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This was a while ago now. We needed to use Ubuntu for a particular application which has now been ported to our default distro, CentOS. I did raise a ticket and there was nothing of any note in any of the logs. Nutanix support also spent quite a while looking into it. Problem has never occurred under CentOS even with the ideintical setup as with Ubuntu.
In my case it was Ubuntu and on one occasion Windows under KVM. VMs paused and the only evidence at all was in /var/log/libvirt/qemu which reportind disk IO errors which was why the VM had been paused. VMs restarted ok withouth corruption. Never seen this issue with CentOS and never with non-cloned drives. If removing the SSD tier stops it (not that I've tried) then I'm suspecting some sort of latency issue. I wonder if copy-on-write on a cloned disk causes the SSD cache layer to trip up briefly where running of spinny disk is slow enough for this not to happen. At that point it might be in the order of magnitude of kernel parameter tweaks which might explain why CentOS doesn't exhibit the same behaviour.
I've noticed similar issues. In our case we have template VMs which are left shut off and we clone off them as required for usable VMs. When running Ubuntu 12.04 LTS we started getting regular disk IO errors which resulted in the VM being paused and in bad cases the drive becoming read only as OP reported. We only needed Ubuntu for a single application which now runs on CentOS 6. We have not seen this issue with CentOS under identical circumstances.
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