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