Tomcat doesn't stop. How can I debug this?

Question

I have a Tomcat 7 running in Linux that I start via $CATALINA_HOME/bin/startup.sh and shutdown via $CATALINA_HOME/bin/shutdown.sh
from /etc/init.d

All is ok except 1 problem. Sometimes tomcat does not stop.
Although I stop it and I see in catalina.out logs that is going down, if I do ps -ef I can still see the process running.

What could be the problem? How can I debug this? My feeling is, that this is related to threads.

So the parts that are suspicious are the following:
1) I use Log4j's LogManager to detect if the log4j configuration has been changed, but I do Log4jManager.shutdown on a contextDestroyed ServletContextListener
2) I use H2 database and I see on shutdown:

SEVERE: The web application [/MyApplication] appears to have started a
thread named [H2 Log Writer MYAPPLICATION] but has failed to stop it.
This is very likely to create a memory leak

SEVERE: The web application [/MyApplication] appears to have started a
thread named [H2 File Lock Watchdog
/opt/myOrg/tomcat/webapps/MyApplication/db/myDatabase.lock.db] but has
failed to stop it. This is very likely to create a memory leak. Apr 2,
2012 9:08:08 AM org.apache.catalina.loader.WebappClassLoader
clearReferencesThreads SEVERE: The web application [/MyApplication]
appears to have started a thread named [FileWatchdog] but has failed
to stop it. This is very likely to create a memory leak.

Any help please? How can I detect the problem here?

UPDATE:
I did a kill -3 as suggested by @daveb, and in the catalina.out I see:

JVMDUMP006I Processing dump event "user", detail "" - please wait. JVMDUMP032I JVM requested Java dump using '/etc/init.d/javacore.20120402.093922.2568.0001.txt' in response to an event JVMDUMP010I Java dump written to /etc/init.d/javacore.20120402.093922.2568.0001.txt JVMDUMP013I Processed dump event "user", detail "".

There is a javacore in /etc/init.d but I don't know how to process it. I.e. what parts should I investigate

Answer 1

If the web application is stopped, all connections to the database should be closed as well. If you don't have a list of connections, then execute the SQL statement "shutdown" (this only works for the H2 and HSQLDB databases).

If you have a registered a Servlet, you can do that in the Servlet.destroy() method.

If you have registered a ServletContextListener, you can execute the "shutdown" statement in the ServletContextListener.contextDestroyed(ServletContextEvent servletContextEvent) method. This is what org.h2.server.web.DbStarter ServletContextListener does (the one that is included in the H2 database).