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Open AccessFeature PaperArticle

Benchmarking a Many-Core Neuromorphic Platform With an MPI-Based DNA Sequence Matching Algorithm

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Interuniversity Department of Regional and Urban Studies and Planning, Politecnico di Torino, 10129 Torino, Italy
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Department of Control and Computer Engineering, Politecnico di Torino, 10129 Torino, Italy
3
Department of Electrical, Electronic, and Information Engineering “Guglielmo Marconi”, University of Bologna, 40126 Bologna, Italy
*
Author to whom correspondence should be addressed.
Electronics 2019, 8(11), 1342; https://doi.org/10.3390/electronics8111342
Received: 29 September 2019 / Revised: 30 October 2019 / Accepted: 12 November 2019 / Published: 14 November 2019
SpiNNaker is a neuromorphic globally asynchronous locally synchronous (GALS) multi-core architecture designed for simulating a spiking neural network (SNN) in real-time. Several studies have shown that neuromorphic platforms allow flexible and efficient simulations of SNN by exploiting the efficient communication infrastructure optimised for transmitting small packets across the many cores of the platform. However, the effectiveness of neuromorphic platforms in executing massively parallel general-purpose algorithms, while promising, is still to be explored. In this paper, we present an implementation of a parallel DNA sequence matching algorithm implemented by using the MPI programming paradigm ported to the SpiNNaker platform. In our implementation, all cores available in the board are configured for executing in parallel an optimised version of the Boyer-Moore (BM) algorithm. Exploiting this application, we benchmarked the SpiNNaker platform in terms of scalability and synchronisation latency. Experimental results indicate that the SpiNNaker parallel architecture allows a linear performance increase with the number of used cores and shows better scalability compared to a general-purpose multi-core computing platform. View Full-Text
Keywords: benchmarking neuromorphic HW; neuromorphic platform; spiNNaker; spinMPI; MPI for neuromorphic HW; Boyer-Moore; DNA matching algorithm benchmarking neuromorphic HW; neuromorphic platform; spiNNaker; spinMPI; MPI for neuromorphic HW; Boyer-Moore; DNA matching algorithm
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Urgese, G.; Barchi, F.; Parisi, E.; Forno, E.; Acquaviva, A.; Macii, E. Benchmarking a Many-Core Neuromorphic Platform With an MPI-Based DNA Sequence Matching Algorithm. Electronics 2019, 8, 1342.

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