Development of the library programs for massively parallel calculation of fragment molecular orbital method

• Project/Area Number: 22550015
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Physical chemistry
• Research Institution: Kyushu University
• Principal Investigator: INADOMI Yuichi 九州大学, 情報基盤研究開発センター, 学術研究員 (70437747)
• Co-Investigator(Kenkyū-buntansha): AOYAGI Mutsumi 九州大学, 情報基盤研究開発センター, 教授 (00260026) ; TAKAMI Toshiya 九州大学, 情報基盤研究開発センター, 准教授 (10270472) ; MAKI Jun 九州先端科学技術研究所, 研究員 (10404047) ; KOBAYASHI Taizo 九州大学, 情報基盤研究開発センター, 学術研究員 (20467880) ; 本田 宏明 財団法人九州先端科学技術研究所, 研究員 (80404044)
• Project Period (FY): 2010 – 2012
• Project Status: Completed (Fiscal Year 2012)
• Budget Amount: ¥4,810,000 (Direct Cost: ¥3,700,000、Indirect Cost: ¥1,110,000); Fiscal Year 2012: ¥1,040,000 (Direct Cost: ¥800,000、Indirect Cost: ¥240,000); Fiscal Year 2011: ¥1,430,000 (Direct Cost: ¥1,100,000、Indirect Cost: ¥330,000); Fiscal Year 2010: ¥2,340,000 (Direct Cost: ¥1,800,000、Indirect Cost: ¥540,000)
• Keywords: フラグメント分子軌道法 / 超並列化 / アプリケーションプログラムインターフェイス(API) / 生物物理化学

Research Abstract

To carry out the effective massively parallel calculation of the fragment molecular orbital (FMO) method, we developed the parallel FMO program, OpenFMO. In addition, we probed the hierarchical structure of the FMO program and designed the interface of subprograms (modules) to make it easy to cooperate with the computer scientists and computer engineers to improve the performance of the parallel FMO program. In this study, we implemented the high performance FMO program and confirmed its high parallelization efficiency. And it was shown that the modules designed and implemented in this work was useful to construct the parallel FMO program in short time.

Research Products

• [Journal Article] Performance Tuning of Parallel Fragment Molecular Orbital Program (OpenFMO) for Effective Execution on K-computer
  • Author(s): Yuichi INADOMI, Jun MAKI, Hiroaki HONDA, Toshiya TAKAMI, Taizo KOBAYASHI, Mutsumi AOYAGI and Kazuo MINAMI
  • Journal Title: Journal of Computer Chemstry, Japan Volume: (accepted)
  • Peer Reviewed
• [Journal Article] Performance Tuning of Parallel Fragment Molecular Orbital Program (OpenFMO) for Effective Execution on K-computer
  • Author(s): Yuichi Inadomi
  • Journal Title: Journal of Computer Chemistry, Japan Volume: accepted(accepted)
  • Peer Reviewed
• [Presentation] スーパーコンピュータ「京」におけるマスク・ワーカ型プログラミングモデルの検討 (2013)
  • Author(s): 村井均
  • Organizer: 情報処理学会報告
  • Place of Presentation: 芦原温泉
  • Year and Date: 2013-02-22
• [Presentation] Performance improvement of FMO program for effective massively parallel execution on K-computer (2013)
  • Author(s): Yuichi Inadomi
  • Organizer: Invited Oral, International Workshop on Massively Parallel Programming Now in Molecular Science
  • Place of Presentation: Waseda University, Japan
  • Year and Date: 2013-01-28
• [Presentation] Performance improvement of FMO program for effective massively parallel execution on K-computer (2013)
  • Author(s): Yuichi Inadomi
  • Organizer: International Workshop on Massively Parallel Programming Now in Molecular Science
  • Place of Presentation: 早稲田大学(招待講演)
  • Year and Date: 2013-01-28
• [Presentation] 並列FMOプログラムOpenFMOの高性能化 (2012)
  • Author(s): 稲富雄一
  • Organizer: 日本コンピュータ化学会秋季年会
  • Place of Presentation: 山形大学
  • Year and Date: 2012-10-13
• [Presentation] 並列FMOプログラムOpenFMOの高性能化 (2012)
  • Author(s): 稲富雄一
  • Organizer: 第6回分子科学討論会
  • Place of Presentation: 東京大学
  • Year and Date: 2012-09-19
• [Presentation] Performance Tuning of FMO Code (OpenFMO) for Effective Massively Parallel Execution (2012)
  • Author(s): Yuichi Inadomi
  • Organizer: Theory and Applications of Computational Chemistry(TACC-2012)
  • Place of Presentation: Pavia, Italy
  • Year and Date: 2012-09-03
• [Presentation] 並列FMOプログラムOpenFMOの性能最適化 (2012)
  • Author(s): 稲富雄一
  • Organizer: HPC研究会2012(HPC-133)
  • Place of Presentation: 有馬温泉(有馬ビューホテルうらら)(兵庫)
  • Year and Date: 2012-03-27
• [Presentation] フラグメント分子軌道法の高性能化 (2012)
  • Author(s): 稲富雄一
  • Organizer: 筑波大学戦略A:若手啓発講演会
  • Place of Presentation: 筑波大学(茨城)(招待講演)
  • Year and Date: 2012-03-19
• [Presentation] Optimization of FMO Code (OpenFMO) for Effective Massively Parallel Execution (2012)
  • Author(s): Yuichi Inadomi
  • Organizer: 日仏計算化学ワークショップ2012
  • Place of Presentation: 志賀島国民休暇村(福岡)
  • Year and Date: 2012-03-05
• [Presentation] 並列FMOプログラムOpenFMOの性能最適化 (2012)
  • Author(s): 稲富雄一,眞木淳,高見利也,小林泰三,青柳睦,南一生
  • Organizer: HPCS2012,ポスター発表 P1-3
  • Place of Presentation: 名古屋大学
  • Year and Date: 2012-01-25
• [Presentation] 並列FMOプログラムOpenFMOの性能最適化 (2012)
  • Author(s): 稲富雄一
  • Organizer: HPCS2012
  • Place of Presentation: 名古屋大学(愛知)
  • Year and Date: 2012-01-25
• [Presentation] Optimization of FMO Code (OpenFMO) for Effective Massively Parallel Execution (2012)
  • Author(s): Yuichi Inadomi
  • Organizer: poster P02, The 4th French-Japanese Workshop on Computational Methods in Chemistry
  • Place of Presentation: Fukuoka, Japan
• [Presentation] 並列FMOプログラムOpenFMOの性能最適化 (2012)
  • Author(s): 稲富雄一,眞木淳,高見利也,本田宏明,小林泰三,南里豪志,青柳睦,南一生
  • Organizer: 情報処理学会研究報告2012-HPC-133,口頭発表
  • Place of Presentation: 有馬温泉
• [Presentation] Performance Tuning of FMO Code (OpenFMO) for Effective Massively Parallel Execution (2012)
  • Author(s): Yuichi Inadomi, Jun Maki, Hiroaki Honda, Toshiya Takami, Takeshi Nanri, Mutsumi Aoyagi and Kazuo Minami
  • Organizer: poster, Theory and Applications of Computational Chemistry(TACC-2012)
  • Place of Presentation: Pavia, Italy
• [Presentation] 並列FMOプログラムOpenFMOの超並列化への取り組み (2011)
  • Author(s): 稲富雄一
  • Organizer: 日本コンピュータ化学会2011秋季年会
  • Place of Presentation: 福井商工会議所(福井)
  • Year and Date: 2011-11-04
• [Presentation] 並列FMOプログラムOpenFMOの超並列化への取り組み (2011)
  • Author(s): 稲富雄一
  • Organizer: 分子科学討論会2011
  • Place of Presentation: 札幌コンベンションセンター(北海道)
  • Year and Date: 2011-09-20
• [Presentation] OpenFMOにおけるフラグメント電子状態計算部分の高並列化 (2011)
  • Author(s): 稲富雄一
  • Organizer: 日本コンピュータ化学会2011春季年会
  • Place of Presentation: 東京工業大学(東京)
  • Year and Date: 2011-06-17
• [Presentation] 並列FMOプログラムOpenFMOの超並列化への取り組み (2011)
  • Author(s): 稲富雄一,眞木淳,本田宏明,高見利也,小林泰三,西田晃,青柳睦,南一生
  • Organizer: 第5回分子科学討論会2011 札幌,ポスター発表 1P108
  • Place of Presentation: 札幌コンベンションセンター
• [Presentation] 並列FMOプログラムOpenFMOの超並列化 (2010)
  • Author(s): 稲富雄一
  • Organizer: 日本コンピュータ化学会秋季年会
  • Place of Presentation: 長岡技術科学大学
  • Year and Date: 2010-10-23
• [Presentation] FMO法の超並列化への取り組み (2010)
  • Author(s): 稲富雄一,眞木淳,本田宏明,西田晃,高見利也,小林泰三,青柳睦,南一生
  • Organizer: 第4回分子科学総合討論会2010大阪,ポスター発表2P095
  • Place of Presentation: 大阪大学豊中キャンパス
  • Year and Date: 2010-09-15
• [Presentation] FMO法の超並列化への取り組み (2010)
  • Author(s): 稲富雄一
  • Organizer: 分子科学総合討論会2010
  • Place of Presentation: 大阪大学豊中キャンパス
  • Year and Date: 2010-09-15
• [Presentation] スーパーコンピュータ「京」におけるマスタ・ワーカ型プログラミングモデルの検討
  • Author(s): 村井均,南一生,横川三津夫,梅田宏明,佐藤三久,辻美和子,稲富雄一,青柳睦,中島真
  • Organizer: 情報処理学会研究報告
  • Place of Presentation: 福井
• [Remarks]
  • URL: http://www.openfmo.org/OpenFMO/index.html
• [Remarks]
  • URL: http://www.openfmo.org/OpenFMO/index.html
• [Remarks]
  • URL: http://www.openfmo.org/OpenFMO/
• [Remarks]
  • URL: http://www.openfmo.org/