Let me first emphasize following the guidance set forth in this article: http://technet.microsoft.com/en-us/library/dd363553.aspx which contains official recommendations when virtualizing domain controllers in Hyper-V. The big 3 “don’t dos” are: never user differencing disks, don’t clone the guest without SYSPREPing it first, and don’t copy a VHD of a previously installed DC as the base for a new one. Those are all pretty straight forward to keep you from having SID conflicts or USN rollback issues which will totally mess up your AD installation.
Now, the next big issue is Time Sync. Microsoft recommends disabling host to guest time synchronization so that all DCs will use the default Windows Time service hierarchy just like a physical server. That’s not so hard, right? Just go into Hyper-V and disable that feature from the Integration Services settings. Easy. Done.
But: what about DCs running virtualized on VMWare [for the sake of discussion, let’s assume the SVVP supported version]? What does VMWare recommend? According to their KB article http://kb.vmware.com/selfservice/viewContent.do?language=en_US&externalId=1318, they say to turn of Windows Time service and use their host-to-guess time sync, except for the PDC Emulator of course, but then they want you to leave that on with “NoSync” turned on.
So: what is one to do?
First, I’d suggest a compromise – one that may avoid some of the issues. Don’t virtualize all your DCs. In fact, this is outlined in the Microsoft article above. You should really keep at least one hardware-based copy of your domain, and it should be the PDC emulator of the root domain of the forest. Preferably, in multi-domain forests, you’d want to keep a physical server for the PDC emulator of each child domain as well. This doesn’t have to be a very large machine, unless you’re a very large organization.
Now, if you virtualize all other DCs on Hyper-V (which I’d recommend not just because it’s Microsoft’s solution and I’m an employee, but because I’ve used both and Hyper-V is SO much easier to manage and configure), then the answer is clear: for DCs, leave the Windows Time service running on the guest DCs, with the root PDC Emulator’s time service configured to point to a highly-accurate external clock and disable Time Synchronization in the Integration settings. The Hyper-V hosts should then be joined to the domain. This will keep all hosts and guests synched to the proper time.
For guest running on VMWare, this is a tough decision since there are competing recommendations. Anecdotally, I have heard of no particular issues with disabling time sync in the VMWare tools and leaving Windows Time to synch the DC time clocks, but I have heard of issues the other way around: letting VMWare tools manage the time sync. In my opinion, such a custom solution as VMWare recommends should only be used if you’ve experience problems with the regular way of doing things. That’s why it’s the default: it generally works well when left that way. You should also configure the hosts to retrieve their time from the physical PDC Emulator in the root domain.
So, in summary, use a physical DC for at least one of your DCs per domain, and when you have to use VMWare, I’d recommend disabling the time sync from host to guest on domain controllers, and setting the hosts to obtain their time information from the root PDC Emulator. All other guests can be configured to obtain time from the host. But, as always, carefully monitor all your event logs for your servers and make sure you don’t have any issues.