MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=145

  • Dataset: 6n4o
  • Software: PMEMD.cuda.MPI (amber/20.12-20.15-gofbc-2020.1.403.114-avx2)
  • Resource: 3 tasks, 1 cores, nodes, 3 GPUs, with NVLink
  • CPU: EPYC 7413 (Milan), 2.65 GHz
  • GPU: NVIDIA-A100-SXM4-40GB, 12 cores/GPU
  • Simulation speed: 15.5305 ns/day
  • Efficiency: 7.5 %
  • Site: Narval
  • Date: Feb. 2, 2022, 4:31 p.m.
  • Submission script:

    #!/bin/bash
    #SBATCH --nodes=1 --ntasks=3 --gpus-per-node=a100:3
    #SBATCH --mem-per-cpu=2000 --time=1:0:0
    # Usage: sbatch $0

    INPFILE=pmemd_prod.in
    STEPS=40000
    TMPFILE=tf_${SLURM_NTASKS}
    LOGFILE=production_${SLURM_NTASKS}.log
    module --force purge
    ml StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 amber/20.12-20.15

    # Print resource info
    echo ${SLURM_NODELIST} running on ${SLURM_NTASKS} tasks
    cat /proc/cpuinfo | grep "model name" | uniq

    srun pmemd.cuda_SPFP.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
    grep "NonSetup CPU time" $LOGFILE > $TMPFILE

    echo -n "ns/day:"
    awk -v steps=$STEPS '{ print 3.6*2.4*steps*0.01/$6 }' $TMPFILE

  • Notes:

  • Simulation input file:

    Benchmark
    &cntrl
    imin=0,irest=1,ntx=5,
    nstlim=20000,dt=0.001,
    ntc=2,ntf=2,
    cut=8.0,
    ntpr=100, ntwx=1000,
    ntb=2, ntp=1, taup=2.0,
    ntt=3, gamma_ln=2.0, temp0=300.0,
    /
    &ewald
    nfft1=128,
    nfft2=128,
    nfft3=128,
    /