Not sure if you managed to resolve this issue but when I had it the last time these are the steps I took.
• Exit M2EE • Get the IDs of all running processes by typing ‘ps aux’ in PuTTY • Identify the JAVA process and get its Process ID (PID) • Force Kill the Java action by typing ‘kill 11111’ (where 11111 = the PID of the JAVA Process • Get back into the Application by typing ‘M2EE’ and you should now have access to the Application to do stop/start.
Hope this helps.
If you want to restart your application more gracefully instead do the following.
As Mohammed sow states get your current process id by using ps -axu | grep java ,but instead of killing this process do the following. Go to the /home/<mxuser>/.m2ee folder and create a new m2ee.pid file. When you now save the file you should be fine.