A method for controlling a plurality of fans operatively disposed in a shipping container. The fans are arranged in a plurality of banks within a closed fluid path. Each bank has a sub-set of the fans arranged in a plurality of horizontal layers. Two banks form an adjacent pair in the closed fluid path if a fluid exiting one of the two banks next enters the other of the two banks. The method includes determining a proposed fluid flow rate for each of the banks. The method also includes modifying each of the flow rates by a respective scaling factor such that the flow rates for each adjacent pair satisfy a continuity criteria. The method further includes controlling the fans based on the modified flow rates.