On Tue, Sep 9, 2014 at 10:58 PM, Mirco Wahab <mirco.wa...@chemie.tu-freiberg.de> wrote: > Thank you very much for your answer. After reading > Mark's very detailed posting on the topic, I played > with some parameters but did not manage to get under > 64K grid dimension. > > On 09.09.2014 21:35, Szilárd Páll wrote: >> >> Is this rather large box a system that can actually be simulated with >> a useful speed on a single Fermi GPU? Even with 5 fs time-step you >> won't get much more than 1-1.5 ns/day on a fast Fermi GPU like a GTX >> 580. > > > This is a rather simple toy system used for machine comparison and > as a hardware reliability test. ~36nm^3 SPC water box, ~1.56x10^6 > water (GTX-780 on 3770K is 0.45ns/day). > > I posted the question because I did not understand why this > happened on the GTX-580. mdrun -nstlist x did not work (4.6.7).
Indeed, -nstlist got exposed as a commnad line option in 5.0. You can use the GMX_NSTLIST environment variable instead. BTW regarding benchmarking: with small systems and single-GPU runs make sure to disable GPU timing (set GMX_DISABLE_CUDA_TIMING)! >> Given that you are quite a bit above the limit, unless you are using a >> quite large nstlist, you may not be able to decrease it enough to fit >> the system on the GPU. What you can do instead is to use >> domain-decomposition and start multiple ranks per GPU. In your case >> two-way DD should be enough. > > > This sounds interesting. I'll try to accomplish that (I never thought > this *this* is possible ...). Not just possible, but it is in fact advantageous from performance point of view with many cores/GPU! > Thank you very much (and Mark) > > Mirco > > > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a > mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.