Can't stop Jira Server "$CATALINA_PID was set but the specified file does not exist"

[Michael Ilewicz]

Hi, I am trying to upgrade Jira but the upgrade script fails failing to shut Jira down. I tried shutting it down manually using both these commands

 sudo /etc/init.d/jira stop

sudo ${installation Directory}/bin/stop-jira.sh

but this fails with the following

executing using dedicated user

Atlassian Jira
Version : 8.12.2

If you encounter issues starting or stopping Jira, please see the Troubleshooting guide at https://docs.atlassian.com/jira/jadm-docs-0812/Troubleshooting+installation

Server startup logs are located in /opt/atlassian/jira/logs/catalina.out
Using CATALINA_BASE: /opt/atlassian/jira
Using CATALINA_HOME: /opt/atlassian/jira
Using CATALINA_TMPDIR: /opt/atlassian/jira/temp
Using JRE_HOME: /opt/atlassian/jira/jre/
Using CLASSPATH: /opt/atlassian/jira/bin/bootstrap.jar:/opt/atlassian/jira/bin/tomcat-juli.jar
Using CATALINA_PID: /opt/atlassian/jira/work/catalina.pid
$CATALINA_PID was set but the specified file does not exist. Is Tomcat running? Stop aborted.

The Catalina startup logs don't seem to hold any valuable information. I am also logged in as root and the installation directory belongs to the root. I used to be able to stop the server before and I have no idea why I can't do so now. I have tried rebooting my VM without change.

Any clues would be highly appreciated!

[Michael Ilewicz · Accepted solution]

I am not sure why but running

sudo systemctl stop jira.service

did shut down my Jira instance as well and I was able to upgrade. Now the above commands work to stop my instance thus the problem is solved. Thanks!

[Daniel Ebers]

Hi @Michael Ilewicz

in case this happens some time in future again you could check for the presence of the file

/opt/atlassian/jira/work/catalina.pid

also you can check using "ls -l" on linux shell what the permissions are - assuming the file is there.
This should give a first clue why Jira complains about this file and letting you not stop Jira.

Cheers,
Daniel

[said kouzibry]

As a temporary workaround, I would search for the PID of the running process by listening port number and kill it,

if the port is 8080 for example : 

#sudo netstat -lnp | grep :8080
tcp6 0 0 :::8080 :::* LISTEN 6871/tomcat9 
#sudo kill 6871

Then I would start Jira service,

You would need to investigate why this has happened in the first place but my bets are on user permissions, it's possible at some point Jira was started as root instead of the dedicated user.