Timed out waiting for server shutdown is an event found in a JVMs stopServer.log. This event typically means it is taking a long time for the JVM to restart. The JVMs SystemOut.log may be helpful in understanding why the JVM restart is taking a long time.

Determine the PID of the JVM. This assumes the operating systme is Linux.

ps -ef | grep jvm_name

Create a heap dump, so that a heap dump is captured while the JVM is in a bad way.

kill -3 the_pid

Kill the PID, which will end all of the processes associated with the JVM that is in a bad way.

kill -9 the_pid

Start the JVM, and ensure the JVM is open for e-business.

cat /usr/local/inet/logs/<cell name>/<jvm name>/SystemOut.log | grep e-business

Determine the new PID of the JVM.

ps -ef | grep jvm_name

Create a heap dump, so that a heap dump is captured while the JVM is in a good way.

kill -3 the_pid

Analyze both heap dumps, to try to understand what happened that caused the JVM to time out.