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Ph.D. Theses

Parallel I/O Optiminations for Large-Scale Scientific Applications

By Jing Fu
Advisor: Christopher Carothers
July 6, 2012

Highly efficient and accurate modeling on advanced computing platforms will enable the relevant science and engineering communities to advance their understanding of complex systems that are too costly or risky for experimental study. However, as the number of processors increases to hundreds of thousands in the recent parallel computer architecture, the failure probability raises correspondingly, making fault tolerance a highly important yet challenging task.

Application-level checkpointing is one of the most popular techniques used to deal with unexpected failures proactively (as well as keeping data for post processing), due to its portability and flexibility. During the checkpoint phase, the local states of the computation spread across thousands of processors are saved to stable storage. Unfortunately, this approach results in heavy I/O load and can cause an I/O bottleneck in a massively parallel system.

In this dissertation, we examine a few parallel I/O approaches for two scientific applications: a computational fluid dynamics solver called PHASTA, and a massively parallel electromagnetics solver system called NekCEM. Both applications scale very well on IBM Blue Gene/L, Blue Gene/P and Cray XK6 supercomputers. We discuss a MPI-IO collective approach (coIO), an application-level I/O staging approach, called "reduced-blocking I/O" (rbIO) and threaded version of rbIO. We demonstrate their respective performance advantages over the traditional "1 POSIX file per processor" approach that is still being used by many scientific applications. We perform scaling tests on PHASTA and NekCEM, and our study shows that rbIO and coIO result in 100x improvement over previous 1PFPP approaches on up to 65,536 processors of the Blue Gene/P using the GPFS. Our study also demonstrates a 25x production performance improvement for NekCEM. We also show how to tune various parameters for those parallel I/O approaches and how to validate performance analysis using I/O profiling techniques.

In addition, we discuss the use of threaded rbIO to achieve near-asynchronous I/O for NekCEM and greatly mitigate the blocking nature of checkpoint. Our experiments on Blue Gene/P and Cray XK6 shows significant production performance improvement of NekCEM over the collective MPI-IO approach. We also discuss the factors that affect the speedup and expect those approaches to maintain their performance advantage on upcoming supercomputers (such as Mira and Blue Waters) as well as future exascale systems.

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