We're in the middle of P2V'ing most of the network, so the current backup method is likely the worst - the backup agent is still installed on the guest OSs, and the backup device is dutifully pulling them onto tape, one file at a time.
I suspect there's a clever way to script (PowerShell?) a suspend on the VMs, then backup of the .vhd files, and unsuspend the VMs. This seems like it would provide big speed benefits, while losing file-level restore (might be best for things like DCs and app servers).
What methods/policies have you hammered out?
Answer
Regular file-level backup of only data should still be used - regardless of if the machine is virtual or not. Backing up the disk file however is a great aid in increasing recovery speed for disasters if the entire guest fails.
There are several approaches to backing up the guests with scripting. You could shut it down, copy the vhd and start it again. A clean system backup. But what you probably want though is creating a snapshot. There's also a mount tool to get to the shadow copies programatically so you could actually move them off the volume as well. There's some debate on how stable the VSS-based snapshot system really is and people have lost data. It's a bit (ok, much more) involved than the approach used by Vmware as far as I can tell and is a bit more annoying to deal with.
I think there's a service pack or patch to the Windows Server 2008 Backup tool that makes it capable of backing up the guests transparently by the way?
Also see Microsofts planning for Backup with Hyper-V.
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