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There are a few methods you can use to run Ubuntu "on top of " Windows:

1. Virtual machines

Virtual machines behave basically just like a real computer, except they run in a window. Running an operating system in one provides the best possible performance without dual-booting. Things like graphics acceleration will be extremely limited or non-existent, however.

2. Emulators

Emulators like QEMU and Bochs can be used to run Ubntu on an emulated machine. This is much slower than a virtual machine, and is thus usually only useful for debugging or for running Ubuntu for a non-native platform, such as PowerPC or ARM.

3. Cooperative Linux (not recommended)

Cooperative Linux runs a Linux kernel as a process on Windows. The reason I don't recommend this is because:

A. It is more difficult to set up than the other methods.

B. It is not supported by Canonical, and thus you cannot file bug reports.

C. It will require installing several pieces of software (such as a terminal emulator and an X server).

D. It has the potential for corrupting your Windows installation.

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Q: Can you run Ubuntu on top of Windows?
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