MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

CPUY: CPU years per 1 microsecond long simulation. GPUY: GPU years per 1 microsecond long simulation. | T: tasks | C: cores | N: nodes. Speed is in ns/day. Integration step = 1 fs. Measured with dataset 6n40 (239,131 atoms).

*More information is available by clicking ID in the table above
ID Software Module Toolch Arch Data Speed CPU CPUeff CPUY GPUY T C N GPU NVLink Site
46 PMEMD.cuda.MPI amber/20.12-20.15 gofbc avx2 6n4o 8.71e+01 EPYC 7413 63.2 0.0 0.063 2 1 1 2A100-SXM4 Yes Narval
  • Benchmark submission script:
    #!/bin/bash
    #SBATCH --nodes=1 --ntasks=2 --gpus-per-node=a100:2
    #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
  • 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,
     /