Modern mathematical modeling on supercomputer systems requires that researchers have both a view of the main aspects of a studied phenomena and a knowledge base of numerical methods and supercomputer technologies for solving natural science problems. Development of intelligent support systems for solving such problems can greatly facilitate the researcher work by providing convenient tools for constructing an efficient scheme of problem solution on a target computational architecture and, if possible, implementing it using already developed program codes.This paper describes an implementation of this idea for the compute-intensive problems of the cosmic plasma hydrodynamics. A knowledge base has been developed, including ontological descriptions of studied astrophysical phenomena, their mathematical representations, numerical methods for solving set problems and supercomputer architectures that can be used for calculations. The paper presents patterns describing the main classes of the constructed ontology and their instances. The ontology can be expanded by a generation system of computational codes for the selected schemes of a problem solution.