[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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