[gmx-users] Gromacs GPU system question
mirco.wahab at chemie.tu-freiberg.de
Sat Jun 22 17:55:51 CEST 2013
On 22.06.2013 17:31, Mare Libero wrote:
> I am assembling a GPU workstation to run MD simulations, and I was wondering if anyone has any recommendation regarding the GPU/CPU combination.
> From what I can see, the GTX690 could be the best bang for my buck in terms of number of cores, memory, clock rate. But being a dual GPU card, I was wondering if there is any latency issue that could make its performances less favorable with respect to a GTX Titan.
> Also, which motherboard, CPU is recommendable for this system.
The most important aspect to consider (by far) is, in my humble
opinion, *your specific workload*:
- Size of the simulation box / number of atoms,
- Specific force field/required integrator (verlet?),
- Handling of long range electrostatics (pme/RF/coulomb).
Furthermore, the effect of the CPU is, imho, much more
pronounced. Remember, mdrun-gpu doesn't 'run' on the
GPU (as, e.g., HOOMD does) but loads work-sets up to
the GPU, runs them, and loads them back. For example: in
one box, I have an AMD FX-8350 and a GTX-660Ti available
for tests, and I didn't see the GPU load going much over 60%,
even with millons of atoms. Here, small differences in the
potential/force field used by the model will probably change
the performance of the GPU-related parts significantly (due
to cu-offs and buffering schemes).
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