I solved this by stopping mysql several times.
$ mysql.server stop
Shutting down MySQL
.. ERROR! The server quit without updating PID file (/usr/local/var/mysql/xxx.local.pid).
$ mysql.server stop
Shutting down MySQL
.. SUCCESS!
$ mysql.server stop
ERROR! MySQL server PID file could not be found! (note: this is good)
$ mysql.server start
All good from here. I suspect mysql had been started more than once.