we can use the cpulimit command to limit cpu usage of any process or application. you can limit a certain running application , either by its name or by it's pid
ex:-
cpulimit -e vlc -l 20
cpulimit -p 5319 -l 40
see:-
http://www.howtoforge.com/how-to-limit-cpu-usage-of-a-process-with-cpulimit-debian-ubuntu
http://ubuntuforums.org/showthread.php?t=992706
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