[BiO BB] remove CTL-M and Buying a bioinformatics workstation

Teletchéa Stéphane steletch at biomedicale.univ-paris5.fr
Thu Sep 4 09:01:48 EDT 2003

Le jeu 04/09/2003 à 14:03, Yannick Wurm a écrit :
> Hi,
> I don't have any hands-on experience with large-volume blasting, but 
> you might want to have a look at Apple's new G5 computers.
> The numbers shown in the "Performance Whitepaper" of june 2003 (you'll 
> find a link at http://www.apple.com/lae/g5/ ) are quite impressive. 
> Apple compared the performance of the dual 2GHz Power Mac G5 running 
> Apple/Genentech BLAST with a 3GHz Pentium 4-based system and a dual 
> 3.06GHz Xeon-based system, both running Red Hat Linux 9.0 and NCBI 
> A/G BLAST is an optimized version of NCBI
> BLAST developed by Apple in collaboration
> with Genentech. Optimized for dual PowerPC
> G5 processors, the Velocity Engine, and the
> symmetric multiprocessing capabilities of
> Mac OS X, A/G BLAST makes a wide variety
> of searches available at higher speeds.
> According to the graph they show, using a word length of 40, the Dual 
> G5 ran 3 million nucleotides per second whereas the Linux boxes did 
> only about 0.75.
> The same paper also states that HMMer runs 4 times faster on the dual 
> g5 than on the dual xeon.
> And Microsoft Word runs on it too :)
> Are the results shown surprising? The code for A/G Blast and HMMer seem 
> to be optimized for the G5, whereas the standard vanilla versions where 
> used on the linux boxes. Could optimization reduce the bias against the 
> xeon?
> Yannick Wurm

Personnaly speaking, i would not that easily accept a benchmark without
doing it myself first ...

Secopnd, why didn't they compare the dual-G5 to its real counterpart
(what you will get for the same price): Opteron or Itanium.

I'll bet they figures will be dramatically different. The dual-G5 is not
a working station but a server for desktop, so let's consider the server
solutions !

See some comparisons at :


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