To resolve it :-
iAS Discovery/Monitoring Fails If Agent Is Installed Under Another OS User Than iAS,
metalink note 437078.1.
Problem: Agent Does Not Discover Other ORACLE_HOME´s, metalink note :371539.1
1) As Ias user:-
cd $IAS_HOME
chmod g+rx $IAS_HOME
chmod g+rx $IAS_HOME/bin
chmod g+rx $IAS_HOME/bin/emtgtctl
chmod ug+s $IAS_HOME/bin/emtgtctl2
chmod g+rx $IAS_HOME/perl
chmod g+rx $IAS_HOME/perl/bin
chmod g+rx $IAS_HOME/perl/bin/perl
chmod g+rx $IAS_HOME/sysman
chmod g+rx $IAS_HOME/sysman/emd
cmod g+rw $IAS_HOME/sysman/emd/targets.xml
touch $IAS_HOME/sysman/emd/centralagents.lst
chmod g+rw $IAS_HOME/sysman/emd/centralagents.lst
chmod g+rx $IAS_HOME/sysman/config
chmod g+rw $IAS_HOME/sysman/config/*.properties
chmod g+rx $IAS_HOME/opmn
chmod g+rx $IAS_HOME/opmn/conf
chmod g+rw $IAS_HOME/opmn/conf/opmn.xml
chmod g+rx $IAS_HOME/config
chmod g+rw $IAS_HOME/config/*.xml
chmod g+rw $IAS_HOME/config/*.properties
chmod g+rx $IAS_HOME/Apache
chmod g+rx $IAS_HOME/Apache/Apache
chmod g+rx $IAS_HOME/Apache/Apache/conf
chmod g+rw $IAS_HOME/Apache/Apache/conf/*conf
chmod g+rw $IAS_HOME/Apache/Apache/conf/*.xml
chmod g+rw $IAS_HOME/Apache/Apache/conf/mime.types
chmod g+rx $IAS_HOME/j2ee
chmod g+rx $IAS_HOME/j2ee/OC4J_SECURITY
chmod g+rx $IAS_HOME/j2ee/OC4J_SECURITY/config
chmod g+rw $IAS_HOME/j2ee/OC4J_SECURITY/config/*
chmod g+rx $IAS_HOME/dcm
chmod g+rx $IAS_HOME/dcm/config
chmod g+rw $IAS_HOME/dcm/config/*.conf
chmod g+rw $IAS_HOME/dcm/config/*.xml
2) as emagent os user
cd $AGENT_HOME
chmod g+rx $AGENT_HOME
chmod g+rx $AGENT_HOME/bin
chmod g+rx $AGENT_HOME/bin/emtgtctl
chmod ug+s $AGENT_HOME/bin/emtgtctl2
chmod g+rx $AGENT_HOME/sysman
chmod g+rx $AGENT_HOME/sysman/emd
chmod g+rw $AGENT_HOME/sysman/emd/targets.xml
chmod g+rx $AGENT_HOME/sysman/opmn
chmod g+rx $AGENT_HOME/sysman/opmn/conf
3) stop and start the agent
emctl stop agent
emctl start agent
4) initialize new discovery through the enterprise manager.
To check the log files , check in the /sysman/log/ emagent.trc & emagent_perl.trc.
Other than that, ensure that the /etc/oratab contains the path to both of the oracle home.
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