[GE users] job dependency question

Rayson Ho rayrayson at gmail.com
Wed Oct 8 03:38:29 BST 2008


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Basically, you submit the first job, and qsub will return its job id.
You then pass first job's job id to -hold_jid when you submit the 2nd
job.

A more advanced way is to use job names, by using -N.

Anyway, play with a few dummy jobs and you will get the concept.

Rayson



On 10/7/08, Mag Gam <magawake at gmail.com> wrote:
> Thanks for the quick reponse.
>
> I believe I have tried this too, but I am still confused with the job
> name and job id.
>
> I looked at https://lists.sdsc.edu/pipermail/npaci-rocks-discussion/2007-June/025538.html,
>  and http://gridengine.sunsource.net/servlets/ReadMsg?list=users&msgNo=447
>
> Do I need another script to check for jobs? Sorry for such a newbie question
>
>
> TIA
>
>
>
> On Tue, Oct 7, 2008 at 10:25 PM, Rayson Ho <rayrayson at gmail.com> wrote:
> > The link in your email is for job arrays.
> >
> > You should read the qsub manpage instead, and look up the "hold_jid"
> > option. If you google "qsub" and "hold_jid", the results should at
> > least include a few examples.
> >
> > Rayson
> >
> >
> >
> > On 10/7/08, Mag Gam <magawake at gmail.com> wrote:
> >> I have been reading many SGE job dependency pages online (such as
> >> http://open.rsp.com.au/?page_id=11) but I am still not able to do the
> >> task I wanted to do. Or perhaps I may be looking at the wrong thing.
> >> Here is what I am looking for:
> >>
> >> I have 2 commands. Command A and Command B. Command A needs to run
> >> first and then execute Command B once Command A is completed. In other
> >> words Command B depends on Command A.
> >>
> >> commandA.sh
> >>
> >> #!/bin/bash
> >> #$ -o output
> >> #$ -S /bin/bash
> >> #$ -S -V
> >> tar -cvf file.tar /large_directory
> >>
> >>
> >> CommandB.sh
> >> #!/bin/bash
> >> #$ -o output
> >> #$ -S /bin/bash
> >> #$ -S -V
> >> gzip file.tar
> >>
> >>
> >> Basically, I want to submit both of the jobs to our GRID but with
> >> commandB running after CommandA
> >>
> >> TIA
> >>
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> >>
> >
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