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See VisualVM issue #346 (https://visualvm.dev.java.net/issues/show_bug.cgi?id=346) for more details.
There seems to be performance bug in retransform classes code in JVM, which redefine classes even if the bytecode is the same. In case of NetBeans profiler, this produces a long (= several minutes) running VM operation, which blocks all Java threads. This explains timeout in JMX connection and the profiler's dialog with "profiled application does not respond". I plan to work-around it in the profiler code.
Fixed in profiler-main. The long transaction is broken into several smaller ones and redefinition of unchanged classes is prevented too. changeset: 155901:ee5a4dcb04e1 user: Tomas Hurka <thurka@netbeans.org> date: Mon Dec 21 12:07:00 2009 +0100 summary: bugfix #178771 and #178792 changeset: 155902:19a0dd9622a0 tag: tip user: Tomas Hurka <thurka@netbeans.org> date: Mon Dec 21 13:07:24 2009 +0100 summary: new profiler native binaries with the following changesets: fbbd58a28aa2 dc7f0d902bee 50e8150a97fe ee5a4dcb04e1
Integrated into 'main-golden', will be available in build *200912230201* on http://bits.netbeans.org/dev/nightly/ (upload may still be in progress) Changeset: http://hg.netbeans.org/main/rev/ee5a4dcb04e1 User: Tomas Hurka <thurka@netbeans.org> Log: bugfix #178771 and #178792 bugfix #178771 - cache loaded classes in several calls instead of one; do not allow to redefine unchanged classes; make sure that retransformIsRunning is initialized bugfix #178792 - allow to cache classes when _ctable_size > 0; cache classes, which was initialy loaded but not linked, in ProfilerInterface.classLoadHook() print error code returned by RetransformClasses()
This issue appears to be a duplicate of http://netbeans.org/bugzilla/show_bug.cgi?id=150662