MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=53

  • Dataset: 6n4o
  • Software: NAMD3.cuda (binary_pack/3.0a9------)
  • Resource: 1 tasks, 1 cores, nodes, 1 GPUs, no NVLink
  • CPU: Xeon E5-2650 (Sandy Bridge), 2.2 GHz
  • GPU: Tesla-P100-PCIE-12GB, 16 cores/GPU
  • Simulation speed: 8.79674 ns/day
  • Efficiency: 100.0 %
  • Site: Cedar
  • Date: Nov. 30, 2021, 6:41 p.m.
  • Submission script:

  • Notes:

    #SBATCH -c1 --gpus=p100:1 --nodes=1

  • Simulation input file:

    # Amber/(t,s,x)leap generated parm and crd file
    parmfile prmtop.parm7
    ambercoor inpcrd.rst7
    # GPU-resident integrator
    CUDASOAintegrate on
    numsteps 10000
    # Input
    bincoordinates equilibration.coor
    binvelocities equilibration.vel
    extendedsystem equilibration.xsc
    # Output
    restartfreq 10000
    dcdfreq 10000
    outputEnergies 10000
    outputPressure 10000
    outputname equilibration
    # AMBER FF 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
    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