In this study, a three-dimensional, high fidelity LES of a fully premixed, lean hydrogen-air deflagration, in a confined and obstructed channel is performed. The experimental configuration studied is the GraVent explosion channel (L. Boeck et al., Shock Waves, 2016). A complete methodology to perform LES of lean hydrogen, strongly compressible deflagrations is presented. The capability of LES to quantitatively reproduce the main Flame Acceleration (FA) mechanisms of the fast deflagration is illustrated. The physics of FA are analysed and the contribution of the unburnt mixture flow aerodynamics to the absolute flame propagation speed, is evaluated. This is made possible by the access to the complete reactive flow fields, which are not available in the experiments. It is shown that the flow contraction, at fence-type obstacles, and the flame/vortex interaction, between the flame front and the turbulent structures in the wake of the obstacles, interact constructively, driving FA.