper(deferred_stageout_logfile, _job.jobId) as logger:
jobStatus, jobAttemptNr, jobStatusCode = pUtil.getJobStatus(_job.jobId, DorE(kwargs,'pshttpurl'),
DorE(kwargs,'psport'),
DorE(kwargs,'pilot_initdir'))
# recover this job?
if jobStatusCode == 20:
log("Received general error code from dispatcher call (leave job for later pilot)")
# release the atomic lockfile and go to the next directory
# releaseAtomicLockFile(fd, lockfile_name)
return False
elif jobStatus in finalJobStates or "tobekilled" in _job.action:
log("Job %s is currently in state \'%s\' with attemptNr = %d (according to server - will not"
" perform staging out)" % (_job.jobId, jobStatus, jobAttemptNr))
# releaseAtomicLockFile(fd, lockfile_name)
return False
# update job state file at this point to prevent a parallel pilot from doing a simultaneous recovery
_retjs = pUtil.updateJobState(_job, _site, _node, _recoveryAttempt)
# releaseAtomicLockFile(fd, lockfile_name)
monitor = Monitor(env)
monitor.monitor_recovery_job(_job, _site, _node, job_command, job_state_file, recover_dir=job_dir)
log("Chdir back to %s" % current_dir)
pUtil.chdir(current_dir)
panda_jobs = glob(job_dir + "/PandaJob_*_*")
panda_logs = glob(job_dir + "/*.log.tgz.*")
if panda_jobs or panda_logs:
log("Number of founded panda jobs: %d, number of panda log tar file %d, will not remove job dir"
% (len(panda_jobs), len(panda_logs)))
else:
log("Number of founded panda jobs: %d, number of panda log tar file %d, will remove job dir"
% (len(panda_jobs), len(panda_logs)))
log("Remove job dir %s" % job_dir)
os.system("rm -rf %s" % job_dir)
return True
except:
log("Failed to start deferred stage out for HPC job: %s" % traceback.format_exc())
return False
# heartbeat jobs due to reassigned panda job id numbers)
if attemptNr != jobAttemptNr:
log("!!WARNING!!1100!! Attempt number mismatch for job %s (according to server - will not be"
" recovered)" % job_state.job.jobId)
log("....Initial attempt number: %d" % attemptNr)
log("....Current attempt number: %d" % jobAttemptNr)
log("....Job status (server) : %s" % jobStatus)
log("....Job status (state) : %s" % job_state.job.result[0])
return lognret(ReturnCode.Cleanup, "Further recovery attempts will be prevented for this job")
else:
log("Attempt numbers from server and job state file agree: %d" % attemptNr)
job_state.recoveryAttempt += 1
currentDir = os.getcwd()
pUtil.chdir(job_state.site.workdir)
# Update state to prevent another pilot to try to recover this job
# This was at the main logic, but I don't see, why should we do that while lockfile is present
pUtil.updateJobState(job_state.job, job_state.site, job_state.node, job_state.recoveryAttempt)
pUtil.chdir(currentDir)
ec = job_state.job.result[2]
logfile = "%s/%s" % (job_state.site.workdir, job_state.job.logFile)
if not ec:
if (not os.path.isfile(logfile)) and os.path.isdir(job_state.job.newDirNM)\
and os.path.isfile(os.path.join(job_state.job.newDirNM, pilotLogFileInNewWD)):
ec = pUtil.getExitCode(job_state.job.newDirNM, "pilotlog.txt")
# Too big nesting, but I don't know how to do better.
# We search an error code, if not found, we get it from the server
if ec == -1: