MySQL 5.7 Reference Manual Including MySQL NDB Cluster 7.5 and NDB Cluster 7.6

14.22.3 Troubleshooting InnoDB Data Dictionary Operations

Information about table definitions is stored both in the .frm files, and in the InnoDB data dictionary. If you move .frm files around, or if the server crashes in the middle of a data dictionary operation, these sources of information can become inconsistent.

If a data dictionary corruption or consistency issue prevents you from starting InnoDB, see Section 14.22.2, “Forcing InnoDB Recovery” for information about manual recovery.

CREATE TABLE Failure Due to Orphan Table

A symptom of an out-of-sync data dictionary is that a CREATE TABLE statement fails. If this occurs, look in the server's error log. If the log says that the table already exists inside the InnoDB internal data dictionary, you have an orphan table inside the InnoDB tablespace files that has no corresponding .frm file. The error message looks like this: 

InnoDB: Error: table test/parent already exists in InnoDB internal
InnoDB: data dictionary. Have you deleted the .frm file
InnoDB: and not used DROP TABLE? Have you used DROP DATABASE
InnoDB: for InnoDB tables in MySQL version <= 3.23.43?
InnoDB: See the Restrictions section of the InnoDB manual.
InnoDB: You can drop the orphaned table inside InnoDB by
InnoDB: creating an InnoDB table with the same name in another
InnoDB: database and moving the .frm file to the current database.
InnoDB: Then MySQL thinks the table exists, and DROP TABLE will
InnoDB: succeed.

You can drop the orphan table by following the instructions given in the error message. If you are still unable to use DROP TABLE successfully, the problem may be due to name completion in the mysql client. To work around this problem, start the mysql client with the --skip-auto-rehash option and try DROP TABLE again. (With name completion on, mysql tries to construct a list of table names, which fails when a problem such as just described exists.)

Cannot Open Datafile

With innodb_file_per_table enabled (the default), the following messages may appear at startup if a file-per-table tablespace file (.ibd file) is missing: 

[ERROR] InnoDB: Operating system error number 2 in a file operation.
[ERROR] InnoDB: The error means the system cannot find the path specified.
[ERROR] InnoDB: Cannot open datafile for read-only: './test/t1.ibd' OS error: 71
[Warning] InnoDB: Ignoring tablespace `test/t1` because it could not be opened.

To address these messages, issue DROP TABLE statement to remove data about the missing table from the data dictionary.

Cannot Open File Error

Another symptom of an out-of-sync data dictionary is that MySQL prints an error that it cannot open an InnoDB file: 

ERROR 1016: Can't open file: 'child2.ibd'. (errno: 1)

In the error log you can find a message like this: 

InnoDB: Cannot find table test/child2 from the internal data dictionary
InnoDB: of InnoDB though the .frm file for the table exists. Maybe you
InnoDB: have deleted and recreated InnoDB data files but have forgotten
InnoDB: to delete the corresponding .frm files of InnoDB tables?

This means that there is an orphan .frm file without a corresponding table inside InnoDB. You can drop the orphan .frm file by deleting it manually.

Orphan Intermediate Tables

If MySQL exits in the middle of an in-place ALTER TABLE operation (ALGORITHM=INPLACE), you may be left with an orphan intermediate table that takes up space on your system. Also, an orphan intermediate table in an otherwise empty general tablespace prevents you from dropping the general tablespace. This section describes how to identify and remove orphan intermediate tables.

Intermediate table names begin with an #sql-ib prefix (e.g., #sql-ib87-856498050). The accompanying .frm file has an #sql-* prefix and is named differently (e.g., #sql-36ab_2.frm).

To identify orphan intermediate tables on your system, you can query the Information Schema INNODB_SYS_TABLES table. Look for table names that begin with #sql. If the original table resides in a file-per-table tablespace, the tablespace file (the #sql-*.ibd file) for the orphan intermediate table should be visible in the database directory. 

SELECT * FROM INFORMATION_SCHEMA.INNODB_SYS_TABLES WHERE NAME LIKE '%#sql%';

To remove an orphan intermediate table, perform the following steps:

  1. In the database directory, rename the #sql-*.frm file to match the base name of the orphan intermediate table: 

    $> mv #sql-36ab_2.frm #sql-ib87-856498050.frm
    Note

    If there is no .frm file, you can recreate it. The .frm file must have the same table schema as the orphan intermediate table (it must have the same columns and indexes) and must be placed in the database directory of the orphan intermediate table.

  2. Drop the orphan intermediate table by issuing a DROP TABLE statement, prefixing the name of the table with #mysql50# and enclosing the table name in backticks. For example: 

    mysql> DROP TABLE `#mysql50##sql-ib87-856498050`;

    The #mysql50# prefix tells MySQL to ignore file name safe encoding introduced in MySQL 5.1. Enclosing the table name in backticks is required to perform SQL statements on table names with special characters such as “#”.

Note

If an unexpected exit occurs during an in-place ALTER TABLE operation that was moving a table to a different tablespace, the recovery process restores the table to its original location but leaves an orphan intermediate table in the destination tablespace.

Note

If MySQL exits in the middle of an in-place ALTER TABLE operation on a partitioned table, you may be left with multiple orphan intermediate tables, one per partition. In this case, use the following procedure to remove the orphan intermediate tables:

  1. In a separate instance of the same MySQL version, create a non-partitioned table with the same schema name and columns as the partitioned table.

  2. Copy the .frm file of the non-partitioned table to the database directory with the orphan intermediate tables.

  3. Make a copy of the .frm file for each table, and rename the .frm files to match names of the orphan intermediate tables (as described above).

  4. Perform a DROP TABLE operation (as described above) for each table.

Orphan Temporary Tables

If MySQL exits in the middle of a table-copying ALTER TABLE operation (ALGORITHM=COPY), you may be left with an orphan temporary table that takes up space on your system. Also, an orphan temporary table in an otherwise empty general tablespace prevents you from dropping the general tablespace. This section describes how to identify and remove orphan temporary tables.

Orphan temporary table names begin with an #sql- prefix (e.g., #sql-540_3). The accompanying .frm file has the same base name as the orphan temporary table.

Note

If there is no .frm file, you can recreate it. The .frm file must have the same table schema as the orphan temporary table (it must have the same columns and indexes) and must be placed in the database directory of the orphan temporary table.

To identify orphan temporary tables on your system, you can query the Information Schema INNODB_SYS_TABLES table. Look for table names that begin with #sql. If the original table resides in a file-per-table tablespace, the tablespace file (the #sql-*.ibd file) for the orphan temporary table should be visible in the database directory. 

SELECT * FROM INFORMATION_SCHEMA.INNODB_SYS_TABLES WHERE NAME LIKE '%#sql%';

To remove an orphan temporary table, drop the table by issuing a DROP TABLE statement, prefixing the name of the table with #mysql50# and enclosing the table name in backticks. For example: 

mysql> DROP TABLE `#mysql50##sql-540_3`;

The #mysql50# prefix tells MySQL to ignore file name safe encoding introduced in MySQL 5.1. Enclosing the table name in backticks is required to perform SQL statements on table names with special characters such as “#”.

Note

If MySQL exits in the middle of an table-copying ALTER TABLE operation on a partitioned table, you may be left with multiple orphan temporary tables, one per partition. In this case, use the following procedure to remove the orphan temporary tables:

  1. In a separate instance of the same MySQL version, create a non-partitioned table with the same schema name and columns as the partitioned table.

  2. Copy the .frm file of the non-partitioned table to the database directory with the orphan temporary tables.

  3. Make a copy of the .frm file for each table, and rename the .frm files to match the names of the orphan temporary tables (as described above).

  4. Perform a DROP TABLE operation (as described above) for each table.

Tablespace Does Not Exist

With innodb_file_per_table enabled, the following message might occur if the .frm or .ibd files (or both) are missing: 

InnoDB: in InnoDB data dictionary has tablespace id N,
InnoDB: but tablespace with that id or name does not exist. Have
InnoDB: you deleted or moved .ibd files?
InnoDB: This may also be a table created with CREATE TEMPORARY TABLE
InnoDB: whose .ibd and .frm files MySQL automatically removed, but the
InnoDB: table still exists in the InnoDB internal data dictionary.

If this occurs, try the following procedure to resolve the problem:

  1. Create a matching .frm file in some other database directory and copy it to the database directory where the orphan table is located.

  2. Issue DROP TABLE for the original table. That should successfully drop the table and InnoDB should print a warning to the error log that the .ibd file was missing.

Restoring Orphan File-Per-Table ibd Files

This procedure describes how to restore orphan file-per-table .ibd files to another MySQL instance. You might use this procedure if the system tablespace is lost or unrecoverable and you want to restore .ibd file backups on a new MySQL instance.

The procedure is not supported for general tablespace .ibd files.

The procedure assumes that you only have .ibd file backups, you are recovering to the same version of MySQL that initially created the orphan .ibd files, and that .ibd file backups are clean. See Section 14.6.1.4, “Moving or Copying InnoDB Tables” for information about creating clean backups.

Table import limitations outlined in Section 14.6.1.3, “Importing InnoDB Tables” are applicable to this procedure.

  1. On the new MySQL instance, recreate the table in a database of the same name. 

    mysql> CREATE DATABASE sakila;

mysql> USE sakila;

mysql> CREATE TABLE actor (
         actor_id SMALLINT UNSIGNED NOT NULL AUTO_INCREMENT,
         first_name VARCHAR(45) NOT NULL,
         last_name VARCHAR(45) NOT NULL,
         last_update TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
         PRIMARY KEY  (actor_id),
         KEY idx_actor_last_name (last_name)
       )ENGINE=InnoDB DEFAULT CHARSET=utf8;

  2. Discard the tablespace of the newly created table. 

    mysql> ALTER TABLE sakila.actor DISCARD TABLESPACE;

  3. Copy the orphan .ibd file from your backup directory to the new database directory. 

    $> cp /backup_directory/actor.ibd path/to/mysql-5.7/data/sakila/

  4. Ensure that the .ibd file has the necessary file permissions.

  5. Import the orphan .ibd file. A warning is issued indicating that InnoDB tries to import the file without schema verification. 

    mysql> ALTER TABLE sakila.actor IMPORT TABLESPACE; SHOW WARNINGS;
Query OK, 0 rows affected, 1 warning (0.15 sec)

Warning | 1810 | InnoDB: IO Read error: (2, No such file or directory)
Error opening './sakila/actor.cfg', will attempt to import
without schema verification

  6. Query the table to verify that the .ibd file was successfully restored. 

    mysql> SELECT COUNT(*) FROM sakila.actor;
+----------+
| count(*) |
+----------+
|      200 |
+----------+
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