MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=164

  • Dataset: 6n4o
  • Software: NAMD2.ucx (namd-ucx/2.14-iimkl-2020a-avx2)
  • Resource: 8 tasks, 1 cores, nodes, 0 GPUs, no NVLink
  • CPU: Xeon Platinum 8160 (Skylake), 2.1 GHz
  • GPU: None
  • Simulation speed: 0.38 ns/day
  • Efficiency: 59.4 %
  • Site: Cedar
  • Date: April 28, 2022, 5:50 p.m.
  • Submission script:

    #!/bin/bash
    #SBATCH -c1 --ntasks=8
    #SBATCH --mem-per-cpu=4000 --time=3:0:0
    module --force purge
    module load StdEnv/2020 intel/2020.1.217 namd-ucx/2.14
    srun --mpi=pmi2 namd2 mdin.in

  • Notes:

  • 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
    # Output
    restartfreq 10000
    dcdfreq 10000
    outputEnergies 10000
    outputPressure 10000
    outputname equilibration
    # Number of steps
    # numsteps 10000
    # AMBER Force Field settings
    amber on
    rigidBonds all
    useSettle on
    rigidTolerance 1.0e-8
    cutoff 9.0
    pairlistdist 11.0
    switching off
    exclude scaled1-4
    readexclusions yes
    1-4scaling 0.83333333
    scnb 2.0
    zeromomentum on
    ljcorrection on
    # Integrator Parameters
    timestep 1.0
    nonbondedFreq 1
    fullElectFrequency 1
    stepspercycle 10
    wrapAll 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
    # PME settings
    PME on
    PMEGridSizeX 144
    PMEGridSizeY 144
    PMEGridSizeZ 144