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If your trying to set up folding on both or one core, make a folder, put the console version in each folder, when you set up the program, it will ask for advance options use it, at the end of the setup program it will let you allocate the cpu's to each folding program.
 

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There's only one physical core, so when you're running one heavy application, it will use the vast majority of the CPU's capabilities even though the task manager only shows 50% usage. Check out the FAQ about how the percentage used math is done on HT rigs.
 
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