Getting good gromacs simulations performance in HPC -reg

GROMACS version: 2020.2 (patched with ramd)
GROMACS modification: Yes/No
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Deal All
I have been using GROMACS for a while now and I was thinking of ways to increase the performance of it (GROMACS 2020.2 installed in HPC). And in the meanwhile I also got a notice regarding the load imbalance which I have listed below for your reference. I would like to know what optimal values for the specific keywords would help me increase the performance. I have listed the 1) load imbalance message, 2) my HPC configuration below.for your kind reference.

  1. Load imbalance message
    vol 0.77 imb F 4% pme/F 0.90 step 278700, will finish Wed Mar 31 06:09:16 2021
    vol 0.77 imb F 5% pme/F 0.88 step 278800, will finish Wed Mar 31 06:09:14 2021
    vol 0.78 imb F 11% pme/F 0.97 step 278900, will finish Wed Mar 31 06:09:18 2021
    vol 0.76 imb F 5% pme/F 0.88 step 279000, will finish Wed Mar 31 06:09:17 2021

  2. My HPC specification, below for your kind reference.

HPC nodes : 20 (each 16 core), total - 320 cores228751 (total number of atoms for system)/320 (cores)= ~714.846 atoms per core
MPI : intel-parallel-studio-2018
fftw : fftw-3.3.4
GCC : gcc-5.5.0

Also, from my side, I went through the following link, gmx mdrun — GROMACS 2020 documentation and got some ideas from the manual . However, I still have some doubts regarding (in my case) which range will fare better for the below listed mdrun options? Kindly request your valuable suggestions.

  1. ntmpi
  2. ntpme
  3. nt

Kindly let me know if I am not clear.

Thank you

Venkat

Dear Venkat,

we have done quite extensive parameter scans involving the parameters you are interested in in the following publications:

https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.26011
https://onlinelibrary.wiley.com/doi/10.1002/jcc.24030

They will point you to finding the optimal parameters for your specific setting.

Best,
Carsten