The present paper reports the added-value of using SPH in the fluid-structure interaction occurring in the run-up and overtopping phenomena for a the rubble mound breakwater, where the seaward layer is made of grooved cubic blocks. The main goal is the study of the equivalent roughness of the outer layer, defined as the ratio of the maximum water level (run-up) on the armoured structure to the run-up on a smooth similar one. Run-up heights and overtopping rates have also been compared with empirical solutions. The complex geometry of the blocks and the surrounding gaps within breakwaters must be efficiently simulated to obtain a detailed description of the flow. Using novel computing solutions such as the new graphics processing unit GPU technology used in the DualSPHysics code (www.dual.sphysics.org), the fluid-structure interaction is being modelled with many armour blocks that are representative of the real structure. GPU computing enables the simulation of millions of particles leading to potentially better accuracy of the numerical run-up and overtopping estimates to obtain the value for the structure roughness.