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protocaller / ProtoCaller

Full automation of relative protein-ligand binding free energy calculations in GROMACS
http://protocaller.readthedocs.io
GNU General Public License v3.0
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Low GPU utilization with default protocol. #17

Closed kexul closed 3 years ago

kexul commented 3 years ago

Hi, I managed to run the simulation with the system prepared by protocaller. I found that the GPU utilization is 3%~5% with my Tesla P40 card. Is that normal? Here is my log about time consuming. 


     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 1 MPI rank, each using 40 OpenMP threads

 Computing:          Num   Num      Call    Wall time         Giga-Cycles
                     Ranks Threads  Count      (s)         total sum    %
-----------------------------------------------------------------------------
 Neighbor search        1   40        501       6.972        613.563   1.0
 Launch GPU ops.        1   40      50001       4.305        378.852   0.6
 Force                  1   40      50001     216.936      19090.346  30.5
 PME mesh               1   40      50001     364.126      32043.018  51.3
 Wait Bonded GPU        1   40       1001       0.007          0.574   0.0
 Wait GPU NB local      1   40      50001       0.760         66.924   0.1
 NB X/F buffer ops.     1   40      99501      20.326       1788.689   2.9
 Write traj.            1   40         11       0.262         23.098   0.0
 Update                 1   40     100002      46.367       4080.316   6.5
 Constraints            1   40     100004      44.149       3885.090   6.2
 Rest                                           6.218        547.217   0.9
-----------------------------------------------------------------------------
 Total                                        710.429      62517.687 100.0
-----------------------------------------------------------------------------
 Breakdown of PME mesh computation
-----------------------------------------------------------------------------
 PME spread             1   40     100002     118.548      10432.218  16.7
 PME gather             1   40     100002      94.478       8314.080  13.3
 PME 3D-FFT             1   40     200004     131.213      11546.690  18.5
 PME solve Elec         1   40     100002       1.376        121.094   0.2
-----------------------------------------------------------------------------
kexul commented 3 years ago

With the new 2021.beta2 version, the GPU utilization can reach 20% now.