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From the Linux side, have you thought about using ACLs in addition to the basic file & directory ownership & permissions? So if you have 20 directories, a user doesn't need to be 20 different groups - with ACLs he needs to be in only one group, and that group can have an ACL entry in each of the 20 directories. Other users that require the same level of access can be put in the same group.
It's still going to need a bit of planning and forethought, but will likely be more manageable than what you describe above.
I must also caution that although I have used this approach when working with lots of users needing access to areas of directory trees on local storage, I haven't used it on EFS and/or NFSv4. So I can't guarantee there's not some technical constraint that will prevent this approach from working (though if that happens it would be interesting to know why it doesn't).
Thanks, that would be ideal but unfortunately EFS doesnt support ACL.
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I am not so sure how to to do this. I mean in the very end, with AP, i will also have to define users and groups right? but doesn't that mean that i will fall back to the old problem of maximum 16 groups per user? Would be Ideal if that could be managed with IAM policies. so that linux users can have access r/w/x to specific folders. any idea?