Ubuntu :: System Stutter Running Heavy Load Through Wine?

I have recently begun contributing to the Folding@Home distributed computing project. Due to oversights in the application's design and to process the most advantageous work units, I need to run this command line app through wine. The application is very CPU/RAM intensive, but it does not put much load on the hard drive. It is multi-threaded and uses up to 100% of all 6 cores in my machine. I run it with a "nice" level of 19 with hopes that it won't slow down my normal desktop use.

Here is the problem... when running this setup, my system will frequently freeze for a fraction of a second and then resume. With the more complicated work units, this can happen 1-2 times per minute. During the freeze, the mouse will stop moving, videos stop playing, music pauses, etc. The system is completely unresponsive. However, each instance only lasts for a very short time. Since this happens so often, my productivity is negatively impacted (and it's very annoying).

I previously ran the native Linux version of F@H without this problem, but that was also processing much less complicated calculations. I have tried with wine 1.2.1 and 1.3.5 with the same results. The application does not have problems running on Windows. It has been suggested that the current Linux CPU scheduler is to blame, but is there anything I can do to resolve this now or work around it?

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