Howto: Clean a mysql InnoDB storage engine?

Question

Is it possible to clean a mysql innodb storage engine so it is not storing data from deleted tables?

Or do I have to rebuild a fresh database every time?

Answer 1

The InnoDB engine does not store deleted data. As you insert and delete rows, unused space is left allocated within the InnoDB storage files. Over time, the overall space will not decrease, but over time the 'deleted and freed' space will be automatically reused by the DB server.

You can further tune and manage the space used by the engine through an manual re-org of the tables. To do this, dump the data in the affected tables using mysqldump, drop the tables, restart the mysql service, and then recreate the tables from the dump files.

Answer 2

You can use OPTIMIZE TABLE query periodically to optimize your storage and speed up SELECT queries a little. Link to MySQL Manual: http://dev.mysql.com/doc/refman/5.1/en/optimize-table.html

Answer 3

There is a more complete answer with regard to InnoDB

Keep in mind the busiest file in the InnoDB infrastructure

/var/lib/mysql/ibdata1

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

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.

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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