Mysql – `thesql_upgrade` is failing with no real reason given

MySQLmysql5.5

I'm upgrading from MySQL 5.1 to 5.5, running mysql_upgrade and getting this output:

# mysql_upgrade
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
FATAL ERROR: Upgrade failed

Any ideas on where to look for what's happening (or, not happening?) so I can fix whatever is wrong and actually run mysql_upgrade?

Thanks!

More output:

# mysql_upgrade --verbose
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
FATAL ERROR: Upgrade failed

# mysql_upgrade --debug-check --debug-info
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
FATAL ERROR: Upgrade failed

# mysql_upgrade --debug-info
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
FATAL ERROR: Upgrade failed

User time 0.00, System time 0.00
Maximum resident set size 1260, Integral resident set size 0
Non-physical pagefaults 447, Physical pagefaults 0, Swaps 0
Blocks in 0 out 16, Messages in 0 out 0, Signals 0
Voluntary context switches 9, Involuntary context switches 5

# mysql_upgrade --debug-check
Looking for 'mysql' as: mysql
Looking for 'mysqlcheck' as: mysqlcheck
FATAL ERROR: Upgrade failed

After shutting down mysqld --skip-grant-tables via mysqladmin shutdown and restarting mysql via service mysql start, the error log loops through this set of errors over and over:

130730 21:03:27 [Note] Plugin 'FEDERATED' is disabled.
/usr/sbin/mysqld: Table 'mysql.plugin' doesn't exist
130730 21:03:27 [ERROR] Can't open the mysql.plugin table. Please run mysql_upgrade to create it.
130730 21:03:27 InnoDB: The InnoDB memory heap is disabled
130730 21:03:27 InnoDB: Mutexes and rw_locks use GCC atomic builtins
130730 21:03:27 InnoDB: Compressed tables use zlib 1.2.3.4
130730 21:03:27 InnoDB: Initializing buffer pool, size = 20.0G
130730 21:03:29 InnoDB: Completed initialization of buffer pool
130730 21:03:30 InnoDB: highest supported file format is Barracuda.
InnoDB: Log scan progressed past the checkpoint lsn 588190222435
130730 21:03:30  InnoDB: Database was not shut down normally!
InnoDB: Starting crash recovery.
InnoDB: Reading tablespace information from the .ibd files...
InnoDB: Restoring possible half-written data pages from the doublewrite
InnoDB: buffer...
InnoDB: Doing recovery: scanned up to log sequence number 588192055067
130730 21:03:30  InnoDB: Starting an apply batch of log records to the database...
InnoDB: Progress in percents: 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 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
InnoDB: Last MySQL binlog file position 0 81298895, file name /var/log/mysql/mysql-bin.006008
130730 21:03:33  InnoDB: Waiting for the background threads to start
130730 21:03:34 InnoDB: 5.5.32 started; log sequence number 588192055067
130730 21:03:34 [Note] Recovering after a crash using /var/log/mysql/mysql-bin
130730 21:03:34 [Note] Starting crash recovery...
130730 21:03:34 [Note] Crash recovery finished.
130730 21:03:34 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
130730 21:03:34 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
130730 21:03:34 [Note] Server socket created on IP: '0.0.0.0'.
130730 21:03:34 [ERROR] Fatal error: Can't open and lock privilege tables: Table 'mysql.host' doesn't exist

MySQL log during start up via mysqld_safe --skip-grant-tables

130730 21:19:36 mysqld_safe Starting mysqld daemon with databases from /var/lib/mysql
130730 21:19:36 [Note] Plugin 'FEDERATED' is disabled.
130730 21:19:36 InnoDB: The InnoDB memory heap is disabled
130730 21:19:36 InnoDB: Mutexes and rw_locks use GCC atomic builtins
130730 21:19:36 InnoDB: Compressed tables use zlib 1.2.3.4
130730 21:19:37 InnoDB: Initializing buffer pool, size = 20.0G
130730 21:19:39 InnoDB: Completed initialization of buffer pool
130730 21:19:39 InnoDB: highest supported file format is Barracuda.
130730 21:19:42  InnoDB: Warning: allocated tablespace 566, old maximum was 0
130730 21:19:42  InnoDB: Waiting for the background threads to start
130730 21:19:43 InnoDB: 5.5.32 started; log sequence number 588192055067
130730 21:19:43 [Note] Server hostname (bind-address): '0.0.0.0'; port: 3306
130730 21:19:43 [Note]   - '0.0.0.0' resolves to '0.0.0.0';
130730 21:19:43 [Note] Server socket created on IP: '0.0.0.0'.
130730 21:19:43 [Warning] Can't open and lock time zone table: Table 'mysql.time_zone_leap_second' doesn't exist trying to live without them
130730 21:19:43 [ERROR] Can't open and lock privilege tables: Table 'mysql.servers' doesn't exist
130730 21:19:43 [ERROR] Native table 'performance_schema'.'events_waits_current' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'events_waits_history' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'events_waits_history_long' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'setup_consumers' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'setup_instruments' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'setup_timers' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'performance_timers' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'threads' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_thread_by_event_name' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'events_waits_summary_by_instance' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'events_waits_summary_global_by_event_name' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'file_summary_by_event_name' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'file_summary_by_instance' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'mutex_instances' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'rwlock_instances' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'cond_instances' has the wrong structure
130730 21:19:43 [ERROR] Native table 'performance_schema'.'file_instances' has the wrong structure
130730 21:19:43 [Note] /usr/sbin/mysqld: ready for connections.
Version: '5.5.32-0ubuntu0.12.04.1-log'  socket: '/var/run/mysqld/mysqld.sock'  port: 3306  (Ubuntu)

As I understand it, all the table structure/existence issues (as it relates to mysql system tables) should be corrected by running mysql_upgrade :

Best Answer

I think that it needs username and password

mysql_upgrade -u root -p

If I don't pass them I get your error

Edit: thanks to the comments now I know that there are other reasons, maybe less frequent but it's best to be aware of them too

So you get that error when

  • you didn't pass username and password
  • you passed your credentials, but they were wrong
  • the MySQL server isn't running
  • the permissions' tables are ruined (then you must restart MySQL with mysqld --skip-grant-table)
  • the table mysql.plugin is missing (you'll see an error about that when starting MySQL which suggests to run... mysql_upgrade, and that fails. You probably have some obsolete configuration in my.cnf)
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