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For example, at the bottom it shows "System: 1.45%, User: 1.55%, Idle: 97%".

Yet in the process list I see under "% CPU" Activity Monitor 20%, WindowServer 13%, Firefox 10%, coreaudiod 9% etc.

I assume this can have to do with multiple cores; in any way this is super confusing and makes it very hard to see what's really using resources.

How can I make these numbers add up (like in the Windows Process Explorer, for example)

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The numbers in the top section are 'per core' [including virtual Hyperthreading cores].
Those at the bottom are 'the whole Mac'

So, depending on how many cores your Mac has, 100% in the top section might be 4, 8 or 12 times the total figures. That's how you can on occasion see huge numbers, like kernel_task trying to cool the Mac by running at 500% - that's 5 entire cores all being marked as busy.

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You might guess that would be a 4-core Mac, with hyperthreading.

Images clipped from How to find cause of high kernel_task cpu usage?

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