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

[Kazem Jahanbakhsh]

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

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