The OS needs to know about hyperthreading, but most OS's written over the past few years support it. Software that uses more than one thread will automatically benefit from hyperthreading, although hyperthreading doesn't duplicate all of a CPU's resources (and of course the threads will share the same cache), so you don't necessarily get a 2:1 speedup. On a multiprocessor hyperthreaded system, software can tell the OS to put its threads on separate physical CPUs instead of being randomly assigned to virtual CPUs if the software knows that that will speed things up.
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