This report focuses on technology of supercomputer simulation of nonlinear processes in the cores, extracted from oil and gas production wells in order to study the properties of hydrocarbon reservoirs. One of modern approaches to solving these kind problems is to create multiphysical mathematical model of core for its study by computer methods. This approach minimizes the number of natural experiments and predicts the evolution of layers properties. Also it allows to predict oil and gas recovery of layers for a long time period. However, implementation of this technology called “virtual core” requires the following: 1) to create multiparametrical model of core as close as possible to the reality; 2) to include the multicomponent and multiphase composition and complex real geometry of core in consideration; 3) to develop a computational framework for modeling the seepage of multicomponent liquid and gas mixtures through the core; 4) to carry out large-scale calibration calculations. In this paper, an attempt to create such a multifactor mathematical model and computational foundations for its computing and supercomputing analysis is made.