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Profiling a JBoss 4.2 instance gives a timeout message. The popup dialog asks to disconnect the profiler or to continue the session. If the session is not aborted eventually it all starts to work though. But in the meantime a cpu runs at 100% until finally the profiler becomes responsive. As I can't ask netbeans to profile its profiler I'm including a thread dump of jvisualvm. It's taken while one of the cpu's ran at 100%
Created attachment 86519 [details] while running at 100% cpu
Created attachment 86520 [details] log while netbeans is running the profiler. maybe it contains a clue.
Actually it works as designed. When profiling memory the profiler needs to change the bytecode for each class loaded in the JVM. This takes a significant amount of time for large applications like JBoss and consumes a lot of CPU cycles in native code. During instrumentation the profiled application doesn't communicate with the profiler tool, that's why the dialog pops up to give you a chance to stop the process. It doesn't seem like we could speed up the instrumentation so the only way is to submit the dialog several times until all classes are instrumented. Based on what's your intention you may just take a heap dump when in Monitor mode (== fast startup) using Profile | Take Heap Dump... to start analyzing classes/instances and/or searching for a memory leak.