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Xian-he Sun Wenyu Qu Ivan Stojmenovic
Wanlei Zhou Zhiyang Li Hua Guo
Geyong Min Tingting Yang Yulei Wu
Lei Liu (Eds.)

Algorithms and
LNCS 8630

Architectures
for Parallel Processing
14th International Conference, ICA3PP 2014
Dalian, China, August 24–27, 2014
Proceedings, Part I

123
Lecture Notes in Computer Science 8630
Commenced Publication in 1973
Founding and Former Series Editors:
Gerhard Goos, Juris Hartmanis, and Jan van Leeuwen

Editorial Board
David Hutchison
Lancaster University, UK
Takeo Kanade
Carnegie Mellon University, Pittsburgh, PA, USA
Josef Kittler
University of Surrey, Guildford, UK
Jon M. Kleinberg
Cornell University, Ithaca, NY, USA
Alfred Kobsa
University of California, Irvine, CA, USA
Friedemann Mattern
ETH Zurich, Switzerland
John C. Mitchell
Stanford University, CA, USA
Moni Naor
Weizmann Institute of Science, Rehovot, Israel
Oscar Nierstrasz
University of Bern, Switzerland
C. Pandu Rangan
Indian Institute of Technology, Madras, India
Bernhard Steffen
TU Dortmund University, Germany
Demetri Terzopoulos
University of California, Los Angeles, CA, USA
Doug Tygar
University of California, Berkeley, CA, USA
Gerhard Weikum
Max Planck Institute for Informatics, Saarbruecken, Germany
Xian-he Sun Wenyu Qu Ivan Stojmenovic
Wanlei Zhou Zhiyang Li Hua Guo
Geyong Min Tingting Yang Yulei Wu
Lei Liu (Eds.)

Algorithms and Architectures


for Parallel Processing
14th International Conference, ICA3PP 2014
Dalian, China, August 24-27, 2014
Proceedings, Part I

13
Volume Editors
Xian-he Sun
Illinois Institute of Technology, Chicago, IL, USA, e-mail: sun@iit.edu
Wenyu Qu
Dalian Maritime University, China, e-mail: wenyu@dlmu.edu.cn
Ivan Stojmenovic
University of Ottawa, ON, Canada, e-mail: ivan@site.ottawa.ca
Wanlei Zhou
Deakin University, Burwood, VIC, Australia, e-mail: wanlei.zhou@deakin.edu.au
Zhiyang Li
Dalian Maritime University, China, e-mail: lizy0205@gmail.com
Hua Guo
BeiHang University, Beijing, China, e-mail: hguo@buaa.edu.cn
Geyong Min
University of Bradford, UK, e-mail: g.min@brad.ac.uk
Tingting Yang
Dalian Maritime University, China, e-mail: yangtingting820523@163.com
Yulei Wu
Chinese Academy of Sciences, Beijing, China, e-mail: yulei.frank.wu@gmail.com
Lei Liu
Shandong University, Jinan City, China, e-mail: l.liu@sdu.edu.cn

ISSN 0302-9743 e-ISSN 1611-3349


ISBN 978-3-319-11196-4 e-ISBN 978-3-319-11197-1
DOI 10.1007/978-3-319-11197-1
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Preface

Welcome to the proceedings of the 14th International Conference on Algorithms


and Architectures for Parallel Processing (ICA3PP 2014) held in Dalian, China.
ICA3PP 2014 is the 14th in this series of conferences started in 1995 that are
devoted to algorithms and architectures for parallel processing. As applications
of computing systems have permeated in every aspect of daily life, the power
of computing system has become increasingly critical. This conference provides
a forum for academics and practitioners from countries around the world to
exchange ideas for improving the efficiency, performance, reliability, security,
and interoperability of computing systems and applications.
It is our great honor to introduce the program for the conference. Thanks to
the Program Committee’s hard work, we were able to finalize the technical pro-
gram. In the selection process, each paper was assigned to at least 4 PC members
as reviewers. The authors and those PC members from the same institution were
separated in the reviewing process to avoid conflicts of interests. We received 285
submissions from all over the world. The large number of submissions indicated
continued excitement in the field worldwide. The manuscripts have been ranked
according to their original contribution, quality, presentation, and relevance to
the themes of the conference. In the end, 70 (24.56%) papers were accepted as
the main conference papers and inclusion in the conference.
ICA3PP 2014 obtained the support of many people and organizations as well
as the general chairs whose main responsibility was various tasks carried out by
other willing and talented volunteers. We want to express our appreciation to
Professor Xian-He Sun for accepting our invitation to be the keynote/invited
speaker.
We would like to give our special thanks to the program chairs of the confer-
ence for their hard and excellent work on organizing the Program Committee,
outstanding review process to select high-quality papers, and making an excellent
conference program. We are grateful to all workshop organizers for their profes-
sional expertise and excellence in organizing the attractive workshops/symposia,
and other committee chairs, advisory members and PC members for their great
support. We appreciate all authors who submitted their high-quality papers to
the main conference and workshops/symposia.
We thank all of you for participating in this year’s ICA3PP 2014 conference,
and hope you find this conference stimulating and interesting.

July 2014 Ivan Stojmenovic


Wanlei Zhou
Organization

General Chairs
Ivan Stojmenovic Ottawa University, Canada
Wanlei Zhou Deakin University, Australia

Program Chairs
Xianhe Sun Illinois Institute of Technology, USA
Wenyu Qu Dalian Maritime University, China

Publicity Chairs
Jaime Lloret Mauri Polytechnic University of Valencia, Spain
Al-Sakib Khan Pathan International Islamic University Malaysia,
Malaysia

Publication Chair
Yang Xiang Deakin University, Australia

Steering Committee Chairs


Andrzej Goscinski Deakin University, Australia
Yi Pan Georgia State University, USA
Yang Xiang Deakin University, Australia

Workshop Chairs
Mianxiong Dong National Institute of Information and
Communications Technology, Japan
Lei Liu Shandong University, China

Local Organizing Chair


Zhiyang Li Dalian Maritime University, China
VIII Organization

Registration Chair
Weijiang Liu Dalian Maritime University, China

Finance Chair
Zhaobin Liu Dalian Maritime University, China

Web Chairs
Yang Shang Dalian Maritime University, China
Tingting Wang Dalian Maritime University, China

Program Committee Members


Zafeirios Papazachos Queen’s University of Belfast, UK
Paolo Trunfio University of Calabria, Italy
Chao-Tung Yang Tunghai University, Taiwan
Yong Zhao University of Electronic Science and Technology
of China, China
Xingquan (Hill) Zhu Florida Atlantic University, USA
Giandomenico Spezzano ICAR-CNR, Italy
Yasuhiko Takenaga The University of Electro-Communications,
Japan
Sushil Prasad University of Georgia, USA
Tansel Ozyer TOBB University of Economics and
Technology, Turkey
Deng Pan Florida International University, USA
Apostolos Papadopoulos Aristotle University of Thessaloniki, Greece
Eric Pardede La Trobe University, Australia
Karampelas Panagiotis Hellenic American University, Greece
Paul Lu University of Alberta, Canada
Kamesh Madduri Penn State University, USA
Ching-Hsien Hsu Chung Hua University, Taiwan
Muhammad Khurram Khan King Saud University, Saudi Arabia
Morihiro Kuga Kumamoto University, Japan
Weiwei Fang Beijing Jiaotong University, China
Franco Frattolillo Università del Sannio, Italy
Longxiang Gao Deakin University, Australia
Javier Garcı́a University Carlos III, Spain
Michael Glass University of Erlangen-Nuremberg, Germany
David E. Singh Universidad Carlos III de Madrid, Spain
Marion Oswald TU Wien, Austria
Rajkumar Buyya The University of Melbourne, Australia
Organization IX

Yue-Shan Chang National Taipei University, Taiwan


Christian Engelman Oak Ridge National Lab, USA
Alessio Bechini University of Pisa, Italy
Hideharu Amano Keio University, Japan
Wei Wei Xi’an University of Technology, China
Toshihiro Yamauchi Okayama University, Japan
Bo Yang University of Electronic Science and Technology
of China, China
Laurence T. Yang St. Francis Xavier University, Canada
Sherali Zeadally University of the District of Columbia, USA
Sotirios G. Ziavras NJIT, USA
Gennaro Della Vecchia Gennaro Della Vecchia - ICAR-CNR, Italy
Olivier Terzo Istituto Superiore Mario Boella, Italy
Hiroyuki Tomiyama Ritsumeikan University, Japan
Tomoaki Tsumura Nagoya Institute of Technology, Japan
Luis Javier Garcı́a Villalba Universidad Complutense de Madrid (UCM),
Spain
Gaocai Wang Guangxi University, China
Chen Wang CSIRO ICT Centre, Australia
Martine Wedlake IBM, USA
Wei Xue Tsinghua University, China
Edwin Sha University of Texas at Dallas, USA
Sachin Shetty Tennessee State University, USA
Ching-Lung Su National Yunlin University of Science and
Technology, Taiwan
Anthony Sulistio High Performance Computing Center Stuttgart
(HLRS), Germany
Magdalena Szmajduch Cracow University of Technology (CDN
Partner Cracow), Poland
Jie Tao University of Karlsruhe (Karlsruhe Institute of
Technology), Germany
Dana Petcu West University of Timisoara, Romania
Florin Pop University Politehnica of Bucharest, Romania
Rajeev Raje Indiana University-Purdue University
Indianapolis, USA
Francoise Sailhan CNAM, France
Subhash Saini NASA, USA
Erich Schikuta University of Vienna, Austria
Alba Amato Second University of Naples, Italy
Cosimo Anglano Università del Piemonte Orientale, Italy
Ladjel Bellatreche ENSMA, France
Ateet Bhalla Oriental Institute of Science and Technology,
India
X Organization

Surendra Byna Lawrence Berkeley National Lab, USA


Aleksander Byrski AGH University of Science and Technology,
Poland
Juan M. Marin University of Murcia, Spain
Francesco Moscato Second University of Naples, Italy
Hirotaka Ono Kyushu University, Japan
Fabrizio Petrini IBM Research, USA
Stefano Marrone Second University of Naples, Italy
Alejandro Masrur Technology University of Munich, Germany
Susumu Matsumae Saga University, Japan
Wei Lu Keene University, USA
Amit Majumdar San Diego Supercomputer Center, USA
Tomas Margalef Universitat Autonoma de Barcelona, Spain
Che-Rung Lee National Tsing Hua University, Taiwan
Keqin Li State University of New York at New Paltz,
USA
Mauro Iacono Second University of Naples, Italy
Shadi Ibrahim Inria, France
Helen Karatza Aristotle University of Thessaloniki, Greece
Soo-Kyun Kim PaiChai University, Korea
Edmund Lai Massey University, New Zealand
Karl Fuerlinger Ludwig-Maximilians-University Munich,
Germany
Jose Daniel Garcia University Carlos III of Madrid, Spain
Harald Gjermundrod University of Nicosia, Cyprus
Houcine Hassan Universidad Politecnica de Valencia, Spain
Raphaël Couturier University of Franche-Comté, France
Eugen Dedu University of Franche-Comté, France
Ciprian Dobre University Politehnica of Bucharest, Romania
Massimo Cafaro University of Salento, Italy
Ruay-Shiung Chang National Dong Hwa University, Taiwan
Dan Chen University of Geosciences, China
Zizhong (Jeffrey) Chen University of California at Riverside, USA
Jing Chen National Cheng Kung University, Taiwan
Carmela Comito University of Calabria, Italy
Yujie Xu Dalian Maritime University, China
Natalija Vlajic York University, Canada
Kenji Saito Keio University, Japan
Thomas Rauber University of Bayreuth, Germany
Pilar Herero Universidad Politecnica de Madrid, Spain
Tania Cerquitelli Politecnico di Torino, Italy
Tzung-Shi Chen National University of Tainan, Taiwan
David Expósito University Carlos III, Spain
Peter Strazdins The Australian National University, Australia
Uwe Tangen Ruhr-Universitaet Bochum, Germany
Organization XI

Luca Tasquier Second University of Naples, Italy


Rafael Santos National Institute for Space Research, Brazil
George Bosilca University of Tennessee, USA
Esmond Ng Lawrence Berkeley National Lab, USA
Laurent Lefevre Laurent Lefevre, Inria, University of Lyon,
France
Giuseppina Cretella Second University of Naples, Italy
Gregoire Danoy University of Luxembourg, Luxembourg
Bernabe Dorronsoro University of Lille 1, France
Massimo Ficco Second University of Naples, Italy
Jorge Bernal Bernabe University of Murcia, Spain
Keynote
C-AMAT: Concurrent Data Access Model for
the Big Data Era

Xian-He Sun

Illinois Institute of Technology, Chicago, USA


sun@iit.edu

Abstract. Scalable data management for big data applications is a chal-


lenging task. It puts even more pressure on the lasting memory-wall prob-
lem, which makes data access the prominent performance bottleneck for
high-end computing. High-end computing is known for its massively par-
allel architectures. A natural way to improve memory performance is to
increase and utilize memory concurrency to a level commensurate with
that of high-end computing. We argue that substantial memory concur-
rency exists at each layer of current memory systems, but it has not been
fully utilized. In this talk we reevaluate memory systems and introduce
the novel C-AMAT model for system design analysis of concurrent data
accesses. C-AMAT is a paradigm shift to support sustained data access-
ing from a data-centric view. The power of C-AMAT is that it has opened
new directions to reduce data access delay. In an ideal parallel memory
system, the system will explicitly express and utilize parallel data ac-
cesses. This awareness is largely missing from current memory systems.
We will review the concurrency available in modern memory systems,
present the concept of C-AMAT, and discuss the considerations and pos-
sibility of optimizing parallel data access for big data applications. We
will also present some of our recent results which quantize and utilize
parallel I/O following the parallel memory concept.

Keywords: Big Data; Parallel memory system; Data access model

1 Bio-Short version
Dr. Xian-He Sun is a Distinguished Professor of Computer Science and the chair-
man of the Department of Computer Science at the Illinois Institute of Technol-
ogy (IIT). He is the director of the Scalable Computing Software laboratory at
IIT and a guest faculty in the Mathematics and Computer Science Division at
the Argonne National Laboratory. Before joining IIT, he worked at DoE Ames
National Laboratory, at ICASE, NASA Langley Research Center, at Louisiana
State University, Baton Rouge, and was an ASEE fellow at Navy Research Lab-
oratories. Dr. Sun is an IEEE fellow and is known for his memory-bounded
speedup model, also called Sun-Nis Law, for scalable computing. His research
XVI X.-H. Sun

interests include parallel and distributed processing, memory and I/O systems,
software systems for big data applications, and performance evaluation. He has
over 200 publications and 4 patents in these areas. He is a former IEEE CS
distinguished speaker and former vice chair of the IEEE Technical Committee
on Scalable Computing, and is serving and served on the editorial board of most
of the leading professional journals in the field of parallel processing. More in-
formation about Dr. Sun can be found at his web site www.cs.iit.edu/~sun/.
Table of Contents – Part I

Porting the Princeton Ocean Model to GPUs . . . . . . . . . . . . . . . . . . . . . . . . 1


Shizhen Xu, Xiaomeng Huang, Yan Zhang, Yong Hu,
Haohuan Fu, and Guangwen Yang
Web Service Recommendation via Exploiting Temporal QoS
Information . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
Chao Zhou, Wancai Zhang, and Bo Li
Optimizing and Scaling HPCG on Tianhe-2: Early Experience . . . . . . . . . 28
Xianyi Zhang, Chao Yang, Fangfang Liu, Yiqun Liu, and Yutong Lu
Understanding the SIMD Efficiency of Graph Traversal on GPU . . . . . . . 42
Yichao Cheng, Hong An, Zhitao Chen, Feng Li, Zhaohui Wang,
Xia Jiang, and Yi Peng
A GPU Implementation of Clipping-Free Halftoning Using the Direct
Binary Search . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Hiroaki Koge, Yasuaki Ito, and Koji Nakano
A Reliable and Secure GPU-Assisted File System . . . . . . . . . . . . . . . . . . . . 71
Shang-Chieh Lin, Yu-Cheng Liao, and Yarsun Hsu
Efficient Detection of Cloned Attacks for Large-Scale RFID Systems . . . . 85
Xiulong Liu, Heng Qi, Keqiu Li, Jie Wu, Weilian Xue,
Geyong Min, and Bin Xiao
Probability Based Algorithms for Guaranteeing the Stability of
Rechargeable Wireless Sensor Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Yiyi Gao, Ce Yu, Jian Xiao, Jizhou Sun, Guiyuan Jiang, and
Hui Wang
PTAS for Minimum k -Path Connected Vertex Cover
in Growth-Bounded Graphs . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
Yan Chu, Jianxi Fan, Wenjun Liu, and Cheng-Kuan Lin
A Simple and Effective Long Duration Contact-Based Utility Metric
for Mobile Opportunistic Networking . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
Chyouhwa Chen, Wei-Chung Teng, and Yu-Ren Wu
Adaptive QoS and Security for Video Transmission over Wireless
Networks: A Cognitive-Based Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 138
Walid Abdallah, Suk kyu Lee, Hwagnam Kim, and
Noureddine Boudriga
Virtual Network Mapping Algorithm in Wireless Data Center
Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 152
Juan Luo, Wenfeng He, Keqin Li, and Yaling Guo
XVIII Table of Contents – Part I

A Weighted Centroid Based Tracking System in Wireless Sensor


Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 166
Hongyang Liu, Qianqian Ren, Longjiang Guo, Jinbao Li, Hui Xu,
Hu Jin, Nan Wang, and Chengjie Song

A Smartphone Location Independent Activity Recognition Method


Based on the Angle Feature . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 179
Changhai Wang, Jianzhong Zhang, Meng Li, Yuan Yuan, and
Yuwei Xu

Reliable and Energy Efficient Routing Algorithm for WirelessHART . . . . 192


Qun Zhang, Feng Li, Lei Ju, Zhiping Jia, and Zhaopeng Zhang

A DSCP-Based Method of QoS Class Mapping between WLAN and


EPS Network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204
Yao Liu, Gang Lu, Wei Zhang, Fengling Cai, and Qian Kong

HostoSink: A Collaborative Scheduling in Heterogeneous


Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 214
Xiaofei Liao, Xiaobao Xiang, Hai Jin, Wei Zhang, and Feng Lu

Load Balancing in MapReduce Based on Data Locality . . . . . . . . . . . . . . . 229


Yi Chen, Zhaobin Liu, Tingting Wang, and Lu Wang

RD-PCA: A Traffic Condition Data Imputation Method Based on


Robust Distance . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 242
XueJin Wan, Yong Du, and Jiong Wang

Network-Aware Re-Scheduling: Towards Improving Network


Performance of Virtual Machines in a Data Center . . . . . . . . . . . . . . . . . . . 255
Gangyi Luo, Zhuzhong Qian, Mianxiong Dong, Kaoru Ota, and
Sanglu Lu

A Novel Petri-Net Based Resource Constrained Multi-project


Scheduling Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 270
Wenbin Hu and Huan Wang

Interconnection Network Reconstruction for Fault-Tolerance of


Torus-Connected VLSI Array . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 285
Longting Zhu, Jigang Wu, Guiyuan Jiang, and Jizhou Sun

An Ant Colony Optimization Algorithm for Virtual Network


Embedding . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299
Wenjie Cao, Hua Wang, and Lei Liu

Temperature-Aware Scheduling Based on Dynamic Time-Slice


Scaling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 310
Gangyong Jia, Youwei Yuan, Jian Wan, Congfeng Jiang,
Xi Li, and Dong Dai
Table of Contents – Part I XIX

An Improved Energy-Efficient Scheduling for Precedence Constrained


Tasks in Multiprocessor Clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 323
Xin Li, Yanheng Zhao, Yibin Li, Lei Ju, and Zhiping Jia

Hierarchical Eventual Leader Election for Dynamic Systems . . . . . . . . . . . 338


Huaguan Li, Weigang Wu, and Yu Zhou

Efficient Resource Provisioning for Mobile Media Traffic Management


in a Cloud Computing Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
Mohammad Mehedi Hassan, Muhammad Al-Qurishi,
Biao Song, and Atif Alamri

A Community Cloud for a Real-Time Financial Application -


Requirements, Architecture and Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . 364
Marcelo Dutra Ös and Graça Bressan

Strategies for Evacuating from an Affected Area with One or Two


Groups . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 378
Qi Wei, Yuan Shi, Bo Jiang, and Lijuan Wang

A Novel Adaptive Web Service Selection Algorithm Based on Ant


Colony Optimization for Dynamic Web Service Composition . . . . . . . . . . . 391
Denghui Wang, Hao Huang, and Changsheng Xie

An Optimization VM Deployment for Maximizing Energy Utility in


Cloud Environment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 400
Jinhai Wang, Chuanhe Huang, Qin Liu, Kai He, Jing Wang,
Peng Li, and Xiaohua Jia

Performance Evaluation of Light-Weighted Virtualization for PaaS in


Clouds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 415
Xuehai Tang, Zhang Zhang, Min Wang, Yifang Wang,
Qingqing Feng, and Jizhong Han

An Access Control Scheme with Direct Cloud-Aided Attribute


Revocation Using Version Key . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 429
Jiaoli Shi, Chuanhe Huang, Jing Wang, Kai He, and Jinhai Wang

Full and Live Virtual Machine Migration over XIA . . . . . . . . . . . . . . . . . . . 443


Dalu Zhang, Xiang Jin, Dejiang Zhou, Jianpeng Wang, and Jiaqi Zhu

A Near-Exact Defragmentation Scheme to Improve Restore Performance


for Cloud Backup Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 457
Rongyu Lai, Yu Hua, Dan Feng, Wen Xia, Min Fu, and Yifan Yang

A Music Recommendation Method for Large-Scale Music Library on a


Heterogeneous Platform . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 472
Yao Zheng, Limin Xiao, Wenqi Tang, and Li Ruan
XX Table of Contents – Part I

GPU-Accelerated Verification of the Collatz Conjecture . . . . . . . . . . . . . . . 483


Takumi Honda, Yasuaki Ito, and Koji Nakano

Reducing the Interconnection Length for 3D Fault-Tolerant Processor


Arrays . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 497
Guiyuan Jiang, Jigang Wu, Jizhou Sun, and Longting Zhu

Feature Evaluation for Early Stage Internet Traffic Identification . . . . . . . 511


Lizhi Peng, Hongli Zhang, Bo Yang, and Yuehui Chen

Hyper-Star Graphs: Some Topological Properties and an Optimal


Neighbourhood Broadcasting Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . 526
F. Zhang, K. Qiu, and J.S. Kim

Customized Network-on-Chip for Message Reduction . . . . . . . . . . . . . . . . . 535


Hongwei Wang, Siyu Lu, Youhui Zhang, Guangwen Yang, and
Weimin Zheng

Athena: A Fault-Tolerant, Efficient and Applicable Routing Mechanism


for Data Centers . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 549
Lijun Lyu, Junjie Xie, Yuhui Deng, and Yongtao Zhou

Performance-Aware Data Placement in Hybrid Parallel File Systems . . . . 563


Shuibing He, Xian-He Sun, Bo Feng, and Kun Feng

Security Analysis and Protection Based on Smali Injection for Android


Applications . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 577
Junfeng Xu, Shoupeng Li, and Tao Zhang

The 1st International Workshop on Emerging Topics


in Wireless and Mobile Computing (ETWMC 2014)
A Novel Key Management Scheme in VANETs . . . . . . . . . . . . . . . . . . . . . . 587
Guihua Duan, Yun Xiao, Rui Ju, and Hong Song

Design and Implementation of Network Hard Disk . . . . . . . . . . . . . . . . . . . 596


Hong Song, Jialong Xu, and Xiaoqiang Cai

Combining Supervised and Unsupervised Learning for Automatic


Attack Signature Generation System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 607
Lili Yang, Jie Wang, and Ping Zhong

The Study on the Increasing Strategy of Detecting Moving Target in


Wireless Sensor Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 619
Jialong Xu, Zhigang Chen, Anfeng Liu, and Hong Song

A CRC-Based Lightweight Authentication Protocol for EPCglobal


Class-1 Gen-2 Tags . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 632
Zhicai Shi, Yongxiang Xia, Yu Zhang, Yihan Wang, and Jian Dai
Table of Contents – Part I XXI

Test Case Prioritization Based on Genetic Algorithm and Test-Points


Coverage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 644
Weixiang Zhang, Bo Wei, and Huisen Du

SAEP: Simulated Annealing Based Ensemble Projecting Method for


Solving Conditional Nonlinear Optimal Perturbation . . . . . . . . . . . . . . . . . 655
Shicheng Wen, Shijin Yuan, Bin Mu, Hongyu Li, and Lei Chen

Converting Ptolemy II Models to SpaceEx for Applied Verification . . . . . 669


Shiwei Ran, Jinzhi Lin, Ying Wu, Jianzhong Zhang, and Yuwei Xu

Research on Interest Searching Mechanism in SNS Learning


Community . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 684
Renfeng Wang, Junpei Liu, Haining Sun, and Zhihuai Li

The 5th International Workshop on Intelligent


Communication Networks (IntelNet 2014)
Improving the Frequency Adaptive Capability of Hybrid Immune
Detector Maturation Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 691
Jungan Chen, ShaoZhong Zhang, and Danjiang Chen

Cluster-Based Time Synchronization Protocol for Wireless Sensor


Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 700
Jian Zhang, Shiping Lin, and Dandan Liu

A Fast CABAC Algorithm for Transform Coefficients in HEVC . . . . . . . . 712


Nana Shan, Wei Zhou, and Zhemin Duan

A Improved PageRank Algorithm Based on Page Link Weight . . . . . . . . . 720


Xinsheng Wang, Jianchu Ma, Kaiyuan Bi, and Zhihuai Li

Computation Offloading Management for Vehicular Ad Hoc Cloud . . . . . 728


Bo Li, Yijian Pei, Hao Wu, Zhi Liu, and Haixia Liu

An Approach to Model Complex Big Data Driven Cyber Physical


Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 740
Lichen Zhang

The 5th International Workshop on Wireless


Networks and Multimedia (WNM 2014)
Reliable Transmission with Multipath and Redundancy for Wireless
Mesh Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 755
Wenze Shi, Takeshi Ikenaga, Daiki Nobayashi, Xinchun Yin, and
Yebin Xu
XXII Table of Contents – Part I

Community Roamer: A Social-Based Routing Algorithm in


Opportunistic Mobile Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 768
Tieying Zhu, Cheng Wang, and Dandan Liu

A Self-adaptive Reliable Packet Transmission Scheme for Wireless


Mesh Networks . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 781
Wenze Shi, Takeshi Ikenaga, Daiki Nobayashi, Xinchun Yin, and
Hui Xu

Distributed Efficient Node Localization in Wireless Sensor Networks


Using the Backtracking Search Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . 794
Alan Oliveira de Sá, Nadia Nedjah, and Luiza de Macedo Mourelle

User Specific QoS and Its Application in Resources Scheduling for


Wireless System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 809
Chao He and Richard D. Gitlin

A Distributed Storage Model for Sensor Networks . . . . . . . . . . . . . . . . . . . . 822


Lee Luan Ling

Relation between Irregular Sampling and Estimated Covariance for


Closed-Loop Tracking Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 836
Bei-bei Miao and Xue-bo Jin

Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 845


Table of Contents – Part II

Parallel Data Processing in Dynamic Hybrid Computing Environment


Using MapReduce . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
Bing Tang, Haiwu He, and Gilles Fedak

Fast Scalable k-means++ Algorithm with MapReduce . . . . . . . . . . . . . . . . 15


Yujie Xu, Wenyu Qu, Zhiyang Li, Changqing Ji, Yuanyuan Li, and
Yinan Wu

Acceleration of Solving Non-Equilibrium Ionization via Tracer Particles


and MapReduce on Eulerian Mesh . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
Jian Xiao, Xingyu Xu, Jizhou Sun, Xin Zhou, and Li Ji

A Continuous Virtual Vector-Based Algorithm for Measuring


Cardinality Distribution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
Xuefei Zhou, Weijiang Liu, Zhiyang Li, and Wenwen Gao

Hmfs: Efficient Support of Small Files Processing over HDFS . . . . . . . . . . 54


Cairong Yan, Tie Li, Yongfeng Huang, and Yanglan Gan

Utilizing Multiple Xeon Phi Coprocessors on One Compute Node . . . . . . 68


Xinnan Dong, Jun Chai, Jing Yang, Mei Wen, Nan Wu, Xing Cai,
Chunyuan Zhang, and Zhaoyun Chen

HPSO: Prefetching Based Scheduling to Improve Data Locality for


MapReduce Clusters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
Mingming Sun, Hang Zhuang, Xuehai Zhou, Kun Lu, and
Changlong Li

Service Scheduling Algorithm in Vehicle Embedded Middleware . . . . . . . . 96


Juan Luo, Xin Jin, and Feng Wu

Similar Samples Cleaning in Speculative Multithreading . . . . . . . . . . . . . . 108


Yuxiang Li, Yinliang Zhao, and Bin Liu

Equi-join for Multiple Datasets Based on Time Cost Evaluation


Model . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 122
Hong Zhu, Libo Xia, Mieyi Xie, and Ke Yan

Identifying File Similarity in Large Data Sets by Modulo File Length . . . 136
Yongtao Zhou, Yuhui Deng, Xiaoguang Chen, and Junjie Xie

Conpy: Concolic Execution Engine for Python Applications . . . . . . . . . . . 150


Ting Chen, Xiao-song Zhang, Rui-dong Chen, Bo Yang, and
Yang Bai
XXIV Table of Contents – Part II

A Platform for Stock Market Simulation with Distributed Agent-Based


Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 164
Chunyu Wang, Ce Yu, Hutong Wu, Xiang Chen, Yuelei Li, and
Xiaotao Zhang

C2CU : A CUDA C Program Generator for Bulk Execution of a


Sequential Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 178
Daisuke Takafuji, Koji Nakano, and Yasuaki Ito

Dynamically Spawning Speculative Threads to Improve Speculative


Path Execution . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 192
Meirong Li, Yinliang Zhao, and You Tao

A Parallel Algorithm of Kirchhoff Pre-stack Depth Migration Based on


GPU . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 207
Yida Wang, Chao Li, Yang Tian, Haihua Yan, Changhai Zhao, and
Jianlei Zhang

An Algorithm to Embed a Family of Node-Disjoint 3D Meshes into


Locally Twisted Cubes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 219
Lantao You and Yuejuan Han

GPU Acceleration of Finding Maximum Eigenvalue of Positive


Matrices . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 231
Ning Tian, Longjiang Guo, Chunyu Ai, Meirui Ren, and Jinbao Li

Improving Speculation Accuracy with Inter-thread Fetching Value


Prediction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 245
Fan Xu, Li Shen, Zhiying Wang, Hui Guo, Bo Su, and Wei Chen

Towards Efficient Distributed SPARQL Queries on Linked Data . . . . . . . 259


Xuejin Li, Zhendong Niu, and Chunxia Zhang

MRFS: A Distributed Files System with Geo-replicated Metadata . . . . . . 273


Jiongyu Yu, Weigang Wu, Di Yang, and Ning Huang

An Advanced Data Redistribution Approach to Accelerate the


Scale-Down Process of RAID-6 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 286
Congjin Du, Chentao Wu, and Jie Li

Thread Mapping and Parallel Optimization for MIC Heterogeneous


Parallel Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 300
Tao Ju, Zhengdong Zhu, Yinfeng Wang, Liang Li, and Xiaoshe Dong
Table of Contents – Part II XXV

Efficient Storage Support for Real-Time Near-Duplicate Video


Retrieval . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 312
Zhenhua Nie, Yu Hua, Dan Feng, Qiuyu Li, and Yuanyuan Sun

Repairing Multiple Data Losses by Parallel Max-min Trees Based on


Regenerating Codes in Distributed Storage Systems . . . . . . . . . . . . . . . . . . 325
Pengfei You, Yuxing Peng, Zhen Huang, and Changjian Wang

Exploiting Content Locality to Improve the Performance and Reliability


of Phase Change Memory . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 339
Suzhen Wu, Zaifa Xi, Bo Mao, and Hong Jiang

Computing, Communication and Control


Technologies in Intelligent Transportation System
(3C in ITS 2014)
Application of Support Vector Machine in the Decision-Making of
Maneuvering . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 352
Zhuang Qi, Zheng Chang, Hanbang Song, and Xinyu Zhang

Mobile Phone Data Reveal the Spatiotemporal Regularity of Human


Mobility . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 359
Zihan Sun, Hanxiao Zhou, Jianfeng Zheng, and Yuhao Qin

Research on Large-Scale Vessel Riding Tidal Current to Promote


Efficiency of Fairway . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 366
Kang Zhou, Ran Dai, and Xingwang Yue

A Vertex-Clustering Algorithm Based on the Cluster-Clique . . . . . . . . . . . 376


Deqiang Wang, Bin Zhang, and Kelun Wang

Designed Slide Mode Controller for Ship Autopilot with Steering Gear
Saturation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 386
Gao-Xiaori, Hong-Biguang, Xing-Shengwei, and Li-Tieshan

Automatic Assessment Model for Sailing in Narrow Channel . . . . . . . . . . . 396


Wang Delong and Ren Hongxiang

Bus Arrival Time Prediction and Release: System, Database and


Android Application Design . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 404
Junhao Fu, Lei Wang, Mingyang Pan, Zhongyi Zuo, and Qian Yang

On Key Techniques of a Radar Remote Telemetry and Monitoring


System . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 417
Jiangling Hao, Mingyang Pan, Deqiang Wang, Lining Zhao, and
Depeng Zhao
XXVI Table of Contents – Part II

PSC Ship-Selecting Model Based on Improved Particle Swarm


Optimization and BP Neural Network Algorithm . . . . . . . . . . . . . . . . . . . . . 425
Tingting Yang, Zhonghua Sun, Shouna Wang,
Chengming Yang, and Bin Lin

LRPON Based Infrastructure Layout Planning of Backbone Networks


for Mobile Cloud Services in Transportation . . . . . . . . . . . . . . . . . . . . . . . . . 436
Song Yingge, Dong Jie, Lin Bin, and Ding Ning

Infrastructure Deployment and Dimensioning of Relayed-Based


Heterogeneous Wireless Access Networks for Green Intelligent
Transportation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 447
Lin Bin, Guo Jiamei, He Rongxi, and Yang Tingting

Vessel Motion Pattern Recognition Based on One-Way Distance and


Spectral Clustering Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 461
Wenyao Ma, Zhaolin Wu, Jiaxuan Yang, and Weifeng Li

Navigation Safety Assessment of Ship in Rough Seas Based on Bayesian


Network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 470
Fengde Qu, Fengwu Wang, Zongmo Yang, and Jian Sun

Optimization of Ship Scheduling Based on One-Way Fairway . . . . . . . . . . 479


Jun Lin, Xin-yu Zhang, Yong Yin, Jin-tao Wang, and Shun Yao

Research on Virtual Crew Path Planning Simulator Based on A*


Algorithm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 487
Huilong Hao, Hongxiang Ren, and Dajun Chen

Speech Recognition Applied in VHF Simulation System . . . . . . . . . . . . . . . 496


Dajun Chen, Hongxiang Ren, and Huilong Hao

The Assessment of Risk of Collision between Two Ships Avoiding


Collision by Altering Course . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 507
Weifeng Li, Wenyao Ma, Jiaxuan Yang, Guoyou Shi, and
Robert Desrosiers

The Merging Algorithm of Radar Simulation Data in Navigational


Simulator . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 516
Shun Yao, Xin-yu Zhang, Yong Yin, Xin Xiong, and Jun Lin

Data Mining Research Based on College Forum . . . . . . . . . . . . . . . . . . . . . . 525


Liming Xue, Zhihuai Li, and Weixin Luan

Simulation of Maritime Joint Sea-Air Search Trend Using 3D GIS . . . . . . 533


Xing Shengwei, Wang Renda, Yang Xuefeng, and Liu Jiandao
Table of Contents – Part II XXVII

Quantitative Analysis for the Development of Maritime Transport


Efficiency . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 543
Wenbo Zhang, Zhaolin Wu, Yong Liu, and Zebing Li

Security and Privacy in Computer and Network


Systems (SPCNS 2014)
Image Compression Based on Time-Domain Lapped Transform and
Quadtree Partition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 553
Xiuhua Ma, Jiwen Dong, and Lei Wang

The Applicability and Security Analysis of IPv6 Tunnel Transition


Mechanisms . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 560
Wei Mi

QOS Performance Analysis for Flexible Workflow Supporting Exception


Handling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 571
Xiaoyan Zhu, Jingle Zhang, and Bo Wang

Analysis of Propagation Characteristics of Variant Worms . . . . . . . . . . . . . 581


Tao Liu, Can Zhang, Mingjing Cao, and Ruping Wu

A Design of Network Behavior-Based Malware Detection System for


Android . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 590
Yincheng Qi, Mingjing Cao, Can Zhang, and Ruping Wu

Detection and Defense Technology of Blackhole Attacks in Wireless


Sensor Network . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 601
Huisheng Gao, Ruping Wu, Mingjing Cao, and Can Zhang

An Improved Remote Data Possession Checking Protocol in Cloud


Storage . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 611
Enguang Zhou and Zhoujun Li

Fault Localization of Concurrency Bugs and Its Application in Web


Security . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 618
Zhenyuan Jiang

Feature Selection Toward Optimizing Internet Traffic Behavior


Identification . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 631
Zhenxiang Chen, Lizhi Peng, Shupeng Zhao, Lei Zhang, and
Shan Jing

ID-Based Anonymous Multi-receiver Key Encapsulation Mechanism


with Sender Authentication . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 645
Bo Zhang, Tao Sun, and Dairong Yu
XXVIII Table of Contents – Part II

Energy Efficient Routing with a Tree-Based Particle Swarm


Optimization Approach . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 659
Guodong Wang, Hua Wang, and Lei Liu

A Context-Aware Framework for SaaS Service Dynamic Discovery in


Clouds . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 671
Shaochong Li and Hao-peng Chen

Author Index . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 685


Porting the Princeton Ocean Model to GPUs

Shizhen Xu1,3 , Xiaomeng Huang1,2,3 , Yan Zhang1,2,3 , Yong Hu1,3 ,


Haohuan Fu1,2,3 , and Guangwen Yang1,2,3
1
Ministry of Education Key Laboratory for Earth System Modeling
2
Center for Earth System Science, Tsinghua University, 100084
3
Joint Center for Global Change Studies, Beijing, 100875, China
{hxm,haohuan,ygw}@tsinghua.edu.cn,
{yan-zhang12,huyong11,xsz12}@mails.tsinghua.edu.cn

Abstract. While GPU is becoming a compelling acceleration solution


for a series of scientific applications, most existing work on climate mod-
els only achieved limited speedup. It is due to partial porting of the
huge code and the memory bound inherence of these models. In this
work, we design and implement a customized GPU-based acceleration
of the Princeton Ocean Model (gpuPOM). Based on Nvidia’s state-of-
the-art GPU architectures (K20X and K40m), we rewrite the original
model from the Fortran into the CUDA-C completely. Several accelerat-
ing methods, including optimizing memory access in a single GPU, over-
lapping communication and boundary operations among multiple GPUs,
are presented. The experimental results show that the gpuPOM on one
K40m GPU achieves 6.9-fold to 17.8-fold speedup and 5.8-fold to 15.5-
fold speedup on one K20X GPU comparing with different Intel CPUs.
Further experiments on multiple GPUs indicate that the performance of
the gpuPOM on a super-workstation containing 4 GPUs is equivalent to
a powerful cluster consisting of 34 pure CPU nodes with over 400 CPU
cores.

1 Introduction

There is no doubt that high-resolution climate modeling is crucial for simulating


global and regional climate change. Most research groups in climate modeling
have established their own roadmaps for high-resolution ranging from several
kilometers down to hundreds of meters. The need for high-resolution exposes
serious problems because the time consumed in running high-resolution climate
models remains a significant scientific and engineering challenge.
Recent years, many scientific codes have been ported to the GPU and well
suited to the GPU. In the area of climate models, most of the previous work
achieved different levels of speedup for entire models on GPUs. For instance,
Michalakes et al accelerated a computationally intensive microphysics process
of the Weather Research and Forecast (WRF) model with a speedup of nearly
25x that speedups the entire WRF model by only 1.23x[1]; Shimokawabe et al
fully accelerated the ASUCA model – a production and non-hydrostatic weather

X.-h. Sun et al. (Eds.): ICA3PP 2014, Part I, LNCS 8630, pp. 1–14, 2014.

c Springer International Publishing Switzerland 2014
2 S. Xu et al.

model – on 528 Nvidia Tesla GT200 GPUs and achieves 15TFlops[2]; [3] accel-
erated a full huge operational weather forecasting model COSMO and achieved
2.8X speedups for its dynamic core.
According to our analysis, further speedup of climate models is limited by
two reasons. Firstly, the partial GPU porting limits the performance of the
whole application. Many scientific models suffer from a flat performance profile
during GPU accerlation. In CAM[4], the most single expensive subroutine only
accounts for about 10% of total runtime and most subroutines accounts for less
than 5%, which is the same in mpiPOM. According to the Amdahl law, the whole
model can not be significantly speedup such as the GPU accerlation of CAM
[4], ROMS [5], WRF [1] and HOMME [6], but it is sometimes a compromised
approach because of the huge code. Secondly, climate models is mainly bounded
by memory access, especially for their dynamic cores[3]. Great work has been
done in the full GPU acceleration of COSMO [3], ASUCA [2] and NIM [7],
including all the dynamic cores and some portion of physics. But the memory-
bound problem exists and can be further eased through better use of state-of-
the-art GPU memory hierarchy.
The objective of our study is to shorten the computation time of high-
resolution ocean models by parallelizing their existing model structures using
the GPU. With the representative ocean model, the mpiPOM, used as an exam-
ple, we demonstrate how to parallelize an ocean model to make it effectively run
on GPU architecture. Using state-of-the-art GPU architecture, we first rewrite
the entire mpiPOM model from the original Fortran version into a new CUDA-
C version. We call the new version gpuPOM. Then, we design and implement
several different optimizing methods from two levels, such as computation opti-
mization in a single GPU, communication optimization among multiple GPUs.
In terms of computation, we concentrate on memory access optimization and
making better use of GPU’s memory hierarchy. We deploy a four-categories
optimizations, including using read-only data cache, local memory blocking, loop
fusion and subroutine fusion, that are especially effective for climate models. The
experimental results demonstrate that one K40m GPU achieves 6.9-fold to 17.8-
fold speedup and one K20X achieves 5.8-fold to 15.5-fold speedup over different
Intel multi-core CPUs.
In terms of communication, we concentrate on the fine-grained overlapping
between the inner-region computation and the outer-region communication and
updating. With the new design, multiple GPUs in one node can communicate
directly bypassing the CPU. In addition, with the fine-grained control of the
CUDA streams and their priorities, inner-region computation can execute con-
currently with outer-region communication and updating.
To understand the accuracy, performance and scalability of the gpuPOM, we
build a customized super-workstation with four K20X GPUs inside. Experimen-
tal results show that the performance of the gpuPOM running on this super-
workstation can compare with a powerful cluster consisted of 34 pure CPU nodes
with over 400 CPU cores, which means this novel gpuPOM version provides a
fast and attractive solution for ocean scientists to conduct simulation research.
Porting the Princeton Ocean Model to GPUs 3

The remainder of this paper is organized as follows. We review the mpiPOM


in Sec. 2, and introduce the structure of the gpuPOM in Sec. 3. In Sec. 4,
we introduce four optimizations to efficiently use GPU’s memory hierarchy for
the gpuPOM. In Section 5, we present detailed techniques about communication
optimization among multiple GPUs. We provide the corresponding experimental
results about correctness, performance and scalability in Section 6 and conclude
our work in Section 7.

2 The mpiPOM
The mpiPOM[8] is a widely used parallel branch of POM based on Message
Passing Interface (MPI) and retains part the physics package of the original
POM[9]. POM is a powerful regional ocean model and has been used in a wide-
range of applications such as circulation and mixing processes in rivers, seas and
oceans.
The mpiPOM solves the primitive equation under hydrostatic and boussi-
nesq approximations. In the horizontal, spatial derivatives are computed us-
ing centered-space differencing on a staggered Arakawa C-grid. In the vertical,
the mpiPOM supports terrain-following sigma coordinates and a fourth-order
scheme option to reduce the internal pressure-gradient errors. The mpiPOM uses
the classical time-splitting technique to separate the vertically integrated equa-
tions (external mode) from the vertical structure equations (internal mode). The
external mode calculation is responsible for updating surface elevation and the
vertically averaged velocities. The internal mode calculation results in updates
for velocity, temperature and salinity, in addition to the turbulence quantities.
The three-dimensional internal mode and the two-dimensional external mode
are both integrated explicitly using a second-order leapfrog scheme. These two
modules are the most time consuming modules of mpiPOM.
To demonstrate the memory-bound problem, the Performance API(PAPI)[10]
is used to estimate floating point operations count and memory access(store/load)
instructions count. Results shows that the computational intensity(flops/byte)
of the mpiPOM is about 1:3.3, while that provided by SandyBridge E5-2670
CPUs is about 7.5:1. Moreover, data are mostly streamed from memory and
shows little locality, which means that mpiPOM is mainly bounded by memory
access. The wider memory bandwidth of GPU has attracted us a lot and to the
best of our knowledge, our work is the first GPU porting of the POM.

3 Structure of the gpuPOM


The flowchart of the gpuPOM is illustrated in Fig. 1. The main difference be-
tween mpiPOM and gpuPOM is that CPU in the gpuPOM implementation is
only responsible for the initializing and output. The gpuPOM begins with ini-
tializing the relevant arrays on CPU host and then copy these data to GPU.
GPU will deal with all the computation including external mode and internal
mode, and so on. During the computation, the variables required for output like
4 S. Xu et al.

CPU GPU
Input data and
MemcpyHostToDevice
Initialization
Advection and
Horizontal diffusion
of U,V

Baroclinic term of
U,V
External
Internal Mode
Mode Sea Surface Hight
+Boundary operation
Update U, V

Vertical Integrated
Continuity equation
moment equations
+Boundary operation

Turbulence equation Compute UT,VT for


+Boundary operation Internal mode
+Boundary operation
Tracer transport
equation(T, S)
+Boundary operation

Momentum equation
+Boundary operation

Output
Netcdf Files

Fig. 1. Flowchart of the gpuPOM

velocity and surface elevation will be copied back to CPU host and then written
to disk at a constant frequency.
In Fig. 1, each module represents a part of the primitive equations and is
implemented by several subroutines. We retained the overall structure of the
original code and rewrote all the subroutines with about 70 CUDA kernel func-
tions. Thus data always resides on GPU during the computation.
In our implementation , the 3D arrays of variables are stored sequentially in
the order of x, y, z (i, j, k ordering) and the 2D arrays are in the order of x,
y, which is the same with the original code. Each GPU thread specifies a (x, y)
point in horizontal direction and performs all the calculations from surface to
bottom(30 to 50 points). The threadblocks are configured with (32, 4, 1) threads
and similar performance can be achieved if configured with (32, 8, 1) or (32, 16, 1)
for the K20X GPU we use.
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He sank into his chair, debating his problem. There was in Rodrigo a
strange intuition about women. His success with them had, apart from his
physical attractiveness, consisted in an ability, far greater than that of the
usual predatory male, to understand them. He thought now that he
understood Mary. In a quiet, conventional way she had fallen in love with
John Dorning, he reasoned from his recent observation of them, and John
with her. Their love was still in its budding state. Unless it were interfered
with, it would grow steadily into a steadfast union. John would ask her to
marry him and she would assent. Her love would be mingled with pity, but
yet it would be as near pure love as modern marriages usually subsist upon.

"Unless it were interfered with." In this last meeting with Mary, brief as
it had been, Rodrigo detected something that would ordinarily have set his
heart to exulting. Mary's coming to him, her eagerness to extend her
personal greetings alone, her face and manner, her desire to remain longer
and her obvious disappointment at his rather, curt reception of her, had
convinced him of something that, never addicted to false modesty, he did not
hide.

"Unless it were interfered with." Well, he took a sad little triumph in


assuring himself, he could interfere if he chose, successfully interfere. Just
now, when she was here, he could have, if he had yielded to his selfish
desire, swept her into his arms and made her his forever. He could have
killed that budding love for John within her by appealing to the force of her
original love for himself, by rushing her off her feet with his superior
strength and feeling. He was sure of this.

Mary Drake still loved him, was the refrain that kept pounding in his
heart. He could have her now if he wanted to take her. If he remained near
her, he would not be able to keep his love silent. He would have to tell her.
Every fibre of his being would revolt against the sacrifice. He would not be
strong enough to give her up to John, though John needed her, loved her,
depended upon her to keep him out of the dark shadows that had so
tragically enveloped him.

No, Rodrigo concluded, he would have to go away—and stay away. Go


away at any cost. Go away as soon as he decently could.
Having spent the day in the details of securing his baggage and
unpacking it amid the familiar scenes of the Park Avenue apartment, he met
John and had dinner with him at their favorite little French restaurant.
Afterward, in the softly lighted living-room of the apartment, over their
pipes they talked.

"I have been wondering," John said, "why you came back so suddenly,
without warning us. I had been expecting a letter or cablegram for weeks. I
had begun to worry about you. You left no forwarding address with me.
And, of course, I would not have asked you to cut short your vacation
anyway. Poor chap, you were tired out, and, to tell you the truth, you don't
look particularly chipper now."

"I received a letter from Mary. She spoke of certain 'developments.'"


Rodrigo said doggedly, anxious to have it over. "She urged me to return and
talk with you."

John asked quietly, "Did she say what those 'developments' were?"

"No."

John smiled, "Wonderful, competent Mary! She insisted I write you to


come back. I refused, because I felt you were coming soon anyway. She,
strangely enough, was not so sure. So she wrote you herself? Well, perhaps
she was wise."

"And the 'developments' she spoke of?" Rodrigo's voice sounded very
small.

John tapped the ashes from his pipe, looked at his friend gravely.
"Rodrigo," he said, "I have found out the truth about Elise."

Rodrigo started with the unexpectedness of the answer, a chaos of


thoughts running suddenly riot within him.

"I know that she is dead," John continued. "And I know that you know
she is dead, that you have always known it. But wait, I will begin at the
beginning! You will remember that I spoke to you before you left about
selling my house in Millbank. Well, I kept putting that off because I dreaded
to enter the place. You see, I had left everything exactly the way it was
before—she went. While my mental condition was still uncertain, I did not
want to disturb things. I felt that the shock of going there, seeing her room,
her clothes, everything that my happiness, my life, had depended upon,
would be too much for me. Even after I came back from California feeling
so much improved, I kept putting it off. I dreaded the ordeal. But three or
four weeks after you left, I pulled myself together, told myself that those
foolish fears were nonsense, a sign even that I had gone a little mad. So I
went over there, and I spent two whole days in the house, alone. I put my
house of memories in order. And, Rodrigo, I found out many terrible things."

Rodrigo, his eyes fixed intensely upon his friend, shuddered.

But John went on calmly. "Well, I had to break into her desk, among
other things, and I found there letters, love-letters from other men. Among
them were letters from you, showing me, Rodrigo, that she loved you and
that you had had the courage to repulse her love. My idol crashed then and
there down to the floor, and the whole world went black again. Rodrigo,
there in that room alone I came as near going crazy as I hope ever to again in
this world. I cursed God for letting me see that He had made life so hideous.
I wanted to die. But I came through it. I think that it was those letters of
yours—those letters were striking blows for my happiness—that brought me
through. That is twice you have saved my life, Rodrigo—once from Rosner
and once—from myself."

Rodrigo rose and cried suddenly, "Don't say that, John! I can't bear it!"

"Please, Rodrigo," John restrained him. "I understand. You have always
tried to protect my happiness. You tried to keep me from knowing that I
loved a woman who never existed. But she is dead now. After I came out of
that house and went back to my father's and told them what I had found, they
confessed to me that anonymous notes had come to me soon after Elise's
disappearance hinting that I might learn something about her if it were
possible to identify the victims of the Van Clair fire. My father and Warren
had kept those notes from me. They felt it was time now to tell me about
them. And it became clear to me. The woman who died in the Van Clair fire
was Elise."
Rodrigo cried out, the secret wrenched from him almost without his
volition, "I know she was! And I sent her there that night, John! You'll
remember you went to Philadelphia and wired me to take the midnight train
and meet you the next morning. Well, she came to me that night in the
office, where I was working on the estimates. I was in a reckless mood,
disappointed—but no matter, it was no excuse for me. I sent her to the Van
Clair, intending to follow. Oh, I didn't go. I got my senses back, thank God!
But I was responsible. I thought I had grown so good, and I knifed my best
friend." He lifted his pale, stricken face to John, pleading for mercy, "I've
been through an ordeal too, John. The difference between us is that—I
deserved it and—the ordeal is going to go right on. Even though I've torn
this awful secret out of me at last!"

John Dorning was silent, stunned, trying to realize the significance of his
friend's confession.

And again Rodrigo cried out, pleadingly, "I couldn't tell you before,
John. I had to let you go on driving yourself crazy from anxiety about her. I
thought it would kill you to know. Mary begged me to tell you—but I
couldn't." Tears were in his eyes. His strong body was shaken with emotion.
Suddenly he flung himself at John's feet and no longer tried to control his
weeping.

And finally John spoke, and Rodrigo wonderingly looked up and saw
that John had a little smile on his face, that he was laying gentle hands upon
the recumbent back. "I knew something was tearing at you," John said, "And
I'm glad you told me about—Elise. Knowing her now for what she really
was, I can forgive you, Rodrigo. None of us are perfect. God knows I have
found that out. You were my friend even that night of the Van Clair—in the
critical moment you were my friend. And you always will be."

Dorning helped Rodrigo to his feet, made him smile again, took his
hand. Rodrigo clutched it, crying, "John, you are a saint. If you hadn't
forgiven me, if you—" He turned his head and went slowly back to his chair.

"I told Mary what I had discovered about Elise," said John. A light of
understanding burst upon him with these words. He ventured, "Rodrigo, had
you told her already of—the Van Clair?"
Rodrigo nodded affirmatively.

John was thinking rapidly.

"What did Mary say?" he asked.

"She called me a coward for not telling you the truth, sick as you were.
She said she could not—respect me, if I didn't."

John said almost to himself, "Mary thought a lot of you, Rodrigo—does


yet."

"She loves you," Rodrigo answered softly, but he could not quite keep
the despair out of his voice.

John glanced at him understandingly at last, but he said nothing. When,


after a long silence, they resumed the conversation, Dorning strove to
change its subject.

"I wish you'd take it easy for a while at the shop, Rodrigo. You don't look
well," he said gently. "Rosner has things quite well in hand. We miss you,
but I do want you well and perfectly happy when you come back to work."

"I was thinking of returning to Europe," Rodrigo replied, attempting to


make his statement as matter-of-fact as possible.

"Not because of anything you have said here to-night, I hope," John
urged at once. "I want you to believe me, old man, that your confession
hasn't made any difference. It's rather relieved my mind, to tell the truth. I
suspected something was up that I did not yet know about. It's made me love
you more than ever, drawn us closer."

"I appreciate that, John. I feel the same way," Rodrigo said.

Nevertheless, he told himself, he was going away. He would see Mary;


deliberately kill her love for him, throw her into John's arms. John needed
her. John deserved happiness. It was the least he could do for John. But it
was not a confession of weakness, his wanting to see Mary again. He must
see her, must do something that would convince her he was unworthy of her
love, that would strangle any desire in her to keep his memory alive after he
was gone. He must disappear from her heart as well as from her sight.

CHAPTER XX

Rodrigo walked slowly into the offices of the Italian-American Line late
the next morning, like a man lately condemned to the scaffold, and booked
passage on a vessel sailing for Naples the following Saturday. Then he took
the subway uptown.

The warm sun drenching the exhibition rooms of Dorning and Son, the
cheerful good mornings of the clerks, mocked at his mood. He summoned a
masking smile on his face and held it while he opened the door of John's
office and strode in. Mary was sitting beside John at the latter's desk, their
heads quite close together. They had been talking confidentially, almost
gayly. Their faces sobered as they looked up at the intruder. It seemed a
warning to Rodrigo that he must go through with his program. The faint
hope, conceived the night before, that the "developments" Mary had written
him about, concerned the discovery of Elise's treachery only and had nothing
to do with an announcement of a troth between Mary and John, vanished. It
was unmistakable. They loved each other. It showed in the quick, warning
glance that passed between them as he entered, in the way they almost
sprang apart at the sight of a third person.

They greeted him warmly enough, and almost immediately John


departed on the excuse of a conference with Henry Madison. Rodrigo took
the seat that his partner had vacated. He did not have to urge Mary to
remain.

His voice simulated a careless nonchalance as he smiled at her and said,


"I hadn't a chance hardly to say a word to you yesterday, Mary."

"That wasn't my fault," she pouted. He was surprised to discover that


Mary could pout. He thought she had never looked more adorable. Sophie,
Rosa, Elise—never in their prime had they been as beautiful as Mary.

"Did you enjoy your vacation?" she asked unexpectedly.

"Very much," he replied, smiling as if in memory. "You know, Mary,


there's no use pretending—I've never changed. I found it out when I got
abroad. I can't play the hermit. It isn't in me. Over here, with you around,
perhaps, I can hold myself in leash. But I am not like you or John, like
Americans, at heart. There is something in my blood. I was torn up
physically and emotionally when I left, and I had to forget somehow. That
isn't an excuse, of course, but it may explain things to you a little. I—I sank
into the old rut over there, Mary. The different environment, the different
sort of women, the liquor, everything." He flung out his hands hopelessly, in
a continental gesture.

"You saw some of your old friends?" she asked quietly.

"Many of them. And they were unchanged too. It was the same old story.
I met a girl in Naples whose father had once blackmailed me for an affair
with her—and now I suppose he'll be blackmailing me over again. In
London, I ran across Sophie Binner. You remember Sophie? We became
quite good friends again. She seems to be my sort. I'm what you called me—
a coward." He sighed, and watched her face.

But her face, strangely enough, did not flinch. She asked him in the same
quiet voice, "You are trying to tell me that you are the same man you were
that first day here, when you tried to play sheik with me, flirted with me?"

He shrugged his shoulders.

"I shouldn't think you would have come back here—after playing fast
and loose all over Europe, after betraying the trust John and I put in you."

"I came in response to your letter," he said with some dignity.

"Nevertheless, you shouldn't have come in that case. You should have
stayed with your—friends."
"I know. You are right," he said. "And I am going back to—them. I
booked my passage this morning. I am sailing in a week for Italy, and this
time I am not coming back."

She started. Her face lost its imperturbability. She said, "And that is all
you have to say to me?"

He leaned toward her, his throat filling with a storm of words. But then
he fell back, lowering his head. "Yes," he said in a low voice. "That is all—
that and—please think as well as you can of me, Mary. And go on—loving
John and taking care of him."

Her lips were twitching a little now. "Do you want to know what I really
think of you?" she asked suddenly.

He raised his tired eyes, his eyes that were saying what his lips were
sealed against, and he nodded his head.

She suddenly left her chair and came to him, laid her hands upon his
shoulders, and said clearly and proudly, "I think that you are a terrible fibber.
I think you have a crazy notion that John and I are in love. And I know this
—I love you, Rodrigo, and you are never going to leave me again."

And then he reached out and clutched her fiercely, devouringly into his
arms, kissed her again and again, crying her name pitifully like a baby. And
when at last he, still holding her tightly, raised her face so that he could look
at it and prove he was not dreaming, he saw that she too was weeping.

He cried, "Mary! Mary! Oh, my dear," again and again. And again and
again he kissed her.

Finally he let her go to adjust her disheveled hair and clothes into some
semblance of order. She smiled at him and asked, "How could you think I
could love anybody but you—coward or no coward? Oh, I found out while
you were gone how foolish I was ever to risk losing you. I lay awake
reviling myself that I had sent you away—yes, I did send you. And I had to
have you back—or dash over to Europe and search for you."

"But John?" he asked. "I thought John and you——"


"I love John too, but as a brother. I always have. And he has felt the same
towards me. But you—oh, my poor, poor boy!" He seized her greedily again,
and his lips were upon hers as a knock sounded upon the door. He released
her, looked at her so guiltily that she laughed aloud.

"It is only John," she said happily. "He knows—about us. He confirmed
my suspicions that you were torturing yourself with this silly idea that he
and I were in love. He even foretold that you would pretend to be the bold,
bad man of old. John is wise, you see, wiser even than you. But not half so
——"

And then John walked in and read their faces at a glance.

CHAPTER XXI

But, after all, Rodrigo sailed for Italy the next Saturday. Though he had
changed his booking from a single to a double cabin and the passenger list
read: The Count and Countess Rodrigo di Torriani.

John Dorning, looking almost as radiant as the bride and groom, saw
them off at the pier. For a long time they stood chatting on the deck of the
great vessel together, these three young people amid the throng of waving,
shouting tourists. When the warning blasts sounded from the smokestack
whistle, John whispered banteringly to Rodrigo, "This time you will not call
upon any of your ex-lady friends, eh? Rosa or Sophie—you bet I was glad to
get that good news of Sophie. Well, cable me when you land. And please
come back on schedule. You are leaving Dorning and Son terribly
handicapped, you know—my two best partners away at once." He kissed
Mary and pressed Rodrigo's hand, and hurried down the gangplank. He
stood there, a thin, but sturdy figure, waving to them while the great ship
backed out into the channel and pointed her bow toward the east.

"John Dorning is the finest of all the men that ever lived," Rodrigo said
solemnly.
"Almost," Mary replied.

Gliding through the magic moonlight over a mirror-like sea, they sat
very close to each other that evening in deck-chairs, and she said to him, at
the end of a long conversation, "And that is why I love you most, Rodrigo—
because you have conquered yourself."

"And so has good old John," he replied.

"Yes, so has John. And both you—and I—have found joy because of
that. It's the only way to win real happiness."
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