Re: AMBER: Opteron vs. Xeon performance

From: Robert Duke <>
Date: Thu, 11 May 2006 22:02:10 -0400

Okay, I do have opteron vs. intel em64t numbers; for the specific opteron
and intel chips I run on they are very close for pme simulations using pmemd
on the benchmarks I have done (pmemd 9). The specifics are 2.2 GHz opteron
dual cpu/infiniband interconnect (note, NOT dual core, which may actually
give you more bang for the buck, though my numbers on this are loose (just
based on some rough benchmarks on dual core cray xd1, which I have not done
a lot of analysis on)) vs 3.6 GHz em64t intel xeon, 2 MB cache/infiniband.
On the two clusters I bench on for these types of chip, the numbers are
pretty darn close for pme. For GB, I would probably tend to prefer the xeon
because I am a little bit chicken about trying to use the Intel MKL with
Opterons, and it really helps GB performance - off the top of my head at
least 20% (this is a very crude recollection from GB which I hacked into
pmemd but have not yet put a lot of effort into optimizing - but it was
clear that the MKL was worth it. I don't know if the AMD equivalent is as
good, and have not tried crossing manufacturers any further than using ifort
to compile on opterons (which is maybe a little slower than pathscale unless
you get adventurous in lying to the compiler about what the chip is (Andreas
Svrcek-Seiler sent me some numbers on this, and has tried lots of different
things in compiling on the opteron; I tend to try to get a few things
working and move on to the next platform). Okay, so the performance is
close, and I could believe that a really well configured opteron can do a
bit better, but I have not seen dramatic differences myself. Don't get me
wrong, I like the opteron very much, but the later intel chips are
delivering too. Now, if I were buying hardware, I would be worried about
getting a reliable cpu + reliable motherboard + reliable interconnect. The
thing that will kill you is if you buy something cheap, and one of the
components is not well balanced, or prone to heat-induced or other failure.
This is stuff where it is handy to be able to ask someone who has a specific
configuration what their experience has been (so ask the vendor for
references, or buy from a manufacturer that is first tier at a bit of a

At this point in time, I find developing performance code for either the
intel ia32 family, opteron or ibm sp4/5 all to be roughly equivalent
experiences, and the chips respond in a similar fashion to attempts at
optimization. RISC architectures, at least the ones I have available, are
falling behind. The itanium is a heck of a chip for brute power, but it is
touchy to optimize and expensive. I mostly develop on the ia32's and move
off to the similar chips first, and then, while grumbling something akin to
"what a pain" over how differently it optimizes, move off to the itanium,
and then I finally make sure everything still runs on the RISC chips. This
gives you a clue or two as to what pmemd will run well on for the near

Regards - Bob Duke

----- Original Message -----
From: "Ross Walker" <>
To: <>
Sent: Thursday, May 11, 2006 7:17 PM
Subject: RE: AMBER: Opteron vs. Xeon performance

> 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.
> E.g.
> 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
> Ross
> /\
> \/
> |\oss Walker
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- |
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Received on Sun May 14 2006 - 06:07:12 PDT
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