I wrote up a CleanUp procedure for InnoDB in StackOverflow
http://stackoverflow.com/a/4056261/491757 (Oct 29, 2010)
Here it is
To shrink ibdata1 once and for all you must do the following:
1) MySQLDump all databases into a SQL text file (call it SQLData.sql)
2) Drop all databases (except mysql schema)
3) Shutdown mysql
4) 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.
5) Delete ibdata1, ib_logfile0 and ib_logfile1
At this point, there should only be the mysql schema in /var/lib/mysql
6) Restart mysql
This will recreate ibdata1 at 10MB, ib_logfile0 and ib_logfile1 at 1G each
7) 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 have done this many times in my career as a MySQL DBA
In fact, the first time I did this, I collapsed a 50GB ibdata1 file into 500MB.
Give it a try. If you have further questions on this, email me. Trust me. This will work in the short term and over the long haul. !!!