[gmx-developers] GROMACS performance on Opteron Dual Core processors!

David van der Spoel spoel at xray.bmc.uu.se
Mon Sep 25 13:50:51 CEST 2006

Kazem Jahanbakhsh wrote:
> Hi everybody,
> I want to prepare required hw for a Linux cluster to run dynamic 
> molcular simulations such as GROMACS. Nowadays we have very advanced 
> Dual-Core Opteron processors in the market that are suitable for high 
> performance computing with good scalability for large clusters. For 
> this reason I selected this type of processors for our Cluster, but 
> when I saw your benchmarks I learned that your application (GROMACS 
> simulation) doesn't have good scalability for Dual Core platform. From 
> your benchmark table we saw that for single Opteron processor we have 
> a performance about 393 picoseconds of simulation time per day (by 
> Intel 8 compiler) and for single Opteron-DC we have  performance about 
> 450 instead of ideal expected performance about 2*393 (by gcc 
> 3.4.3 compiler) . According with these results and by considering cost 
> per performance ratio it seems that Single-Core architecture is better 
> than advanced Dual-Core architecture. If I am in a mistake, pls 
> correct me. And if this conclusion is true, would you intend to 
> improve your application so that it can utilize better the DC-Opteron 
> platform. All we know that in the dual core platform we have two real 
> core on one chipset, and to utilize this type of configuration the 
> application should be aware from and tuned for it.
> Any suggestion is appreciated, Jahanbakhsh

check benchmarks on he website. DC opterons are very fast, but the 
latest Intels are still slightly better.
The intel compiler does not help.

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