For Glassfish, we normally put the log4j.properties in the "domain / config" directory.
To enable Glassfish to find it, add the following to the Glassfish JVM settings. Easiest way is to use the Admin console i.e. Application Server / JVM Settings / JVM Options.
Add this line:
-Dlog4j.configuration=file:///${com.sun.aas.instanceRoot}/config/log4j.properties
Enjoy!
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