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I have around a 40+ user network running Ubuntu 12.04 Desktop and Ubuntu Server. What is the best tool to use to run authentication on users? Webmin? Similar to what AD does for Windows.

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You will probably want to create an OpenLDAP server for clients to authenticate against. Webmin is just a frontend (or rather, it has a plugin that is a frontend) to LDAP. I didn't really find a good GUI frontend for OpenLDAP (if that is what you are looking for).

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Active Directory is not just LDAP! –  Jorge Castro Jul 24 '12 at 1:07
    
Thank you. Was looking at that a while ago. But thought if there was a nice gui for the client to be able to use :( –  Tommy45 Jul 24 '12 at 2:16
    
@JorgeCastro That is true, but since he didn't mention he needed any support for Windows machines (and I don't know of anything else similar to Active Directory), I didn't think Samba4 was the right move. –  tgm4883 Jul 24 '12 at 12:26
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