Ask Questions and Find Answers

You need to find the root cause, I'd suggest you enable some logging.

But before you do that, stop Liferay, delete osgi/state, both work folders and the tomcat/temp folder and start it again. You might also try to undeploy all your own modules to find if it also happens without any of your code.

To enable logging:
Go to Control Panel -> Configuration -> Server Administration -> Log Levels
A good start is to set "com.liferay.portal.servlet.MainServlet" to all. Maybe this gives you a hint.

Also, you could enable slow query log in mysql.

Also, try to get some stacktraces: "kill -3 <Tomcat_PID>" should give you a hint in which methods it waits. Look for locks. If CPU is used, you might also do a "top -H" to find the thread that uses the CPU. You can then convert the pid to hex and look into the stacktrace to find it. This article describes the idea:
http://www.nurkiewicz.com/2012/08/which-java-thread-consumes-my-cpu.html

With those stacktraces you might get an idea which part of the code gets stuck and enable logging for those classes to get a clearer picture.

hth