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)
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_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_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_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_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_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_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)
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))
ft = FinishedTrigger(outputfile)
jh.add_job(name=name,
run_script=skim_script.format(inputfile=f,
outputfile=outputfile,
treenames=treenames,
branches=branchnames,
finished_func=ft,
selection=selection))
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()
