Windows Data Deduplication and Cluster Operating System Rolling Upgrades


Have you considered when Windows data deduplication and cluster operating system rolling upgrades from Windows Server 2012 R2 to Windows Server 2016 Clusters are discussed we often hear people talk about Hyper-V or Scale Out File Server clusters, sometimes SQL but not very often for a General-Purpose File Share server with continuous availability. Which is the kind I’ve done quite a number of actually.


Being active in an industry that produces and consumes file data in large quantities and sizes we have been early implementers of Windows cluster for General-Purpose File Shares with continuous availability. This provides us the benefits of SMB 3, ODX for both the clients and IT Operations for workloads that are not suited for Scale Out File Server deployments.

As such we have dealt with a number of Windows 2012 R2 GPFS with GA cluster that we wanted to move to Windows Serer 2016. Partially to keep the environment up to date and partially because we want to leverage the new Windows deduplication capabilities that this OS version offers. The SOFS and Hyper clusters that I upgraded didn’t have data deduplication enabled.

The process to perform this upgrade is straight forward and has been documented well by others as well as by me in regards to issues we saw in the field . We even dove behind the scenes a bit in Cluster Operating System Rolling Upgrade Leaves Traces. I have also presented on this topic in public at conferences around Europe (Ireland, Germany and Belgium) as part of our community contributions. No surprises there.

Test your assumptions

This is a scenario you can perform without any downtime for your clients when all things go well. And normally it should. I have upgraded a couple of Scale Out File Server (SOFS) and General-Purpose File Server (GPFS) cluster with Continuous availability now and those went very well. Just make sure your cluster is perfectly healthy at the start.

Naturally there are some check you need to make that are outside of Microsoft scope:

I’m pretty sure you have good backups for your file data and you should check this works with Windows Server 2016 and how it reacts during the upgrade while the server is in mixed mode. Perhaps you will or won’t be able to run backups or restore data. Check and know this.

Verify your storage solution supports and words with Windows Server 2016. It sounds obvious but I have seen people forget such details.

Another point of attention is any Anti-Virus you might have running on the file server cluster nodes. Verify that this is fully supported on Windows Server 2016. On top of that validate that the Anti-Virus still works well with ODX so you don’t run into surprises there. Don’t assume anything.

Check if the server and it components (HBA, NICs, BIOS, …) its firmware and drivers support Windows Server 2016. Sure, the rolling upgrade allows for some testing before committing but that doesn’t mean you should go ahead blindly into the unknown.

Make sure your nodes are fully patched before and after the upgrade of a cluster node.

As the file server cluster is already leveraging SMB 3 with continuous availability al the prerequisites to make that work are already take care of. If you are upgrading a File server cluster without continuous availability and are planning to start using this, that’s another matter and you’ll need to address any issues. You can do this before or after moving to Windows Server 2016. This means you’d move to a solution before you upgrade or after you have performed the upgrade to Windows Server 2016.

You can take a look at my blogs on this subject from the Windows 2012 R2 time frame such as More Tips On Dealing With Removing Short File Names When Migrating To a SMB3 Transparent Failover File Server Cluster, Migrate an old file server to a transparent failover file server with continuous availability and SMB 3, ODX, Windows Server 2012 R2 & Windows 8.1 perform magic in file sharing for both corporate & branch offices

Data deduplication takes some extra consideration

I have blogged before on how Windows Server 2016 Data Deduplication performs and scales better than it did it Windows Server 2012 R2. This also means that it works at least partially different than it did Windows Server 2012 R2. You can see this in some of the updates that came out in regards to a data corruption bug with data deduplication which only affected Windows Server 2016.


Given this difference, what would happen if you fail over a LUN with deduplication enable from Windows Server 2012 to Windows Server 2016 and vice versa? That’s the question I had to consider when combining Windows data deduplication and cluster operating system rolling upgrades for the first time.

Windows Server 2016 is backward compatible and will work just fine with a LUN that from and Windows Server 2012 Server that has Windows data deduplication enabled. The reverse is not the case. Windows Server 2012 R2 is not forward compatible. When dealing with data deduplication in an Operating System Rolling Upgrade scenario I’m extra careful as I cannot guarantee any LUN movement scenario will go well. With a standalone server

Once I have failed over a LUN to Windows Server 2016 node in a mixed cluster I avoid moving it back to a Windows Server 2012 R2 node in that cluster. I only move them between Windows Server 2016 nodes when needed.

I move through the rolling upgrade as fast as I can to minimize the time frame in which a LUN with data deduplication could end up moving from a Windows Server 2016 o a Windows Server 2012 cluster node.

Should I need to reverse the Operating System Rolling Upgrade to end up with a Windows Server 2012 R2 cluster again I’ll make absolutely sure I can restore the data from LUNs with data deduplication from backup and/or a snapshot from a SAN or such. You cannot guarantee that this will work out fine. So be prepared.

For “standard” non deduplicated NTFS LUNs you can fail back if needed. When data deduplication is enabled you should try to avoid that and be prepared to restore data if needed.

Final advise is always the same

Even when you have tested your upgrade scenario and made sure your assumptions are correct you must have a way out. And as always, “One is none, two is one”.

As always during such endeavors you need to make sure that you have a roll back scenario in things do not work out. You must also have a fail back plan for when things turn really bad. For most scenarios has the ability to return to the original situation built in. But things can go wrong badly and Murphy’s Law does apply. So also have the backups and restore verified just in case.

The last thing you need after a failed upgrade is telling your customer or employer “it almost worked” but unfortunately, they’ve lost that 200TB of continuous available data. Better next time doesn’t really cut it.

An error occurred connecting to the cluster

An error occurred connecting to the cluster

This morning I woke up to a bunch of failed backup notifications of our trusted Veeam Backup & Replication v9.5 update 2 solution. After 3:30 AM the backups of one particular cluster started failing.

I went to have a look but I could not connect to the 3 node cluster.


I logged on to the cluster nodes themselves and did a quick verification of network connectivity, DNS etc. That was all fine. WMI services were running on all nodes but on node 2 and 3 they were not functional.

Cleary we have a WMI issue. And sure enough, no Hyper-V manager available on those 2 nodes but we did have it on the one properly functioning node.

We tested some PowerShell WMI queries (get-wmiobject mscluster_resourcegroup -computer NodeToTest -namespace “ROOT\MSCluster“) to the cluster and this confirmed that WMI was toast on those two nodes.

Fixing the issue

The good news was that all the VMs were all up and running  – a few that had RHS.exe issues – but were still alive pure Hyper-V wise. That explains why they didn’t have any support calls come in. So if we can fix this without causing down time this would be great. To try this we decided to restart the WMI service.

On problematic node 2 this worked. It restarted depending services as well such as Hyper-V Virtual Machine Management, User Access Logging Service, IP Helper and the Veeam Installer Service and the Veeam Hyper-V Integration Service. We got connectivity back via Hyper-V manager but the Failover Cluster manager GUI remained an issue but now only complained about node 3.


We wanted to avoid rebooting node 3 to avoid downtime to the VMs. So what we did there is stop the depending services that we could stop. It was vmms.exe that was stuck in shutdown we just killed the process manually with stop-Process -name “vmms” -force
That allowed the WMI service to be restarted. We then started the depending services manually and we got back the connectivity to Hyper-V Manager on node 3.

The Failover Cluster manager GUI could also connect again to the cluster. We checked the cluster for other issues. When done and found OK we live migrated the VMs node per node and did a reboot of every node one by one. This to have cleanly started nodes and to see if any trouble some event were logged during the startup. Normal operations were resumed.

Do note that there is a blog on TechNet about a similar issue but with a different error message. That was caused by missing cluswmi.mof file due to an ill advised use of run mofcomp.exe *.mof. This was not the case here. A reboot of the misbehaving nodes would have done the trick as well (as blogged here Trouble Connecting to Cluster Nodes? Check WMI! ) but we avoided as much downtime as possible here by going the route we did.

Continuous available general purpose file shares & ReFSv3 provide high available backup targets


In our previous two blog posts on Veeam and SMB 3 we’ve seen how and when Veeam Backup & Replication can leverage SMB Multichannel and SMB Direct. See Veeam Backup & Replication leverages SMB Multichannel and Veeam Backup & Replication Preferred Subnet & SMB Multichannel.The benefits of this are more bandwidth, high availability, better throughput and with RDMA low latency and CPU offload. What’s not to like, right? In a world where the compute and networks need keeps rising due to the storage capabilities (flash storage) pushing the limits this is all very welcome.

We have also seen earlier that Veeam B & R 9.5 leverages ReFSv3 in Windows Server 2016. This provides clear and present benefits in regards to space efficiencies and speed with many backup file related operations. Read Veeam Leads the way by leveraging ReFSv3 capabilities

When it comes to ReFSv3 in Windows Server 2016 most of the focus has gone to solutions based around Storage Spaces Direct (S2D). That’s a great solution and it is the poster child use case of these technologies.

But what other options do you have out there to build efficient and effective high available backup targets creatively except for S2D? What if you would like to repurpose existing hardware to build those? Let’s take a look together at how continuous available general purpose file shares & ReFSv3v3 provide high available backup targets

CSV, S2D, ReFSv3 & Archival Data

In Windows Server 2016, traditional shared storage (iSCSI, FC, Shared SAS, Shared RAID) with CSV are not recommend to be used with ReFSv3. Why isn’t exactly clear. The biggest impact you’ll see is the performance difference when not writing to the owner node of the CSV in this use case. Even with a well configured RDMA network that difference is significant. But that doesn’t mean that the performance is bad. It’s just that many of the super-fast meta data operations are relatively and significantly slower when compared each other, not that any of these two are slow.


Microsoft does state that an S2D with ReFSv3 and SOFS shares can be used for archival data. Storage spaces and ReFSv3 also have the benefit of offering automatic repair of corrupt data from a redundant copy on the fly even when needed. So yes, the best know supported scenario is this one.

Continuous available general purpose file shares and ReFSv3 provide high available backup targets

But what if we need a high available backup target and would love to leverage ReFSv3 with Veeam Backup & Replication 9.5? Well, you can have 95% of your cookie and eat it to. All this without ignoring the cautions offered.

We could set up SOFS shares on a Windows Server 2016 Cluster with ReFSv3 with traditional shared storage. Some storage vendors do state this is supported actually.

That only means you don’t have the auto repair functionality ReFSv3 combined with storage spaces offers. But perhaps you want to avoid the risk of using ReFSv3 with CSV in a non S2D scenario all together. What you could do is forgo ReFSv3 and use NTFS. How well this will work for archival data or backup is something you’ll need to test and find out how well this holds up. There is not much info is out there, only other cautions and warnings that might keep you up at night.

There is another scenario however and that is using Windows Server 2016 failover clustering to set up continuously available general purpose file shares that leverage SMB3 transparent failover.

The good news is that general purpose file shares (no CSV) do work consistently with ReFSv3 because such a share/LUN is only exposed on one cluster node at the time, the owner. By having multiple shares and setting preferred owners we can load balance the workload across all cluster nodes.

Thank to continuous availability for general file shares and SMB 3 transparent failover we can still get a high available backup target this way. The failover is fast enough to make this happen and all we see with Veeam Backup & Replication is a short pause in throughput before it resumes after failover. To put the icing on the cake, you can leverage SMB multichannel SMB Direct for both backup and restores.

I would take a sizeable whitepaper to walk through the setup so instead I’ll show you a a quick video of a POC we did in the lab here


If you want to learn more come to the community & other conferences I’m speaking at and will be around for Ask The Experts time opportunities. I’ll be at the German Hyper-V community meet up, The Cloud & Datacenter Conference in Germany 2017, Dell EMC World 2017 and last but not least VeeamON 2017 (see  May 2017 will be a travelling month). 


What do you lose?

Potentially there is one big loss in regards to the capabilities of ReFSv3 with this solution when you are not using storage spaces. This is that you lose the capability to automatic repair of corrupt data. The ability of ReFSv3 to do so is tied into the redundant copies of Storage Spaces (parity/mirror).

What do you get?

That’s fine, the strength of this design is that you get the speed and space efficiencies of ReFSv3and high available backup targets in way more scenarios than “just” S2D. After all, not everyone is in a position to choose their storage fabric for backup targets green field or at will. But they might be able to leverage existing storage and opt to use SMB 3 for their data transport.

So even if you can’t have it all, you can still build very good solutions. It offers ReFSv3 benefits and high availability for your backup target via transparent failover with SMB transparent failover on continuous available general purpose file shares. This also only requires Windows Server 2016 Standard Edition, which is a cost saving. You get to leverage SMB Multichannel and SMB Direct. All this while not ignoring the cautions of using ReFSv3 in certain scenarios.

On top of that, if you use NTFS with this approach it will also work for Windows Server 2012 (R2) as the OS for the backup target cluster hosts.


I do not work for or at Microsoft, nor am I perfect or infallible just because I’m an MVP. You’ll have to do your own testing and validation. From our testing and without ReFSv3 bugs ruining the show, to me this is a very valid and cost effective approach.

Cluster Operating System Rolling Upgrade Leaves Traces


When you perform a cluster OS rolling upgrade of Windows Server 2012 R2 cluster to a Windows Server 2016 Cluster you’ll have two options.

1. You evict the nodes, one after the other, perform a clean OS install and join them to the existing cluster.

2. You do an in-place OS upgrade of the nodes (no need to evict the nodes, you can if you want to). I tested this and blogged about it in In Place upgrades of cluster nodes to Windows Server 2016  

Both of these give you the benefits that you can keep your workloads (Hyper-V, SOFS, SQL Server) running and you don’t have to create a new cluster to do so. The moment you have Windows Server 2016 Nodes added to an existing Windows Server 2012 R2 cluster you are running in Mixed mode. Until all your nodes have been upgraded to Windows Server 2016 will remain running in mixed mode.

Illustration showing the three stages of a cluster OS rolling upgrade: all nodes Windows Server 2012 R2, mixed-OS mode, and all nodes Windows Server 2016

When there are only Windows Server 2016 nodes you can decide to also upgrade the cluster functional level.  This enables all the new capabilities in Windows Server 2016 Failover Clustering and also means you cannot go back to a Windows 2012 R2 cluster anymore. So, only take this step after a final validation of all drivers and firmware to make sure you don’t need to go back and you’re ready to fully commit to a fully functional Windows Server 2016 Failover Cluster.

A cluster operating system rolling upgrade does leave some traces, but that’s OK. Let’s take a look. 

This is what a get-cluster against Windows Server 2016 that was upgraded from Windows Server 2012 R2 looks like.


As you can see the cluster functional level is 8 and not 9 yet. This means that we have not yet run the Update-ClusterFunctionalLevel command on this cluster yet. Which still allows us to roll back all the way to a cluster running only Windows 2012 R2 nodes. The ClusterUpgradeVersion has a value of 3.

We now execute the Update-ClusterFunctionalLevel command and take a look at Get-Cluster again.


As you can see we are now at cluster functional level 9 which enables all the capabilities offered by Windows Server 2016 Failover Clustering. The cluster Upgrade version is 8. That’s the previous cluster functional level we were at before we executed Update-ClusterFunctionalLevel.

Note that both properties ClusterFunctionalLevel and ClusterUpgradeVersion are only available with Windows Server 2016. You will not find it on a Windows Server 2012 R2 or lower cluster. If you run this command from Windows Server 2016 against a Windows Server 2012 R2 cluster both properties will be empty. If you run it on a Windows Server 2012 R2 host against Windows Server 2012 R2 or lower and even a Windows Server 2016 cluster these properties are not even there. The commandlet is older on those OS versions and didn’t know about these properties yet.

What about if you create a brand-new cluster, perhaps even on freshly installed windows Server 2016 Nodes? What does ClusterUpgradeVersion have as a value then? Well it’s also 8. In the end, there is no difference between an in-place upgrade Windows Server 2016 cluster and a cleanly created one. So where are those traces?

Cluster Operating System Rolling Upgrade Leaves Traces

What gives a rolling upgrade away is that in the registry, under the HKLM\Cluster the OS and OSVersion values are not updated (purple in the picture below). This is a benign artifact and I don’t know if this if on purpose or not.  I have changed them to Windows Server 2016 Datacenter as an experiment and I have not found any issues by doing so. Now, please don’t take this as recommendation to do so. The smartest and safest thing is to leave it alone. These are not used, so don’t worry about them.


But even if you would change those values a cluster resulting from of a cluster operating system rolling upgrade still has other ways of telling it was not born as a Window Server 2016 Cluster.

Under HKLM\Cluster (and Cluster.0) you’ll find the value CusterFunctionaLevel that does not exist on a cleanly installed Windows Server 2016 Cluster (green in the picture above). As you can see this is a Window Server 2016 cluster running at functional level 9.

There is even an extra key OperatingVersion under HKLM\Cluster that you will not find on a cleanly installed cluster either. It also has a Mixed Mode value under that key which indicates whether the cluster is still running in mixed mode or not.


Here is a screenshot of newly installed/created Windows Server 2016 cluster. No ClusterFunctionalLevel value, the OS and OSVersion Values are correct and there is no OperatingVersion key to be found.


What if you don’t like traces?

First of all, these traces are harmless. One thing you can do if you want to weed out all traces of a rolling upgrade (as far as the cluster is concerned) is to destroy the cluster and create one with the same CNO (and IP address if that was a fixed one). This might all be a bit more involved when it comes to CSV naming and other existing resources but then these remnants will be gone in a supported way. Now this does defeat one of the main purposes of this feature: no down time. The operating system itself might also contain traces if you did in-place OS upgrades but the cluster will not. Just adapting OS/OSVersion, ClusterFunctionalLevel and deleting the key OperatingVersion from HKLM\Cluster (and HKLM\Cluster.0) are not supported actions and messing around in the cluster registry keys can lead to problems, so don’t! The advice is to just leave it all alone. Microsoft developed cluster operating system rolling upgrade the way they did for a reason and by leaving things as Microsoft has set or left them will make sure you are always in a fully supported condition. So, use it if it fits the circumstances & you comply with all the prerequisites. Look at these traces a flag of honor, not a smudge on your shining armor. When I see these artifacts, I see people who have used this feature to their own benefits. Well done I say.

Learn more about the Cluster OS Rolling Upgrade process

Next to my blogs like First experiences with a rolling cluster upgrade of a lab Hyper-V Cluster (Technical Preview) and In Place upgrades of cluster nodes to Windows Server 2016 there are many resources out there by fellow blogger and Microsoft. A great video on the subject is Introducing Cluster OS Rolling Upgrades in Windows Server 2016 with Rob Hindman, who actually works on this feature and knows it inside out.

An important thing to keep in mind is that this can be automated using PowerShell or by leveraging SCVMM for orchestration for example. 3rd party tools could also support this and help you automate this process in order to scale it when needed.

Finally, the official documentation can be found here Cluster operating system rolling upgrade