Hi, Regarding the K40 vs GTX 960 question, the K40 will likely be a bit faster (though it'l consume more power if that matters). The difference will be at most 20% in total performance, I think -- and with small systems likely negligible (as a smaller card with higher clocks is more efficient at small tasks than a large card with lower clocks).
Regarding the load balance note, you are correct, the "pme mesh/force" means the ratio of time spent in computing PME forces on a separate task/rank and the rest of the forces (including nonbonded, bonded, etc.). With GPU offload this is a bit more tricky as the observed time is the time spent waiting for the GPU results, but the take-away is the same: when a run shows "pme mesh/force" far from 1, there is imbalance affecting performance. However, note that with a single GPU I've yet to see a case where you get better performance by running multiple ranks rather than simply running OpenMP-only. Also note that what a "weak GPU" can case-by-case, so I recommend taking the 1-2 minutes to do a short run and check for a certain hardware + simulation setup is it better to offload all of PME or keep the FFTs on the CPU. We'll do our best to automate more of these choices, but for now if you care about performance it's useful to test before doing long runs. Cheers, -- Szilárd On Thu, Jun 14, 2018 at 2:09 AM, Alex <nedoma...@gmail.com> wrote: > Question: in the DD output (md.log) that looks like "DD step xxxxxx pme > mesh/force 1.229," what is the ratio? Does it mean the pme calculations > take longer by the shown factor than the nonbonded interactions? > With GTX 960, the ratio is consistently ~0.85, with Tesla K40 it's ~1.25. > My mdrun line contains -pmefft cpu (per Szilard's advice for weak GPUs, I > believe). Would it then make sense to offload the fft to the K40? > > Thank you, > > Alex > > On Wed, Jun 13, 2018 at 4:53 PM, Alex <nedoma...@gmail.com> wrote: > >> So, swap, then? Thank you! >> >> >> >> On Wed, Jun 13, 2018 at 4:49 PM, paul buscemi <pbusc...@q.com> wrote: >> >>> flops trumps clock speed….. >>> >>> > On Jun 13, 2018, at 3:45 PM, Alex <nedoma...@gmail.com> wrote: >>> > >>> > Hi all, >>> > >>> > I have an old "prototyping" box with a 4-core Xeon and an old GTX 960. >>> We >>> > have a Tesla K40 laying around and there's only one PCIE slot available >>> in >>> > this machine. Would it make sense to swap the cards, or is it already >>> > bottlenecked by the CPU? I compared the specs and 960 has a higher clock >>> > speed, while K40's FP performance is better. Should I swap the GPUs? >>> > >>> > Thanks, >>> > >>> > Alex >>> > -- >>> > 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. >> >> >> > -- > 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.
