This paper considers the efficient methods and high- performance parallel technologies for the numerical solution of the multi-dimensional initial boundary value problems, with a complicated geometry of a computational domain and contrast properties of a material on the heterogeneous multi-processor systems with distributed and hierarchical shared memory. The approximations with respect to time and space are carried out by implicit schemes on the quasi-structured grids. At each time step, the iterative algorithms are used for solving the systems of linear or nonlinear equations that, in general, are non-symmetric with a special choice of the initial guess. The scalable parallelism is provided by two-level iterative domain decomposition methods, with parameterized intersection of subdomains in the Krylov subspaces, which are accelerated by means of a coarse grid correction and polynomial or other types of preconditioning. A comparative analysis of the performance and speed up of the computational processes is presented, based on a simple model of parallel computing and data structures.