ID=259

• Dataset: 6n4o
• Software: PMEMD.cuda (amber/24.3-gofbc-2023a-avx512)
• Resource: 1 tasks, 1 cores, nodes, 1 GPUs, with NVLink
• CPU: EPYC 9654 (Genoa), 2.4 GHz
• GPU: NVidia-H100-SXM5-80GB, 16 cores/GPU
• Simulation speed: 110.12 ns/day
• Efficiency: 100.0 %
• Site: Rorqual
• Date: Aug. 8, 2025, 2:57 a.m.
• Submission script:

  #!/bin/bash
  #SBATCH -c1 --gres=gpu:h100:1  --mem-per-cpu=2000 --time=20:0
  
  module --force purge
  module load StdEnv/2023  gcc/12.3  openmpi/4.1.5  cuda/12.2 amber/24.3
  
  # Run simulation 
  pmemd.cuda -O -i pmemd_prod.in -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,
   /