ID=308

• Dataset: 9naw
• Software: GROMACS.ROCm (container/2026.0-SYCL (Adaptive CPP)-rocm-7.2.0-avx512)
• Resource: 2 tasks, 24 cores, 1 nodes, 2 GPUs, no NVLink
• CPU: AMD Instinct Accelerator MI300A (Aqua Vanjaram), 2.0 GHz
• GPU: AMD Instinct-MI300A-128GB, 24 cores/GPU
• Simulation speed: 12.613 ns/day
• Efficiency: 35.0 %
• Site: Nibi
• Date: March 12, 2026, 4:04 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH --gpus=mi300a:2
  #SBATCH --mem-per-cpu=4000 
  #SBATCH --time=1:0:0 
  #SBATCH --ntasks=4
  #SBATCH --cpus-per-task=24
  
  module load apptainer/1.3.5
  
  apptainer run --rocm gromacs_amd.sif gmx mdrun \
    -ntmpi 16 \
    -ntomp 6 \
    -npme 1 \
    -nb gpu \
    -pme gpu \
    -update gpu \
    -bonded gpu \
    -nstlist 300 \
    -noconfout \
    -s topol.tpr \

• Notes:

• Simulation input file:

  title                   = benchmark 
  ; Run parameters
  integrator              = md     
  nsteps                  = 100000    
  dt                      = 0.002    
  ; Output control
  nstxout                 = 0       
  nstvout                 = 0     
  nstfout                 = 0        
  nstenergy               = 1000    
  nstlog                  = 500    
  nstxout-compressed      = 5000   
  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              = 324
  fourier-ny              = 324
  fourier-nz              = 324
  ; 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