Got it! Thanks Mark.
On Fri, Jul 25, 2014 at 10:41 AM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > They report the time since the step that the timers were reset. The log > file will note this event. Whether load is balanced by then/ever depends on > the load. > > Mark > On Jul 25, 2014 7:31 PM, "Sikandar Mashayak" <symasha...@gmail.com> wrote: > > > 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? 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