According to http://dev.mysql.com/doc/refman/5.0/en/dynamic-system-variables.html there is a number of global system variables that can be changed at runtime, without taking the server down. However, the values are only valid until the server has been shut down, because they have not been stored in my.cnf. Using the Instance Manager, it is of course now possible to instruct it to add the variable to the instance's my.cnf file and store it. However, this is not very intuitive or comfortable as the same value has to be set twice, at different locations. As the server itself does not modify the my.cnf file, there currently is probably no way to implement this on the server level. However, it may be possible to modify the IM so it would be able to set these dynamic variables *and* save them to the my.cnf file with a single command.