Facing the Multicore-Challenge III: Aspects of New Paradigms and Technologies in Parallel Computing

155 Pages·2013·11.57 MB·English

by  Michael Bader, Hans-Joachim Bungartz, Martin Schreiber (auth.), Rainer Keller, David Kramer, Jan-Philipp Weiss (eds.)

Lecture Notes in Computer Science 7686
CommencedPublicationin1973
FoundingandFormerSeriesEditors:
GerhardGoos,JurisHartmanis,andJanvanLeeuwen
EditorialBoard
DavidHutchison
LancasterUniversity,UK
TakeoKanade
CarnegieMellonUniversity,Pittsburgh,PA,USA
JosefKittler
UniversityofSurrey,Guildford,UK
JonM.Kleinberg
CornellUniversity,Ithaca,NY,USA
AlfredKobsa
UniversityofCalifornia,Irvine,CA,USA
FriedemannMattern
ETHZurich,Switzerland
JohnC.Mitchell
StanfordUniversity,CA,USA
MoniNaor
WeizmannInstituteofScience,Rehovot,Israel
OscarNierstrasz
UniversityofBern,Switzerland
C.PanduRangan
IndianInstituteofTechnology,Madras,India
BernhardSteffen
TUDortmundUniversity,Germany
MadhuSudan
MicrosoftResearch,Cambridge,MA,USA
DemetriTerzopoulos
UniversityofCalifornia,LosAngeles,CA,USA
DougTygar
UniversityofCalifornia,Berkeley,CA,USA
GerhardWeikum
MaxPlanckInstituteforInformatics,Saarbruecken,Germany
Rainer Keller David Kramer
Jan-Philipp Weiss (Eds.)
Facing the
Multicore-Challenge III
Aspects of New Paradigms and Technologies
in Parallel Computing
1 3
VolumeEditors
RainerKeller
UniversityofAppliedScience
FacultyforSurveying,ComputerScienceandMathematics
Schellingstraße24,70174Stuttgart,Germany
E-mail:[e-mail]
DavidKramer
KarlsruheInstituteofTechnology(KIT)
InstituteofComputerScienceandEngineering
Haid-und-Neu-Straße7,76131Karlsruhe,Germany
E-mail:[e-mail]
Jan-PhilippWeiss
KarlsruheInstituteofTechnology(KIT)
InstituteforAppliedandNumericalMathematics4
Fritz-Erler-Straße23,76133Karlsruhe,Germany
E-mail:[e-mail]
ISSN0302-9743 e-ISSN1611-3349
ISBN978-3-642-35892-0 e-ISBN978-3-642-35893-7
DOI10.1007/978-3-642-35893-7
SpringerHeidelbergDordrechtLondonNewYork
LibraryofCongressControlNumber:2010935359
CRSubjectClassification(1998):C.1.4,C.1.3,C.4,D.1.3,D.3.4,I.3.1,B.2.1,B.2.4,
B.3.2,D.4.2,D.4.8,F.2.2
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Preface
Welcome to the proceedings of the third conference “Facing the Multicore-
Challenge,”whichwasheldinStuttgart,Germany,duringSeptember19–21,2012.
RecenthardwaredevelopmentshaveagainpresentedtheMulticore-Challengeto
software developers: this applies to the development of software with regard to
scientific computing, system-level software, as well as compilers. The introduc-
tionof highly parallelarchitecturesbasedoncommodity processors,suchasthe
IntelXeon(cid:2)R PhiTM,orthehighlythreadedKeplerGPGPUsbyNVIDIA,requires
programmersevenmoretoidentifysectionsofcodeamenabletoparallelizationon
variouslevels,identifyloadimbalance,reorderinefficientdatastructureaccesses,
andfinallyanalyzeandoptimizedatatransfers.
By“FacingtheMulticore-Challenge”weinitiatedaseriesofconferencesthat
allow young scientists to present high-quality, relevant, and up-to-date research
onscalableapplications,middleware,andcompilersonthesearchitectures.These
proceedings, together with the previous two, attest to the importance of this
series’ approach. The first conference was organized in 2010 at the Heidelberg
Academy of Science, the second conference in the following year was held at
the KarlsruheInstitute ofTechnology(KIT). This year’sconferencewas heldat
the Hochschule fu¨r Technik Stuttgart, University of Applied Science, in the city
center of Stuttgart, Germany.
Inallwereceived21fullpapersoutofwhichtenwereselectedbytheProgram
Committee–eachpaperwasreviewedbyatleastthreeindependentexpertswith
a short rebuttal period to balance differing opinions. Apart from the full-paper
presentations,theconferencefeaturedapostersessionwith12selectedcontribu-
tions.Anotherfeature ofthe conferenceis asetofshorttalksshowingthe latest
results that are not yet ready for publication but allow the speakers to present
their firstdata,toreceivefeedback,andtodiscuss novelideas.Inasimilarvein,
the conference features invited talks: this year they comprised a keynote on the
technology obstacles to be tackled for the exascale with reality checks, a talk
presenting the status of MPI-3, one presentation on the Extoll network inter-
connect, and last but not least a talk on the exascale preparations at sandia
nationallabs.Todigintodetailto overcomeroadblockstoscalability,wehosted
threetutorials:thefirstwasprovidedbyCrayonlarge-scalecomputing,another
tutorialfromRoguewavefocusedonsingle-nodeperformanceusingThreadspot-
ter, and the last tutorial by Intel introduced the programming for Intel Xeon(cid:2)R
TM
Phi .
Thanks to the German Gauß-Allianz for Supercomputing, the conference
was able to offer best paper, best poster, and best presentation awards. The
best paper awards were selected by the Program Committee; the best paper
in the application category was awarded to the group of authors represented
by Christoph Altmann, Institute of Aerodynamics and Gas Dynamics of the
VI Preface
University of Stuttgart, with their paper “An Efficient High-Performance Par-
allelization of a Discontinuous Galerkin Spectral Element Method.” The best
paper with regard to theory was awarded to Marek Pal(cid:4)kowski from the West
PomeranianUniversity ofTechnologyfor his paper “ImpactofVariable Privati-
zationonExtractingSynchronization-FreeSlices.”Thebestposterandbesttalk
awardswereselectedbythe55participants.Bothawardsweregrantedtopartic-
ipants from the Technical University of Denmark. The best poster award went
to Peter E. Aackermann, Peter J. Dinesen Pedersen, and co-authors for their
contribution “Development of a GPU-Accelerated MIKE 21 Solver for Water
Wave Dynamics,” while the best presentation was awarded to Allan S. Nielsen
for his presentation “The PararealAlgorithm for Multi-layered Parallelism.”
The conference organizers and editors would like to thank the paper and
poster authors for submitting their novel material, making this event an in-
teresting conference. We would especially like to thank all the members of the
ProgramCommitteefortheirexperience,guidance,andgreateffortinthereview
process, not only for selecting the material, but also for providing authors with
valuable feedback on improvementsandcomments for future work.In the name
of all participants and invited speakers, we would especially like to thank the
Gauß-Allianz for Supercomputing in Germany for sponsorship, which allowed
the conference to provide awards and travel grants.
September 2012 Rainer Keller
David Kramer
Jan-Philipp Weiss
Organization
General Chair
Rainer Keller University of Applied Sciences Stuttgart,
Germany
David Kramer Karlsruhe Institute of Technology, Germany
Jan-Philipp Weiss Karlsruhe Institute of Technology, Germany
Program Committee
Michael Bader University of Stuttgart, Germany
Richard Barrett Oak Ridge National Labs, Oak Ridge, USA
Carlo Bertolli Imperial College London, UK
Christian Bischof RWTH Aachen, Germany
Arndt Bode TU Munich, Germany
George Bosilca University of Tennessee Knoxville, USA
Rainer Buchty TU Braunschweig,Germany
Mark Bull EPCC, Edinburgh, UK
Hans-Joachim Bungartz TU Munich, Germany
Franck Capello LRI, Universit´e Paris Sud, France
Jack Dongarra University of Tennessee, USA
David Ediger Georgia Tech, USA
Claudia Fohry Kassel University, Germany
Dominik G¨oddeke TU Dortmund, Germany
Georg Hager University of Erlangen-Nuremberg,Germany
Thomas Herault Universit´e Paris Sud, France
Hans J. Herrmann ETH, Zu¨rich, Switzerland
Peter Heusch HfT Stuttgart, Germany
Vincent Heuveline Karlsruhe Institute of Technology, Germany
Lee Howes AMD, UK
Wolfgang Karl Karlsruhe Institute of Technology, Germany
David Kramer Karlsruhe Institute of Technology, Germany
Rainer Keller HfT Stuttgart, Germany
Michael Klemm Intel, Germany
Hiroaki Kobayashi Tohoku University, Japan
Dimitar Lukarski Uppsala University, Sweden
Norihiro Nakajima JAEA and CCSE, Tokyo, Japan
Dieter an Mey RWTH Aachen, Germany
Claus-Dieter Munz Stuttgart University, Germany
Fabian Oboril Karlsruhe Institute of Technology, Germany
Christian Perez INRIA, France
VIII Organization
Franz-Josef Pfreundt ITWM Kaiserslautern,Germany
Michael Philippsen University of Erlangen-Nuremberg,Germany
Thomas Rauber Bayreuth University, Germany
Rolf Rabenseifner HLRS, Stuttgart, Germany
Gudula Ru¨nger Chemnitz Technical University, Germany
Olaf Schenk Basel University, Switzerland
Martin Schulz Lawrence Livermore National Labs, USA
Christian Simmendinger T-Systems SfR, Germany
Masha Sosonkina Ames Lab, USA
Thomas Steinke ZIB, Berlin, Germany
Mehdi Tahoori Karlsruhe Institute of Technology, Germany
Walter Tichy Karlsruhe Institute of Technology, Germany
Carsten Trinitis TUM, Munich, Germany
Stefan Turek Dortmund University, Germany
Josef Weidendorfer TUM, Munich, Germany
Jan-Philipp Weiss Karlsruhe Institute of Technology, Germany
Felix Wolf FZ Ju¨lich, Germany
Table of Contents
Full Papers
Invasive Computing on High Performance Shared Memory Systems..... 1
Michael Bader, Hans-Joachim Bungartz, and Martin Schreiber
A Similarity-Based Analysis Tool for Porting OpenMP Applications.... 13
Wei Ding, Oscar Hernandez, and Barbara Chapman
Array-BasedReduction Operations for a Parallel Adaptive FEM....... 25
Martina Balg, Jens Lang, Arnd Meyer, and Gudula Ru¨nger
An Efficient High Performance Parallelization of a Discontinuous
Galerkin Spectral Element Method................................. 37
Christoph Altmann, Andrea D. Beck, Florian Hindenlang,
Marc Staudenmaier, Gregor J. Gassner, and Claus-Dieter Munz
Reducing the Memory Footprint of ParallelApplications with KSM .... 48
Nathalie Rauschmayr and Achim Streit
Recalibrating Fine-Grained Locking in ParallelBucket Hash Tables .... 60
A´kos Dud´as, Sa´ndor Juha´sz, and S´andor Kolumba´n
Impact of Variable Privatization on Extracting Synchronization-Free
Slices for Multi-core Computers.................................... 72
Marek Palkowski
Parallel Collision Queries on the GPU: A Comparative Study
of Different CUDA Implementations................................ 84
Rainer Erbes, Anja Mantel, Elmar Scho¨mer, and Nicola Wolpert
ÆminiumGPU: An Intelligent Framework for GPU Programming ...... 96
Alcides Fonseca and Bruno Cabral
Parallel k-Means Image Segmentation Using Sort, Scan and Connected
Components on a GPU ........................................... 108
Michael Backer, Jan Tu¨nnermann, and Ba¨rbel Mertsching
Poster Abstracts
Solving High-Dimensional Problems on Processors with Integrated
GPU ........................................................... 121
Alexander Heinecke
X Table of Contents
Pulsar Searching with Many-Cores ................................. 123
Alessio Sclocco and Rob V. van Nieuwpoort
Scheduling Overheads for Task-BasedParallel Programming Models.... 125
Mathias Nachtmann, Jose Gracia, and Colin W. Glass
PINstruct – Efficient Memory Access to Data Structures.............. 127
Rainer Keller and Shiqing Fan
Development of a GPU-Accelerated Mike 21 Solver for Water Wave
Dynamics ....................................................... 129
Peter Edward Aackermann, Peter Juhler Dinesen Pedersen,
Allan Peter Engsig-Karup, Thomas Clausen, and Jesper Grooss
GPU-Accelerated and CPU SIMD Optimized Monte Carlo Simulation
of φ4 Model ..................................................... 131
Piotr Bialas, Jakub Kowal, and Adam Strzelecki
Protable Codes on New HPC Architectures ......................... 133
Mhd. Amer Wafai, Colin W. Glass, and Christoph Niethammer
GASPI – A Partitioned Global Address Space Programming
Interface........................................................ 135
Thomas Alrutz, Jan Backhaus, Thomas Brandes, Vanessa End,
Thomas Gerhold, Alfred Geiger, Daniel Gru¨newald,
Vincent Heuveline, Jens J¨agersku¨pper, Andreas Knu¨pfer,
Olaf Krzikalla, Edmund Ku¨geler, Carsten Lojewski, Guy Lonsdale,
Ralph Mu¨ller-Pfefferkorn, Wolfgang Nagel, Lena Oden,
Franz-Josef Pfreundt, Mirko Rahn, Michael Sattler,
Mareike Schmidtobreick, Annika Schiller, Christian Simmendinger,
Thomas Soddemann, Godehard Sutmann, Henning Weber, and
Jan-Philipp Weiss
ParallelFully Adaptive Tsunami Simulations ........................ 137
Michael Bader, Alexander Breuer, and Martin Schreiber
Implementation of Stable Skew–Symmetric Matrix Factorization
for Fermi GPUs Using CUDA ..................................... 139
Neven Krajina
The IMData Approach to Accelerate Data Intensive Workloads ........ 141
Marcus Vo¨lp, Nils Asmussen, and Hermann Ha¨rtig
PRAgMaTIc – ParallelAnisotropic Adaptive Mesh Toolkit............ 143
Georgios Rokos and Gerard Gorman
Author Index.................................................. 145
Invasive Computing on High Performance
Shared Memory Systems
Michael Bader, Hans-Joachim Bungartz, and Martin Schreiber
Department of Informatics,
Boltzmannstrasse 3, 85748 Garching, Germany
{bader,bungartz,martin.schreiber}@in.tum.de
http://www5.in.tum.de/
Abstract. In this work, we tackle several important issues to improve
thethroughputofruntime-adaptiveapplicationsonstate-of-the-artHPC
systems. A first issue is the, in general, missing information about the
actual impact of unforeseeable workload by adaptivity and of the un-
known number of time steps or iterations on the runtime of adaptive
applications. Anotherissue is that resource scheduling on HPC systems
iscurrentlydonebeforeanapplicationisstartedandremainsunchanged
afterwards,evenincaseofvaryingrequirements.Furthermore,anappli-
cation cannot be started after another running application allocated all
resources. We combine addressing these issues with the design of algo-
rithms that adapt their use of resources during runtime,by releasing or
requesting compute cores, for example. If concurrent applications com-
pete for resources, this requires the implementation of an appropriate
resource management.
We show a solution for these issues by using invasive paradigms to
startapplicationsandscheduleresourcesduringruntime.Thescheduling
ofthedistributionofcorestotheapplicationsisachievedbyaglobalre-
sourcemanager.Weintroducescalabilitygraphstoimproveloadbalanc-
ingofmultipleapplications.Foradaptivesimulations,severalscalability
graphs exist to consider different phases of scalability due to changing
workload.
Foraproof-of-concept,weshowruntime/throughputresultsforafully
adaptive shallow-water simulation.
Keywords: Invasive computing, resource awareness, shared-memory,
runtimeadaptive applications, OpenMP, TBB.
1 Introduction
The current trend to many-core systems was forced to still fulfill Moore’s Law
for performance and energy efficiency reasons [1]. The parallel efficiency of ap-
plicationsonsuchmany-coresystemsis usuallyrepresentedbythe scalabilityof
a parallel application[2]. To overcomescalability problems of applications (e.g.
due to a small workload), the execution of multiple programs in parallel is one
of the main approaches in HPC (among others [3,4]). So far, those scheduling
R.Kelleretal.(Eds.):FacingtheMulticore-ChallengeIII2012,LNCS7686,pp.1–12,2013.
(cid:2)c Springer-VerlagBerlinHeidelberg2013