Preliminary investigation of accelerating molecular dynamics simulation on godson-T many-core processor

Liu Peng; Guangming Tan; Rajiv K. Kalia; Aiichiro Nakano; Priya Vashishta; Dongrui Fan; Ninghui Sun

doi:10.1007/978-3-642-21878-1_43

Preliminary investigation of accelerating molecular dynamics simulation on godson-T many-core processor

Liu Peng
, Guangming Tan
, Rajiv K. Kalia
, Aiichiro Nakano
, Priya Vashishta
, Dongrui Fan
, Ninghui Sun

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

2 Scopus citations

Abstract

Molecular dynamics (MD) simulation is widely used in computational science, however, its irregular memory-access pattern imposes great difficulty on performance optimization. This paper presents a joint application/architecture study to accelerate MD on an emerging unconventional computing platform-Godson-T many-core architecture. We propose three incremental optimizations: (1) a divide-and-conquer algorithm adaptive to on-chip memory; (2) a novel data-layout to re-organize linked-list cell data structures to improve data locality; (3) an on-chip locality-aware parallel algorithm to enhance data reuse. Experiments on an event-driven, cycle-accurate Godson-T simulator achieve excellent speedup of 62 on 64 cores. © 2011 Springer-Verlag Berlin Heidelberg.

Original language	English
Title of host publication	Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Pages	349-356
Number of pages	8
Volume	6586 LNCS
DOIs	https://doi.org/10.1007/978-3-642-21878-1_43
State	Published - Aug 19 2011
Externally published	Yes

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10.1007/978-3-642-21878-1_43

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Peng, L., Tan, G., Kalia, R. K., Nakano, A., Vashishta, P., Fan, D., & Sun, N. (2011). Preliminary investigation of accelerating molecular dynamics simulation on godson-T many-core processor. In Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 6586 LNCS, pp. 349-356) https://doi.org/10.1007/978-3-642-21878-1_43

@inproceedings{c6bd7f2f40f94c71b004720782b6a6d8,

title = "Preliminary investigation of accelerating molecular dynamics simulation on godson-T many-core processor",

abstract = "Molecular dynamics (MD) simulation is widely used in computational science, however, its irregular memory-access pattern imposes great difficulty on performance optimization. This paper presents a joint application/architecture study to accelerate MD on an emerging unconventional computing platform-Godson-T many-core architecture. We propose three incremental optimizations: (1) a divide-and-conquer algorithm adaptive to on-chip memory; (2) a novel data-layout to re-organize linked-list cell data structures to improve data locality; (3) an on-chip locality-aware parallel algorithm to enhance data reuse. Experiments on an event-driven, cycle-accurate Godson-T simulator achieve excellent speedup of 62 on 64 cores. {\textcopyright} 2011 Springer-Verlag Berlin Heidelberg.",

author = "Liu Peng and Guangming Tan and Kalia, \{Rajiv K.\} and Aiichiro Nakano and Priya Vashishta and Dongrui Fan and Ninghui Sun",

year = "2011",

month = aug,

day = "19",

doi = "10.1007/978-3-642-21878-1\_43",

language = "English",

isbn = "9783642218774",

volume = "6586 LNCS",

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booktitle = "Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)",

}

Peng, L, Tan, G, Kalia, RK, Nakano, A, Vashishta, P, Fan, D & Sun, N 2011, Preliminary investigation of accelerating molecular dynamics simulation on godson-T many-core processor. in Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). vol. 6586 LNCS, pp. 349-356. https://doi.org/10.1007/978-3-642-21878-1_43

Preliminary investigation of accelerating molecular dynamics simulation on godson-T many-core processor. / Peng, Liu; Tan, Guangming; Kalia, Rajiv K. et al.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 6586 LNCS 2011. p. 349-356.

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

TY - GEN

T1 - Preliminary investigation of accelerating molecular dynamics simulation on godson-T many-core processor

AU - Peng, Liu

AU - Tan, Guangming

AU - Kalia, Rajiv K.

AU - Nakano, Aiichiro

AU - Vashishta, Priya

AU - Fan, Dongrui

AU - Sun, Ninghui

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N2 - Molecular dynamics (MD) simulation is widely used in computational science, however, its irregular memory-access pattern imposes great difficulty on performance optimization. This paper presents a joint application/architecture study to accelerate MD on an emerging unconventional computing platform-Godson-T many-core architecture. We propose three incremental optimizations: (1) a divide-and-conquer algorithm adaptive to on-chip memory; (2) a novel data-layout to re-organize linked-list cell data structures to improve data locality; (3) an on-chip locality-aware parallel algorithm to enhance data reuse. Experiments on an event-driven, cycle-accurate Godson-T simulator achieve excellent speedup of 62 on 64 cores. © 2011 Springer-Verlag Berlin Heidelberg.

AB - Molecular dynamics (MD) simulation is widely used in computational science, however, its irregular memory-access pattern imposes great difficulty on performance optimization. This paper presents a joint application/architecture study to accelerate MD on an emerging unconventional computing platform-Godson-T many-core architecture. We propose three incremental optimizations: (1) a divide-and-conquer algorithm adaptive to on-chip memory; (2) a novel data-layout to re-organize linked-list cell data structures to improve data locality; (3) an on-chip locality-aware parallel algorithm to enhance data reuse. Experiments on an event-driven, cycle-accurate Godson-T simulator achieve excellent speedup of 62 on 64 cores. © 2011 Springer-Verlag Berlin Heidelberg.

UR - https://www.scopus.com/pages/publications/80051683478

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DO - 10.1007/978-3-642-21878-1_43

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VL - 6586 LNCS

SP - 349

EP - 356

BT - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

ER -

Preliminary investigation of accelerating molecular dynamics simulation on godson-T many-core processor

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