[Bioclusters] [Fwd: [Mpihmmer] new release of GPU-HMMER]

Joe Landman landman at scalableinformatics.com
Sun Feb 8 20:36:03 EST 2009

Forwarded for those in need of accelerated HMMer.

-------- Original Message --------
Subject: [Mpihmmer] new release of GPU-HMMER
Date: Sun, 08 Feb 2009 20:32:27 -0500
From: John Paul Walters <waltersj at buffalo.edu>
To: mpihmmer at mpihmmer.org

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

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

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