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Accelerating K-mer Frequency Counting with GPU and Non-Volatile Memory

Author
Cadenelli, N.; Polo, J.; Carrera, D.
Type of activity
Presentation of work at congresses
Name of edition
19th IEEE Intl Conference on High Performance Computing and Communications
Date of publication
2018
Presentation's date
2017-12-20
Book of congress proceedings
Proceedings - 2017 IEEE 19th Intl Conference on High Performance Computing and Communications, HPCC 2017, 2017 IEEE 15th Intl Conference on Smart City, SmartCity 2017 and 2017 IEEE 3rd Intl Conference on Data Science and Systems, DSS 2017
First page
434
Last page
441
DOI
https://doi.org/10.1109/HPCC-SmartCity-DSS.2017.57 Open in new window
Project funding
BSC Severo Ochoa Program 2
Computación de Altas Prestaciones VII
HiEST: Holistic Integration of Emerging Supercomputing Technologies
Models de Programacio i Entorns d'eXecució PARal.lels
Repository
http://hdl.handle.net/2117/127558 Open in new window
https://arxiv.org/pdf/1712.03254.pdf Open in new window
Abstract
The emergence of Next Generation Sequencing (NGS) platforms has increased the throughput of genomic sequencing and in turn the amount of data that needs to be processed, requiring highly efficient computation for its analysis. In this context, modern architectures including accelerators and non-volatile memory are essential to enable the mass exploitation of these bioinformatics workloads. This paper presents a redesign of the main component of a state-of-the-art reference-free method for varian...
Citation
Cadenelli, N.; Polo, J.; Carrera, D. Accelerating K-mer Frequency Counting with GPU and Non-Volatile Memory. A: IEEE International Performance Computing and Communications Conference. "Proceedings - 2017 IEEE 19th Intl Conference on High Performance Computing and Communications, HPCC 2017, 2017 IEEE 15th Intl Conference on Smart City, SmartCity 2017 and 2017 IEEE 3rd Intl Conference on Data Science and Systems, DSS 2017". 2018, p. 434-441.
Keywords
Acceleration, Bioinformatics, DNA sequences, Data communication systems, Efficient computation, Energy utilization, GPU, Genes, Genomic sequencing, Genomics, Graphics processing unit, K-mer, Modern architectures, NVM, Next-generation sequencing, Non-Volatile Memory, Non-volatile memory, Nonvolatile storage, Program processors, Reduction in energy consumption, Scale-up, Scale-up Acceleration, Scheduling algorithms, Smart city
Group of research
CAP - High Performace Computing Group
GRUP ISI - Instrumentation, Sensors and Interfaces Group

Participants

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