A system comprising a chassis that includes a plurality of modules and a fan assembly disposed in a distal end of the chassis for drawing air in parallel pathways through the plurality of modules. At least one of the modules is a compute module having a thermal sensor disposed to sense the temperature of air flowing across a processor mounted on a motherboard. The system further comprises a fan controller receiving output from the thermal sensor, wherein the fan controller operates the fan assembly to cool the plurality of modules and maintain the thermal sensor output within an operating temperature range. The fan controller controls the fan speed according to predetermined thermal profile settings associated with one of the compute modules received in the chassis. For example, the predetermined thermal profile settings may include a minimum fan speed, a maximum fan speed, and control loop feedback settings.