Paper Info
Title
Scalability study of molecular dynamics simulation on Godson-T many-core architecture
Abstract
Molecular dynamics (MD) simulation has broad applications, and an increasing amount of computing power is needed to satisfy the large scale of the real world simulation. The advent of the many-core paradigm brings unprecedented computing power, but it remains a great challenge to harvest the computing power due to MD's irregular memory-access pattern. To address this challenge, this paper presents a joint application/architecture study to enhance the scalability of MD on Godson-T-like many-core architecture. First, a preprocessing approach leveraging an adaptive divide-and-conquer framework is designed to exploit locality through memory hierarchy with software controlled memory. Then three incremental optimization strategies-a novel data-layout to improve data locality, an on-chip locality-aware parallel algorithm to enhance data reuse, and a pipelining algorithm to hide latency to shared memory-are proposed to enhance on-chip parallelism for Godson-T many-core processor. Experiments on Godson-T simulator exhibit strong-scaling parallel efficiency of 0.99 on 64 cores, which is confirmed by a field-programmable gate array emulator. Also the performance per watt of MD on Godson-T is much higher than MD on a 16-cores Intel core i7 symmetric multiprocessor (SMP) and 26 times higher than MD on an 8-core 64-thread Sun T2 processor. Detailed analysis shows that optimizations utilizing architectural features to maximize data locality and to enhance data reuse benefit scalability most. Furthermore, a hierarchical parallelization scheme is designed to map the MD algorithm to Godson-T many-core cluster and a simple performance model is derived, which suggests that the optimization scheme is likely to scale well toward exascale. Certain architectural features are found essential for these optimizations, which could guide future hardware developments.
Year
DOI
Venue
2013
10.1016/j.jpdc.2012.07.007
J. Parallel Distrib. Comput.
Keywords
Field
DocType
data reuse benefit scalability,godson-t many-core processor,computing power,godson-t simulator exhibit,many-core paradigm,many-core cluster,data locality,scalability study,md algorithm,data reuse,molecular dynamics simulation,godson-t-like many-core architecture,godson-t many-core architecture,molecular dynamics,scalability
Pipeline (computing),Locality,Computer architecture,Memory hierarchy,Parallel algorithm,Computer science,Parallel computing,Multiprocessing,Gate array,Performance per watt,Distributed computing,Scalability
Journal
Volume
Issue
ISSN
73
11
0743-7315
Citations 
PageRank 
References 
1
0.35
22
Authors
8
Name
Order
Citations
PageRank
Liu Peng1716.17
Guangming Tan243648.90
Rajiv K. Kalia323935.66
Aiichiro Nakano427947.53
Priya Vashishta524337.69
FAN Dong-Rui622238.18
Hao Zhang7245.81
Fenglong Song8669.09