[gmx-users] Gromacs GPU system question

Szilárd Páll szilard.pall at cbr.su.se
Mon Jun 24 16:43:57 CEST 2013

On Sat, Jun 22, 2013 at 5:55 PM, Mirco Wahab
<mirco.wahab at chemie.tu-freiberg.de> wrote:
> 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

Without DD you should be able to get up to 75-80% CPU-GPU overlap
(slighly less with vsites).

> 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.
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