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In my setup, the network's core router (MikroTik hEX S) has switching hardware acceleration which would drastically lower CPU consumption from switching tasks. This interests me as I intend to run a VPN server on the router.

However, STP needs to be disabled to enable hardware acceleration. I'm still interested in STP though, but I'm not sure if it needs to enabled for the entire network, or if I need it in the first place.

If I want STP, do I need to enable it everywhere? Or can I enable it sparingly where it seems to be needed (e.g. only between Site 1 SW1 and Site 2 SW2 in the diagram)?

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It depends on the connections between your switches.

If you (plan to) have redundant paths between switches STP must be enabled in both switches in your case between SW1 and SW2 (it also must be the same implementation/protocol otherwise it will cause timing issues between the different port states so please check if the switches are different models or from different vendors).

As far as I see you only have one path (cable) between switch and router and the other SW connected to the router has no connection to any other switches therefore there is no loop. So it shouldn't be necessary to enable the router's STP. Then you'll just need to be careful when attaching new connections to the router so you don't create a loopback.

Same goes for SW3 and SW4. Each has only one connection to SW2 and no connections to other switches so there can not be a loop.

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