I/O Performance of the Santos Dumont Supercomputer

Abstract : In this paper, we study the I/O performance of the Santos Dumont supercomputer, since the gap between processing and data access speeds causes many applications to spend a large portion of their execution on I/O operations. For a large-scale, expensive, supercomputer, it is essential to ensure applications achieve the best I/O performance to promote efficient usage. We monitor a week of the machine's activity and present a detailed study on the obtained metrics, aiming at providing an understanding of its workload. From experiences with one numerical simulation, we identified large I/O performance differences between the MPI implementations available to users. We investigated the phenomenon and narrowed it down to collective I/O operations with small request sizes. For these, we concluded the customized MPI implementation by the machine's vendor (used by more than 20% of the jobs) presents the worst performance. By investigating the issue, we provide information to help improve future MPI-IO collective write implementations, and practical guidelines to help users and steer future system upgrades. Finally, we discuss the challenge of describing applications I/O behavior without depending on information from users. That allows for identifying the applications I/O bottlenecks and proposing ways of improving its I/O performance. We propose a methodology to do so, and use GROMACS, the application with the largest number of jobs in 2017, as a case study.
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https://hal.inria.fr/hal-02270908
Contributor : Francieli Zanon Boito <>
Submitted on : Monday, August 26, 2019 - 1:49:19 PM
Last modification on : Monday, September 2, 2019 - 4:24:01 PM

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Jean Luca Bez, André Ramos Carneiro, Pablo Pavan, Valéria Soldera Girelli, Francieli Zanon Boito, et al.. I/O Performance of the Santos Dumont Supercomputer. International Journal of High Performance Computing Applications, SAGE Publications, In press. ⟨hal-02270908⟩

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