[Bioclusters] [Fwd: [Mpihmmer] Announcing GPU-HMMER]

Joe Landman landman at scalableinformatics.com
Sat Dec 13 22:05:19 EST 2008

-------- Original Message --------
Subject: [Mpihmmer] Announcing GPU-HMMER
Date: Sat, 13 Dec 2008 21:50:55 -0500
From: John Paul Walters <waltersj at buffalo.edu>
To: mpihmmer at mpihmmer.org

Hi Folks,

We'd like to announce the availability of GPU-HMMER, a port of HMMER's
hmmsearch utility to NVIDIA CUDA-enabled GPUs.  Anyone who is interested
is invited to visit www.mpihmmer.org to get the source.  A brief user's
guide and installation guide are provided at mpihmmer.org as well.  This
version has been tested on 8800 GTX Ultra and Tesla C1060 GPUs, though
we expect that the code should work on a wider range of GPUs than has
been tested.

The current source code supports a single GPU with speedups that range
from 20x-38x, depending on the size of the HMM.  In the coming weeks we
plan to release support for multiple GPUs within a single node.  Current
tests demonstrate speedups that exceed 100x using 3 Tesla GPUs, also
depending on the size of the HMM.  Thereafter we plan to integrate GPU
support directly into MPI-HMMER to support multiple GPUs via MPI.

As always we welcome any feedback or bug reports.  We are especially
interested in compatibility reports and will post compatibility updates
to www.mpihmmer.org as necessary.

best regards,
JP Walters

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

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