[Bioclusters] G5

landman bioclusters@bioinformatics.org
Wed, 25 Jun 2003 08:50:13 -0500


There has been serious discussion on other sites
(http://www.haxial.com/spls-soapbox/apple-powermac-G5/) discounting some of
the marketing speak associated with it.  That said, using the specialized SIMD
versions of BLAST/HMMer, you can indeed achieve significantly better results
on a SIMD processor than running the non-SIMD on a single processor.

However, noting what the folks noted on that website above about benchmark
"gaming" (e.g. not really doing an "apples" to "apples" comparison, if you
could pardon the pun, by purposely overoptimizing the machine far beyond what
an ordinary user would do, tuning the prefetch cache, using a better compiler
for one and a known worse compiler for the one you wish to show the poorer
performance for ... ) makes me suspicious if any of that occured for the BLAST
and HMMer benchmarks.

That said, the A/G BLAST does look good w/o the gaming, and so does HMMer. 
Hopefully those of us working on the SIMD versions for the IA32/x86-64
platforms will be able to finally help out with a real "apples" to "apples"
comparison.  Basic results (using the poor compiler, and no SIMD) on Opteron
are quite interesting.

Joe

On Wed, 25 Jun 2003 13:05:26 +0200 (CEST), L ben wrote
> Hi all,
> probably it' s not a news , but I ' ve just found
> it :-)
> http://www.apple.com/g5/
> Particular interesting the 2nd pdf linked :
> brings some benchmarks on blast and hmmer.
> greetings
> ben
> 
> ______________________________________________________________________
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Joseph Landman, Ph.D
Scalable Informatics LLC,
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