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I have a network of linux clients and servers that are used for numerical computations; and I'm using NIS for user authentication. After a successful login, every user lands in her / his home directory (via NFS automount).

I have now a second set of linux clients that are not part of the compute machines above. I was thinking of setting up NIS for user authentication, ideally reusing the same usernames / passwords. However, since these are 'personal' desktop machines, it would make sense to have /home/username point to a local drive, instead of the NFS mounted /home from above.

One of the reason for having two different home directories is that I have quotas enabled for NFS homes. On a users 'personal' desktop however, the user should be allowed to store as much data in her / his home directory as (s)he needs.

So if there are no conceptual draw backs with this approach (please point them out to me if there are!), is there a way to automatically create the home directory on the desktop machines, once the first NIS login has been successfully?

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Yes - you can use the pam_mkhomedir module. A man page is available at http://linux.die.net/man/8/pam_mkhomedir, though I've never used this module before.

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