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Is it possible to limit usage of a program to specific kernel or limit usage of processor capacity?

It otherwise runs on 100% during long time.

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Read man bash, and look for the ulimit section that starts with:

   ulimit [-HSTabcdefilmnpqrstuvx [limit]]
          Provides  control over the resources available to the shell and to processes started by it, on systems that allow such control.  

Also read man nice:

NAME
   nice - run a program with modified scheduling priority

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