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OpenGL games running in Ubuntu 12.04 and Ubuntu 12.10 in fullscreen mode very slow. FPS is very low (it lags). When I switch in the game settings in Windows Mode (same resolution 1680*1050) the game runs perfectly.

Graphics: NVIDIA GeForce GTX 460
Driver: NVIDIA 304.48 (I now use a beta driver, but in the older drivers the games are slower.)

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If you change your native screen resolution to whatever your window size was, fullscreen will/should be as performant as windowed.

to clarify, game running at 1680x1050 windowed and fullscreen means your native resolution >= 1680x1050 ... probably

If some random openGL app has to render a viewport, then scale it...performance is going to suffer.

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Enable Unredirect Fullscreen Windows in CompizConfig Settings Manager:

In my opinion it should be enabled by default.

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