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The paper considers a job shop scheduling problem similar to those taking place in many fields such as project management, educational sphere and operational planning of manufacturing process. The considered problem, in real life, has high dimensionality and it is quite hard to find even a feasible solution, therefore, making necessary a problem-oriented heuristic for solving it in reasonable time. Manufacturing process stability requires special care about restriction and, at the same time, operational planning requires finding solutions quickly. In this paper, hierarchical problem structure is proposed where the top-level problem is the traveling salesman problem and the nested resource-constrained project scheduling problem is replaced by the simulation model. This paper considers combinatorial genetic algorithm (GA) and Lin-Kernigan heuristic (LKH). The performance comparison is fulfilled and competitive results are demonstrated.