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Kill all grid engine jobs on shutdown #5083

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merged 1 commit into from
Sep 16, 2024
Merged

Kill all grid engine jobs on shutdown #5083

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9 changes: 8 additions & 1 deletion src/toil/batchSystems/abstractGridEngineBatchSystem.py
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Original file line number Diff line number Diff line change
Expand Up @@ -256,6 +256,8 @@ def _runStep(self):
newJob = self.newJobsQueue.get()
if newJob is None:
logger.debug('Received queue sentinel.')
# Send out kill signals before stopping
self.killJobs()
return False
if self.killJobs():
activity = True
Expand Down Expand Up @@ -413,7 +415,7 @@ def issueBatchJob(self, command: str, jobDesc, job_environment: Optional[Dict[st
gpus = accelerator['count']
else:
gpus = jobDesc.accelerators

self.newJobsQueue.put((jobID, jobDesc.cores, jobDesc.memory, command, get_job_kind(jobDesc.get_names()),
job_environment, gpus))
logger.debug("Issued the job command: %s with job id: %s and job name %s", command, str(jobID),
Expand Down Expand Up @@ -496,6 +498,11 @@ def shutdown(self) -> None:
"""
Signals thread to shutdown (via sentinel) then cleanly joins the thread
"""

for jobID in self.getIssuedBatchJobIDs():
# Send kill signals to any jobs that might be running
self.killQueue.put(jobID)

self.shutdownLocal()
newJobsQueue = self.newJobsQueue
self.newJobsQueue = None
Expand Down
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