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fix: logfile quoting and scancel error handling #140

Merged
merged 6 commits into from
Sep 7, 2024
Merged

fix: logfile quoting and scancel error handling #140

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ceec90f
fix: quote sbatch logfile in order to avoid problems with whitespaces…
johanneskoester Aug 27, 2024
a0cccb4
capture errors in scancel
johanneskoester Aug 27, 2024
d48c726
superfluous decode
johanneskoester Aug 29, 2024
1ede6fa
Update __init__.py
johanneskoester Aug 30, 2024
6f0e3e1
Update snakemake_executor_plugin_slurm/__init__.py
cmeesters Sep 1, 2024
fc7973d
Merge branch 'main' into fix/logfile-quoting
johanneskoester Sep 7, 2024
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10 changes: 9 additions & 1 deletion snakemake_executor_plugin_slurm/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -137,7 +137,7 @@ def run_job(self, job: JobExecutorInterface):
f"sbatch "
f"--parsable "
f"--job-name {self.run_uuid} "
f"--output {slurm_logfile} "
f"--output '{slurm_logfile}' "
f"--export=ALL "
f"--comment {comment_str}"
)
Expand Down Expand Up @@ -408,6 +408,14 @@ def cancel_jobs(self, active_jobs: List[SubmittedJobInfo]):
)
except subprocess.TimeoutExpired:
self.logger.warning("Unable to cancel jobs within a minute.")
except subprocess.CalledProcessError as e:
msg = e.stderr.strip()
if msg:
msg = f": {msg}"
raise WorkflowError(
"Unable to cancel jobs with scancel "
f"(exit code {e.returncode}){msg}"
) from e

async def job_stati(self, command):
"""Obtain SLURM job status of all submitted jobs with sacct
Expand Down
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