def submit_job(brunel_app, reco_type, input_files=None, local=RUN_LOCAL):
# Set EvtMax depending on if this is a local job
brunel_app.extraOpts += 'from Configurables import Brunel\n'
brunel_app.extraOpts += 'Brunel().EvtMax = {}'.format(2 * int(local) - 1)
# Configure the corresponding Job
job = Job(name='VP hybrid distortions',
comment='{reco_type} reconstruction {suffix}'.format(
reco_type=reco_type, suffix=['', '(local)'][local]),
application=brunel_app,
splitter=SplitByFiles(filesPerJob=1, ignoremissing=True),
parallel_submit=True)
if local:
job.backend = Local()
job.outputfiles = [LocalFile('*.xdst'), LocalFile('*.root')]
job.inputdata = dataset[:1]
else:
job.backend = Dirac()
job.outputfiles = [DiracFile('*.xdst'), DiracFile('*.root')]
job.inputdata = dataset
job.inputfiles = input_files or []
queues.add(job.submit)
return True
def test_lcg(gpi):
from Ganga.GPI import Job, LCG, VomsProxy, credential_store, jobs
logger.info('Submitting first job')
j1 = Job()
j1.backend = LCG()
j1.submit()
logger.info('Submitting second job')
j2 = Job()
j2.backend = LCG(credential_requirements=VomsProxy(vo='lhcb'))
j2.submit()
# Wipe out all the credentials to make sure they can be created on cue
for cred in credential_store:
cred.destroy()
logger.info('Monitoring jobs')
for j in jobs:
stripProxy(j).backend.master_updateMonitoringInformation(
[stripProxy(j)])
# Wipe out all the credentials to make sure they can be created on cue
credential_store.clear()
logger.info('Monitoring jobs')
for j in jobs:
stripProxy(j).backend.master_updateMonitoringInformation(
[stripProxy(j)])
# Wipe out all the credentials to make sure they can be created on cue
for cred in credential_store:
cred.destroy()
credential_store.clear()
logger.info('Monitoring jobs')
for j in jobs:
stripProxy(j).backend.master_updateMonitoringInformation(
[stripProxy(j)])
# Wipe out all the credentials to make sure they can be created on cue
for cred in credential_store:
cred.destroy()
credential_store.clear()
logger.info('Killing jobs')
for j in jobs:
j.kill()
def Savannah19123(self):
from Ganga.GPI import Job, Local
from GangaTest.Framework.utils import sleep_until_state
# check if stdout and stderr exists or not, flag indicates if files are required to exist or not
def check(exists_flag):
for fn in ['stdout','stderr']:
fn = os.path.join(j.outputdir,fn)
file_exists = os.path.exists(fn)
if exists_flag:
self.assertTrue(file_exists, 'file %s should exist but it does not' % fn)
else:
self.assertFalse(file_exists, 'file %s should not exist but it does' % fn)
j = Job()
j.application.exe = 'bash'
j.application.args = ['-c', 'for i in `seq 1 30`; do echo $i; sleep 1; done']
j.backend = Local()
j.submit()
check(False)
sleep_until_state(j, 5, 'running')
j.kill()
check(True)
def test_a_CreateJob(self):
from Ganga.GPI import jobs, Job, Executable, Local
jobs.remove()
j = Job()
j.application = Executable()
j.backend = Local()
def test_job_complete(gpi):
from Ganga.GPI import Job, LCG
j = Job()
j.backend = LCG()
j.submit()
assert run_until_completed(j, timeout=1200, sleep_period=10), 'Timeout on job submission: job is still not finished'
def test_submit_kill_resubmit(gpi):
"""
Test that a simple submit-kill-resubmit-kill cycle works
"""
from Ganga.GPI import Job, LCG
j = Job()
j.backend = LCG()
with patch('Ganga.Lib.LCG.Grid.submit', return_value='https://example.com:9000/42') as submit:
j.submit()
submit.assert_called_once()
assert j.backend.id == 'https://example.com:9000/42'
with patch('Ganga.Lib.LCG.Grid.cancel', return_value=True) as cancel:
j.kill()
cancel.assert_called_once()
assert j.status == 'killed'
with patch('Ganga.Lib.LCG.Grid.submit', return_value='https://example.com:9000/43') as submit:
j.resubmit()
submit.assert_called_once()
assert j.backend.id == 'https://example.com:9000/43'
with patch('Ganga.Lib.LCG.Grid.cancel', return_value=True):
j.kill()
def test_job_kill(gpi):
from Ganga.GPI import Job, LCG
j = Job()
j.backend = LCG()
j.submit()
j.kill()
def test_job_kill(gpi):
from Ganga.GPI import Job, CREAM
vo = getConfig('LCG')['VirtualOrganisation']
call = subprocess.Popen(['lcg-infosites', 'ce', 'cream', '--vo', vo],
stdout=subprocess.PIPE)
stdout, stderr = call.communicate()
# Based on output of:
#
# # CPU Free Total Jobs Running Waiting ComputingElement
# ----------------------------------------------------------------
# 19440 2089 17760 17351 409 arc-ce01.gridpp.rl.ac.uk:2811/nordugrid-Condor-grid3000M
# 3240 0 1594 1250 344 carceri.hec.lancs.ac.uk:8443/cream-sge-grid
# 1176 30 1007 587 420 ce01.tier2.hep.manchester.ac.uk:8443/cream-pbs-long
#
# Select the CREAM CEs (URL path starts with '/cream') and how many free slots they have
ces = re.findall(
r'^\s*\d+\s*(?P<free>\d+)\s*\d+\s*\d+\s*\d+\s*(?P<ce>[^:/\s]+uk:\d+/cream.*)$',
stdout, re.MULTILINE)
# Grab the one with the most empty slots
ce = sorted(ces)[-1][1]
j = Job()
j.backend = CREAM(CE=ce)
j.submit()
j.kill()
def test_job_kill(gpi):
from Ganga.GPI import Job, LCG
j = Job()
j.backend = LCG()
j.submit()
j.kill()
def test_submit_kill_resubmit(gpi):
"""
Test that a simple submit-kill-resubmit-kill cycle works
"""
from Ganga.GPI import Job, LCG
j = Job()
j.backend = LCG()
with patch('Ganga.Lib.LCG.Grid.submit',
return_value='https://example.com:9000/42') as submit:
j.submit()
submit.assert_called_once()
assert j.backend.id == 'https://example.com:9000/42'
with patch('Ganga.Lib.LCG.Grid.cancel', return_value=True) as cancel:
j.kill()
cancel.assert_called_once()
assert j.status == 'killed'
with patch('Ganga.Lib.LCG.Grid.submit',
return_value='https://example.com:9000/43') as submit:
j.resubmit()
submit.assert_called_once()
assert j.backend.id == 'https://example.com:9000/43'
with patch('Ganga.Lib.LCG.Grid.cancel', return_value=True):
j.kill()
def test_e_testInMemory(self):
"""
Test the resubmit on a job in memory vs a job which has been loaded from disk
"""
from Ganga.GPI import Job, Local
j = Job()
j.splitter = self._getSplitter()
j.backend = Local()
j.submit()
from GangaTest.Framework.utils import sleep_until_completed
sleep_until_completed(j)
# Job has ben created, split, run and now exists in Memory (NOT SJXML)
from Ganga.Utility.Config import setConfigOption
setConfigOption('Configuration', 'resubmitOnlyFailedSubjobs', 'True')
j.resubmit()
sleep_until_completed(j)
j.subjobs(0).resubmit()
# We should get here if calling resubmit doesn't stall
j.subjobs(0).force_status('failed', force=True)
j.resubmit()
sleep_until_completed(j)
assert j.subjobs(0).status == 'completed'
# Test resubmit from the master job worked
j.subjobs(0).force_status('failed')
j.subjobs(0).resubmit()
sleep_until_completed(j)
assert j.subjobs(0).status == 'completed'
# Test that the resubmit from the subjob worked
setConfigOption('Configuration', 'resubmitOnlyFailedSubjobs', 'False')
j.resubmit()
sleep_until_completed(j)
j.subjobs(0).force_status('failed')
j.resubmit()
sleep_until_completed(j)
def test_e_testInMemory(self):
"""
Test the resubmit on a job in memory vs a job which has been loaded from disk
"""
from Ganga.GPI import Job, Local
j=Job()
j.splitter = self._getSplitter()
j.backend = Local()
j.submit()
from GangaTest.Framework.utils import sleep_until_completed
sleep_until_completed(j)
# Job has ben created, split, run and now exists in Memory (NOT SJXML)
from Ganga.Utility.Config import setConfigOption
setConfigOption('Configuration', 'resubmitOnlyFailedSubjobs', 'True')
j.resubmit()
sleep_until_completed(j)
j.subjobs(0).resubmit()
# We should get here if calling resubmit doesn't stall
j.subjobs(0).force_status('failed')
j.resubmit()
sleep_until_completed(j)
assert j.subjobs(0).status == 'completed'
# Test resubmit from the master job worked
j.subjobs(0).force_status('failed')
j.subjobs(0).resubmit()
sleep_until_completed(j)
assert j.subjobs(0).status == 'completed'
# Test that the resubmit from the subjob worked
setConfigOption('Configuration', 'resubmitOnlyFailedSubjobs', 'False')
j.resubmit()
sleep_until_completed(j)
j.subjobs(0).force_status('failed')
j.resubmit()
sleep_until_completed(j)
def test_lcg(gpi):
from Ganga.GPI import Job, LCG, VomsProxy, credential_store, jobs
logger.info("Submitting first job")
j1 = Job()
j1.backend = LCG()
j1.submit()
logger.info("Submitting second job")
j2 = Job()
j2.backend = LCG(credential_requirements=VomsProxy(vo="lhcb"))
j2.submit()
# Wipe out all the credentials to make sure they can be created on cue
for cred in credential_store:
cred.destroy()
logger.info("Monitoring jobs")
for j in jobs:
stripProxy(j).backend.master_updateMonitoringInformation([stripProxy(j)])
# Wipe out all the credentials to make sure they can be created on cue
credential_store.clear()
logger.info("Monitoring jobs")
for j in jobs:
stripProxy(j).backend.master_updateMonitoringInformation([stripProxy(j)])
# Wipe out all the credentials to make sure they can be created on cue
for cred in credential_store:
cred.destroy()
credential_store.clear()
logger.info("Monitoring jobs")
for j in jobs:
stripProxy(j).backend.master_updateMonitoringInformation([stripProxy(j)])
# Wipe out all the credentials to make sure they can be created on cue
for cred in credential_store:
cred.destroy()
credential_store.clear()
logger.info("Killing jobs")
for j in jobs:
j.kill()
def test_job_submit_and_monitor(gpi):
from Ganga.GPI import Job, LCG
j = Job()
j.backend = LCG()
j.submit()
assert j.status != 'new'
stripProxy(LCG).master_updateMonitoringInformation([stripProxy(j)])
def test_job_submit_and_monitor(gpi):
from Ganga.GPI import Job, LCG
j = Job()
j.backend = LCG()
j.submit()
assert j.status != 'new'
stripProxy(LCG).master_updateMonitoringInformation([stripProxy(j)])
def testInterfaceLookFeel(self):
from Ganga.GPI import Job, LSF, Executable, DaVinci
j1 = Job(name='my',application='DaVinci')
j2 = Job(application = DaVinci())
j1.backend = LSF()
j1.backend.queue = '8nm'
j2.backend = j1.backend # deepcopy
j2.backend.queue = '16nh' # shortcut
bk2 = j2.backend # reference
assert j2.backend.queue == '16nh'
bk2.queue = '100nh'
assert j2.backend.queue == '100nh'
ap = Executable()
j1.application = ap # deepcopy
def test_e_UsingDifferentBackends(self):
from Ganga.GPI import Job, plugins, Local
# -- USINGDIFFERENTBACKENDS PLUGINS START
plugins("backends")
# -- USINGDIFFERENTBACKENDS PLUGINS STOP
# -- USINGDIFFERENTBACKENDS LOCAL START
j = Job()
j.backend = Local()
j.submit()
def test_e_UsingDifferentBackends(self):
from Ganga.GPI import Job, plugins, Local
# -- USINGDIFFERENTBACKENDS PLUGINS START
plugins("backends")
# -- USINGDIFFERENTBACKENDS PLUGINS STOP
# -- USINGDIFFERENTBACKENDS LOCAL START
j = Job()
j.backend = Local()
j.submit()
def testInterfaceLookFeel(self):
"""
This test tests the Executable app and that the DaVinci are assignable
"""
from Ganga.GPI import Job, LSF, Executable, DaVinci
j1 = Job(name='my',application='DaVinci')
j2 = Job(application = DaVinci())
j1.backend = LSF()
j1.backend.queue = '8nm'
j2.backend = j1.backend # deepcopy
j2.backend.queue = '16nh' # shortcut
bk2 = j2.backend # reference
assert j2.backend.queue == '16nh'
bk2.queue = '100nh'
assert j2.backend.queue == '100nh'
ap = Executable()
j1.application = ap # deepcopy
def testMergeThatAlwaysFailsOverwrite(self):
from Ganga.GPI import Job, Executable, Local, LocalFile
j = Job()
j.application = Executable(exe='sh', args=['-c', 'echo foo > out.txt'])
j.backend = Local()
j.outputfiles = [LocalFile('out.txt')]
j.splitter = CopySplitter()
j.postprocessors = MergerTester(files=['out.txt'], overwrite=True)
j.submit()
assert run_until_state(j, 'failed', timeout=60)
assert os.path.exists(os.path.join(j.outputdir, 'out.txt.merge_summary')), 'Summary file should be created'
def test_a_JobSubmission(self):
"""
Create lots of subjobs and submit it
"""
from Ganga.GPI import Job, Local
j = Job()
j.application.exe = "sleep"
j.splitter = self._getSplitter()
j.backend = Local()
j.submit()
# Test we can submit a job and we're going to check the sj are created
assert len(j.subjobs) == TestSJSubmit.n_subjobs
def testMergeThatAlwaysFailsOverwrite(self):
from Ganga.GPI import Job, Executable, Local, LocalFile
j = Job()
j.application = Executable(exe='sh', args=['-c', 'echo foo > out.txt'])
j.backend = Local()
j.outputfiles = [LocalFile('out.txt')]
j.splitter = CopySplitter()
j.postprocessors = MergerTester(files=['out.txt'], overwrite=True)
j.submit()
assert run_until_state(j, 'failed', timeout=60)
assert os.path.exists(os.path.join(j.outputdir, 'out.txt.merge_summary')), 'Summary file should be created'
def test_a_JobSubmission(self):
"""
Create lots of subjobs and submit it
"""
from Ganga.GPI import Job, Local
j = Job()
j.application.exe = "sleep"
j.splitter = self._getSplitter()
j.backend = Local()
j.submit()
# Test we can submit a job and we're going to check the sj are created
assert len(j.subjobs) == TestSJSubmit.n_subjobs
def testLargeJobSubmission(self):
"""
Create lots of subjobs and submit it
"""
from Ganga.GPI import Job, GenericSplitter, Local
j = Job()
j.application.exe = "sleep"
j.splitter = GenericSplitter()
j.splitter.attribute = 'application.args'
j.splitter.values = [['400'] for _ in range(0, 20)]
j.backend = Local()
j.submit()
assert len(j.subjobs) == 20
def testLargeJobSubmission(self):
"""
Create lots of subjobs and submit it
"""
from Ganga.GPI import Job, GenericSplitter, Local
j = Job()
j.application.exe = "sleep"
j.splitter = GenericSplitter()
j.splitter.attribute = 'application.args'
j.splitter.values = [['400'] for _ in range(0, 20)]
j.backend = Local()
j.submit()
assert len(j.subjobs) == 20
def test_Savannah44116(self):
from Ganga.GPI import Job, TestApplication, TestSubmitter
from GangaTest.Framework.utils import sleep_until_state
j = Job()
j.application = TestApplication()
j.application.postprocess_mark_as_failed = True
j.backend = TestSubmitter()
j.backend.time = 1
j.submit()
self.assertTrue(sleep_until_state(j, 10, 'failed'), 'Job is not marked as failed despite app.postprocess() hook')
def test_SubmitAndRemoval(self):
from Ganga.GPI import Job, TestSubmitter
j = Job()
j.backend = TestSubmitter(time=1, update_delay=5)
j.submit()
all = [j]
for i in range(10):
j2 = j.copy()
j2.submit()
all.append(j2)
for j in all:
j.remove()
def testMergeThatAlwaysFailsIgnoreFailed(self):
from Ganga.GPI import Job, Executable, Local, LocalFile
j = Job()
j.application = Executable(exe='sh', args=['-c', 'echo foo > out.txt'])
j.backend = Local()
j.outputfiles = [LocalFile('out.txt')]
j.splitter = CopySplitter()
j.postprocessors = MergerTester(files=['out.txt'], ignorefailed=True)
j.submit()
sleep_until_completed(j, 60)
assert j.status == 'failed'
assert os.path.exists(os.path.join(j.outputdir, 'out.txt.merge_summary')), 'Summary file should be created'
def test_SubmitAndRemoval(self):
from Ganga.GPI import Job, TestSubmitter
j = Job()
j.backend = TestSubmitter(time=1, update_delay=5)
j.submit()
all = [j]
for i in range(10):
j2 = j.copy()
j2.submit()
all.append(j2)
for j in all:
j.remove()
def test_Savannah15630(self):
from Ganga.GPI import Job, Executable, Local, LocalFile
from GangaTest.Framework.utils import sleep_until_completed
j = Job()
j.application = Executable(exe='touch', args=['out.dat'])
j.backend = Local()
j.outputfiles = [LocalFile('out.dat')]
j.submit()
self.assertTrue(sleep_until_completed(j, 60), 'Timeout on job submission: job is still not finished')
import os.path
p = os.path.join(j.outputdir, j.application.args[0])
self.assertTrue(os.path.exists(p))
def testMergeThatAlwaysFailsFlagsSet(self):
from Ganga.GPI import Job, Executable, Local, LocalFile
j = Job()
j.application = Executable(exe="sh", args=["-c", "echo foo > out.txt"])
j.backend = Local()
j.outputfiles = [LocalFile("out.txt")]
j.splitter = CopySplitter()
j.postprocessors = MergerTester(files=["out.txt"], ignorefailed=True, overwrite=True)
j.submit()
run_until_completed(j, timeout=60)
assert j.status == "failed"
assert os.path.exists(os.path.join(j.outputdir, "out.txt.merge_summary")), "Summary file should be created"
def test_Savannah44116(self):
from Ganga.GPI import Job, TestApplication, TestSubmitter
from GangaTest.Framework.utils import sleep_until_state
j = Job()
j.application = TestApplication()
j.application.postprocess_mark_as_failed = True
j.backend = TestSubmitter()
j.backend.time = 1
j.submit()
self.assertTrue(
sleep_until_state(j, 10, 'failed'),
'Job is not marked as failed despite app.postprocess() hook')
def test_Savannah15630(self):
from Ganga.GPI import Job, Executable, Local, LocalFile
from GangaTest.Framework.utils import sleep_until_completed
j = Job()
j.application = Executable(exe='touch', args=['out.dat'])
j.backend = Local()
j.outputfiles = [LocalFile('out.dat')]
j.submit()
self.assertTrue(
sleep_until_completed(j, 60),
'Timeout on job submission: job is still not finished')
import os.path
p = os.path.join(j.outputdir, j.application.args[0])
self.assertTrue(os.path.exists(p))
def test_Savannah19123(self):
from Ganga.GPI import Job, Local
from GangaTest.Framework.utils import sleep_until_state
# check if stdout and stderr exists or not, flag indicates if files are required to exist or not
def check(exists_flag):
for fn in ['stdout', 'stderr']:
fn = os.path.join(j.outputdir, fn)
file_exists = os.path.exists(fn)
if exists_flag:
self.assertTrue(
file_exists,
'file %s should exist but it does not' % fn)
else:
self.assertFalse(
file_exists,
'file %s should not exist but it does' % fn)
j = Job()
j.application.exe = 'bash'
j.application.args = [
'-c', 'for i in `seq 1 30`; do echo $i; sleep 1; done'
]
j.backend = Local()
j.submit()
check(False)
if not sleep_until_state(j, 5, 'running'):
# problem with the test - print out stdout/stderr and assert
for fn in ['stdout', 'stderr']:
fn = os.path.join(j.outputdir, fn)
print " ---- Contents of " + fn
if os.path.exists(fn):
print open(fn).read()
else:
print "NO FILE AVAILABLE"
self.assertEqual(j.status, 'running')
j.kill()
check(True)
def testJobCopy(self):
"""Test that a job copy copies everything properly"""
from Ganga.GPI import Job, ARC, GenericSplitter, GangaDataset, LocalFile, FileChecker
from Ganga.GPIDev.Base.Proxy import isType
j = Job()
j.application.exe = "sleep"
j.application.args = ['myarg']
j.backend = ARC()
j.backend.CE = "my.ce"
j.inputdata = GangaDataset()
j.inputdata.files = [ LocalFile("*.txt") ]
j.inputfiles = [ LocalFile("*.txt") ]
j.name = "testname"
j.outputfiles = [ LocalFile("*.txt") ]
j.postprocessors = FileChecker(files=['stdout'], searchStrings = ['my search'])
j.splitter = GenericSplitter()
j.splitter.attribute = "application.args"
j.splitter.values = ['arg 1', 'arg 2', 'arg 3']
j2 = j.copy()
# test the copy has worked
self.assertTrue( isType(j2, Job) )
self.assertEqual( j2.application.exe, "sleep" )
self.assertEqual( j2.application.args, ["myarg"] )
self.assertTrue( isType(j2.backend, ARC) )
self.assertEqual( j2.backend.CE, "my.ce" )
self.assertTrue( isType(j2.inputdata, GangaDataset) )
self.assertEqual( len(j2.inputdata.files), 1 )
self.assertTrue( isType(j2.inputdata.files[0], LocalFile) )
self.assertEqual( j2.inputdata.files[0].namePattern, "*.txt" )
self.assertEqual( len(j2.inputfiles), 1 )
self.assertTrue( isType(j2.inputfiles[0], LocalFile) )
self.assertEqual( j2.inputfiles[0].namePattern, "*.txt" )
self.assertEqual( j2.name, "testname" )
self.assertEqual( len(j2.outputfiles), 1 )
self.assertTrue( isType(j2.outputfiles[0], LocalFile) )
self.assertEqual( j2.outputfiles[0].namePattern, "*.txt" )
self.assertEqual( len(j2.postprocessors), 1 )
self.assertTrue( isType(j2.postprocessors[0], FileChecker) )
self.assertEqual( j2.postprocessors[0].files, ["stdout"] )
self.assertEqual( j2.postprocessors[0].searchStrings, ["my search"] )
self.assertTrue( isType(j2.splitter, GenericSplitter) )
self.assertEqual( j2.splitter.attribute, "application.args" )
self.assertEqual( j2.splitter.values, ['arg 1', 'arg 2', 'arg 3'])
def test_CondorConfigDefaults(self):
from Ganga.GPI import Job, TestSplitter, TestSubmitter
j = Job()
j.splitter = TestSplitter()
j.splitter.backs = [TestSubmitter(), TestSubmitter(), TestSubmitter()]
j.backend = TestSubmitter()
b = j.splitter.backs[1]
b.fail = 'submit'
assert j.status == 'new'
j.submit(keep_going=False)
assert j.status in ['submitted', 'running']
assert j.subjobs[0].status in ['submitted', 'running']
assert j.subjobs[1].status == 'new'
assert j.subjobs[2].status == 'new'
def testInterfaceLookFeel(self):
# Just testing that the job construction works
from Ganga.GPI import Job, Im3ShapeApp, Im3ShapeSplitter, DiracFile, LocalFile, GangaDataset, Dirac
j=Job()
app = Im3ShapeApp(
im3_location=DiracFile(lfn='/lsst/y1a1-v2-z/software/2016-02-24/im3shape-grid.tar.gz'),
ini_location=LocalFile('/afs/cern.ch/user/r/rcurrie/cmtuser/GANGA/GANGA_LSST/install/ganga/python/params_disc.ini'),
blacklist=LocalFile('/afs/cern.ch/user/r/rcurrie/cmtuser/GANGA/GANGA_LSST/install/ganga/python/blacklist-y1.txt')
)
j.application = app
j.backend=Dirac()
mydata=GangaDataset()
mydata.append(DiracFile(lfn='/lsst/DES0005+0043-z-meds-y1a1-gamma.fits.fz'))
j.inputdata = mydata
j.splitter=Im3ShapeSplitter(size=20)
j.outputfiles = [DiracFile('*.main.txt'), DiracFile('*.epoch.txt')]
def test_CondorConfigDefaults(self):
# A test with sequential submission
from Ganga.GPI import Job, TestSplitter, TestSubmitter
j = Job()
j.splitter = TestSplitter()
j.splitter.backs = [TestSubmitter(),TestSubmitter(),TestSubmitter()]
j.backend= TestSubmitter()
b = j.splitter.backs[1]
b.fail = 'submit'
j.parallel_submit = False
assert j.status == 'new'
with pytest.raises(IncompleteJobSubmissionError):
j.submit(keep_going=True)
assert j.subjobs[0].status in ['submitted', 'running']
assert j.subjobs[1].status == 'new'
assert j.subjobs[2].status == 'new'
def test_CondorConfigDefaults(self):
# A test with sequential submission
from Ganga.GPI import Job, TestSplitter, TestSubmitter
j = Job()
j.splitter = TestSplitter()
j.splitter.backs = [TestSubmitter(), TestSubmitter(), TestSubmitter()]
j.backend = TestSubmitter()
b = j.splitter.backs[1]
b.fail = 'submit'
j.parallel_submit = False
assert j.status == 'new'
with pytest.raises(IncompleteJobSubmissionError):
j.submit(keep_going=True)
assert j.subjobs[0].status in ['submitted', 'running']
assert j.subjobs[1].status == 'new'
assert j.subjobs[2].status == 'new'
def test_Savannah19123(self):
from Ganga.GPI import Job, Local
from GangaTest.Framework.utils import sleep_until_state
# check if stdout and stderr exists or not, flag indicates if files are required to exist or not
def check(exists_flag):
for fn in ['stdout','stderr']:
fn = os.path.join(j.outputdir,fn)
file_exists = os.path.exists(fn)
if exists_flag:
self.assertTrue(file_exists, 'file %s should exist but it does not' % fn)
else:
self.assertFalse(file_exists, 'file %s should not exist but it does' % fn)
j = Job()
j.application.exe = 'bash'
j.application.args = ['-c', 'for i in `seq 1 30`; do echo $i; sleep 1; done']
j.backend = Local()
j.submit()
check(False)
if not sleep_until_state(j, 5, 'running'):
# problem with the test - print out stdout/stderr and assert
for fn in ['stdout','stderr']:
fn = os.path.join(j.outputdir,fn)
print " ---- Contents of " + fn
if os.path.exists(fn):
print open(fn).read()
else:
print "NO FILE AVAILABLE"
self.assertEqual(j.status, 'running')
j.kill()
check(True)
def test_submit_monitor(gpi):
"""
Test that an LCG job can be monitored
"""
from Ganga.GPI import Job, LCG
j = Job()
j.backend = LCG()
job_id = 'https://example.com:9000/42'
with patch('Ganga.Lib.LCG.Grid.submit', return_value=job_id) as submit:
j.submit()
submit.assert_called_once()
assert j.backend.id == job_id
status_info = {
'status': 'Submitted',
'name': '',
'destination': '',
'reason': '',
'exit': '',
'is_node': False,
'id': job_id
}
status_results = [
([status_info], []), # Once for the proper status call
([], []) # Once for the bulk monitoring call
]
with patch('Ganga.Lib.LCG.Grid.status',
side_effect=status_results) as status:
stripProxy(j).backend.master_updateMonitoringInformation(
[stripProxy(j)])
assert status.call_count == 1
with patch('Ganga.Lib.LCG.Grid.cancel', return_value=True):
j.kill()
def testKilling(self):
"""
Create some subjobs and kill them
"""
from Ganga.GPI import Job, GenericSplitter, Local
from GangaTest.Framework.utils import sleep_until_state
j = Job()
j.application.exe = "sleep"
j.splitter = GenericSplitter()
j.splitter.attribute = 'application.args'
j.splitter.values = [['400'] for _ in range(0, 5)]
j.backend = Local()
j.submit()
sleep_until_state(j, None, 'running')
assert j.status == 'running'
j.subjobs(0).kill()
assert j.subjobs(0).status == 'killed'
assert j.subjobs(1).status != 'killed'
j.kill()
assert j.status == 'killed'
assert all(sj.status == 'killed' for sj in j.subjobs)
def testMergeRemoval(self):
from Ganga.GPI import Job, Executable, Local, LocalFile, jobs
# see Savannah 33710
j = Job()
jobID = j.id
# job will run for at least 20 seconds
j.application = Executable(exe="sh", args=["-c", "sleep 20; echo foo > out.txt"])
j.backend = Local()
j.outputfiles = [LocalFile("out.txt")]
j.splitter = CopySplitter()
j.postprocessors = MergerTester(files=["out.txt"])
j.postprocessors[0].ignorefailed = True
j.postprocessors[0].alwaysfail = True
j.postprocessors[0].wait = 10
j.submit()
run_until_state(j, state="running")
j.remove()
with pytest.raises(KeyError):
jobs(jobID)
def testKilling(self):
"""
Create some subjobs and kill them
"""
from Ganga.GPI import Job, GenericSplitter, Local
from GangaTest.Framework.utils import sleep_until_state
j = Job()
j.application.exe = "sleep"
j.splitter = GenericSplitter()
j.splitter.attribute = 'application.args'
j.splitter.values = [['400'] for _ in range(0, 5)]
j.backend = Local()
j.submit()
sleep_until_state(j, None, 'running')
assert j.status == 'running'
j.subjobs(0).kill()
assert j.subjobs(0).status == 'killed'
assert j.subjobs(1).status != 'killed'
j.kill()
assert j.status == 'killed'
assert all(sj.status == 'killed' for sj in j.subjobs)
def submit(N, K):
jobs = []
for i in range(K):
j = Job()
j.backend = LCG()
j.backend.middleware = 'GLITE'
j.splitter = GenericSplitter()
j.splitter.attribute = 'application.args'
j.splitter.values = [['x']] * N
j.submit()
jobs.append(j)
import time
def finished():
for j in jobs:
if not j.status in ['failed', 'completed']:
return False
return True
while not finished():
time.sleep(1)
return jobs
def submit(N, K):
jobs = []
for i in range(K):
j = Job()
j.backend = LCG()
j.backend.middleware = 'GLITE'
j.splitter = GenericSplitter()
j.splitter.attribute = 'application.args'
j.splitter.values = [['x']] * N
j.submit()
jobs.append(j)
import time
def finished():
for j in jobs:
if not j.status in ['failed', 'completed']:
return False
return True
while not finished():
time.sleep(1)
return jobs
def test_submit_monitor(gpi):
"""
Test that an LCG job can be monitored
"""
from Ganga.GPI import Job, LCG
j = Job()
j.backend = LCG()
job_id = 'https://example.com:9000/42'
with patch('Ganga.Lib.LCG.Grid.submit', return_value=job_id) as submit:
j.submit()
submit.assert_called_once()
assert j.backend.id == job_id
status_info = {
'status': 'Submitted',
'name': '',
'destination': '',
'reason': '',
'exit': '',
'is_node': False,
'id': job_id
}
status_results = [
([status_info], []), # Once for the proper status call
([], []) # Once for the bulk monitoring call
]
with patch('Ganga.Lib.LCG.Grid.status', side_effect=status_results) as status:
stripProxy(j).backend.master_updateMonitoringInformation([stripProxy(j)])
assert status.call_count == 2
with patch('Ganga.Lib.LCG.Grid.cancel', return_value=True):
j.kill()
def testMergeRemoval(self):
from Ganga.GPI import Job, Executable, Local, LocalFile, jobs
# see Savannah 33710
j = Job()
jobID = j.id
# job will run for at least 20 seconds
j.application = Executable(exe='sh',
args=['-c', 'sleep 20; echo foo > out.txt'])
j.backend = Local()
j.outputfiles = [LocalFile('out.txt')]
j.splitter = CopySplitter()
j.postprocessors = MergerTester(files=['out.txt'])
j.postprocessors[0].ignorefailed = True
j.postprocessors[0].alwaysfail = True
j.postprocessors[0].wait = 10
j.submit()
run_until_state(j, state='running')
j.remove()
with pytest.raises(KeyError):
jobs(jobID)
def test_job_kill(gpi):
from Ganga.GPI import Job, CREAM
vo = getConfig("LCG")["VirtualOrganisation"]
call = subprocess.Popen(["lcg-infosites", "ce", "cream", "--vo", vo], stdout=subprocess.PIPE)
stdout, stderr = call.communicate()
# Based on output of:
#
# # CPU Free Total Jobs Running Waiting ComputingElement
# ----------------------------------------------------------------
# 19440 2089 17760 17351 409 arc-ce01.gridpp.rl.ac.uk:2811/nordugrid-Condor-grid3000M
# 3240 0 1594 1250 344 carceri.hec.lancs.ac.uk:8443/cream-sge-grid
# 1176 30 1007 587 420 ce01.tier2.hep.manchester.ac.uk:8443/cream-pbs-long
#
# Select the CREAM CEs (URL path starts with '/cream') and how many free slots they have
ces = re.findall(r"^\s*\d+\s*(?P<free>\d+)\s*\d+\s*\d+\s*\d+\s*(?P<ce>[^:/\s]+:\d+/cream.*)$", stdout, re.MULTILINE)
# Grab the one with the most empty slots
ce = sorted(ces)[-1][1]
j = Job()
j.backend = CREAM(CE=ce)
j.submit()
j.kill()
def Savannah19123(self):
from Ganga.GPI import Job, Local
from GangaTest.Framework.utils import sleep_until_state
# check if stdout and stderr exists or not, flag indicates if files are required to exist or not
def check(exists_flag):
for fn in ['stdout', 'stderr']:
fn = os.path.join(j.outputdir, fn)
file_exists = os.path.exists(fn)
if exists_flag:
self.assertTrue(
file_exists,
'file %s should exist but it does not' % fn)
else:
self.assertFalse(
file_exists,
'file %s should not exist but it does' % fn)
j = Job()
j.application.exe = 'bash'
j.application.args = [
'-c', 'for i in `seq 1 30`; do echo $i; sleep 1; done'
]
j.backend = Local()
j.submit()
check(False)
sleep_until_state(j, 5, 'running')
j.kill()
check(True)
def makeIPResolutionsJob( jobName, dataFile, brunelVersion="", dataType = '2012', extraFiles = [],
ddDBTag = None, condDBTag = None ) :
"""Call this method to make a job that will run Brunel with the IP resolutions
ntupling algorithm, using the given config file (data type, etc) and data file.
Add this method to your ~/.ganga.py file to have it automatically loaded whenever
you run ganga."""
print "Creating an IP resolutions monitoring job named \'%s\'" % jobName
dataFile = os.path.expandvars(dataFile)
if not os.path.exists(dataFile) :
print "Could not find the data file \"%s\"!" % dataFile
return None
dataFile = os.path.abspath(dataFile)
print "Using data file \'%s\'" % dataFile
print "Parsing data file for options."
stepInfos = parseDataFileForSteps(dataFile)
productionOptsFiles = None
if len(stepInfos) > 0 :
for step in stepInfos :
# Get any additional options files used for the Brunel step.
if step['ApplicationName'] == "Brunel" :
productionOptsFiles = []
for optsFile in step['OptionFiles'].split(";") :
productionOptsFiles.append(optsFile.replace(" \n",""))
# Get the DB tags used for the Gauss step. This should be the
# same as for the Brunel step but it seems there's a bug in bkk.
if step['ApplicationName'] == "Gauss" or step['ApplicationName'] == 'DaVinci' or step['ApplicationName'] == 'Brunel' :
if ddDBTag == None :
ddDBTag = step['DDDB']
if condDBTag == None :
condDBTag = step['CONDDB']
if None == ddDBTag and len(extraFiles) == 0 :
print "The DB tags could not be retrieved from the data file and no extra options\
files have been specified! The job cannot be made."
return None
j = Job( name = jobName )
if brunelVersion == "" :
j.application = Brunel()
else :
j.application = Brunel(version=brunelVersion)
j.application.extraopts = 'Brunel().OutputLevel = 5\nBrunel().PrintFreq = 10000\nBrunel().DataType = "{0}"\n'.format(dataType)
if None != ddDBTag :
print "Using DDDBTag \"%s\" and CondDBTag \"%s\"" % (ddDBTag, condDBTag)
j.application.extraopts += "\nBrunel().DDDBtag = \"%s\"\nBrunel().CondDBtag = \"%s\"\n" % (ddDBTag, condDBTag)
if 'sim' in ddDBTag.lower() :
j.application.extraopts += '\nBrunel().Simulation = True\n'
#j.application.extraopts += '\nBrunel().WithMC = True\n'
else :
print "The DB tags could not be retrieved from the data file."
print "If they are not defined in one of the extra options files default values will be used."
j.application.optsfile = [ mainIPConfigFile ] + extraFiles
print "Using options files:"
for optsFile in j.application.optsfile :
print optsFile.name
if None != productionOptsFiles and len(productionOptsFiles) > 0 :
for optsFile in productionOptsFiles :
print optsFile
j.application.extraopts += "\nimportOptions(\"%s\")\n" % optsFile
print "Reading in data ..."
j.inputdata = j.application.readInputData( dataFile )
print "Data read. %s files found." % len(j.inputdata.files)
if len(j.inputdata.files) > 0 :
j.application.extraopts += '\nBrunel().InputType = "{0}"\n'.format(j.inputdata.files[0].name.split('.')[-1].upper())
j.splitter = SplitByFiles( filesPerJob = 10 )
j.backend = Dirac()
j.outputfiles = [DiracFile('*.root')]
return j
def test_f_InputAndOutputData(self):
from Ganga.GPI import Job, File, LocalFile, GangaDataset, Local, plugins
# -- INPUTANDOUTPUTDATA BASIC START
# create a script to send
open('my_script2.sh', 'w').write("""#!/bin/bash
ls -ltr
more "my_input.txt"
echo "TESTING" > my_output.txt
""")
import os
os.system('chmod +x my_script2.sh')
# create a script to send
open('my_input.txt', 'w').write('Input Testing works!')
j = Job()
j.application.exe = File('my_script2.sh')
j.inputfiles = [ LocalFile('my_input.txt') ]
j.outputfiles = [ LocalFile('my_output.txt') ]
j.submit()
# -- INPUTANDOUTPUTDATA BASIC STOP
# -- INPUTANDOUTPUTDATA PEEKOUTPUT START
j.peek() # list output dir contents
j.peek('my_output.txt')
# -- INPUTANDOUTPUTDATA PEEKOUTPUT STOP
# -- INPUTANDOUTPUTDATA FAILJOB START
# This job will fail
j = Job()
j.application.exe = File('my_script2.sh')
j.inputfiles = [ LocalFile('my_input.txt') ]
j.outputfiles = [ LocalFile('my_output_FAIL.txt') ]
j.submit()
# -- INPUTANDOUTPUTDATA FAILJOB STOP
# -- INPUTANDOUTPUTDATA WILDCARD START
# This job will pick up both 'my_input.txt' and 'my_output.txt'
j = Job()
j.application.exe = File('my_script2.sh')
j.inputfiles = [LocalFile('my_input.txt')]
j.outputfiles = [LocalFile('*.txt')]
j.submit()
# -- INPUTANDOUTPUTDATA WILDCARD STOP
# -- INPUTANDOUTPUTDATA OUTPUTFILES START
j.outputfiles
# -- INPUTANDOUTPUTDATA OUTPUTFILES STOP
# -- INPUTANDOUTPUTDATA INPUTDATA START
# Create a test script
open('my_script3.sh', 'w').write("""#!/bin/bash
echo $PATH
ls -ltr
more __GangaInputData.txt__
echo "MY TEST FILE" > output_file.txt
""")
import os
os.system('chmod +x my_script3.sh')
# Submit a job
j = Job()
j.application.exe = File('my_script3.sh')
j.inputdata = GangaDataset(files=[LocalFile('*.sh')])
j.backend = Local()
j.submit()
# -- INPUTANDOUTPUTDATA INPUTDATA STOP
# -- INPUTANDOUTPUTDATA GANGAFILES START
plugins('gangafiles')
def test_f_InputAndOutputData(self):
from Ganga.GPI import Job, File, LocalFile, GangaDataset, Local, plugins
# -- INPUTANDOUTPUTDATA BASIC START
# create a script to send
open('my_script2.sh', 'w').write("""#!/bin/bash
ls -ltr
more "my_input.txt"
echo "TESTING" > my_output.txt
""")
import os
os.system('chmod +x my_script2.sh')
# create a script to send
open('my_input.txt', 'w').write('Input Testing works!')
j = Job()
j.application.exe = File('my_script2.sh')
j.inputfiles = [LocalFile('my_input.txt')]
j.outputfiles = [LocalFile('my_output.txt')]
j.submit()
# -- INPUTANDOUTPUTDATA BASIC STOP
# -- INPUTANDOUTPUTDATA PEEKOUTPUT START
j.peek() # list output dir contents
j.peek('my_output.txt')
# -- INPUTANDOUTPUTDATA PEEKOUTPUT STOP
# -- INPUTANDOUTPUTDATA FAILJOB START
# This job will fail
j = Job()
j.application.exe = File('my_script2.sh')
j.inputfiles = [LocalFile('my_input.txt')]
j.outputfiles = [LocalFile('my_output_FAIL.txt')]
j.submit()
# -- INPUTANDOUTPUTDATA FAILJOB STOP
# -- INPUTANDOUTPUTDATA WILDCARD START
# This job will pick up both 'my_input.txt' and 'my_output.txt'
j = Job()
j.application.exe = File('my_script2.sh')
j.inputfiles = [LocalFile('my_input.txt')]
j.outputfiles = [LocalFile('*.txt')]
j.submit()
# -- INPUTANDOUTPUTDATA WILDCARD STOP
# -- INPUTANDOUTPUTDATA OUTPUTFILES START
j.outputfiles
# -- INPUTANDOUTPUTDATA OUTPUTFILES STOP
# -- INPUTANDOUTPUTDATA INPUTDATA START
# Create a test script
open('my_script3.sh', 'w').write("""#!/bin/bash
echo $PATH
ls -ltr
more __GangaInputData.txt__
echo "MY TEST FILE" > output_file.txt
""")
import os
os.system('chmod +x my_script3.sh')
# Submit a job
j = Job()
j.application.exe = File('my_script3.sh')
j.inputdata = GangaDataset(files=[LocalFile('*.sh')])
j.backend = Local()
j.submit()
# -- INPUTANDOUTPUTDATA INPUTDATA STOP
# -- INPUTANDOUTPUTDATA GANGAFILES START
plugins('gangafiles')
j = Job(name=JNAME.format(
polarity, year, mode
))
j.comment = (
'{1} {2} MC {0} ntuple creation for k3pi mixing measurement.'
.format(event_type, year, polarity)
)
j.application = DaVinci(version='v41r3')
j.application.optsfile = [s.format(path=base, year=year) for s in OPTIONS]
if args.test:
# If testing, run over a couple of files locally,
# saving the results to the sandbox
j.inputdata = dataset[0:1]
j.backend = Local()
# Prepend test string to job name
j.name = 'TEST_{0}'.format(j.name)
j.outputfiles = [LocalFile(tfn)]
else:
# If not testing, run over everything on the grid, splitting jobs
# into groups of 10 files, notifying me on job completion/subjob failure,
# and save the results on the grid storage
j.inputdata = dataset
j.backend = Dirac()
j.backend.settings['CPUTime'] = 60*60*24*7
j.do_auto_resubmit = True
j.splitter = SplitByFiles(filesPerJob=5, ignoremissing=True)
j.postprocessors = [Notifier(address=email)]
j.outputfiles = [DiracFile(tfn)]
