def submit_run(workdir: str, runnumber: int):
logfile = os.path.join(workdir, "trendingExtractor.log")
jobname = "TD_{RUN}".format(RUN=runnumber)
executable = os.path.join(repo, "Trending", "runExtractTrendingTree.sh")
cmd = "{EXE} {REPO} {WD} {RUN}".format(EXE=executable,
REPO=repo,
WD=workdir,
RUN=runnumber)
slurm.submit(cmd, jobname, logfile)
def submit_download(self, sample: str) -> int:
cert = self._tokens["cert"]
key = self._tokens["key"]
if not key or not cert:
logging.error("Alien token not provided - cannot download ...")
return None
executable = os.path.join(self._repo, "downloader",
"runDownloadAndMergeMCBatch.sh")
jobname = "down_{SAMPLE}".format(SAMPLE=sample)
outputdir = os.path.join(self._outputbase, sample)
if not os.path.exists(outputdir):
os.makedirs(outputdir, 0o755)
logfile = os.path.join(outputdir, "download.log")
downloadcmd = "{EXE} {DOWNLOADREPO} {OUTPUTDIR} {DATASET} {LEGOTRAIN}/{TRAINID} {ALIEN_CERT} {ALIEN_KEY}".format(
EXE=executable,
DOWNLOADREPO=self._repo,
OUTPUTDIR=outputdir,
DATASET=sample,
LEGOTRAIN=self._legotrain,
TRAINID=self._trainrun,
ALIEN_CERT=cert,
ALIEN_KEY=key)
jobid = submit(command=downloadcmd,
jobname=jobname,
logfile=logfile,
partition=self._partitionDownload,
numnodes=1,
numtasks=4,
maxtime=self._maxtime)
return jobid
def submit_final(self, wait_jobid: int = 0) -> int:
executable = os.path.join(self.__repo, "processMergeFinal.sh")
command = "{EXECUTABLE} {OUTPUTDIR} {FILENAME} {REPO} {CHECK}".format(
EXECUTABLE=executable,
OUTPUTDIR=self.__outputdir,
FILENAME=self.__filename,
REPO=os.path.dirname(self.__repo),
CHECK=1 if self.__check else 0)
logfile = "{OUTPUTDIR}/mergefinal.log".format(
OUTPUTDIR=self.__outputdir)
jobname = "mergefinal"
try:
jobid = submit(command=command,
jobname=jobname,
logfile=logfile,
partition=self.__partition,
dependency=wait_jobid,
maxtime=self.__maxtime)
return jobid
except UnknownClusterException as e:
logging.error("Submission error: %s", e)
return -1
except PartitionException as e:
logging.error("Submission error: %s", e)
return -1
def submit_pthardbins(self, wait_jobid: int = 0) -> int:
executable = os.path.join(self.__repo, "processMergeRun.sh")
commmand = "{EXECUTABLE} {INPUTDIR} {OUTPUTDIR} {FILENAME}".format(
EXECUTABLE=executable,
INPUTDIR=self.__inputdir,
OUTPUTDIR=self.__outputdir,
FILENAME=self.__filename)
logfile = "{OUTPUTDIR}/joboutput_%a.log".format(
OUTPUTDIR=self.__outputdir)
jobname = "mergebins"
try:
jobid = submit(command=commmand,
jobname=jobname,
logfile=logfile,
partition=self.__partition,
jobarray=[1, 20],
dependency=wait_jobid,
maxtime=self.__maxtime)
return jobid
except UnknownClusterException as e:
logging.error("Submission error: %s", e)
return -1
except PartitionException as e:
logging.error("Submission error: %s", e)
return -1
def submit(self):
if not self.__trainrun:
logging.error("Failed initializing train run")
return
cert = self.__tokens["cert"]
key = self.__tokens["key"]
if not key or not cert:
logging.error("Alien token not provided - cannot download ...")
return None
executable = os.path.join(self.__repo, "downloader", "runDownloadRunwise.sh")
samples = {}
try:
samples = self.__sampleDB.getDataSamples(self.__year)
except SampleDB.YearNotFoundException as e:
logging.error(e)
raise LaunchHandler.SampleException(self.__year)
jobids = {}
for period,recpass in samples.items():
logging.info("Downloading period %s, reconstruction pass %s", period, recpass)
perioddir = os.path.join(self.__outputbase, period)
if not os.path.exists(perioddir):
os.makedirs(perioddir, 0o755)
jobname = "down_{PERIOD}".format(PERIOD=period)
logfile = os.path.join(perioddir, "download.log")
filenamestr = self.__filename if self.__filename != None else "NONE"
aodprodstr = self.__aodset if self.__aodset != None else "NONE"
downloadcmd = "{EXE} {DOWNLOADREPO} {ALIEN_CERT} {ALIEN_KEY} {OUTPUTDIR} {TRAINRUN} {LEGOTRAIN} {DATASET} {RECPASS} {AODPROD} {FILENAME}".format(EXE=executable, DOWNLOADREPO = self.__repo, ALIEN_CERT=cert, ALIEN_KEY=key, OUTPUTDIR=perioddir, TRAINRUN=self.__trainrun, LEGOTRAIN=self.__legotrain, DATASET=period, RECPASS=recpass, AODPROD=aodprodstr, FILENAME=filenamestr)
logging.debug("Download command: %s", downloadcmd)
jobid = submit(command=downloadcmd, jobname=jobname, logfile=logfile, partition=self.__partitionDownload, numnodes=1, numtasks=1)
logging.info("Submitting download job for period {}: {}".format(period, jobid))
jobids[period] = jobid
return jobids
def launch(self):
print("launching jobs for {}".format(self.__year))
executable = os.path.join(self.__repo, "EMCALTrigger",
"FastorAcceptance", "runFindIsolated.sh")
commonoutputdir = os.path.join(self.__outputdir, "%d" % self.__year)
if not os.path.exists(commonoutputdir):
os.makedirs(commonoutputdir, 0o755)
logdir = os.path.join(commonoutputdir, "logs")
if not os.path.exists(logdir):
os.makedirs(logdir, 0o755)
runlist = self.read_runlists()
for run in runlist:
logfile = os.path.join(logdir, "filter_{}".format(run))
jobname = "{}_{}".format(self.__year, run)
cmd = "{} {} {} {}".format(executable, self.__repo,
commonoutputdir, run)
submit(cmd, jobname, logfile)
def submit(self, year: int):
if not self.__trainrun:
logging.error("Failed initializing train run")
return
cert = self.__tokens["cert"]
key = self.__tokens["key"]
if not key or not cert:
logging.error("Alien token not provided - cannot download ...")
return None
executable = os.path.join(self.__repo, "downloader", "runDownloadAndMergeDataBatch.sh")
jobname = "down_{YEAR}".format(YEAR=year)
logfile = os.path.join(self.__outputbase, "download.log")
downloadcmd = "{EXE} {DOWNLOADREPO} {OUTPUTDIR} {YEAR} {TRAINRUN} {ALIEN_CERT} {ALIEN_KEY}".format(EXE=executable, DOWNLOADREPO = self.__repo, OUTPUTDIR=self.__outputbase, YEAR=year, TRAINRUN=self.__trainrun, ALIEN_CERT=cert, ALIEN_KEY=key)
jobid = submit(command=downloadcmd, jobname=jobname, logfile=logfile, partition=self.__partitionDownload, numnodes=1, numtasks=1, maxtime=self.__maxtime)
logging.info("Submitting download job: {}".format(jobid))
return jobid
def merge_submitter_datasets(repo: str, inputdir: str, filename: str,
partition: str, maxtime: str, wait: list,
check: bool) -> dict:
outputbase = os.path.join(inputdir, "merged")
if not os.path.exists(outputbase):
os.makedirs(outputbase, 0o755)
executable = os.path.join(repo, "processMergeMCDatasets.sh")
exefinal = os.path.join(repo, "processMergeFinal.sh")
runcmd_bins = "{EXECUTABLE} {INPUTDIR} {OUTPUTDIR} {FILENAME}".format(
EXECUTABLE=executable,
INPUTDIR=inputdir,
FILENAME=filename,
OUTPUTDIR=outputbase)
logfile_bins = os.path.join(outputbase, "joboutput_%a.log")
jobid = submit_dependencies(runcmd_bins,
"mergebins",
logfile_bins,
partition,
jobarray=[1, 20],
dependency=wait,
maxtime=maxtime)
print("Submitted merge job under JobID %d" % jobid)
finalcmd = "{EXECUTABLE} {OUTPUTDIR} {FILENAME} {REPO} {CHECK}".format(
EXECUTABLE=exefinal,
OUTPUTDIR=outputbase,
FILENAME=filename,
REPO=os.path.dirname(repo),
CHECK=1 if check else 0)
jobidFinal = submit(
finalcmd,
"mergefinal",
"{OUTPUTDIR}/mergefinal.log".format(OUTPUTDIR=outputbase),
partition,
dependency=jobid,
maxtime=maxtime)
print("Submitted final merging job under JobID %d" % jobidFinal)
return {"pthard": jobid, "final": jobidFinal}
EXE=unfoldingexecutable,
REPO=repo,
WDIR=args.workdir,
DATAFILE=args.datafile,
MCFILE=args.mcfile,
SYSVAR=args.sysvar,
MACRO=args.macro)
logfile = "joboutput_R0%a.log"
workdir = os.path.abspath(args.workdir)
if not os.path.exists(workdir):
os.makedirs(workdir, 0o755)
os.chdir(workdir)
unfoldingjob = slurm.submit(unfoldingcmd,
args.jobtag,
logfile,
args.queue,
1,
1, [2, 6],
maxtime=args.time)
print("Submitting processing job under %d" % unfoldingjob)
mergeexecutable = os.path.join(repo, "unfolding", "postprocess1D.sh")
mergecmd = "{EXE} {WORKDIR}".format(EXE=mergeexecutable,
WORKDIR=os.getcwd())
logfile = "merge"
mergejob = slurm.submit(mergecmd,
"merge_{TAG}".format(TAG=args.jobtag),
logfile,
args.queue,
1,
1,
None,
#! /usr/bin/env python3
from argparse import ArgumentParser
from SubstructureHelpers.slurm import submit
import os
if __name__ == "__main__":
repo = os.path.abspath(os.getenv("SUBSTRUCTURE_ROOT"))
parser = ArgumentParser("submitRepack.py", description="Submitter for repacking")
parser.add_argument("inputdir", metavar="INPUTDIR", type=str, help="Input directory")
parser.add_argument("-p", "--partition", metavar="PARTITION", type=str, default="short", help="Partition")
args = parser.parse_args()
executable = os.path.join(repo, "downloader", "runRepackStandalone.sh")
cmd = "{EXE} {WD}".format(EXE=executable, WD=args.inputdir)
logfile = os.path.join(args.inputdir, "repack.log")
submit(cmd, "repack", logfile, args.partition)
type=float,
default=1.3,
help="Reweighting factor")
args = parser.parse_args()
repo = os.path.abspath(os.path.dirname(sys.argv[0]))
unfoldingexecutable = os.path.join(
repo, "runUnfolding1D_local_SysAngularity.sh")
reweighthigh = 1 if args.reweighthigh else 0
angularityweight = args.angularityweight
unfoldingcmd = "{EXE} {WDIR} {DATAFILE} {MCFILE} {SYSVAR} {MACRO} {REWEIGHTHIGH} {WEIGHT}".format(
EXE=unfoldingexecutable,
WDIR=args.workdir,
DATAFILE=args.datafile,
MCFILE=args.mcfile,
SYSVAR=args.sysvar,
MACRO=args.macro,
REWEIGHTHIGH=reweighthigh,
WEIGHT=angularityweight)
logfile = "joboutput_R0%a.log"
os.chdir(args.workdir)
unfoldingjob = slurm.submit(unfoldingcmd, args.jobtag, logfile, args.queue,
1, 1, [2, 6])
print("Submitting processing job under %d" % unfoldingjob)
mergeexecutable = os.path.join(repo, "postprocess1D.sh")
mergecmd = "{EXE} {WORKDIR}".format(EXE=mergeexecutable,
WORKDIR=os.getcwd())
logfile = "merge"
mergejob = slurm.submit(mergecmd, "merge_{TAG}".format(TAG=args.jobtag),
logfile, args.queue, 1, 1, None, unfoldingjob)
print("Submitting merging job under %d" % mergejob)