HPC-BLAST: Distributed BLAST for Modern HPC Clusters.

14 pages•Published: March 18, 2019

Shane Sawyer, Mitchel Horton, Chad Burdyshaw, Glenn Brook and Bhanu Rekapalli

Abstract

The near exponential growth in sequence data available to bioinformaticists, and the emergence of new fields of biological research, continue to fuel an incessant need for in- creases in sequence alignment performance. Today, more than ever before, bioinformatics researchers have access to a wide variety of HPC architectures including high core count Intel Xeon processors and the many-core Intel Xeon Phi.
In this work, the implementation of a distributed, NCBI compliant, BLAST+ (C++ toolkit) code, targeted for multi- and many-core clusters, such as those containing the Intel Xeon Phi line of products is presented. The solution is robust: distributed BLAST runs can use the CPU only, the Xeon Phi processor or coprocessor, or both by utilizing the CPU or Xeon Phi processor plus a Xeon Phi coprocessor. The distributed BLAST implementation employs static load balancing, fault tolerance, and contention aware I/O. The distributed BLAST implementation, HPC-BLAST, maintains greater than 90% weak scaling efficiency on up to 160 Xeon Phi (Knights Landing) nodes.
The source code and instructions, are available under the Apache License, Version 2.0 at https://github.com/UTennessee-JICS/HPC-BLAST.

Keyphrases: bioinformatics, high performance computing, sequence alignment

In: Oliver Eulenstein, Hisham Al-Mubaid and Qin Ding (editors). Proceedings of 11th International Conference on Bioinformatics and Computational Biology, vol 60, pages 1-14.

Links:	https://easychair.org/publications/paper/BxHL
	https://doi.org/10.29007/qm7h

BibTeX entry

@inproceedings{BiCOB2019:HPC_BLAST_Distributed_BLAST,
  author    = {Shane Sawyer and Mitchel Horton and Chad Burdyshaw and Glenn Brook and Bhanu Rekapalli},
  title     = {HPC-BLAST: Distributed BLAST for Modern HPC Clusters.},
  booktitle = {Proceedings of 11th International Conference on Bioinformatics and Computational Biology},
  editor    = {Oliver Eulenstein and Hisham Al-Mubaid and Qin Ding},
  series    = {EPiC Series in Computing},
  volume    = {60},
  publisher = {EasyChair},
  bibsource = {EasyChair, https://easychair.org},
  issn      = {2398-7340},
  url       = {/publications/paper/BxHL},
  doi       = {10.29007/qm7h},
  pages     = {1-14},
  year      = {2019}}

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