def main():
channels = args.channels
years = args.years
batchSystem = 'psibatch_runner.sh'
chunkpattern = re.compile(r".*_(\d+)_[a-z]+\.root")
for year in years:
# GET LIST
samplelist = []
outdir = "output_%s/" % (year)
for directory in sorted(os.listdir(outdir)):
if not os.path.isdir(outdir + directory): continue
if args.samples and not matchSampleToPattern(
directory, args.samples):
continue
if args.veto and not matchSampleToPattern(directory, args.veto):
continue
if args.type == 'mc' and any(
s in directory[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau']):
continue
if args.type == 'data' and not any(
s in directory[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau']):
continue
samplelist.append(directory)
if not samplelist:
print "No samples found in %s!" % (outdir)
if args.verbose:
print samplelist
# RESUBMIT samples
for channel in channels:
print header(year, channel)
for directory in samplelist:
#if directory.find('W4JetsToLNu_TuneCP5_13TeV-madgraphMLM-pythia8__ytakahas-NanoTest_20180507_W4JetsToLNu_TuneCP5_13TeV-madgraphMLM-pythia8-a7a5b67d3e3590e4899e147be08660be__USER')==-1: continue
outdir = "output_%s/%s" % (year, directory)
outfilelist = glob.glob(outdir + '/*_' + channel + '.root')
nFilesPerJob = args.nFilesPerJob
jobName = getSampleShortName(directory)[1]
if not outfilelist: continue
# GET INPUT FILES
if 'LQ' in directory:
infiles = getFileListPNFS(directory)
else:
infiles = getFileListDAS('/' +
directory.replace('__', '/'))
# NFILESPERJOBS CHECKS
# Diboson (WW, WZ, ZZ) have very large files and acceptance,
# and the jet-binned DY and WJ files need to be run separately because of a bug affecting LHE_Njets
if nFilesPerJob > 1 and any(vv in jobName[:8] for vv in [
'WW', 'WZ', 'ZZ', 'DY', 'WJ', 'W1J', 'W2J', 'W3J',
'W4J', 'Single', 'Tau'
]):
print bcolors.BOLD + bcolors.WARNING + "[WN] setting number of files per job from %s to 1 for %s" % (
nFilesPerJob, jobName) + bcolors.ENDC
nFilesPerJob = 1
infilelists = list(split_seq(infiles, nFilesPerJob))
badchunks = []
misschunks = range(0, len(infilelists))
jobList = 'joblist/joblist%s_%s_retry.txt' % (directory,
channel)
with open(jobList, 'w') as jobslog:
for filename in outfilelist:
match = chunkpattern.search(filename)
if match:
chunk = int(match.group(1))
else:
print bcolors.BOLD + bcolors.FAIL + '[NG] did not recognize output file %s !' % (
filename) + bcolors.ENDC
exit(1)
if chunk in misschunks:
misschunks.remove(chunk)
elif chunk >= len(infilelists):
print bcolors.BOLD + bcolors.FAIL + '[WN] %s: found chunk %s >= total number of chunks %s ! Please make sure you have chosen the correct number of files per job (-n=%s) !' % (
filename, chunk, len(infilelists),
nFilesPerJob) + bcolors.ENDC
else:
print bcolors.BOLD + bcolors.FAIL + '[WN] %s: found weird chunk %s ! Please check if there is any overcounting !' % (
filename, chunk,
len(infilelists)) + bcolors.ENDC
file = TFile(filename, 'READ')
if not file.IsZombie() and file.GetListOfKeys(
).Contains('tree') and file.GetListOfKeys().Contains(
'cutflow'):
continue
infiles = infilelists[chunk]
createJobs(jobslog,
infiles,
outdir,
directory,
chunk,
channel,
year=year)
badchunks.append(chunk)
# BAD CHUNKS
if len(badchunks) > 0:
badchunks.sort()
chunktext = ('chunks ' if len(badchunks) > 1 else
'chunk ') + ', '.join(
str(ch) for ch in badchunks)
print bcolors.BOLD + bcolors.WARNING + '[NG] %s, %d/%d failed! Resubmitting %s...' % (
directory, len(badchunks), len(outfilelist),
chunktext) + bcolors.ENDC
# MISSING CHUNKS
if len(misschunks) > 0:
chunktext = ('chunks ' if len(misschunks) > 1 else
'chunk ') + ', '.join(
str(i) for i in misschunks)
print bcolors.BOLD + bcolors.WARNING + "[WN] %s missing %d/%d files ! Resubmitting %s..." % (
directory, len(misschunks), len(outfilelist),
chunktext) + bcolors.ENDC
for chunk in misschunks:
infiles = infilelists[chunk]
createJobs(jobslog,
infiles,
outdir,
directory,
chunk,
channel,
year=year)
# RESUBMIT
jobName += "_%s_%s" % (channel, year)
nChunks = len(badchunks) + len(misschunks)
if nChunks == 0:
print bcolors.BOLD + bcolors.OKBLUE + '[OK] ' + directory + bcolors.ENDC
elif args.force:
submitJobs(jobName, jobList, nChunks, outdir, batchSystem)
else:
submit = raw_input(
"Do you also want to submit %d jobs to the batch system? [y/n] "
% (nChunks))
if submit.lower() == 'force':
submit = 'y'
args.force = True
if submit.lower() == 'quit':
exit(0)
if submit.lower() == 'y':
submitJobs(jobName, jobList, nChunks, outdir,
batchSystem)
else:
print "Not submitting jobs"
print
def main():
channels = args.channels
years = args.years
tes = args.tes
ltf = args.ltf
jtf = args.jtf
Zmass = args.Zmass
prefetch = args.prefetch
batchscript = 'submit_SGE.sh'
tag = args.tag
if tag and tag[0]!='_': tag = '_'+tag
if tes!=1.: tag += "_TES%.3f"%(tes)
if ltf!=1.: tag += "_LTF%.3f"%(ltf)
if jtf!=1.: tag += "_JTF%.3f"%(jtf)
if Zmass: tag += "_Zmass"
tag = tag.replace('.','p')
for year in years:
# READ SAMPLES
directories = [ ]
samplelist = "samples_%s.cfg"%(year)
with open(samplelist, 'r') as file:
for line in file:
line = line.rstrip().lstrip().split(' ')[0].rstrip('/')
if line[:2].count('#')>0: continue
if line=='': continue
if line.count('/')<2: continue
sample = '/'.join(line.split('/')[-3:])
if args.samples and not matchSampleToPattern(sample,args.samples): continue
if args.vetoes and matchSampleToPattern(sample,args.vetoes): continue
if args.type=='mc' and any(s in sample[:len(s)+2] for s in ['SingleMuon','SingleElectron','Tau','EGamma']): continue
if args.type=='data' and not any(s in sample[:len(s)+2] for s in ['SingleMuon','SingleElectron','Tau','EGamma']): continue
directories.append(line)
if args.testrun:
directories = directories[:1]
#print directories
blacklist = getBlackList("filelist/blacklist.txt")
tasks = []
for channel in channels:
print header(year,channel,tag)
# SUBMIT SAMPLES
for directory in directories:
if args.verbose:
print "\ndirectory =",directory
# FILTER
if 'SingleMuon' in directory and channel not in ['mutau','mumu','elemu']: continue
if ('SingleElectron' in directory or 'EGamma' in directory) and channel!='eletau': continue
if 'Tau' in directory[:5] and channel!='tautau': continue
if 'LQ3' in directory[:5] and channel not in ['mutau','eletau','tautau']: continue
# GET SKIMMED
if args.useSkim and isSkimmed(directory,year):
directory = isSkimmed(directory,year)
if args.verbose:
print "skimmed:", directory
print bcolors.BOLD + bcolors.OKGREEN + directory + bcolors.ENDC
# FILE LIST
files = [ ]
if not args.useDAS:
files = getFileListLocal(directory,blacklist=blacklist)
if not files:
if not args.useDAS:
print "Getting file list from DAS/PNFS..."
files = getFileList(directory,blacklist=blacklist)
if files:
saveFileListLocal(directory,files,blacklist=blacklist)
if not files:
print bcolors.BOLD + bcolors.WARNING + "Warning! EMPTY filelist for " + directory + bcolors.ENDC
continue
elif args.verbose:
print "FILELIST = "+files[0]
for file in files[1:]:
print " "+file
if args.testrun:
files = files[:1]
# JOB LIST
sample = '__'.join(directory.split('/')[-3:])
ensureDirectory('joblist')
jobList = 'joblist/joblist_%s_%s%s.txt'%(sample,channel,tag)
print "Creating job file %s..."%(jobList)
jobName = getSampleShortName(directory)[1]
jobName += "_%s_%s"%(channel,year)+tag
jobs = open(jobList,'w')
# outdir = ensureDirectory("output_%s/%s"%(year,sample))
outdir = "$PWD"
ensureDirectory(outdir+'/logs/')
# NFILESPERJOBS
nFilesPerJob = args.nFilesPerJob
if nFilesPerJob<1:
for default, patterns in nFilesPerJob_defaults:
if matchSampleToPattern(sample,patterns):
nFilesPerJob = default
break
else:
nFilesPerJob = nFilesPerJob_default
if args.verbose:
print "nFilesPerJob = %s"%nFilesPerJob
filelists = chunkify(files,nFilesPerJob)
# CREATE JOBS
nChunks = 0
checkExistingFiles(outdir,channel,len(filelists))
#filelists = chunkify(files,1)
for file in filelists:
#print "FILES = ",f
createJobs(jobs,file,outdir,sample,nChunks,channel,year=year,tes=tes,ltf=ltf,jtf=jtf,Zmass=Zmass,tag=tag,prefetch=prefetch)
nChunks = nChunks+1
jobs.close()
# SUBMIT
if args.force:
submitJobs_gc(jobName,jobList,nChunks,outdir,batchscript, args.workdir, year, channel)
else:
submit = raw_input("Do you also want to submit %d jobs to the batch system? [y/n] "%(nChunks))
if submit.lower()=='force':
submit = 'y'
args.force = True
if submit.lower()=='quit':
exit(0)
if submit.lower()=='y':
submitJobs_gc(jobName,jobList,nChunks,outdir,batchscript, args.workdir, year, channel)
else:
print "Not submitting jobs"
print
tasks.append("_".join([jobName, str(year), channel]))
# Assemble while script to start every gc task.
while_temp = open(os.environ["CMSSW_BASE"]+"/src/NanoTreeProducer/while_temp.sh", "r").read()
task_list = ["go.py {}gc_conf/{}.conf".format(args.workdir,task) for task in tasks]
while_temp = while_temp.format(TASK_COMMANDS="\n".join(task_list))
with open(os.path.join(args.workdir, "while.sh"), "w") as out:
out.write(while_temp)
print 'Submit samples with: "bash {}"'.format(os.path.join(args.workdir, "while.sh"))
def main():
channels = args.channels
years = args.years
tes = args.tes
ltf = args.ltf
jtf = args.jtf
batchSystem = 'slurm_runner.sh'
chunkpattern = re.compile(r".*_(\d+)_[a-z]+(?:_[A-Z]+\dp\d+)?\.root")
tag = ""
if tes != 1.:
tag += "_TES%.3f" % (tes)
if ltf != 1.:
tag += "_LTF%.3f" % (ltf)
if jtf != 1.:
tag += "_JTF%.3f" % (jtf)
tag = tag.replace('.', 'p')
for year in years:
# GET LIST
samplelist = []
outdir = "/work/pbaertsc/heavy_resonance/output_%s/" % (year)
for directory in sorted(os.listdir(outdir)):
if not os.path.isdir(outdir + directory): continue
if args.samples and not matchSampleToPattern(
directory, args.samples):
continue
if args.vetos and matchSampleToPattern(directory, args.vetos):
continue
if args.type == 'mc' and any(s in directory[:len(s) + 2] for s in [
'SingleMuon', 'SingleElectron', 'EGamma', 'MET',
'SinglePhoton'
]):
continue
if args.type == 'data' and not any(
s in directory[:len(s) + 2] for s in [
'SingleMuon', 'SingleElectron', 'EGamma', 'MET',
'SinglePhoton'
]):
continue
samplelist.append(directory)
if not samplelist:
print "No samples found in %s!" % (outdir)
if args.verbose:
print samplelist
# RESUBMIT samples
for channel in channels:
print header(year, channel, tag)
for directory in samplelist:
#if directory.find('W4JetsToLNu_TuneCP5_13TeV-madgraphMLM-pythia8__ytakahas-NanoTest_20180507_W4JetsToLNu_TuneCP5_13TeV-madgraphMLM-pythia8-a7a5b67d3e3590e4899e147be08660be__USER')==-1: continue
outdir = "/work/pbaertsc/heavy_resonance/output_%s/%s" % (
year, directory)
outfilelist = glob.glob("%s/*_%s%s.root" %
(outdir, channel, tag))
nFilesPerJob = args.nFilesPerJob
jobName = getSampleShortName(directory, year)[1]
jobName += "_%s_%s" % (channel, year) + tag
#if not outfilelist: continue
# FILE LIST
infiles = []
if not args.useDAS:
infiles = getFileListLocal(directory)
if not infiles:
if not args.useDAS:
print "Getting file list from DAS..."
infiles = getFileListDAS('/' + directory)
if infiles:
saveFileListLocal(directory, infiles)
if not infiles:
print bcolors.BOLD + bcolors.WARNING + "Warning!!! FILELIST empty" + bcolors.ENDC
continue
elif args.verbose:
print "FILELIST = " + infiles[0]
for file in infiles[1:]:
print " " + file
# NFILESPERJOBS
nFilesPerJob = 1
if args.verbose:
print "nFilesPerJob = %s" % nFilesPerJob
infilelists = list(split_seq(infiles, nFilesPerJob))
# JOB LIST
badchunks = []
misschunks = range(0, len(infilelists))
jobList = '/work/pbaertsc/heavy_resonance/NanoTreeProducer/joblist/joblist_%s_%s%s_retry.txt' % (
directory, channel, tag)
with open(jobList, 'w') as jobslog:
for filename in outfilelist:
match = chunkpattern.search(filename)
if match:
chunk = int(match.group(1))
else:
print bcolors.BOLD + bcolors.FAIL + '[NG] did not recognize output file %s !' % (
filename) + bcolors.ENDC
exit(1)
if chunk in misschunks:
misschunks.remove(chunk)
elif chunk >= len(infilelists):
print bcolors.BOLD + bcolors.FAIL + '[WN] %s: found chunk %s >= total number of chunks %s ! Please make sure you have chosen the correct number of files per job (-n=%s), check DAS, or resubmit everything!' % (
filename, chunk, len(infilelists),
nFilesPerJob) + bcolors.ENDC
else:
print bcolors.BOLD + bcolors.FAIL + '[WN] %s: found weird chunk %s ! Please check if there is any overcounting !' % (
filename, chunk,
len(infilelists)) + bcolors.ENDC
file = TFile(filename, 'READ')
if not file.IsZombie() and (
file.GetListOfKeys().Contains('tree')
and file.GetListOfKeys().Contains('pileup')
and file.GetListOfKeys().Contains('Events')):
continue
infiles = infilelists[chunk]
createJobs(jobslog,
infiles,
outdir,
directory,
chunk,
channel,
year=year,
tes=tes,
ltf=ltf,
jtf=jtf)
badchunks.append(chunk)
# BAD CHUNKS
if len(badchunks) > 0:
badchunks.sort()
chunktext = ('chunks ' if len(badchunks) > 1 else
'chunk ') + ', '.join(
str(ch) for ch in badchunks)
print bcolors.BOLD + bcolors.WARNING + '[NG] %s, %d/%d failed! Resubmitting %s...' % (
directory, len(badchunks), len(outfilelist),
chunktext) + bcolors.ENDC
# MISSING CHUNKS
if len(misschunks) > 0:
chunktext = ('chunks ' if len(misschunks) > 1 else
'chunk ') + ', '.join(
str(i) for i in misschunks)
print bcolors.BOLD + bcolors.WARNING + "[WN] %s missing %d/%d files ! Resubmitting %s..." % (
directory, len(misschunks), len(outfilelist),
chunktext) + bcolors.ENDC
for chunk in misschunks:
infiles = infilelists[chunk]
createJobs(jobslog,
infiles,
outdir,
directory,
chunk,
channel,
year=year,
tes=tes,
ltf=ltf,
jtf=jtf)
# RESUBMIT
nChunks = len(badchunks) + len(misschunks)
if nChunks == 0:
print bcolors.BOLD + bcolors.OKBLUE + '[OK] ' + directory + bcolors.ENDC
elif args.force:
submitJobs(jobName, jobList, nChunks, outdir, batchSystem)
else:
submit = raw_input(
"Do you also want to submit %d jobs to the batch system? [y/n] "
% (nChunks))
if submit.lower() == 'force':
submit = 'y'
args.force = True
if submit.lower() == 'quit':
exit(0)
if submit.lower() == 'y':
submitJobs(jobName, jobList, nChunks, outdir,
batchSystem)
else:
print "Not submitting jobs"
print
def main():
channels = args.channels
years = args.years
tes = args.tes
ltf = args.ltf
jtf = args.jtf
batchSystem = 'psibatch_runner.sh'
tag = ""
if tes != 1.:
tag += "_TES%.3f" % (tes)
if ltf != 1.:
tag += "_LTF%.3f" % (ltf)
if jtf != 1.:
tag += "_JTF%.3f" % (jtf)
tag = tag.replace('.', 'p')
for year in years:
# READ SAMPLES
directories = []
samplelist = "samples_%s.cfg" % (year)
with open(samplelist, 'r') as file:
for line in file:
line = line.rstrip().lstrip().split(' ')[0].rstrip('/')
if line[:2].count('#') > 0: continue
if line == '': continue
if args.samples and not matchSampleToPattern(
line, args.samples):
continue
if args.vetos and matchSampleToPattern(line, args.vetos):
continue
if args.type == 'mc' and any(
s in line[:len(s) + 2] for s in
['SingleMuon', 'SingleElectron', 'EGamma', 'MET']):
continue
if args.type == 'data' and not any(
s in line[:len(s) + 2] for s in
['SingleMuon', 'SingleElectron', 'EGamma', 'MET']):
continue
directories.append(line)
#print directories
for channel in channels:
print header(year, channel, tag)
# SUBMIT SAMPLES
for directory in directories:
if args.verbose:
print "\ndirectory =", directory
# FILTER
print bcolors.BOLD + bcolors.OKGREEN + directory + bcolors.ENDC
# FILE LIST
files = []
name = directory.split('/')[-3].replace(
'/', '') + '__' + directory.split('/')[-2].replace(
'/', '') + '__' + directory.split('/')[-1].replace(
'/', '')
if not args.useDAS:
files = getFileListLocal(directory)
if not files:
if not args.useDAS:
print "Getting file list from DAS..."
if 'pnfs' in directory:
files = getFileListPNFS(directory)
else:
files = getFileListDAS(directory)
if files:
saveFileListLocal(name, files)
if not files:
print bcolors.BOLD + bcolors.WARNING + "Warning!!! FILELIST empty" + bcolors.ENDC
continue
elif args.verbose:
print "FILELIST = " + files[0]
for file in files[1:]:
print " " + file
# JOB LIST
ensureDirectory('joblist_skim')
jobList = 'joblist_skim/joblist_%s_%s%s.txt' % (name, channel,
tag)
print "Creating job file %s..." % (jobList)
jobName = getSampleShortName(directory, year)[1]
jobName += "_%s_%s" % (channel, year) + tag
jobs = open(jobList, 'w')
outdir = ensureDirectory(
"/work/pbaertsc/heavy_resonance/output_skim_%s/%s" %
(year, name))
ensureDirectory(outdir + '/logs/')
# NFILESPERJOBS
nFilesPerJob = 1
if nFilesPerJob < 1:
for default, patterns in nFilesPerJob_defaults:
if matchSampleToPattern(directory, patterns):
nFilesPerJob = default
break
else:
nFilesPerJob = 4 # default
if args.verbose:
print "nFilesPerJob = %s" % nFilesPerJob
filelists = list(split_seq(files, nFilesPerJob))
# CREATE JOBS
nChunks = 0
checkExistingFiles(outdir, channel, len(filelists))
#filelists = list(split_seq(files,1))
for file in filelists:
#print "FILES = ",f
createJobs(jobs,
file,
outdir,
name,
nChunks,
channel,
year=year,
tes=tes,
ltf=ltf,
jtf=jtf)
nChunks = nChunks + 1
jobs.close()
# SUBMIT
if args.force:
submitJobs(jobName, jobList, nChunks, outdir, batchSystem)
else:
submit = raw_input(
"Do you also want to submit %d jobs to the batch system? [y/n] "
% (nChunks))
if submit.lower() == 'force':
submit = 'y'
args.force = True
if submit.lower() == 'quit':
exit(0)
if submit.lower() == 'y':
submitJobs(jobName, jobList, nChunks, outdir,
batchSystem)
else:
print "Not submitting jobs"
print
def main(args):
years = args.years
tag = args.tag
checkEvents = args.checkEvents
outbasedir = "/scratch/ineuteli"
batchscript = 'submit_SGE.sh'
director = "root://t3dcachedb.psi.ch:1094/" #"root://xrootd-cms.infn.it/"
for year in years:
samplesdir = args.outdir if args.outdir else "/pnfs/psi.ch/cms/trivcat/store/user/ineuteli/samples/NANOAOD_%s" % (
year)
# GET LIST
samplelist = []
if args.instance == None:
directories = glob.glob(samplesdir +
"/*/*/NANOAOD*") + glob.glob(samplesdir +
"/*/*/USER*")
else:
directories = glob.glob(samplesdir + "/*/*/" + args.instance)
for directory in sorted(directories):
sample = '/'.join(directory.split('/')[-3:])
if args.samples and not matchSampleToPattern(sample, args.samples):
continue
if args.vetos and matchSampleToPattern(sample, args.vetos):
continue
if args.type == 'mc' and any(
s in sample[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau', 'EGamma'
]):
continue
if args.type == 'data' and not any(
s in sample[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau', 'EGamma'
]):
continue
if not os.path.isdir(directory): continue
samplelist.append(directory)
if not samplelist:
print "No samples found in %s!" % (samplesdir)
if args.verbose:
print 'samplelist = %s\n' % (samplelist)
# CHECK samples
print header(year, tag)
for directory in samplelist:
sample = '__'.join(directory.split('/')[-3:])
filelist = '%s/*_skim%s*.root' % (directory, tag)
if args.verbose:
print "directory = %s" % (directory)
print "filelist = %s" % (filelist)
print "sample = %s" % (sample)
# FILE LIST ON SE
filelist = [
director + d
for d in sorted(glob.glob(filelist), key=naturalSort)
]
if not filelist:
print bcolors.BOLD + bcolors.WARNING + "[WN] %s empty filelist" % directory + bcolors.ENDC
elif args.verbose:
print "filelist = %s" % (filelist[0])
for file in filelist[1:]:
print " " + file
# FILE LIST ON DAS
infilelist = []
if args.useLocal:
infilelist = getFileListLocal(sample)
if not infilelist:
if args.useLocal:
print "Getting file list from DAS/PNFS..."
infilelist = getFileListDAS(sample)
if not infilelist:
print bcolors.BOLD + bcolors.WARNING + "Warning! EMPTY filelist for " + directory + bcolors.ENDC
elif args.verbose:
print "infilelist = %s" % (infilelist[0])
for file in infilelist[1:]:
print " " + file
# FILE LIST FOR RESUBMISSION
nevents, resubmitfiles = checkFiles(
filelist,
infilelist,
directory,
clean=args.removeBadFiles,
force=args.force,
cleanBug=args.removeBuggedFiles,
checkEvents=checkEvents)
if len(resubmitfiles) == 0:
print bcolors.BOLD + bcolors.OKGREEN + '[OK] %s is complete ! ' % sample + bcolors.ENDC
elif len(resubmitfiles) > len(infilelist):
print bcolors.BOLD + bcolors.FAIL + 'WARNING! %s has more output files %d than %d input files from DAS!' % (
sample, len(resubmitfiles), len(infilelist)) + bcolors.ENDC
else:
print bcolors.BOLD + bcolors.WARNING + '[WN] %d / %d of %s need to be resubmitted...' % (
len(resubmitfiles), len(infilelist), sample) + bcolors.ENDC
if checkEvents and not any(s in directory for s in ['LQ3']):
compareEventsToDAS(nevents, sample, treename='Events')
if len(resubmitfiles) == 0:
print
continue
# JOB LIST
ensureDirectory('joblist')
jobList = 'joblist/joblist_%s_skim%s_retry.txt' % (sample, tag)
print "Creating job file %s..." % (jobList)
jobName = getSampleShortName(directory)[1]
jobName += "_%s_skim" % (year) + tag
outdir = "%s/output_%s/%s" % (outbasedir, year, sample)
logdir = ensureDirectory("skim_logs_%s/%s" % (year, sample))
# NFILESPERJOBS
nFilesPerJob = args.nFilesPerJob
if nFilesPerJob < 1:
for default, patterns in nFilesPerJob_defaults:
if matchSampleToPattern(directory, patterns):
nFilesPerJob = default
break
else:
nFilesPerJob = 1 # default
if args.verbose:
print "nFilesPerJob = %s" % nFilesPerJob
filelists = chunkify(resubmitfiles, nFilesPerJob)
# CREATE JOBS
with open(jobList, 'w') as jobs:
nChunks = 0
for filelist in filelists:
createSkimJobs(jobs,
year,
sample,
filelist,
outdir,
prefetch=args.prefetch)
nChunks = nChunks + 1
# SUBMIT
if args.force:
submitSkimJobs(jobName, jobList, nChunks, logdir, batchscript)
else:
submit = raw_input(
"Do you also want to submit %d jobs to the batch system? [y/n] "
% (nChunks))
if submit.lower() == 'force':
submit = 'y'
args.force = True
if submit.lower() == 'quit':
exit(0)
if submit.lower() == 'y':
submitSkimJobs(jobName, jobList, nChunks, logdir,
batchscript)
else:
print "Not submitting jobs"
print
def main(args):
years = args.years
channels = args.channels
njobs = args.njobs
getFilesOfRunningJobs()
exit(0)
if args.running:
getSubmittedJobs()
return
for year in years:
indir = "output_%s/" % (year)
os.chdir(indir)
# GET LIST
samplelist = []
for directory in sorted(os.listdir('./')):
if not os.path.isdir(directory): continue
if args.samples and not matchSampleToPattern(
directory, args.samples):
continue
if args.veto and matchSampleToPattern(directory, args.veto):
continue
if args.type == 'mc' and any(
s in directory[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau']):
continue
if args.type == 'data' and not any(
s in directory[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau']):
continue
samplelist.append(directory)
if not samplelist:
print "No samples found in %s!" % (indir)
if args.verbose:
print 'samplelist = %s\n' % (samplelist)
# CHECK samples
for channel in channels:
print header(year, channel)
for directory in samplelist:
print ">>> %s" % (directory)
infiles = "%s/logs/*%s_%d*.o*.*" % (directory, channel, year)
filelist = glob.glob(infiles)
if not filelist:
continue
jobids = []
for filename in filelist:
jobid, taskid = getJobID(filename)
if jobid not in jobids:
jobids.append(jobid)
jobids.sort(reverse=True)
jobids_max = jobids[:njobs]
jobs = {id: [] for id in jobids_max}
stuck = {id: [] for id in jobids_max}
failed = {id: [] for id in jobids_max}
running = {id: [] for id in jobids_max}
done = {id: [] for id in jobids_max}
for filename in filelist:
if not any(".o%d." % (id) in filename
for id in jobids_max):
continue
job = Job(filename)
jobs[job.jobid].append(job)
if job.stuck:
stuck[job.jobid].append(job)
if job.running:
running[job.jobid].append(job)
if job.failed:
failed[job.jobid].append(job)
if job.done:
done[job.jobid].append(job)
for jobid, joblist in sorted(jobs.iteritems()):
ntot = len(joblist)
jobs[jobid].sort()
stuck[jobid].sort()
failed[jobid].sort()
running[jobid].sort()
done[jobid].sort()
print ">>> %d" % (jobid)
if running[jobid]:
print ">>> running: %4d /%4d, %12s" % (len(
running[jobid]), ntot, average(running[jobid]))
if failed[jobid]:
print ">>> failed: %4d /%4d" % (
len(failed[jobid]), ntot
) #+ ', '.join([str(j) for j in failed[jobid]])
if stuck[jobid]:
print ">>> stuck: %4d /%4d" % (len(
stuck[jobid]), ntot)
print ">>> done: %4d /%4d, %12s" % (
len(done[jobid]), ntot,
average(done[jobid]) if done[jobid] else ""
) #+ ', '.join([str(j) for j in done[jobid]])
print ">>>"
os.chdir('..')
def main():
channels = args.channels
years = args.years
tes = args.tes
batchSystem = 'psibatch_runner.sh'
for year in years:
# READ SAMPLES
directories = []
samplelist = "samples_%s.cfg" % (year)
for line in open(samplelist, 'r'):
line = line.rstrip().lstrip().split(' ')[0]
if line[:2].count('#') > 0: continue
if line == '': continue
if args.samples and not matchSampleToPattern(line, args.samples):
continue
if args.veto and matchSampleToPattern(line, args.veto): continue
if args.type == 'mc' and any(
s in line[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau']):
continue
if args.type == 'data' and not any(
s in line[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau']):
continue
directories.append(line)
#print directories
for channel in channels:
print header(year, channel)
# SUBMIT SAMPLES
for directory in directories:
if args.verbose:
print "\ndirectory =", directory
# FILTER
if 'SingleMuon' in directory and channel not in [
'mutau', 'mumu'
]:
continue
if 'SingleElectron' in directory and channel != 'eletau':
continue
if 'Tau' in directory[:5] and channel != 'tautau': continue
if 'LQ3' in directory[:5] and channel not in [
'mutau', 'eletau', 'tautau'
]:
continue
print bcolors.BOLD + bcolors.OKGREEN + directory + bcolors.ENDC
files = None
name = None
if 'pnfs' in directory:
name = directory.split('/')[8].replace(
'/', '') + '__' + directory.split('/')[9].replace(
'/', '') + '__' + directory.split('/')[10].replace(
'/', '')
#files = getFileListPNFS(directory)
files = getFileListPNFS(name)
else:
files = getFileListDAS(directory)
name = directory.split('/')[1].replace(
'/', '') + '__' + directory.split('/')[2].replace(
'/', '') + '__' + directory.split('/')[3].replace(
'/', '')
if not files:
print bcolors.BOLD + bcolors.WARNING + "Warning!!! FILELIST empty" + bcolors.ENDC
continue
elif args.verbose:
print "FILELIST = " + files[0]
for file in files[1:]:
print " " + file
# JOBLIST
ensureDirectory('joblist')
jobList = 'joblist/joblist%s_%s.txt' % (name, channel)
print "Creating job file %s..." % (jobList)
jobName = getSampleShortName(directory)[1]
jobs = open(jobList, 'w')
nFilesPerJob = args.nFilesPerJob
outdir = ensureDirectory("output_%s/%s" % (year, name))
# NFILESPERJOBS CHECKS
# Diboson (WW, WZ, ZZ) have very large files and acceptance,
# and the jet-binned DY and WJ files need to be run separately because of a bug affecting LHE_Njets
if nFilesPerJob > 1 and any(vv in jobName[:8] for vv in [
'WW', 'WZ', 'ZZ', 'DY', 'WJ', 'W1J', 'W2J', 'W3J',
'W4J', 'Single', 'Tau'
]):
print bcolors.BOLD + bcolors.WARNING + "[WN] setting number of files per job from %s to 1 for %s" % (
nFilesPerJob, jobName) + bcolors.ENDC
nFilesPerJob = 1
try:
os.stat(outdir)
except:
os.mkdir(outdir)
try:
os.stat(outdir + '/logs/')
except:
os.mkdir(outdir + '/logs/')
# CREATE JOBS
nChunks = 0
filelists = list(split_seq(files, nFilesPerJob))
checkExistingFiles(outdir, channel, len(filelists))
#filelists = list(split_seq(files,1))
for file in filelists:
#print "FILES = ",f
createJobs(jobs,
file,
outdir,
name,
nChunks,
channel,
year=year)
nChunks = nChunks + 1
jobs.close()
# SUBMIT
jobName += "_%s_%s" % (channel, year)
if args.force:
submitJobs(jobName, jobList, nChunks, outdir, batchSystem)
else:
submit = raw_input(
"Do you also want to submit %d jobs to the batch system? [y/n] "
% (nChunks))
if submit.lower() == 'force':
submit = 'y'
args.force = True
if submit.lower() == 'quit':
exit(0)
if submit.lower() == 'y':
submitJobs(jobName, jobList, nChunks, outdir,
batchSystem)
else:
print "Not submitting jobs"
print
def main():
channels = args.channels
years = args.years
tes = args.tes
ltf = args.ltf
jtf = args.jtf
Zmass = args.Zmass
prefetch = args.prefetch
batchSystem = 'submit_SGE.sh'
tag = args.tag
if tag and tag[0] != '_': tag = '_' + tag
if tes != 1.: tag += "_TES%.3f" % (tes)
if ltf != 1.: tag += "_LTF%.3f" % (ltf)
if jtf != 1.: tag += "_JTF%.3f" % (jtf)
if Zmass: tag += "_Zmass"
tag = tag.replace('.', 'p')
chunkpattern = re.compile(r".*_(\d+)_[a-z]+%s\.root" % tag)
for year in years:
# GET LIST
samplelist = []
outdir = "output_%s/" % (year)
for directory in sorted(os.listdir(outdir)):
if not os.path.isdir(outdir + directory): continue
if args.samples and not matchSampleToPattern(
directory, args.samples):
continue
if args.vetoes and matchSampleToPattern(directory, args.vetoes):
continue
if args.type == 'mc' and any(
s in directory[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau', 'EGamma'
]):
continue
if args.type == 'data' and not any(
s in directory[:len(s) + 2]
for s in ['SingleMuon', 'SingleElectron', 'Tau', 'EGamma'
]):
continue
samplelist.append(directory)
if not samplelist:
print "No samples found in %s!" % (outdir)
if args.verbose:
print samplelist
blacklist = getBlackList("filelist/blacklist.txt")
# RESUBMIT samples
for channel in channels:
print header(year, channel, tag)
for directory in samplelist:
#if directory.find('W4JetsToLNu_TuneCP5_13TeV-madgraphMLM-pythia8__ytakahas-NanoTest_20180507_W4JetsToLNu_TuneCP5_13TeV-madgraphMLM-pythia8-a7a5b67d3e3590e4899e147be08660be__USER')==-1: continue
outdir = "output_%s/%s" % (year, directory)
outfilelist = glob.glob("%s/*_%s%s.root" %
(outdir, channel, tag))
nFilesPerJob = args.nFilesPerJob
jobName = getSampleShortName(directory)[1]
jobName += "_%s_%s" % (channel, year) + tag
if not outfilelist: continue
# GET SKIMMED
if args.useSkim and isSkimmed(directory, year):
directory = isSkimmed(directory, year)
# FILE LIST
infiles = []
if not args.useDAS:
infiles = getFileListLocal(directory)
if not infiles:
if not args.useDAS:
print "Getting file list from DAS..."
infiles = getFileList(directory)
if infiles:
saveFileListLocal(directory, infiles)
if not infiles:
print bcolors.BOLD + bcolors.WARNING + "Warning! EMPTY filelist for " + directory + bcolors.ENDC
continue
elif args.verbose:
print "FILELIST = " + infiles[0]
for file in infiles[1:]:
print " " + file
# NFILESPERJOBS
sample = '__'.join(directory.split('/')[-3:])
nFilesPerJob = args.nFilesPerJob
if nFilesPerJob < 1:
for default, patterns in nFilesPerJob_defaults:
if matchSampleToPattern(sample, patterns):
nFilesPerJob = default
break
else:
nFilesPerJob = nFilesPerJob_default
if args.verbose:
print "nFilesPerJob = %s" % nFilesPerJob
infilelists = chunkify(infiles, nFilesPerJob)
# JOB LIST
badchunks = []
misschunks = range(0, len(infilelists))
jobList = 'joblist/joblist_%s_%s%s_retry.txt' % (sample,
channel, tag)
with open(jobList, 'w') as jobslog:
for filename in outfilelist:
match = chunkpattern.search(filename)
if match:
chunk = int(match.group(1))
else:
print bcolors.BOLD + bcolors.FAIL + '[NG] did not recognize output file %s !' % (
filename) + bcolors.ENDC
exit(1)
if chunk in misschunks:
misschunks.remove(chunk)
elif chunk >= len(infilelists):
print bcolors.BOLD + bcolors.FAIL + '[WN] %s: found chunk %s >= total number of chunks %s ! Please make sure you have chosen the correct number of files per job (-n=%s), check DAS, or resubmit everything!' % (
filename, chunk, len(infilelists),
nFilesPerJob) + bcolors.ENDC
else:
print bcolors.BOLD + bcolors.FAIL + '[WN] %s: found weird chunk %s ! Please check if there is any overcounting !' % (
filename, chunk,
len(infilelists)) + bcolors.ENDC
file = TFile(filename, 'READ')
if not file.IsZombie() and file.GetListOfKeys(
).Contains('tree') and file.GetListOfKeys().Contains(
'cutflow'):
continue
infiles = infilelists[chunk]
for filename in blacklist:
if filename in infiles:
print ">>> removing blacklisted %s" % filename
infiles.remove(filename)
createJobs(jobslog,
infiles,
outdir,
sample,
chunk,
channel,
year=year,
tes=tes,
ltf=ltf,
jtf=jtf,
Zmass=Zmass,
tag=tag,
prefetch=prefetch)
badchunks.append(chunk)
# BAD CHUNKS
if len(badchunks) > 0:
badchunks.sort()
chunktext = ('chunks ' if len(badchunks) > 1 else
'chunk ') + ', '.join(
str(ch) for ch in badchunks)
print bcolors.BOLD + bcolors.WARNING + '[NG] %s, %d/%d jobs failed!\n Resubmitting %s...' % (
directory, len(badchunks), len(outfilelist),
chunktext) + bcolors.ENDC
# MISSING CHUNKS
if len(misschunks) > 0:
chunktext = ('chunks ' if len(misschunks) > 1 else
'chunk ') + ', '.join(
str(i) for i in misschunks)
print bcolors.BOLD + bcolors.WARNING + "[WN] %s missing %d/%d files !\n Resubmitting %s..." % (
directory, len(misschunks), len(outfilelist),
chunktext) + bcolors.ENDC
for chunk in misschunks:
infiles = infilelists[chunk]
createJobs(jobslog,
infiles,
outdir,
sample,
chunk,
channel,
year=year,
tes=tes,
ltf=ltf,
jtf=jtf,
Zmass=Zmass,
tag=tag,
prefetch=prefetch)
# RESUBMIT
nChunks = len(badchunks) + len(misschunks)
if nChunks == 0:
print bcolors.BOLD + bcolors.OKGREEN + '[OK] %s' % directory + bcolors.ENDC
elif args.force:
submitJobs(jobName, jobList, nChunks, outdir, batchSystem)
else:
submit = raw_input(
"Do you also want to submit %d jobs to the batch system? [y/n] "
% (nChunks))
if submit.lower() == 'force':
submit = 'y'
args.force = True
if submit.lower() == 'quit':
exit(0)
if submit.lower() == 'y':
submitJobs(jobName, jobList, nChunks, outdir,
batchSystem)
else:
print "Not submitting jobs"
print
def main():
years = args.years
outbasedir = "/scratch/ineuteli"
batchscript = 'submit_SGE.sh'
tag = ""
for year in years:
# READ SAMPLES
directories = []
samplelist = "samples_%s.cfg" % (year)
with open(samplelist, 'r') as file:
for line in file:
line = line.rstrip().lstrip().split(' ')[0].rstrip('/')
if line[:2].count('#') > 0: continue
if line == '': continue
if '/pnfs/' in line: continue
if args.samples and not matchSampleToPattern(
line, args.samples):
continue
if args.vetos and matchSampleToPattern(line, args.vetos):
continue
if args.type == 'mc' and any(
s in line[:len(s) + 2] for s in
['SingleMuon', 'SingleElectron', 'Tau', 'EGamma']):
continue
if args.type == 'data' and not any(
s in line[:len(s) + 2] for s in
['SingleMuon', 'SingleElectron', 'Tau', 'EGamma']):
continue
directories.append(line)
if args.testrun:
directories = directories[:1]
blacklist = [] #getBlackList("filelist/blacklist.txt")
print header(year, tag)
# SUBMIT SAMPLES
for directory in directories:
if args.verbose:
print "\ndirectory =", directory
print bcolors.BOLD + bcolors.OKGREEN + directory + bcolors.ENDC
# FILE LIST
files = []
name = '__'.join(directory.split('/')[-3:])
sample = '/' + name.replace('__', '/')
###if not args.useDAS:
### files = getFileListLocal(directory,blacklist=blacklist)
###if not files:
###if not args.useDAS:
### print "Getting file list from DAS..."
files = getFileListDAS(directory, blacklist=blacklist)
### if files:
### saveFileListLocal(name,files,blacklist=blacklist)
if not files:
print bcolors.BOLD + bcolors.WARNING + "Warning! EMPTY filelist for " + directory + bcolors.ENDC
continue
elif args.verbose:
print "FILELIST = " + files[0]
for file in files[1:]:
print " " + file
if args.testrun:
files = files[:1]
# JOB LIST
ensureDirectory('joblist')
jobList = 'joblist/joblist_%s_skim%s.txt' % (name, tag)
print "Creating job file %s..." % (jobList)
jobName = getSampleShortName(directory)[1]
jobName += "_%s_skim" % (year) + tag
outdir = "%s/output_%s/%s" % (outbasedir, year, name)
logdir = ensureDirectory("skim_logs_%s/%s" % (year, name))
# NFILESPERJOBS
nFilesPerJob = args.nFilesPerJob
if nFilesPerJob < 1:
for default, patterns in nFilesPerJob_defaults:
if matchSampleToPattern(directory, patterns):
nFilesPerJob = default
break
else:
nFilesPerJob = nFilesPerJob_default # default
if args.verbose:
print "nFilesPerJob = %s" % nFilesPerJob
filelists = chunkify(files, nFilesPerJob)
# CREATE JOBS
with open(jobList, 'w') as jobs:
nChunks = 0
for filelist in filelists:
createSkimJobs(jobs,
year,
name,
filelist,
outdir,
prefetch=args.prefetch)
nChunks = nChunks + 1
# SUBMIT
if args.force:
submitSkimJobs(jobName, jobList, nChunks, logdir, batchscript)
else:
submit = raw_input(
"Do you also want to submit %d jobs to the batch system? [y/n] "
% (nChunks))
if submit.lower() == 'force':
submit = 'y'
args.force = True
if submit.lower() == 'quit':
exit(0)
if submit.lower() == 'y':
submitSkimJobs(jobName, jobList, nChunks, logdir,
batchscript)
else:
print "Not submitting jobs"
print
