On Mon, Jun 24, 2013 at 4:43 PM, Szilárd Páll <szilard.p...@cbr.su.se> wrote: > On Sat, Jun 22, 2013 at 5:55 PM, Mirco Wahab > <mirco.wa...@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).
Note that you can increase GPU utilization by running two or more *independent* runs (as part of a multi-run or not) on the same GPU (for details see: http://goo.gl/dv1iK). So in practice, if you have to simulate e.g. two confirmations of a protein, running the two on half of the CPU cores, both using the same GPU(s) can give substantial aggregate performance. Cheers, -- Szilárd > >> 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. >> >> >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the www >> interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
