[gmx-users] Questions about how to set up PME options correctly

[Yunlong Liu]

Hi Gromacs Users,

I have experienced a very high loading imbalance for a long time. And 
each time the loading imbalance increased to a high level, Gromacs 5.0 
turned on the dynamic loading automatically and this lowered the loading 
imbalance. However, when running my simulations on 1 GPU- 16CPU cores 
hybrid, the high loading imbalance will cause memory allocation problem 
and the simulation will shut down.

Here is my loading imbalance:

DD  step 3559999 load imb.: force 21.8%
At step 3560000 the performance loss due to force load imbalance is 5.0 %
NOTE: Turning on dynamic load balancing

            Step           Time         Lambda
         3560000     7120.00000        0.00000

I read the notes from Gromacs website and it seems that I need to adjust 
the PME parameters to lower down this loading imbalance, or increase 
-ntpme threads. So I have a few questions on that:

1) how to correctly set up the PME md options: fourierspacing, PME order 
or fourier grid options?
2) Do I really need to increase my PME nodes? (since I run this 
simulation on 2 nodes, each has 16 physical cores and 1 Nvidia Tesla K20 
GPU. And I initiated 4 MPI processes in total with 8 threads each MPI 
process.)

Thank you.
Yunlong


-- 

========================================
Yunlong Liu, PhD Candidate
Computational Biology and Biophysics
Department of Biophysics and Biophysical Chemistry
School of Medicine, The Johns Hopkins University
Email: yliu120 at jhmi.edu
Address: 725 N Wolfe St, WBSB RM 601, 21205
========================================