Added code to support Singularity on HiperGator #389
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manthey
reviewed
Jan 10, 2024
| logger.info(f'Job {jobid} was cancelled by user.') | ||
| return JOB_STATUS.CANCELLED | ||
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| time.sleep(5) # Sleep to avoid busy waiting |
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I think it'd be better to call s.wait(5) and catch ExitTimeoutException.
manthey
reviewed
Jan 10, 2024
| bind_paths[temporary_directory] = '/output' | ||
| super().__call__(*args,**kwargs) | ||
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| qos = kwargs.pop('qos', 'pinaki.sarder') |
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I'd recommend having these from environment variables. And, rather than construct the slurm script ourselves, we could use the simple_slurm package to do it (it does the same thing, but has been validated by others and escapes command line parameters appropriately).
manthey
reviewed
Jan 10, 2024
| bind_option = ','.join([f"{host}:{container}" for host, container in bind_paths.items()]) | ||
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| # Construct the Singularity command | ||
| singularity_command = f'singularity exec --bind {bind_option} docker://{image} {" ".join(container_args)}' |
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The join is unsafe -- if the container args contain spaces or quotes or shell characters, odd things will happen.
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