I don't understand why the author used "It is" rather than They are in the following sentence.
It is threads, not processes, that are the units scheduled by the system for execution on the processor.
Why don't we say the following?
They are threads, not processes, that are the units scheduled by the system for execution on the processor.
Answer
This is a cleft sentence: "It is noun phrase that clause." In this construct, the pronoun is always "it"; it doesn't agree with the number (or gender) of anything. So it doesn't matter that threads or are are plural.
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