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Multi-scale molecular dynamics of the systems of nanomagnets is investigated by numerical simulation using parallel algorithms. Fortran- code Magnetodynamics-F provides next types of research: study of the possibility of regulation time of switching of the magnetic moment of the nanostructure; estimation of the role of nanocrystal geometry on super-radiation of 1-, 2- and 3-dimensional objects; study of magnetodynamics of a nanodots inductively coupled with the passive resonator; depending on the solution from initial orientation of the magnetic moment in order to find the configurations for which the super-radiance and radiative damping are maximal. The parallel programs created using application programming interfaces OpenMP and OpenACC. The estimates of speedup and efficiency of implemented algorithms in comparison with sequential algorithms have been obtained. It is shown that the use of NVIDIA Tesla accelerates simulation for study of magnetic dynamics systems which include thousands of magnetic nanoparticles.Back