[torqueusers] Interacting with Torque/Maui from Perl scripts

William Nelson bnelson at arabidopsis.org
Wed Aug 17 09:35:53 MDT 2011

Hi Anthony,
I don't have a specific answer to your question but I can point you to some
example code. InterProScan (http://www.ebi.ac.uk/Tools/pfa/iprscan/) is a
PERL project that integrates with PBS, LSF, or SGE. We use it with Torque by
making small modifications to the PBS conf files. It runs several analysis
tool in parallel on the cluster and then merges the results.

On Wed, Aug 17, 2011 at 1:33 AM, Anthony Ferrari <ferraria at gmail.com> wrote:

> Hi all,
> Basically, I would like to launch a job on a cluster with specific
> resources and dependencies, wait for the job to complete or fail, check that
> all has gone OK, then do something with the generated files ...
> To launch jobs, I am using a customized version of PBS-Client-0.09 package
> written by Ka-Wai Mak.
> I also saw that packages named PBS-0.03 by Todd Merritt and perl-PBS by
> Garrick Staples exist but they do not seem maintained or seem outdated
> (please correct me if I am wrong).
> What do you personally use ?
> My problem here is more after the job submission, to keep 'control' of the
> job.
> Because with the PBS-Client module, once the job is submitted, Torque does
> what it has to do and that's it. It does not give any information in return
> to my Perl script.
> I was thinking about several solutions to achieve this but I do not find
> them very smart ... like :
>  - using qstat | grep '^myjobid' in a while loop (with open3 perl function)
>  - waiting for the output & error files to be written where I expect them
> (hum...)
>  - use an epilogue script in the job to do something useful...
> But there may exist brighter answers to this question. Perhaps with some
> modules I don't know about.
> Do you have any advice ?
> And actually this is to know when the job has finished but how do you check
> that the job completed and did not crash ?
> Do you always parse the created logs ?
> Is there a way to propagate the exit code of the program launched with qsub
> to the perl script running on the master node ?
> Thank you very much.
> Cheers,
> Anthony
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> torqueusers at supercluster.org
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Bill Nelson
Bioinformatics Developer
Carnegie Institution of Washington
Dept. of Plant Biology
260, Panama
Stanford, CA 94305

Cell: (650) 720-5708
Phone: Phone: (650) 739-4343
Fax: (650) 325-6857
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