The number and arrangement of fans are important considerations in any computer case using airflow for cooling. Your computer's internal components produce a lot of heat, especially the CPU, graphics card and hard drive. The flow of air is what will remove this heat from your case, keeping the components cool enough to perform well and preventing their premature failure. By altering the placement of fans on your case, you can redirect the flow of air to target hotter components and move the air out of the computer more efficiently.
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Consider the overall flow of air into, out of, and through your case before deciding on a fan arrangement. There are a lot of varying opinions out there, but for the typical vertical rectangular box case, there is a general consensus, as seen in articles from The Heatsink Guide and Icrontic, as well as the "Builder's Guide for Desktop/Tower Systems" by AMD, that air should enter the case near the bottom of the front side and exit through the rear side near the top. For that style of case, this arrangement will cause fresh air to pass over the motherboard and CPU, and will prevent hot air from being drawn back into the case. Of course, not all cases are shaped this way, and if you are designing your own, another logical path for airflow may present itself. In any case, however, the fact that hot air rises will influence the airflow regardless of the overall form, so venting hot air near the top of the case is almost certainly a guideline to follow.
Devise a placement of fans on your case that will reinforce the desired airflow and target any components that need special cooling. Keep in mind the conclusions of thorough tests by Icrontic that showed more fans do not necessarily mean better cooling or airflow. In fact, adding fans may hinder the effectiveness of the system by introducing turbulent flows which move hot air around in the case instead of venting it. Every fan added also presents another path for dust to enter the case, which will degrade the cooling performance of your case over time. In addition, the noise produced by the fans in your case should not be ignored unless you are designing with cooling as the highest priority.
Decide whether each fan in your system should face outward or inward, that is, whether it will push air into the case or pull air out. A case cooling design document by AMD indicates that for typical cases, a rear exhaust fan pushing air out is more important than an intake fan. The balance between intake and exhaust fans and their airflow capacities (typically measured in cubic feet per minute, or CFM) will determine whether the pressure inside the case is higher or lower than the ambient pressure of the room. According to an article from Technibble, higher pressure inside the case is generally best, because hot air and dust will tend to exit the case by default. The pressure in the case and the airflow will be affected by any holes in the case, including the I/O ports and optical drives, so seal your case or add vent holes to control where air can escape and enter. Remember that you want air to flow through your case, not keep it filled like a hot air balloon, so balance your efforts toward higher internal pressure with adequate ventilation. Components that need special cooling, like the CPU, graphics card or hard drives, might merit a dedicated intake fan positioned so as to pull outside air directly onto them, especially if you are overclocking your system. In addition, many such high-heat components are designed for, and should be used with, a heat sink that has an attached fan inside the case.
Test your set-up by running the computer through typical tasks while monitoring the temperatures of the CPU and other components. Most motherboards make the CPU and motherboard temperatures available to the operating system, so you can keep track of the heat with software tools. Newer hard drives using SMART technology also report their temperatures for monitoring purposes. Finally, you can add your own thermometers, or even use an infrared camera if you have one, to get a better idea of how the airflow is moving heat in your case. Run the same tests while changing the configuration of the fans; you may find areas that need more attention, and you may find that some fans are redundant and don't contribute much to your cooling strategy.
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