[Beowulf] RE: OT: Announcing MPI-HMMER

David Mathog mathog at caltech.edu
Thu Jan 4 08:54:44 PST 2007

> There's also my PVM version of 2.3.2 from 2003/2004

I ought to clarify that slightly.  Sean Eddy's original code had
a PVM mode.  My variant retained the original but defaults to
a new "database sliced" mode - where each query
runs on every node against a fraction of the database.  (Similar to
what Joe's MPI-BLAST and my PVM parallel BLAST do.)  To support that
hmmfetch was also modified to work over PVM, which wasn't required in
SE's original since the master node always had a complete database,
so there was no need to fetch entries back from the database slices
on the compute nodes.

Now back to your regularly scheduled topics...


David Mathog
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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