[gmx-users] Recommendations on how to increase performance

[Yunlong Liu]

Hi Gromacs Users,


I got an time accounting table from a single run. Can anyone give me any advice on how to further increase performance?


     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 16 MPI ranks, each using 8 OpenMP threads

 Computing:          Num   Num      Call    Wall time         Giga-Cycles
                     Nodes Threads  Count      (s)         total sum    %
-----------------------------------------------------------------------------
 Domain decomp.        16    8      10001      42.603      14723.278   3.3
 DD comm. load         16    8       2001       0.034         11.807   0.0
 Neighbor search       16    8      10001      50.194      17346.533   3.9
 Comm. coord.          16    8     190000      33.143      11454.105   2.6
 Force                 16    8     200001     530.787     183435.628  41.7
 Wait + Comm. F        16    8     200001      30.357      10491.253   2.4
 PME mesh              16    8     200001     491.803     169963.077  38.7
 NB X/F buffer ops.    16    8     580001      12.216       4221.874   1.0
 Write traj.           16    8          4       0.081         28.145   0.0
 Update                16    8     200001       5.612       1939.518   0.4
 Constraints           16    8     200001      67.633      23373.282   5.3
 Comm. energies        16    8      20001       2.636        910.895   0.2
 Rest                                           4.649       1606.573   0.4
-----------------------------------------------------------------------------
 Total                                       1271.748     439505.968 100.0
-----------------------------------------------------------------------------
 Breakdown of PME mesh computation
-----------------------------------------------------------------------------
 PME redist. X/F       16    8     400002     135.738      46909.937  10.7
 PME spread/gather     16    8     400002     119.991      41467.827   9.4
 PME 3D-FFT            16    8     400002      59.470      20552.340   4.7
 PME 3D-FFT Comm.      16    8     800004     170.363      58876.121  13.4
 PME solve Elec        16    8     200001       5.465       1888.524   0.4
-----------------------------------------------------------------------------


Thank you.

Yunlong



Davis Yunlong Liu

BCMB - First Year PhD Candidate

School of Medicine

The Johns Hopkins University

E-mail: yliu120 at jhmi.edu<mailto:yliu120 at jhmi.edu>