[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:
0.24
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
set
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,
Pu,
**
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