I recently blogged about the new Base OS MP that was recently released: HERE
One of the things you will notice RIGHT off the bat… is that a huge percentage of your logical disks will go into a warning state, if you don't already have some sort of scheduled defragmentation set up. This will be true for virtual machines and physical machines…. anything over 10 percent file fragmentation (or the OS recommended setting) will get hit:

You will also get many warning alerts on this monitor…. the first time the condition is detected and the state changes for this monitor. This monitor checks status every Saturday, at 3:00AM by default, for all logical disks discovered.
If you don't care about this monitoring in SCOM – disable this monitor using overrides.
If you do care about seeing the state change – but don't want the alerts – turn the “Generates Alert” property to False, using overrides.
You can adjust the threshold from 10% to some other number…. but make sure you take note – this monitor will ignore the “File Percent Fragmentation” property by default, and always use the OS recommended setting. If you want to control this – you also need to set “Use OS Recommendation” to FALSE.
Here is an example of hard coding the frag percentage to 20% from the OS default:
“Use OS Recommendation” property description:
Lastly – one thing of interest…. If you want SCOM to “fix” the fragmentation issue…. it can. There is a recovery on this very monitor that can run a VBScript that will run a defrag job against your logical disks. It is disabled by default.
Keep in mind – if you turn on this defrag…. on your physical boxes – it wont be a big deal… it will simply fix the fragmentation issue. However – this will also run on ALL yours VM’s. If this was triggered all at the same time – Saturday at 3:00AM by default – this can kill the disk I/O on the disk subsystem hosting your VM/VHD files. Keep this in mind if you decide to enable this…. This recovery will only run when the state change is detected… as a recovery to the condition, so any disks that are already in a warning state will not run this recovery should you enable it. This defrag has a timeout of 1 hour…. so it should kill the defrag if it cannot complete within an hour.
Another cool thing to do – is to use the recovery action as a single run-time task. You can do this right from health explorer, to fix the disks on your own schedule:
Just click the link, and run the task:
Minimize this…. and just let it run – you can come back in 1 hour – and see if it completed, or timed out.
You can also monitor for task status in the Task Status list in the console:
On the agent – you will see the following events logged in the OpsMgr event log:
Log Name: Operations Manager
Source: Health Service Script
Date: 9/28/2009 10:50:04 AM
Event ID: 4002
Task Category: None
Level: Information
Keywords: Classic
User: N/A
Computer: OMDW.opsmgr.net
Description:
Microsoft.Windows.Server.LogicalDisk.Defrag.vbs : Perform Defragmentation (disk: C:; computer: OMDW.opsmgr.net).
And when completed:
Log Name: Operations Manager
Source: Health Service Script
Date: 9/28/2009 11:03:44 AM
Event ID: 4002
Task Category: None
Level: Information
Keywords: Classic
User: N/A
Computer: OMDW.opsmgr.net
Description:
Microsoft.Windows.Server.LogicalDisk.Defrag.vbs : Defragmentation completed (disk: C:; computer: OMDW.opsmgr.net): FilePercentFragmentation = 0.