ID=212

• Dataset: 6n4o
• Software: GROMACS.cuda.mpi (gromacs/2023.2-gofbfc-2020.1.403.114-avx2)
• Resource: 2 tasks, 8 cores, nodes, 2 GPUs, with NVLink
• CPU: Xeon Silver 4216 (Cascade Lake), 2.1 GHz
• GPU: Tesla-V100-SXM2-32GB, 8 cores/GPU
• Simulation speed: 43.875 ns/day
• Efficiency: 49.2 %
• Site: Cedar
• Date: Aug. 10, 2023, 12:35 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH  --mem-per-cpu 2000 --time 1:0:0   
  #SBATCH  --nodes 1 --ntasks 2 -c 8 --gpus-per-task 1  
  
  module load StdEnv/2020 gcc/9.3.0 cuda/11.4 openmpi/4.0.3 gromacs/2023.2
  
  td=$SLURM_TMPDIR
  wd=$SLURM_SUBMIT_DIR
  cp topol.tpr $td && cd $td
  
  srun 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: 43.875 0.547
  Performance: 41.948 0.572
  Performance: 41.407 0.580
  Performance: 23.830 1.007

• 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