Problem
On occasion I've had to restart a Jira server abruptly. While I try to avoid this sometimes it can't be helped. A problem can occur when Jira doesn't have time to shutdown nicely and remove several of its lock files. When this occurs Jira may not be able to startup again without removing said lock files.
Solution
If Jira complains about files being locked and won't startup, first stop any Jira instance:
sudo service jira stop
and make sure the following files do NOT exist (if they do then delete them):
/opt/atlassian/jira/work/catalina.pid/var/atlassian/application-data/jira/.jira-home.lock
Note (2) refers to your Jira home folder, which may differ from the above.
References
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