Applied Parallel and Scientific Computing: 11th International Conference, PARA 2012, Helsinki, Finland, June 10-13, 2012, Revised Selected Papers

568 Pages·2013·17.308 MB·English

by  Ari Harju, Topi Siro, Filippo Federici Canova, Samuli Hakala, Teemu Rantalaiho (auth.), Pekka Manninen, Per Öster (eds.)

Lecture Notes in Computer Science 7782
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TakeoKanade
CarnegieMellonUniversity,Pittsburgh,PA,USA
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UniversityofSurrey,Guildford,UK
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CornellUniversity,Ithaca,NY,USA
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MicrosoftResearch,Cambridge,MA,USA
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UniversityofCalifornia,LosAngeles,CA,USA
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UniversityofCalifornia,Berkeley,CA,USA
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MaxPlanckInstituteforInformatics,Saarbruecken,Germany
Pekka Manninen Per Öster (Eds.)
Applied Parallel
and Scientific Computing
11th International Conference, PARA 2012
Helsinki, Finland, June 10-13, 2012
Revised Selected Papers
1 3
VolumeEditors
PekkaManninen
CSC-ITCenterforScienceLtd
02101Espoo,Finland
E-mail:pekka.manninen@csc.fi
PerÖster
CSC-ITCenterforScienceLtd
02101Espoo,Finland
E-mail:per.oster@csc.fi
ISSN0302-9743 e-ISSN1611-3349
ISBN978-3-642-36802-8 e-ISBN978-3-642-36803-5
DOI10.1007/978-3-642-36803-5
SpringerHeidelbergDordrechtLondonNewYork
LibraryofCongressControlNumber:2013932191
CRSubjectClassification(1998):G.1.0,G.1.3-6,F.2.1-2,C.1.4,F.1.2,C.4,G.4
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Preface
TheseproceedingscontainasetofpaperspresentedatthePARA2012conference
heldduringJune10–13,2012,inHelsinki,Finland.Itwasthe11th inthe PARA
conferenceseries.ThegeneralthemeofthePARAconferenceseriesisthe“State
of the Art in Scientific and Parallel Computing,” and a special theme of the
PARA 2012 conference was “TowardExascale.”
JuneinHelsinkimeanslongdays.Thesunapproachesthehorizonnotbefore
11 pm, which gives plenty of time for long and interesting discussions. For the
PARA 2012 participants, many of the discussions were likely around this year’s
theme,exascalecomputing.Exascalesupercomputersarepredictedtoemergein
6 to 10 years’ time. The path toward this regime of computing has been pretty
clear for more than a decade and implies dramatically increased parallelism in
all levels of the computing systems. We already know how to handle massive
parallelism, but now we are talking about excessively massive parallelism: two
orthree ordersofmagnitude abovetoday’sleading petaflop/ssystems.The real
challenge is not just to build a computer system of theoretical exascale perfor-
mance,butrathertobeabletodevisereal-worldscientificapplicationsthathar-
nesstheexaflop/scomputingpower.Thisfactwasthebackgroundforthechoice
of the theme for the conference:Addressing the challengesdue to exploiting the
ever-increasingparallelismand to the changing balance betweenthe computers’
subsystems performance requiresnovel,more suitable algorithms,programming
models, performance optimization techniques, and numerical libraries.
The conference itself consisted of a number of selected contributed talks di-
vided into topicalparallelsessions,and five thematic minisymposia.These were
accompanied by keynote talks and interactive sessions. In these proceedings,
we have, based on a peer-review process, selected 35 technical full articles for
publication, categorized as follows:
(cid:129) Advances in HPC Applications
(cid:129) ParallelAlgorithms
(cid:129) Performance Analysis and Optimization
(cid:129) Applications of ParallelComputing in Industry and Engineering
(cid:129) HPC Interval Methods
In addition to these, three of the topical minisymposia are described by a
correspondingoverviewarticleontheminisymposiumtopic.Inordertocoverthe
state ofthe artof the field, we haveincluded atthe endofthe proceedingsa set
of extended abstracts that describe some of the conference talks not elaborated
by a full article. These extended abstracts have not been peer-reviewed.
We would like to thank everyone who contributed to the PARA 2012 con-
ference: keynote speakers Jack Dongarra, Bjo¨rn Engquist, and Mark Parsons;
Minisymposium Chairs; presenters of contributed talks; tutorial instructors; all
VI Preface
attendees; and everyone involved in practical arrangements. Especially all the
authors of these proceedings as well as the numerous reviewers are gratefully
acknowledged.
December 2012 P. Manninen
P. O¨ster
Organization
Steering Committee
Jack Dongarra,Honorary Chair University of Tennessee, USA
Jerzy Wasniewski, Chair Technical University of Denmark
Petter Bjørstad University of Bergen, Norway
Anne C. Elster Norwegian University of Science and
Technology, Norway
Bjo¨rn Engquist University of Texas at Austin, USA
Hja´lmty´r Hafsteinsson University of Iceland
Kristja´n Jo´nasson University of Iceland
Kimmo Koski CSC – IT Center for Science Ltd, Finland
Bo K˚agstr¨om University of Ume˚a, Sweden
Kaj Madsen Technical University of Denmark
Per O¨ster CSC – IT Center for Science Ltd, Finland
Organizing Committee
Per O¨ster, Chair CSC – IT Center for Science Ltd, Finland
Pekka Manninen, Co-chair CSC – IT Center for Science Ltd, Finland
Juha Fagerholm CSC – IT Center for Science Ltd, Finland
Table of Contents
Part I: Overview Articles of Topical Minisymposia
Computational Physics on Graphics Processing Units................. 3
Ari Harju, Topi Siro, Filippo Federici Canova, Samuli Hakala, and
Teemu Rantalaiho
Preparing Scientific Application Software for Exascale Computing...... 27
J.A. ˚Astr¨om, A. Carter, J. Hetherington, K. Ioakimidis,
E. Lindahl, G. Mozdzynski, R.W. Nash, P. Schlatter,
A. Signell, and J. Westerholm
PRACE DECI (Distributed European Computing Initiative)
Minisymposium.................................................. 43
Chris Johnson, Adam Carter, Iain Bethune, Kevin Statford,
Mikko Alava, Vitor Cardoso, Muhammad Asif,
Bernhard S.A. Schuberth, and Tobias Weinzierl
Part II: Advances in HPC Applications
Parallel Electronic Structure Calculations Using Multiple Graphics
Processing Units (GPUs) ......................................... 63
Samuli Hakala, Ville Havu, Jussi Enkovaara, and Risto Nieminen
An Environment for Service Composition, Execution and Resource
Allocation ...................................................... 77
Jan Kwiatkowski, Krzysztof Juszczyszyn, and Grzegorz Kolaczek
Multicore and Accelerator Development for a Leadership-Class Stellar
Astrophysics Code ............................................... 92
O.E. Bronson Messer, J. Austin Harris, Suzanne Parete-Koon, and
Merek A. Chertkow
Steering and In-situ Visualization for Simulation of Seismic Wave
Propagationon Graphics Cards.................................... 107
David Mich´ea, Joachim Pouderoux, Fabrice Dupros, and Hideo Aochi
PCJ - New Approach for Parallel Computations in Java .............. 115
Marek Nowicki and Piotr Bal(cid:2)a
PortingProductionLevelQuantumChromodynamicsCodetoGraphics
Processing Units – A Case Study .................................. 126
Teemu Rantalaiho
X Table of Contents
Time Propagation of Many-Body Quantum States on Graphics
Processing Units ................................................. 141
Topi Siro and Ari Harju
ParallelNumerical Simulation of Seismic Waves Propagationwith Intel
Math Kernel Library ............................................. 153
Mikhail A. Belonosov, Clement Kostov, Galina V. Reshetova,
Sergey A. Soloviev, and Vladimir A. Tcheverda
Part III: Parallel Algorithms
Blocked Schur Algorithms for Computing the Matrix Square Root ..... 171
Edvin Deadman, Nicholas J. Higham, and Rui Ralha
Distributed Evolutionary Computing System Based on Web Browsers
with JavaScript.................................................. 183
Jerzy Duda and Wojciech Dl(cid:2)ubacz
Use of Direct Solvers in TFETI Massively Parallel Implementation ..... 192
V´aclav Hapla, David Hor´ak, and Michal Merta
Parallel Implementation of the Sherman-Morrison Matrix Inverse
Algorithm....................................................... 206
Xin He, Marcus Holm, and Maya Neytcheva
Multi-threaded Nested Filtering Factorization Preconditioner.......... 220
Pawan Kumar, Karl Meerbergen, and Dirk Roose
An Approach of the QR Factorization for Tall-and-Skinny Matrices on
Multicore Platforms.............................................. 235
Sergey V. Kuznetsov
Approximate Incomplete Cyclic Reduction for Systems Which Are
Tridiagonal and Strictly Diagonally Dominant by Rows ............... 250
Carl Christian Kjelgaard Mikkelsen and Bo K˚agstr¨om
Fast Poisson Solvers for Graphics Processing Units ................... 265
Mirko Myllykoski, Tuomo Rossi, and Jari Toivanen
ParallelFeature Selection for Regularized Least-Squares .............. 280
Sebastian Okser, Antti Airola, Tero Aittokallio,
Tapio Salakoski, and Tapio Pahikkala
Part IV: Performance Analysis and Optimization
Topology Aware Process Mapping.................................. 297
Sebastian von Alfthan, Ilja Honkonen, and Minna Palmroth
Table of Contents XI
Numprof: A Performance Analysis Framework for Numerical
Libraries........................................................ 309
Olli-Pekka Lehto
Multi-core Scalability Measurements: Issues and Solutions............. 319
Mattias Linde
AutoTune: A Plugin-Driven Approach to the Automatic Tuning of
ParallelApplications ............................................. 328
Renato Miceli, Gilles Civario, Anna Sikora, Eduardo C´esar,
Michael Gerndt, Houssam Haitof, Carmen Navarrete,
Siegfried Benkner, Martin Sandrieser, Laurent Morin, and
Franc¸ois Bodin
Vectorized Higher Order Finite Difference Kernels.................... 343
Gerhard Zumbusch
Part V: Applications of Parallel Computing in
Industry and Engineering
Preconditioning for Large Scale Micro Finite Element Analyses of 3D
Poroelasticity.................................................... 361
Peter Arbenz and Erhan Turan
ParallelSolvers for Numerical Upscaling ............................ 375
R. Blaheta, O. Jakl, J. Star´y, and Erhan Turan
Parallel Numerical Algorithms for Simulation of Multidimensional
Ill-Posed Nonlinear Diffusion-Advection-Reaction Models ............. 387
Raimondas Cˇiegis and Andrej Bugajev
Efficient Setup of AggregationAMG for CFD on GPUs............... 398
Maximilian Emans and Manfred Liebmann
Accelerating 2D-to-3D Video Conversionon Multi-core Systems........ 410
Jiangbin Feng, Yurong Chen, Eric Li, Yangzhou Du, and
Yimin Zhang
Solution of Multi-objective Competitive Facility Location Problems
Using Parallel NSGA-II on Large Scale Computing Systems ........... 422
Algirdas Lanˇcinskas and Julius Z˘ilinskas
Simulation Software for Flow of Fluid with Suspended Point Particles
in Complex Domains: Application to Matrix Diffusion ................ 434
Jukka I. Toivanen, Keijo Mattila, Jari Hyva¨luoma,
Pekka Kek¨ala¨inen, Tuomas Puurtinen, and Jussi Timonen
XII Table of Contents
Part VI: HPC Interval Methods
Introduction to the “HPC Interval Methods”Minisymposium .......... 449
Bart(cid:2)lomiej Jacek Kubica
ParallelInterval Newton Method on CUDA ......................... 454
Philip-Daniel Beck and Marco Nehmeier
HeterogeneousMulti-agentEvolutionarySystemforSolvingParametric
Interval Linear Systems........................................... 465
Jerzy Duda and Iwona Skalna
Interval Finite Difference Method for Solving the One-Dimensional
Heat Conduction Problem with Heat Sources........................ 473
Malgorzata A. Jankowska and Grazyna Sypniewska-Kaminska
Interval Arithmetic and Automatic Differentiation on GPU Using
OpenCL ........................................................ 489
Grzegorz Kozikowski and Bartl(cid:2)omiej Jacek Kubica
Tuning the Interval Algorithm for Seeking Pareto Sets of Multi-criteria
Problems ....................................................... 504
Bart(cid:2)lomiej Jacek Kubica and Adam Wo´zniak
A Central-BackwardDifference Interval Method for Solving the Wave
Equation........................................................ 518
Andrzej Marciniak and Barbara Szyszka
Part VII: Collection of Extended Abstracts
Using State-of-the-Art Sparse Matrix Optimizations for Accelerating
the Performance of Multiphysics Simulations ........................ 531
Vasileios Karakasis, Georgios Goumas, Konstantinos Nikas,
Nectarios Koziris, Juha Ruokolainen, and Peter R˚aback
Schedule Optimisation for Interactive Parallel Structure Simulations.... 536
Jovana Kneˇzevi´c, Ralf-Peter Mundani, and Ernst Rank
A Shared Memory Parallel Implementation of the IRKA Algorithm for
H2 Model Order Reduction (Extended Abstract)..................... 541
Martin Ko¨hler and Jens Saak
ParallelBlock Preconditioning by Using the Solver of Elmer........... 545
Mika Malinen, Juha Ruokolainen, Peter R˚aback, Jonas Thies, and
Thomas Zwinger
Distributed High-Performance Parallel Mesh Generation with
ViennaMesh..................................................... 548
Jorge Rodr´ıguez, Josef Weinbub, Dieter Pahr, Karl Rupp, and
Siegfried Selberherr