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.
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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 -
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.
- ntmpi
- ntpme
- nt
Kindly let me know if I am not clear.
Thank you
Venkat