MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=105

  • Dataset: 6n4o
  • Software: PMEMD.cuda.MPI (amber/20.9-20.15-gomklc-2020a-avx512)
  • Resource: 4 tasks, 1 cores, nodes, 4 GPUs, with NVLink
  • CPU: Xeon Silver 4216 (Cascade Lake), 2.1 GHz
  • GPU: Tesla-V100-SXM2-32GB, 5 cores/GPU
  • Simulation speed: 53.6896 ns/day
  • Efficiency: 32.4 %
  • Site: Cedar
  • Date: Jan. 14, 2022, 3:02 p.m.
  • Submission script:

    #!/bin/bash
    #SBATCH --nodes=1 --ntasks=4 --gpus-per-node=v100l:4
    #SBATCH --mem-per-cpu=2000 --time=1:0:0

    INPFILE=pmemd_prod.in
    LOGFILE=production_${SLURM_JOBID}.log

    module --force purge
    ml StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 amber/20.9-20.15

    srun pmemd.cuda.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7

  • Notes:

    Benchmark submission:

    #!/bin/bash
    #SBATCH --nodes=1 --ntasks=4 --gpus-per-node=v100l:4
    #SBATCH --mem-per-cpu=2000 --time=1:0:0
    # Usage: sbatch submit.cuda.sh]

    INPFILE=pmemd_prod.in
    LOGFILE=production_${SLURM_JOBID}.log

    module --force purge
    ml StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 amber/20.9-20.15

    # Print resource info
    echo ${SLURM_NODELIST} running on ${SLURM_NTASKS} tasks
    cat /proc/cpuinfo | grep "model name" | uniq
    # Run simulation
    srun pmemd.cuda.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7

    Calculate speed:

    #!/bin/bash
    STEPS=40000
    grep "NonSetup CPU time" production_*.log > tmp
    awk -v steps=$STEPS '{ print 3.6*2.4*steps*0.01/$6 }' tmp
    rm tmp

  • 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,
    /