- Dataset: 6n4o
- Software: GROMACS.cuda.mpi (gromacs/2024.1-gofbfc-2023a-avx512)
- Resource: 2 tasks, 12 cores, 1 nodes, 2 GPUs, with NVLink
- CPU: Xeon Gold 5418Y (Sapphire Rapids), 2.0 GHz
- GPU: NVidia-H100-NVL-94GB, 12 cores/GPU
- Simulation speed: 148.586 ns/day
- Efficiency: 50.0 %
- Site: Argo
- Date: Oct. 5, 2024, 1:31 p.m.
- Submission script:
#!/bin/bash
#SBATCH --ntasks=2 --mem-per-cpu=1000 -c12
#SBATCH --gpus-per-task=h100:1 --time=0:30:0 --partition=gpu_general
ml StdEnv/2023 gcc/12.3 openmpi/4.1.5 cuda/12.2 gromacs/2024.1
srun gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK:-1} \
-nb gpu -pme gpu -update gpu -bonded cpu -s topol.tpr
- Notes:
(ns/day) (hour/ns)
Performance: 148.019 0.162
Performance: 148.586 0.162
Performance: 148.343 0.162
- Simulation input file:
title = benchmark
; Run parameters
integrator = md
nsteps = 400000
dt = 0.001
; Output control
nstxout = 0
nstvout = 0
nstfout = 0
nstenergy = 10000
nstlog = 10000
nstxout-compressed = 50000
compressed-x-grps = System
; Bond parameters
continuation = yes
constraint_algorithm = lincs
constraints = h-bonds
; Neighborsearching
cutoff-scheme = Verlet
ns_type = grid
nstlist = 10
rcoulomb = 0.8
rvdw = 0.8
DispCorr = Ener ; anaytic VDW correction
; Electrostatics
coulombtype = PME
pme_order = 4
fourier-nx = 144
fourier-ny = 144
fourier-nz = 144
; Temperature coupling is on
tcoupl = V-rescale
tc-grps = system
tau_t = 0.1
ref_t = 300
; Pressure coupling is on
pcoupl = Parrinello-Rahman
pcoupltype = isotropic
tau_p = 2.0
ref_p = 1.0
compressibility = 4.5e-5
; Periodic boundary conditions
pbc = xyz
; Velocity generation
gen_vel = no