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pls go through this: http://docs.oracle.com/cd/E24628_01/upgrade.121/e22625/upgrading_10205_111_PS1_agents.htm#CIHHABAD
If you are using option: Use Oracle Home Preferred Credentials then use have to set the oracle home credentails in EM using emcli first. Since in 10g or 11g we neverhad oracle home credentails you cannt use UI do it .
Else use the Override Oracle Home Preferred Credentials and enter one set of credentials that can be used for all Oracle homes. Run Privilege section, by default, None
Also, check that the 10/11g agents have had root.sh run on them by looking at the owner of $AGENT_HOME/bin/nm* executables. Should be root. This is a common reason for ERROR: NMO not setuid-root (Unix-only) message. If not, you'll need to run $AGENT_HOME/root.sh as root before any jobs can be run against those agents. To test, try a simple job on the agent such as 'id' or something to see if it can communicate.
It turns out that indeed the root.sh had not been run. RUnning it solved the problem.