ID=183

• Dataset: 6n4o
• Software: PMEMD.cuda.MPI (amber/20.9-20.15-gomklc-2020a-avx512)
• Resource: 4 tasks, 1 cores, nodes, 4 GPUs, no NVLink
• CPU: Xeon Gold 5120 (Skylake), 2.2 GHz
• GPU: Tesla-V100-PCIE-16GB, 4 cores/GPU
• Simulation speed: 32.9624 ns/day
• Efficiency: 20.4 %
• Site: Graham
• Date: Oct. 19, 2022, 12:38 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH --nodes=1 --ntasks=4 --gpus-per-node=v100:4
  #SBATCH --mem-per-cpu=2000 --time=1:0:0
  INPFILE=pmemd_prod.in
  LOGFILE=md_${SLURM_JOBID}.log 
  module --force purge
  ml StdEnv/2020  gcc/9.3.0 cuda/11.0 openmpi/4.0.3 amber/20.9-20.15 
  srun pmemd.cuda.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7

• Notes:

  Benchmark submission:

  #!/bin/bash
  #SBATCH --nodes=1 --ntasks=4 --gpus-per-node=v100:4
  #SBATCH --mem-per-cpu=2000 --time=1:0:0
  # Usage: sbatch submit.cuda.sh]
  INPFILE=pmemd_prod.in
  STEPS=20000
  # End of user input
  TMPFILE=tf_${SLURM_NTASKS}
  LOGFILE=production_${SLURM_NTASKS}.log
  module --force purge
  ml StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 amber/20
  # Print resource info
  echo ${SLURM_NODELIST} running on ${SLURM_NTASKS} cores
  cat /proc/cpuinfo | grep "model name" | uniq
  # Run simulation three times
  srun pmemd.cuda.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
  grep "NonSetup CPU time" $LOGFILE > $TMPFILE
  srun pmemd.cuda.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
  grep "NonSetup CPU time" $LOGFILE >> $TMPFILE
  srun pmemd.cuda.MPI -O -i $INPFILE -o $LOGFILE -p prmtop.parm7 -c restart.rst7
  grep "NonSetup 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

• 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,
   /