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I am using superduper to mirror my server harddrive nightly. Should I be shutting down the mail services before I do this.

Or any other service?

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OS X server uses Postfix for mail. It's reasonably safe to back up a host while Postfix is running. After restoring the queue may be a little messed up. These queue problems can be repaired by running postsuper -s after restoring. In fact, postsuper -s is required after restoring even if you don't shut down Postfix. Postfix relies on certain files in its queue having a name that's the same as their inode number. Obviously, this can no longer be guaranteed after restoring from backup.

Regarding other services: Hard to say without knowing what other services you're running. Databases, for example, frequently require special care when backing up.

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