Because the MySQL server as distributed by MySQL includes a built-in copy of InnoDB, if you are using the dynamic InnoDB Plugin and have INSTALLed it into the MySQL server, you must always start the server with the option ignore_builtin_innodb, either in the option file or on the mysqld command line. Also, remember that the startup option skip_grant_tables prevents MySQL from loading any plugins. Neither of these options is needed when using a specialized version of MySQL that you build from source.

By default, the InnoDB Plugin does not create tables in a format that is incompatible with the built-in InnoDB in MySQL. Tables in the new format may be compressed, and they may store portions of long columns off-page, outside the B-tree nodes. You may wish to enable the creation of tables in the new format, using one of these techniques:

You may also want to enable the new InnoDB strict mode, which guards SQL or certain operational errors that otherwise generate warnings and possible unintended consequences of ignored or incorrect SQL commands or parameters. As described in Section 8.5, “InnoDB Strict Mode”, the GLOBAL parameter innodb_strict_mode can be set ON or OFF in the same way as the parameters just mentioned. You can also use the command SET SESSION innodb_strict_mode=mode (where mode is ON or OFF) to enable or disable InnoDB strict mode on a per-session basis.

Take care when using new InnoDB configuration parameters or values that apply only when using the InnoDB Plugin. When the MySQL server encounters an unknown option, it fails to start and returns an error: unknown variable. This happens, for example, if you include the new parameter innodb_file_format when you start the MySQL server with the built-in InnoDB rather than the plugin. This can cause a problem if you accidentally use the built-in InnoDB after a system crash, because InnoDB crash recovery runs before MySQL checks the startup parameters. See Section 11.4, “Possible Problems” why this can be a problem. One safeguard is to specify the prefix loose_ before the names of new options, so that if they are not recognized on startup, the server gives a warning instead of a fatal error.