Beginning with MySQL 5.1 as an additional plugin and included by default in MySQL 5.5 the InnoDB plugin includes many performance improvements. To leverage the support of new file formats however a very important setting is necessary.
#my.cnf [mysqld] innodb_file_per_table
The use of innodb_file_per_table with an existing system or during an upgrade to 5.1 or 5.5 requires a complete reload of your database to use effectively. In summary.
- Backup all InnoDB tables via mysqldump
- Drop InnoDB tables
- Verify InnoDB not used
- Stop MySQL …