MPI/PVM for BLAST and FASTA

Robert B Heckendorn heckendo at cs.uidaho.edu
Sun Apr 14 13:05:39 EDT 2002


Bill Pearson's paragraph introduces so many great questions that
maybe Bill or others can answer.

> The advantage of an ES40 or other large shared memory machine for
> BLAST is that it has been optimized for searching databases that are
> large memory mapped files, and it runs multithreaded.  PVM and MPI
> versions of BLAST are not available but, it is important to remember
> that BLAST is extremely fast, and highly optimized to go through a
> large amount of memory very quickly; it would be difficult to provide
> an equally efficient distributed version - but, of course, a
> distributed memory machine would be much cheaper.

I think I could learn a lot by listening to the details of why this
is not done.  So here goes:

Why is it that BLAST is not available for MPI/PVM?  I would think
clusters would be the prefect host for such an application.
Is it there is no need because BLAST is already so fast and
no one wants to break the database out onto node-resident disks?
Or is it that BLAST is kept running on single processor or shared memory 
machines BLAST so that the DB is always in memory ready to roll without
loading and doing the same for a cluster is not worth it
because the same trick is difficult to do on a node given the current
way clusters are built?  I assume the same is true for FASTA?

thanks for the clarification,

-- 
| Robert Heckendorn                        | We may not be the only
| heckendo at cs.uidaho.edu                   | species on the planet but
| http://www.cs.uidaho.edu/~heckendo       | we sure do act like it.
| CS Dept, University of Idaho             |
| Moscow, Idaho, USA   83844-1010          |
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