ID=9, NAMD2.ucx

• Module/Version: namd-ucx/2.14
• Toolchain/Version: iimkl/2020a
• CPU instruction set: avx2
• Example job submission script:

  #!/bin/bash 
  #SBATCH -c1 --ntasks=20 
  #SBATCH --mem-per-cpu=500 --time=1:0:0  
  module --force purge  
  module load StdEnv/2020 intel/2020.1.217 namd-ucx/2.14  
  srun --mpi=pmi2 namd2 namd.in
  

• Benchmark submission script:

  #!/bin/bash
  #SBATCH -c1 --ntasks=160
  #SBATCH --mem-per-cpu=500 --time=1:0:0
  # Usage: sbatch submit.sh [nsteps] 
  INPFILE=namd.in
  #------- End of user input ------
  STEPS=$1
  NP=${SLURM_NTASKS}
  TMPFILE=tf_$NP
  cp $INPFILE run_$NP.in
  echo numsteps $1 >> run_$NP.in
  module --force purge
  module load StdEnv/2020 intel/2020.1.217 namd-ucx/2.14
  
  echo ${SLURM_NODELIST} running on ${NP} cores
  cat /proc/cpuinfo | grep "model name" | uniq
  # Run simulation three times
  srun --mpi=pmi2 namd2 run_$NP.in > $TMPFILE
  srun --mpi=pmi2 namd2 run_$NP.in >> $TMPFILE
  srun --mpi=pmi2 namd2 run_$NP.in >> $TMPFILE
  
  # Print average of three runs. 
  echo -n "ns/day:"
  grep CPUTime $TMPFILE  | cut -f5 -d " " | awk  -v steps=$STEPS  '{ total += $1; count++ } END { print count*3.6*2.4*steps*0.01/total}'
  rm -f tf_$NP *.restart.* *.old *.BAK *.dcd run_$NP.in