Contributions of hybrid architectures to depth imaging : a CPU, APU and GPU comparative study Issam Said To cite this version: Issam Said. Contributions of hybrid architectures to depth imaging : a CPU, APU and GPU com- parative study. Hardware Architecture [cs.AR]. Université Pierre et Marie Curie - Paris VI, 2015. English. NNT : 2015PA066531. tel-01248522v2 HAL Id: tel-01248522 https://tel.archives-ouvertes.fr/tel-01248522v2 Submitted on 20 May 2016 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. THESE` DE DOCTORAT DE l’UNIVERSITE´ PIERRE ET MARIE CURIE sp´ecialit´e Informatique Ecole´ doctorale Informatique, T´el´ecommunications et Electronique´ (Paris) pr´esent´eeet soutenue publiquement par Issam SAID pour obtenir le grade de DOCTEUR en SCIENCES de l’UNIVERSITE´ PIERRE ET MARIE CURIE Apports des architectures hybrides `a l’imagerie profondeur : ´etude comparative entre CPU, APU et GPU Th`esedirig´eepar Jean-Luc Lamotte et Pierre Fortin soutenue le Lundi 21 D´ecembre 2015 apr`es avis des rapporteurs M. Fran¸cois Bodin Professeur, Universit´ede Rennes 1 M. Christophe Calvin Chef de projet, CEA devant le jury compos´ede M. Fran¸cois Bodin Professeur, Universit´ede Rennes 1 M. Henri Calandra Expert en imagerie profondeur et calcul haute performance, Total M. Christophe Calvin Chef de projet, CEA M. Pierre Fortin Maˆıtrede conf´erences, Universit´ePierre et Marie Curie M. Lionel Lacassagne Professeur, Universit´ePierre et Marie Curie M. Jean-Luc Lamotte Professeur, Universit´ePierre et Marie Curie M. Mike Mantor Senior Fellow Architect, AMD M. St´ephane Vialle Professeur, SUPELEC campus de Metz “If I have seen further it is by standing on the shoulders of Giants.” — Isaac Newton Acknowledgements Foremost, I would like to express my deepest thanks to my two directors, Pr. Jean-Luc Lamotte and Dr. Pierre Fortin. Their patience, encouragement, and immense knowledge were key motivations throughout my Ph.D. I thank them for having instructed me, for having guided me to compose this thesis, and for having steered me to the end. I thank them for having cheerfully assisted me in moments of frustration and of doubt. I would like to gratefully thank Henri Calandra for his trust, valuable recommendations, insights and useful discussions. He accompanied me throughout this adventure, I look forward to the next one. I have been privileged and honored to have had my work been reviewed by Pr. Fran¸cois Bodin and Dr. Christophe Calvin. I am indebted to them for having taken the time out of their busy schedules, and for having spent efforts to go through, to give insightful comments, and to correct the ideas shared in this dissertation. I also thank the rest of the committee members: Pr. Lionel Lacassagne, M. Mike Mantor and Pr. St´ephaneVialle for having accepted to examine this dissertation and to give valuable feedbacks. This work was a close partnership between Total, AMD, CAPS and Lip6. I would like to extend my gratitude to Total for funding this project. AMD is acknowledged for providing the hardware which was used at the heart of this work. CAPS is kindly acknowledged for the technical support and the sophisticated skills. Immeasurable appreciation and deepest gratitude for the help and support are ex- tended to the following persons, who in one way or another, have contributed in making this study possible. Bruno Conche for his endless support and logistic help, and more importantly for his energy that he did not spare in order to put this project together, without him it would not have been a success. Bruno Stefanizzi for having pointed me to the right way whenever I had questions or needed support from AMD. Laurent Morichetti, Joshua Mora and Robert Engel, each of whom had made each journey of mine to the AMD Sunnyvale campus, a pleasant experience. I thank them for sharing their experiences with me, and for finding answers to all of my questions. Greg Stoner and Gregory Rodgers, for the helpful discussions and the valuable information about the AMD hardware and software stack roadmaps. Terrence Liao and Rached Abdelkhalek, for their precious advices and for the brain storming sessions during my trips to Pau, France. Harry Zong, Jing Wen, Donny Cooper, Matthew Bettinger and Russell Jones for their precious help in setting up a remote work environment. Romain Dolbeau, for having put his rich technical expertise at my disposal. My fellow colleagues in the PE- QUAN team with whom I have shared memorable moments throughout this experience. The administrative staff of the PEQUAN team is also kindly acknowledged for having taken care of my professional trips. On a more personal note, words cannot express my gratitude for my parents, Khalifa and Moufida, the reason of what I become today thank you for your great support and continuous care. I profusely thank my brothers Bilel and Zied for being there for me no matter what. Asma, thank you for being supportive and for the great moments we spent together discussing this project. Rached, thank you for your hospitality, for the time, for the trips and for the laughs and fears we lived together. Saber, thank you immensely for your wise thoughtful advices, and for the numerous funny moments we spent together. I thank my cousins and friends (Khaled, Yasser, Rafik, Haithem, Fethi, Mohammed, Elkhal, John, Erick, Nefili, Layla, Justyna, Chris, Daniel, Jeaven, Binomi, Sahma, Saif, Sana, Sari, Hanen, and the list goes on) for the precious moments of joy that were much needed during this journey. Moktar and Souad, I owe you a deep sense of gratitude for you unconditional love and attention. Ludmila, Igor, Anna, Beji, and Lorita thank you for your never ending support, and more importantly for the initiation to the Russian “banya”. To my wonderful wife Tatjana, whose sacrificial care for me, her quiet patience, her tolerance to my occasional vulgar moods, and her unwavering love made it possible for me to finish this work, I express my genuine appreciation. Finally, I thank my son Arsen, a treasure from the Lord that was offered to me and to my wife in the middle of this adventure, and who was the source of my inspiration and of my greatest happiness. vi Contents Contents vi 1 Introduction 1 I State of the art 5 2 Geophysics and seismic applications 7 2.1 Introduction to seismic exploration ...................... 8 2.1.1 Seismic acquisition ........................... 9 2.1.2 Seismic processing ........................... 11 2.1.3 Seismic interpretation ......................... 14 2.2 Seismic migrations and Reverse Time Migration (RTM) . 14 2.2.1 Description and overview of migration methods . 14 2.2.2 Reverse Time Migration ........................ 16 2.3 Numerical methods for the wave propagation phenomena . 18 2.3.1 The wave equation ........................... 19 2.3.1.1 Seismic waves and propagation media . 19 2.3.1.2 The elastic wave equation . 19 2.3.1.3 The acoustic wave equation . 21 2.3.2 Numerical methods for wave propagation . 22 2.3.2.1 Integral methods ....................... 22 2.3.2.2 Asymptotic methods ..................... 23 2.3.2.3 Direct methods ........................ 23 2.3.2.3.1 Pseudo-Spectral Methods . 23 2.3.2.3.2 Finite Difference Methods . 23 2.3.2.3.3 Finite Element Methods . 24 2.3.3 Application to the acoustic wave equation . 25 2.3.3.1 Numerical approximation . 25 2.3.3.2 Stability analysis and CFL . 27 2.3.3.3 Boundary conditions ..................... 28 3 High performance computing 29 3.1 Overview of HPC hardware architectures . 30 3.1.1 Central Processing Unit: more and more cores . 30 3.1.2 Hardware accelerators: the other chips for computing . 33 3.1.3 Towards the fusion of CPUs and accelerators: the emergence of the Accelerated Processing Unit ................... 36 Contents vii 3.2 Programming models in HPC ......................... 41 3.2.1 Dedicated programming languages for HPC . 41 3.2.1.1 Overview ........................... 41 3.2.1.2 The OpenCL programming model . 43 3.2.2 Directive-based compilers and language extensions . 45 3.3 Power consumption in HPC and the power wall . 45 4 Overview of accelerated seismic applications 49 4.1 Stencil computations .............................. 49 4.2 Reverse time migration ............................. 52 4.2.1 Evolution of RTM algorithms ..................... 52 4.2.2 Wave-field reconstruction methods . 53 4.2.2.1 Re-computation of the forward wavefield . 54 4.2.2.2 Storing all the forward wavefield . 54 4.2.2.3 Selective wavefield storage (linear checkpointing) . 54 4.2.2.4 Checkpointing ........................ 55 4.2.2.5 Boundaries storage ...................... 56 4.2.2.6 Random boundary condition . 56 4.2.3 RTM on multi-cores and hardware accelerators . 56 4.2.3.1 RTM on multi-core CPUs . 57 4.2.3.2 RTM on GPUs ........................ 58 4.2.3.3 RTM on other accelerators . 59 4.3 Close to seismics workflows .......................... 61 5 Thesis position and contributions 63 5.1 Position of the study .............................. 63 5.2 Contributions .................................. 65 5.3 Hardware and seismic material configurations . 67 5.3.1 The hardware configuration ...................... 68 5.3.2 The numerical configurations of the seismic materials . 69 5.3.2.1 The seismic source ...................... 69 5.3.2.2 The velocity model and the compute grids .