- Dataset: 6n4o
- Software: GROMACS.mpi (gromacs/2024.4-gofb-2023a-avx512)
- Resource: 384 tasks, 1 cores, nodes, 0 GPUs, no NVLink
- CPU: EPYC 9654 (Genoa), 2.4 GHz
- GPU: None
- Simulation speed: 86.467 ns/day
- Efficiency: 25.7 %
- Site: Rorqual
- Date: Aug. 1, 2025, 9:05 p.m.
- Submission script:
#!/bin/bash
#SBATCH --mem-per-cpu=2000 --time=1:0:0 -c1 --ntasks=384--nodes=1
export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
module load StdEnv/2023 gcc/12.3 openmpi/4.1.5 gromacs/2024.4
srun gmx_mpi mdrun -s topol.tpr
- Notes:
Trial speeds (ns/day): 86.467 86.059 85.844 85.588 84.596 84.493 83.737 83.333 83.148 81.704 78.816
- 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