Parallel Programming with OpenACC PDF
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Parallel Programming with OpenACC Parallel Programming with OpenACC Edited By Rob Farber AMSTERDAM (cid:127) BOSTON (cid:127) HEIDELBERG (cid:127) LONDON NEW YORK (cid:127) OXFORD (cid:127) PARIS (cid:127) SAN DIEGO SAN FRANCISCO (cid:127) SINGAPORE (cid:127) SYDNEY (cid:127) TOKYO Morgan Kaufmann is an imprint of Elsevier Morgan Kaufmann is an imprint of Elsevier 50 Hampshire Street, 5th Floor, Cambridge, MA 02139, United States Copyright © 2017 Elsevier Inc. All rights reserved. Designations used by companies to distinguish their products are often claimed as trademarks or registered trademarks. In all instances in which Morgan Kaufmann Publishers is aware of a claim, the product names appear in initial capital or all capital letters. Readers, however, should contact the appropriate companies for more complete information regarding trademarks and registration. Some material may be © 2017 NVIDIA Corporation. All rights reserved. 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Library of Congress Cataloging-in-Publication Data A catalog record for this book is available from the Library of Congress British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library ISBN: 978-0-12-410397-9 For information on all Morgan Kaufmann publications visit our website at https://www.elsevier.com/ Publisher: Todd Green Acquisition Editor: Todd Green Editorial Project Manager: Lindsay Lawrence Production Project Manager: Priya Kumaraguruparan Cover Designer: Miles Hitchens Typeset by SPi Global, India Contributors C. Keith Cassidy University of Illinois at Urbana-Champaign, United States Keith is a graduate student in the Department of Physics at the University of Illinois Urbana- Champaign. As part of the Theoretical and Computational Biophysics Group, his research centers on the use of computational methodolo- gies to study molecular signal transduction and information processing within the context of bac- terial chemotaxis. Sunita Chandrasekaran University of Delaware, United States Sunita is an Assistant Professor at the Computer & Information Sciences department and an af- filiated faculty member with the Center for Bioinformatics & Computational Biology (CBCB) at the University of Delaware. She explores high- level programming abstractions for HPC and em- bedded systems. She also creates validation suites testing conformance of compiler implementations to programming standard specifications. She is a member of the OpenMP and OpenACC standard communities. She also contributes scientific paral- lel applications to SPEC HPG, of which she is a member. She has worked with the Multicore Association consortium to design and use open standard APIs for embed- ded systems. Dr. Chandrasekaran earned her PhD in Computer Science Engineering from Nanyang Technological University, Singapore for creating a high-level soft- ware stack for FPGAs. xi xii Contributors Barbara Chapman Stony Brook University, United States Barbara is a Professor of Applied Mathematics and Statistics, and of Computer Science, at Stony Brook University, where she is affiliated with the Institute for Advanced Computational Science. She has per- formed research on parallel programming interfaces and the related implementation technology for over 20 years and has been involved in efforts to develop community standards for parallel programming, in- cluding OpenMP, OpenACC, and OpenSHMEM. Her group at the University of Houston developed the OpenUH compiler that enabled practical experi- mentation with proposed extensions and implementation techniques. Dr. Chapman has participated in the work of the Multicore Association and explores the use of accelera- tors to obtain high performance on a broad variety of applications. Mathew Colgrove The Portland Group, United States Mat is an NVIDIA Dev Tech working with the PGI compiler team. Mat’s primary focus is on training, customer support, and programming advice on us- ing the PGI compilers, as well as OpenACC. Mat is also NVIDIA’s representative on SPEC’s CPU and HPG benchmarking committees. Janus Juul Eriksen Aarhus University, Denmark Janus is a postdoctoral researcher employed at the qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Denmark. His work is concerned in part with new theoretical developments in the area of accurate wave function-based quantum chemistry and in part the HPC adaption of the resulting models. Contributors xiii Robert Dietrich Technische Universität Dresden, Germany Robert studied Information Systems Technology at Technische Universitaet Dresden and gradu- ated in 2009. The focus as junior researcher and his diploma thesis was FPGA programmability in the context of high-performance computing. After graduation, he worked on the support of hardware accelerators and coprocessors in known performance analysis tools such as VampirTrace, Score-P, and Vampir. He is an active member in the OpenACC consortium and the OpenMP com- mittee, focusing on the standardization of tools support. He has carried out recent research in automatic analysis techniques for ap- plications on heterogeneous architectures. Rob Farber TechEnablement.com, United States Rob is a scientist and consultant with an extensive background in HPC and a long history of starting companies as well as working with national labo- ratories and corporations engaged in HPC, real- time, and machine learning. Rob is well published in technical and peer-reviewed literature. He has authored/edited several books and is the CEO/ Publisher of TechEnablement.com. xiv Contributors Saber Feki King Abdullah University of Science and Technology, Saudi Arabia Saber leads the Computational Scientists Team at the Supercomputing Core Laboratory at King Abdullah University of Science and Technology. He was part of the technical team for the procure- ment and led the acceptance of the world’s top 10 supercomputer, Shaheen XC40. Saber received his MSc and PhD degrees in computer science from the University of Houston in 2008 and 2010, respectively. He then joined the oil and gas company TOTAL in 2011 as HPC Research Scientist. Saber has been with KAUST since 2012. His research interests include parallel programming models and automatic performance tuning of MPI communications and OpenACC accelerated applications such as computational electromagnetics and seismic imaging. Oliver Fuhrer MeteoSwiss, Switzerland Oliver is the team leader of the model develop- ment group at the Federal Office of Meteorology and Climatology MeteoSwiss, Zurich. He has over 10 years’ experience in the fields of high- performance computing, regional climate simu- lation, and numerical weather prediction. He has applied and developed parallel software on vector (NEC SX-5) as well as massively parallel (HPC Cluster Brutus, Cray XT-4/5, XE6, XK7, XC30, as well as several experimental heterogeneous cluster solutions) architectures. He studied phys- ics at ETH Zurich, where he also completed his PhD in 2000 at the Institute of Atmospheric and Climate Science (IAC, ETH) on the topic of numerical simulation of convection at very high resolutions. He regularly lectures a course on numerical methods at ETH Zurich. Contributors xv Wayne Gaudin AWE plc., United Kingdom Wayne is a Computational Physicist with over 20 years of experience working on complex codes in an HPC environment. Over the last 3 years, he has concentrated on assessing emerging technologies and programming models in a number of algo- rithmic areas. Andy Herdman AWE plc., United Kingdom Andy is Head of the High Performance Computing section at AWE plc. He graduated from Newcastle University with a BSc (Hons) in Mathematics and Statistics; he also holds an MSc in Applied Mathematics. He has worked in the HPC applications field for over 20 years. Roles have included Technical Team Leader, responsible for code porting and optimization, and Group Leader of mul- tidisciplined teams, covering engineering codes, data visualization, and advanced technologies. He is currently a Visiting Fellow at the University of Warwick, researching his doctorate in the field of high-performance computing. Guido Juckeland Helmholtz-Zentrum Dresden-Rossendorf (HZDR), Germany Guido runs the Computational Science Group at Helmholtz-Zentrum Dresden-Rossendorf (HZDR) and coordinates the work of the GPU Center of Excellence at Dresden. He and also represents HZDR at the SPEC High Performance Group and OpenACC committee. He received his PhD for his work on performance analysis for hardware accelerators. xvi Contributors Jiri Kraus NVIDIA GmbH, Germany Jiri is a senior developer in NVIDIA’s European Developer Technology team. As a consultant for GPU HPC applications at the NVIDIA Julich Applications Lab and the Power Acceleration and Design Center (PADC), Jiri collaborates with developers and scien- tists at the Julich Supercomputing Centre and the Forschungszentrum Julich. Before joining NVIDIA, he worked on the parallelization and optimization of scientific and technical applica- tions for clusters of multicore CPUs and GPUs at Fraunhofer SCAI in St. Augustin. He holds a diploma in mathematics from the University of Cologne, Germany. Xavier Lapillonne MeteoSwiss, Switzerland Xavier is a senior scientist in the model develop- ment group at the Federal Office of Meteorology and Climatology MeteoSwiss, Zurich since 2015. He is working in the field of high-performance computing, in particular on hybrid systems, and is currently the project leader of the Performance on Massively Parallel Architectures project for the Consortium for Small-Scale Modeling (COSMO). He received a PhD in physics from EPF Lausanne in 2010, where he worked on massively parallel codes to simulate turbulence in hot plasmas. He has experience in developing and running scientific models on many supercomputers, including hybrid architectures (IBM blue gene, Bull NovaScale, Cray XT-4/5, XE6, XK7, XC30, CS-Storm).
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