just subscribed for rsync-qa from bugzilla via rsync wrote:
Hard link handling seems to be broken when using "rsync -aH --compare-dest". I
found two possible scenarios:

1) rsync completes without error message and exit code 0, although some files
are missing from the backup
2) rsync blocks and must be interrupted/killed
....

Further information
===================

This problem exists at least for rsync versions 3.1.0, 3.1.1, and 3.1.2 for
different Linux varieties using various file systems:
https://lists.samba.org/archive/rsync/2015-April/030092.html
---

   I ran rsync 3.1.1 for over a year to help generate
snapshots.  I can't say if it copied all the files or not, as
it was backing up a large "/home" partition, BUT, it never hung.
It did take 45min to a few hours to do the compare, but it
was comparing a large amount of data (>750G) w/a snapshot
(another 750G) to dump diffs to a third, and my /home partion
has a *very* large number of hard links.

   So I know that hardlinks are handled 'fine' on comparing
'xfs' to 'xfs'.
Latest test on openSUSE 42.2 (x86_64) on ext4 + on nfs with
----
   Ah...  I'd suspect nfs...
Why are you using nfs? rsync was designed to compare
against local file systems.  You should try running rsync
directly from the nfs-host machine to the client and bypassing
NFS.  I.e. -- you need to bypass NFS, since local->local
with hardlinks works.

   Just checked my /home partition.
   find shows 9295431 names (of any type), but du shows
(using du --inodes) shows 4407458 inodes.  That means over
half of the filenames are hard linked.  While my home
partition takes up 60% more space now, even cutting
those counts in half would still a large number of
hard links -- and rsync didn't crash doing an
rsync of the partition to an empty one, but first comparing
to a previous snapshot (the empty partition ended up
with differences between the main partition & the snapshot.

   I'd remove NFS...




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