run as root? newb question

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New to linux and was wondering what is the best
practice for choosing a user and group for running
applications? Is running an app as root the normal
thing to do? Is running apps as root a bad thing? Huge
security risk? Sorry for the stupid question but have
seen different docs saying what to run a directory as.
The RH docs say if you want to run directory on
default ports run as root. Thats what I plan to do.

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