[Bioclusters] Grid BLAST

Yannick Gingras ygingras at ygingras.net
Fri Sep 23 23:53:02 EDT 2005

Hi, I'm the administrator the bioinformatics laboratory at Université
du Québec à Montréal.  I have a room filled with dual P4 3GHz
workstations.  The boxen are dual booted with Windows and GNU/Linux but
they spend most of their time on GNU/Linux.  Each box have 2Gb of RAM
so I expected decent performance with local BLAST jobs but the sad
truth is that my jobs are run about 4 times slower with blast2 than
with blastcl3 with the same parameters.  The hard drive is IDE so I
suspect a bottle neck here.  Strangely if I set the number of threads
to 2 or 3 with -a my jobs run slower.

Do you think there is a way to like those machines together in order
to get better performance ?  I think that I can't use something like
mpiBlast because there is always a risk that a node be rebooted
under windows making a part of the database suddenly unavailable.

Yannick Gingras

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