[Beowulf] RE: [Bioclusters] FPGAin bioinformatics clusters (again?)

Lukasz Salwinski lukasz at mbi.ucla.edu
Mon Jan 16 09:05:47 PST 2006

Michael Will wrote:
> I have always been amazed at the promises of massivelyparallel. Now
> their
> technique is so good they don't even need the source code to
> parallelize?
> ...but if I tell you how I would have to kill you...
> Michael Will 

uh.. just a quick comment on bioinformatics and parallelizing things...

please note, that most of the bioinformatic problems are already
embarrassingly parallel and, with the new genomes showing up at an 
amazing rate, getting more and more so. Thus, in most cases, it just
doesn't make much sense to parallelize anything - if one's got to
run 300x4000 blasts against a library of 300x4000 sequences (ie 300
genomes, 4000 genes/proteins, all vs all) the simplest solution -
a lot of nodes, blast optimized for a single cpu and a decent queing
system will ultimately win (as long as one stays within the same
architecture; FPGAs are a diferent story ;o)


  Lukasz Salwinski                             PHONE:        310-825-1402
  UCLA-DOE Institute for Genomics & Proteomics   FAX:        310-206-3914
  UCLA, Los Angeles                            EMAIL: lukasz at mbi.ucla.edu

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