If I have 2 core Layer 3 switches that are in an HSRP config, each of the active router vlans are setup already as the root bridge for those particular vlans, who should I designate as the root bridge for VLAN 1 ?
If you are carrying any traffic in VLAN 1, then best option is to set up active router as root bridge as you have done in case of other VLANs. If you are not carrying any user traffic in VLAN1, you can use any of the two core switches as root bridge
Root bridge and the active router in hsrp are not really related.
Root bridge selection is only used to control which paths are blocked if any. The actual path of the traffic does not have to pass via the root bridge. It will always take the most direct path between the machines.
It is much more important to see where the blocked link is if you have any.
As a example you have a distribution switch connected to your 2 core switches and the 2 core switches connected to each other. You design you spanning tree to block the link between the 2 core switches by setting the cost very high. In this case any machine on the distribution switch can directly access either core switch. Since only the core switch that is the active HSRP router for a vlan will advertise the common mac address the distribution switch will only see the mac address on one of the two links. Either core switch can be set as the root but the traffic will alway directly flow to the active HSRP device.
Of course you don't want to block the line between the switches because the HSRP keepalive message will be layer 2 routed via the distribution switch. In a very simple design it is common to have the root bridge be the HSRP active device just because its easier to configure but the concepts are not really related. Root bridge placement is more related to traffic volumes than anything else it just tends to be true that the switch has the gateway is also the highest volume of traffic
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