I think it should be the exact size of the core, ignoring any IHS. If you want you could take an IHS off of a dead P4 and sandwich it in there for P4 simulation (exact die height would need to be done then also). A design such as the one Cathar made could not be tested correctly if the die size did not simulate the real thing.
What about in a real die, there are hotter spots on the die itself, such as over where the cache is located, how do you simulate that?
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