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You can use 'emctl setproperty agent'.
1: stop the agent
2: emctl setproperty agent -name EMD_URL -value https://hostname.domain:port/emd/main/
3: start agent
Note that this procedure will change the agent port but will not update the agent target name (which includes the port number).
To change the OMS secure upload port:
emctl secure oms -secure port (no load balancer)
emctl secure oms -slb_port (access via load balancer)
See Enterprise Manager Cloud Control Administrator’s Guide for the detailed syntax. You will need to resecure your agents and load balancer configuration after changing the port.