2082 Supercomputing Frontiers 6Th Asian Conference, SCFA 2020 Singapore, February 24–27, 2020 Proceedings Lecture Notes in Computer Science 12082
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Dhabaleswar K. Panda (Ed.) LNCS 12082 Supercomputing Frontiers 6th Asian Conference, SCFA 2020 Singapore, February 24–27, 2020 Proceedings Lecture Notes in Computer Science 12082 Founding Editors Gerhard Goos Karlsruhe Institute of Technology, Karlsruhe, Germany Juris Hartmanis Cornell University, Ithaca, NY, USA Editorial Board Members Elisa Bertino Purdue University, West Lafayette, IN, USA Wen Gao Peking University, Beijing, China Bernhard Steffen TU Dortmund University, Dortmund, Germany Gerhard Woeginger RWTH Aachen, Aachen, Germany Moti Yung Columbia University, New York, NY, USA More information about this series at http://www.springer.com/series/7407 Dhabaleswar K. Panda (Ed.) Supercomputing Frontiers 6th Asian Conference, SCFA 2020 Singapore, February 24–27, 2020 Proceedings Editor Dhabaleswar K. Panda Department of Computer Science and Engineering The Ohio State University Columbus, OH, USA ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notes in Computer Science ISBN 978-3-030-48841-3 ISBN 978-3-030-48842-0 (eBook) https://doi.org/10.1007/978-3-030-48842-0 LNCS Sublibrary: SL1 – Theoretical Computer Science and General Issues The Editor(s) (if applicable) and The Author(s) 2020. This book is an open access publication. Open Access This book is licensed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license and indicate if changes were made. The images or other third party material in this book are included in the book’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the book’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, express or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland Preface As the share of supercomputers in Asia continues to increase, the relevance of supercomputing merits a supercomputing conference for Asia. Supercomputing Asia (SCA 2020) was planned to be an umbrella of notable supercomputing events that promote a vibrant HPC ecosystem in Asian countries. With over 600 speakers, par- ticipants, and exhibitors already pre-registered to attend, SCA20 was on course to be the biggest SCA conference yet. It was planned to be held during February 24–27, 2020, at Suntec Singapore Convention and Exhibition Centre. Unfortunately, the physical conference was canceled due to the COVID-19 pandemic. However, the current proceedings contain the list of papers selected under its technical paper program. The technical program of SCA19 provided a platform for leaders from both aca- demia and industry to interact and to discuss visionary ideas, important global trends, and substantial innovations in supercomputing. SCA19 was attended by over 700 delegates from over 20 different countries. In March 2017, the National Supercom- puting Centre (NSCC) Singapore hosted the Supercomputing Frontiers (SCF 2017). NSCC expanded the scope of SCF by embarking on the first Supercomputing Frontiers Asia (SCFA) technical paper program at SCA 2018. NSCC was established in 2015 and manages Singapore’s first national petascale facility with available HPC resources to support science and engineering computing needs for academic, research, and industry communities. SCFA represents the technical program for SCA 2020, consisting of four tracks: – Application, Algorithms, and Libraries – Architecture, Network/Communications, and Management – Data, Storage, and Visualization – Programming Models and Systems Software The submitted papers for the technical papers program went through a rigorous peer review process by an International Program Committee. A set of eight papers were finally selected for inclusion in these proceedings. The accepted papers cover a range of topics including file systems, memory hierarchy, HPC cloud platform, container image configuration workflow, large-scale applications, and scheduling. I would like thank all authors for their submissions to this conference. My sincere thanks to all Program Committee members for doing high-quality and in-depth reviewing of the submissions and selecting the papers for this year’s program. I would like to thank the conference organizers for giving me an opportunity to serve this year’s conference as the technical papers chair. To the readers, please enjoy these proceedings. April 2020 Dhabaleswar K. (DK) Panda Organization Program Chair Dhabaleswar K. (DK) Panda The Ohio State University, USA Program Committee Ritu Arora Texas Advanced Computing Center, USA Costas Bekas IBM Zurich, Switzerland Hal Finkel Argonne National Laboratory, USA Piotr R. Luszczek University of Tennessee at Knoxville, USA Antonio Pena Barcelona Supercomputing Center, Spain Nathan Tallent Pacific Northwest National Laboratory, USA Pradeep Dubey Intel Corporation, USA Rajkumar Buyya The University of Melbourne, Australia Albert Zomaya The University of Sydney, Australia Kishore Kothapalli IIIT Hyderabad, India Jianfeng Zhan Institute of Computing Technology (ICT), China Amitava Majumdar San Diego Supercomputing Centre, USA Nikhil Jain Google Inc., USA Ron Brightwell Sandia National Laboratories, USA John Kim Korea Advanced Institute of Science and Technology (KISTI), South Korea Ryota Shioya Nagoya University, Japan R. Govindarajan Indian Institute of Science Bangalore, India Quincey Koziol Lawrence Berkeley National Laboratory, USA Amelie Chi Zhou Shenzen University, China Ugo Varetto Pawsey Supercomputing Center, Australia Fang-Pang Lin National Center for High-performance Computing (NCHC), Taiwan Olivier Aumage Inria, France Sunita Chandrasekaran University of Delaware, USA Bilel Hadri King Abdullah University of Science and Technology, Saudi Arabia Hai Jin Huazong University of Science and Technology, China Arthur Maccabe Oak Ridge National Laboratory, USA Naoya Maruyama Lawrence Livermore National Laboratory, USA Ronald Minnich Google Inc., USA Yogesh Simmhan Indian Institute of Science Bangalore, India Sandra Gesing University of Notre Dame, USA viii Organization Michela Taufer University of Tennessee at Knoxville, USA Depei Qian Sun Yat-sen University, China Frances Lee Nanyang Technological University, Singapore Martin Schulz Technical University of Munich, Germany Tin Wee Tan National Supercomputing Centre, Singapore Contents File Systems, Storage and Communication A BeeGFS-Based Caching File System for Data-Intensive Parallel Computing . 3 David Abramson, Chao Jin, Justin Luong, and Jake Carroll Multiple HPC Environments-Aware Container Image Configuration Workflow for Large-Scale All-to-All Protein–Protein Docking Calculations. 23 Kento Aoyama, Hiroki Watanabe, Masahito Ohue, and Yutaka Akiyama DAOS: A Scale-Out High Performance Storage Stack for Storage Class Memory . 40 Zhen Liang, Johann Lombardi, Mohamad Chaarawi, and Michael Hennecke Cloud Platform Optimization for HPC . 55 Aman Verma Applications and Scheduling swGBDT: Efficient Gradient Boosted Decision Tree on Sunway Many-Core Processor . 67 Bohong Yin, Yunchun Li, Ming Dun, Xin You, Hailong Yang, Zhongzhi Luan, and Depei Qian Numerical Simulations of Serrated Propellers to Reduce Noise . 87 Wee-beng Tay, Zhenbo Lu, Sai Sudha Ramesh, and Boo-cheong Khoo High-Performance Computing in Maritime and Offshore Applications . 104 Kie Hian Chua, Harrif Santo, Yuting Jin, Hui Liang, Yun Zhi Law, Gautham R. Ramesh, Lucas Yiew, Yingying Zheng, and Allan Ross Magee Correcting Job Walltime in a Resource-Constrained Environment . 118 Jessi Christa Rubio, Aira Villapando, Christian Matira, and Jeffrey Aborot Author Index ............................................ 139 File Systems, Storage and Communication A BeeGFS-Based Caching File System for Data-Intensive Parallel Computing David Abramson(&) , Chao Jin , Justin Luong , and Jake Carroll The University of Queensland, St Lucia, QLD 4072, Australia {david.abramson,c.jin,justin.luong, jake.carroll}@uq.edu.au Abstract. Modern high-performance computing (HPC) systems are increas- ingly using large amounts of fast storage, such as solid-state drives (SSD), to accelerate disk access times. This approach has been exemplified in the design of “burst buffers”, but more general caching systems have also been built. This paper proposes extending an existing parallel file system to provide such a file caching layer. The solution unifies data access for both the internal