MerBench: PGAS Benchmarks for High Performance Genome Assembly
MerBench: PGAS Benchmarks for High Performance Genome Assembly
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MerBench：高性能基因组组装的 PGAS 基准
DOI：
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发表时间：
2017
期刊：
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通讯作者：
K. Yelick
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作者：
E. Georganas;Marquita Ellis;R. Egan;S. Hofmeyr;A. Buluç;B. Cook;L. Oliker;K. Yelick
从头基因组组装是现代基因组学中最重要和最具挑战性的计算问题之一;此外，它与其他图形分析和不规则应用程序共享重要的算法和通信模式。与模拟不同，它没有浮点运算，并且由计算节点内和计算节点之间的小内存事务主导。在这项工作中，我们引入MerBench，一组紧凑的PGAS基准测试，捕获整个HipMer，并行基因组组装流水线，已被证明可扩展到大规模并发的并行算法的通信模式。我们还介绍了这些微基准测试的结果在爱迪生超级计算机上，并说明这些经验结果可以用来评估管道的缩放行为。
De novo genome assembly is one of the most important and challenging computational problems in modern genomics; further, it shares algorithms and communication patterns important to other graph analytic and irregular applications. Unlike simulations, it has no floating point arithmetic and is dominated by small memory transactions within and between computing nodes. In this work, we introduce MerBench, a compact set of PGAS benchmarks that capture the communication patterns of the parallel algorithms throughout HipMer, a parallel genome assembler pipeline that has been shown to scale to massive concurrencies. We also present results of these microbenchmarks on the Edison supercomputer and illustrate how these empirical results can be used to assess the scaling behavior of the pipeline.