Fatal error: Please read "Security" section of the manual to find out how to run mysqld as root

I'm using OS X (Yosemite) and this error happened to me when I upgraded from Mavericks to Yosemite. It was solved by using this command

sudo /usr/local/mysql/support-files/mysql.server start

The MySQL daemon should not be executed as the system user root which (normally) do not has any restrictions.

According to your cli, I suppose you wanted to execute the initscript instead:

sudo /etc/init.d/mysql stop

Another way would be to use the mysqladmin tool (note, root is the MySQL root user here, not the system root user):

/usr/local/mysql/bin/mysqladmin --port=8889 -u root shutdown

you might try this if you logged in with root:

mysqld --user=root