ID=119

• Dataset: 6n4o
• Software: NAMD2.cuda.ofi (namd-ofi-smp/2.14-iimklc-2020a-avx2)
• Resource: 4 tasks, 6 cores, nodes, 4 GPUs, no NVLink
• CPU: Xeon E5-2650 (Sandy Bridge), 2.2 GHz
• GPU: Tesla-P100-PCIE-12GB, 6 cores/GPU
• Simulation speed: 6.3307 ns/day
• Efficiency: 46.8 %
• Site: Cedar
• Date: Jan. 22, 2022, 5:55 p.m.
• Submission script:

  !!! MEMORY LEAK !!!
  
  #!/bin/bash
  #SBATCH --ntasks=4 --nodes=1
  #SBATCH --cpus-per-task=6
  #SBATCH --gpus-per-node=p100:4
  #SBATCH --mem-per-cpu=2000 --time=1:0:0
  # Usage: sbatch $0 number_of_steps
  INPFILE=namd.in
  
  STEPS=$1
  TMPFILE=tf_${SLURM_JOBID}
  RUN_IN=run_${SLURM_JOBID}.in
  cp ${INPFILE} ${RUN_IN}
  echo numsteps $1 >> run_${SLURM_JOBID}.in
  ml StdEnv/2020 cuda/11.0 namd-ofi-smp/2.14
  
  echo ${SLURM_NODELIST} running on ${SLURM_CPUS_PER_TASK} cores
  cat /proc/cpuinfo | grep "model name" | uniq
  
  (( NUM_PES=$SLURM_CPUS_PER_TASK - 1 ))
  srun --mpi=pmi2 namd2 ++ppn $NUM_PES +idlepoll ${RUN_IN} > ${TMPFILE}

• Notes:

  # calc_speed.sh
  #!/bin/bash
  echo "Usage: sh cal_speed.sh output_filename nsteps"
  grep CPUTime $1 | cut -f5 -d " " | awk -v steps=$2 '{ print 3.6*2.4*steps*0.01/$1}'

• Simulation input file:

  # Amber/(t,s,x)leap generated parm and crd file  
  parmfile       prmtop.parm7  
  ambercoor      inpcrd.rst7
  # Input 
  bincoordinates  equilibration.coor
  binvelocities   equilibration.vel
  extendedsystem  equilibration.xsc
  # Output 
  restartfreq         10000      
  dcdfreq             10000 
  outputEnergies      10000
  outputPressure      10000 
  outputname          equilibration
  # Number of steps
  # numsteps 10000
  # AMBER Force Field settings
  amber on
  rigidBonds     all 
  useSettle      on 
  rigidTolerance 1.0e-8 
  cutoff         9.0 
  pairlistdist   11.0 
  switching      off 
  exclude        scaled1-4 
  readexclusions yes 
  1-4scaling     0.83333333 
  scnb           2.0 
  zeromomentum   on
  ljcorrection   on
  # Integrator Parameters 
  timestep            1.0 
  nonbondedFreq       1 
  fullElectFrequency  1 
  stepspercycle       10 
  wrapAll on
  # Temperature control
  langevin on
  langevinTemp 300
  langevinDamping 1.0
  # Pressure control
  useGroupPressure yes
  LangevinPiston on
  LangevinPistonTarget 1.0
  LangevinPistonPeriod 200
  LangevinPistonDecay 100
  LangevinPistonTemp 300
  # PME settings 
  PME                 on 
  PMEGridSizeX        144 
  PMEGridSizeY        144 
  PMEGridSizeZ        144