ID=28

• Dataset: 6n4o
• Software: NAMD3.cuda (binary_pack/3.0a9------)
• Resource: 1 tasks, 2 cores, nodes, 2 GPUs, no NVLink
• CPU: Xeon Gold 6148 (Skylake), 2.4 GHz
• GPU: Tesla-V100-PCIE-32GB, 8 cores/GPU
• Simulation speed: 22.7408 ns/day
• Efficiency: 56.3 %
• Site: Siku
• Date: Jan. 31, 2022, 1:44 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH -c2 --gres=gpu:v100:2
  #SBATCH --mem-per-cpu=2000 --time=1:0:0
  # Usage: sbatch submit.cuda.sh [number_of_steps]
  INPFILE=namd.in
  #------- End of user input ------
  STEPS=$1
  TMPFILE=tf_${SLURM_CPUS_PER_TASK}
  cp $INPFILE run_${SLURM_CPUS_PER_TASK}.in
  echo numsteps $1 >> run_${SLURM_CPUS_PER_TASK}.in
  echo "CUDASOAintegrate on" >> run_${SLURM_CPUS_PER_TASK}.in 
  NAMDHOME=$HOME/NAMD_3.0alpha9_Linux-x86_64-multicore-CUDA
  
  echo ${SLURM_NODELIST} running on ${SLURM_CPUS_PER_TASK} cores
  cat /proc/cpuinfo | grep "model name" | uniq
  nvidia-smi -L 
  # Run simulation three times
  $NAMDHOME/namd3 +p${SLURM_CPUS_PER_TASK} +idlepoll run_${SLURM_CPUS_PER_TASK}.in > $TMPFILE
  $NAMDHOME/namd3 +p${SLURM_CPUS_PER_TASK} +idlepoll run_${SLURM_CPUS_PER_TASK}.in > $TMPFILE
  $NAMDHOME/namd3 +p${SLURM_CPUS_PER_TASK} +idlepoll run_${SLURM_CPUS_PER_TASK}.in > $TMPFILE
  
  # Print average of three runs. 
  echo -n "ns/day:"
  grep CPUTime $TMPFILE  | cut -f5 -d " " | awk  -v steps=$STEPS  '{ total += $1; count++ } END { print count*3.6*2.4*steps*0.01/total}' 
  rm -f tf_* *.restart.*  *.old  *.BAK run_${SLURM_CPUS_PER_TASK}.in

• Notes:

• Simulation input file:

  # Amber/(t,s,x)leap generated parm and crd file  
  parmfile       prmtop.parm7
  ambercoor      inpcrd.rst7
  # GPU-resident integrator
  CUDASOAintegrate on
  numsteps 10000
  # Input 
  bincoordinates  equilibration.coor
  binvelocities   equilibration.vel
  extendedsystem  equilibration.xsc
  # Output 
  restartfreq         10000
  dcdfreq             10000
  outputEnergies      10000
  outputPressure      10000
  outputname          equilibration
  # AMBER FF settings
  amber on
  rigidBonds     all
  useSettle      on
  rigidTolerance 1.0e-8
  cutoff         9.0
  pairlistdist   11.0
  switching      off
  exclude        scaled1-4
  readexclusions yes
  1-4scaling     0.83333333
  scnb           2.0
  ljcorrection   on
  # Integrator Parameters 
  timestep            1.0
  nonbondedFreq       1
  fullElectFrequency  1
  stepspercycle       10
  wrapAll on
  # Temperature control
  langevin on
  langevinTemp 300
  langevinDamping 1.0
  # Pressure control
  useGroupPressure yes
  LangevinPiston on
  LangevinPistonTarget 1.0
  LangevinPistonPeriod 200
  LangevinPistonDecay 100
  LangevinPistonTemp 300
  # PME settings 
  PME                 on
  PMEGridSizeX        144
  PMEGridSizeY        144
  PMEGridSizeZ        144