ID=63

• Dataset: 6n4o
• Software: GROMACS.cuda (gromacs/2021.2-gomklc-2020a-avx512)
• Resource: 2 tasks, 8 cores, nodes, 2 GPUs, no NVLink
• CPU: Xeon Gold 6148 (Skylake), 2.4 GHz
• GPU: Tesla-V100-PCIE-32GB, 8 cores/GPU
• Simulation speed: 12.222 ns/day
• Efficiency: 15.8 %
• Site: Siku
• Date: Dec. 15, 2021, 3:41 p.m.
• Submission script:

• Notes:

  #!/bin/bash
  #SBATCH --mem-per-cpu=2000 --time=1:0:0 -c8 --ntasks=2 --nodes=1 --gpus-per-node=v100:2
  export OMP_NUM_THREADS="${SLURM_CPUS_PER_TASK:-1}"
  module load StdEnv/2020 gcc/9.3.0 cuda/11.0 openmpi/4.0.3 gromacs/2021.2
  srun gmx_mpi mdrun -s next.tpr -cpi state.cpi

• 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