Paper Info
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.
Year
DOI
Venue
2010
10.1007/978-3-642-21878-1_43
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
Keywords
Field
DocType
great difficulty,godson-t many-core processor,linked-list cell data structure,computational science,preliminary investigation,incremental optimizations,data locality,on-chip locality-aware parallel algorithm,data reuse,architecture study,divide-and-conquer algorithm adaptive,molecular dynamics simulation,excellent speedup
Data structure,Locality,Unconventional computing,Memory hierarchy,Computer science,Parallel algorithm,Parallel computing,Molecular dynamics,Multi-core processor,Speedup,Distributed computing
Conference
Volume
Issue
ISSN
6586 LNCS
null
16113349
Citations 
PageRank 
References 
0
0.34
7
Authors
7
Name
Order
Citations
PageRank
Liu Peng1716.17
Guangming Tan243648.90
Rajiv K. Kalia323935.66
Aiichiro Nakano427947.53
Priya Vashishta524337.69
FAN Dong-Rui622238.18
SUN Ning-Hui7126897.37