ID=87

• Dataset: 6n4o
• Software: GROMACS.mpi (gromacs/2021.4-gofb-2020a-avx2)
• Resource: 1024 tasks, 1 cores, nodes, 0 GPUs, with NVLink
• CPU: EPYC 7532 (Rome), 2.4 GHz
• GPU: None
• Simulation speed: 45.772 ns/day
• Efficiency: 9.1 %
• Site: Narval
• Date: Dec. 14, 2021, 3:08 a.m.
• Submission script:

• Notes:

  #!/bin/bash
  #SBATCH --mem-per-cpu=4000 --time=2:0:0 -c1 --ntasks=1024 --nodes=16 -A def-svassili

  export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
  module load StdEnv/2020 gcc/9.3.0 openmpi/4.0.3 gromacs/2021.4
  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

  NOTE: 8.6 % of the available CPU time was lost due to load imbalance
  in the domain decomposition.
  Dynamic load balancing was automatically disabled, but it might be benefic
  ial to manually tuning it on (option -dlb on.)
  You can also consider manually changing the decomposition (option -dd);
  e.g. by using fewer domains along the box dimension in which there is
  considerable inhomogeneity in the simulated system.
  NOTE: 19.3 % performance was lost because the PME ranks
  had more work to do than the PP ranks.
  You might want to increase the number of PME ranks
  or increase the cut-off and the grid spacing.

  Will use 640 particle-particle and 384 PME only ranks

• 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