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Modeling of astrophysical processes requires the use of modern tools to support time-consuming calculations with more effective parallelization of operations. In this study, we analyze the results obtained using parallelization technique in numerical simulation for the case of direct collision of clouds in situations where they collide in head-on scenario or in the case with penetration one cloud to another which rotating in contrary directions. These mutual penetrations are accompanied by periodical perturbations of matter density in new-formed cloud residues. In clumps containing more condensed matter, the gas density can reach values that are at the initial level of pre-stellar formations, in zones where new stars can form with a high probability. The generation of revealed coherent structures unbalanced after a collision is determined by Kelvin-Helmholtz and Nonlinear Thin Shell Instability effects. Issues related to the modification of the computational code, which must be done to use new processor technologies, are discussed.