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E-grāmata: Exascale Scientific Applications: Scalability and Performance Portability

Edited by (Oak Ridge National Laboratory, Oak Ridge, TN, USA), Edited by , Edited by
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From the Foreword:

"The authors of the chapters in this book are the pioneers who will explore the exascale frontier. The path forward will not be easy... These authors, along with their colleagues who will produce these powerful computer systems will, with dedication and determination, overcome the scalability problem, discover the new algorithms needed to achieve exascale performance for the broad range of applications that they represent, and create the new tools needed to support the development of scalable and portable science and engineering applications. Although the focus is on exascale computers, the benefits will permeate all of science and engineering because the technologies developed for the exascale computers of tomorrow will also power the petascale servers and terascale workstations of tomorrow. These affordable computing capabilities will empower scientists and engineers everywhere." Thom H. Dunning, Jr., Pacific Northwest National Laboratory and University of Washington, Seattle, Washington, USA

"This comprehensive summary of applications targeting Exascale at the three DoE labs is a must read." Rio Yokota, Tokyo Institute of Technology, Tokyo, Japan

"Numerical simulation is now a need in many fields of science, technology, and industry. The complexity of the simulated systems coupled with the massive use of data makes HPC essential to move towards predictive simulations. Advances in computer architecture have so far permitted scientific advances, but at the cost of continually adapting algorithms and applications. The next technological breakthroughs force us to rethink the applications by taking energy consumption into account. These profound modifications require not only anticipation and sharing but also a paradigm shift in application design to ensure the sustainability of developments by guaranteeing a certain independence of the applications to the profound modifications of the architectures: it is the passage from optimal performance to the portability of performance. It is the challenge of this book to demonstrate by example the approach that one can adopt for the development of applications offering performance portability in spite of the profound changes of the computing architectures." Christophe Calvin, CEA, Fundamental Research Division, Saclay, France

"Three editors, one from each of the High Performance Computer Centers at Lawrence Berkeley, Argonne, and Oak Ridge National Laboratories, have compiled a very useful set of chapters aimed at describing software developments for the next generation exa-scale computers. Such a book is needed for scientists and engineers to see where the field is going and how they will be able to exploit such architectures for their own work. The book will also benefit students as it provides insights into how to develop software for such computer architectures. Overall, this book fills an important need in showing how to design and implement algorithms for exa-scale architectures which are heterogeneous and have unique memory systems. The book discusses issues with developing user codes for these architectures and how to address these issues including actual coding examples. Dr. David A. Dixon, Robert Ramsay Chair, The University of Alabama, Tuscaloosa, Alabama, USA

Recenzijas

"Numerical simulation is now a need in many fields of science, technology, and industry. The complexity of the simulated systems coupled with the massive use of data makes the HPC essential to move towards predictive simulations. Advances in computer architecture have so far permitted scientific advances, but at the cost of continually adapting algorithms and applications. The next technological breaks force us to rethink the applications by taking energy consumption into account. These profound modifications require not only anticipation and sharing but also a paradigm shift in application design to ensure the sustainability of developments by guaranteeing a certain independence of the applications to the profound modifications of the architectures: it is the passage from optimal performance to the portability of performance. It is the challenge of this book to demonstrate by example the approach that one can adopt for the development of applications offering a portability of the performances in spite of the profound changes of the computing architectures." Christophe Calvin, CEA, Fundamental Research Division, Scalay, France

"This comprehensive summary of applications targeting Exascale at the three DoE labs is a must read." Rio Yokota, Tokyo Institute of Technology, Tokyo, Japan

"Three editors, one from each of the High Performance Computer Centers at Lawrence Berkeley, Argonne, and Oak Ridge National Laboratories, have complied a very useful set of chapters aimed at describing software developments for the next generation exa-scale computers. Such a book is needed for scientists and engineers to see where the field is going and how they will be able to exploit such architectures for their own work. The book will also benefit students as it provides insights into how to develop software for such computer architectures. Overall, this book fills an important need in showing how to design and implement algorithms for exa-scale architectures which are heterogeneous and have unique memory systems. The book discusses issues with developing user codes for these architectures and how to address these issues including actual coding examples. Dr. David A. Dixon, Robert Ramsay Chair, The University of Alabama, USA "Numerical simulation is now a need in many fields of science, technology, and industry. The complexity of the simulated systems coupled with the massive use of data makes the HPC essential to move towards predictive simulations. Advances in computer architecture have so far permitted scientific advances, but at the cost of continually adapting algorithms and applications. The next technological breaks force us to rethink the applications by taking energy consumption into account. These profound modifications require not only anticipation and sharing but also a paradigm shift in application design to ensure the sustainability of developments by guaranteeing a certain independence of the applications to the profound modifications of the architectures: it is the passage from optimal performance to the portability of performance. It is the challenge of this book to demonstrate by example the approach that one can adopt for the development of applications offering a portability of the performances in spite of the profound changes of the computing architectures." Christophe Calvin, CEA, Fundamental Research Division, Scalay, France

"This comprehensive summary of applications targeting Exascale at the three DoE labs is a must read." Rio Yokota, Tokyo Institute of Technology, Tokyo, Japan

"Three editors, one from each of the High Performance Computer Centers at Lawrence Berkeley, Argonne, and Oak Ridge National Laboratories, have complied a very useful set of chapters aimed at describing software developments for the next generation exa-scale computers. Such a book is needed for scientists and engineers to see where the field is going and how they will be able to exploit such architectures for their own work. The book will also benefit students as it provides insights into how to develop software for such computer architectures. Overall, this book fills an important need in showing how to design and implement algorithms for exa-scale architectures which are heterogeneous and have unique memory systems. The book discusses issues with developing user codes for these architectures and how to address these issues including actual coding examples. Dr. David A. Dixon, Robert Ramsay Chair, The University of Alabama, USA

Foreword xi
Preface xiii
About the Editors xvii
Contributors xix
Chapter 1 Portable Methodologies for Energy Optimization on Large-Scale Power-Constrained Systems
1(16)
Kevin J. Barker
Darren J. Kerbyson
Chapter 2 Performance Analysis and Debugging Tools at Scale
17(34)
Scott Parker
John Mellor-Crummey
Dong H. Ahn
Heike Jagode
Holger Brunst
Sameer Shende
Allen D. Malony
David Lecomber
John V. DelSignore, Jr.
Ronny Tschuter
Ralph Castain
Kevin Harms
Philip Carns
Ray Loy
Kalyan Kumaran
Chapter 3 Exascale Challenges in Numerical Linear and Multilinear Algebras
51(44)
Dmitry I. Lyakh
Wayne Joubert
Chapter 4 Exposing Hierarchical Parallelism in the FLASH Code for Supernova Simulation on Summit and Other Architectures
95(24)
Thomas Papatheodore
O. E. Bronson Messer
Chapter 5 NAMD: Scalable Molecular Dynamics Based on the Charm++ Parallel Runtime System
119(26)
Bilge Acun
Ronak Buch
Laxmikant Kale
James C. Phillips
Chapter 6 Developments in Computer Architecture and the Birth and Growth of Computational Chemistry
145(6)
Wim Nieuwpoort
Ria Broer
Chapter 7 On Preparing the Super Instruction Architecture and Aces4 for Future Computer Systems
151(14)
Jason Byrd
Rodney Bartlett
Beverly A. Sanders
Chapter 8 Transitioning NWChem to the Next Generation of Manycore Machines
165(22)
Eric J. Bylaska
Edoardo Apra
Karol Kowalski
Mathias Jacquelin
Wibe A. de Jong
Abhinav Vishnu
Bruce Palmer
Jeff Daily
Tjerk P. Straatsma
Jeff R. Hammond
Michael Klemm
Chapter 9 Exascale Programming Approaches for Accelerated Climate Modeling for Energy
187(20)
Matthew R. Norman
Azamat Mametjanov
Mark Taylor
Chapter 10 Preparing the Community Earth System Model for Exascale Computing
207(24)
John M. Dennis
Christopher Kerr
Allison H. Baker
Brian Dobbins
Kevin Paul
Richard Mills
Sheri Mickelson
Youngsung Kim
Raghu Kumar
Chapter 11 Large Eddy Simulation of Reacting Flow Physics and Combustion
231(26)
Joseph C. Oefelein
Ramanan Sankaran
Chapter 12 S3D-Legion: An Exascale Software for Direct Numerical Simulation of Turbulent Combustion with Complex Multicomponent Chemistry
257(22)
Sean Treichler
Michael Bauer
Ankit Bhagatwala
Giulio Borghesi
Ramanan Sankaran
Hemanth Kolla
Patrick S. McCormick
Elliott Slaughter
Wonchan Lee
Alex Aiken
Jacqueline Chen
Chapter 13 Data and Workflow Management for Exascale Global Adjoint Tomography
279(28)
Matthieu Lefebvre
Yangkang Chen
Wenjie Lei
David Luet
Youyi Ruan
Ebru Bozdag
Judith Hill
Dimitri Komatitsch
Lion Krischer
Daniel Peter
Norbert Podhorszki
James Smith
Jeroen Tromp
Chapter 14 Scalable Structured Adaptive Mesh Refinement with Complex Geometry
307(12)
Brian Van Straalen
David Trebotich
Andrey Ovsyannikov
Daniel T. Graves
Chapter 15 Extreme Scale Unstructured Adaptive CFD for Aerodynamic Flow Control
319(26)
Kenneth E. Jansen
Michel Rasquin
Jed Brown
Cameron Smith
Mark S. Shephard
Chris Carothers
Chapter 16 Lattice Quantum Chromodynamics and Chroma
345(30)
Balint Joo
Robert G. Edwards
Frank T. Winter
Chapter 17 PIC Codes on the Road to Exascale Architectures
375(34)
Henri Vincenti
Mathieu Lobet
Remi Lehe
Jean-Luc Vay
Jack Deslippe
Chapter 18 Extreme-Scale De Novo Genome Assembly
409(22)
Evangelos Georganas
Steven Hofmeyr
Leonid Oliker
Rob Egan
Daniel Rokhsar
Aydin Buluc
Katherine Yelick
Chapter 19 Exascale Scientific Applications: Programming Approaches for Scalability, Performance, and Portability: KKRnano
431(18)
Paul F. Baumeister
Marcel Bornemann
Dirk Pleiter
Rudolf Zeller
Chapter 20 Real-Space Multiple-Scattering Theory and Its Applications at Exascale
449(12)
Markus Eisenbach
Yang Wang
Chapter 21 Development of QMCPACK for Exascale Scientific Computing
461(20)
Anouar Benali
David M. Ceperley
Ed D'Azevedo
Mark Dewing
Paul R. C. Kent
Jeongnim Kim
Jaron T. Krogel
Ying Wai Li
Ye Luo
Tyler McDaniel
Miguel A. Morales
Amrita Mathuria
Luke Shulenburger
Norm M. Tubman
Chapter 22 Preparing an Excited-State Materials Application for Exascale
481(26)
Jack Deslippe
Felipe H. da Jornada
Derek Vigil-Fowler
Taylor Barnes
Thorsten Kurth
Steven G. Louie
Chapter 23 Global Gyrokinetic Particle-in-Cell Simulation
507(22)
William Tang
Zhihong Lin
Chapter 24 The Fusion Code XGC: Enabling Kinetic Study of Multiscale Edge Turbulent Transport in ITER
529(24)
Eduardo D'Azevedo
Stephen Abbott
Tuomas Koskela
Patrick Worley
Seung-Hoe Ku
Stephane Ethier
Eisung Yoon
Mark Shephard
Robert Hager
Jianying Lang
Jong Choi
Norbert Podhorszki
Scott Klasky
Manish Parashar
Choong-Seock Chang
Index 553
Tjerk P. Straatsma, Katerina B. Antypas, Timothy J. Williams