def main():
parser = getBasicOptionParser()
parser.add_argument(
"jobStore",
type=str,
help=(
"Store in which to place job management files \
and the global accessed temporary files"
"(If this is a file path this needs to be globally accessible "
"by all machines running jobs).\n"
"If the store already exists and restart is false an"
" ExistingJobStoreException exception will be thrown."
),
)
parser.add_argument("--version", action="version", version=version)
options = parseBasicOptions(parser)
jobStore = Toil.loadOrCreateJobStore(options.jobStore)
logger.info("Starting routine to kill running jobs in the toil workflow: %s" % options.jobStore)
####This behaviour is now broken
batchSystem = Toil.createBatchSystem(
jobStore.config
) # This should automatically kill the existing jobs.. so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(): # Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
def main():
parser = getBasicOptionParser()
parser.add_argument(
"jobStore",
type=str,
help=("Store in which to place job management files \
and the global accessed temporary files"
"(If this is a file path this needs to be globally accessible "
"by all machines running jobs).\n"
"If the store already exists and restart is false an"
" JobStoreCreationException exception will be thrown."))
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
jobStore = Toil.loadOrCreateJobStore(options.jobStore)
logger.info(
"Starting routine to kill running jobs in the toil workflow: %s" %
options.jobStore)
####This behaviour is now broken
batchSystem = Toil.createBatchSystem(
jobStore.config
) #This should automatically kill the existing jobs.. so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(
): #Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
def main():
parser = parser_with_common_options()
options = parser.parse_args()
set_logging_from_options(options)
config = Config()
config.setOptions(options)
config.jobStore = config.jobStore[5:] if config.jobStore.startswith('file:') else config.jobStore
# ':' means an aws/google jobstore; use the old (broken?) method
if ':' in config.jobStore:
jobStore = Toil.resumeJobStore(config.jobStore)
logger.info("Starting routine to kill running jobs in the toil workflow: %s", config.jobStore)
# TODO: This behaviour is now broken: https://github.com/DataBiosphere/toil/commit/a3d65fc8925712221e4cda116d1825d4a1e963a1
batchSystem = Toil.createBatchSystem(jobStore.config) # Should automatically kill existing jobs, so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(): # Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
# otherwise, kill the pid recorded in the jobstore
else:
pid_log = os.path.join(os.path.abspath(config.jobStore), 'pid.log')
with open(pid_log, 'r') as f:
pid2kill = f.read().strip()
try:
os.kill(int(pid2kill), signal.SIGKILL)
logger.info("Toil process %s successfully terminated." % str(pid2kill))
except OSError:
logger.error("Toil process %s could not be terminated." % str(pid2kill))
raise
def main():
parser = getBasicOptionParser()
parser.add_argument(
"jobStore",
type=str,
help=
"The location of the job store used by the workflow whose jobs should "
"be killed." + jobStoreLocatorHelp)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
jobStore = Toil.resumeJobStore(options.jobStore)
logger.info(
"Starting routine to kill running jobs in the toil workflow: %s" %
options.jobStore)
####This behaviour is now broken
batchSystem = Toil.createBatchSystem(
jobStore.config
) #This should automatically kill the existing jobs.. so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(
): #Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
def main():
parser = getBasicOptionParser()
parser.add_argument("jobStore", type=str,
help="The location of the job store used by the workflow whose jobs should "
"be killed." + jobStoreLocatorHelp)
parser.add_argument("--version", action='version', version=version)
options = parseBasicOptions(parser)
jobStore = Toil.resumeJobStore(options.jobStore)
logger.info("Starting routine to kill running jobs in the toil workflow: %s" % options.jobStore)
####This behaviour is now broken
batchSystem = Toil.createBatchSystem(jobStore.config) #This should automatically kill the existing jobs.. so we're good.
for jobID in batchSystem.getIssuedBatchJobIDs(): #Just in case we do it again.
batchSystem.killBatchJobs(jobID)
logger.info("All jobs SHOULD have been killed")
def main() -> None:
parser = parser_with_common_options()
options = parser.parse_args()
set_logging_from_options(options)
config = Config()
config.setOptions(options)
job_store_type, _ = Toil.parseLocator(config.jobStore)
if job_store_type != 'file':
# Remote (aws/google) jobstore; use the old (broken?) method
job_store = Toil.resumeJobStore(config.jobStore)
logger.info("Starting routine to kill running jobs in the toil workflow: %s", config.jobStore)
# TODO: This behaviour is now broken: https://github.com/DataBiosphere/toil/commit/a3d65fc8925712221e4cda116d1825d4a1e963a1
# There's no guarantee that the batch system in use can enumerate
# running jobs belonging to the job store we've attached to. And
# moreover we don't even bother trying to kill the leader at its
# recorded PID, even if it is a local process.
batch_system = Toil.createBatchSystem(job_store.config) # Should automatically kill existing jobs, so we're good.
for job_id in batch_system.getIssuedBatchJobIDs(): # Just in case we do it again.
batch_system.killBatchJobs([job_id])
logger.info("All jobs SHOULD have been killed")
else:
# otherwise, kill the pid recorded in the jobstore.
# TODO: We assume thnis is a local PID.
job_store = Toil.resumeJobStore(config.jobStore)
assert isinstance(job_store, FileJobStore), "Need a FileJobStore which has a sharedFilesDir"
pid_log = os.path.join(job_store.sharedFilesDir, 'pid.log')
with open(pid_log) as f:
pid_to_kill = f.read().strip()
try:
os.kill(int(pid_to_kill), signal.SIGTERM)
logger.info("Toil process %s successfully terminated." % str(pid_to_kill))
except OSError:
logger.error("Toil process %s could not be terminated." % str(pid_to_kill))
raise
