Cannot restart the MySQL Docker container, gives errors like `Can't open the mysql.plugin table` and `Table 'mysql.user' doesn't exist`

Question

After running out of space on the server, it seems that the file of Docker MySQL got corrupted.

When trying to relaunch mysql:5.6 container I get the error [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist.

I cannot locate the file that is corrupted, and possibly delete it or fix the permissions.

Here is a full error output:

$ docker start -a  mysql_1
2016-11-23 10:22:17 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2016-11-23 10:22:17 0 [Note] mysqld (mysqld 5.6.34) starting as process 1 ...
2016-11-23 10:22:17 1 [Note] Plugin 'FEDERATED' is disabled.
mysqld: Table 'mysql.plugin' doesn't exist
2016-11-23 10:22:17 1 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2016-11-23 10:22:17 1 [Note] InnoDB: Using atomics to ref count buffer pool pages
2016-11-23 10:22:17 1 [Note] InnoDB: The InnoDB memory heap is disabled
2016-11-23 10:22:17 1 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2016-11-23 10:22:17 1 [Note] InnoDB: Memory barrier is not used
2016-11-23 10:22:17 1 [Note] InnoDB: Compressed tables use zlib 1.2.8
2016-11-23 10:22:17 1 [Note] InnoDB: Using Linux native AIO
2016-11-23 10:22:17 1 [Note] InnoDB: Using CPU crc32 instructions
2016-11-23 10:22:17 1 [Note] InnoDB: Initializing buffer pool, size = 128.0M
2016-11-23 10:22:17 1 [Note] InnoDB: Completed initialization of buffer pool
2016-11-23 10:22:17 1 [Note] InnoDB: Highest supported file format is Barracuda.
2016-11-23 10:22:17 1 [Note] InnoDB: Log scan progressed past the checkpoint lsn 49463
2016-11-23 10:22:17 1 [Note] InnoDB: Database was not shutdown normally!
2016-11-23 10:22:17 1 [Note] InnoDB: Starting crash recovery.
2016-11-23 10:22:17 1 [Note] InnoDB: Reading tablespace information from the .ibd files...
2016-11-23 10:22:17 1 [Note] InnoDB: Restoring possible half-written data pages
2016-11-23 10:22:17 1 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Doing recovery: scanned up to log sequence number 1600607
2016-11-23 10:22:17 1 [Note] InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percent: 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99
InnoDB: Apply batch completed
2016-11-23 10:22:18 1 [Note] InnoDB: 128 rollback segment(s) are active.
2016-11-23 10:22:18 1 [Note] InnoDB: Waiting for purge to start
2016-11-23 10:22:18 1 [Note] InnoDB: 5.6.34 started; log sequence number 1600607
2016-11-23 10:22:18 1 [Note] Server hostname (bind-address): '*'; port: 3306
2016-11-23 10:22:18 1 [Note] IPv6 is available.
2016-11-23 10:22:18 1 [Note]   - '::' resolves to '::';
2016-11-23 10:22:18 1 [Note] Server socket created on IP: '::'.
2016-11-23 10:22:18 1 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist

Answer 1

So docker-compose rm mysql was needed to remove the broken connection, and then launch again the container.