How to run Rsync with preserving Ownership, Permission, Group?
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Just run a chmod on /home2/user1.backup, you should only have to do it once.
What's happening is your source has a trailing slash, that means it doesn't copy /home2/user1, it copies everything inside of /home2/user1. And with rsync -r when the destination is an existing directory, it copies into the destination directory, without touching the directory itself at all.
All of this means that the way you're running the command, rsync is completely ignoring the permissions on both /home/user1 and /home2/user1.backup themselves, and only maintaining the permissions on the contents of these two directories.
I have more than 100 VIP's mailbox that required to be backup every night to a folder in the same machine, source Maildir is under /Home2/Users/* and the target is under /Home3/Users/*.
How to backup their mailbox with their original ownership, permission, group?
rsync -vaxAX /Home2/Users /Home3/
This will recursively replicate Users from /Home2/Users to /Home3/Users, preserving original ownership, permission, group, etc. In particular, it will replicate the original ownership/permission/group of the "Users" folder itself also.