ID=145

• Dataset: 6n4o
• Software: PMEMD.cuda.MPI (amber/20.12-20.15-gofbc-2020.1.403.114-avx2)
• Resource: 3 tasks, 1 cores, nodes, 3 GPUs, with NVLink
• CPU: EPYC 7413 (Milan), 2.65 GHz
• GPU: NVIDIA-A100-SXM4-40GB, 12 cores/GPU
• Simulation speed: 15.5305 ns/day
• Efficiency: 7.5 %
• Site: Narval
• Date: Feb. 2, 2022, 4:31 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH --nodes=1 --ntasks=3 --gpus-per-node=a100:3
  #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

• Notes:

• 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,
   /