Can you use Samba as primary domain controller with Active Directory?

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You are right -- Samba can't fully replace Microsoft's Active Directory. However, you can use Samba as a Primary Domain Controller (PDC)at each site. If you only have one domain at each of your sites, I would think you could leave that infrastructure in place and then authenticate against your AD servers. However, I am not sure in what capacity (just authentication, or roaming profiles etc.) you are using AD... but there may be a place for Microsoft AD and Samba in your setup.