A mechanism is provided for improving the performance and efficiency of multi-core processors. A system controller in a data processing system determines an operational function for each primary processor core in a set of primary processor cores in a primary processor core logic layer and for each secondary processor core in a set of secondary processor cores in a secondary processor core logic layer, thereby forming a set of determined operational functions. The system controller then generates an initial configuration, based on the set of determined operational functions, for initializing the set of primary processor cores and the set of secondary processor cores in the three-dimensional processor core architecture. The initial configuration indicates how at least one primary processor core of the set of primary processor cores collaborate with at least one secondary processor core of the set of secondary processor cores.