Andreas got this answer first in terms of what to do. +1 for Andreas !!!
I would like clarify why that answer is the only way and how to do it.
By default ibdata1 normally houses four types of information
- Table Data
- Table Indexes
- MVCC (Multiversioning Concurrency Control) Data
- Table Metadata
Running OPTIMIZE TABLE against an InnoDB table stored ibdata1 will make things worse because here is what it does:
- Makes the table's data and indexes contiguous inside ibdata1
- It makes ibdata1 grow because the contiguous data is appended to ibdata1
You can segregate Table Data and Table Indexes from ibdata1 and manage them independently using innodb_file_per_table. That way, only MVCC and Table MetaData would reside in ibdata1.
If you already use it, then you must have a high-write environment that stores lots of MVCC to support transaction isolation. Once the transactions holding the MVCC is done, the space is simply abandoned for re-use.
To shrink ibdata1 once and for all you must do the following:
STEP 01) MySQLDump all databases into a SQL text file (call it SQLData.sql)
STEP 02) Drop all databases (except mysql schema)
service mysql stop
STEP 04) Add the following lines to /etc/my.cnf
Sidenote: Whatever your set for innodb_buffer_pool_size, make sure innodb_log_file_size is 25% of innodb_buffer_pool_size.
rm -f /var/lib/mysql/ibdata1 /var/lib/mysql/ib_logfile
At this point, there should only be the mysql schema in /var/lib/mysql
service mysql start
This will recreate ibdata1 at 10MB, ib_logfile0 and ib_logfile1 at 1G each
STEP 07) Reload SQLData.sql into mysql
ibdata1 will grow but only contain table metadata
Each InnoDB table will exist outside of ibdata1
Suppose you have an InnoDB table named mydb.mytable. If you go into /var/lib/mysql/mydb, you will see two files representing the table
- mytable.frm (Storage Engine Header)
- mytable.ibd (Home of Table Data and Table Indexes for mydb.mytable)
ibdata1 will never contain InnoDB data and Indexes anymore.
With the innodb_file_per_table option in /etc/my.cnf, you can run
OPTIMIZE TABLE mydb.mytable; and the file /var/lib/mysql/mydb/mytable.ibd will actually shrink.
I would like to suggest a formula for you to query on sizing your InnoDB Buffer Pool from my post on What are the main differences between InnoDB and MyISAM?