In this paper the approach to simulation of unsteady fluid dynamic problems in terms of the Navier-Stokes system of equations is considered. The numerical scheme is built using the Runge-Kutta discontinuous Galerkin method, approximating the viscous terms with the local discontinuous Galerkin method. A modification of the DiamondTorre algorithm is developped for the geterogeneous implementation of the scheme. The solver based on this algorithm is included into the DTGV software for solving three-dimensional fluid dynamic problems, the results of its validation and performance tests are given. An example of solving the problem of flow past a sphere in three-dimensional setting is presented.