MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

SOFTWARE DETAILS

ID=4, PMEMD.mpi

  • Module/Version: amber/20.9-20.15
  • Toolchain/Version: gomkl/2020a
  • CPU instruction set: avx512
  • Example job submission script:

    #!/bin/bash
    #SBATCH --ntasks=40 --mem-per-cpu=2000 --time=1:0:0
    module --force purge
    module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 amber/20.9-20.15
    srun pmemd.MPI -O -i pmemd_prod.in -o production.log -p prmtop.parm7 -c restart.rst7

  • Benchmark submission script:
      

    #!/bin/bash
    #SBATCH -c1 --ntasks=40
    #SBATCH --mem-per-cpu=2000 --time=1:0:0
    # Usage: sbatch submit.MPI.sh
    INPFILE=pmemd_prod.in
    STEPS=5000
    # End of user input
    TMPFILE=tf_${SLURM_NTASKS}
    LOGFILE=production_${SLURM_NTASKS}.log
    module --force purge
    ml StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 amber/20
    # Print resource info
    echo ${SLURM_NODELIST} running with ${SLURM_NTASKS} tasks
    cat /proc/cpuinfo | grep "model name" | uniq
    # Run simulation three times
    srun pmemd.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
    grep "Master Total CPU time" $LOGFILE > $TMPFILE
    srun pmemd.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
    grep "Master Total CPU time" $LOGFILE >> $TMPFILE
    srun pmemd.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
    grep "Master Total CPU time" $LOGFILE >> $TMPFILE
    # Print average of three runs.
    echo -n "ns/day:"
    awk -v steps=$STEPS '{total += $6; count++ } END { print count*3.6*2.4*steps*0.01/total}' $TMPFILE
    rm $TMPFILE $LOGFILE mdinfo mdcrd restrt logfile