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If you are not using the patched Mininet version as mentioned in the below link

and installed it directly from the repository (apt-get), then to enable the openflow 1.3 mode in openvswitch, you will have to use the following command on each openvswitch instance mininet creates

ovs-vsctl set bridge <switch-name> protocols=OpenFlow13
e.g : ovs-vsctl set bridge s0 protocols=OpenFlow13

This command will disconnect the switch from controller ( if it's connected ) and then set the mode to openflow 1.3 and will again attempt to connect to the controller.