This document should explain how to configure Oracle EM console in SAP environment, because there is one big issue with ORACLE_HOME environment variable.
As in SAP installation on Linux (or other unix OS), normally installation is done into /oracle/<SID>/11203 or /oracle/<SID>/112_64 directory, but ORACLE_HOME is set to /oracle/<SID>/112, which is soft link, there is a problem with configuration of EM.
In Oracle notes 1106623.1 and 550484.1 it is described that ORACLE_HOME should be set to physical directory, not to linked one.
Solution is to change scripts emca and emctl which are located in /oracle/<SID>/112/bin directory and replace physical directory with linked one and then start command for configuration:
emca -config dbcontrol db -repos create
Also for RAC database there is two other prerequisites:
1. parameter remote_listener must be set to scan VIP
2. password files for all instances must exists in /oracle/<SID>/112/dbs directory
Then you can start configuration:
emca -config dbcontrol db -repos create -cluster