As with a dynamically installed InnoDB storage engine, you must perform a “slow” shutdown of the MySQL server. If you have built MySQL from source code and replaced the built-in InnoDB in MySQL with the InnoDB storage engine in the source tree, you will have a special version of the mysqld executable that contains the InnoDB storage engine.

If you intend to upgrade to a dynamically linked InnoDB storage engine, you can follow the advice of Section 11.3.4, “Uninstalling a Statically Built InnoDB Storage Engine”.

If you intend to upgrade a statically built InnoDB storage engine to another statically built plugin, rebuild the mysqld executable, shut down the server, and replace the mysqld executable before starting the server.

Either way, please be sure to follow the instructions of Section 10.3, “Converting Compressed Tables Created Before Version 1.0.2” if any compressed tables were created.