You could try going into the task manager once it's running, and changing the process's base priority to a lower setting. That way it wouldn't interfere with other processes that try to access the CPU.
That's the same way that programs like SETI@home work. They claim to use "idle" CPU cycles, because they set the process priority very low, so that any other applications that attempt to access the CPU will take priority over it, so it doesn't interfere with normal computing.
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