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I have a i3 2nd gen system with nvidia 1GB graphics card and running ubuntu . The cpu usage becomes 99% when i run a 3D simulator and other OpenGL 2D application and i acquire the mouse movement data from another program but the mouse movement is slowed due to too much usage , is there any way in which i can give priority to some process or decrease my CPU usage .

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Go into your distribution's system monitor and adjust the priorities for the relevant processes? – Thomas Oct 16 '12 at 10:16
up vote 2 down vote accepted

Use the nice command from the command line shell to change the priority of a process.

man nice and man renice should give you the information you need.

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