MySQL version 5.1 comes with an alternative, faster InnoDB implementation (called "InnoDB Plugin").

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Switching is easy:

• Stop your mysqld with sudo stop mysql
• Add the following lines to your /etc/mysql/my.cnf under the [mysqld] section
  ignore-builtin-innodb
  plugin-load=innodb=ha_innodb_plugin.so
• Start your mysqld with sudo start mysql

The file format has not changed, your tables should survive this.

Note: This is not necessary in MySQL 5.5, where the new implementation is the default.