From brokenpoet.org wiki

The purpose of this script is to check all sites on a cPanel server to see if the domains are using the local nameservers or external nameservers.

It gets a domain list from the user files in /var/cpanel/users/ and the nameserver info from /etc/nameserverips

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wget http://scripts.brokenpoet.org/chkdns.sh

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#!/bin/bash
#
# written by benjamin cathey on 2008.11.22

# for cPanel servers, this script runs a whois lookup for all domains hosted 
# on the server to see if they use the servers nameservers or if they use
# external DNS

domains=$(cat /var/cpanel/users/* | grep -e '.*\..*' | grep DNS | cut -d'=' -f2| awk '!/[a-z].*\.[a-z].*\.[a-z].*/')

nameservers=$(cat /etc/nameserverips | cut -d'=' -f2 | awk '/[a-zA-Z].*\.[a-zA-Z].*\.[a-zA-Z].*/')

echo "DOMAINS"
echo "-------"
printf "$domains\n"
echo
echo "NAMESERVERS"
echo "-----------"
printf "$nameservers\n"
echo
for domain in $domains
do
  for nameserver in $nameservers
  do
    if [ -z "`whois $domain | grep -i $nameserver`" ]
    then
      user=$(basename `grep -lr "$domain" /var/cpanel/users/`)
      dns=$(whois $domain | awk '/[a-zA-Z].*\.[a-zA-Z].*\.[a-zA-Z]/' | grep -i ns | sed 's/\ //g')
      if [ -z $count ]
      then
        echo "DNS NOT ON THIS SERVER"
        echo "----------------------"
        echo "$domain ($user)"
        printf "$dns\n"
        echo
        count=1
        break
      else
        echo "$domain ($user)"
        printf "$dns\n"
        echo
        count=$(( $count + 1 ))
        break
      fi
    fi
  done
done
if [ -z $count ]
then
  exit 1
else
  echo
  echo "$count domain(s) not on this server"
fi