If you have the resources (CPU + RAM) available on your server then its can be a great troubleshooting tool if you enable MySQL logging which includes server messages, SQL query logs, and slow query logs. If you do not have the resources I would suggest only enable minimal logging such as only server messages and the slow query log since enabling all queries to be written to a file can become expensive rather quickly. Below I discuss enabling three different types of MySQL logging, adding a MySQL configuration file to logrotate, and configuring root to run mysqladmin commands without having to type the password out each time.

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