Problem Description :

The UNIX/Linux Discovery Wizard in SCOM 2012 R2 can fail with the error message : “Data at the root level is invalid. Line 2, position 1” .

Solution :

This problem can of course have different reasons but in our case we figured out that the problem is caused because of a problem in the Linux Resource Pool. We basically created a new Resource Pool and tried to discover the Linux computer again and we were able to discover it successfully.

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Hope it helps.