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I am using CentOS 6.5 - users authenticate using winbind, all are domain users except for root.

/home is mapped to a cifs share on a windows server in /etc/fstab with this line: \\server\home$ /home cifs credentials=/root/samba.txt,_netdev 0 0

Under the home$ share there are folders corresponding to each username, that are their home directories in windows. Each user has full windows permissions to their individual folders.

However, when on the linux system, users only have read and execute access to /home/$username Chmodding and chowning does not throw any errors, but neither have any effect on the subdirectories, which are all owned by root.

Each user should ideally own, but at least have full access to read/write to their home directories, but they must not be able to read another users home dir.

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If you're mounting them with shared credentials, that's going to result in all users on the system seeing the same user owning the files (root by default). You probably want to work with cifs.upcall so that each individual user authenticates to the CIFS share using their kerberos credentials. Not where I can write a full answer but here is a reference. –  Joel Davis Mar 13 at 13:34
    
Also note, Samba 3 clients have issues with using Kerberos authentication with DFS in general. If you're using DFS, keep that in mind. –  Joel Davis Mar 13 at 13:35

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