Simulation of the water flow around a ship hull and a marine propeller operation are considered in this paper as popular problems of ship propulsion, which are frequently investigated through CFD approach now. CFD technologies are used for determination of ship hull resistance as well as the open water curves of the propeller according to usual methods of ship design. FlowVision CFD software is used for simulations based on solving RANS equations. The software was used together with supercomputer "HPC 2" of National Research Center "Kurchatov Institute". The original features of the numerical models and technologies, software algorithms and the supercomputer's hardware are submitted and discussed. There are the method of grid formation based on Cartesian initial grid and chimerical overlapping boundary layer grid, special versions of turbulence models, modified method of free surface simulation and many other things among them. Governing equations for water flow, which are integrated using an implicit numerical method, are given as well. The generated systems of linear equations are solved by an aggregative algebraic multigrid method. The scalability of this method on the supercomputer has been studied and analyzed.