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I've set up virtual users paired with a SQL-configured pam file on CentOS, but logging in with system users no longer work. How would I make it so system users can still login when configured with virtual users? Would this be in the pam file?

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You can configure PAM to accept either MySQL or passwd authentication, probably using the sufficient option like so:

auth    sufficient  pam_mysql.so
auth    sufficient  pam_unix.so use_first_pass

You probably need to configure the account type similarly.

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