ID=17, NAMD2.cuda

• Module/Version: namd-multicore/2.14
• Toolchain/Version: iccifortcuda/2020.1.114
• CPU instruction set: avx2
• Example job submission script:

  #!/bin/bash
  #SBATCH -c8 --gpus=1
  #SBATCH --mem-per-cpu=2000 --time=1:0:0
  
  module load StdEnv/2020 intel/2020.1.217 cuda/11.4 namd-multicore/2.14
  namd2 +p${SLURM_CPUS_PER_TASK} +idlepoll run.in

• Benchmark submission script:

    
  #!/bin/bash
  #SBATCH -c8 --gpus=1
  #SBATCH --mem-per-cpu=2000 --time=1:0:0
  # Usage: sbatch submit.cuda.sh [number_of_steps]
  INPFILE=namd.in
  #------- End of user input ------
  STEPS=$1
  TMPFILE=tf_${SLURM_CPUS_PER_TASK}
  cp $INPFILE run.in
  echo numsteps $1 >> run.in
  module load StdEnv/2020 intel/2020.1.217 cuda/11.4 namd-multicore/2.14
  
  echo ${SLURM_NODELIST} running on ${SLURM_CPUS_PER_TASK} cores
  cat /proc/cpuinfo | grep "model name" | uniq
  # Run simulation three times
  namd2 +p${SLURM_CPUS_PER_TASK} +idlepoll run.in > $TMPFILE
  namd2 +p${SLURM_CPUS_PER_TASK} +idlepoll run.in >> $TMPFILE
  namd2 +p${SLURM_CPUS_PER_TASK} +idlepoll run.in >> $TMPFILE
  
  # Print average of three runs. 
  echo -n "ns/day:"
  grep CPUTime $TMPFILE  | cut -f5 -d " " | awk  -v steps=$STEPS  '{ total += $1; count++ } END { print count*3.6*2.4*steps*0.01/total}' 
  #rm -f tf_* *.restart.*  *.old  *.BAK run.in