def test_trigger_success_listener(self):
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_trigger_success_listener')
jh.add_job(run_script=self.run_script_trigger_success, name='test')
jh.run_jobs()
self.assertIs(jh.jobs.test.status, Status.SUCCESS)
def test_run_max(self):
## This effectively only tests if run_jobs finishes or not
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_run_max',
run_max=1)
for i in range(3):
jh.add_job(run_script=self.run_script, name='test_{}'.format(i))
jh.run_jobs()
for i in range(3):
self.assertIs(jh['test_{}'.format(i)].status, Status.SUCCESS)
def test_post_process(self):
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_post_process')
output_file = os.path.join(jh.config.output_dir, 'test')
post_func = TestPostFunction(output_file)
jh.add_job(run_script=self.run_script,
name='test',
post_func=post_func)
jh.run_jobs()
time.sleep(1)
self.assertIs(jh.jobs.test.status, Status.SUCCESS)
self.assertTrue(os.path.isfile(output_file))
def test_chain_fail(self):
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_chain',
listens=False)
jh.add_job(run_script=self.run_script_fail,
name='test_parent',
tags='parent')
jh.add_job(run_script=self.run_script_success,
name='test_child',
parent_tags='parent')
jh.run_jobs()
self.assertIs(jh.jobs.test_parent.status, Status.FAILED)
self.assertIs(jh.jobs.test_child.status, Status.CANCELLED)
def test_output_listener(self):
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_output_listener')
jh.add_job(run_script=self.run_script_touch_file,
name='test',
output=self.output_file)
jh.run_jobs()
self.assertIs(jh.jobs.test.status, Status.SUCCESS)
jh.reset()
jh.jobs.test.config.backend.run_script = self.run_script_success
jh.jobs.test.config.output = 'jwoigjwoijegoijwoijegoiwoeg'
jh.run_jobs()
self.assertIs(jh.jobs.test.status, Status.FAILED)
def test_chain(self):
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_chain',
listens=False)
jh.add_job(run_script=self.run_script_touch_file,
name='test_parent',
tags='parent')
jh.add_job(run_script=self.run_script_ls_file,
name='test_child',
parent_tags='parent')
jh.run_jobs()
self.assertIs(jh.jobs.test_parent.status, Status.SUCCESS)
self.assertIs(jh.jobs.test_child.status, Status.SUCCESS)
def test_batch_listener(self):
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_batch_listener')
jh.add_job(run_script=self.run_script_fail, name='test')
jh.run_jobs()
status_fail = jh.jobs.test.status
id_first = jh.jobs.test.id
jh.jobs.test.config.backend.run_script = self.run_script_success
jh.run_jobs(retry=True)
status_success = jh.jobs.test.status
id_second = jh.jobs.test.id
self.assertIsNot(id_first, id_second)
self.assertIs(status_fail, Status.FAILED)
self.assertIs(status_success, Status.SUCCESS)
def main():
"""Batch submission using slurmy."""
## Set up the JobHandler
jh = JobHandler(
local_max=8,
local_dynamic=True,
work_dir=mkdir('batch'),
printer_bar_mode=True,
wrapper=SingularityWrapper('docker://philippgadow/checkmate'))
## Define the run script content
## Add a job
jh.add_job(run_script='/work/run_example_in_docker.sh',
job_type=Type.LOCAL)
## Run all jobs
jh.run_jobs()
def test_reset(self):
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_reset',
listens=False)
jh.add_job(run_script=self.run_script, name='test')
jh.run_jobs()
self.assertIs(jh.jobs.test.status, Status.SUCCESS)
id_first = jh.jobs.test.id
jh.reset()
self.assertIs(jh.jobs.test.status, Status.CONFIGURED)
jh.run_jobs()
self.assertIs(jh.jobs.test.status, Status.SUCCESS)
id_second = jh.jobs.test.id
self.assertIsNot(id_first, id_second)
def test_type_local(self):
from slurmy import JobHandler, Type
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_jobconfig_type_local',
do_snapshot=False,
local_max=1)
job = jh.add_job(run_script=self.run_script, job_type=Type.LOCAL)
self.assertIs(job.type, Type.LOCAL)
def test_mix_batch_local_listener(self):
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_mix_batch_local_listener',
local_max=1,
local_dynamic=True)
jh.add_job(run_script=self.run_script_fail, name='test_1')
jh.add_job(run_script=self.run_script_fail, name='test_2')
jh.run_jobs()
self.assertIsNot(jh.jobs.test_1.type, jh.jobs.test_2.type)
self.assertIs(jh.jobs.test_1.status, Status.FAILED)
self.assertIs(jh.jobs.test_2.status, Status.FAILED)
jh.jobs.test_1.config.backend.run_script = self.run_script_success
jh.jobs.test_2.config.backend.run_script = self.run_script_success
jh.run_jobs(retry=True)
self.assertIs(jh.jobs.test_1.status, Status.SUCCESS)
self.assertIs(jh.jobs.test_2.status, Status.SUCCESS)
def test_local_listener(self):
from slurmy import JobHandler, Status, Type, test_mode
test_mode(True)
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_local_listener',
local_max=1)
jh.add_job(run_script=self.run_script_fail,
name='test',
job_type=Type.LOCAL)
jh.run_jobs()
status_fail = jh.jobs.test.status
jh.jobs.test.config.backend.run_script = self.run_script_success
jh.run_jobs(retry=True)
status_success = jh.jobs.test.status
test_mode(False)
self.assertIs(status_fail, Status.FAILED)
self.assertIs(status_success, Status.SUCCESS)
def test_chain_multiparent(self):
from slurmy import JobHandler, Status
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_chain_multiparent',
listens=False)
output1 = '@SLURMY.output_dir/parent1'
run_script1 = '#!/bin/bash\ntouch {}; sleep 2;'.format(output1)
jh.add_job(run_script=run_script1,
name='test_parent1',
tags='parent1',
output=output1)
output2 = '@SLURMY.output_dir/parent2'
run_script2 = '#!/bin/bash\ntouch {}; sleep 2;'.format(output2)
jh.add_job(run_script=run_script2,
name='test_parent2',
tags='parent2',
output=output2)
run_script3 = '#!/bin/bash\nls {} {};'.format(output1, output2)
jh.add_job(run_script=run_script3,
name='test_child',
parent_tags=['parent1', 'parent2'])
jh.run_jobs()
self.assertIs(jh.jobs.test_parent1.status, Status.SUCCESS)
self.assertIs(jh.jobs.test_parent2.status, Status.SUCCESS)
self.assertIs(jh.jobs.test_child.status, Status.SUCCESS)
"MET_SoftTrk_ScaleUp",
"MUON_ID",
"MUON_MS",
"MUON_SAGITTA_RESBIAS",
"MUON_SAGITTA_RHO",
"MUON_SCALE",
# "NoSys",
]
for process in processes:
print "Starting with process {}".format(process)
for sys in systematics:
outputfile= os.path.join(output_path, "{}_merged_{}.root".format(process,sys))
name = "{}_merged_{}".format(process,sys)
to_merge = []
for campaign in ["mc16e","mc16d","mc16a"]:
# for f in glob.glob("/project/etp4/eschanet/ntuples/common/{}/{}/merged/{}_*tree_{}*done_noLHE.root".format(campaign,tag,process,sys)):
for f in glob.glob("/project/etp4/eschanet/ntuples/common/{}/{}/merged/{}_*merged_processed_tree_{}*.root*".format(campaign,tag,process,sys)):
if process == "ttbar" and "ttbar_allhad" in f:
continue
print f
to_merge.append(f)
# if len(to_merge)%3!=0:
# print("{} probably incomplete!".format(process))
print(len(to_merge))
ft = FinishedTrigger(outputfile)
jh.add_job(name=name+"_hadd", run_script=merge_script.format(outputfile=outputfile,finished_func=ft, inputfiles=" ".join(to_merge)))
jh.run_jobs()
# print(inputfile)
for skipEvents in range(0, totalEvents - maxEvents + 1, maxEvents):
# print("Adding job for inputfile={}, skipEvents={}".format(inputfile, skipEvents))
dirname = os.path.basename(os.path.normpath(indirectory))
dirname = dirname.replace("EVNT",
"DAOD_TRUTH3").replace("evgen", "deriv")
outputfile = os.path.join(outdir, dirname, inputfile).replace(
"EVNT", "DAOD_TRUTH3")
myoutdir = os.path.join(outdir, dirname)
outputfile = outputfile + "_{}".format(skipEvents)
st = SuccessTrigger(outputfile, 20)
test_finished = os.path.join(outdir, dirname,
inputfile + "_testfile")
# print(test_finished)
jh.add_job(
run_script=run_script.format(inputfile=inputfile,
indir=indirectory,
outdir=myoutdir,
outputfile=outputfile,
finished_file=test_finished,
skipEvents=skipEvents,
maxEvents=maxEvents),
name="pantagruel_{}_{}".format(inputfile.replace(".", "_"),
skipEvents),
output=outputfile,
success_func=st,
backend=Slurm(mem="3500mb"))
jh.run_jobs()
class Test(unittest.TestCase):
def setUp(self):
from slurmy import JobHandler, test_mode
test_mode(True)
self.test_dir = 'slurmy_unittest/jobconfig'
self.jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_jobconfig',
do_snapshot=False)
self.run_script = 'echo "test"'
self.run_script_trigger = '@SLURMY.FINISHED; @SLURMY.SUCCESS;'
def tearDown(self):
from slurmy import test_mode
test_mode(False)
##TODO: run_script test --> with direct string and path to file
def test_run_args(self):
job = self.jh.add_job(run_script=self.run_script, run_args='test')
self.assertIs(job.config.backend.run_args, 'test')
def test_name(self):
job = self.jh.add_job(run_script=self.run_script, name='test')
self.assertIs(job.name, 'test')
self.assertIn('test', self.jh.jobs)
self.assertIs(self.jh.jobs.test.name, 'test')
def test_type_local(self):
from slurmy import JobHandler, Type
jh = JobHandler(work_dir=self.test_dir,
verbosity=0,
name='test_jobconfig_type_local',
do_snapshot=False,
local_max=1)
job = jh.add_job(run_script=self.run_script, job_type=Type.LOCAL)
self.assertIs(job.type, Type.LOCAL)
def test_finished_func(self):
from slurmy import Status, Mode
job = self.jh.add_job(run_script=self.run_script,
finished_func=lambda x: x)
self.assertIs(job.get_mode(Status.RUNNING), Mode.ACTIVE)
self.assertTrue(job.config.finished_func(True))
def test_success_func(self):
from slurmy import Status, Mode
job = self.jh.add_job(run_script=self.run_script,
success_func=lambda x: x)
self.assertIs(job.get_mode(Status.FINISHED), Mode.ACTIVE)
self.assertTrue(job.config.success_func(True))
def test_post_func(self):
from slurmy import Status
job = self.jh.add_job(run_script=self.run_script,
post_func=lambda x: x)
self.assertTrue(job.config.post_func(True))
def test_output(self):
from slurmy import Status, Mode
job = self.jh.add_job(run_script=self.run_script, output='test')
self.assertIs(job.get_mode(Status.FINISHED), Mode.PASSIVE)
self.assertIsNotNone(job.output)
def test_tags(self):
job = self.jh.add_job(run_script=self.run_script, tags='hans')
self.assertIn('hans', job.tags)
job = self.jh.add_job(run_script=self.run_script,
tags=['hans', 'horst'])
self.assertIn('hans', job.tags)
self.assertIn('horst', job.tags)
def test_parent_tags(self):
job = self.jh.add_job(run_script=self.run_script, parent_tags='hans')
self.assertIn('hans', job.parent_tags)
job = self.jh.add_job(run_script=self.run_script,
parent_tags=['hans', 'horst'])
self.assertIn('hans', job.parent_tags)
self.assertIn('horst', job.parent_tags)
def test_variable_substitution(self):
from slurmy import Status
job = self.jh.add_job(run_script=self.run_script,
output='@SLURMY.output_dir/test')
output = os.path.join(self.jh.config.output_dir, 'test')
self.assertTrue(job.output == output)
print point
#TODO: make nicer
if "onestep" in point.lower():
#onestep points have different formatting at tree- and AOD-level
point = point.replace("onestepCC", "oneStep")
elif "LQ" in point:
point = "leptoquark_" + point.replace('ld_0p3_beta_0p5_hnd_1p0_','') + "_"
searcher = "{}*merged_processed*.root".format(point)
print(searcher)
files_mc16a = glob.glob("/project/etp4/eschanet/ntuples/common/mc16a/{}/merged/{}".format(args.production,searcher))
files_mc16d = glob.glob("/project/etp4/eschanet/ntuples/common/mc16d/{}/merged/{}".format(args.production,searcher))
files_mc16e = glob.glob("/project/etp4/eschanet/ntuples/common/mc16e/{}/merged/{}".format(args.production,searcher))
if len(files_mc16a)==0 or len(files_mc16d)==0 or len(files_mc16e)==0:
print "mc16a: %i"%len(files_mc16a)
print "mc16d: %i"%len(files_mc16d)
print "mc16e: %i"%len(files_mc16e)
print "WARNING - {} is not complete".format(point)
if not args.ignore_incomplete:
continue
print "WARNING - Ignoring incomplete!".format(point)
inputfiles = " ".join(sorted(files_mc16a)) + " " + " ".join(sorted(files_mc16d)) + " " + " ".join(sorted(files_mc16e))
#pprint.pprint(inputfiles)
outputfile = output_path + "{}_merged_processed.root".format(point)
jh.add_job(name=point+"_campaignHadder", run_script=merge_script.format(outputfile=outputfile, inputfiles=inputfiles), output=outputfile)
jh.run_jobs()
def run():
parser = argparse.ArgumentParser(description='Run stuff locally on etp')
parser.add_argument('files', type=argparse.FileType('r'), nargs='+')
parser.add_argument("-s",help="input sample",default=None)
parser.add_argument("-selector",help="selector",default="OneLep")
parser.add_argument("-writeTrees",help="sys or nominal",default="1")
parser.add_argument("-deepConfig",help="input sample",default="SusySkim1LInclusive_Rel21.config")
parser.add_argument("-outputPath",help="output path",default=None)
parser.add_argument("-process",help="process tag to find your output",default=None)
args = parser.parse_args()
jobscript = """
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
shopt -s expand_aliases
export ATLAS_LOCAL_ROOT_BASE=/cvmfs/atlas.cern.ch/repo/ATLASLocalRootBase
source ${ATLAS_LOCAL_ROOT_BASE}/user/atlasLocalSetup.sh
pushd $testarea
set -- ""
acmSetup
popd
echo "run_xAODNtMaker"
echo " -s $sample"
echo " -selector $selector"
echo " -writeTrees $writeTrees"
echo " -deepConfig $deepConfig"
echo " -MaxEvents $maxEvents"
echo " -SkipEvents $skipEvents"
run_xAODNtMaker -s $sample -selector $selector -writeTrees $writeTrees -deepConfig $deepConfig -MaxEvents $maxEvents -SkipEvents $skipEvents
[[ "$?" = "0" ]] && mv ${outputPath}/submitDir/data-tree/ ${outputPath}/${groupset}/${mytag}/merged/${process}_${minEvent}_${maxEvent}_merged_processed_${writeTrees}.root
"""
sw = SingularityWrapper('/cvmfs/atlas.cern.ch/repo/containers/images/singularity/x86_64-centos7.img')
jh = JobHandler(wrapper = sw,work_dir="/project/etp2/eschanet/collect", name="run_ntuple")#, run_max=50)
# sf = SuccessOutputFile()
for exportopts, optDict in params:
slurm = Slurm(export = exportopts)
outputfile = os.path.abspath("{path}/{groupset}/{mytag}/merged/{process}_{minEvent}_{maxEvent}_merged_processed_{sys}.root.done".format(**optDict))
jobname = "run_xAODNtMaker_{groupset}_{process}_{sys}_{minEvent}".format(**optDict)
jobname = clean_jobname(jobname)
print(jobname)
ft = FinishedTrigger(outputfile)
jh.add_job(backend = slurm, run_script = jobscript, output = outputfile, success_func = ft, name = jobname)
jh.run_jobs()
['"{}"'.format(b) for b in lhe_weights])
# if there are more than 50 trees, split into several jobs and merge later
if len(treenames) > 50:
i = 1
to_merge = []
for chunk in chunks(treenames, 25):
print("creating chunk #{:02d}".format(i))
trees = " ,".join(['"{}"'.format(t) for t in chunk])
basename = "{:}_part{:03d}.root".format(
os.path.splitext(os.path.basename(f))[0], i)
outputfile = os.path.join(output_path, basename)
jh.add_job(name=name + "_part{:03d}".format(i),
run_script=skim_script.format(inputfile=f,
outputfile=outputfile,
treenames=trees,
branches=branchnames,
selection=selection),
tags=name + "_skim")
to_merge.append(outputfile)
i += 1
outputfile = os.path.join(output_path, os.path.basename(f))
ft = FinishedTrigger(outputfile)
jh.add_job(name=name + "_merge",
run_script=merge_script.format(outputfile=outputfile,
inputfiles=" ".join(to_merge)),
finished_func=ft,
parent_tags=name + '_skim')
else:
treenames = " ,".join(['"{}"'.format(t) for t in treenames])
outputfile = os.path.join(output_path, os.path.basename(f))
