[Bioclusters] mpiBLAST

[Lapointe, David]

I am still trying to figure out the numerology behind mpiblast. I
haven't applied the patches to mpiformatdb yet.

16 nodes dual cpu 2.4G XEON
1 node dual cpu 2.4G XEON

That makes 34 cpus total.

So is the N the number of cpu's ( minus 1 or 2) in the mpiformatdb
command or the number of dual nodes? Jeremy seemed to do well with the
number of cpus, but I'm not getting results that way.

On the other hand, using 30 as N for mpiformatdb (31 sections of nr) and
mpirun -np 16 mpiblast -p blastp -d nr -a 2 -i in.file -o out.file

gives me about 4-5 sec per query, using the -a 2 (use 2 cpus) flag.


Also I am curious about Eric Engelhard's statement last year (
Mar01,2002) "but my
work cluster (18 nodes 2GB RAM/node) cuts through >1500 queries/minute
against nr."  That's 40 msec per query. He didn't indicate running
special hardware. If that is true how is that achieved?  It's >100 times
what people ( Jeremy, John) have been reporting recently.

David
--------
David Lapointe
Information Services
UMass Medical School
Worcester MA 01655