ID=108

• Dataset: 6n4o
• Software: PMEMD.mpi (amber/20.9-20.15-gomkl-2020a-avx2)
• Resource: 512 tasks, 1 cores, nodes, 0 GPUs, with NVLink
• CPU: EPYC 7532 (Rome), 2.4 GHz
• GPU: None
• Simulation speed: 11.7359 ns/day
• Efficiency: 24.3 %
• Site: Narval
• Date: Dec. 27, 2021, 2:09 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH --nodes=8 --ntasks=512 
  #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 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.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7

• Notes:

  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,
   /