Subject: opteron performance

From: David van der Spoel <D.van.der.Spoel[at]chem.rug.nl>
Date: Mon, 17 Nov 2003 22:31:10 +0100

On Mon, 2003-11-17 at 19:35, pderosa-Latech wrote:
> Dear all:
>  
>         Can any of you give me your opinion about AMD Opteron.  They
> are intended to run Gaussian 03, MD simulations, and a cellular
> simulator.  I believe Opteron do not have the problem associated with
> 32 bit processors that cannot handle files larger than 2 GB.  But how
> they perform compared to Alpha?, how are they for integer
> operations?.  Opteron is much cheaper than alphas, thus I can take
> some loss in performance, but not too much.
>  
>         I apologize if this issue was already treated in CCL, I tried
> to check the CCL archives but they seem to be unavailable at this
> moment.
>     
>         Thanks,
Since you ask, I recently did some tests with the GROMACS MD package
(http://www.gromacs.org), see below.

Hi,

FYI, I've done some benchmarks on our new 2 GHz Opterons. I have two
dual machines which are connected directly by a Gbit ethernet cable
running at full duplex. The numbers are the regular gromacs benchmarks
run using grompp -shuffle -sort. For comparison results on our Dual 2.2
GHz Xeon are given as well. Results in ps/day (higher is better!)

	natoms	Delta t	1 CPU	2 CPU	4 CPU	2Xeon
Villin	9389	2 fs	9340	18180	19190	13280
LZM	23207	4 fs	2541	5080	7200	3756
LZM-PME	23207	4 fs	1600	3086	3756	1920
DPPC	121856	2 fs	185	419	702	330
Polymer	6000	2 fs	4192	7714	9394	5268

Conclusion: scaling to 2 CPUs is excellent, four CPU's is only worth it
for DPPC. Furthermore the Opterons are quite a bit faster (35%) than the
Xeons, this might be due in part to the larger cache (1 Mb iso 512 kb).
The Opterons are more expensive than the Xeons, but their GROMACS speed
at 2 GHz is roughly comparable to a 3 GHz Xeon. Preliminary tests imply 
that similar GROMACS performance can also be obtained on a 900 MHz
Itanium.
 
The LZM-PME result on 2 Opterons is roughly 0.12s per integration step, 
which compares favorably to the recently posted PMEMD and NAMD results
(PMEMD at 0.43 s per integration step on 2 x 1 GHz Alpha processors). One 
should be careful interpreting these results however, because simulation
systems and parameters were not completely identical. Obviously GROMACS
scaling (with PME) is still a problem.

Hope this helps...
> Pedro
-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel[at]xray.bmc.uu.se	spoel[at]gromacs.org   http://xray.bmc.uu.se/~spoel
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