[Bioclusters] GCG Winsconsin Package and GridEngine

[Ron Chen]

--- Rick Westerman <westerman@purdue.edu> wrote:
> 
> >Does anyone have any experience of distributing GCG
> applications (e.g.
> >pileup and srsupdate) using Sun's GridEngine? 
> After a trawl through the web
> >it seems that some GCG applications FrameSearch,
> BLAST, FASTA, FASTAX,
> >FASTX, TFASTA, TFASTX and SSearch) are threaded and
> can take advantage of a
> >multi-processor architecture.  I am more interested
> in distributing
> >cpu-intensive jobs like pileup and srsupdate that
> are not threaded.  For
> >pileup I suppose the way to go is to split up the
> input file and kick off a
> >number of jobs on different servers using
> GridEnginec - does anyone have any
> >comments?  As for srsupdate, I'm not sure how to
> procede, but its pig slow
> >and I am sure there must be a way to speed it up
> with distribution.
> 
>     No experience.  And I am not sure if many other
> people have gone down 
> this path because I suspect that your GCG license
> does not allow running on 
> more than 'X' number of boxes -- 'X' being the
> number of RTR (right to run) 
> licenses you have purchased.   Yet another reason to
> migrate to Emboss, et.al.

I also don't have any experience with pileup or
srsupdate, but what is the exact problem you want to
solve?

If you only have X number of licenses, you can
set up a requestable resource, then SGE will make sure
it starts less then or equal to X jobs that request
the license. This way you can have your license used
up
7x24 (as long as you have jobs queued up waiting for
the license).

-Ron

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