In this paper we address efficient decentralised coordination for cooperative multi-agent systems (framed as DCOPs) by taking into account the communication and computational resources of the system. We focus on techniques that exploit structural independence among agents' actions to provide optimal solutions to the coordination problem, and, in particular, we use the Generalized Distributed Law (GDL) algorithm. In this settings, we propose a novel resource aware heuristic to build junction trees and to schedule GDL computations across the agents. Our approach aims at minimising directly the total running time of the coordination process, rather than the theoretical complexity of the computation, by considering computational and communication capabilities of agents.