[Bioclusters] G5

[Benjamin Horsman]

Apple has addressed these issues.
(http://apple.slashdot.org/apple/03/06/24/2154256.shtml?tid=126&tid=181)
Essentially, an Apple VP claims that disabling hyperthreading on the
Intel system improved performance, and that adjustments made to the G5
(memory read bypass, prefetching, beefed-up malloc) represent default
settings when the machines ship in a few months.

Ben


On Wed, 2003-06-25 at 06:50, landman wrote:
> 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,
> email: landman@scalableinformatics.com
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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