As you may have noticed in your MySQL’s data directory (in Debian/Ubuntu – /var/lib/mysql) lies a file called ‘ibdata1′. It holds almost all the InnoDB data (it’s not a transaction log) of the MySQL instance and could get quite big. By default this file has a initial size of 10Mb and it automatically extends. Unfortunately, by design InnoDB data files cannot be shrinked. That’s why DELETEs, TRUNCATEs, DROPs, etc. can’t will not reclaim the space used by the file. Instead any freed regions are marked as unused and can be used later. Theoretically speaking the file could reach the maximum size allowed by the filesystem if no limit is set in the my.cnf file (in Debian/Ubuntu it’s located in /etc/mysql/my.cnf). Guess what ? It’s not set by default.
