[Bioclusters] SSE2 HMMer

[Benjamin Horsman]

Any chance we can see the source for your A/G BLAST port?

Ben

On Wed, 2003-06-25 at 15:07, David Huen wrote:
> I did quite a bit of work of this in January.  I got a modest speedup but
> nothing like the performance of the Apple version.  The reasons for this I
> posted to this group earlier this year:-
> http://bioinformatics.org/pipermail/biodevelopers/2003-January/000150.html
> 
> Anyway, I have put my sources up for download from here:-
> http://gadfly.gen.cam.ac.uk/~davidh/hmmer-2.2g-cache.tgz
> I hope this is the right version as i proliferated versions during
> development :-).
> 
> Compile with the Intel compiler, not gcc.  The versions I have tried
> seriously mangle SSE2 intrinsics and generate the weirdest code around
> them (like elaborate register swaps with no conceivable purpose).
> 
> There are multiple versions of the key file as I was messing around with
> trying to speed it up.  I think the G4/G5 is clearly the best HMMer
> platform around (excepting FPGA implementations of course).
> 
> As for the Apple-Genentech Blast speedup - it is bunkum.  The improvements
> are solely from a superior algorithm and I did port their version over to
> x86 and it shows the same speedups too.  I am very disappointed that
> they have repeated these claims for the G5 as I had spoken to one of their
> bioinformatics support team about it early this year.  He adamantly denied
> that there was anything in their claim that remotely implied it was down
> to their hardware and that they had provided the algorithmic improvements
> back to the community.  I left it as that.  I regret it will force me to
> go back and repeat all those measurements and this time document it
> publically with sources and all.
> 
> Actually their changes are not all that useful in that there is no effect
> at the default wordlength and I think it is not sensible to use Blast at
> large wordlengths - what would you achieve that other algorthms won't do
> better (thinking SSAHA)?
> 
> Regards,
> David Huen
> 
> 
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-- 

Benjamin Horsman 
Student Researcher 
Brinkman Laboratory, Department of Molecular Biology and Biochemistry
Simon Fraser University 
Burnaby, B.C., Canada, V5A 1S6 604-291-5414
www.pathogenomics.sfu.ca/brinkman