ID=102

• Dataset: 6n4o
• Software: PMEMD.cuda (amber/20.9-20.15-gomklc-2020a-avx512)
• Resource: 1 tasks, 1 cores, nodes, 1 GPUs, no NVLink
• CPU: Xeon E5-2650 (Sandy Bridge), 2.2 GHz
• GPU: Tesla-P100-PCIE-12GB, 16 cores/GPU
• Simulation speed: 14.9455 ns/day
• Efficiency: 100.0 %
• Site: Cedar
• Date: Dec. 23, 2021, 4:29 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH --mem-per-cpu=2000 --time=1:0:0 --gpus=p100:1 
  
  module --force purge
  module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 amber/20.9-20.15
  
  nvidia-smi --query-gpu=gpu_name --format=csv
  pmemd.cuda -O -i pmemd_prod.in -o production.log -p prmtop.parm7 -c restart.rst7

• Notes:

• 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,
   /