Optimizing Production Run with GPUs and CHARMM36

b-omics
Tue, 25 Feb 2025 14:44:28 +0000
User discussions

GROMACS version: 2024.4
GROMACS modification: Yes/No

I am simulating a system of approximately 330,000 atoms using CHARMM36 and aiming to significantly improve the performance of my production run. Currently, I am utilizing 3 GPUs (Nvidia A100) and 64 CPUs on a single node (my node can support up to 6 GPUs). I have also increased the nstlist from 10 to 40 to enhance the efficiency of the pair search. Currently I am getting 134 nsec/day but I see that the PME wait and GPU state copy is 30-35 percent. I am looking for further optimizations to increase the production rate of the mdrun.
With -tunepme I managed to get 138 nsec. Any suggestions?

Log file:

gmx mdrun -ntmpi 3 -ntomp 10 -npme 3 -nb gpu -bonded gpu -pme gpu -update gpu
-g gpu3_test_multigpu_pme_optimized -nsteps -1 -maxh 0.017 -resethway -notunepme
-s benchmark.tpr -deffnm gpu3_test_multigpu_pme_optimized

4 posts - 3 participants