I/O performance of the Santos Dumont supercomputer

Abstract

In this article, 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 that 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 application’s 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.