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The document discusses the proceedings of the Big Scientific Data Benchmarks, Architecture, and Systems (SDBA) workshop held in Beijing on June 12, 2018, focusing on the importance of efficient management and analysis of big scientific data for scientific discovery. It highlights the need for comprehensive benchmarks to aid researchers in designing high-performance data management systems tailored to specific scientific domains. The document includes ten selected papers from the workshop, addressing various topics related to benchmarking and optimizing big scientific data architectures and systems.

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8 views124 pages

46204

The document discusses the proceedings of the Big Scientific Data Benchmarks, Architecture, and Systems (SDBA) workshop held in Beijing on June 12, 2018, focusing on the importance of efficient management and analysis of big scientific data for scientific discovery. It highlights the need for comprehensive benchmarks to aid researchers in designing high-performance data management systems tailored to specific scientific domains. The document includes ten selected papers from the workshop, addressing various topics related to benchmarking and optimizing big scientific data architectures and systems.

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Rui Ren
Chen Zheng
Jianfeng Zhan (Eds.)

Communications in Computer and Information Science 911

Big Scientific Data


Benchmarks, Architecture,
and Systems
First Workshop, SDBA 2018
Beijing, China, June 12, 2018
Revised Selected Papers

123
Communications
in Computer and Information Science 911
Commenced Publication in 2007
Founding and Former Series Editors:
Phoebe Chen, Alfredo Cuzzocrea, Xiaoyong Du, Orhun Kara, Ting Liu,
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Pontifical Catholic University of Rio de Janeiro (PUC-Rio),
Rio de Janeiro, Brazil
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Polytechnic Institute of Setúbal, Setúbal, Portugal
Ashish Ghosh
Indian Statistical Institute, Kolkata, India
Igor Kotenko
St. Petersburg Institute for Informatics and Automation of the Russian
Academy of Sciences, St. Petersburg, Russia
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Indian Institute of Technology Madras, Chennai, India
Takashi Washio
Osaka University, Osaka, Japan
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University at Buffalo, The State University of New York, Buffalo, USA
Lizhu Zhou
Tsinghua University, Beijing, China
More information about this series at http://www.springer.com/series/7899
Rui Ren Chen Zheng

Jianfeng Zhan (Eds.)

Big Scientific Data


Benchmarks, Architecture,
and Systems
First Workshop, SDBA 2018
Beijing, China, June 12, 2018
Revised Selected Papers

123
Editors
Rui Ren Jianfeng Zhan
Institute of Computing Technology Institute of Computing Technology
Chinese Academy of Sciences Chinese Academy of Sciences
Beijing, China Beijing, China
Chen Zheng
Institute of Computing Technology
Chinese Academy of Sciences
Beijing, China

ISSN 1865-0929 ISSN 1865-0937 (electronic)


Communications in Computer and Information Science
ISBN 978-981-13-5909-5 ISBN 978-981-13-5910-1 (eBook)
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Singapore
Big Scientific Data: A Rich and Fertile Land

The past several decades witnessed that many scientific projects are data-driven. For
example, Aronova et al. [1] discussed the historical connections between two
large-scale scientific projects about 50 or 60 years ago that became exemplars for
worldwide data-driven scientific initiatives after World War II: the International
Geophysical Year (1957–1958; in short, IGY) and the International Biological Program
(1964–1974). They concluded [1] that one of the important features of the IGY was its
data-driven mode of research, as contrasted with the hypothesis- [3, 4] or
instrument-driven mode [5] of most physicists’ work and with the platform-driven [6]
character of much of the space program.
In recent years, this trend has accelerated, and big scientific data have become the
foundation and strategic resources for science discovery and technology innovation.
There is increasing interest to generate value from big scientific data. However, effi-
cient management and analysis of big scientific data comprise the first step toward
scientific discovery. Scientific data in different domains have unique data schemas, i.e.,
event data in high-energy physics, RDF data in microbiology, and spatial-temporal data
in astronomy. In this context, widely used data management and analytic systems are
not necessarily the best choices. The unique characteristics of big scientific data pro-
vide new research opportunities. To achieve higher efficiency, we need to tailor both
software and hardware architecture to the characteristics of a domain of applications [6,
7]. However, the first step is to fully understand big scientific data.
Without comprehensive big scientific data benchmarks, it is very difficult for sci-
entific researchers and computer system researchers to design and implement
high-performance and energy-efficient data management and analytics systems.
The NAS parallel benchmarks [8] provide a good example for understanding scientific
workloads in terms that the common requirements are specified only algorithmically in
a paper-and-pencil approach [8] and are reasonably divorced from individual imple-
mentations [9].
In recent years there has been progress in our understanding and modeling of
modern big data and AI workloads. Gao et al. [7] consider each big data and AI
workload as a pipeline of one or more classes of units of computation performed on
different initial or intermediate data inputs, each class of which is called a data motif.
They [7] also identify eight data motifs taking up most of the runtime of a wide variety
of big data and AI workloads, including Matrix, Sampling, Transform, Graph, Logic,
Set, Sort and Statistic computation. Furthermore, they found [7] that significantly
different from the traditional kernels [8, 9], a data motif’s behaviors are affected by the
sizes, patterns, types, and sources of different data inputs. Finally, they [9, 10] propose
using the combination of one or more data motifs, to represent diversity of big data and
AI workloads, and release a unified big data and AI benchmark suite—BigDataBench
4.0 [9, 10]. This unified benchmark suite sheds new light on domain-specific hardware
and software co-design in terms of tailoring the system and architecture to the
VI Big Scientific Data: A Rich and Fertile Land

characteristics of the unified eight data motifs other than one or more applications case
by case [7, 9, 10]. However, there is still a long way ahead for big scientific
data-specific hardware and software system co-design as there are huge recognition
gaps between scientific researchers and computer system researchers. Fortunatelsy,
pioneer researchers have paved a path. For example, SciDB [11] is a good attempt of
data management system intended primarily for use in application domains that involve
very large (petabyte)- scale array data.
Following the past success of BPOE (Big Data benchmarks, Performance Opti-
mization, and Emerging Hardware) workshops [12, 13], we organized the first work-
shop on Big Scientific Data Benchmarks, Architecture, and Systems (SDBAA 2018;
http://prof.ict.ac.cn/sdba18/), which was co-located with ICS 2018 (http://prof.ict.ac.cn/
sdba18/)— an ACM International Conference on Supercomputing. The workshop
seeks papers that address hot topics in benchmarking, designing, implementing and
optimizing big scientific data architecture and systems. This book includes ten papers
from the SDBA 2018 workshop.
The call for papers for the workshop attracted a number of high-quality submissions.
During a rigorous review process, in which each paper was reviewed by at least three
experts, we select ten papers for presentation as SDBA 2018. In addition, we also
invited a keynote speaker, Prof. Ziming Zou from the Chinese Academy of Sciences,
whose topic was “Big Data Processing and Application Use Cases from China Space
Science Missions.”
We are very grateful for the efforts of all authors related to writing, revising, and
presenting their papers at the SDBA workshop. Finally, we appreciate the indispens-
able support of the SDBA Program Committee and thank them for their efforts and
contributions in maintaining the high standards of the SDBA workshop.

December 2018 Rui Ren


Chen Zheng
Jianfeng Zhan

References

1. E. Aronova, K. S. Baker, and N. Oreskes, Big science and big data in biology:
From the international geophysical year through the international biological pro-
gram to the long term ecological research (lter) network, 1957—present, Hist Stud
Nat Sci, vol. 40, no. 2, pp. 183–224, 2010.
2. D. B. Kell and S. G. Oliver, Here is the evidence, now what is the hypothesis? the
complementary roles of inductive and hypothesis-driven science in the
post-genomic era, Bioessays, vol. 26, no. 1, pp. 99–105, 2004.
3. U. Krohs and W. Callebaut, Data without models merging with models without
data, in Systems biology. Elsevier, 2007, pp. 181–213.
4. P. Galison, Image and logic: A material culture of microphysics. University of
Chicago Press, 1997.
Big Scientific Data: A Rich and Fertile Land VII

5. D. H. DeVorkin, Science with a vengeance: how the military created the us space
sciences after world war ii, Science With A Vengeance. How the Military Created
the US Space Sciences After World War II, XXII, 404 pp. 109 figs.
Springer-Verlag Berlin Heidelberg New York. Also Springer Study Edition,
p. 109, 1992.
6. J. Hennessy and D. Patterson, A new golden age for computer architecture:
Domain-specific hardware/software co-design, enhanced security, open instruction
sets, and agile chip development, 2018.
7. W. Gao, J. Zhan, L. Wang, C. Luo, D. Zheng, F. Tang, B. Xie, C. Zheng, X. Wen,
X. He, H. Ye, and R. Ren, Data motifs: A lens towards fully understanding big
data and ai workloads, Parallel Architectures and Compilation Techniques
(PACT), 27th International Conference on, 2018.
8. D. H. Bailey, E. Barszcz, J. T. Barton, D. S. Browning, R. L. Carter, L. Dagum, R.
A. Fatoohi, P. O. Frederickson, T. A. Lasinski, R. S. Schreiber et al., The nas
parallel benchmarks, The International Journal of Supercomputing Applications,
vol. 5, no. 3, pp. 63–73, 1991.
9. K. Asanovic, R. Bodik, B. C. Catanzaro, J. J. Gebis, P. Husbands, K. Keutzer, D.
A. Patterson,W. L. Plishker, J. Shalf, S.W. Williams, and Y. Katherine, The
landscape of parallel computing research: A view from berkeley, Technical Report
UCB/EECS-2006-183, EECS Department, University of California, Berkeley,
Tech. Rep., 2006.
10. W. Gao, J. Zhan, L. Wang, C. Luo, D. Zheng, X. Wen, R. Ren, C. Zheng, H. Ye,
J. Dai, Z. Cao, et al., Bigdatabench: A scalable and unified big data and ai
benchmark suite, Under review of IEEE Transaction on Parallel and Distributed
Systems, 2018.
11. L. Wang, J. Zhan, C. Luo, Y. Zhu, Q. Yang, Y. He, W. Gao, Z. Jia, Y. Shi, S.
Zhang et al., Bigdatabench: A big data benchmark suite from internet services,
IEEE International Symposium On High Performance Computer Architecture
(HPCA), 2014.
12. Stonebraker, M., Brown, P., Zhang, D., & Becla, J. (2013). SciDB: A database
management system for applications with complex analytics. Computing in Sci-
ence & Engineering, 15(3), 54-62.
13. J. Zhan, R. Han, C. Weng. Big Data Benchmarks, Performance Optimization, and
Emerging Hardware, Springer LNCS, volume 8807, 2014.
14. J. Zhan, R. Han, R. V. Zicari. Big Data Benchmarks, Performance Optimization,
and Emerging Hardware, Springer LNCS, volume 9495, 2016.
Organization

Program Co-chairs
Rui Ren Institute of Computing Technology, Chinese Academy
of Sciences and University of Chinese Academy
of Sciences, China
Xiaoyong Du Renmin University of China, China
Jianfeng Zhan Institute of Computing Technology, Chinese Academy
of Sciences and University of Chinese Academy
of Sciences, China

General Chairs
Chen Zheng Institute of Computing Technology, Chinese Academy
of Sciences and University of Chinese Academy
of Sciences, China
Jianhui Li Computer Network Information Center, Chinese Academy
of Sciences, China

Program Committee
Xiaoyi Lu The Ohio State University, USA
Hyogi Sim Oak Ridge National Laboratory, USA
Gwangsun Kim ARM Ltd.
Nikhil Jain Lawrence Livermore National Laboratory, USA
Weijia Xu The University of Texas at Austin, USA
Zhihui Du Tsinghua University, China
Lei Wang Institute of Computing Technology, Chinese Academy
of Sciences, China
Shengzhong Feng Shenzhen Institutes of Advanced Technology, Chinese
Academy of Sciences, China
Jiaquan Gao Nanjing Normal University, China
Hua Zhong Institute of Software, Chinese Academy of Sciences, China
Li Zha Institute of Computing Technology, Chinese Academy
of Sciences, China
Yunquan Zhang Institute of Computing Technology, Chinese Academy
of Sciences, China
Cheqing Jin East China Normal University, China
Yuanming Zhang Zhejiang University of Technology, China
Wenyao Zhang Beijing Institute of Technology, China
Xiaoru Yuan Peking University, China
X Organization

Jianyan Wei National Astronomical Observatories, Chinese Academy


of Sciences, China
Yuanchun Zhou Computer Network Information Center, Chinese Academy
of Sciences, China
Gang Chen Institute of High Energy Physics, Chinese Academy
of Sciences, China
Jungang Xu University of Chinese Academy of Sciences, China
Yue Liu Shanghai University, China
Rong Zhang East China Normal University, China
Yaodong Cheng Institute of High Energy Physics, Chinese Academy
of Sciences, China
Lizhe Wang Institute of Remote Sensing Applications, Chinese Academy
of Sciences, China
Ce Yu Tianjin University, China
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