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Tower coolers are preferable to the heat sink and fan combinations that blow air down into the processors (incidentally, both AMD and Intel include these with their retail boxed processors). However, it is of paramount importance that you pay attention to the correct installation orientation.
Because a lot of mistakes can crop up here, we'll take a look at the various installation options before summarizing the most important rules.
The vertical assembly is mostly applicable to Intel-based systems. Machines with Socket AM2+- or AM3-based motherboards need a cooler with a special mounting system that allows it to be installed at a 90° angle.
Of course, tower coolers can also be installed in enclosures with power supplies mounted up top. In those cases, the schematic diagram looks like this:
It should be noted that the rear wall must either be perforated or contain a vent. It's even better if there's an exhaust fan in place, which can replace a second heat sink fan in many cases. Of course, it's possible to improve on this scenario as well:
Even with a top-mounted PSU, airflow can be improved by taking in extra cool air from the floor: