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First, dont run the server as root. It should be run as the user that has ownership of the library files.
As for your extra CPU usage, normally, I'd be willing to help you track it down, but I am currently in the middle of rewriting the entire server, so the effort would be largely wasted as the new server has no code in common with the old one. So I suggest you just live with the high CPU usage for a few months until calibre 3.0 is released.
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