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Open Access Publications from the University of California

MerBench: PGAS benchmarks for high performance genome assembly

  • Author(s): Georganas, E
  • Ellis, M
  • Egan, R
  • Hofmeyr, S
  • Buluç, A
  • Cook, B
  • Oliker, L
  • Yelick, K
  • Editor(s): Morris, Karla
  • Iancu, Costin
  • Filippone, Salvatore
  • Chamberlain, Bradford L
  • Long, Bill
  • et al.

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.

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