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I've got a .Net application that runs as a service. I'd like to run it on a machine that is dedicated to that service. For other machines that have a very dedicated purpose, I use instance of Windows Server Core. But from what I've read and seen, Windows Server Core doesn't support .Net.

Is there away to run a .Net application without running a full blown version of Windows?

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Depending on the specific application, you may be able to run it using Mono. Mono lets you run most .NET programs. You can check the application's compatibility with Mono using this tool.

If your application can run on Mono, you can try installing it on your Windows Server Core. If it doesn't work, there's always many, many lightweight versions of Linux that can run Mono. I won't make any specific recommendations here, as I don't use them myself.

Edit: If you are running Windows Server Core 2008 R2, there's a cut down version of .NET for it, but some features may be missing. An additional standalone installer is available.

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There is the .Net Micro Framework which is a very limited version of the .Net framework/runtime for embedded devices. To my knowledge, it doesn't require Windows.
Wikipedia, as always, has additional information.

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Can it run on a PC or does it have to run on an embedded device? – epotter Mar 15 '12 at 19:19
I've never worked with it myself. There are also other alternative implementations. – Oliver Salzburg Mar 15 '12 at 19:31

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