[gmx-users] time accounting in log file with GPU

Sikandar Mashayak symashayak at gmail.com
Fri Jul 25 19:31:28 CEST 2014


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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