ID=246

• Dataset: 6n4o
• Software: NAMD3.cuda (binary_pack/3.0------)
• Resource: 1 tasks, 2 cores, nodes, 2 GPUs, with NVLink
• CPU: Xeon Gold 5418Y (Sapphire Rapids), 3.8 GHz
• GPU: NVIDIA-H100 NVL-94GB, 12 cores/GPU
• Simulation speed: 91.6243 ns/day
• Efficiency: 72.7 %
• Site: Argo
• Date: Oct. 6, 2024, 1:57 p.m.
• Submission script:

  #!/bin/bash
  
  if [ $# -ne 1 ] 
  then
  	echo 'Usage: bash submit.namd3.cuda.sh <nGPUs>'
  	exit 1
  fi
  
  sbatch << EOF
  #!/bin/bash
  #SBATCH -c${1} --gres=gpu:h100:${1} 
  #SBATCH --mem-per-cpu=2000  --time=0:30:0 --partition=tech
  
  INPUT=namd3_input.in 
  NAMDHOME=\$HOME/NAMD_3.0_Linux-x86_64-multicore-CUDA
  
  nvidia-smi -L 
  
  \$NAMDHOME/namd3 +p\${SLURM_CPUS_PER_TASK} +idlepoll \${INPUT} 
  
  cat /proc/cpuinfo | grep "model name" | uniq
  grep  TIMING: slurm*.out | awk '{printf "Performance %f %s ",\$9,\$10}'
  echo -n $1 "GPUs, " 
  hostname -s
  
  EOF

• Notes:

  Performance 90.895700 ns/days
  Performance 91.109300 ns/days
  Performance 91.624300 ns/days

• Simulation input file:

  # Amber/(t,s,x)leap generated parm and crd file  
  parmfile       prmtop.parm7  
  ambercoor      inpcrd.rst7
  
  # Input 
  bincoordinates  equilibration.coor
  binvelocities   equilibration.vel
  extendedsystem  equilibration.xsc
  numsteps 100000
  outputtiming 100000
  
  # Output 
  restartfreq         100000      
  dcdfreq             100000 
  outputEnergies      2000
  outputPressure      100000 
  outputname          _prod
  
  # AMBER FF settings
  amber on
  rigidBonds     all 
  useSettle      on 
  rigidTolerance 1.0e-8 
  cutoff         8.0 
  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
  CUDASOAintegrate 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