This work is dedicated to development of mathematical modelling software. In this dissertation numerical methods and algorithms are investigated in software making context. While applying a numerical method it is important to take into account the limited computer resources, the architecture of these resources and how do methods affect software robustness. Three main aspects of this investigation are that software implementation must be efficient, robust and be able to utilize specific hardware resources. The hardware specificity in this work is related to distributed computations of different types: single CPU with multiple cores, multiple CPUs with multiple cores and highly parallel multithreaded GPU device. The investigation is done in three directions: GPU usage for 3D FDTD calculations, FVM method usage to implement efficient calculations of a very specific heat transferring problem, and development of special techniques for software for specific bacteria self organization problem when the results are sensitive to numerical methods, initial data and even computer round-off errors. All these directions are dedicated to create correct technological components that make a software implementation robust and efficient. The time prediction model for 3D FDTD calculations is proposed, which lets to evaluate the efficiency of different GPUs. A reasonable speedup with GPU comparing to CPU is obtained. For FVM implementation the OpenFOAM open source software is selected as a basis for implementation of calculations and a few algorithms and their modifications to solve efficiency issues are proposed. The FVM parallel solver is implemented and analyzed, it is adapted to heterogeneous cluster Vilkas. To create robust software for simulation of bacteria self organization mathematically robust methods are applied and results are analyzed, the algorithm is modified for parallel computations
