I had this error message having started up a second Tomcat server on a Linux server.
$CATALINA_PID was set but the specified file does not exist. Is Tomcat running? Stop aborted.
When starting up the 2nd Tomcat I had set CATALINA_PID as asked but my mistake was to set it to a directory (I assumed Tomcat would write a default file name in there with the pid).
The fix was simply to change my CATALINA_PID to add a file name to the end of it (I chose catalina.pid from the above examples). Next I went to the directory and did a simple:
touch catalina.pid
creating an empty file of the correct name. Then when I did my shutdown.sh I got the message back saying:
PID file is empty and has been ignored.
Tomcat stopped.
I didn’t have the option to kill Tomcat as the JVM was in use so I was glad I found this.