[Bioclusters] GCG Winsconsin Package and GridEngine

Rick Westerman bioclusters@bioinformatics.org
Thu, 09 May 2002 08:33:43 -0500

>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.

-- Rick

Rick Westerman

Phone: (765) 494-0505                         FAX: (765) 496-7255
S049 WSLR bldg. Purdue Univ. W. Lafayette, IN 47907-1153

Bioinformatics specialist at the Genomics Initiative.