[gmx-users] How can I control PME domain decomposition

柯谱 kepu at csrc.ac.cn
Thu Mar 10 03:27:09 CET 2016

Hi everyone,
                          I am working on PP/PME optimization.  But I 
found while PP ranks could be controlled by, say -dd  9 8 8, PME node 
decomposition CANNOT be tuned.
                          For instance,  below is the basic information 
for optimization:

    - Using a fourier grid of 216x192x192, spacing 0.065 0.062 0.062
    - Estimate for the relative computational load of the PME mesh part:

                         I would like to run this simulation by -dd 9 8 
8 and the PME nodes setting 24 * 8, in which PME grid_x (216) and grid_y 
(192) is divisible by #PME_ranks_x (24)
       and PME grid_y (192) and grid_z (192) is divisible by 
#PME_ranks_y (8).  However, when I used -npme=192, gromacs automatically 

    Domain decomposition grid *9 x 8 x 8*, separate PME ranks *192*
    PME domain decomposition: *192 x 1 x 1*

which significantly slowed down the simulation.  Then my question is 
what can I do to control PME node decomposition?  Thanks for your help!
         Best wishes,

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