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.
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