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Before installing confirm that you can ssh to target from OMS host.

1. Setup --> Add Target --> Add Targets Manually
2. Enter hostname including domain and select Linux x86-64
3. Installation Base Directory   : /u01/app/oracle/middleware12c
   Instance Directory            : /u01/app/oracle/middleware12c/agent_inst
   Named Credential              : Use previous or create new one
   Privileged Delegation Setting : Remove default text, should be blank
   Port                          : 3872
4. Login as root user and run /u01/app/oracle/middleware12c/core/12.1.0.4.0/root.sh

http://docs.oracle.com/cd/E24628_01/install.121/e24089/install_agent_usng_rsp.htm#EMADV137

1. Create Directories "D:\Oracle\Cloud12c" and "D:\AgentInst" on Agent Host
2. Use emcli to download latest Agent software from OMS
   cd $OMS_HOME/bin
   export ZIP_LOC=/usr/bin/zip
   ./emcli login -username=sysman
   ./emcli get_agentimage -destination=/tmp -platform="Microsoft Windows x64 (64-bit)" -version=12.1.0.4.0
3. Transfer downloaded software to Windows Host (D:\AgentInst)
4. Unzip and edit agent.rsp file (Change 4 parameters)
   OMS_HOST=hostname
   EM_UPLOAD_PORT=Usually 4903 or 4904
   AGENT_REGISTRATION_PASSWORD=<Secure Key Password>
   AGENT_PORT=3872
5. Open DOS prompt as administrator and navigate to D:\AgentInst
   agentDeploy.bat AGENT_BASE_DIR=D:\Oracle\Cloud12c RESPONSE_FILE=D:\AgentInst\agent.rsp

export OMS_HOME=/u01/app/oracle/middleware12/oms
$OMS_HOME/bin/emctl status oms
$OMS_HOME/bin/emctl stop oms
$OMS_HOME/bin/emctl start oms

export OMS_HOME=/u01/app/oracle/middleware12c/core/12.1.0.1.0
$OMS_HOME/bin/emctl status agent
$OMS_HOME/bin/emctl stop agent
$OMS_HOME/bin/emctl start agent
$OMS_HOME/bin/emctl upload agent : Upload data to OMS
$OMS_HOME/bin/emctl clearstate agent : Force agent to re-read status of host and re-send data to OMS
$OMS_HOME/bin/emctl pingOMS : Check connectivity between agent and OMS

On Target

./emctl stop agent

On OMS Host

./emcli login -username
./emcli sync
./emcli delete_target -name="hostname:3872" -type="oracle_emd" -delete_monitored_targets