Supercomputing Frontiers

301 Pages·2018·25.439 MB·English

by  Rio Yokota, Weigang Wu

Rio Yokota
Weigang Wu (Eds.)
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Supercomputing Frontiers
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4th Asian Conference, SCFA 2018
Singapore, March 26–29, 2018
Proceedings
Lecture Notes in Computer Science 10776
Commenced Publication in 1973
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Carnegie Mellon University, Pittsburgh, PA, USA
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ETH Zurich, Zurich, Switzerland
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Stanford University, Stanford, CA, USA
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Weizmann Institute of Science, Rehovot, Israel
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Indian Institute of Technology Madras, Chennai, India
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TU Dortmund University, Dortmund, Germany
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University of California, Berkeley, CA, USA
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Max Planck Institute for Informatics, Saarbrücken, Germany
More information about this series at http://www.springer.com/series/7407
Rio Yokota Weigang Wu (Eds.)
(cid:129)
Supercomputing Frontiers
4th Asian Conference, SCFA 2018
–
Singapore, March 26 29, 2018
Proceedings
Editors
RioYokota WeigangWu
Tokyo Institute of Technology SunYat-sen University
Tokyo Guangzhou
Japan China
ISSN 0302-9743 ISSN 1611-3349 (electronic)
Lecture Notesin Computer Science
ISBN 978-3-319-69952-3 ISBN978-3-319-69953-0 (eBook)
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Preface
As the share of supercomputers in Asia continues to increase, the relevance of
supercomputing in Asia has achieved a critical mass to merit the inauguration of a
supercomputing conference for Asia. Supercomputing Asia (SCA) 2018 encompassed
an umbrella of notable supercomputing events with the key objective of promoting a
vibrant and relevant HPC ecosystem in Asian countries, and was held during March
26–29, 2018, at Resorts World Convention Centre, Singapore.
The technical program of SCA18 had its roots inSupercomputing Frontiers (SCF),
whichisSingapore’sannualinternationalHPCconferencethatprovidesaplatformfor
leaders from both academia and industry to interact and discuss visionary ideas,
important global trends, and substantial innovations in supercomputing. The confer-
ence was inaugurated in 2015 and helmed by A*STAR Computational Resource
Centre (A*CRC). In March 2017, the National Supercomputing Centre (NSCC)
Singapore took over hosting of Supercomputing Frontiers 2017 (SCF17). 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. SCF17 was attended by over 450
delegates from over 12 different countries.
Riding on the success from the previous year, the SCA18 program highlights will
included:
– HPC technology updates and case studies
– Scientific paper presentations
– Academic activities and workshop for students
The co-located HPC events include:
– Asia-Pacific Advanced Network Meeting (APAN45)
– Towards an Asia Research Platform (ARP)
– Conference on Next-Generation Arithmetic (CoNGA)
– Singapore–Japan Joint Sessions
– Supercomputing Frontiers Asia (SCFA)
SCFA represented the technical program for SCA18, consisting offour tracks:
– Application, Algorithms, and Libraries
– Programming and System Software
– Data, Storage, and Visualization
– Architecture, Network/Communications, and Management
VI Preface
Wewouldliketoexpressourgratitudetoallourcolleaguesforsubmittingpapersto
theSCA18scientificsessions,aswellastothemembersoftheProgramCommitteefor
organizing this year’s attractive program.
March 2018 Rio Yokota
Weigang Wu
Organization
Technical Program Committee
Technical Papers Co-chairs
Rio Yokota Tokyo Institute of Technology, Japan
Weigang Wu Sun Yat-sen University, China
Application, Algorithms, and Libraries
Emmanuel Agullo Inria, France
Ariful Azad Lawrence Berkeley National Laboratory, USA
Costas Bekas IBM, Switzerland
Aparna Chandramowlishwaran University of California Irvine, USA
Kate Clark NVIDIA, USA
Hal Finkel Argonne National Laboratory, USA
Michael Heroux Sandia National Laboratories, USA
Johannes Langguth Simula, Norway
Piotr R. Luszczek University of Tennessee at Knoxville, USA
Maciej Malawski AGH University of Science and Technology,
Poland
John Owens UC Davis, USA
Vivek Pallipuram University of the Pacific, USA
Antonio Pena Barcelona Supercomputing Center, Spain
Min Si Argonne National Laboratory, USA
Hari Sundar University of Utah, USA
Nathan Tallent Pacific Northwest National Laboratory, USA
Programming and System Software
Olivier Aumage Inria, France
Sunita Chandrasekaran University of Delaware, USA
Florina M. Ciorba University of Basel, Switzerland
Bilel Hadri King Abdullah University of Science
and Technology, Saudi Arabia
Zbigniew Kalbarczyk University of Illinois, USA
Hatem Ltaief King Abdullah University of Science
and Technology, Saudi Arabia
Arthur Maccabe Oak Ridge National Laboratory, USA
Naoya Maruyama Lawrence Livermore National Laboratory, USA
Ronald Minnich Google Inc., USA
Raymond Namyst University of Bordeaux, France
C. J. Newburn NVIDIA, USA
Christian Perez Inria, France
VIII Organization
Miquel Pericas Chalmers University of Technology, Sweden
Mohamed Wahib National Institute of Advanced Industrial Science
and Technology, Japan
Data, Storage, and Visualization
Janine Bennett Sandia National Laboratories, USA
Mahdi Bohlouli University of Koblenz, Germany
Steffen Frey University of Stuttgart, Germany
Shadi Ibrahim Inria, France
Hai Jin Huazhong University of Science and Technology,
China
Hideyuki Kawashima University of Tsukuba, Japan
Quincey Koziol Lawrence Berkeley National Laboratory, USA
Suzanne McIntosh New York University, USA
Bogdan Nicolae Huawei Technologies, China
David Pugmire Oak Ridge National Laboratory, USA
Shinji Sumimoto Fujitsu, Japan
Bronis R. de Supinski Lawrence Livermore National Laboratory, USA
Daniela Ushizima Lawrence Berkeley National Laboratory, USA
Jon Woodring Los Alamos National Laboratory, USA
Amelie Chi Zhou Inria, France
Architecture, Network/Communications, and Management
David Abramson The University of Queensland, Australia
Eishi Arima The University of Tokyo, Japan
Ali R. Butt Virginia Tech, USA
Nikhil Jain University of Illinois, USA
John Kim Korea Advanced Institute of Science
and Technology, Korea
John Shalf Lawrence Berkeley National Laboratory, USA
Ryota Shioya Nagoya University, Japan
Jeremiah J. Wilke Sandia National Laboratories, USA
Weikuan Yu Florida State University, USA
Contents
Big Data
HHVSF: A Framework to Accelerate Drug-Based High-Throughput
Virtual Screening on High-Performance Computers. . . . . . . . . . . . . . . . . . . 3
Pin Chen, Xin Yan, Jiahui Li, Yunfei Du, and Jun Xu
HBasechainDB – A Scalable Blockchain Framework
on Hadoop Ecosystem. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 18
Manuj Subhankar Sahoo and Pallav Kumar Baruah
DETOUR: A Large-Scale Non-blocking Optical Data Center Fabric . . . . . . . 30
Jinzhen Bao, Dezun Dong, and Baokang Zhao
Querying Large Scientific Data Sets with Adaptable IO System ADIOS . . . . 51
Junmin Gu, Scott Klasky, Norbert Podhorszki, Ji Qiang,
and Kesheng Wu
On the Performance of Spark on HPC Systems: Towards
a Complete Picture . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
Orcun Yildiz and Shadi Ibrahim
Experiences of Converging Big Data Analytics Frameworks
with High Performance Computing Systems. . . . . . . . . . . . . . . . . . . . . . . . 90
Peng Cheng, Yutong Lu, Yunfei Du, and Zhiguang Chen
GPU/FPGA
MACC: An OpenACC Transpiler for Automatic Multi-GPU Use . . . . . . . . . 109
Kazuaki Matsumura, Mitsuhisa Sato, Taisuke Boku, Artur Podobas,
and Satoshi Matsuoka
Acceleration of Wind Simulation Using Locally Mesh-Refined
Lattice Boltzmann Method on GPU-Rich Supercomputers . . . . . . . . . . . . . . 128
Naoyuki Onodera and Yasuhiro Idomura
Architecture of an FPGA-Based Heterogeneous System
for Code-Search Problems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 146
Yuki Hiradate, Hasitha Muthumala Waidyasooriya,
Masanori Hariyama, and Masaaki Harada