How to Recover an Orphaned .ibd File with MySQL 5.6

This post comes from Michael Rikmas at the MySQL Performance Blog.

A few years ago Yves Trudeau and Aleksandr Kuzminsky wrote posts about different ways for recovering orphaned .ibd files:

• Connecting orphaned .ibd files
• A recovery trivia or how to recover from a lost ibdata1 file

Today I want to show you how to do that in an easier and quicker way. In my example I’ll restore a “payment.ibd” file (payment table) from Sakila DB on a server with MySQL 5.5 (but with help from MySQL 5.6 and sandbox).

In my case the OS is CentOS. So I needed to:

• install mysqlsandbox(check instructions there)
• download latest Percona Server 5.6:

wget http://www.percona.com/redir/downloads/Percona-Server-5.6/LATEST/release-5.6.14-62.0/483/binary/linux/i686/Percona-Server-5.6.14-rel62.0-483.Linux.i686.tar.gz

Create sandbox:

make_sandbox Percona-Server-5.6.14-rel62.0-483.Linux.i686.tar.gz

Test it:

mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "select @@version\G"
*************************** 1. row ***************************
@@version: 5.6.14-rel62.0

It works!

Check datadir and if the innodb_file_per_table option enabled (this is requirement):

mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "show variables like 'datadir'"
+---------------+---------------------------------------+
| Variable_name | Value                                 |
+---------------+---------------------------------------+
| datadir       | /home/mixa/sandboxes/msb_5_6_14/data/ |
+---------------+---------------------------------------+

mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "show variables like '%per_table'"
+-----------------------+-------+
| Variable_name         | Value |
+-----------------------+-------+
| innodb_file_per_table | ON    |
+-----------------------+-------+

If it’s not enabled then you’ll need to enable it

mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "SET GLOBAL innodb_file_per_table=1"

Create empty payment table on 5.6 sandbox

mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 test < payment_table.sql

Payment_table.sql – is file with “SHOW CREATE TABLE” statement for payment table. The table structure should be the same.

cat payment_table.sql
CREATE TABLE `payment` (
  `payment_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
  `customer_id` smallint(5) unsigned NOT NULL,
  `staff_id` tinyint(3) unsigned NOT NULL,
  `rental_id` int(11) DEFAULT NULL,
  `amount` decimal(5,2) NOT NULL,
  `payment_date` datetime NOT NULL,
  `last_update` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
  PRIMARY KEY (`payment_id`),
  KEY `idx_fk_staff_id` (`staff_id`),
  KEY `idx_fk_customer_id` (`customer_id`),
  KEY `fk_payment_rental` (`rental_id`)
) ENGINE=InnoDB

Stop sandbox

./sandboxes/msb_5_6_14/stop

Replace .ibd file (in my case the correct copy of it is located in my homedir)

cp ~/payment.ibd ~/sandboxes/msb_5_6_14/data/test/ -f

Make sure permissions are ok for .ibd file

sudo chmod 660 ~/sandboxes/msb_5_6_14/data/test/payment.ibd
sudo chown : ~/sandboxes/msb_5_6_14/data/test/payment.ibd

Start sandbox

./sandboxes/msb_5_6_14/start

Currently if you’ll try to select something from the table you’ll get an error:

Select from table

mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "select count(*) from test.payment"
ERROR 2013 (HY000) at line 1: Lost connection to MySQL server during query
mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "select count(*) from test.payment"
ERROR 1146 (42S02) at line 1: Table 'test.payment' doesn't exist

Error log

2013-11-02 14:36:34 b7eff990  InnoDB: Error: table 'test/payment'
InnoDB: in InnoDB data dictionary has tablespace id 7,
InnoDB: but a tablespace with that id does not exist. There is
InnoDB: a tablespace of name test/payment and id 10, though. Have
InnoDB: you deleted or moved .ibd files?
...  ...
2013-11-02 14:36:36 11640 [ERROR] InnoDB: Failed to find tablespace for table '"test"."payment"' in the cache. Attempting to load the tablespace with space id 7.
2013-11-02 14:36:36 11640 [ERROR] InnoDB: In file './test/payment.ibd', tablespace id and flags are 10 and 0, but in the InnoDB data dictionary they are 7 and 0. Have you moved InnoDB .ibd files around without using the commands DISCARD TABLESPACE and IMPORT TABLESPACE? Please refer to http://dev.mysql.com/doc/refman/5.6/en/innodb-troubleshooting-datadict.html for how to resolve the issue.
2013-11-02 14:36:36 a31a2b90  InnoDB: Operating system error number 2 in a file operation.
InnoDB: The error means the system cannot find the path specified.
2013-11-02 14:36:36 11640 [ERROR] InnoDB: Could not find a valid tablespace file for 'test/payment'. See http://dev.mysql.com/doc/refman/5.6/en/innodb-troubleshooting-datadict.html for how to resolve the issue.
2013-11-02 14:36:36 a31a2b90 InnoDB: cannot calculate statistics for table "test"."payment" because the .ibd file is missing. For help, please refer to http://dev.mysql.com/doc/refman/5.6/en/innodb-troubleshooting.html

How to Fix it? In 5.6 tablespacemanagement is very improved so the only thing needed is “ALTER TABLE .. DISCARD TABLESPACE” and “ALTER TABLE .. IMPORT TABLESPACE”.

Please check also limitations: Tablespace Copying Limitations

Look at example:

Discard tablespace

mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "alter table test.payment discard tablespace; show warnings;"
+---------+------+--------------------------------------------------------+
| Level   | Code | Message                                                |
+---------+------+--------------------------------------------------------+
| Warning | 1812 | InnoDB: Tablespace is missing for table 'test/payment' |
| Warning | 1812 | InnoDB: Tablespace is missing for table 'payment'      |
+---------+------+--------------------------------------------------------+

Import tablespace

mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "alter table test.payment import tablespace; show warnings"
+---------+------+----------------------------------------------------------------------------------------------------------------------------------------------+
| Level   | Code | Message                                                                                                                                      |
+---------+------+----------------------------------------------------------------------------------------------------------------------------------------------+
| Warning | 1810 | InnoDB: IO Read error: (2, No such file or directory) Error opening './test/payment.cfg', will attempt to import without schema verification |
+---------+------+----------------------------------------------------------------------------------------------------------------------------------------------+

That’s it, data recovered, payment table accessible on 5.6 sandbox.

Now check if data exists in payment table on sandbox:

mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "select count(*) from test.payment"
+----------+
| count(*) |
+----------+
|    16049 |
+----------+
mysql -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 -e "select * from test.payment limit 1\G"
*************************** 1. row ***************************
  payment_id: 1
 customer_id: 1
    staff_id: 1
   rental_id: 76
      amount: 2.99
payment_date: 0000-00-09 03:49:32
 last_update: 2028-02-08 12:32:35

Exists.

So dump it from sandbox and restore on 5.5:

Dump from 5.6

mysqldump -umsandbox -pmsandbox --host=127.0.0.1 --port=5614 --add-drop-table test payment > ~/payment_dump.sql

Restore to 5.5

mysql -u user -p  < ~/payment_dump.sql

Check if data exists on 5.5

mysql -u root -e "select * from test.payment limit 3;"
+------------+-------------+----------+-----------+--------+---------------------+---------------------+
| payment_id | customer_id | staff_id | rental_id | amount | payment_date        | last_update         |
+------------+-------------+----------+-----------+--------+---------------------+---------------------+
|          1 |           1 |        1 |        76 |   2.99 | 0000-00-09 03:49:32 | 2028-02-08 12:32:35 |
|          2 |           1 |        1 |       573 |   0.99 | 0000-00-09 03:49:32 | 0000-00-00 00:00:00 |
|          3 |           1 |        1 |      1185 |   5.99 | 0000-00-09 03:49:37 | 0000-00-00 00:00:00 |
+------------+-------------+----------+-----------+--------+---------------------+---------------------+

During my work with this case I got into a situation in which the drop table payment on 5.5 wasn’t possible because payment.idb there wasn’t correct – so the server crashed each time I tried to access to this table. The workaround is:
- stop server
- rm .ibd file
- start server
- drop table as usually by DROP TABLE command