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Logging in to my Webmin control panel, I noticed that virtually all of my disk space is full. I searched for the ten largest files/ directories on my system and found that a file called ibdata1 is taking up around 94GB of space. It resides in my /var/lib/mysql directory.

What does ibdata1 do? Am I safe to remove it? My assumption is that it's a dump of some kind, but that's just a wild guess.

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3 Answers

The file ibdata1 is the system tablespace for the InnoDB infrastructure.

It contains several classes for information vital for InnoDB

  • Table Data Pages
  • Table Index Pages
  • Data Dictionary
  • MVCC Control Data
    • Undo Space
    • Rollback Segments
  • Double Write Buffer (Pages Written in the Background to avoid OS caching)
  • Insert Buffer (Changes to Secondary Indexes)
  • Click Here to see a Pictorial Representation

You can separate Data and Index Pages from ibdata1 by enabling innodb_file_per_table. This will cause any newly created InnoDB table to store data and index pages in an external .ibd file.

Example

  • datadir is /var/lib/mysql
  • CREATE TABLE mydb.mytable (...) ENGINE=InnoDB;, creates /var/lib/mysql/mydb/mytable.frm
    • innodb_file_per_table enabled, Data/Index Pages Stored in /var/lib/mysql/mydb/mytable.ibd
    • innodb_file_per_table disabled, Data/Index Pages Stored in ibdata1

No matter where the InnoDB table is stored, InnoDB's functionality requires looking for table metadata and storing and retrieving MVCC info to support ACID compliance and Transaction Isolation.

Here are my past articles on separating table data and indexes from ibdata1

WHAT TO DO NEXT

You can continue having ibdata1 stored everything, but that makes doing LVM snapshots real drudgery (my personal opinion).

You need to use My StackOverflow post and shrink that file permanently.

Please run this query:

SELECT 
    ((POWER(1024,3)*94 - InnoDBDiskDataAndIndexes))/POWER(1024,3) SpaceToReclaim
FROM
(SELECT SUM(data_length+index_length) InnoDBDiskDataAndIndexes
FROM information_schema.tables WHERE engine='InnoDB') A;

This will tell how much wasted space can be reclaimed after applying the InnoDB Cleanup.

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Thanks for your input. My disk quota has since filled completely - before I act on any of the advice in your posts, will I need free space? I note that your original post on SO mentions about doing an SQL dump, but this would presumably create a ~90GB file with nowhere to go. –  James Mar 13 '13 at 22:21
    
mysqldump will only the logical representation of the data pages, not the indexes. You will need another disk mount, perhaps a remote server, to dump the data. –  RolandoMySQLDBA Mar 14 '13 at 3:18
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That file is ibdata1, not ibdatal and it contains all of your InnoDB databases. If you delete it, you lose all your data.

For some ideas on how to deal with it, see How to shrink/purge ibdata1 file in MySQL.

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If you use innodb as MySQL engine by default will store all your databases into ibdata1. Also there are log files ib_logfile0 and ib_logfile1. Do not delete those files.

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