MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=236

  • Dataset: 6n4o
  • Software: NAMD3.cuda (binary_pack/3.0b3------)
  • Resource: 1 tasks, 3 cores, nodes, 3 GPUs, no NVLink
  • CPU: Xeon Gold 6148 (Skylake), 2.4 GHz
  • GPU: Tesla-V100-PCIE-32GB, 10 cores/GPU
  • Simulation speed: 8.252 ns/day
  • Efficiency: 11.2 %
  • Site: Siku
  • Date: Sept. 5, 2023, 8:19 p.m.
  • Submission script:

    #!/bin/bash
    #SBATCH -c3 --gpus-per-node=v100:3
    #SBATCH --mem-per-cpu=2000 --time=1:0:0

    INPUT=namd3_input.in
    NAMDHOME=$HOME/NAMD_3.0b3_Linux-x86_64-multicore-CUDA

    $NAMDHOME/namd3 +p${SLURM_CPUS_PER_TASK} +idlepoll ${INPUT}

  • Notes:

    Performance 8.223050 ns/days, 3 GPUs, cg001
    Performance 8.252000 ns/days, 3 GPUs, cg001

  • Simulation input file:

    # Amber/(t,s,x)leap generated parm and crd file
    parmfile prmtop.parm7
    ambercoor inpcrd.rst7

    # Input
    bincoordinates equilibration.coor
    binvelocities equilibration.vel
    extendedsystem equilibration.xsc
    numsteps 100000
    outputtiming 100000

    # Output
    restartfreq 100000
    dcdfreq 100000
    outputEnergies 2000
    outputPressure 100000
    outputname _prod

    # AMBER FF settings
    amber on
    rigidBonds all
    useSettle on
    rigidTolerance 1.0e-8
    cutoff 8.0
    pairlistdist 11.0
    switching off
    exclude scaled1-4
    readexclusions yes
    1-4scaling 0.83333333
    scnb 2.0
    ljcorrection on

    # Integrator Parameters
    timestep 1.0
    nonbondedFreq 1
    fullElectFrequency 1
    stepspercycle 10
    wrapAll on
    CUDASOAintegrate on

    # Temperature control
    langevin on
    langevinTemp 300
    langevinDamping 1.0

    # Pressure control
    useGroupPressure yes
    LangevinPiston on
    LangevinPistonTarget 1.0
    LangevinPistonPeriod 200
    LangevinPistonDecay 100
    LangevinPistonTemp 300