[gmx-users] Should I use separate PME nodes

[Gaurav Goel]

I ran my simulation in parallel on 4 nodes (with zero separate PME
nodes). Below is the information printed in md.log.

I see that PME-Mesh calculations took 60% of CPU time. Any
recommendations on using 1 or more separate PME nodes to speed up?


 Computing:                         M-Number         M-Flops  % Flops
-----------------------------------------------------------------------
 Coul(T) + VdW(T)             1761401.496982   119775301.795    20.2
 Outer nonbonded loop          106414.135764     1064141.358     0.2
 Calc Weights                   32400.006480     1166400.233     0.2
 Spread Q Bspline             2332800.466560     4665600.933     0.8
 Gather F Bspline             2332800.466560    27993605.599     4.7
 3D-FFT                      47185929.437184   377487435.497    63.6
 Solve PME                     675840.135168    43253768.651     7.3
 NS-Pairs                      823453.927656    17292532.481     2.9
 Reset In Box                    2160.002160        6480.006     0.0
 CG-CoM                          2160.004320        6480.013     0.0
 Virial                         11700.002340      210600.042     0.0
 Ext.ens. Update                10800.002160      583200.117     0.1
 Stop-CM                        10800.002160      108000.022     0.0
 Calc-Ekin                      10800.004320      291600.117     0.0
-----------------------------------------------------------------------
 Total                                         593905146.863   100.0
-----------------------------------------------------------------------

  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

 Computing:         Nodes     Number     G-Cycles    Seconds     %
-----------------------------------------------------------------------
 Domain decomp.         4    1000001     3859.416     1488.1     0.6
 Comm. coord.           4    5000001     1874.635      722.8     0.3
 Neighbor search        4    1000001    78640.722    30322.2    11.2
 Force                  4    5000001   180659.902    69658.5    25.8
 Wait + Comm. F         4    5000001     2578.994      994.4     0.4
 PME mesh               4    5000001   422268.834   162817.7    60.4
 Write traj.            4      10001       17.526        6.8     0.0
 Update                 4    5000001     2981.794     1149.7     0.4
 Comm. energies         4    5000001     2633.176     1015.3     0.4
 Rest                   4                3580.341     1380.5     0.5
-----------------------------------------------------------------------
 Total                  4              699095.342   269556.0   100.0
-----------------------------------------------------------------------

Thanks,
Gaurav