run

#!/bin/bash

DIR=$(pwd)
PROGRAM="simulator"

OPTIND=1
BIRDS=512
FILE=""
CLUSTERS=0
RANKS=1
THREADS=1
SIZE=500
STEP=1
TIME=100
OUTDIR="tmp"

while getopts "hb:d:f:g:i:n:p:s:t:" opt; do
    case "$opt" in
    h)  echo "Usage: ./run [options]"
        echo "             -b <number of birds to simulate>"
        echo "             -f <file with bird info>"
        echo "             -g <number of bird groups to create> (0 uses a uniform random distribution)"
        echo "             -i <step size, which iterations to show graphs for"
        echo "             -n <number of MPI ranks>"
        echo "             -p <number of pthreads per rank>"
        echo "             -s <size of the universe>"
        echo "             -t <number of iterations>"
        exit 0
        ;;
    b)  BIRDS=$OPTARG
        ;;
    d)  OUTDIR=$OPTARG
        ;;
    f)  FILE=$OPTARG
        ;;
    g)  CLUSTERS=$OPTARG
        ;;
    i)  STEP=$OPTARG
        ;;
    n)  RANKS=$OPTARG
        ;;
    p)  THREADS=$OPTARG
        ;;
    s)  SIZE=$OPTARG
        ;;
    t)  TIME=$OPTARG
        ;;
    esac
done

shift $((OPTIND-1))
[ "$1" = "--" ] && shift

echo groups = $CLUSTERS

if [ $CLUSTERS == 0 ]
then
  # Run the simulation with a uniform random distribution of birds
  echo "Running $PROGRAM with"
  echo "  RANKS=$RANKS, THREADS=$THREADS"
  mpirun -N $RANKS "$DIR/$PROGRAM" -p $THREADS -b $BIRDS -s $SIZE -t $TIME
else
  # Use n groups of birds
  if [ "$FILE" == "" ]
  then
    # Generate birds if not provided with file
    echo "Generating Birds"
    python generateBirds.py $CLUSTERS $SIZE $BIRDS all.birds
    FILE="all.birds"
  fi

  # Split birds up into a single input file per rank
  echo "Splitting Birds into separate input files"
  python splitInputFile.py $FILE $RANKS

  # Run the simulation
  echo "Running $PROGRAM with"
  echo "  RANKS=$RANKS, THREADS=$THREADS"
  mpirun -N $RANKS "$DIR/$PROGRAM" -p $THREADS -b $BIRDS -s $SIZE -t $TIME -f

  # Clean up
  echo "Cleaning up input files"
  rm *.birds
fi

#---------------Uncomment to visualize simulation output-----------------------
#
#
#echo "Generating Plots"
#mkdir $OUTDIR
#rm $OUTDIR/*.png
#rm $OUTDIR/Rplots.gif
#Rscript plot_birds.R $SIZE $OUTDIR $TIME --vanilla

#echo "Creating .gif"
#convert -delay 10x100 $OUTDIR/* $OUTDIR/Rplots.gif
#
#echo "Cleaning up"
#rm simout.csv
#----------------------------End commented section-----x-----------------------


echo "Finished!"