Today advanced research is based on complex simulations which require a lot of computational resources that usually are organized in a very complicated way from technical part of the view. It means that a scientist from physics, biology or even sociology should struggle with all technical issues on the way of building distributed multi-scale application supported by a stack of specific technologies on high-performance clusters. As the result, created applications have partly implemented logic and are extremely inefficient in execution. In this paper, we present an approach which takes away the user from the necessity to care about an efficient resolving of imbalance of computations being performed in different processes and on different scales of his application. The efficient balance of internal workload in distributed and multi-scale applications may be achieved by introducing: a special multi-level model; a contract (or domain-specific language) to formulate the application in terms of this model; and a scheduler which operates on top of that model. The multi-level model consists of computing routines, computational resources and executed processes, determines a mapping between them and serves as a mean to evaluate the resulting performance of the whole application and its individual parts. The contract corresponds to unification interface of application integration in the proposed framework while the scheduling algorithm optimizes the execution process taking into consideration the main computational environment aspects. © 2019, Springer Nature Switzerland AG.