AMBER Archive (2006)

Subject: Re: AMBER: Opteron vs. Xeon performance

From: Robert Duke (
Date: Fri May 12 2006 - 07:46:08 CDT

Ye -
Thanks for posting your results. I presume this is a pme run of pmemd 9?
What's the size of the benchmark? One note - If you do runs of different
lengths, there will be slight variation in runtimes as the system settles.
So it becomes hard to compare absolutely down to the level of 3%.
Generally, also, I can find minor things to do that will have a 1-3% impact.
So with slight differences you may be able to throw the numbers either way.
An exciting thing to me, though, is the dual core/dual cpu config, because
this basically gives you a relatively inexpensive 4 cpu node that is not
doing mpi i/o over the interconnect. I would expect the scaling to be
pretty good. The only experience I have with this is on a cray xd1, and the
dual cpu/dual core nodes are indeed nice; I can't see the differential in
scaling though because the xd1 has a good inter-node interconnect. Still, I
think there is a future down this path. One other issue I have not been
following, and that is how each of these architectures is "topping out".
The xeon is cranking out around 3.6 GHz these days; I am mostly seeing 2.2
GHz opterons. I don't know where intel takes the xeon next, but it would
seem that highspeed clock heating is an issue. On the other hand, the
opteron already has heat issues down around 2 GHz, so I don't know how much
further it is going. I think we are in the fortunate position these days of
having two good and relatively inexpensive alternatives, though.
Best Regards - Bob Duke

----- Original Message -----
From: "Ye Mei" <>
To: <>
Sent: Friday, May 12, 2006 4:04 AM
Subject: Re: AMBER: Opteron vs. Xeon performance

>I ever did some tests for IBM new Xeon Blade, and compared with my
>"homemade" Opteron workstation.
> Molecular Dynamics
> Software: Amber 8 with all patches
> Compiler and LIB: Inter Fortran 9.0 with IMKL8.1
> Parallel Environment: Intel MPI 2.0
> Intel Xeon Dual Dual-Core 3.2GHz
> Simulation time: 100ps CPU time: 467min speed: 0.214ps/min
> AMD opteron 275 (2.2GHz) Dual Dual-Core
> Simulation time: 5000ps CPU time: 22571min speed: 0.222ps/min
> Speed: Intel:AMD=1:1.03
> AMD is a little bit faster.
> Best regards,
> Ye Mei
> Institute of Theoretical and Computational Chemistry
> Key Laboratory of Mesoscopic Chemistry
> School of Chemistry and Chemical Engineering
> Nanjing University
> Nanjing 210093
> P.R.China
> 2006-05-12
> ======= 2006-05-12 02:47:42 Jim Paugh wrote=======
>>I am looking for recent data comparing the performance between Opterons
>>and Xeons using Amber, as well as interpretation of that data.
>>The AMBER Mail Reflector
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