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Multi threading is useful for programs that will not saturate a processor core, so you run 2 light programs on one core. For Seti@home this is not the case. It is written to completly ulitlize a processor core, so you'll want to only have 4 tasks running on a quad core processor. Running 8 will only cause overhead to increase, decreasing actual work.
As for the GPU, you could test to see what it wants from the processor, by clearing your cache, accept only GPU tasks and observe how much cpu is being used by the one GPU task alone. GPU's are generally designed to ONLY handle one task at a time.
On my imac qc i5 i run 4 S@H MB tasks (cpu) and one Einstein@home task on GPU (only uses .5% cpu) so I have no need to throttle S@H
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