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If I run quota I get:

Disk quotas for user XXXXXX (uid xxxx):
 Filesystem  blocks   quota   limit   grace   files   quota   limit   grace
   /dev/md2 1119132* 1048576 2097152    none       6       0       0
   /dev/md3 6816256       0 10485760            4529       0       0

The first is a temp directory and can be ignored. Home is on the second disk (md3). If I run du -sh inside my home directory I get:

3.3G    .
3.3G    total

I've run du without switches and the numbers all seem to coincide with what I should get (not listing for the sake of privacy).

So, why is quota showing ~6.8GB used while du is showing 3.3GB used? I am on a shared server and have a pretty small allowed storage space, of which about 33% seems to be missing!

I checked for "deleted" files that might be held open by a process:

lsof | grep "$USER" | grep deleted

Nothing. I ran a list of open files but nothing seemed out of the ordinary (though it might have been and I didn't realize it):

lsof | grep "$USER" > list.txt

I'm not sure of what else to try. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++

Without a solution this has become kind of moot as I got to a superuser and had them eliminate my quota and then reinstate it a day later. My quota now is showing LESS than du. So it might be worth investigating but I can live with the ability to use approx. 1 GB MORE space then my quota!

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    The quota is showing ~6 million blocks. How big are your blocks? If they are 512KB then this adds up.
    – Paul
    Sep 7, 2015 at 4:40
  • @Paul - My temp directory (on /dev/md2) shows a quota of 1 million blocks and a hard limit of 2 million blocks while the actual real-world limits are 1GB and 2GB. That corresponds to an effective "block" size for quota of 1024B or 1.0KB, which as I see it is the "modern" quota block size. When I write a single letter to a file then du reports the size as 4.0KB, which would be the hard-drive block size. Sep 8, 2015 at 5:47

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