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I have a Mac mini late 2012 running the i5 2.5 processor. In the mac system information it has number of cores - 2, however if I boot to Windows 7 on the bootcamp partition the system information shows i5 2.5 with 4 cores.

Im inclined to assume OS X is going to be more accurate and correct, but does anyone know why this might be showing as different?

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That is a dual core processor (Ivybridge Core i5 2.5GHz 3210M). I am guessing that Apple's system information is telling you about the physical cores and Windows is including hyper-threading which lets you run two tasks per core.

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