[gmx-users] Gromacs GPU system question

[Mirco Wahab]

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).

Regards

M.