GROMACS version: GROMACS/2021-foss-2020b
GROMACS modification: No
GROMACS version: GROMACS/2021-foss-2020b
GROMACS modification: No
Hi, I have a problem with parameter setup on HPC. There are only CPUs available, so I can’t run the simulation on a GPU. My system has 116,347 atoms, and the best speed of the simulation was 5.46 ns/day. :(
My SLURM script:
#!/bin/bash
#SBATCH -p normal
#SBATCH -J gromacs_sim
#SBATCH -N 1
#SBATCH -n 16
#SBATCH --time=1-00:00:00
#SBATCH --mem=128G
#SBATCH --output=gromacs-%j.out
#SBATCH --error=gromacs-%j.err
source /usr/local/sbin/modules.sh
module load GROMACS/2021-foss-2020b
export OMP_NUM_THREADS=16
gmx mdrun -v -s step5_1.tpr -ntomp 16 2> gromacs_errors-%j.err
exit
How can I improve the perfomance of the simulation? Thanks in advance!