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

[Elia Stupka]

> 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.

Any idea what the speed up is for hmmpfam (which is actually what we are
interested in)?

Elia

> > 

> > 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
> 
> 
> 

Elia

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