http://askubuntu.com/a/297285/79266

PdfDiff.sh

#!/bin/bash
#
# Compare two PDF files.
# Dependencies:
#  - pdfinfo (xpdf)
#  - pdfjam  (texlive-extra-utils)
#  - diffpdf
#

MAX_HEIGHT=15840  #The maximum height of a page (in points), limited by pdfjam.

TMPFILE1=$(mktemp /tmp/XXXXXX.pdf)
TMPFILE2=$(mktemp /tmp/XXXXXX.pdf)

usage="usage: scrolldiff -h FILE1.pdf FILE2.pdf
  -h print this message

v0.0"

while getopts "h" OPTIONS ; do
    case ${OPTIONS} in
        h|-help) echo "${usage}"; exit;;
    esac
done
shift $(($OPTIND - 1))

if [ -z "$1" ] || [ -z "$2" ] || [ ! -f "$1" ] || [ ! -f "$2" ]
then
  echo "ERROR: input files do not exist."
  echo
  echo "$usage"
  exit
fi

    #Get the number of pages:
pages1=$( pdfinfo "$1" | grep 'Pages' - | awk '{print $2}' )
pages2=$( pdfinfo "$2" | grep 'Pages' - | awk '{print $2}' )
numpages=$pages2
if [[ $pages1 > $pages2 ]]
then
  numpages=$pages1
fi

     #Get the paper size:
width1=$( pdfinfo "$1" | grep 'Page size' | awk '{print $3}' )
height1=$( pdfinfo "$1" | grep 'Page size' | awk '{print $5}' )
width2=$( pdfinfo "$2" | grep 'Page size' | awk '{print $3}' )
height2=$( pdfinfo "$2" | grep 'Page size' | awk '{print $5}' )

if [ $(bc <<< "$width1 < $width2") -eq 1 ]
then
  width1=$width2
fi
if [ $(bc <<< "$height1 < $height2") -eq 1 ]
then
  height1=$height2
fi

height=$( echo "scale=2; $height1 * $numpages" | bc )
if [ $(bc <<< "$MAX_HEIGHT < $height") -eq 1 ]
then
  height=$MAX_HEIGHT
fi
papersize="${width1}pt,${height}pt"



    #Make the scrolls:
pdfj="pdfjam --nup 1x$numpages --papersize {${papersize}} --outfile"
$pdfj "$TMPFILE1" "$1"
$pdfj "$TMPFILE2" "$2"

diffpdf "$TMPFILE1" "$TMPFILE2"

rm -f $TMPFILE1 $TMPFILE2