[gridengine users] submitting a job that submits jobs
robert.hutton at well.ox.ac.uk
Thu Feb 2 18:01:04 UTC 2012
On 02/02/12 15:50, Reuti wrote:
> Can you put the workflow in a loop at submission time? In each loop iteration you do:
> JOB_ID=$(qsub -terse command1)
> This will give you the JOB_ID of the submitted job.
> Then submit the next steps like:
> qsub -hold_jid $JOB_ID command2
> qsub -hold_jid $JOB_ID command3
> They will only start, after command1 finished.
On 02/02/12 16:04, William Hay wrote:
> I don't know about better but a more conventional way would be to have
> the front end script submit three jobs per file. One regular and two
> using -hold_jid on the first job.
> To get fancier with it you could have your initial submit script
> generate a list of files and the intended name of the corresponding
> derived file. Then submit three suitably sized array jobs using
> -hold_jid_ad for the second one. Each would then use its $SGE_TASK_ID to
> pick the right file to work on from your list.
Great, thanks guys, this is exactly the kind of sage advice I was
looking for, you've saved me barking up the wrong tree! :)
Senior Systems and Database Administrator
Centre for Genomics and Global Health <http://cggh.org>
The Wellcome Trust Centre for Human Genetics
Tel: +44 (0)1865 287721
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