title: Cannot restart the MySQL Docker container, gives errors like `Can't open the mysql.plugin table` and `Table 'mysql.user' doesn't exist`
body: <p>After running out of space on the server, it seems that the file of Docker MySQL got corrupted. </p>
  
  <p>When trying to relaunch <code>mysql:5.6</code> container I get the error <code>[ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.user' doesn't exist</code>.</p>
  
  <p>I cannot locate the file that is corrupted, and possibly delete it or fix the permissions.</p>
  
  <p>Here is a full error output:</p>
  
  <pre><code>$ 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
  </code></pre>