MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=107

  • Dataset: 6n4o
  • Software: PMEMD.cuda.MPI (amber/20.9-20.15-gomklc-2020a-avx512)
  • Resource: 2 tasks, 1 cores, nodes, 2 GPUs, no NVLink
  • CPU: Xeon E5-2650 (Sandy Bridge), 2.2 GHz
  • GPU: Tesla-P100-PCIE-12GB, 16 cores/GPU
  • Simulation speed: 17.3381 ns/day
  • Efficiency: 58.0 %
  • Site: Cedar
  • Date: Jan. 14, 2022, 3:03 p.m.
  • Submission script:

    #!/bin/bash
    #SBATCH --nodes=1 --ntasks=2 --gpus-per-node=p100:2
    #SBATCH --mem-per-cpu=2000 --time=1:0:0

    INPFILE=pmemd_prod.in
    STEPS=40000
    # End of user input
    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
    #rm $TMPFILE $LOGFILE mdinfo mdcrd restrt

  • Notes:

    Inconsistent performance. One day on nodes, cdr340 and cdr341 speed was only about 9 ns/day. Two days later speed was back to normal.

    Compare jobs 22449024 and 22503974. Note abnormal RAM usage of the slow job 22449024. Nvidia-smi showed only three running processes for 22449024, while normal jobs had four.

    Script to 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,
    /