Hi Jochen, For that particular benchmark I only measured performance with 1,2,4,8,16 cores with a few different kinds of GPUs. It would be easy to do the runs on all possible core counts with increments of 1, but that won't tell a whole lot more than what the performance is of a run using a E5-2620 v4 CPU (with some GPUs) on a certain core count. Even extrapolating from that 2620 to a E5-2630 v4 and expecting to get a good estimate is tricky (given that the latter has 25% more cores for the same TDP!), let alone to any 26xxv4 CPU or the current-gen Skylake chips which have different performance characteristics.
As Mark notes, there are some mdp option as well as some system charateristics that will have a strong influence on performance -- if tens of % is something you consider "strong" (some users are fine to be within a 2x ballpark :). What's worth considering is to try to avoid ending up strongly CPU or GPU bound from start. That may admittedly could be a difficult task you would run e.g. both biased MD with large pull groups and all-bonds constraints with Amber FF on large-ish (>100k) systems as well as vanilla MD with CHARMM FF with small-ish (<25k) systems. On the same hardware the former will be more prone to be CPU-bound while the latter will have relatively more GPU-heavy workload. There are many factors that influence the performance of a run and therefore giving a the one right answer to your question is not really possible. What can say is that 7-10 "core-GHz" per fast Pascal GPU is generally sufficient for "typical" protein simulations to run at >=85% of peak. Cheers, -- Szilárd On Wed, Mar 28, 2018 at 4:31 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > On Tue, Mar 27, 2018 at 6:43 PM Jochen Hub <j...@gwdg.de> wrote: > >> Dear Gromacs community, dear Mark, >> >> Mark showed in the webinar today that having more than 8 Xeon E5-26XXv4 >> cores does not help when using a GTX 1080Ti and PME on the GPU. >> > > ... for that particular simulation system. > > >> Unfortunately, there were no data points between 4 and 8 CPU cores, >> hence it was not clear at which #cores the performance actually levels >> off. With a GTX 1080 (not Ti) I once found that having more than 5 Xeon >> cores does not help, if not having UB potentials, but I don't have a >> 1080Ti at hand to test for that. >> > > Those data points may not have been run. Szilard might have the data - this > was GLIC 2fs comparing 1080 with 1080Ti from the recent plots he shared. > > >> So my questions are: >> >> - At which number of E5-26XXv4 cores does the performance for common >> systems level off with a 1080Ti for your test system (GLIC)? >> >> - Does the answer depend strongly on the mdp settings (in particular on >> the LJ cutoff)? >> > > Longer LJ cutoff (e.g. from different forcefields) will certainly require > more non-bonded work, so then fewer CPU cores would be needed to do the > remaining non-offloaded work. However any sweet spot for a particular .tpr > would be highly dependent on other effects, such as the ratio of solvent > (which typically has less LJ and simpler update) to solute, or the density > of dihedral or U-B interactions. And doing pulling or FEP is very different > again. The sweet spot for the next project will be elsewhere, sadly. > > This would help us a lot when choosing the appropriate CPU for a 1080Ti. >> >> Many thanks for any suggestions, >> Jochen >> >> -- >> --------------------------------------------------- >> Dr. Jochen Hub >> Computational Molecular Biophysics Group >> Institute for Microbiology and Genetics >> Georg-August-University of Göttingen >> Justus-von-Liebig-Weg 11, 37077 Göttingen, Germany >> <https://maps.google.com/?q=Justus-von-Liebig-Weg+11,+37077+G%C3%B6ttingen,+Germany&entry=gmail&source=g> >> . >> Phone: +49-551-39-14189 <+49%20551%203914189> >> http://cmb.bio.uni-goettingen.de/ >> --------------------------------------------------- >> -- >> 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.