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

Authors:
Liu Peng;Guangming Tan;Rajiv K. Kalia;Aiichiro Nakano;Priya Vashishta;Dongrui Fan;Ninghui Sun
Affiliations:
Collaboratory for Advanced Computing and Simulation, University of Southern California, Los Angeles, CA;Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China;Collaboratory for Advanced Computing and Simulation, University of Southern California, Los Angeles, CA;Collaboratory for Advanced Computing and Simulation, University of Southern California, Los Angeles, CA;Collaboratory for Advanced Computing and Simulation, University of Southern California, Los Angeles, CA;Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China;Institute of Computing Technology, Chinese Academy of Sciences, Beijing, China
Venue:
Euro-Par 2010 Proceedings of the 2010 conference on Parallel processing
Year:
2010

Citing 5
Cited 0

Scalable atomistic simulation algorithms for materials research

Proceedings of the 2001 ACM/IEEE conference on Supercomputing
A Quantitative Study of the On-Chip Network and Memory Hierarchy Design for Many-Core Processor

ICPADS '08 Proceedings of the 2008 14th IEEE International Conference on Parallel and Distributed Systems
A metascalable computing framework for large spatiotemporal-scale atomistic simulations

IPDPS '09 Proceedings of the 2009 IEEE International Symposium on Parallel&Distributed Processing
Study on Fine-Grained Synchronization in Many-Core Architecture

SNPD '09 Proceedings of the 2009 10th ACIS International Conference on Software Engineering, Artificial Intelligences, Networking and Parallel/Distributed Computing
A Low-Complexity Synchronization Based Cache Coherence Solution for Many Cores

CIT '09 Proceedings of the 2009 Ninth IEEE International Conference on Computer and Information Technology - Volume 02

Quantified Score

Hi-index	0.00

Visualization

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.