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

2012 Fiscal Year Final Research Report

• 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)
• Project Period (FY): 2010 – 2012
• Keywords: フラグメント分子軌道法 / 超並列化

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
• [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 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
  • Year and Date: 20120902-07
• [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
  • Year and Date: 20120326-27
• [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
  • Year and Date: 20120305-06
• [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
  • Year and Date: 20110920-23
• [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] 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