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The problem of analyzing the delays arising in the transmission of data in a multiprocessor computing system is considered. This problem is actual due the need to create parallel programs that effectively use the resources of a cluster computing system. Also, the analysis of delays in the communication environment is helpful for system administrators. They can use it for automated troubleshooting and fine-tuning of computing cluster system software. This paper proposes special approach of analysis of delays, appearing in supercomputers. Clustering algorithm is proposed, which allows smoothing out overshoots to significantly reduce the amount of stored data of delay values and find the nodes with similar behavior of delays. The research was conducted using K60 supercomputer of Keldysh Institute of Applied Mathematics and Lomonosov supercomputer of Lomonosov Moscow State University.