Table Of ContentCloud, Grid and High
Performance Computing:
Emerging Applications
Emmanuel Udoh
Indiana Institute of Technology, USA
http://avaxho.me/blogs/ChrisRedfield
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Library of Congress Cataloging-in-Publication Data
Cloud, grid and high performance computing: emerging applications / Emmanuel Udoh, editor.
p. cm.
Includes bibliographical references and index.
Summary: “This book offers new and established perspectives on architectures, services and the resulting impact of
emerging computing technologies, including investigation of practical and theoretical issues in the related fields of grid,
cloud, and high performance computing”--Provided by publisher.
ISBN 978-1-60960-603-9 (hardcover) -- ISBN 978-1-60960-604-6 (ebook) 1. Cloud computing. 2. Computational grids
(Computer systems) 3. Software architecture. 4. Computer software--Development. I. Udoh, Emmanuel, 1960-
QA76.585.C586 2011
004.67’8--dc22
2011013282
British Cataloguing in Publication Data
A Cataloguing in Publication record for this book is available from the British Library.
All work contributed to this book is new, previously-unpublished material. The views expressed in this book are those of the
authors, but not necessarily of the publisher.
Table of Contents
Preface .................................................................................................................................................xvi
Section 1
Introduction
Chapter 1
Supercomputers in Grids .........................................................................................................................1
Michael M. Resch, University of Stuttgart, Germany
Edgar Gabriel, University of Houston, USA
Chapter 2
Porting HPC Applications to Grids and Clouds ....................................................................................10
Wolfgang Gentzsch, Independent HPC, Grid, and Cloud Consultant, Germany
Chapter 3
Grid-Enabling Applications with JGRIM .............................................................................................39
Cristian Mateos, ISISTAN - UNCPBA, Argentina
Alejandro Zunino, ISISTAN - UNCPBA, Argentina
Marcelo Campo, ISISTAN - UNCPBA, Argentina
Section 2
Scheduling
Chapter 4
Moldable Job Allocation for Handling Resource Fragmentation in Computational Grid ....................58
Kuo-Chan Huang, National Taichung University of Education, Taiwan
Po-Chi Shih, National Tsing Hua University, Taiwan
Yeh-Ching Chung, National Tsing Hua University, Taiwan
Chapter 5
Speculative Scheduling of Parameter Sweep Applications Using Job Behaviour
Descriptions ..........................................................................................................................................72
Attila Ulbert, Eötvös Loránd University, Hungary
László Csaba Lőrincz, Eötvös Loránd University, Hungary
Tamás Kozsik, Eötvös Loránd University, Hungary
Zoltán Horváth, Eötvös Loránd University, Hungary
Chapter 6
A Security Prioritized Computational Grid Scheduling Model: An Analysis .......................................90
Rekha Kashyap, Jawaharlal Nehru University, India
Deo Prakash Vidyarthi, Jawaharlal Nehru University, India
Chapter 7
A Replica Based Co-Scheduler (RBS) for Fault Tolerant Computational Grid .................................101
Zahid Raza, Jawaharlal Nehru University, India
Deo Prakash Vidyarthi, Jawaharlal Nehru University, India
Section 3
Security
Chapter 8
A Policy-Based Security Framework for Privacy-Enhancing Data Access and Usage
Control in Grids ..................................................................................................................................118
Wolfgang Hommel, Leibniz Supercomputing Centre, Germany
Chapter 9
Adaptive Control of Redundant Task Execution for Dependable Volunteer Computing ...................135
Hong Wang, Tohoku University, Japan
Yoshitomo Murata, Tohoku University, Japan
Hiroyuki Takizawa, Tohoku University, Japan
Hiroaki Kobayashi, Tohoku University, Japan
Chapter 10
Publication and Protection of Sensitive Site Information in a Grid Infrastructure .............................155
Shreyas Cholia, Lawrence Berkeley National Laboratory, USA
R. Jefferson Porter, Lawrence Berkeley National Laboratory, USA
Chapter 11
Federated PKI Authentication in Computing Grids: Past, Present, and Future ..................................165
Massimiliano Pala, Dartmouth College, USA
Shreyas Cholia, Lawrence Berkeley National Laboratory, USA
Scott A. Rea, DigiCert Inc., USA
Sean W. Smith, Dartmouth College, USA
Chapter 12
Identifying Secure Mobile Grid Use Cases ........................................................................................180
David G. Rosado, University of Castilla-La Mancha, Spain
Eduardo Fernández-Medina, University of Castilla-La Mancha, Spain
Javier López, University of Málaga, Spain
Mario Piattini, University of Castilla-La Mancha, Spain
Chapter 13
Trusted Data Management for Grid-Based Medical Applications ......................................................208
Guido J. van ‘t Noordende, University of Amsterdam, The Netherlands
Silvia D. Olabarriaga, Academic Medical Center - Amsterdam, The Netherlands
Matthijs R. Koot, University of Amsterdam, The Netherlands
Cees T.A.M. de Laat, University of Amsterdam, The Netherlands
Section 4
Applications
Chapter 14
Large-Scale Co-Phylogenetic Analysis on the Grid ...........................................................................222
Heinz Stockinger, Swiss Institute of Bioinformatics, Switzerland
Alexander F. Auch, University of Tübingen, Germany
Markus Göker, University of Tübingen, Germany
Jan Meier-Kolthoff, University of Tübingen, Germany
Alexandros Stamatakis, Ludwig-Maximilians-University Munich, Germany
Chapter 15
Persistence and Communication State Transfer in an Asynchronous Pipe Mechanism .....................238
Philip Chan, Monash University, Australia
David Abramson, Monash University, Australia
Chapter 16
Self-Configuration and Administration of Wireless Grids ..................................................................255
Ashish Agarwal, Carnegie Mellon University, USA
Amar Gupta, University of Arizona, USA
Chapter 17
Push-Based Prefetching in Remote Memory Sharing System ............................................................269
Rui Chu, National University of Defense Technology, China
Nong Xiao, National University of Defense Technology, China
Xicheng Lu, National University of Defense Technology, China
Chapter 18
Distributed Dynamic Load Balancing in P2P Grid Systems ..............................................................284
You-Fu Yu, National Taichung University, Taiwan, ROC
Po-Jung Huang, National Taichung University, Taiwan, ROC
Kuan-Chou Lai, National Taichung University, Taiwan, ROC
Chapter 19
An Ontology-Based P2P Network for Semantic Search .....................................................................299
Tao Gu, University of Southern Denmark, Denmark
Daqing Zhang, Institut Telecom SudParis, France
Hung Keng Pung, National University of Singapore, Singapore
Chapter 20
FH-MAC: A Multi-Channel Hybrid MAC Protocol for Wireless Mesh Networks ............................313
Djamel Tandjaoui, Center of Research on Scientific and Technical Information, Algeria
Messaoud Doudou, University of Science and Technology Houari Boumediène, Algeria
Imed Romdhani, Napier University School of Computing, UK
Chapter 21
A Decentralized Directory Service for Peer-to-Peer-Based Telephony ..............................................330
Fabian Stäber, Siemens Corporate Technology, Germany
Gerald Kunzmann, Technische Universität München, Germany
Jörg P. Müller, Clausthal University of Technology, Germany
Compilation of References ...............................................................................................................345
About the Contributors ....................................................................................................................374
Index ...................................................................................................................................................385
Detailed Table of Contents
Preface .................................................................................................................................................xvi
Section 1
Introduction
Chapter 1
Supercomputers in Grids .........................................................................................................................1
Michael M. Resch, University of Stuttgart, Germany
Edgar Gabriel, University of Houston, USA
This article describes the state of the art in using supercomputers in Grids. It focuses on various ap-
proaches in Grid computing that either aim to replace supercomputing or integrate supercomputers in
existing Grid environments. We further point out the limitations to Grid approaches when it comes to
supercomputing. We also point out the potential of supercomputers in Grids for economic usage. For
this, we describe a public-private partnership in which this approach has been employed for more than
10 years. By giving such an overview we aim at better understanding the role of supercomputers and
Grids and their interaction.
Chapter 2
Porting HPC Applications to Grids and Clouds ....................................................................................10
Wolfgang Gentzsch, Independent HPC, Grid, and Cloud Consultant, Germany
A Grid enables remote, secure access to a set of distributed, networked computing and data resources.
Clouds are a natural complement to Grids towards the provisioning of IT as a service. To “Grid-enable”
applications, users have to cope with: complexity of Grid infrastructure; heterogeneous compute and
data nodes; wide spectrum of Grid middleware tools and services; the e-science application architectures,
algorithms and programs. For clouds, on the other hand, users don’t have many possibilities to adjust
their application to an underlying cloud architecture, because of its transparency to the user. Therefore,
the aim of this chapter is to guide users through the important stages of implementing HPC applica-
tions on Grid and cloud infrastructures, together with a discussion of important challenges and their
potential solutions. As a case study for Grids, we present the Distributed European Infrastructure for
Supercomputing Applications (DEISA) and describe the DEISA Extreme Computing Initiative (DECI)
for porting and running scientific grand challenge applications on the DEISA Grid. For clouds, we pres-
ent several case studies of HPC applications running on Amazon’s Elastic Compute Cloud EC2 and its
recent Cluster Compute Instances for HPC. This chapter concludes with the author’s top ten rules of
building sustainable Grid and cloud e-infrastructures.
Chapter 3
Grid-Enabling Applications with JGRIM .............................................................................................39
Cristian Mateos, ISISTAN - UNCPBA, Argentina
Alejandro Zunino, ISISTAN - UNCPBA, Argentina
Marcelo Campo, ISISTAN - UNCPBA, Argentina
The development of massively distributed applications with enormous demands for computing power,
memory, storage and bandwidth is now possible with the Grid. Despite these advances, building Grid
applications is still very difficult. We present JGRIM, an approach to easily gridify Java applications by
separating functional and Grid concerns in the application code, and report evaluations of its benefits
with respect to related approaches. The results indicate that JGRIM simplifies the process of porting
applications to the Grid, and the Grid code obtained from this process performs in a very competitive
way compared to the code resulting from using similar tools.
Section 2
Scheduling
Chapter 4
Moldable Job Allocation for Handling Resource Fragmentation in Computational Grid ....................58
Kuo-Chan Huang, National Taichung University of Education, Taiwan
Po-Chi Shih, National Tsing Hua University, Taiwan
Yeh-Ching Chung, National Tsing Hua University, Taiwan
In a computational Grid environment, a common practice is to try to allocate an entire parallel job onto
a single participating site. Sometimes a parallel job, upon its submission, cannot fit in any single site due
to the occupation of some resources by running jobs. How the job scheduler handles such situations is
an important issue which has the potential to further improve the utilization of Grid resources, as well
as the performance of parallel jobs. This paper adopts moldable job allocation policies to deal with such
situations in a heterogeneous computational Grid environment. The proposed policies are evaluated
through a series of simulations using real workload traces. The moldable job allocation policies are also
compared to the multi-site co-allocation policy, which is another approach usually used to deal with the
resource fragmentation issue. The results indicate that the proposed moldable job allocation policies can
further improve the system performance of a heterogeneous computational Grid significantly.
Chapter 5
Speculative Scheduling of Parameter Sweep Applications Using Job Behaviour
Descriptions ..........................................................................................................................................72
Attila Ulbert, Eötvös Loránd University, Hungary
László Csaba Lőrincz, Eötvös Loránd University, Hungary
Tamás Kozsik, Eötvös Loránd University, Hungary
Zoltán Horváth, Eötvös Loránd University, Hungary
The execution of data intensive Grid applications raises several questions regarding job scheduling, data
migration, and replication. This paper presents new scheduling algorithms using more sophisticated
job behaviour descriptions that allow estimating job completion times more precisely thus improving
scheduling decisions. Three approaches of providing input to the decision procedure are discussed: a)
single job description, b) multiple job descriptions, and c) multiple job descriptions with mutation. The
proposed Grid middleware components (1) monitor the execution of jobs and gather resource access
information, (2) analyse the compiled information and generate a description of the behaviour of the job,
(3) refine the already existing job description, and (4) use the refined behaviour description to schedule
the submitted jobs.
Chapter 6
A Security Prioritized Computational Grid Scheduling Model: An Analysis .......................................90
Rekha Kashyap, Jawaharlal Nehru University, India
Deo Prakash Vidyarthi, Jawaharlal Nehru University, India
Grid supports heterogeneities of resources in terms of security and computational power. Applications
with stringent security requirement introduce challenging concerns when executed on the grid resources.
Though grid scheduler considers the computational heterogeneity while making scheduling decisions,
little is done to address their security heterogeneity. This work proposes a security aware computational
grid scheduling model, which schedules the tasks taking into account both kinds of heterogeneities. The
approach is known as Security Prioritized MinMin (SPMinMin). Comparing it with one of the widely
used grid scheduling algorithm MinMin (secured) shows that SPMinMin performs better and sometimes
behaves similar to MinMin under all possible situations in terms of makespan and system utilization.
Chapter 7
A Replica Based Co-Scheduler (RBS) for Fault Tolerant Computational Grid .................................101
Zahid Raza, Jawaharlal Nehru University, India
Deo Prakash Vidyarthi, Jawaharlal Nehru University, India
Grid is a parallel and distributed computing network system comprising of heterogeneous computing
resources spread over multiple administrative domains that offers high throughput computing. Since the
Grid operates at a large scale, there is always a possibility of failure ranging from hardware to software.
The penalty paid of these failures may be on a very large scale. System needs to be tolerant to various
possible failures which, in spite of many precautions, are bound to happen. Replication is a strategy
often used to introduce fault tolerance in the system to ensure successful execution of the job, even when
some of the computational resources fail. Though replication incurs a heavy cost, a selective degree of
