There is a more complete answer with regard to InnoDB
Keep in mind the busiest file in the InnoDB infrastructure
This file normally houses four types of information
1) Table Data
2) Table Indexes
3) MVCC (Multiversioning Concurrency Control) Data
4) Table Metadata
Many people create multiple ibdata files hoping for better diskspace management and performance. SORRY, NOT HAPPENING !!!
Unfortunately, OPTIMIZE TABLE against an InnoDB table stored ibdata1 does two things: 1) Makes the table’s data and indexes contiguous inside ibdata1 2) It makes ibdata1 grow because the contiguous data is appended to ibdata1
You can segragate Table Data and Table Indexes from ibdata1 and manage them independently. 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 time in my career as a MYSQL DBA
In fact, the first time I did this, I collapsed a 50GB ibdata1 file into 50MB.
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. !!!
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