ID=88

• Dataset: 6n4o
• Software: GROMACS.cuda (gromacs/2021.4-gofbc-2020a-avx2)
• Resource: 1 tasks, 12 cores, nodes, 1 GPUs, with NVLink
• CPU: EPYC 7413 (Milan), 2.65 GHz
• GPU: NVIDIA-A100-SXM4-40GB, 12 cores/GPU
• Simulation speed: 50.911 ns/day
• Efficiency: 61.9 %
• Site: Narval
• Date: Dec. 16, 2021, 8:32 p.m.
• Submission script:

• Notes:

  Inconsistent performance:
  jobs 946956-58
  19.267, 30.403, 50.911
  jobs #947618-20
  44.807, 28.639, 45.942
  jobs 948067-69
  22.320 , 33.170 , 45.191

  Without -update gpu:
  27.690 , 29.114 , 30.437, 20.010, 33.940, 28.225, 31.716 , 27.610,

  Set constraint algorithm to LINCS because -update gpu is not supported with SHAKE

  10000 step is not enough for reliable timing, becuse gromacs reports WALL TIME, not CPU TIME.
  I will submit another benchmark done with 400,000 steps.

  ---------8><---------><8----------
  #!/bin/bash
  #SBATCH --mem-per-cpu=2000 --time=1:0:0 -c12 --ntasks=1 --gpus-per-node=1 --nodes=1 -A def-svassili

  export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
  module load StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 gromacs/2021.4
  gmx mdrun -ntomp $OMP_NUM_THREADS -nb gpu -pme gpu -bonded gpu -update gpu -s topol.tpr -cpi state.cpi

  grep Brand md.log
  grep -A1 "Number of GPUs detected:" md.log | tail -n1
  grep "The number of OpenMP threads" md.log
  grep Performance: md.log

• 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