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

[Sikandar Mashayak]

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?

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