MySQL Fatal error: Can't open and lock privilege tables: Incorrect file format 'user'

Question

MySQL (Percona 5.6) will not start.

This error has happened to me several times. Each time, I have had to remove MySQL data directories and reinstall MySQL.

Answer 1

Here is the setup for @John Linhart's answer, if you're running Docker:

First, start a new docker container with the appropriate tag from the mysql-container (the same you used to write the DB with).

$ docker run --rm -it -v :/var/lib/mysql mysql: /bin/bash

This will launch a new container with the correct named volume (or mounted volume) mounted in the container and drop you into a shell as root. The mysqld-Daemon will refuse to launch as root though, so we'll run it as the mysql-user:

$ whoami
root
$ which mysqld
/usr/sbin/mysqld
$ su mysql
$ whoami
mysql
$ /usr/sbin/mysqld --skip-grant-tables
....

Now to run the SQL commands, we'll connect to the running container from a new terminal:

$ docker ps 
CONTAINER ID [...]
abc123 [...]
$ docker exec -it abc123 /bin/bash
# We're on the container now!
$ whoami
root
$ mysql
...

And continue from there. When you're done, leave the container on the second terminal via exit. The terminal running mysqld will not respond to CMD+C, so we'll stop the container via Docker:

$ docker ps
CONTAINER ID [...]
abc123 [...]
$ docker stop abc123