There is a long list of possibilities, but let's assume that these are down-blow units delivering air under the raised floor, that the air conditioners are all set for the same temperature and humidity, that the sensor calibrations have been field-checked by the manufacturer, that they are running as they were designed, and that the equipment cabinets have either highly perforated doors, or no doors, so air can flow freely into the equipment.
The three primary causes of poor air delivery are bypass air, air leakage, and under-floor blockage.
Bypass air is simply air from the hot aisle getting back into the cold aisle and going back through the equipment, or vice-versa (cold air going through into the hot aisle). Every unused space in every cabinet should have a blank panel installed. In future use cabinets that have no equipment installed, at least tape a piece of heavy construction plastic inside to separate the front from the back. Also block any spaces between cabinets. And never install perforated tiles in the hot aisle. It not only wastes useful cold air; it also lowers the return air temperature, making the air conditioners think less cooling is needed, which also happens when cold air bypasses through cabinets into the hot aisle.
Air leakage comes through openings in the floor that do not deliver useful air to the equipment. Cable holes under racks and cabinets; gaps between the floor tiles and the walls or air conditioners, or around conduit penetrations; missing tiles; perforated tiles where there is no equipment; gaps between poorly aligned tiles; perimeter walls that do not extend to the floor or have openings to adjacent rooms – all these not only waste cold air, but also reduce the air pressure under the floor which lowers air delivery through the tiles that need it. Fill and seal gaps, get tiles re-aligned, install under-floor air dams to keep air within the data center, and install good quality seals (such as those from air distribution optimization product maker, KoldLok) on cable openings.
Under-floor blockage is usually due to large cable pile ups in front of air conditioners and/or under too low a raised floor. Floors of 12-in. height or less are destined to have problems, but higher floors can also be over-filled. Power and cable runs must be planned so as to avoid blocking air flow, and cables must be spread out in order to reduce air dam situations.
There are many more factors that affect data center cooling, but until the above are addressed, it is probably not worth the effort to delve into the more complex possibilities.
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