We're having the same problem --- the underlying bricks seem fine and the 
problem appears to be that ls is reporting the wrong thing rather than there 
are actually duplicate files.

We are using gluster 3.6.1-1 on machines running Scientific Linux 6.3 (we're 
use the glusterfs-epel packages). The underlying bricks are all ext3.

Different client machines report different duplicate files.  There doesn't seem 
to be pattern to why files duplicated -- some bricks seem to have more files 
that are listed as duplicates than others but no obvious pattern.

Some other oddities. We have a directory called dm512 that contains some 
duplicate files.

If I do  ls dm512, the duplicate files appear -- one of which is called 
restart.12

But if I say "ls restart.36", the file appears only once

But if I say "ls restart.36*", the file appears twice.  And using, find

find . -iname "restart.36" -exec echo "<{}>" \;

gives

<./restart.36>
<./restart.36>

We upgraded from 3.5 to 3.6 about two weeks ago and user only reported the 
problem about a week ago. I don't think this necessarily means the problem 
didn't occur before -- our gluster file system is a storage area for us for 
relatively infrequently but important large data sets. 

It's a bit unnerving for the user and causes some scripts to break, e.g., "for 
x in `ls dm512`; do"

Scott



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