ID=236

• Dataset: 6n4o
• Software: NAMD3.cuda (binary_pack/3.0b3------)
• Resource: 1 tasks, 3 cores, nodes, 3 GPUs, no NVLink
• CPU: Xeon Gold 6148 (Skylake), 2.4 GHz
• GPU: Tesla-V100-PCIE-32GB, 10 cores/GPU
• Simulation speed: 8.252 ns/day
• Efficiency: 11.2 %
• Site: Siku
• Date: Sept. 5, 2023, 8:19 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH -c3 --gpus-per-node=v100:3
  #SBATCH --mem-per-cpu=2000 --time=1:0:0
  
  INPUT=namd3_input.in 
  NAMDHOME=$HOME/NAMD_3.0b3_Linux-x86_64-multicore-CUDA
  
  $NAMDHOME/namd3 +p${SLURM_CPUS_PER_TASK} +idlepoll ${INPUT}

• Notes:

  Performance 8.223050 ns/days, 3 GPUs, cg001
  Performance 8.252000 ns/days, 3 GPUs, cg001

• 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