Symptoms

The following appears during stopping the JIRA instance with the embedded stop script:

Killing Tomcat with the PID: <PID>
Tomcat has not been killed completely yet. The process might be waiting on some system call or might be UNINTERRUPTIBLE.

Cause

Sometimes there are threads remain uninterrupted, even after issuing a shutdown on the instance and the Java process fails to stop gracefully. 

Resolution

These messages can generally be ignored, as the bundled start scripts will kill the process after 20 seconds. Should it fail, please open a support request, attaching your application logs for review.