1. For a particular controller for managing a network by generating configuration data for a plurality of managed forwarding elements that forward data to each other in the network, a method for computing sets of managed forwarding element configuration outputs using corresponding sets of configuration inputs from first and second controllers, the method comprising: receiving a first set of inputs that are part of a particular transaction relating to a logical forwarding element that is implemented by the plurality of managed forwarding elements from the first controller and a second set of inputs that are redundant of the first set of inputs and are part of the particular transaction relating to the logical forwarding element from the second controller, wherein the inputs of the particular transaction are (i) for processing together to compute a set of managed forwarding element configuration output changes and (ii) for processing separately from other, separate transactions processed by the particular controller that relate to other logical forwarding elements; storing the second set of inputs while computing a first portion of the set of managed forwarding element configuration output changes using the first set of inputs; after a failure of the first controller, receiving a third set of inputs from the second controller, the third set of inputs comprising inputs that are part of the particular transaction relating to the logical forwarding element and are not in the second set of inputs; while maintaining the first portion of the set of managed forwarding element configuration output changes, computing a second portion of the set of managed forwarding element configuration output changes using the second and third sets of inputs; and after computing the complete set of managed forwarding element configuration output changes, outputting the set of managed forwarding element configuration output changes for distribution to a set of managed forwarding elements.