Public bug reported:

Opening this report for Xenial and later as this problem does surface
again due to moving to systemd.

Background:

mdadm is used to create md raid volumes based on Intel Matrix Storage
Manager fakeraid metadata. The setup usually consists of a container set
that contains one or more raid volumes. Which is the reason that those
fakeraid volume are more affected by timing issues on shutdown/reboot.

In my specific setup I am using one of the IMSM raid volumes as a LVM PV
and one LV of that is mounted as /home. The problem is that unmounting
/home on shutdown/reboot will update the filesystem superblock which
causes the raid state to become dirty for a small period of time. For
that reason with sysvinit scripts there is a mdadm-waitidle script which
*must* be run after the umountroot (or for /home at least after
umountfs) script has run.

With Xenial both umountroot and umountfs are softlinks to /dev/null in 
/lib/systemd/system, so I am not sure they are good to cause the mdadm-waitidle 
to be delayed *after* all filesystems are unmounted.
Practically I see that if /home is mounted on shutdown/reboot, the raid set 
will go into a full resync the next time I boot (additional pain but different 
problem: the resync appears to be much more aggressive than in the past, 
delaying boot a lot and rendering the system barely usable until it finishes). 
If I manually unmount /home before the reboot, the raid set is good.

** Affects: mdadm (Ubuntu)
     Importance: Undecided
         Status: New

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https://bugs.launchpad.net/bugs/1608495

Title:
  IMSM fakeraid handled by mdadm: unclean mounted volumes on
  shutdown/reboot

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