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An extended linear algebra library for electronic structure calculation and its optimization for many-core processors

Research Project

Project/Area Number 26286087
Research Category

Grant-in-Aid for Scientific Research (B)

Allocation TypePartial Multi-year Fund
Section一般
Research Field Computational science
Research InstitutionThe University of Electro-Communications

Principal Investigator

Yamamoto Yusaku  電気通信大学, 大学院情報理工学研究科, 教授 (20362288)

Co-Investigator(Kenkyū-buntansha) 横川 三津夫  神戸大学, 先端融合研究環, 教授 (70358307)
星 健夫  鳥取大学, 工学研究科, 准教授 (80272384)
Co-Investigator(Renkei-kenkyūsha) IMAMURA TOSHIYUKI  理化学研究所, 計算科学研究センター, チームリーダー (60361838)
INADOMI YUICHI  九州大学, 大学院システム情報科学研究院, 研究員 (70437747)
Research Collaborator Vajtersic Marian  ザルツブルグ大学, コンピュータサイエンス学科, 教授
Project Period (FY) 2014-04-01 – 2018-03-31
Project Status Completed (Fiscal Year 2017)
Budget Amount *help
¥11,440,000 (Direct Cost: ¥8,800,000、Indirect Cost: ¥2,640,000)
Fiscal Year 2016: ¥4,290,000 (Direct Cost: ¥3,300,000、Indirect Cost: ¥990,000)
Fiscal Year 2015: ¥3,250,000 (Direct Cost: ¥2,500,000、Indirect Cost: ¥750,000)
Fiscal Year 2014: ¥3,900,000 (Direct Cost: ¥3,000,000、Indirect Cost: ¥900,000)
Keywords固有値計算 / 連立1次方程式 / 直交化 / 並列計算 / メニーコア / 電子状態計算 / 計算科学 / 確率的アルゴリズム / 並列化 / 非線形固有値問題 / 理論流体力学 / 連立1次方程式解法 / 有機高分子系 / 前処理付き反復法 / 線形計算 / 固有値 / 行列関数 / 通信回避型アルゴリズム / 電子波ダイナミクス / 固有値問題
Outline of Final Research Achievements

In this project, we aimed at developing solvers for numerical linear algebra functions used in electronic structure calculations. The main achievements of this project are as follows. (1) We performed an error analysis of the CholeskyQR2 method, which is a promising communication-avoiding algorithm for the QR decomposition, and proved its numerical stability. (2) We developed a parallel linear equation solver based on the one-way dissection for quantum wave dynamics. (3) We developed a generalized eigenvalue solver EigenKernel, which is a hybrid solver that combines three eigenvalue solvers for dense matrices. These results will be useful for accelerating electronic structure calculations on many-core processors.

Report

(5 results)
  • 2017 Annual Research Report   Final Research Report ( PDF )
  • 2016 Annual Research Report
  • 2015 Annual Research Report
  • 2014 Annual Research Report
  • Research Products

    (42 results)

All 2018 2017 2016 2015 2014 Other

All Int'l Joint Research (4 results) Journal Article (13 results) (of which Int'l Joint Research: 3 results,  Peer Reviewed: 12 results,  Acknowledgement Compliant: 8 results,  Open Access: 2 results) Presentation (22 results) (of which Int'l Joint Research: 7 results,  Invited: 6 results) Book (2 results) Remarks (1 results)

  • [Int'l Joint Research] ザルツブルグ大学(オーストリア)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] スロバキア国立科学アカデミー(スロバキア)

    • Related Report
      2016 Annual Research Report
  • [Int'l Joint Research] Salzburg University(Austria)

    • Related Report
      2015 Annual Research Report
  • [Int'l Joint Research] Slovak Academy of Sciences(Slovakia)

    • Related Report
      2015 Annual Research Report
  • [Journal Article] Solution of a Nonlinear Eigenvalue Problem Using Signed Singular Values2018

    • Author(s)
      Ooi Kouhei、Mizuno Yoshinori、Sogabe Tomohiro、Yamamoto Yusaku、Zhang Shao-Liang
    • Journal Title

      East Asian J. Appl. Math.

      Volume: 7 Issue: 4 Pages: 799-809

    • DOI

      10.4208/eajam.181016.300517c

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] On the optimality and sharpness of Laguerre's lower bound on the smallest eigenvalue of a symmetric positive definite matrix2017

    • Author(s)
      Yusaku Yamamoto
    • Journal Title

      Appl. Math.

      Volume: 62 Issue: 4 Pages: 319-331

    • DOI

      10.21136/am.2017.0022-17

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] The danger of combining block red?black ordering with modified incomplete factorizations and its remedy by perturbation or relaxation2017

    • Author(s)
      Shioya Akemi、Yamamoto Yusaku
    • Journal Title

      Japan J. Indust. Appl. Math.

      Volume: 35 Issue: 1 Pages: 195-216

    • DOI

      10.1007/s13160-017-0277-5

    • NAID

      210000166851

    • Related Report
      2017 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Asymptotic quadratic convergence of the serial block-Jacobi EVD algorithm for Hermitian matrices2017

    • Author(s)
      Gabriel Oksa, Yusaku Yamamoto and Marian Vajtersic
    • Journal Title

      Numerische Mathematik

      Volume: 印刷中 Issue: 4 Pages: 1071-1095

    • DOI

      10.1007/s00211-016-0863-5

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] Performance analysis and optimization of the parallel one-sided block Jacobi SVD algorithm with dynamic ordering and variable blocking2017

    • Author(s)
      Shuhei Kudo, Yusaku Yamamoto, Martin Becka and Marian Vajtersic
    • Journal Title

      Concurrency and Computation: Practice and Experience

      Volume: 印刷中 Issue: 9

    • DOI

      10.1002/cpe.4059

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] On constructing cost models for online automatic tuning using ATMathCoreLib2016

    • Author(s)
      Seiji Nagashima, Takeshi Fukaya and Yusaku Yamamoto
    • Journal Title

      Proceedings of the IEEE 10th International Symposium on Embedded Multicore/Many-core Systtems-on-Chip (MCSoC-16)

      Volume: - Pages: 345-352

    • DOI

      10.1109/mcsoc.2016.52

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Extremely scalable algorithm for 10^8-atom quantum material simulation on the full system of the K computer2016

    • Author(s)
      Takeo Hoshi, Hiroto Imachi, Kiyoshi Kumahata, Masaaki Terai, Kengo Miyamoto, Kazuo Minami and Fumiyoshi Shoji
    • Journal Title

      Proceeding of ScalA16: Workshop on Latest Advances in Scalable Algorithms for Large-Scale Systems

      Volume: -

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] One-hundred-nm-scale electronic structure and transport calculations of organic polymers on the K computer2016

    • Author(s)
      Hiroto Imachi, Seiya Yokoyama, Takami Kaji, Yukiya Abe, Tomofumi Tada, Takeo Hoshi
    • Journal Title

      AIP Conf. Proc.

      Volume: 1790 Pages: 020010-020010

    • DOI

      10.1063/1.4968636

    • Related Report
      2016 Annual Research Report
    • Peer Reviewed / Acknowledgement Compliant
  • [Journal Article] Hybrid numerical solvers for massively parallel eigenvalue computation and their benchmark with electronic structure calculations2016

    • Author(s)
      H. Imachi and T. Hoshi
    • Journal Title

      J. Inf. Process

      Volume: 164 -- 172 Pages: 164-172

    • NAID

      130005119986

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed
  • [Journal Article] Roundoff error analysis of the CholeskyQR2 algorithm in an oblique inner product2016

    • Author(s)
      Y. Yamamoto, Y. Nakatsukasa, Y. Yanagisawa and T. Fukaya
    • Journal Title

      JSIAM Letters

      Volume: 8 Pages: 5-8

    • NAID

      130005125235

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Open Access / Acknowledgement Compliant
  • [Journal Article] Performance of the parallel one-sided block Jacobi SVD algorithm on a modern distributed-memory parallel computer2016

    • Author(s)
      S. Kudo, Y. Yamamoto, M. Becka and M. Vajtersic
    • Journal Title

      Lecture Notes in Computer Science

      Volume: 9573

    • Related Report
      2015 Annual Research Report
    • Peer Reviewed / Int'l Joint Research / Acknowledgement Compliant
  • [Journal Article] 大規模連立一次方程式の反復解法の 実問題への適用と性能評価2015

    • Author(s)
      俵谷 健太郎,横川 三津夫
    • Journal Title

      情報処理学会研究報告ハイパフォーマンスコンピュー ティング(HPC)

      Volume: 2015-HPC-152 Pages: 1-7

    • Related Report
      2015 Annual Research Report
    • Acknowledgement Compliant
  • [Journal Article] Convergence analysis of the parallel classical block Jacobi method for the symmetric eigenvalue problem2014

    • Author(s)
      Y. Yamamoto, L. Zhang and S. Kudo
    • Journal Title

      JSIAM Letters

      Volume: 6 Pages: 57-60

    • NAID

      130004713955

    • Related Report
      2014 Annual Research Report
    • Peer Reviewed
  • [Presentation] Block Red-Black Milu(0) Preconditioner with Relaxation on GPU2018

    • Author(s)
      Akemi Shioya and Yusaku Yamamoto
    • Organizer
      18th SIAM Conference on Parallel Processing for Scientific Computing
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] Roundoff error analysis of the CholeskyQR2 and related algorithms2017

    • Author(s)
      Yusaku Yamamoto
    • Organizer
      PARNUM2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ブロック赤-黒順序付けされた摂動/緩和MILU(0) 前処理法のGPUとマルチコアCPUにおける性能評価2017

    • Author(s)
      塩谷明美,山本有作
    • Organizer
      SWoPP 2017
    • Related Report
      2017 Annual Research Report
  • [Presentation] On using the Cholesky QR method in the full-blocked one-sided Jacobi algorithm2017

    • Author(s)
      Shuhei Kudo and Yusaku Yamamoto
    • Organizer
      PPAM2017
    • Related Report
      2017 Annual Research Report
    • Int'l Joint Research
  • [Presentation] 虚数シフトを行った実対称行列のための COCG法と一般化MINRES法の性能比較2017

    • Author(s)
      清藤 博暉, 山本 有作
    • Organizer
      日本応用数理学会「行列・固有値問題 の解法とその応用」研究部会 第24回研究会
    • Related Report
      2017 Annual Research Report
  • [Presentation] 色数を抑えた改良reverse Cuthill-McKee法による線形ソルバの並列化について2017

    • Author(s)
      俵谷 健太郎,横川 三津夫
    • Organizer
      情報処理学会 第159回ハイパフォーマンスコンピューティング研究発表会
    • Place of Presentation
      東京大学 情報基盤センター(千葉県柏市)
    • Related Report
      2016 Annual Research Report
  • [Presentation] π共役ポリマーの電子状態計算に現れる連立一次方程式の並列解法2016

    • Author(s)
      横川三津夫,熊澤賢一郎,山本有作
    • Organizer
      計算物質科学における時空間アップスケーリングと数理手法
    • Place of Presentation
      電気通信大学(東京都調布市)
    • Year and Date
      2016-11-28
    • Related Report
      2016 Annual Research Report
  • [Presentation] One-hundred-nanometer-scale electronic state and transport calculations of organic device material on the K computer2016

    • Author(s)
      Takeo Hoshi, Hiroto Imachi
    • Organizer
      The 19th Asian Workshop on First-Principles Electronic Structure Calculations, National Chiao Tung University, Hsinchu, Taiwan
    • Place of Presentation
      National Chiao Tung University, Hsinchu, Taiwan
    • Year and Date
      2016-10-31
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] Convergence and Performance Analysis of the Parallel Block Jacobi SVD Algorithm with Dynamic Ordering2016

    • Author(s)
      Yusaku Yamamoto
    • Organizer
      Parallel Numerical Computing and Its Applications
    • Place of Presentation
      Smolenice, Slovakia
    • Year and Date
      2016-09-07
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] 100M atom electronic structure calculation of organic device materials on full system of K Computer2016

    • Author(s)
      Takeo Hoshi
    • Organizer
      ISC2016
    • Place of Presentation
      Frankfurt, Germany
    • Year and Date
      2016-06-19
    • Related Report
      2016 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] Massively parallel electronic structure calculations and transport property of organic materials2016

    • Author(s)
      T. Hoshi
    • Organizer
      Computational Chemistry Symposium of 12th International Conference of Computational Methods in Sciences and Engineering (ICCMSE 2016)
    • Place of Presentation
      Metropolitan Hotel, Athens, Greece
    • Year and Date
      2016-03-17
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research / Invited
  • [Presentation] エネルギー保存数値解法の大規模物質計算への展開2016

    • Author(s)
      井町 宏人, 宮武 勇登, 星 健夫
    • Organizer
      日本応用数理学会研究部会連合発表会
    • Place of Presentation
      神戸学院大学
    • Year and Date
      2016-03-04
    • Related Report
      2015 Annual Research Report
  • [Presentation] ブロックヤコビ法に基づく強スケーリング型固有値・特異値計算アルゴリズム2016

    • Author(s)
      山本 有作
    • Organizer
      日本応用数理学会「行列・固有値問題の解法とその応用」研究部会 第22回研究会
    • Place of Presentation
      東京大学(東京都文京区)
    • Related Report
      2016 Annual Research Report
    • Invited
  • [Presentation] 正規行列のトレースに対する確率的推定法の分散について2015

    • Author(s)
      山本有作
    • Organizer
      日本応用数理学会「行列・固有値問題の解法とその応用」研究部会
    • Place of Presentation
      東京大学
    • Year and Date
      2015-12-11
    • Related Report
      2015 Annual Research Report
  • [Presentation] コレスキーQR法と古典的グラム・シュミット法の数値的安定性について2015

    • Author(s)
      山本有作
    • Organizer
      京大数理研 研究集会「現象解明に向けた数値解析学の新展開」
    • Place of Presentation
      京都大学数理解析研究所
    • Year and Date
      2015-11-18
    • Related Report
      2015 Annual Research Report
  • [Presentation] Roundoff Error Analysis of the CholeskyQR2 and Related Algorithms2015

    • Author(s)
      Y. Yamamoto, Y. Nakatsukasa, Y. Yanagisawa and T. Fukaya
    • Organizer
      SIAM Conference on Applied Linear Algebra
    • Place of Presentation
      Hyatt Regency Atlanta
    • Year and Date
      2015-10-28
    • Related Report
      2015 Annual Research Report
    • Int'l Joint Research
  • [Presentation] ブロック化ハウスホルダー・コレスキーQR法の安定性について2015

    • Author(s)
      山本有作
    • Organizer
      日本応用数理学会2015年度年会
    • Place of Presentation
      金沢大学
    • Year and Date
      2015-09-10
    • Related Report
      2015 Annual Research Report
  • [Presentation] 超並列固有値計算のための最適複合化数理ソルバと電子状態計算におけるベンチマーク2015

    • Author(s)
      井町宏人,星健夫
    • Organizer
      日本応用数理学会2015年研究部会連合発表会
    • Place of Presentation
      明治大学,東京
    • Year and Date
      2015-03-06 – 2015-03-07
    • Related Report
      2014 Annual Research Report
  • [Presentation] CholeskyQR2: a simple and communication-avoiding algorithm for computing a tall-skinny QR factorization on a large-Scale parallel system2014

    • Author(s)
      T. Fukaya, Y. Nakatsukasa, Y. Yanagisawa and Y. Yamamoto
    • Organizer
      Scalable Algorithms for Large-Scale Systems (ScalA'14)
    • Place of Presentation
      New Orleans, LA, USA
    • Year and Date
      2014-11-17
    • Related Report
      2014 Annual Research Report
  • [Presentation] 実応用・アルゴリズム連携研究のための固有値ソルバ 性能評価環境の開発2014

    • Author(s)
      井町宏人,星 健夫
    • Organizer
      日本応用数理学会年会
    • Place of Presentation
      政策研究大学院大学,東京
    • Year and Date
      2014-09-03 – 2014-09-05
    • Related Report
      2014 Annual Research Report
  • [Presentation] A nonlinear eigenvalue problem arising in theoretical fluid dynamics and its solution using signed singular values2014

    • Author(s)
      Y. Yamamoto
    • Organizer
      The Fifth China-Japan-Korea Conference on Numerical Mathematics
    • Place of Presentation
      Yinchuan, China
    • Year and Date
      2014-08-25 – 2014-08-28
    • Related Report
      2014 Annual Research Report
    • Invited
  • [Presentation] Performance analysis of the Householder-type parallel tall-skinny QR factorizations toward automatic algorithm selection2014

    • Author(s)
      T. Fukaya, T. Imamura and Y. Yamamoto
    • Organizer
      The Ninth International Workshop on Automatic Performance Tuning (iWAPT2014)
    • Place of Presentation
      Eugene, Oregon, USA
    • Year and Date
      2014-07-01
    • Related Report
      2014 Annual Research Report
  • [Book] Eigenvalue Problems: Algorithms, Software and Applications in Petascale Computing2018

    • Author(s)
      Yusaku Yamamoto
    • Publisher
      Springer
    • ISBN
      9783319624266
    • Related Report
      2017 Annual Research Report
  • [Book] ストラング:計算理工学(第1章「応用線形代数」の翻訳を担当)2016

    • Author(s)
      ルバート ストラング(著), 今井 桂子, 岡本 久, 日本応用数理学会(監訳)
    • Total Pages
      735
    • Publisher
      近代科学社
    • Related Report
      2016 Annual Research Report
  • [Remarks] Parallel One-Sided Block Jacobi SVD Algorithm

    • URL

      http://uni-salzburg.at/fileadmin/multimedia/Computerwissenschaften/3_Forschung/2016-02_Kudo_Yamamoto_Becka_Vajtersic.pdf

    • Related Report
      2015 Annual Research Report

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Published: 2014-04-04   Modified: 2019-03-29  

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