MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=203

  • Dataset: 6n4o
  • Software: GROMACS.cuda.mpi (gromacs/2023.2-gofbfc-2020.1.403.114-avx2)
  • Resource: 2 tasks, 12 cores, nodes, 2 GPUs, with NVLink
  • CPU: EPYC 7413 (Milan), 2.65 GHz
  • GPU: NVIDIA-A100-SXM4-40GB, 12 cores/GPU
  • Simulation speed: 98.394 ns/day
  • Efficiency: 55.7 %
  • Site: Narval
  • Date: Aug. 9, 2023, 1:29 a.m.
  • Submission script:

    #!/bin/bash
    #SBATCH --mem-per-cpu 2000 --time 1:0:0
    #SBATCH --nodes 1 --ntasks 2 -c 12 --gpus-per-task 1

    module load StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 gromacs/2023.2

    td=$SLURM_TMPDIR
    wd=$SLURM_SUBMIT_DIR
    cp topol.tpr $td && cd $td

    srun gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK:-1} \
    -nb gpu -pme gpu -update gpu -bonded cpu -s topol.tpr

    cp md.log $wd

  • Notes:

    (ns/day) (hour/ns)
    Performance: 98.394 0.244
    Performance: 96.326 0.249
    Performance: 94.558 0.254
    Performance: 93.623 0.256
    Performance: 93.050 0.258
    Performance: 93.032 0.258
    Performance: 92.584 0.259
    Performance: 91.398 0.263
    Performance: 88.407 0.271
    Performance: 85.253 0.282
    Performance: 84.896 0.283
    Performance: 83.536 0.287
    Performance: 81.737 0.294
    Performance: 81.563 0.294
    Performance: 80.620 0.298
    Performance: 80.316 0.299
    Performance: 77.790 0.309
    Performance: 75.781 0.317
    Performance: 75.455 0.318
    Performance: 73.165 0.328

  • 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