I am not sure how to fix this:
dyn-72-33-214-45:python mona$ sudo /usr/local/mysql/bin/mysqld stop 2014-09-06 09:49:04 0 [Warning] TIMESTAMP with implicit DE
Very weird, but I got this error when I made a typo in the my.cnf file. So it had nothing to do with the user directive not defined or not running as root-user.
my.cnf
user
root
My mistake was:
bind=192.168.1.2
instead of
bind-address=192.168.1.2