Thanks Szilárd. I am bit confused about the -resethway or -resetstep options. Do they exclude the time spent on initialization and load-balancing from the total time reported in the log file, i.e., the time reported is the total time spent only in the loop/iterations over time-steps?
Thanks, Sikandar On Thu, Jul 24, 2014 at 4:30 PM, Szilárd Páll <pall.szil...@gmail.com> wrote: > On Fri, Jul 25, 2014 at 12:48 AM, Sikandar Mashayak > <symasha...@gmail.com> wrote: > > Thanks Mark. -noconfout option helps. > > For benchmarking purposes, additionally to -noconfout I suggest also using: > * -resethway or -resetstep: to exclude initialization and > load-balancing at the beginning of the run to get a more realistic > performance measurement from a short run > * -nsteps N or -maxh: the former is useful if you want to directly > compare (e.g. two-sided diff) the timings from the end of the log > between multiple runs > > Cheers, > -- > Szilárd > > > > > -- > > Sikandar > > > > > > On Thu, Jul 24, 2014 at 3:25 PM, Mark Abraham <mark.j.abra...@gmail.com> > > wrote: > > > >> On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak < > symasha...@gmail.com> > >> wrote: > >> > >> > Hi > >> > > >> > I am running a benchmark test with the GPU. The system consists of > simple > >> > LJ atoms. > >> > And I am running only very basic simulation with NVE ensemble and not > >> > writing any > >> > trajectories or energy values. My grompp.mdp file is attached below. > >> > > >> > However, in the time accounting table in the md.log, I observe that > write > >> > traj. and comm energies > >> > operations take 40% of time each. So, my question is that even if I > have > >> > specified not to write > >> > trajectories and energies, why is 80% of time being spent on those > >> > operations? > >> > > >> > >> Because you're writing a checkpoint file (hint, use mdrun -noconfout), > and > >> that load is imbalanced so the other cores wait for it in the global > >> communication stage in Comm. energies (fairly clear, since they have the > >> same "Wall time"). Hint - make benchmarks run for about a minute, so you > >> are not dominated by setup and load-balancing time. Your compute time > was > >> about 1/20 of a second... > >> > >> Mark > >> > >> > >> > Thanks, > >> > Sikandar > >> > > >> > R E A L C Y C L E A N D T I M E A C C O U N T I N G > >> > > >> > On 2 MPI ranks > >> > > >> > Computing: Num Num Call Wall time > Giga-Cycles > >> > Ranks Threads Count (s) total sum > % > >> > > >> > > >> > ----------------------------------------------------------------------------- > >> > Domain decomp. 2 1 11 0.006 0.030 > >> 2.1 > >> > DD comm. load 2 1 2 0.000 0.000 > >> 0.0 > >> > Neighbor search 2 1 11 0.007 0.039 > >> 2.7 > >> > Launch GPU ops. 2 1 202 0.007 0.036 > >> 2.5 > >> > Comm. coord. 2 1 90 0.002 0.013 > >> 0.9 > >> > Force 2 1 101 0.001 0.003 > >> 0.2 > >> > Wait + Comm. F 2 1 101 0.004 0.020 > >> 1.4 > >> > Wait GPU nonlocal 2 1 101 0.004 0.020 > >> 1.4 > >> > Wait GPU local 2 1 101 0.000 0.002 > >> 0.2 > >> > NB X/F buffer ops. 2 1 382 0.001 0.008 > >> 0.6 > >> > Write traj. 2 1 1 0.108 0.586 > >> 40.2 > >> > Update 2 1 101 0.005 0.025 > >> 1.7 > >> > Comm. energies 2 1 22 0.108 0.588 > >> 40.3 > >> > Rest 0.016 0.087 > >> 5.9 > >> > > >> > > >> > ----------------------------------------------------------------------------- > >> > Total 0.269 1.459 > >> 100.0 > >> > > >> > > >> > ----------------------------------------------------------------------------- > >> > > >> > > >> > grompp.mdp file: > >> > > >> > integrator = md-vv > >> > dt = 0.001 > >> > nsteps = 100 > >> > nstlog = 0 > >> > nstcalcenergy = 0 > >> > cutoff-scheme = verlet > >> > ns_type = grid > >> > nstlist = 10 > >> > pbc = xyz > >> > rlist = 0.7925 > >> > vdwtype = Cut-off > >> > rvdw = 0.7925 > >> > rcoulomb = 0.7925 > >> > gen_vel = yes > >> > gen_temp = 296.0 > >> > -- > >> > 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? 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