GNU/Linux Desktop Survival Guide by Graham Williams
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MySQL Root Password

Once mysql-server is installed it is ready for immediate use. However, it is best to at least set an admin password with:

  $ /usr/bin/mysqladmin -u root password 'new-password'

You will then also need to let cron jobs work on the database so create a personal mysql config file for root in /root/.my.cnf containing:

  [mysqladmin] 
  user            = root
  password        = <secret>

Make sure the permissions are set appropriately:

  # chmod 0600 /root/.my.cnf
  # ls -l /root/.my.cnf
  4.0k -rw-------    1 root root  64 Oct 12 10:52 /root/.my.cnf