What is the best way to reduce the size of ibdata in mysql?
Keep in mind the busiest file in the InnoDB infrastructure is /var/lib/mysql/ibdata1

This file normally houses many classes of information (when innodb_file_per_table is 0)


Table Data
Table Indexes
MVCC (Multiversioning Concurrency Control) Data


Rollbacks Segments
Undo Tablespace

Table Metadata
See Pictorial Representation


Many people create multiple ibdata files hoping for better diskspace management and performance. It does not help.

Unfortunately, OPTIMIZE TABLE against an InnoDB table stored in ibdata1 does two things: 


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.
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) (More details here)

Step 02) Drop all databases (except mysql, performance_schema, and information_schema)

Step 03) Shutdown mysql

Step 04) Add the following lines to /etc/my.cnf

[mysqld]
innodb_file_per_table
innodb_flush_method=O_DIRECT
innodb_log_file_size=1G
innodb_buffer_pool_size=4G


Sidenote: Whatever your set for innodb_buffer_pool_size, make sure innodb_log_file_size is 25% of innodb_buffer_pool_size.

Step 05) Delete ibdata1, ib_logfile0 and ib_logfile1

At this point, there should only be the mysql schema in /var/lib/mysql

Step 06) Restart mysql

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 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. !!!

If you would like to see how much actual data is stored in MyISAM and InnoDB, please run this query:

SELECT IFNULL(B.engine,'Total') "Storage Engine",
CONCAT(LPAD(REPLACE(FORMAT(B.DSize/POWER(1024,pw),3),',',''),17,' '),' ',
SUBSTR(' KMGTP',pw+1,1),'B') "Data Size", CONCAT(LPAD(REPLACE(
FORMAT(B.ISize/POWER(1024,pw),3),',',''),17,' '),' ',
SUBSTR(' KMGTP',pw+1,1),'B') "Index Size", CONCAT(LPAD(REPLACE(
FORMAT(B.TSize/POWER(1024,pw),3),',',''),17,' '),' ',
SUBSTR(' KMGTP',pw+1,1),'B') "Table Size"
FROM (SELECT engine,SUM(data_length) DSize,SUM(index_length) ISize,
SUM(data_length+index_length) TSize FROM information_schema.tables
WHERE table_schema NOT IN ('mysql','information_schema','performance_schema')
AND engine IS NOT NULL GROUP BY engine WITH ROLLUP) B,
(SELECT 3 pw) A ORDER BY TSize;