Here is how I enable remote debugging with WebLogic Server (11g) and Eclipse IDE. (Actually the java option is for any JVM, just the instruction here is WLS specific.)
1. Edit <my_domain>/bin/setDomainEnv.sh file and add this on top:
JAVA_OPTIONS="$JAVA_OPTIONS -Xrunjdwp:transport=dt_socket,address=8000,server=y,suspend=y"
The suspend=y will start your server and wait for you to connect with IDE before continue. If you don't want this, then set to suspend=n instead.
2. Start/restart your WLS with <my_domain>/bin/startWebLogic.sh
3. Once WLS is running, you may connect to it using Eclipse IDE. Go to Menu: Run > Debug Configuration ... > Remote Java Application and create a new entry. Ensure your port number is matching to what you used above.
Read more java debugging options here: http://www.oracle.com/technetwork/java/javase/tech/vmoptions-jsp-140102.html#DebuggingOptions
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