ID=311

• Dataset: 6n4o
• Software: OPENMM.ROCm (container/8.5.0-rocm-7.2.0-avx512)
• Resource: 3 tasks, 24 cores, 1 nodes, 3 GPUs, no NVLink
• CPU: AMD Instinct Accelerator MI300A (Aqua Vanjaram), 2.0 GHz
• GPU: AMD Instinct-MI300A-128GB, 24 cores/GPU
• Simulation speed: 62.863 ns/day
• Efficiency: 42.3 %
• Site: Nibi
• Date: March 13, 2026, 5:10 p.m.
• Submission script:

  #!/bin/bash
  #SBATCH -c72 --gpus-per-node=mi300a:3
  #SBATCH --mem-per-cpu=2000  --time=1:0:0 --partition=debug
  
  module load apptainer
  
  apptainer exec \
  	--cleanenv \
  	--rocm \
          --env SLURM_JOB_GPUS=\$SLURM_JOB_GPUS \
  	--bind /home:/home \
  	--bind /project:/project \
  	ROCm-7.2-dev.sif python3 openmm_input_rocm.py

• Notes:

• Simulation input file:

  import openmm as mm
  import openmm.app as app
  from openmm.unit import *
  import os, time, netCDF4
  from parmed import load_file
  from parmed.openmm import StateDataReporter, NetCDFReporter
  
  nsteps=100000
  dt=1.0
  
  amber_sys=load_file("prmtop.parm7", "restart.rst7")
  ncrst=app.amberinpcrdfile.AmberInpcrdFile("restart.rst7")
  
  system=amber_sys.createSystem(
              nonbondedMethod=app.PME, 
              ewaldErrorTolerance=0.0005,
              nonbondedCutoff=8.0*angstroms,
              constraints=app.HBonds,
              removeCMMotion = True,
  )
  
  integrator = mm.LangevinMiddleIntegrator(300*kelvin, 1.0/picoseconds, dt*femtoseconds,)
  barostat = mm.MonteCarloBarostat(1.0*atmosphere, 300.0*kelvin, 50)
  system.addForce(barostat)
  
  platform = mm.Platform.getPlatformByName("HIP")
  
  prop = dict(
      Precision="mixed", 
      UseCpuPme='false', 
      DeterministicForces="false", 
      DeviceIndex=os.environ["SLURM_JOB_GPUS"],
     )
  
  sim = app.Simulation(amber_sys.topology, system, integrator, platform, prop)
  sim.context.setPositions(amber_sys.positions)
  sim.context.setVelocities(ncrst.velocities)
  
  nonbonded = next(f for f in system.getForces()
                   if isinstance(f, mm.NonbondedForce))
  params = nonbonded.getPMEParametersInContext(sim.context)
  print("Nonbonded settings:")
  print("  Cutoff:", nonbonded.getCutoffDistance())
  print("  Switching enabled:", nonbonded.getUseSwitchingFunction())
  print("  PME alpha:", params[0])
  print("  PME grid:", params[1], params[2], params[3])
  print("  Ewald tolerance:", nonbonded.getEwaldErrorTolerance())
  print("  Method:", nonbonded.getNonbondedMethod())
  
  print("\nAll system forces:")
  for i, force in enumerate(system.getForces()):
      print(f"  {i}: {force.__class__.__name__}")
      if isinstance(force, mm.MonteCarloBarostat):
          print("    Frequency:", force.getFrequency())
          print("    Pressure:", force.getDefaultPressure())
          print("    Temperature:", force.getDefaultTemperature())
  
  print("Warming up")
  sim.step(100)  # Compile all kernels
  sim.context.setTime(0)  # Reset time
  sim.currentStep = 0 
  
  sim.reporters.append(
          StateDataReporter(
              sys.stdout,
              1000,
              step=True,
              time=False,
              potentialEnergy=True,
              kineticEnergy=True,
              temperature=True,
              volume=True
          )
  )
  
  sim.reporters.append(
          NetCDFReporter(
              "trajectory.nc",
              50000,
              crds=True
          )
  )
  
  print("Running dynamics")
  start = time.time()
  sim.step(nsteps)
  elapsed=time.time() - start
  benchmark_time = 0.0864 * nsteps * dt / elapsed
  print(f"Elapsed time: {elapsed} sec\nBenchmark time: {benchmark_time} ns/day, ", end="")