Massively Parallel Applications in Sequence Analysis

Anne Juelich anne at chpc.utexas.edu
Mon Mar 29 17:50:30 EST 1993

In article <C4novr.Knt at murdoch.acc.Virginia.EDU>, wrp at cyclops.micr.Virginia.EDU (Bill Pearson) writes:
|> [ ... ]
|> 	I should note also, since some readers of this group may be
|> interested, that I now have a version of our parallel "platform" for
|> sequence comparison ( Despande, Richards, and Pearson (1991) CABIOS "A
|> platform for biological sequence comparison on parallel computers"
|> 7:237-247) running on networks of workstations using PVM (parallel
|> virtual machine), a freely available package for almost any machine.
|> If you are doing lots of sequence comparisons, I can provide you with 
|> PVM versions for FASTA and Smith-Waterman, with BLAST to be available 
|> in about a month.
|> [ ...]

At The University of Texas System Center for High Performance Computing, 
we have developed a PVM based version of BLAST running as part of GenTools(TM).

GenTools is a distributed genomic tool suite designed to provide
the experimental molecular biologist and/or geneticist transparent
access to computational tools on high performance platforms. (To
obtain more information about GenTools, please send E-mail to
gentools at chpc.utexas.edu.)

For example, blastp, comparing a 799 residues query sequence
versus PIR, release 32 (40.298 sequences) ran on a net of up to 
8 SPARC 2 workstations (times are elapsed times in seconds):

# processors            time
      1                 194.6
      2                 100.1
      4                  53.2
      6                  38.1
      8                  29.6

These timings were obtained with blastp, version 1.2.5 and PVM,
version 2.4.2. We are now using PVM, version 3.0, but I haven't redone
the timings yet.

Anne Juelich

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