Before you shut down the InnoDB Plugin and start the basic built-in InnoDB in MySQL, review the configuration files. Changes to the startup options do not take effect until the server is restarted, or the InnoDB Plugin is uninstalled and reinstalled.
The InnoDB Plugin introduces several configuration parameters
that are not recognized by the built-in InnoDB in MySQL, including:
innodb_file_format, innodb_file_format_check, and
innodb_strict_mode. See
Section C.1, “New Parameters” for a complete list of
new configuration parameters in the InnoDB Plugin. You can
include these parameters in the configuration file, only if you
use the loose_ form of the parameter names,
so that the built-in InnoDB in MySQL can start.
If the InnoDB Plugin was installed as a dynamic plugin, the
startup option ignore_builtin_innodb or skip_innodb must
have been set to disable the built-in InnoDB in MySQL. These options must be
removed, so that the built-in InnoDB in MySQL is enabled the next time the
server is started.
If the InnoDB Plugin was loaded using plugin-load option.
This option has to be removed, too.
In MySQL, configuration options can be specified in the
mysqld command line or the option file
(my.cnf or my.ini). See
the MySQL manual on Using Option Files for more
information.

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