[gmx-users] time accounting in log file with GPU
Sikandar Mashayak
symashayak at gmail.com
Fri Jul 25 19:47:31 CEST 2014
Got it! Thanks Mark.
On Fri, Jul 25, 2014 at 10:41 AM, Mark Abraham <mark.j.abraham at 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" <symashayak at 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.szilard at gmail.com>
> > wrote:
> >
> > > On Fri, Jul 25, 2014 at 12:48 AM, Sikandar Mashayak
> > > <symashayak at 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.abraham at gmail.com>
> > > > wrote:
> > > >
> > > >> On Fri, Jul 25, 2014 at 12:12 AM, Sikandar Mashayak <
> > > symashayak at 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
> > > >> >
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