I just restarted MySQL (following a tip from here: https://stackoverflow.com/a/14238800) and it solved the issue.
I had the same issue on MacOS (10.10.2) and MySql (5.6.21) installed via homebrew.
The confusing thing was that one of my apps connected to the database fine and the other did not.
After trying many things on the app that threw the exception com.mysql.jdbc.CommunicationsException as suggested by the accepted answer of this question to no avail, I was surprised that restarting MySQL worked.
The cause of my issue might have been the following as suggested in the answer in the aforementioned link:
Are you using connection pool ? If yes, then try to restart the
server. Probably few of the connections in your connection pool are in closed state.