Problem

After stopping confluence via catalina.sh stop Confluence says, in the logs, that it is stopping, as below:

INFO [main] [com.atlassian.confluence.lifecycle] contextDestroyed Stopping Confluence
 INFO [main] [confluence.cluster.tangosol.TangosolClusterManager] shutdown Shutting down Coherence services

but the java process never terminates.

Resolution

Pass the -force parameter to catalina.sh as:

catalina.sh stop -force

This will kill the java process and stop Confluence.

If the above results in an error, such as:

Kill failed: $CATALINA_PID not set

Please add the following line of code to the top of your <Confluence-Installation-Directory>/bin/setenv.sh file (Standalone instance):

CATALINA_PID="<Change this to your preferred location>/id.pid"
export CATALINA_PID

Tomcat will automatically write its process id to id.pid in your specified path and kill its process with the -force parameter.

For Linux or Mac user:
In addition to the above, you can try a custom script that runs shutdown.sh first before forcing Tomcat to shutdown. This script will sleep 60 seconds then look inside ./id.pid to check if Tomcat is still running. If Tomcat is still running, it will issue a catalina.sh stop -force.

The script needs to be saved in <confluence install>/bin and assumes id.pid is located in the same location.

Note that this script is provided as is and not supported.