Problem:
A port is being used by some process but the pid of process is not visible
Reason:
When the process is started by root, other users not in the root group cannot view the process ids. So when you do:
netstat -atnp
process id will not be visible to normal user.
You have to run netstat command with sudo, to view all process ids.
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A scenario I came across is when Apache tomcat was started as a Java service with jsvc command. The daemon.sh was run by the root user, so the process belonged to root.