Well, forcing an application/task to use "only" CPU "0" isn't useful, since Windows XP manages that itself.
You get advantage of having a HT CPU most of the time when there is more than one thread to execute. If you only run "After Effects", it depends if this is coded multithreaded. If you run "After Effects" and another task in the background, for example video or audio player, you will for sure have an advantage with a HT CPU.
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I have noticed that when rendering video (after effects) I get a CPU usage of up to 95% (w/o HT) Now, correct me if I am wrong: if I enable HT with after effects and set affinity to one CPU only, I should notice a decrease of performance since I am forcing after effects to use only 1 CPU (50% of the physcical CPU)?
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Wrong, thats not a "real" Duo Core CPU. In fact, I would estimate no change of performance when you set affinity to one CPU only.
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How Due Core would handle all this?
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Duo Cores can handle identical threads at the same time, a HT CPU can only handle different threads at the same time, because the 2 virtual CPUs have to share their ressources (If CPU "0" calculates floating point, CPU "1" cannot calculate also floating point at the same time. A Duo Core can do that.)