The numerical simulation of Friction Stir Welding (FSW) is carried out using an Arbitrary Lagrangian or Eulerian (ALE) formulation. Its computational cost is reduced by appealing to the parallel version recently developed within the Forge software. The accuracy of the numerical model is increased by enhancing the state variables remapping algorithm and by introducing a better suited time integration scheme based on the cylindrical coordinates. The pin and shoulder threads are modelled in order to account for this crucial phenomenon on material heating. The developed model provides quite satisfactory temperature fields for the FSW of a butt joint of 6061 aluminium, as compared to experimental results. It allows simulating welding defects such as tunnels holes or flashes. The study then focuses on numerical simulations and experimental measurements of a lap joint of a 7175 aluminium sheet on a 2024 aluminium sheet for an aeronautical application.