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In decomposition methods, the memory costs for solving the interface problem are increasing significantly with the number of subdomains increasing. Using of the substructuring method allows you to reduce the number of iterations when the system is being solved. At the same time, the global boundary stiffness matrix takes up more memory in comparison with global stiffness matrix. This imposes restrictions on the maximum size of the problem for which you can apply this method. Different approaches to reduce the costs and limitations of memory on stage of the construction and solving of the interface system exist. A layer-by-layer approach to the partitioning of a triangulated multiply connected domain into connected subdomains without branching of inner boundaries was presented. This makes it possible to avoid conflicts with concurrent operations of the assembly type without using synchronization and critical sections. Parallel algorithm of the construction global boundary stiffness matrix with distributed storage of the matrix are considered when implementing using OpenMP and MPI technologies. This approach allows not only to reduce the limits on the maximum size of the solved problem, but also to resolve conflicts of shared memory access by increasing the number of independent parallel tasks.