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
The correct answer that worked for me on CentOS is
/etc/init.d/mysql restart
which is an init script and not /etc/init.d/mysqld restart, which is binary
The is in fact comment of @MrTux on the question which worked for me. It took quite a bit of my time hence posting it as answer.