[Beowulf] updated GPU-HMMer/mpiHMMer bits

Joe Landman landman at scalableinformatics.com
Mon Feb 9 00:11:42 EST 2009


This time compared to a loaner AMD shanghai 2.3 GHz (same one I did the 
rzf tests on a few weeks ago).

 From the mpihmmer mailing list:

---
A new release of GPU-HMMER is available at www.mpihmmer.org.  The most
notable change in the new code is support for multi-GPU systems.  We
have tested the current GPU-HMMER with up to 3 GPUs, and have achieved
over 100x speedup with sufficiently large HMMs.  A few bug fixes have
been applied as well, so I would encourage users to update.  Users who
update should be aware that several command line options have changed,
and should check the GPU-HMMER user guide for details
(http://www.mpihmmer.org/userguideGPUHMMER.htm).

While the system requirements haven't changed from the last version,
users who intend to use multiple GPUs should be aware that they will
need a substantial amount of system memory in order to do so.  The 3 GPU
system I've been using has 16GB RAM.  This is probably a bit overkill,
but 8GB or so would probably be appropriate.

As always, any comments, bug reports, etc. are welcome.

best regards,
JP Walters

---

Updated mpiHMMer results were shown at SC08, the graph I saw showed 
maxing out about 180x over a single thread, though I think the parallel 
IO version can scale higher still.

Cudos to JP and the team for doing a great job on this!

-- 
Joseph Landman, Ph.D
Founder and CEO
Scalable Informatics LLC,
email: landman at scalableinformatics.com
web  : http://www.scalableinformatics.com
        http://jackrabbit.scalableinformatics.com
phone: +1 734 786 8423 x121
fax  : +1 866 888 3112
cell : +1 734 612 4615
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