[Beowulf] CCL:dual-core Opteron
mathog at mendel.bio.caltech.edu
Thu Jul 7 14:23:19 EDT 2005
> I am sure it is possible to find codes and test cases which will
> bandwidth for the memory controller. The usual suspects (Amber8, GAMESS,
> BLAST, HMMer) did not.
Regarding HMMer, did you try running tests where you step through
a range of query sequence sizes (all vs. the same HMM database)?
On the Athlon MP 2200+ machines in our cluster there was
a large variation in run time resulting from complex cache interactions.
This processor has a relatively small cache and is presumably much
more sensitive to this than would be the Opterons. A substantial
amount of reorganization of the data structures minimized this effect
but at least initially going from n residues to n+1 residues in the
same sequence could change the run time for the query by a factor of 3.
You may be able to trigger the same effect on an Opteron by using
a largish query sequence, say 4000 amino acids or so. Admittedly
there are not very many proteins which are that large.
mathog at caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech
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