AMBER Archive (2006)

Subject: RE: AMBER: Opteron vs. Xeon performance

From: Ross Walker (
Date: Thu May 11 2006 - 18:17:12 CDT

Dear Joseph

> I am looking for recent data comparing the performance
> between Opterons
> and Xeons using Amber, as well as interpretation of that data.

This sort of thing is never a simple as it sounds. As with all comparissons
it very much depends what you compare. E.g. periodic boundary PME
simulations on a top end Opteron will probably be better than a top end
Xeon, however, this may be reversed when one tries Generalized Born implicit
solvent calculations. This is all a function of cache hits, code branching
etc. I.e. some problems do well on some chips but worse on others and vice
versa. This is certainly the case with IA64 chips.


JAC Benchmark (PME) (PMEMD v9.0)
Pentium-D 3.2GHz = 231.79 ps/day
Itanium 2 1.5GHz = 395.37 ps/day
Ratio IA64/P4 = 1.71

GB_MB Benchmark (GB) (PMEMD v9.0)
Pentium-D 3.2GHz = 266.03 ps/day
Itanium 2 1.5GHz = 191.51 ps/day
Ratio IA64/P4 = 0.72

Anyway, I know that this is not dealing with Opterons which is what you are
interested in but at present we don't have any amber9 timings on Opteron
chips. However, there are some timings here for dual core opterons:

JAC Benchmark (PME) (PMEMD v8.0)
Dual Core Opteron 875 (2.2GHz) = 187.0 ps/day
Single Core Opteron (1.4GHz) = 124.0 ps/day

All the best

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
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