High Performance Computing on Vector Systems 2007

264 Pages·2008·19.344 MB·English

by  Seiji Tsuboi (auth.), Michael Resch, Sabine Roller, Peter Lammers, Toshiyuki Furui, Martin Galle, Wolfgang Bez (eds.)

High Performance Computing on Vector Systems 2007
Michael Resch · Sabine Roller · Peter Lammers
Toshiyuki Furui ·Martin Galle · Wolfgang Bez
Editors
High Performance
Computing
on Vector Systems
2007
123
MichaelResch ToshiyukiFurui
SabineRoller NECCorporation
PeterLammers Nisshin-cho1-10
Höchstleistungsrechenzentrum 183-8501Tokyo,Japan
Stuttgart(HLRS) [e-mail]
UniversitätStuttgart
Nobelstraße19
WolfgangBez
70569Stuttgart,Germany
MartinGalle
[e-mail]
[e-mail] NECHighPerformanceComputing
[e-mail] EuropeGmbH
Prinzenallee11
40459Düsseldorf,Germany
[e-mail]
[e-mail]
Frontcoverfigure:ImpressionoftheprojectedtidalcurrentpowerplanttobebuiltintheSouthKorean
province ofWando.Picture duetoRENETEC,Jongseon Park, incooperation withInstitute ofFluid
MechanicsandHydraulicMachinery,UniversityofStuttgart
ISBN 978-3-540-74383-5 e-ISBN 978-3-540-74384-2
DOI 10.1007/978-3-540-74384-2
LibraryofCongressControlNumber:2007936175
MathematicsSubjectClassification(2000):68Wxx,68W10,68U20,76-XX,86A05,86A10,70Fxx
©2008Springer-VerlagBerlinHeidelberg
Thisworkissubjecttocopyright.Allrightsarereserved,whetherthewholeorpartofthematerialis
concerned,specificallytherightsoftranslation,reprinting,reuseofillustrations,recitation,broadcasting,
reproductiononmicrofilmorinanyotherway,andstorageindatabanks.Duplicationofthispublication
orpartsthereofispermittedonlyundertheprovisionsoftheGermanCopyrightLawofSeptember9,
1965,initscurrentversion,andpermissionforusemustalwaysbeobtainedfromSpringer.Violations
areliabletoprosecutionundertheGermanCopyrightLaw.
Theuseofgeneral descriptive names, registered names, trademarks, etc. inthis publication does not
imply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfromtherelevantprotective
lawsandregulationsandthereforefreeforgeneraluse.
Typesetting:bytheeditorsusingaSpringerTEXmacropackage
Production:LE-TEXJelonek,Schmidt&VöcklerGbR,Leipzig
Coverdesign:WMXDesignGmbH,Heidelberg
Printedonacid-freepaper
987654321
springer.com
Preface
In2004theHighPerformanceComputingCenteroftheUniversityofStuttgart
andNECestablishedtheTERAFLOPWorkbenchcollaboration.TheTERA-
FLOP Workbench is a research & Service Project for which the following
targets have been defined:
• Make new science and engineering possible that requires TFLOP/s sus-
tained application performance
• Support the HLRS user community to achieve capability science by im-
proving existing codes
• Integrate different system architectures for simulation, pre- and post-
processing, visualisation into a computational engineering workbench
• Assess and demonstrate system capabilities for industry relevant applica-
tions
IntheTERAFLOPWorkbenchsignificanthardwareandhumanresources
have been made available by both partners. The hardware provided within
the TERAFLOP project consists of 8 nodes NEC SX-8 Vector Computers
and a cluster of 200 Intel Xeon nodes. The complete NEC installation at
HLRS comprises 72 nodes SX-8, two TX-7 (i.e. 32-way Itanium based SMP
systems)whicharealsousedasfrontendfortheSXnodesandthepreviously
described Xeon cluster.
Six computer experts,who arededicated to advancedapplicationsupport
anduserservices,arefunded overthe complete projectruntime.The support
is carried out on the basis of small project groups working on specific ap-
plications. These groups usually consist of application experts, in most cases
members of the development team, and TERAFLOP workbench represen-
tatives. This setup to combines detailed application know-how and physical
backgroundwith computer science and engineering knowledgeand sound nu-
merical mathematics expertise. The combination of these capabilities forms
the basis for leading edge research and computational science.
Following the above formulated targets, the cooperation was successful
in achieving sustained application performance of more than 1 TFLOP/s for
VI Preface
morethan10applicationssofar.Thebestperformingapplicationisthehydro-
dynamicscodeBEST,whichisbasedonthesolutionoftheLatticeBoltzmann
equations. This application achieves a performance of 5.7 TFLOP/s on the
72 nodes SX-8. Also other hydrodynamics as well as oceanography and cli-
matology applications are running highly efficient on the SX-8 architecture.
The enhancement of applications and their adaptation to the SX-8 Vector
architecture within the collaborationwill continue.
On the other hand, the Teraflop Workbench project works on supporting
future applications, looking at the requirements users ask for. In that con-
text,we see anincreasinginterestin CoupledApplications,in whichdifferent
codesareinteractingtosimulatecomplexsystemsofmultiplephysicalregimes.
Examples for such couplings are Fluid-Structure or Ocean-Atmosphereinter-
actions. The codes in these coupled applications may have completely dif-
ferent requirements concerning the computer architecture which often results
in the situation that they are running most efficient on different platforms.
The efficient execution of coupled application requires a close integration of
the different platforms. The platform integration and the support for cou-
pled applications will become another important share in the TERAFLOP
Workbench collaboration.
WithintheframeworkoftheTERAFLOPWorkbenchcollaboration,semi-
annual workshops are carried out in which researchers and computer experts
come together to exchange their experiences. The workshop series started in
2004 with the 1st TERAFLOP Workshop in Stuttgart. In autumn 2005, the
TERAFLOP Workshop Japan session was established with the 3rd TERA-
FLOP Workshop in Tokyo.
The following book presents contributions from the 6th TERAFLOP
Workshop which was hosted by Tohoku University in Sendai, Japan in au-
tumn 2006and the 7th Workshopin Stuttgart which was held in spring 2007
in Stuttgart. Focus is layed on current applications and future requirements,
aswellasdevelopmentsofnextgenerationhardwarearchitecturesandinstal-
lations.
Starting with a section on geophysics and climate simulations, the suit-
ability and necessity of vector systems is justified showing sustained teraflop
performance.Earthquakesimulations basedonthe Spectral-ElementMethod
demonstrate that the systhetic seismic waves computed by this numerical
technique match with the observed seismic waves accurately. Further papers
addresscloud-resolvingsimulationoftropicalcyclones,orthe question:What
is the impact of small-scale phenomena on the large-scale ocean and climate
modeling? Ensemble climate model simulation discribed in the closing paper
in this section enable scientists to better distinguish the forced signal due to
the increase of greenhouse gases from internal climat variability.
A section on computational fluid dynamics (CFD) starts with a paper
discussing the current capability of CFD and the maturity to reduce wind
tunnel testings. Further papers in this section show simulations in applied
Preface VII
fields as aeronautics and flows in gas and steam turbines, as well as basic
research and detailed performance analysis.
The following section considers multi-scale and multi-physics simulations
based on CFD. Current applications in aero-acoustics and the coupling of
Large-Eddy Simulation (LES) with acoustic perturbation equations (APE)
start the section, followed by fluid-structure interaction (FSI) in such differ-
ent aereas as tidal current turbines or the respiratory systems. The section is
closed by a paper addressing the algorithmic and imlementation issues asso-
ciated with FSI simulations on vector architecture. These examples show to
usthetendencytocoupledapplicationsandtherequirementscomingupwith
future simulation techniques.
The section on chemistry and astrophysics combines simulation of pre-
mixedswirlingflamesandsupernovasimulations.The commonbasisforboth
applications is the combination of a hydrodynamic module with processes as
chemicalkineticsormulti-floavour,multi-frequenceyneutrinotransportbased
on the Boltzmann transport equation, respectively.
A section on material science closes the applications part. Green chem-
istry from supercomputers considers Car-Parrinello simulations of ionic liq-
uids.Micromagneticsimulationsofmagneticrecordingmedia allownew head
and media designs to be evaluated and optimized prior to fabrications.
Thesesectionsshowthewiderangeofapplicationareasperformedoncur-
rentvectorsystems.TheclosingsectiononFutureHighPerformanceSystems
consider the potential of on-chip memory systems for future vector archi-
tectures. A technical note describing the TSUBAME installation at Tokyo
Institute of Technology (TiTech) closes the book.
The papers presented in this book lay out the wide range of fields in
which sustained performance can be achieved if engineering knowledge, nu-
merical mathematics and computer science skills are brought together. With
the advent of hybrid systems, the Teraflop workbench project will continue
the support of leading edge computations for future applications.
The editors would like to thank all authors and Springer for making this
publication possible and wouldlike to express their hope that the entire high
performance computing community will benefit from it.
Stuttgart, Juli 2007 M. Resch, W. Bez
S. Roller, M. Galle
P. Lammers, T. Furui
Contents
Applications I Geophysics and Climate Simulations
Sustained Performance of 10+ Teraflop/s in Simulation on
Seismic Waves Using 507 Nodes of the Earth Simulator
Seiji Tsuboi ..................................................... 3
Cloud-Resolving Simulation of Tropical Cyclones
Toshiki Iwasaki, Masahiro Sawada ................................. 15
OPA9 – French Experiments on the Earth Simulator and
Teraflop Workbench Tunings
S. Masson, M.-A. Foujols, P. Klein, G. Madec, L. Hua, M. Levy, H.
Sasaki, K. Takahashi, F. Svensson ................................ 25
TERAFLOP Computing and Ensemble Climate Model
Simulations
Henk A. Dijkstra................................................. 35
Applications II Computational Fluid Dynamics
Current Capability of Unstructured-Grid CFD and a
Consideration for the Next Step
Kazuhiro Nakahashi .............................................. 45
Smart Suction – an Advanced Concept for Laminar Flow
Control of Three-Dimensional Boundary Layers
Ralf Messing, Markus Kloker ...................................... 53
Supercomputing of Flows with Complex Physics and the
Future Progress
Satoru Yamamoto................................................ 61
X Contents
Large-Scale Computations of Flow Around a Circular
Cylinder
Jan G. Wissink, Wolfgang Rodi.................................... 71
Performance Assessment and Parallelisation Issues of the
CFD Code NSMB
J¨org Ziefle, Dominik Obrist and Leonhard Kleiser .................... 83
Applications III Multiphysics Computational Fluid Dynamics
High Performance Computing Towards Silent Flows
E. Gr¨oschel1, D. Ko¨nig2, S. Koh, W. Schro¨der, M. Meinke............115
Fluid-Structure Interaction: Simulation of a Tidal Current
Turbine
Felix Lippold, Ivana Buntic´Ogor...................................137
Coupled Problems in Computational Modeling of the
Respiratory System
Lena Wiechert, Timon Rabczuk, Michael Gee, Robert Metzke, Wolfgang
A. Wall.........................................................145
FSI Simulations on Vector Systems – Development of a Linear
Iterative Solver (BLIS)
Sunil R. Tiyyagura, Malte von Scheven .............................167
Applications IV Chemistry and Astrophysics
Simulations of Premixed Swirling Flames Using a Hybrid
Finite-Volume/Transported PDF Approach
Stefan Lipp, Ulrich Maas .........................................181
Supernova Simulations with the Radiation Hydrodynamics
Code PROMETHEUS/VERTEX
B. Mu¨ller, A. Marek, K. Benkert, K. Kifonidis, H.-Th. Janka .........195
Applications V Material Science
Green Chemistry from Supercomputers: Car–Parrinello
Simulations of Emim-Chloroaluminates Ionic Liquids
Barbara Kirchner, Ari P Seitsonen.................................213
Micromagnetic Simulations of Magnetic Recording Media
Simon Greaves ..................................................229
Contents XI
Future High Performance Systems
The Potential of On-Chip Memory Systems for Future Vector
Architectures
Hiroaki Kobayashi, Akihiko Musa, Yoshiei Sato, Hiroyuki Takizawa,
Koki Okabe .....................................................247
The Road to TSUBAME and Beyond
Satoshi Matsuoka ................................................265
List of Contributors
Benkert, K., 193 Metzke, R., 143
Dijkstra, H. A., 34 Mu¨ller, B., 193
Foujols, M.-A., 24 Musa, A., 247
Gee, M., 143 Nakahashi, K., 45
Greaves, S., 227 Obrist, D., 81
Hua, L., 24 Gro¨schel, E., 115
Iwasaki, T., 14 Ogor, I. B., 135
Janka, H.-Th., 193 Okabe, K., 247
Kifonidis, K., 193 Rabczuk, T., 143
Kirchner, B., 213 Rodi, W., 69
Klein, P., 24 Sasaki, H., 24
Kleiser, L., 81 Sato, Y., 247
Kloker, M., 52 Sawada, M., 14
Kobayashi,H., 247 Scheven, M. v., 166
Koh, S., 115 Seitsonen, A. P., 213
Ko¨nig, D., 115 Schro¨der, W., 115
Levy, M., 24 Svensson, F., 24
Lipp, S., 181 Takahashi, K., 24
Lippold, F., 135 Takizawa, H., 247
Maas, U., 181 Tiyyagura,S. R., 166
Madec, G., 24 Tsuboi, S., 3
Marek, A., 193 Wall, W. A., 143
Masson, S., 24 Wiechert, L., 143
Matsuoka, S., 264 Wissink, J. G., 69
Meinke, M., 115 Yamamoto, S., 60
Messing, R., 52 Ziefle, J., 81