[Bioclusters] how can I know jobs over ?

chris dagdigian bioclusters@bioinformatics.org
Mon, 25 Nov 2002 10:01:50 -0500


I don't use PBS myself but had ocasion to install PBSPro for someone
recently. From reading the manual I remember that PBS supports 'job
dependencies' just like LSF and SGE does -- a feature that neatly solves
your problem.

Read the documentation in order to get the exact syntax needed for the
qsub program. The basic idea is that you can submit your merge job to
the system with a resource requirement that states 'do not run me until
jobs A, B and C have successfully run to completion without error'. If
you do this correctly your merge job will remain pending while the other
jobs run.

A quick google search turned up this NASA tutorial page:
http://www.nas.nasa.gov/Groups/SciCon/Tutorials/usingpbs/dependency1.html

This is from that page:

> Job 3 should start after jobs 1 and 2 have ended:
> 
> qsub script1
> 0001.vn
> qsub script2
> 0002.vn
> qsub -W depend=afterany:0001:0002 script3
> 0003.vn
> 





zzar wrote:
> I using openPBS.
>  
> I want make many output file merge script ,after all job is over..
>  
> ex)
>  ------------------------------
>   #!/bin/sh
>  qsub test.one.job
>  qsub test.two.job
>  qsub test.three.job
>  
>  
> XXXXX if < all job over > XXXXXX
>  
>  cat test.one.job >> all.job
>  cat test.two.job >>  all.job
>  cat test.three.job >> all.job
>  --------------------------
>  
>  output : test.one.job.o1 (2.3)
>  
>  
> how can I know all job over ?
>  
> and I read qsub man page , -bb or -be option   but error message => 
> qsub: invalid option -- b
>  
>  
> thank you !
>  
> --



-- 
Chris Dagdigian, <dag@sonsorol.org>
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