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.

Is there another way to fix MySQL? (Specifically one in which the data not blown away?)

/var/log/mysql/error.log

150214 16:36:39 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
2015-02-14 16:36:40 0 [Warning] Using unique option prefix key_buffer instead of key_buffer_size is deprecated and will be removed in a future release. Please use the full name instead.
2015-02-14 16:36:40 0 [Warning] 'THREAD_CONCURRENCY' is deprecated and will be removed in a future release.
2015-02-14 16:36:40 0 [Warning] TIMESTAMP with implicit DEFAULT value is deprecated. Please use --explicit_defaults_for_timestamp server option (see documentation for more details).
2015-02-14 16:36:40 1018 [Warning] Using unique option prefix myisam-recover instead of myisam-recover-options is deprecated and will be removed in a future release. Please use the full name instead.
2015-02-14 16:36:40 1018 [Note] Plugin 'FEDERATED' is disabled.
/usr/sbin/mysqld: Incorrect file format 'plugin'
2015-02-14 16:36:40 1018 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
2015-02-14 16:36:40 1018 [Note] InnoDB: Using atomics to ref count buffer pool pages
2015-02-14 16:36:40 1018 [Note] InnoDB: The InnoDB memory heap is disabled
2015-02-14 16:36:40 1018 [Note] InnoDB: Mutexes and rw_locks use GCC atomic builtins
2015-02-14 16:36:40 1018 [Note] InnoDB: Memory barrier is not used
2015-02-14 16:36:40 1018 [Note] InnoDB: Compressed tables use zlib 1.2.8
2015-02-14 16:36:40 1018 [Note] InnoDB: Using Linux native AIO
2015-02-14 16:36:40 1018 [Note] InnoDB: Using CPU crc32 instructions
2015-02-14 16:36:40 1018 [Note] InnoDB: Initializing buffer pool, size = 256.0M
2015-02-14 16:36:40 1018 [Note] InnoDB: Completed initialization of buffer pool
2015-02-14 16:36:40 1018 [Note] InnoDB: Highest supported file format is Barracuda.
2015-02-14 16:36:40 1018 [Note] InnoDB: The log sequence numbers 714340126 and 714340126 in ibdata files do not match the log sequence number 716513090 in the ib_logfiles!
2015-02-14 16:36:40 1018 [Note] InnoDB: Database was not shutdown normally!
2015-02-14 16:36:40 1018 [Note] InnoDB: Starting crash recovery.
2015-02-14 16:36:40 1018 [Note] InnoDB: Reading tablespace information from the .ibd files...
2015-02-14 16:36:40 1018 [Note] InnoDB: Restoring possible half-written data pages 
2015-02-14 16:36:40 1018 [Note] InnoDB: from the doublewrite buffer...
InnoDB: Last MySQL binlog file position 0 292596, file name binlog.000056
2015-02-14 16:36:40 1018 [Note] InnoDB: 128 rollback segment(s) are active.
2015-02-14 16:36:40 1018 [Note] InnoDB: Waiting for purge to start
2015-02-14 16:36:40 1018 [Note] InnoDB:  Percona XtraDB (http://www.percona.com) 5.6.21-70.1 started; log sequence number 716513090
2015-02-14 16:36:40 1018 [Note] Recovering after a crash using binlog
2015-02-14 16:36:40 1018 [Note] Starting crash recovery...
2015-02-14 16:36:40 1018 [Note] Crash recovery finished.
2015-02-14 16:36:40 1018 [Note] RSA private key file not found: /var/lib/mysql//private_key.pem. Some authentication plugins will not work.
2015-02-14 16:36:40 1018 [Note] RSA public key file not found: /var/lib/mysql//public_key.pem. Some authentication plugins will not work.
2015-02-14 16:36:40 1018 [Note] Server hostname (bind-address): '*'; port: 3306
2015-02-14 16:36:40 1018 [Note] IPv6 is available.
2015-02-14 16:36:40 1018 [Note]   - '::' resolves to '::';
2015-02-14 16:36:40 1018 [Note] Server socket created on IP: '::'.
2015-02-14 16:36:40 1018 [ERROR] Fatal error: Can't open and lock privilege tables: Incorrect file format 'user'
150214 16:36:40 mysqld_safe mysqld from pid file /tmp/mysqld.pid ended

Answer 1

I managed so solve this problem with answer from ruby.b

You'll have to repair your host table. To do this, issue the following command to start your server bypassing the privilege system

In one terminal, run

$ sudo mysqld --skip-grant-tables

Open another terminal and execute these commands

$ mysql
mysql> use mysql
mysql> repair table host use_frm;
mysql> exit

And restart the mysql service

$ sudo service mysql restart

Answer 2

Thanks to John for putting me on the right track, I had a few other hoops to jump through on my system. Hope this helps someone.

This is a corrupt privilege table. Maybe caused by an upgrade or power failure. My system OpenSUSE 13.2, MySQL 5.6. Simple reinstall does not fix, must delete all traces of MySQL before reinstall OR…

Close down all instances of MySQL

$ systemctl stop mysql.service
$ pkill -9 mysqld

Start server bypassing privilege system

$ sudo mysqld_safe --user=root --skip-grant-tables

Start MySQL command line tool

$ mysql

If you receive

ERROR 2002 (HY000): Can't connect to local MySQL server through socket '/var/run/mysqld/mysqld.sock' (2)

mysqld_safe is running with its socket somewhere else. Find it with.

$ sudo find / -type s

Mine was in /var/run/mysql/ Edit the socket line in my.cnf, making a note of your existing socket setting. My line became

socket=/var/run/mysql/mysql.sock

Return to 'Close down all instances of MySQL' (the top of these instructions). Follow them through to 'Start MySQL command line tool'. Hopefully you can open mysql successfully. From mysql command line.

mysql> use mysql
mysql> repair table user use_frm;
mysql> exit

Close down all instances of MySQL

$ systemctl stop mysql.service
$ pkill -9 mysqld

Re-edit my.cnf, returning the socket line to its original setting.

I had to reset permissions on 2 files in my mysql data directory.

$ chown mysql:mysql server2.err
$ chown mysql:mysql server2.pid

Start the MySQL server

$ systemctl start mysql.service

I then got the same original error with another table (db)

[ERROR] Fatal error: Can't open and lock privilege  tables: Incorrect file format 'db'

And had to repeat the above procedure multiple times altering the 'repair' command until all privilege tables were fixed.

mysql> repair table db use_frm;