[Bioclusters] GCG Winsconsin Package and GridEngine

Andrew Hynes bioclusters@bioinformatics.org
Thu, 9 May 2002 11:24:00 +0100


Hi All,

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.

Thanks,

Andrew

Andrew M Hynes PhD
Bioinformatician
Software Engineering
Oxford GlycoSciences
The Forum
86 Milton Park
Abingdon
Oxon OX14 4RY
01235 208065


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