To select a master controller from a plurality of controllers, a computing system may consider whether connections between components within field replaceable units (FRUs) are functional as well as the data dependencies between the FRUs. For example, in addition to identifying whether the connections between the FRUs and the controllers are functional, the computing system sends instructions to each of the FRUs coupled to the controllers to determine if inter- and intra-FRU connections required for booting a compute node hosting the FRUs are functional. For instance, one FRU may depend on data from another FRU in order to boot. If a communication link between the FRUs is non-functional, the compute node may fail to boot. The computer system uses these evaluations to determine which of the controllers to select as the master.