poptbench

#!/bin/bash
#
# script to benchmark COPASI's parallel optimization
# make sure that the .cps files passed on to this script are set
# executable for parameter estimation or optimization and that the
# correct optimization algorithm is selected

# PARAMETERS (edit as needed)

# the executable with serial algorithm
OPTSER=/usr/bin/CopasiSE

# the executable with parallel algorithm
OPTPAR=/usr/local/COPASI-DEVEL/bin/CopasiSE

# CopasiSE options
CLOPT="--nologo"

# default number of iterations
RUNITER=20

# default number of threads
THREADS=4

#DON'T EDIT BELOW THIS LINE

# check command line options
if [[ $# -ge 1 ]]; then
  INFILE=$1
  if [[ "$1" =~ ^-h$ ]]; then
   printf "usage: poptbench infile [iterations [threads [serial|parallel]]]\n"
   exit 0
  fi
else
  printf "usage: poptbench infile [iterations [threads [serial|parallel]]]\n"
 exit 1
fi

if [[ $# -ge 2 ]]; then
  if [[ "$2" =~ ^[0-9]+$ ]]; then
    RUNITER=$2
  else
    printf "usage: poptbench infile [iterations [threads [serial|parallel]]]\n"
    printf "error: iterations must be an integer"
    exit 1
  fi
fi

if [[ $# -ge 3 ]]; then
  if [[ "$3" =~ ^[0-9]+$ ]]; then
    THREADS=$3
  else
    printf "usage: poptbench infile [iterations [threads [serial|parallel]]]\n"
    printf "error: threads must be an integer\n"
    exit 1
  fi
fi

if [ $# -ge 4 ]; then
  SERIAL=0
  PARALLEL=0
  if [[ "$4" == "serial" ]]; then
    SERIAL=1
  else
    if [[ "$4" == "parallel" ]]; then
      PARALLEL=1
    else
      printf "usage: poptbench infile [iterations [threads [serial|parallel]]]\n"
      printf '%s\n' "error: option '$4' not allowed"
      exit 1
	fi
  fi
else
 SERIAL=1
 PARALLEL=1
fi

# OMP directives,number of threads to be used, etc
export OMP_THREAD_LIMIT=$THREADS
export OMP_NUM_THREADS=$OMP_THREAD_LIMIT
export OMP_SCHEDULE=guided

#find the name of the outfile in the parameter estimation report
line=$(grep -A 1 "name=\"Parameter Estimation" $INFILE)
# Check if "target=" is present in the result
if [[ $line == *"target="* ]]; then
  OUTFILE=$(echo $line | sed 's/.*target="\([^"]*\)".*/\1/')
fi

#check if variable is empty
if [[ -z "$OUTFILE" ]]; then
  #maybe it's in the optimization report?
  line=$(grep -A 1 "name=\"Optimization" $INFILE)
  # Check if "target=" is present in the result
  if [[ $line == *"target="* ]]; then
    OUTFILE=$(echo $line | sed 's/.*target="\([^"]*\)".*/\1/')
  fi
  if [[ -z "$OUTFILE" ]]; then
    printf "No output file specified, aborting.\n"
    exit 1
  else
    TASK="Optimization"
  fi
else
  TASK="Parameter Estimation"
fi

printf "started on "
date

printf '%s\n' "$TASK writing output to $OUTFILE"

# keep a backup of OUTFILE if it exists
if [[ -e $OUTFILE ]]; then
  mv $OUTFILE $OUTFILE.bak
fi

#write a header
date >> $OUTFILE
echo "$0 $@" >> $OUTFILE
grep -m 1  "model name" /proc/cpuinfo >> $OUTFILE
grep -m 1  "bogomips" /proc/cpuinfo >> $OUTFILE
grep -m 1  "cpu cores" /proc/cpuinfo >> $OUTFILE
printf 'threads used\t: %s\n' "$OMP_THREAD_LIMIT" >> $OUTFILE
printf "\n" >> $OUTFILE

# run the serial version
if [[ $SERIAL == 1 ]]; then
  printf '%s' "running serial PS $RUNITER times "
  printf "SERIAL\n" >> $OUTFILE
  for ((i=1;i<=$RUNITER;i++));
  do
     $OPTSER $CLOPT $INFILE 2>&1 > /dev/null
 	 if [ $((i % 10)) -eq 0 ]; then
       printf "|"
	 else
       printf "."
	 fi
  done

  # add empty line to report file
  echo >> $OUTFILE
  # and to the console
  echo
fi

# run the parallel version (the "!" is used to make sure script doesn't abort)
if [[ $PARALLEL == 1 ]]; then
  printf '%s' "running parallel PS $RUNITER times "
  printf 'PARALLEL %d THREADS\n' $THREADS >> $OUTFILE
  for ((i=1;i<=$RUNITER;i++));
  do
     ! $OPTPAR $CLOPT $INFILE 2>&1 > /dev/null
     if [ $((i % 10)) -eq 0 ]; then
       printf "|"
     else
       printf "."
     fi
  done
fi

printf "\nfinished on "
date