Parallel fock matrix construction with distributed shared memory model for the FMO-MO method

Journal of Computational Chemistry

Volumn 31, Issue 13, 2010, Pages 2381-2388

  Umeda, Hiroaki ^a,b,c   Inadomi, Yuichi ^d   Watanabe, Toshio ^c,e   Yagi, Toru ^c,f   Ishimoto, Takayoshi ^c,g   Ikegami, Tsutomu ^c   Tadano, Hiroto ^a   Sakurai, Tetsuya ^a,c   Nagashima, Umpei ^c  

^a UNIVERSITY OF TSUKUBA   (Japan)

^b INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

^c NATIONAL INSTITUTE OF ADVANCED INDUSTRIAL SCIENCE AND TECHNOLOGY AIST   (Japan)

^d Fukuoka Industry Academia Symphonicity   (Japan)

^e TOKYO INSTITUTE OF TECHNOLOGY   (Japan)

^f EDOGAWA UNIVERSITY   (Japan)

^g KYUSHU UNIVERSITY   (Japan)

Author keywords

Distributed shared memory; FMO MO method; Large MO calculation; Parallel fock matrix construction; Sakurai Sugiura method

Indexed keywords

DISTRIBUTED SHARED MEMORY; FOCK MATRIX; MO CALCULATIONS; MO METHOD; SAKURAI;

PARALLEL ALGORITHMS;

CLUSTER COMPUTING;

CRAMBIN PROTEIN, CRAMBE ABYSSINICA; EPIDERMAL GROWTH FACTOR RECEPTOR; VEGETABLE PROTEIN;

ARTICLE; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; QUANTUM THEORY;

COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; MODELS, MOLECULAR; PLANT PROTEINS; QUANTUM THEORY; RECEPTOR, EPIDERMAL GROWTH FACTOR;

EID: 77957557718     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21531     Document Type: Article

References (43)

1. Helgaker, T.; Jørgensen, P.; Olsen, J. Molecular Electronic-Structure Theory; Wiley: Chichester, 2000.
2. Kitaura, K.; Sawai, T.; Asada, T.; Nakano, T.; Uebayasi, M. Chem Phys Lett 1999, 312, 319.
3. Kitaura, K.; Ikeo, E.; Asada, T.; Nakano, T.; Uebayasi, M. Chem Phys Lett 1999, 313, 701.
4. Nakano, T.; Kaminuma, T.; Sato, T.; Akiyama, Y.; Uebayasi, M.; Kitaura, K. Chem Phys Lett 2000, 318, 614.
5. Nakano, T.; Kaminuma, T.; Sato, T.; Fukuzawa, K.; Akiyama, Y.; Uebayasi, M.; Kitaura, K. Chem Phys Lett 2002, 351, 475.
6. Fedorov, D. G.; Kitaura, K. J Phys Chem A 2007, 111, 6904.
7. Fedorov, D. G.; Kitaura, K., Eds. The Fragment Molecular Orbital Method: Practical Applications to Large Molecular Systems; CRC Press: Boca Raton, FL, 2009.
8. Fedorov, D. G.; Olson, R. M.; Kitaura, K.; Gordon, M. S.; Koseki, S. J Comput Chem 2004, 25, 872.
9. Ikegami, T.; Ishida, T.; Fedorov, D. G.; Kitaura, K.; Inadomi, Y.; Umeda, H.; Yokokawa, M.; Sekiguchi, S.In Proceedings of the 2005 ACM/IEEE conference on Supercomputing; IEEE Comput Soc, 2005.
10. Inadomi, Y.; Nakano, T.; Kitaura, K.; Nagashima, U. Chem Phys Lett 2002, 364, 139.
11. Watanabe, T.; Inadomi, Y.; Umeda, H.; Fukuzawa, K.; Tanaka, S.; Nakano, T.; Nagashima, U. J Comput Theor Nanosci 2009, 6, 1328.
12. Furlani, T. R.; King, H. F. J Comput Chem 1995, 16, 91.
13. Foster, I. T.; Tilson, J. L.; Wagner, A. F.; Shepard, R. L.; Harrison, R. J.; Kendall, R. A.; Littlefield, R. J. J Comput Chem 1996, 17, 109.
14. Harrison, R. J.; Guest, M. F.; Kendall, R. A.; Bernholdt, D. E.; Wong, A. T.; Stave, M.; Anchell, J. L.; Hess, A. C.; Littlefield, R. J.; Fann, G. L.; Nieplocha, J.; Thomas, G. S.; Elwood, D.; Tilson, J. L.; Shepard, R. L.; Wagner, A. F.; Foster, I. T.; Lusk, E.; Stevens, R. J Comput Chem 1996, 17, 124.
15. Takashima, H.; Yamada, S.; Obara, S.; Kitamura, K.; Inabata, S.; Miyakawa, N.; Tanabe, K.; Nagashima, U. J Comput Chem 2002, 23, 1337.
16. Nieplocha, J.; Palmer, B.; Tipparaju, V.; Krishnan, M.; Trease, H.; Apra, E. Int J High Perf Comput Appl 2006, 20, 203; available at: http://www.emsl.pnl.gov/docs/global/. Accessed on January 9, 2009.
17. Tilson, J. L.; Minkoff, M.; Wagner, A. F.; Shepard, R.; Sutton, P.; Harrison, R. J.; Kendall, R. A.; Wong, A. T. Int J High Perf Comput Appl 1999, 13, 291.
18. White, C. A.; Johnson, B. G.; Gill, P. M. W.; Head-Gordon, M. Chem Phys Lett 1994, 230, 8.
19. Rudberg, E.; Salek, P. J Chem Phys 2006, 125, 084106.
20. White, C. A.; Head-Gordon, M. J Chem Phys 1996, 104, 2620.
21. Füsti-Molnár, L.; Pulay, P. J Chem Phys 2002, 117, 7827.
22. Früchtl, H. A.; Kendall, R. A.; Harrison, R. J.; Dyall, K. G. Int J Quantum Chem 1997, 64, 63.
23. Tamura, K.; Watanabe, T.; Ishimoto, T.; Umeda, H.; Inadomi, Y.; Nagashima, U. Bull Chem Soc Jpn 2008, 81, 254.
24. Umeda, H.; Inadomi, Y.; Honda, H.; Nagashima, U. J Comput Chem 2009, 30, 826.
25. Almlöf, J.; Faegri, K., Jr.; Korsell, K. J Comput Chem 1982, 3, 385.
26. Ochsenfeld, C.; White, C. A.; Head-Gordon, M. J Chem Phys 1998, 109, 1663.
27. Häser, M.; Ahlrichs, R. J Comput Chem 1989, 10, 104.
28. Millam, J. M.; Scuseria, G. E. J Chem Phys 1997, 106, 5569.
29. Barrett, R.; Berry, M.; Chan, T. F.; Demmel, J.; Donato, J.; Dongarra, J.; Eijkhout, V.; Pozo, R.; Romine, C.; Van der Vorst, H. Templates for the Solution of Linear Systems: Building Blocks for Iterative Methods; SIAM: Philadelphia, PA, 1994.
30. ABINIT-MP: Ab initio Fragment MO Method Program. Available at: http://moldb.nihs.go.jp/abinitmp/. Accessed on June 26, 2002.
31. T2K Open Supercomputer Alliance. Availble at: http://www. opensupercomputer. org/. Accessed on June 18, 2009.
32. Blume-Jensen, P.; Hunter, T. Nature 2001, 411, 355.
33. Holbro, T.; Civenni, G.; Hynes, N. E. Exp Cell Res. 2003, 284, 99.
34. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kalé, L.; Schulten, K. J Comput Chem 2005, 26, 1781.
35. MacKerell, A. D.; Bashford, D.; Bellott, M.; Dunbrac, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
36. AIST Super Cluster. Available at: http://unit.aist.go.jp/tacc/en/ supercluster.html. Accessed on May 10, 2004.
37. Sakurai, T.; Sugiura, H. J Comput Appl Math 2003, 159, 119.
38. Sakurai, T.; Kodaki, Y.; Umeda, H.; Inadomi, Y.; Watanabe, T.; Nagashima, U. In Large-Scale Scientific Computing; LNCS 3743, Springer: Berlin, 2006; pp 438-445.
39. Sakurai, T.; Tadano, H. Hokkaido Math J 2007, 36, 745.
40. Blackford, L. S.; Choi, J.; Cleary, A.; Azeuedo, E. D.; Demmel, J.; Dhillon, I.; Hammarling, S.; Henry, G.; Petitet, A.; Stanley, K.; Walker, D.; Whaley, R. C. ScaLAPACK user's guide; Society for Industrial and Applied Mathematics, Philadelphia, 1997. Available at: http://www.netlib.org/scalapack/. Accessed on April 6, 2007.
41. Rudberg, E.; Rubensson, E. H.; Salek, P. J Chem Phys 2008, 128, 184106.
42. Tsuneyuki, S.; Kobori, T.; Akagi, K.; Sodeyama, K.; Terakura, K.; Fukuyama, H. Chem Phys Lett 2009, 476, 104.
43. Tanaka, Y.; Nakada, H.; Sekiguchi, S.; Suzumura, T.; Matsuoka, S. J Grid Comput 2003, 1, 41. Available at: http://ninf.apgrid.org/. Accessed on October 23, 2008.