The artificial intelligence problems in creating the integrated computational environment (ICE) for the mathematical modeling on the modern supercomputers are considered. The mathematical tasks to be solved present the direct and inverse interdisciplinary problems which are described by the systems of partial differential and/or integral equations in the multi-dimensional computational domains with real complicated multiscale geometry and contrast material properties. The conception of ICE consists in developing the instrumental media to support all main stages of large scale computational experiments, with a long life cycle of the products. The technical requirements for ICE include the flexible extension of the mathematical models and methods, the adaption to evolution of the computer platforms, the reusing external program products, and coordinated participation in the project of the different groups of developers. The objectives of intelligent tools consist in automatic construction of algorithms as well as generating and executing the applied software packages for the end users in particular domains.