Pulling the official MySQL image from the docker registry https://hub.docker.com/r/mysql/mysql-server to start a MySQL instance with your configuration file (and MySQL binary files). Adding the “–volume” option for the configuration directory (or file) and MySQL binary files and you stumble on the error:

2019-12-03 01:13:38 0 [Note] mysqld (mysqld 5.6.46-log) starting as process 67 ...
2019-12-03 01:13:38 67 [ERROR] Fatal error: Please read "Security" section of the manual to find out how to run mysqld as root!

2019-12-03 01:13:38 67 [ERROR] Aborting

2019-12-03 01:13:38 67 [Note] Binlog end
2019-12-03 01:13:38 67 [Note] mysqld: Shutdown complete

Apparently, the server option is not configured to run properly as a root user and you do not want to run it, but why it keeps insisting to run it as root?

Because of the entry point script will execute only “mysqld” as a command, which expects to have a “user” option in the “[mysqld]” section of your my.cnf configuration file!

Do not miss the user option in my.cnf! This is how the MySQL server will be using the “mysql” username not the root!

user=mysql

Typical error, because it is not so common to include the username in my.cnf configuration file of the mysqld process to run as. If you use the official docker MySQL image to create your configuration file you would not encounter the above error, but if you use an existing (probably old and from non virtualized environment) my.cnf make sure to include the username, which should be used to run the mysqld process as.

Here is our command to execute the container:

docker run --privileged -d -v /mnt/storage/docker/mysql-slave/files:/var/lib/mysql -v /mnt/storage/docker/mysql-slave/etc/my.cnf:/etc/my.cnf mysql/mysql-server:5.6