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dnsmasq is run to help make the user experience smoother for the desktop users. If I run bind/named on this same server will there be conflicts between the two? What are the limitations of dnsmasq, where I should use bind/named instead?

In particular, I've set up bind to run a psuedo-domain locally. It works, but I'm just curious to know if I should've done this through dnsmasq instead of running yet another service that seems to duplicate functionality.

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By default you won't be able to run bind and dnsmasq simultaneously, because they will both try to bind to port 53 and one of the will fail. (It is possible to run them simultaneously if you configure them to bind to different IP addresses.) Based on what you want to accomplish, I would personally use dnsmasq instead of bind, because it's smaller and simpler. The main difference is that dnsmasq is not intended to be used as an authoritative nameserver, whereas bind is.

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