mysql_upgrade failed - innodb tables doesn't exist?

This is a known bug in MySQL 5.6, it is documented here.

According to the replies to the bug report, you can manually create the missing tables. The structure of the missing tables is provided as attachment here.

Steps to follow:

1) Drop these tables from Mysql:

 innodb_index_stats
 innodb_table_stats
 slave_master_info
 slave_relay_log_info
 slave_worker_info

2) Delete *.frm and *.ibd files for the 5 tables above.

3) Create the tables by running the following queries:

CREATE TABLE `innodb_index_stats` (
  `database_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `table_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `index_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
  `stat_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `stat_value` bigint(20) unsigned NOT NULL,
  `sample_size` bigint(20) unsigned DEFAULT NULL,
  `stat_description` varchar(1024) COLLATE utf8_bin NOT NULL,
  PRIMARY KEY (`database_name`,`table_name`,`index_name`,`stat_name`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin STATS_PERSISTENT=0;

CREATE TABLE `innodb_table_stats` (
  `database_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `table_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
  `n_rows` bigint(20) unsigned NOT NULL,
  `clustered_index_size` bigint(20) unsigned NOT NULL,
  `sum_of_other_index_sizes` bigint(20) unsigned NOT NULL,
  PRIMARY KEY (`database_name`,`table_name`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin STATS_PERSISTENT=0;

CREATE TABLE `slave_master_info` (
  `Number_of_lines` int(10) unsigned NOT NULL COMMENT 'Number of lines in the file.',
  `Master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL COMMENT 'The name of the master binary log currently being read from the master.',
  `Master_log_pos` bigint(20) unsigned NOT NULL COMMENT 'The master log position of the last read event.',
  `Host` char(64) CHARACTER SET utf8 COLLATE utf8_bin NOT NULL DEFAULT '' COMMENT 'The host name of the master.',
  `User_name` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The user name used to connect to the master.',
  `User_password` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The password used to connect to the master.',
  `Port` int(10) unsigned NOT NULL COMMENT 'The network port used to connect to the master.',
  `Connect_retry` int(10) unsigned NOT NULL COMMENT 'The period (in seconds) that the slave will wait before trying to reconnect to the master.',
  `Enabled_ssl` tinyint(1) NOT NULL COMMENT 'Indicates whether the server supports SSL connections.',
  `Ssl_ca` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The file used for the Certificate Authority (CA) certificate.',
  `Ssl_capath` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The path to the Certificate Authority (CA) certificates.',
  `Ssl_cert` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The name of the SSL certificate file.',
  `Ssl_cipher` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The name of the cipher in use for the SSL connection.',
  `Ssl_key` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The name of the SSL key file.',
  `Ssl_verify_server_cert` tinyint(1) NOT NULL COMMENT 'Whether to verify the server certificate.',
  `Heartbeat` float NOT NULL,
  `Bind` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'Displays which interface is employed when connecting to the MySQL server',
  `Ignored_server_ids` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The number of server IDs to be ignored, followed by the actual server IDs',
  `Uuid` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The master server uuid.',
  `Retry_count` bigint(20) unsigned NOT NULL COMMENT 'Number of reconnect attempts, to the master, before giving up.',
  `Ssl_crl` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The file used for the Certificate Revocation List (CRL)',
  `Ssl_crlpath` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The path used for Certificate Revocation List (CRL) files',
  `Enabled_auto_position` tinyint(1) NOT NULL COMMENT 'Indicates whether GTIDs will be used to retrieve events from the master.',
  PRIMARY KEY (`Host`,`Port`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 STATS_PERSISTENT=0 COMMENT='Master Information';

CREATE TABLE `slave_relay_log_info` (
  `Number_of_lines` int(10) unsigned NOT NULL COMMENT 'Number of lines in the file or rows in the table. Used to version table definitions.',
  `Relay_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL COMMENT 'The name of the current relay log file.',
  `Relay_log_pos` bigint(20) unsigned NOT NULL COMMENT 'The relay log position of the last executed event.',
  `Master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL COMMENT 'The name of the master binary log file from which the events in the relay log file were read.',
  `Master_log_pos` bigint(20) unsigned NOT NULL COMMENT 'The master log position of the last executed event.',
  `Sql_delay` int(11) NOT NULL COMMENT 'The number of seconds that the slave must lag behind the master.',
  `Number_of_workers` int(10) unsigned NOT NULL,
  `Id` int(10) unsigned NOT NULL COMMENT 'Internal Id that uniquely identifies this record.',
  PRIMARY KEY (`Id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 STATS_PERSISTENT=0 COMMENT='Relay Log Information';

CREATE TABLE `slave_worker_info` (
  `Id` int(10) unsigned NOT NULL,
  `Relay_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
  `Relay_log_pos` bigint(20) unsigned NOT NULL,
  `Master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
  `Master_log_pos` bigint(20) unsigned NOT NULL,
  `Checkpoint_relay_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
  `Checkpoint_relay_log_pos` bigint(20) unsigned NOT NULL,
  `Checkpoint_master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
  `Checkpoint_master_log_pos` bigint(20) unsigned NOT NULL,
  `Checkpoint_seqno` int(10) unsigned NOT NULL,
  `Checkpoint_group_size` int(10) unsigned NOT NULL,
  `Checkpoint_group_bitmap` blob NOT NULL,
  PRIMARY KEY (`Id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 STATS_PERSISTENT=0 COMMENT='Worker Information';

4) Restart your MySQL server.


UPDATED Fix For: MariaDB 10

6 tables (includes gtid_slave_pos table)

note: MariaDB and MySQL have different GTID implementations that are not compatible with each other.

Use at your own risk.

--
-- Table structure for table `gtid_slave_pos`
--

DROP TABLE IF EXISTS `gtid_slave_pos`;
/*!40101 SET @saved_cs_client     = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `gtid_slave_pos` (
  `domain_id` int(10) unsigned NOT NULL,
  `sub_id` bigint(20) unsigned NOT NULL,
  `server_id` int(10) unsigned NOT NULL,
  `seq_no` bigint(20) unsigned NOT NULL,
  PRIMARY KEY (`domain_id`,`sub_id`)
) ENGINE=InnoDB DEFAULT CHARSET=latin1 COMMENT='Replication slave GTID position';
/*!40101 SET character_set_client = @saved_cs_client */;

--
-- Dumping data for table `gtid_slave_pos`
--

LOCK TABLES `gtid_slave_pos` WRITE;
/*!40000 ALTER TABLE `gtid_slave_pos` DISABLE KEYS */;
/*!40000 ALTER TABLE `gtid_slave_pos` ENABLE KEYS */;
UNLOCK TABLES;

--
-- Table structure for table `innodb_index_stats`
--

DROP TABLE IF EXISTS `innodb_index_stats`;
/*!40101 SET @saved_cs_client     = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `innodb_index_stats` (
  `database_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `table_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `index_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
  `stat_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `stat_value` bigint(20) unsigned NOT NULL,
  `sample_size` bigint(20) unsigned DEFAULT NULL,
  `stat_description` varchar(1024) COLLATE utf8_bin NOT NULL,
  PRIMARY KEY (`database_name`,`table_name`,`index_name`,`stat_name`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin STATS_PERSISTENT=0;
/*!40101 SET character_set_client = @saved_cs_client */;

--
-- Dumping data for table `innodb_index_stats`
--

LOCK TABLES `innodb_index_stats` WRITE;
/*!40000 ALTER TABLE `innodb_index_stats` DISABLE KEYS */;
/*!40000 ALTER TABLE `innodb_index_stats` ENABLE KEYS */;
UNLOCK TABLES;

--
-- Table structure for table `innodb_table_stats`
--

DROP TABLE IF EXISTS `innodb_table_stats`;
/*!40101 SET @saved_cs_client     = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `innodb_table_stats` (
  `database_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `table_name` varchar(64) COLLATE utf8_bin NOT NULL,
  `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
  `n_rows` bigint(20) unsigned NOT NULL,
  `clustered_index_size` bigint(20) unsigned NOT NULL,
  `sum_of_other_index_sizes` bigint(20) unsigned NOT NULL,
  PRIMARY KEY (`database_name`,`table_name`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 COLLATE=utf8_bin STATS_PERSISTENT=0;
/*!40101 SET character_set_client = @saved_cs_client */;

--
-- Dumping data for table `innodb_table_stats`
--

LOCK TABLES `innodb_table_stats` WRITE;
/*!40000 ALTER TABLE `innodb_table_stats` DISABLE KEYS */;
/*!40000 ALTER TABLE `innodb_table_stats` ENABLE KEYS */;
UNLOCK TABLES;

--
-- Table structure for table `slave_master_info`
--

DROP TABLE IF EXISTS `slave_master_info`;
/*!40101 SET @saved_cs_client     = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `slave_master_info` (
  `Number_of_lines` int(10) unsigned NOT NULL COMMENT 'Number of lines in the file.',
  `Master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL COMMENT 'The name of the master binary log currently being read from the master.',
  `Master_log_pos` bigint(20) unsigned NOT NULL COMMENT 'The master log position of the last read event.',
  `Host` char(64) CHARACTER SET utf8 COLLATE utf8_bin NOT NULL DEFAULT '' COMMENT 'The host name of the master.',
  `User_name` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The user name used to connect to the master.',
  `User_password` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The password used to connect to the master.',
  `Port` int(10) unsigned NOT NULL COMMENT 'The network port used to connect to the master.',
  `Connect_retry` int(10) unsigned NOT NULL COMMENT 'The period (in seconds) that the slave will wait before trying to reconnect to the master.',
  `Enabled_ssl` tinyint(1) NOT NULL COMMENT 'Indicates whether the server supports SSL connections.',
  `Ssl_ca` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The file used for the Certificate Authority (CA) certificate.',
  `Ssl_capath` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The path to the Certificate Authority (CA) certificates.',
  `Ssl_cert` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The name of the SSL certificate file.',
  `Ssl_cipher` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The name of the cipher in use for the SSL connection.',
  `Ssl_key` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The name of the SSL key file.',
  `Ssl_verify_server_cert` tinyint(1) NOT NULL COMMENT 'Whether to verify the server certificate.',
  `Heartbeat` float NOT NULL,
  `Bind` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'Displays which interface is employed when connecting to the MySQL server',
  `Ignored_server_ids` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The number of server IDs to be ignored, followed by the actual server IDs',
  `Uuid` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The master server uuid.',
  `Retry_count` bigint(20) unsigned NOT NULL COMMENT 'Number of reconnect attempts, to the master, before giving up.',
  `Ssl_crl` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The file used for the Certificate Revocation List (CRL)',
  `Ssl_crlpath` text CHARACTER SET utf8 COLLATE utf8_bin COMMENT 'The path used for Certificate Revocation List (CRL) files',
  `Enabled_auto_position` tinyint(1) NOT NULL COMMENT 'Indicates whether GTIDs will be used to retrieve events from the master.',
  PRIMARY KEY (`Host`,`Port`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 STATS_PERSISTENT=0 COMMENT='Master Information';
/*!40101 SET character_set_client = @saved_cs_client */;

--
-- Dumping data for table `slave_master_info`
--

LOCK TABLES `slave_master_info` WRITE;
/*!40000 ALTER TABLE `slave_master_info` DISABLE KEYS */;
/*!40000 ALTER TABLE `slave_master_info` ENABLE KEYS */;
UNLOCK TABLES;

--
-- Table structure for table `slave_relay_log_info`
--

DROP TABLE IF EXISTS `slave_relay_log_info`;
/*!40101 SET @saved_cs_client     = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `slave_relay_log_info` (
  `Number_of_lines` int(10) unsigned NOT NULL COMMENT 'Number of lines in the file or rows in the table. Used to version table definitions.',
  `Relay_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL COMMENT 'The name of the current relay log file.',
  `Relay_log_pos` bigint(20) unsigned NOT NULL COMMENT 'The relay log position of the last executed event.',
  `Master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL COMMENT 'The name of the master binary log file from which the events in the relay log file were read.',
  `Master_log_pos` bigint(20) unsigned NOT NULL COMMENT 'The master log position of the last executed event.',
  `Sql_delay` int(11) NOT NULL COMMENT 'The number of seconds that the slave must lag behind the master.',
  `Number_of_workers` int(10) unsigned NOT NULL,
  `Id` int(10) unsigned NOT NULL COMMENT 'Internal Id that uniquely identifies this record.',
  PRIMARY KEY (`Id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 STATS_PERSISTENT=0 COMMENT='Relay Log Information';
/*!40101 SET character_set_client = @saved_cs_client */;

--
-- Dumping data for table `slave_relay_log_info`
--

LOCK TABLES `slave_relay_log_info` WRITE;
/*!40000 ALTER TABLE `slave_relay_log_info` DISABLE KEYS */;
/*!40000 ALTER TABLE `slave_relay_log_info` ENABLE KEYS */;
UNLOCK TABLES;

--
-- Table structure for table `slave_worker_info`
--

DROP TABLE IF EXISTS `slave_worker_info`;
/*!40101 SET @saved_cs_client     = @@character_set_client */;
/*!40101 SET character_set_client = utf8 */;
CREATE TABLE `slave_worker_info` (
  `Id` int(10) unsigned NOT NULL,
  `Relay_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
  `Relay_log_pos` bigint(20) unsigned NOT NULL,
  `Master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
  `Master_log_pos` bigint(20) unsigned NOT NULL,
  `Checkpoint_relay_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
  `Checkpoint_relay_log_pos` bigint(20) unsigned NOT NULL,
  `Checkpoint_master_log_name` text CHARACTER SET utf8 COLLATE utf8_bin NOT NULL,
  `Checkpoint_master_log_pos` bigint(20) unsigned NOT NULL,
  `Checkpoint_seqno` int(10) unsigned NOT NULL,
  `Checkpoint_group_size` int(10) unsigned NOT NULL,
  `Checkpoint_group_bitmap` blob NOT NULL,
  PRIMARY KEY (`Id`)
) ENGINE=InnoDB DEFAULT CHARSET=utf8 STATS_PERSISTENT=0 COMMENT='Worker Information';
/*!40101 SET character_set_client = @saved_cs_client */;

--
-- Dumping data for table `slave_worker_info`
--

LOCK TABLES `slave_worker_info` WRITE;
/*!40000 ALTER TABLE `slave_worker_info` DISABLE KEYS */;
/*!40000 ALTER TABLE `slave_worker_info` ENABLE KEYS */;
UNLOCK TABLES;

I was able to fix this by deleting /var/lib/mysql/ibdata* files from the old container(5.5). I am copying content inside /var/lib/mysql directory of my old container(5.5) to the new container(5.6) /var/lib/mysql. It's working if i skip copying /var/lib/mysql/ibdata* file.

  +---------------------------+
  | Tables_in_mysql           |
  +---------------------------+
  | columns_priv              |
  | db                        |
  | event                     |
  | func                      |
  | general_log               |
  | help_category             |
  | help_keyword              |
  | help_relation             |
  | help_topic                |
- | host                      |
+ | innodb_index_stats        |
+ | innodb_table_stats        |
  | ndb_binlog_index          |
  | plugin                    |
  | proc                      |
  | procs_priv                |
  | proxies_priv              |
  | servers                   |
+ | slave_master_info         |
+ | slave_relay_log_info      |
+ | slave_worker_info         |
  | slow_log                  |
  | tables_priv               |
  | time_zone                 |
  | time_zone_leap_second     |
  | time_zone_name            |
  | time_zone_transition      |
  | time_zone_transition_type |
  | user                      |
  +---------------------------+

Found that these are tables are added/removed in mysql-5.6. Copying/Using old ibdata files leads to inconsistency with innodb tables and ibdata files. Though the .frm,.idb files are present, because of older ibdata its failing.

As mentioned in this link, tried to delete that file and mysql_upgrade finished successfully.

The ibdata* data files created by mysql_install_db are corrupt and must be trashed before starting mysqld !

Tags:

Docker

Mysql

Innodb

Mysqlupgrade

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