Avaliação de desempenho da paralelização do sequenciamento genético em GPU
Resumo
Como incrementar o desempenho de sistemas paralelos tem despertado muitas pesquisas para a construção de novos sistemas em grande escala. Em resposta a esse desafio, este artigo propõe uma avaliação de desempenho de aplicativos de pesquisa de DNA em CPU e GPU.
Palavras-chave:
Arquiteturas Dedicadas e Específicas (GPUs, FPGAs, e outras)
Referências
Baskett, W., Spencer, M., and Shyu, C. (2017). Efficient gpu-accelerated extraction of imperfect inverted repeats from dna sequences. In 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), pages 516–520.
Batzoglou, S. (2005). The many faces of sequence alignment. Briefings in bioinformatics, 6(1):6–22.
Edgar, R. C. and Batzoglou, S. (2006). Multiple sequence alignment. Current opinion in structural biology, 16(3):368–373.
Martínez, V., Serpa, M., Navaux, P. O. A., Padoin, E. L., and Panetta, J. (2018). Performance prediction of geophysics numerical kernels on accelerator architectures. In The Eighth International Conference on Smart Grids, Green Communications and IT Energy-aware Technologies (ENERGY 2018), pages 1–6, Nice - França.
Mount, D. W. (2004). Bioinformatics: sequence and genome analysis. 2nd, volume 692. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. xii.
Padoin, E. L., Pilla, L. L., Boito, F. Z., Kassick, R. V., Velho, P., and Navaux, P. O. A. (2013). Evaluating application performance and energy consumption on hybrid CPU+GPU architecture. Cluster Computing, 16(3):511–525. 10.1007/s10586-012-0219-6.
Pavan, P. J., Serpa, M., Carreno, E. D., Martínez, V., Padoin, E. L., Navaux, P., Panetta, J., and Méhaut, J.-F. (2018). Improving performance and energy efficiency of geophysics applications on gpu architectures. High Performance Computing: 5th Latin American Conference, CARLA 2018, Bucaramanga, pages 1–11.
Rastogi, P. and Guddeti, R. (2014). Gpu accelerated inexact matching for multiple patterns in dna sequences. In 2014 International Conference on Advances in Computing, Communications and Informatics (ICACCI), pages 163–167.
Samsi, S., Helfer, B., Kepner, J., Reuther, A., and Ricke, D. O. (2017). A linear algebra approach to fast dna mixture analysis using gpus. In 2017 IEEE High Performance Extreme Computing Conference (HPEC), pages 1–6.
Batzoglou, S. (2005). The many faces of sequence alignment. Briefings in bioinformatics, 6(1):6–22.
Edgar, R. C. and Batzoglou, S. (2006). Multiple sequence alignment. Current opinion in structural biology, 16(3):368–373.
Martínez, V., Serpa, M., Navaux, P. O. A., Padoin, E. L., and Panetta, J. (2018). Performance prediction of geophysics numerical kernels on accelerator architectures. In The Eighth International Conference on Smart Grids, Green Communications and IT Energy-aware Technologies (ENERGY 2018), pages 1–6, Nice - França.
Mount, D. W. (2004). Bioinformatics: sequence and genome analysis. 2nd, volume 692. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press. xii.
Padoin, E. L., Pilla, L. L., Boito, F. Z., Kassick, R. V., Velho, P., and Navaux, P. O. A. (2013). Evaluating application performance and energy consumption on hybrid CPU+GPU architecture. Cluster Computing, 16(3):511–525. 10.1007/s10586-012-0219-6.
Pavan, P. J., Serpa, M., Carreno, E. D., Martínez, V., Padoin, E. L., Navaux, P., Panetta, J., and Méhaut, J.-F. (2018). Improving performance and energy efficiency of geophysics applications on gpu architectures. High Performance Computing: 5th Latin American Conference, CARLA 2018, Bucaramanga, pages 1–11.
Rastogi, P. and Guddeti, R. (2014). Gpu accelerated inexact matching for multiple patterns in dna sequences. In 2014 International Conference on Advances in Computing, Communications and Informatics (ICACCI), pages 163–167.
Samsi, S., Helfer, B., Kepner, J., Reuther, A., and Ricke, D. O. (2017). A linear algebra approach to fast dna mixture analysis using gpus. In 2017 IEEE High Performance Extreme Computing Conference (HPEC), pages 1–6.
Publicado
15/04/2020
Como Citar
KÜNAS, Cristiano Alex; SCHULZE, Vinicios Dutra; PADOIN, Edson Luiz.
Avaliação de desempenho da paralelização do sequenciamento genético em GPU. In: ESCOLA REGIONAL DE ALTO DESEMPENHO DA REGIÃO SUL (ERAD-RS), 20. , 2020, Santa Maria.
Anais [...].
Porto Alegre: Sociedade Brasileira de Computação,
2020
.
p. 13-16.
ISSN 2595-4164.
DOI: https://doi.org/10.5753/eradrs.2020.10744.
