MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=99

  • Dataset: 6n4o
  • Software: GROMACS.mpi (gromacs/2021.2-gomkl-2020.a-avx512)
  • Resource: 40 tasks, 1 cores, nodes, 0 GPUs, no NVLink
  • CPU: Xeon Gold 6148 (Skylake), 2.4 GHz
  • GPU: None
  • Simulation speed: 10.998 ns/day
  • Efficiency: 63.2 %
  • Site: Niagara
  • Date: Dec. 22, 2021, 4:47 p.m.
  • Submission script:
    #!/bin/bash
    #SBATCH --nodes=1 --ntasks=40 --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
    grep Performance: md.log
  • Notes:

  • 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