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I have a physical server with 4 NICs running Debian 8. I want to install KVM and configure guest vm's.

One of the guest vm's will run the controller software to manage my network devices (ie managed switches and WAPs).

How can I create a bond of two ports to pass to this guest OS if I can't also configure it on the switch to support it? Or are there other methods of doing this (ie pass each NIC separately, configure the guest vm and switch, then reconfigure the host and guest afterwards)?

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You say you have 4 NICs? Connect one of them (third, for example) to the third interface of a switch.

Bridge controller VM with that NIC and configure first two interfaces of a switch to be a bond. Do same with first two interfaces of a server. Connect them and have a bonded connection.

Now, delete third interface from the bridge on a server and add bond there. It is easy (say, bond0 is up and working over eth0 and eth1):

brctl delif vmbr0 eth2
brctl addif vmbr0 bond0

Now, pull out cable from third interface (eth2). You have a bonded connection between server and a switch. Now it's time to reflect this change in /etc/network/interfaces.

Though, only two physical lines. You could get further and add another interfaces, that is not so hard.

By the way, if you plan to use 802.1q vlans, in Linux you have to create vlan sub-interfaces on your bond, not on individual physical interfaces.

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