[Biodevelopers] altivec-HMMER bechmark results from Erik Lindahl - 6x faster than dual Athlon

[chris dagdigian]

Some nice data from Erik Lindahl at Stanford regarding the new apple 
altivec enhancements that were added to the hmmer codebase:

> Hmmsearch on the dual-1.25 GHz G4 is 6.2 times faster than on a dual Athlon!
> 
> Hmmpfam is less impressive, mainly because it spends less time in the
> core routines, but as far as I know hmmsearch is the most important program anyway.
> 
> Sean Eddy has also confirmed that he will be including this altivec
> optimization in the next official version of HMMer, whenever that is released. In the
> meantime I've put my optimized version at
> 
> http://csb.stanford.edu/lindahl/altivec/
> 
> Since it is licensed under the GPL anybody can use and distribute it.

Benchmark data from Erik is enclosed in PDF form.

BioTeam has built a double-clickable Mac OS X package installer for this 
code but I've been a slacker and have yet to put it on our website. 
Interested parties should email me directly if they want the package 
version of these binaries.

-Chris


-- 
Chris Dagdigian, <dag at sonsorol.org>
Independent life science IT & informatics consulting
Office: 617-666-6454, Mobile: 617-877-5498, Fax: 425-699-0193
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