gerris 20131206+dfsg-7 / usr / bin / gfsjoin

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/usr/bin/gfsjoin is in gerris 20131206+dfsg-7.

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#!/bin/bash
# script to join gerris output files in parallel simulations


help ()
{
    echo ""
    echo "Usage: gfsjoin Simfile Directory Rootname NP Tailname > Joined"
    echo ""
    echo "Simfile:        Name of the simulation file"
    echo "Directory:      Directory where results are located"
    echo "Rootname:       File root name"
    echo "NP:             Number of processors"
    echo "Tailname:       File tail name"
    echo ""
    exit
}

#verbose=1

message ()
{
    if test $verbose; then
	echo $1 > /dev/stdout
    fi
}

errmessage ()
{
        echo $1 > /dev/stderr
}


#------------------------------------------------------------------------------

#checking input
if [ $# -ne 5 ]; then
   if [ $1 == '-h' ]; then
       help
   else
        errmessage "Input error, this command requires 5 arguments"
        errmessage "Type gfsjoin -h for more info"
   fi
exit
fi

# removing all blanks and tabs immediately before the end of line.
# Comments are also removed to avoid errors
tmp=`mktemp -d`
sed -e 's/#.*//' -e 's/[ ^I]*$//' -e '/^$/ d' $1 | sed '/^#/ d'  > $tmp/sim.tmp

c1=$3
c2=$5
c3="$tmp/sim.tmp"
numproc=$4
dir=$2

# checking operations
y=`expr ${#c2} - 2`
tailst=`expr substr $c2 $y 3`

if [ $tailst == 'gfs' ]; then
   compress=0
else
        if [ $tailst == '.gz' ]; then
          compress=1
          c2=`expr substr $c2 1 $[$y-1]`
        else
          errmessage "Your simulation file has not a valid extension ("$tailst")"
          errmessage "The correct file extensions are either .gfs or .gz"
          exit
        fi
fi

p1=$(awk '/GfsSimulation/ {print $1}' $c3)
p2=$(awk '/GfsSimulation/ {print $2}' $c3)

i=1
if [ $compress -eq 1 ]; then
while [ $i -le $numproc ]; do
    gunzip -q ${dir}'/'$c1$[$i-1]$c2
    i=$[$i+1]
done
fi

message 'Creating output................'

# Variables to handle the files names
i=0
while [ $i -lt $numproc ]; do
    mainfile[$i]=${dir}'/'$c1$i$c2
    message "${mainfile[$i]}"
    i=$[$i+1]
done

# Copying the first two lines of the simulation file
head -2 ${mainfile[0]} > $tmp/tmp.tmp
# Inserting the correct number of boxes and connections
sed -e '/GfsSimulation/ s/[0-9]*/'$p1'/1' -e '/GfsSimulation/s/[0-9]*/'$p2'/2' $tmp/tmp.tmp

# Copying solid file (if any)
sed -n '/SurfaceFile/ p' $c3

# The first two lines are removed because they have useless information.
# As I have already inserted the solid, this information is also removed from the files
i=0
while [ $i -lt $numproc ]; do
    nend=$(echo -n $(sed -n '/GtsSurface/,/Gfs/ p' ${mainfile[$i]} | tail -1 | awk '{print $1}' ))
    nend=$(echo -n $(awk '$1 ~ /'$nend'/ {print NR}' ${mainfile[$i]} | head -1 ))
    nend=$[$nend+0]
    if [ $nend -ne 0 ]; then
	sed -e '1,2 d' -e '/GtsSurface/,'$[$nend-1]' d' ${mainfile[$i]} > $tmp/tmpfile$i
    else
	more +3 ${mainfile[$i]} > $tmp/tmpfile$i
    fi
    i=$[$i+1]
done

#Taking the initial common arguments
sed -n '1,/GfsBox/p' $tmp/tmpfile0 | sed '$ d' 

# Creating temporal file with all the boxes (sed is used to remove the 
# local connectivities in case they will be equal)
# boxes in proc 0
(sed -n '/GfsBox/,$p' $tmp/tmpfile0 | awk '
BEGIN{}
{
condition1 = ( $3 == "right" || $3 == "left" || $3 == "top" || $3 == "bottom" || $3 == "front" || $3 == "back" )
if(!(NF == 3 && condition1)) {print $0}
}
END{}') > $tmp/tmp.tmp

# the rest of boxes
i=1
while [ $i -lt $numproc ]; do
    (sed -n '/GfsBox/,$p' $tmp/tmpfile$i | awk '
BEGIN{}
{
condition1= ( $3 == "right" || $3 == "left" || $3 == "top" || $3 == "bottom" || $3 == "front" || $3 == "back" )
if(!(NF == 3 && condition1)) {print $0}
}
END{}') >> $tmp/tmp.tmp
    i=$[$i+1]
done

message
message "IMPORTANT: This script assumes that the \"id\" is in correlative order in your simulation file (not the pid)"
message

awk '$1 ~ /GfsBox/ && /id =/ {print $0}' $tmp/tmp.tmp | \
    awk 'BEGIN{}
     { i = 0
       do {
           i++
       } while ( $i !~ /^id/ )
        print $(i+2)
}
END{}' > $tmp/tmp.tmp2

# The last box in the temporal file is:
lastid=$(tail -1 $tmp/tmp.tmp2)
# And the total number of boxes:
numboxes=$(wc -l $tmp/tmp.tmp2 | awk '{print $1}')

message "Putting boxes in order in the final file"
# Boxes are pasted in the final file in order (it is assumed to be sequential)
i=1
while [ $i -le $numboxes ]; do
    if [ $i -ne $lastid ]; then
	message -n "$i ,"
        n0=$(awk '{if($1 == '$i') {print NR}}' $tmp/tmp.tmp2)
        n1=$(awk 'FNR == '$[$n0+1]' {print $1}' $tmp/tmp.tmp2)
        # Taking the lines of this range (the last line is removed
	# because it corresponds to the next box)
        (awk '/id = '$i' pid/,/id = '$n1' pid/ {print $0}' $tmp/tmp.tmp | head -n -1)
        i=$[$i+1]
    else
	message -n "$i ,"
        nf=$(awk '$1 ~ /GfsBox/ && $5 == '$i' && $3 ~ /id/ {print NR}' $tmp/tmp.tmp)
        more +$nf $tmp/tmp.tmp
        i=$[$i+1]
    fi
done

# Copying the global conectivities
tail -n $p2 $c3

message
message
if [ $compress -eq 1 ]; then
	message 'compressing files again'
	gzip -f -q ${dir}'/'${c1}*'.gfs'
fi

rm -rf $tmp

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