#!/bin/ksh
# SETUP    SET UP General Circulation Model run    2007/06/06

# OMDIR=$HOME  ;  IFDIR=$HOME/IFDIR  ;  OPDIR=$HOME

# Rundeck (runID.R) is assumed to reside in Present Working Directory.
# Compiled object modules are assumed to reside in Present Working
# Directory or else in the directory OMDIR.
# Input files are assumed to be an absolute path or else to reside in
# the directory IFDIR.
# Run will be executed and output files will be saved in the directory
# OPDIR/RUNID .

  if [[ $# -eq 0 ]] then
     echo " Usage: SETUP runID     2007/06/06"
     echo "        SETUP Fortran-90 Model run"
     echo "        Default directory of compiled object modules: $OMDIR"
     echo "        Default directory of input files: $IFDIR"
     echo "        Output parent directory: $OPDIR"
     exit ; fi

  RUNID=$1  ;  RFILE=$RUNID.R  ;  OUTPUT=$OPDIR/$RUNID

  if ps -e  |  grep $RUNID[.]exe  >  /dev/null  ;  then
     echo "$RUNID is already running."  ;  exit 1  ;  fi

  if [[ ! -s $RFILE ]] then
     echo "File does not exist: $RFILE"  ;  exit 2  ;  fi

  echo "Setting up run: $RUNID"
  echo "Output files are saved in: $OUTPUT"

  export XLFRTEOPTS=namelist=old:nlwidth=133  ##  needed for IBM xlf

# Make RFILE the standard input
   exec  <  $RFILE

# Create the run directory, OUTPUT, if it does not already exist
  umask 002
  if [[ ! -d $OUTPUT ]] ; then  mkdir $OUTPUT ; fi
  echo "0Run $RUNID"  >  $OUTPUT/$RUNID.PRT

# First token of RFILE should contain this file's name
  read VAR1 VAR2
  if [[ ! $VAR1 = $RFILE ]] then
     echo "The first token in runID.R file should be the file's name."
     echo "Filename: $RFILE , first token: $VAR1"  ;  exit 3  ;  fi
  echo " $VAR1 $VAR2"  >>  $OUTPUT/$RUNID.PRT

# Read RFILE until "Object modules:" is encountered
  until [[ $VAR1 = 'Object' && $VAR2 = 'modules:' ]] ; do
     read VAR1 VAR2
     if [[ $? -ne 0 ]] then
        echo "'"Object modules:"' not found in $RFILE" ; exit 4 ; fi
     echo " $VAR1 $VAR2"  >>  $OUTPUT/$RUNID.PRT ; done

# Set beginning of link command that creates executable module
  LINK="  f90 -o $OUTPUT/$RUNID.exe -O3 -64 -mips4"          ## SGI
# LINK="  f90 -o $OUTPUT/$RUNID.exe -O4 -convert big_endian" ## Compaq
# LINK="xlf90 -o $OUTPUT/$RUNID.exe -O2"                     ## IBM xlf
# LINK="ifort -o $OUTPUT/$RUNID.exe -O3 -xN -ipo -fpconstant -pc80 \
#   -openmp -fpp -parallel -ansi_alias -convert big_endian" ## Intel 8.1
# LINK="ifort -o $OUTPUT/$RUNID.exe -O3 -xN -ipo -static \
#   -openmp -fpp -parallel -ansi_alias -convert big_endian" ## Pent4 9.0

# Add the names of all object modules to LINK command
  while true ; do
     read VAR1 VAR2 VAR3
     if [[ $? -ne 0 ]] then
        echo "'"Data input files:"' not found in $RFILE" ; exit 5 ; fi
     echo " $VAR1 $VAR2 $VAR3"  >>  $OUTPUT/$RUNID.PRT
     if [[ $VAR1 = 'Data' && $VAR2 = 'input' && $VAR3 = 'files:' ]]
        then  break  ;  fi
     if [[ $VAR1 != '' ]] then
        for VAR in $VAR1 $VAR2 $VAR3 ; do
           if [[ $VAR = '!' ]] ; then  break ; fi
           OM=$VAR.o
           if [[ ! -r $OM ]] then  OM=$OMDIR/$VAR.o ; fi
           if [[ ! -r $OM ]] then
              echo "Neither $VAR.o nor $OM exists." ; exit 6 ; fi
           LINK="$LINK $OM" ; done ; fi ; done

# Create the executable module OUTPUT/RUNID.exe
  rm -f $OUTPUT/$RUNID.exe WARN.f90
  $LINK  2>  WARN.f90
  if [[ -s WARN.f90 ]] then
     echo "Compiler warnings saved in: WARN.f90 .  Inspect them." ; fi
  if [[ ! -s $OUTPUT/$RUNID.exe ]] then
     echo "Link errors.  SETUP terminated." ; exit 7 ; fi

# Change directory to model run directory where output will go
  cd $OUTPUT
# Remove any old link and unlink files after switching to run directory
  if [[ -a $RUNID.ln  ]] then  rm $RUNID.ln  ;  fi
  if [[ -a $RUNID.uln ]] then  rm $RUNID.uln ;  fi

# Use the subsequent information to create the link and unlink files
  echo "#!/bin/ksh"  >  $RUNID.ln
  echo "#!/bin/ksh"  >  $RUNID.uln
  while true ; do
     read VAR1 VAR2 VAR3
     if [[ $? -ne 0 ]] then
        echo "'"Label and Namelist:"' not found in $RFILE" ; exit 8 ; fi
     if [[ $VAR1 = 'Label' && $VAR2 = 'and' && $VAR3 = 'Namelist:' ]]
        then  break ; fi
     echo " $VAR1 $VAR2 $VAR3"  >>  $RUNID.PRT
     if [[ $VAR1 != '' ]] then
        for VAR in $VAR1 $VAR2 $VAR3 ; do
           if [[ $VAR = '!'* ]] then  break ; fi
           UN=${VAR%%'='*}
           FN=${VAR##*'='}
           IFN=$FN
           if [[ ! -r $IFN ]] then  IFN=$IFDIR/$FN ; fi
           if [[ ! -r $IFN ]] then
              echo "Neither file $FN nor $IFN exists." ; exit 9 ; fi
           echo "ln -s $IFN fort.$UN"  >>  $RUNID.ln
           echo "rm fort.$UN"  >>  $RUNID.uln ; done ; fi ; done
  echo "chmod ugo+rw *"  >>  $RUNID.uln

# Copy Label and Namelist to RUNID.I.
  rm -f I
# Check that beginning of Label is RUNID
  read VAR1 VAR2
  echo "$VAR1 $VAR2"  >  I
  if [[ ! $VAR1 = $RUNID ]] then
     echo "Beginning of Label ($VAR1) is not equal to runID ($RUNID)."
     exit 10 ; fi
  read LINE
  echo "$LINE"  >>  I
# Remaining lines need a leading blank
  read LINE
  until [[ $? -ne 0 ]] ; do
     echo " $LINE"  >>  I
     read LINE ; done

# Make initial run
  chmod ugo+x $RUNID.ln
  chmod ugo+x $RUNID.uln
  $RUNID.ln
  $RUNID.exe  <  I  >>  $RUNID.PRT
  RETC=$?
  $RUNID.uln
# if [[ $RETC -ne 13 && $retc -ne 12 ]] then
#    echo "Problem encountered during initial run." ; exit 11 ; fi

# Create executable script file E
  echo "$RUNID.ln"  >  E
# echo "export XLFRTEOPTS=namelist=old:nlwidth=133"  >>  E  ##  for IBM
  echo "$RUNID.exe  <  I  >  $RUNID.PRT"  >>  E
  echo "$RUNID.uln"  >>  E
  chmod ugo+x E

# Overwrite I file omitting lines with "ISTART=" in them
  exec  <  I
  read LINE
  echo "$LINE"  >  $RUNID.tmp
  read LINE
  echo "$LINE"  >>  $RUNID.tmp
  read LINE
  until [[ $? -ne 0 ]] ; do
     if [[ $LINE != *'ISTART='* ]] then
       echo " $LINE"  >>  $RUNID.tmp ; fi
     read LINE ; done
  mv $RUNID.tmp I

  chmod go+rw fort.* *.PRT
  QRSF $RUNID