Without seeing any additional information, here is my best guess why MySQL is trying to shutdown for a long time: I suspect mysqld no longer has a socket file.
About 1.5 years ago, I answered mysql restart issue after move database. I learned that mysqld depends on the presence of a socket file. If there is no socket, mysqld just draws lots of dots on the screen and then gives up.
In that old post, I wrote three instructions
- kill mysqld_safe
- kill mysqld
- start mysqld
Please go do this now ...
I have discussed MySQL behavior with the socket file (or lack of it) 4 years ago (See my older post mysql restart won't kill child processes on CentOS)