Don't want to start a processor war but the current Intel chip is a 3.06GHz Pentium 4 not a 1GHz Pentium 3. IMHO, benchmark results should match current hardware or don't make them at all. -----Original Message----- From: chris dagdigian [mailto:dag@sonsorol.org]=20 Sent: Wednesday, December 11, 2002 10:56 AM To: bioclusters@bioinformatics.org; biodevelopers@bioinformatics.org Subject: [Bioclusters] altivec-HMMER bechmark results from Erik Lindahl - 6x faster than dual Athlon Some nice data from Erik Lindahl at Stanford regarding the new apple=20 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! >=20 > 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. >=20 > 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 >=20 > http://csb.stanford.edu/lindahl/altivec/ >=20 > 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.=20 Interested parties should email me directly if they want the package=20 version of these binaries. -Chris --=20 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