def test_bad_command(self, patcher):
patcher.side_effect = [subprocess.CalledProcessError(1, 'cmd')]
sched = _scheduler.TorqueScheduler()
job = _job.Job(SUBCOMMAND.VALIDATE, '', job_ident='1234')
sched.cancel(job)
patcher.assert_called_with(['qdel', '1234'])
self.assertNotEqual(_constants.JOB_STATUS.CANCELLED, job.status)
def test_job_with_mixed_deps(self, patcher):
patcher.side_effect = ['141.torque01.bcgsc.ca\n']
job = _job.Job(stage=SUBCOMMAND.VALIDATE,
queue='all',
output_dir='output_dir',
name='MV1',
memory_limit=1,
mail_user='******',
mail_type=_constants.MAIL_TYPE.ALL,
script='script.sh',
dependencies=[
_job.Job(stage=SUBCOMMAND.VALIDATE,
output_dir='output_dir',
job_ident='1234.torque01.bcgsc.ca'),
_job.Job(stage=SUBCOMMAND.VALIDATE,
output_dir='output_dir',
job_ident='54.torque01.bcgsc.ca'),
_job.TorqueArrayJob(
stage=SUBCOMMAND.VALIDATE,
output_dir='output_dir',
job_ident='99[].torque01.bcgsc.ca',
task_list=5)
])
sched = _scheduler.TorqueScheduler()
sched.submit(job)
self.assertEqual('141.torque01.bcgsc.ca', job.job_ident)
patcher.assert_called_with([
'qsub', '-j', 'oe', '-q', 'all', '-l', 'mem=1mb', '-l',
'walltime=16:00:00', '-V',
'-W depend=afterokarray:99[][5].torque01.bcgsc.ca,afterok:1234.torque01.bcgsc.ca:54.torque01.bcgsc.ca',
'-N', 'MV1', '-o', 'output_dir/job-$PBS_JOBNAME-$PBS_JOBID.log',
'-m', 'abef', '-M', '*****@*****.**', 'script.sh'
])
def test_array_job(self, patcher):
sched = _scheduler.TorqueScheduler()
job = _job.ArrayJob(SUBCOMMAND.VALIDATE, 10, output_dir='', job_ident='1234')
sched.cancel(job)
self.assertEqual(_constants.JOB_STATUS.CANCELLED, job.status)
for task in job.task_list:
self.assertEqual(_constants.JOB_STATUS.CANCELLED, task.status)
patcher.assert_called_with(['qdel', '1234'])
def test_array_job_task(self, patcher):
sched = _scheduler.TorqueScheduler()
job = _job.ArrayJob(SUBCOMMAND.VALIDATE, 10, output_dir='', job_ident='1234')
sched.cancel(job, task_ident='4')
self.assertEqual(_constants.JOB_STATUS.NOT_SUBMITTED, job.status)
for i, task in enumerate(job.task_list):
if i == 3:
self.assertEqual(_constants.JOB_STATUS.CANCELLED, task.status)
else:
self.assertEqual(_constants.JOB_STATUS.NOT_SUBMITTED, task.status)
patcher.assert_called_with(['qdel', '1234', '-t', '4'])
def test_array(self, patcher):
patcher.side_effect = ['142[].torque01.bcgsc.ca\n']
job = _job.TorqueArrayJob(
stage=SUBCOMMAND.VALIDATE,
queue='all',
output_dir='output_dir',
name='MV1',
memory_limit=1,
mail_user='******',
mail_type=_constants.MAIL_TYPE.ALL,
script='script.sh',
task_list=[1, 2, 3, 6, 9],
)
sched = _scheduler.TorqueScheduler(concurrency_limit=2)
sched.submit(job)
self.assertEqual('142[].torque01.bcgsc.ca', job.job_ident)
patcher.assert_called_with(
[
'qsub',
'-j',
'oe',
'-q',
'all',
'-l',
'mem=1mb',
'-l',
'walltime=16:00:00',
'-V',
'-N',
'MV1',
'-o',
'output_dir/job-$PBS_JOBNAME-$PBS_JOBID-$PBS_ARRAYID.log',
'-m',
'abef',
'-M',
'*****@*****.**',
'-t',
'1-3,6,9%2',
'script.sh',
]
)
def test_array_job(self):
content = """
Job Id: 48[1].torque01.bcgsc.ca
Job_Name = MA_mock-A47933_batch-JT3CUggKXNStHcoFXYaGR3-1
Job_Owner = [email protected]
job_state = C
queue = batch
server = torque01.bcgsc.ca
Checkpoint = u
ctime = Tue May 29 18:27:33 2018
depend = afterokarray:43[].torque01.bcgsc.ca
Error_Path = torque01.bcgsc.ca:/projects/trans_scratch/validations/workspa
ce/creisle/temp/test_submission/output_torque/mock-A47933_diseased_tra
nscriptome/annotate/batch-JT3CUggKXNStHcoFXYaGR3-/job---.log-1
Join_Path = oe
Keep_Files = n
Mail_Points = a
mtime = Tue May 29 18:27:33 2018
Output_Path = torque01.bcgsc.ca:/projects/trans_scratch/validations/worksp
ace/creisle/temp/test_submission/output_torque/mock-A47933_diseased_tr
anscriptome/annotate/batch-JT3CUggKXNStHcoFXYaGR3-/job---.log-1
Priority = 0
qtime = Tue May 29 18:27:33 2018
Rerunable = True
Resource_List.mem = 12000mb
Resource_List.walltime = 16:00:00
Resource_List.nodes = 1
Resource_List.nodect = 1
Variable_List = PBS_ARRAYID=1,PBS_O_QUEUE=batch,PBS_O_HOME=/home/creisle,
PBS_O_LOGNAME=creisle,
PBS_O_PATH=/home/creisle/git/mavis/venv/bin:/home/creisle/application
s/node-v10.1.0-linux-x64/bin:/home/creisle/.npm-packages/bin:/home/cre
isle/bin:/home/creisle/applications/centos06/python-3.6.1/bin:/project
s/tumour_char/analysis_scripts/bin/pog:/gsc/software/linux-x86_64-cent
os6/git-2.12.0/bin/:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr
/bin:/usr/local/sbin:/usr/sbin:/projects/trans_scratch/software/pipeli
ne_commands/:/home/creisle/bin,PBS_O_MAIL=/var/spool/mail/creisle,
PBS_O_SHELL=/bin/bash,PBS_O_LANG=en_US.UTF-8,
PBS_O_WORKDIR=/projects/trans_scratch/validations/workspace/creisle/t
emp/test_submission,PBS_O_HOST=torque01.bcgsc.ca,
PBS_O_SERVER=torque01.bcgsc.ca,
MANPATH=/home/creisle/.npm-packages/share/man:/home/creisle/applicati
ons/centos06/python-3.6.1/man:/usr/local/share/man:/usr/share/man/over
rides:/usr/share/man,XDG_SESSION_ID=1340,HOSTNAME=torque01.bcgsc.ca,
SHELL=/bin/bash,TERM=xterm-256color,HISTSIZE=1000,CLICOLOR=1,
SSH_CLIENT=10.9.202.242 35994 22,TMPDIR=/var/tmp/,
PYTHONUNBUFFERED=True,MAVIS_MIN_CLUSTERS_PER_FILE=2,
NODE_OPTIONS=--trace-warnings,SSH_TTY=/dev/pts/0,USER=creisle,
SVN_EDITOR=vim,LS_COLORS=di=34;01;47:mi=100;31;01:ln=36;01:ex=01;32,
MAVIS_SCHEDULER=TORQUE,VIRTUAL_ENV=/home/creisle/git/mavis/venv,
SACCT_FORMAT=jobid%-18\\,jobname%45\\,user%-8\\,reqmem\\,elapsed\\,state\\,
MaxRSS\\,AveRSS\\,Partition,
PATH=/home/creisle/git/mavis/venv/bin:/home/creisle/applications/node
-v10.1.0-linux-x64/bin:/home/creisle/.npm-packages/bin:/home/creisle/b
in:/home/creisle/applications/centos06/python-3.6.1/bin:/projects/tumo
ur_char/analysis_scripts/bin/pog:/gsc/software/linux-x86_64-centos6/gi
t-2.12.0/bin/:/usr/local/bin:/usr/local/sbin:/usr/local/bin:/usr/bin:/
usr/local/sbin:/usr/sbin:/projects/trans_scratch/software/pipeline_com
mands/:/home/creisle/bin,MAIL=/var/spool/mail/creisle,
_=/usr/local/bin/qsub,
PWD=/projects/trans_scratch/validations/workspace/creisle/temp/test_s
ubmission,XMODIFIERS=@im=none,LANG=en_US.UTF-8,
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles,
LOADEDMODULES=,
NODE_PATH=/home/creisle/.npm-packages/lib/node_modules,
SQUEUE_FORMAT=%.12i %9P %45j %.8u %.2t %.10M %.6D %.8m %.14l %.4c %.2
0R %E,HISTCONTROL=ignoredups,MAVIS_MAX_FILES=1,HOME=/home/creisle,
SHLVL=2,LOGNAME=creisle,
PYTHONPATH=/home/creisle/applications/centos06/python-3.6.1/bin:,
SSH_CONNECTION=10.9.202.242 35994 10.9.220.231 22,
ORIENTDB_HOME=/home/creisle/applications/orientdb/orientdb-community-
2.2.34,MODULESHOME=/usr/share/Modules,
LESSOPEN=||/usr/bin/lesspipe.sh %s,BROWSER=/usr/bin/google-chrome,
NPM_PACKAGES=/home/creisle/.npm-packages,
XDG_RUNTIME_DIR=/run/user/1365,
BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`\\
}
euser = creisle
egroup = users
queue_type = E
comment = Job 48[].torque01.bcgsc.ca deleted because its dependency of arr
ay 43[].torque01.bcgsc.ca can never be satisfied
etime = Tue May 29 18:27:33 2018
exit_status = 271
submit_args = -j oe -l mem=12000mb -l walltime=16:00:00 -V -W depend=after
okarray:43[].torque01.bcgsc.ca -N MA_mock-A47933_batch-JT3CUggKXNStHco
FXYaGR3 -o /projects/trans_scratch/validations/workspace/creisle/temp/
test_submission/output_torque/mock-A47933_diseased_transcriptome/annot
ate/batch-JT3CUggKXNStHcoFXYaGR3-/job---.log -t 1 /projects/trans_scra
tch/validations/workspace/creisle/temp/test_submission/output_torque/m
ock-A47933_diseased_transcriptome/annotate/submit.sh
job_array_id = 1
fault_tolerant = False
job_radix = 0
submit_host = torque01.bcgsc.ca
init_work_dir = /projects/trans_scratch/validations/workspace/creisle/temp
/test_submission
request_version = 1
"""
rows = _scheduler.TorqueScheduler().parse_qstat(content)
self.assertEqual(1, len(rows))
row = rows[0]
self.assertEqual('48[].torque01.bcgsc.ca', row['job_ident'])
self.assertIs(1, row['task_ident'])
def test_single_job(self, patcher):
sched = _scheduler.TorqueScheduler()
job = _job.Job(SUBCOMMAND.VALIDATE, '', job_ident='1234')
sched.cancel(job)
self.assertEqual(_constants.JOB_STATUS.CANCELLED, job.status)
patcher.assert_called_with(['qdel', '1234'])
def test_single_job_complete(self):
content = """
Job Id: 9.torque01.bcgsc.ca
Job_Name = subtest.sh
Job_Owner = [email protected]
resources_used.cput = 00:00:00
resources_used.vmem = 346716kb
resources_used.walltime = 00:01:00
resources_used.mem = 3624kb
resources_used.energy_used = 0
job_state = C
queue = batch
server = torque01.bcgsc.ca
Checkpoint = u
ctime = Tue May 29 09:37:00 2018
Error_Path = torque01.bcgsc.ca:/projects/trans_scratch/validations/workspa
ce/creisle/temp/subtest.sh.e9
exec_host = torque01.bcgsc.ca/0
Hold_Types = n
Join_Path = n
Keep_Files = n
Mail_Points = a
mtime = Tue May 29 09:38:01 2018
Output_Path = torque01.bcgsc.ca:/projects/trans_scratch/validations/worksp
ace/creisle/temp/subtest.sh.o9
Priority = 0
qtime = Tue May 29 09:37:00 2018
Rerunable = True
Resource_List.walltime = 01:00:00
Resource_List.nodes = 1
Resource_List.nodect = 1
session_id = 25438
Variable_List = PBS_O_QUEUE=batch,PBS_O_HOME=/home/creisle,
PBS_O_LOGNAME=creisle,
PBS_O_PATH=/home/creisle/applications/node-v10.1.0-linux-x64/bin:/hom
e/creisle/.npm-packages/bin:/home/creisle/bin:/home/creisle/applicatio
ns/centos06/python-3.6.1/bin:/projects/tumour_char/analysis_scripts/bi
n/pog:/gsc/software/linux-x86_64-centos6/git-2.12.0/bin/:/usr/local/bi
n:/usr/local/sbin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/p
rojects/trans_scratch/software/pipeline_commands/:/home/creisle/bin,
PBS_O_MAIL=/var/spool/mail/creisle,PBS_O_SHELL=/bin/bash,
PBS_O_LANG=en_US.UTF-8,
PBS_O_WORKDIR=/projects/trans_scratch/validations/workspace/creisle/t
emp,PBS_O_HOST=torque01.bcgsc.ca,PBS_O_SERVER=torque01.bcgsc.ca
euser = creisle
egroup = users
queue_type = E
comment = Job started on Tue May 29 at 09:37
etime = Tue May 29 09:37:00 2018
exit_status = 0
submit_args = subtest.sh
start_time = Tue May 29 09:37:01 2018
start_count = 1
fault_tolerant = False
comp_time = Tue May 29 09:38:01 2018
job_radix = 0
total_runtime = 60.481239
submit_host = torque01.bcgsc.ca
init_work_dir = /projects/trans_scratch/validations/workspace/creisle/temp
request_version = 1
"""
rows = _scheduler.TorqueScheduler().parse_qstat(content)
self.assertEqual(1, len(rows))
row = rows[0]
self.assertEqual(_constants.JOB_STATUS.COMPLETED, row['status'])
self.assertEqual('9.torque01.bcgsc.ca', row['job_ident'])
self.assertEqual('subtest.sh', row['name'])
self.assertIs(None, row['task_ident'])
self.assertEqual('', row['status_comment'])