title: MySQL Fatal error: Can't open and lock privilege tables: Incorrect file format 'user'
body: <p>MySQL (Percona 5.6) will not start.</p>
  
  <p>This error has happened to me several times. Each time, I have had to remove MySQL data directories and reinstall MySQL.</p>
  
  <p>Is there another way to fix MySQL? (Specifically one in which the data not blown away?)</p>
  
  <p><strong>/var/log/mysql/error.log</strong></p>
  
  <pre><code>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
  </code></pre>