MOLECULAR DYNAMICS PERFORMANCE GUIDE - Digital Research Alliance of CANADA

BENCHMARK DETAILS

ID=210

  • Dataset: 6n4o
  • Software: GROMACS.cuda (gromacs/2023.2-gofbfc-2020.1.403.114-avx2)
  • Resource: 1 tasks, 32 cores, nodes, 4 GPUs, with NVLink
  • CPU: Xeon Silver 4216 (Cascade Lake), 2.1 GHz
  • GPU: Tesla-V100-SXM2-32GB, 8 cores/GPU
  • Simulation speed: 48.287 ns/day
  • Efficiency: 27.1 %
  • Site: Cedar
  • Date: Aug. 9, 2023, 4:46 p.m.
  • Submission script:
    #!/bin/bash
    #SBATCH  --mem-per-cpu 2000 --time 1:0:0   
    #SBATCH -c 32 --gpus-per-node v100l:4
    


    td=$SLURM_TMPDIR
    wd=$SLURM_SUBMIT_DIR
    cp topol.tpr $td && cd $td
    


    module load StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 gromacs/2023.2
    


    gmx mdrun -ntomp ${SLURM_CPUS_PER_TASK:-1} \
    -nb gpu -pme gpu -update gpu -bonded cpu -s topol.tpr
    


    cp md.log $wd
  • Notes:

    (ns/day) (hour/ns)
    Performance: 48.287 0.497
    Performance: 48.235 0.498
    Performance: 48.217 0.498
    Performance: 48.216 0.498
    Performance: 48.113 0.499

  • 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