The answer is in the log files, in particular the performance summary should indicate where is the performance difference. If you post your log files somewhere we can probably give further tips on optimizing your run configurations.
Note that with such a small system the scaling with the group scheme surely becomes limited by imbalance and probably it won't scale much further than 72 cores. At the same time, simulations with the verlet scheme have shown scaling to below 100 atoms/core. Cheers, -- Szilárd On Fri, May 17, 2013 at 11:07 AM, Djurre de Jong-Bruinink <djurredej...@yahoo.com> wrote: > Dear all, > > We recently did some comparisons of gmx 4.5.5, 4.6.1+group and 4.6.1+verlet > cutoff scheme. The system was a protein (amber99) in water (tip3p) in a > triclinic box (23k atoms total). We're using pme with a realspace > cutoff=0.9nm, gridspacing=0.12nm, npme=-1, which based on g_tune_pme gives > (close to) best performance. Below some performance measure (ns/day) from > 100,000 step runs: > > CPUs G455 G461+group G461+verlet > 24 34.9 43.1 35.3 > 36 47.6 57.8 49.7 > 48 50.8 65.9 60.4 > 60 59.9 81.8 71.1 > 72 57.7 78.7 78.2 > > The scaling to more CPUs in 4.6.1 is much better (thank you developers for > putting up all the hard work!), however I would have expected more > improvements from the verlet scheme. Note that both 455 and 461 have been > compiled with MPI only (no OMP, GPU), and 461 was compiled with gcc (4.7.2). > I did change the nstlist from 5 to 10 for the verlet scheme only. > > > Are these results expected given the setup? Is there anything I'm doing wrong? > > Thanks in advance, > Djurre de Jong > -- > 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
