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I have seen this before and it was because the link learning process was not working. That happens via LLDP packets that the controller issues out of each port that it knows about. The controller also programs a flow in each switch to punt all LLDP packets the switch receives to the controller. So, when a packet-out sends the LLDP from one switch to the connected switch, the controller will get that LLDP and it can then know/learn that link.

to debug, in this order:

  • check that all the ports you expect are known to the controller. (a request to http://$CONTROLLER_IP:8181/restconf/operational/opendaylight-inventory:nodes/node/openflow:1 will show you the ports for the switch "openflow:1")

  • check that your switches have the flow to punt LLDP packets to the controller (sudo ovs-ofctl dump-flows <switch name=""> -O OpenFlow13)

  • verify that the controller is sending packet-out with LLDP packets (tcpdump is how I would check)

  • verify that the switches are sending packet-ins for each received LLDP packet.

  • check the controller logs for any trouble (Exceptions, ERRORS, etc)

hope it helps figure it out