[Bioclusters] Apple Altivec enhanced version of HMMER-2.2g is available (and very fast)

chris dagdigian bioclusters@bioinformatics.org
Wed, 06 Nov 2002 08:33:20 -0600

Hi everyone,

Bill Van Etten at BioTeam Inc. has added support for Apple's 'Altivec'
vector coprocessor to HMMER2.2 as one several side projects we have
going on behind the scenes. Our version was not quite ready for prime
time and we've just learned from Erik Lindahl at Stanford that he has a
Altivec-HMMER2.2g version that is ready to go.  Bittersweet news for us,
but excellent news for the community.

Early benchmarking looks impressive -- Erik has seen HMMER run 8x faster
on his Apple TiBook than some Athalon CPUs and predicts that the code
will be even faster on a dual-CPU Apple since the package is multithreaded.

BioTeam is running the code on other Apple hardware including the new
Xserve boxes. We've also taken Erik's source distribution and packaged
it up as a traditional "click and install" binary MacOS X installer 
package. We'll post the results of our benchmark results.

Both are available now for people who want to try this code for themselves:

(1) Source code for Erik's Altivec-enchanced HMMER

(2) Binary MacOS X Package installer for Altivec-enhanced HMMER

Sean Eddy has been given the code but we are not sure when/if it will be 
accepted into the actual HMMER codebase.


Chris Dagdigian, <dag@sonsorol.org>
Independent life science IT & informatics consulting
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
PGP KeyID: 83D4310E Yahoo IM: craffi Web: http://bioteam.net