无法重新启动 MySQL Docker 容器，出现“无法打开 mysql.plugin 表”和“表 'mysql.user' 不存在”等错误

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

因此需要docker-compose rm mysql删除断开的连接，然后再次启动容器。

Answer 2

I have meet same issue, in my case, it is since I have create db dir for volume before I run cmd 'docker-compose up', after I delete image and delete db dir I have created, it will ok below is my docker.yml

volumes: - "./db:/var/lib/mysql"

we should notice that not to create db dir before rum cmd.