As you spotted john my killing loop was killing the system V script itself also hence it never starting my_app again, so instead a simple if skips the process ID of the system V script itself so it can continue on to start my_app again:

> I'd think that the pgrep is matching both the processes you want
> to kill _and_ the init.d script itself.

My script looks like the following:

restart)
echo "Stopping my_app:"
pgrep my_app | while read PIDS
do
        if [ "$PIDS" -eq $$ ]; then
                continue
        fi
        kill -9 $PIDS
done
echo "Starting my_app:"
/etc/init.d/my_app start &
exit $?
;;

Thanks for the help everyone its greatly appreciated.

Regards,
James ;)

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