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

[Sikandar Mashayak]

Thanks Mark. -noconfout option helps.

--
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
> > --
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