The prerequisite check script exadataDiscoveryPreCheck.pl that is bundled in the EM Exadata plug-in 12.1.0.3 does not support the catalog.xml file.
Download the latest exadataDiscoveryPreCheck.pl file from MOS as described in the “Discovery Precheck Script” section of the Oracle Enterprise Manager Exadata Management Getting Started Guide at:
http://docs.oracle.com/cd/E24628_01/doc.121/e27442/title.htm
If multiple database clusters share the same storage server, in one Enterprise Manager management server environment, you can discover and monitor the first DB machine target and all its components. However, for additional DB machine targets sharing the same storage server, the Oracle Storage Server Grid system and the Oracle Database Storage Server System have no storage server members because they are already monitored.
If the perfquery command installed on your SuperCluster system is version 1.5.8 or later (see Check the perfquery Version), you might encounter a bug (ID 15919339) where most columns in the HCA Port Errors metric in the host targets for the compute nodes are blank. Any errors occurring on the HCA ports are not reported in Enterprise Manager.