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Shrinking Ibdata1 file and using Multiple Table spaces

The ibdata1 file usually grows up to a very large size. The bad new is that the  ibdata1 file can´t actually be shrunk unless you delete all databases, remove the files and reload a dump.

But you can configure MySQL so that each table, including its indexes, is stored as a separate file. In that way ibdata1 will not grow as large.
It was a while ago I did this. However, to setup your server to use separate files for each table you need to change my.cnf in order to enable this:

In this regard I found the following excerpt from the Mysql documents very enlightening:

"You can store each InnoDB table and its indexes in its own file. This feature is called “multiple tablespaces” because in effect each table has its own tablespace.
Using multiple tablespaces can be beneficial to users who want to move specific tables to separate physical disks or who wish to restore backups of single tables quickly without interrupting the use of other InnoDB tables.

To enable multiple tablespaces, start the server with the --innodb_file_per_table option. For example, add a line to the [mysqld] section of my.cnf:
With multiple tablespaces enabled, InnoDB stores each newly created table into its own tbl_name.ibd file in the database directory where the table belongs. This is similar to what the MyISAM storage engine does, but MyISAM divides the table into a tbl_name.MYD data file and an tbl_name.MYI index file. For InnoDB, the data and the indexes are stored together in the .ibd file. The tbl_name.frm file is still created as usual.

You cannot freely move .ibd files between database directories as you can with MyISAM table files. This is because the table definition that is stored in the InnoDB shared tablespace includes the database name, and because InnoDB must preserve the consistency of transaction IDs and log sequence numbers.
If you remove the innodb_file_per_table line from my.cnf and restart the server, InnoDB creates tables inside the shared tablespace files again.

The --innodb_file_per_table option affects only table creation, not access to existing tables. If you start the server with this option, new tables are created using .ibd files, but you can still access tables that exist in the shared tablespace. If you start the server without this option, new tables are created in the shared tablespace, but you can still access any tables that were created using multiple tablespaces.
InnoDB always needs the shared tablespace because it puts its internal data dictionary and undo logs there. The .ibd files are not sufficient for InnoDB to operate.
To move an .ibd file and the associated table from one database to another, use a RENAME TABLE statement:
RENAME TABLE db1.tbl_name TO db2.tbl_name;
If you have a “clean” backup of an .ibd file, you can restore it to the MySQL installation from which it originated as follows:
  1. Issue this ALTER TABLE statement to delete the current .ibd file:
  2. Copy the backup .ibd file to the proper database directory.
  3. Issue this ALTER TABLE statement to tell InnoDB to use the new .ibd file for the table:
In this context, a “clean.ibd file backup is one for which the following requirements are satisfied:
  • There are no uncommitted modifications by transactions in the .ibd file.
  • There are no unmerged insert buffer entries in the .ibd file.
  • Purge has removed all delete-marked index records from the .ibd file.
  • mysqld has flushed all modified pages of the .ibd file from the buffer pool to the file.
You can make a clean backup .ibd file using the following method:
  1. Stop all activity from the mysqld server and commit all transactions.
  2. Wait until SHOW ENGINE INNODB STATUS shows that there are no active transactions in the database, and the main thread status of InnoDB is Waiting for server activity. Then you can make a copy of the .ibd file.
Another method for making a clean copy of an .ibd file is to use the commercial InnoDB Hot Backup tool:
  1. Use InnoDB Hot Backup to back up the InnoDB installation.
  2. Start a second mysqld server on the backup and let it clean up the .ibd files in the backup.

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