On Tue, Apr 3, 2018 at 3:41 PM, Jochen Hub <j...@gwdg.de> wrote: > > > Am 29.03.18 um 20:57 schrieb Szilárd Páll: > >> 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. > > > Hi Szilárd, > > many thanks, this alrady helps me a lot. Just to get it 100% clear what you > mean with core-GHz: A 10-core E5-2630v4 with 2.2 GHz would have 22 core-GHz, > right?
Yes, that's what I was referring to; note that a 2630v4 won't be running at a 2.2 GHz base clock if you run AVX code ;) > Thanks, > Jochen > > >> >> 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. > > > -- > --------------------------------------------------- > 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. > Phone: +49-551-39-14189 > > 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.