ID=152

• Dataset: 6n4o
• Software: NAMD3.cuda (binary_pack/3.0a9------)
• Resource: 1 tasks, 3 cores, nodes, 3 GPUs, with NVLink
• CPU: Xeon Silver 4216 (Cascade Lake), 2.1 GHz
• GPU: Tesla-V100-SXM2-32GB, 5 cores/GPU
• Simulation speed: 39.023 ns/day
• Efficiency: 70.4 %
• Site: Cedar
• Date: Feb. 7, 2022, 11:29 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH -c3 --gpus=v100l:3 --nodes=1
  #SBATCH --mem-per-cpu=2000 --time=1:0:0
  # Usage: sbatch $0 numsteps
  INPFILE=namd.in
  
  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
  $NAMDHOME/namd3 +p${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}'

• 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