I was just wondering, if MySQL is running when you shutdown does the OS shut it down cleanly or does it just kill the process?

I Installed via the .DMG image from the MySQL site. Also started it with the System Preferences panel option. In Fedora Linux you can switch to the terminal during shutdown and watch all the programs being shut down. Is there a way to do something similiar?

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That will depend on how it was installed, I guess. The default installation on OS X Server will of course shutdown cleanly, as will an installation that created valid launchd entries for MySQL (ie. with the official installers and/or MacPorts/Fink). If you rolled your own and just start it from some global init script or even manually it will likely just be killed.

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