MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

SOFTWARE DETAILS

ID=12, NAMD2.ucx

  • Module/Version: namd-ucx/2.14
  • Toolchain/Version: iimkl/2020a
  • CPU instruction set: avx512
  • Example job submission script:

    #!/bin/bash
    #SBATCH -c1 --ntasks=20
    #SBATCH --mem-per-cpu=500 --time=1:0:0
    module --force purge
    module load StdEnv/2020 intel/2020.1.217 namd-ucx/2.14
    srun --mpi=pmi2 namd2 namd.in

  • Benchmark submission script:
      

    #!/bin/bash
    #SBATCH -c1 --ntasks=160
    #SBATCH --mem-per-cpu=500 --time=1:0:0
    # Usage: sbatch submit.sh [nsteps]
    INPFILE=namd.in
    #------- End of user input ------
    STEPS=$1
    NP=${SLURM_NTASKS}
    TMPFILE=tf_$NP
    cp $INPFILE run_$NP.in
    echo numsteps $1 >> run_$NP.in
    module --force purge
    module load StdEnv/2020 intel/2020.1.217 namd-ucx/2.14

    echo ${SLURM_NODELIST} running on ${NP} cores
    cat /proc/cpuinfo | grep "model name" | uniq
    # Run simulation three times
    srun --mpi=pmi2 namd2 run_$NP.in > $TMPFILE
    srun --mpi=pmi2 namd2 run_$NP.in >> $TMPFILE
    srun --mpi=pmi2 namd2 run_$NP.in >> $TMPFILE

    # Print average of three runs.
    echo -n "ns/day:"
    grep CPUTime $TMPFILE | cut -f5 -d " " | awk -v steps=$STEPS '{ total += $1; count++ } END { print count*3.6*2.4*steps*0.01/total}'
    rm -f tf_$NP *.restart.* *.old *.BAK *.dcd run_$NP.in