After several futile attempts to get my deployment units to log to Glassfish I finally figured out to use Log4J in Glassfish which is not really well documented there. So that is what I had to do:
Now you will find the log file relative to the<Glassfish Domain Directory>/configdirectory. Now I can read the log4j output like usual even though not in the same file as the Glassfish log statements.
Now some feedback to the responses I got:
Moral of the story is that if Sun could have swallowed their pride and either kept Log4J out of the JDK or just incorporated Log4J as is like they did with Corba we would not have this discussion. Now we have several frameworks on top of them that are trying to fix that and each of them fail one way or the other, what a mess. Thank you - Sun.