ID=94

• Dataset: 6n4o
• Software: GROMACS.mpi (gromacs/2021.2-gomkl-2020.a-avx512)
• Resource: 1280 tasks, 1 cores, nodes, 0 GPUs, no NVLink
• CPU: Xeon Gold 6148 (Skylake), 2.4 GHz
• GPU: None
• Simulation speed: 53.027 ns/day
• Efficiency: 9.5 %
• Site: Niagara
• Date: Dec. 15, 2021, 5:32 p.m.
• Submission script:

• Notes:

  #!/bin/bash
  #SBATCH --nodes=16 --ntasks=1280 --time=0:30:0

  export OMP_NUM_THREADS="1"
  module load CCEnv StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.2
  srun gmx_mpi mdrun -s topol.tpr -cpi state.cpi
  
  grep Brand md.log
  grep "The number of OpenMP threads" md.log
  grep "MPI pro" md.log
  echo ntasks=$SLURM_TASKS_PER_NODE

• Simulation input file:

  title                   = benchmark 
  ; Run parameters
  integrator              = md     
  nsteps                  = 400000     
  dt                      = 0.001    
  ; Output control
  nstxout                 = 0       
  nstvout                 = 0     
  nstfout                 = 0        
  nstenergy            = 10000    
  nstlog                  = 10000   
  nstxout-compressed     = 50000   
  compressed-x-grps       = System 
  ; Bond parameters
  continuation            = yes      
  constraint_algorithm    = lincs    
  constraints             = h-bonds  
  
  ; Neighborsearching
  cutoff-scheme           = Verlet   
  ns_type                 = grid  
  nstlist                 = 10  
  rcoulomb                = 0.8    
  rvdw                    = 0.8
  DispCorr                = Ener ; anaytic VDW correction 
  ; Electrostatics
  coulombtype             = PME    
  pme_order               = 4        
  fourier-nx              = 144
  fourier-ny              = 144
  fourier-nz              = 144
  ; Temperature coupling is on
  tcoupl                  = V-rescale 
  tc-grps                 = system
  tau_t                   = 0.1             
  ref_t                   = 300   
  ; Pressure coupling is on
  pcoupl                  = Parrinello-Rahman  
  pcoupltype              = isotropic   
  tau_p                   = 2.0      
  ref_p                   = 1.0   
  compressibility         = 4.5e-5   
  ; Periodic boundary conditions
  pbc                     = xyz 
  ; Velocity generation
  gen_vel                 = no