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The overall performance of a distributed system is often depends on the effectiveness of its interconnection network. Thus, the study of the communication networks for distributed systems is very important, which is the focus of this paper. In particular, we address the problem of fat-tree based interconnection networks performance modeling for multi-user heterogeneous multi-cluster computing systems. To this end, we present an analytical model and validate the model through comprehensive simulation. The results of the simulation demonstrated that the proposed model exhibits a good degree of accuracy for various system organizations and under different working conditions.