Running Gromacs in HPC

Ligand1
Wed, 15 May 2024 00:40:18 +0000
User discussions

GROMACS version: 2022.5
GROMACS modification: No
Hi everyone!

I am trying to optimize the duration of my simulations using Gromacs on a HPC cluster. I am using Lysozyme in water tutorial for this optimization exercise. I am submitting my jobs using the Slurm script. My current slurm script looks something like this:

#!/bin/bash
#SBATCH --job-name=Lysozyme_in_water_Job
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=70
#SBATCH --time=01:00:00
#SBATCH --partition=standard
#SBATCH --account=lab

module load gromacs/2022.5
srun gmx mdrun -deffnm md_1ns -v

The simulation speed that I am getting here is:
Core t (s) Wall t (s) (%)
Time: 2538.208 36.267 6998.7
(ns/day) (hour/ns)
Performance: 238.239 0.101

Now when i am trying to increase the number of nodes from one to four using the following slurm script:

#SBATCH --job-name=Lysozyme_in_water_Job
#SBATCH --ntasks=4
#SBATCH --nodes=4
#SBATCH --cpus-per-task=70
#SBATCH --time=01:00:00
#SBATCH --partition=standard
#SBATCH --account=lab

module load gromacs/2022.5
srun gmx mdrun -deffnm md_1ns -v

The performance is:
Core t (s) Wall t (s) (%)
Time: 29466.398 420.952 6999.9
(ns/day) (hour/ns)
Performance: 20.525 1.169

Now I am a bit confused regarding this since increasing the number of nodes should speedup the process; however, in my case the performance is going down. Can someone help me with this. I am sure I am missing out on something.

Thanks in advance

7 posts - 4 participants