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Add --parsable option #156

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gdevenyi opened this issue Apr 26, 2018 · 5 comments
Open

Add --parsable option #156

gdevenyi opened this issue Apr 26, 2018 · 5 comments
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@gdevenyi
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qbatch needs an option where it only returns the jobids of jobs submitted.

This would allow qbatch to be used in other pipelines that may want to monitor job IDs themselves rather than using the cluster's proper dependency tracking (see ANTs pipelines...)

@gdevenyi
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Best way to implement is a combination of proper options to the submission and parsing the outputs so that the qbatch outputs are always consistent.

In addition, parsing the outputs is important for eventual python module qbatch.

@gdevenyi
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Related to #163

@gdevenyi
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SLURM will report back:

JOBID:CLUSTERNAME

With option sbatch --parsable

@gdevenyi
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SGE uses qsub -terse to report only job IDs

@gdevenyi
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PBS isn't documented very well, but it looks like it just returns Job ids by default:
http://www.arc.ox.ac.uk/content/torque-job-scheduler#PBScondExecution

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