On Wed, Sep 6, 2017 at 4:58 AM, Alex <nedoma...@gmail.com> wrote: > Hi all, > > We just got the new machines that were actually built with Szilárd's > advice (a while back) and I am doing some preliminary tests. "My" machine > has two 22-core Xeon E5 CPUs (44 cores / 88 threads total) + 3 Titan Xp > GPUs. So far, I got good test system performance (~11K atoms, 92 ns/day) > from '-nt 36' and running on all GPUs. Further increasing the number of > threads only reduces performance. The test system is a CHARMM-based > lipid+water setup, elongated in the Z-direction (6.7 nm x 6.7 nm x 11.2 > nm).Very decent performance (70 ns/day) for 16 CPU cores and two GPUs. > > Any suggestions on further increase what we can squeeze out of this thing > for a single simulation? The relevant mdp section is below (CHARMM > defaults, really). What would you try in your mdrun line? > > Thanks! > > Alex > > **** > cutoff-scheme = Verlet > nstlist = 20 > rlist = 1.2 > coulombtype = pme > rcoulomb = 1.2 > vdwtype = Cut-off > vdw-modifier = Force-switch > rvdw_switch = 1.0 > rvdw = 1.2 > >
You really just have to try different options for different systems. The performance will be system-dependent. Expect larger systems to benefit more from GPU acceleration. Try different combinations of MPI ranks and OMP threads along with specifying the GPU's multiple times. I always do a series of short runs with different combinations before choosing the fastest one for a particular system and then doing a longer production run. See http://www.gromacs.org/Documentation/Acceleration_and_parallelization -- James "Wes" Barnett Postdoctoral Research Scientist Department of Chemical Engineering Kumar Research Group <http://www.columbia.edu/cu/kumargroup/> Columbia University w.barn...@columbia.edu http://wbarnett.us -- 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.