GPU linear algebra libraries and GPGPU programming for accelerating MOPAC semiempirical quantum chemistry calculations

Journal of Chemical Theory and Computation

Volumn 8, Issue 9, 2012, Pages 3072-3081

  Maia, Julio Daniel Carvalho ^a   Urquiza Carvalho, Gabriel Aires ^a   Mangueira, Carlos Peixoto ^a   Santana, Sidney Ramos ^a   Cabral, Lucidio Anjos Formiga ^a   Rocha, Gerd B ^a  

^a FEDERAL UNIVERSITY OF PARAÍBA   (Brazil)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84866184290     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct3004645     Document Type: Article

References (57)

1. De Jong, W. A.; Bylaska, E.; Govind, N.; Janssen, C. L.; Kowalski, K.; Müller, T.; Nielsen, I. M. B.; Dam, H. J. J.; Van; Veryazov, V.; Lindh, R. Phys. Chem. Chem. Phys. 2010, 12, 6896-6920
2. Seeger, R. J. Comput. Chem. 1981, 2, 168-176
3. GPU Computing Gems Emerald, 1st ed.; Hwu, W. W., Ed.; Elsevier Inc.: Burlington, MA, 2011.
4. Stone, J. E.; Hardy, D. J.; Ufimtsev, I. S.; Schulten, K. J. Mol. Graphics Modell. 2010, 29, 116-125
5. Xu, D.; Williamson, M. J.; Walker, R. C. Annu. Rep. Comput. Chem. 2010, 6, 1-19
6. Anderson, J.; Lorenz, C.; Travesset, A. J. Comput. Phys. 2008, 227, 5342-5359
7. Friedrichs, M. S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Legrand, S.; Beberg, A. L.; Ensign, D. L.; Bruns, C. M.; Pande, V. S. J. Comput. Chem. 2009, 30, 864-872
8. Brown, P.; Woods, C. J.; McIntosh-Smith, S.; Manby, F. R. J. Comput. Chem. 2010, 31, 2008-2013
9. Ufimtsev, I. S.; Martinez, T. J. J. Chem. Theory Comput. 2009, 5, 3138-3138
10. Luehr, N.; Ufimtsev, I. S.; Martínez, T. J. J. Chem. Theory Comput. 2011, 7, 949-954
11. Kindratenko, V.; Wilhelmson, R.; Brunner, R.; Martinez, T. J.; Hwu, W. M. Comput. Sci. Eng. 2010, 12, 12-16
12. Ufimtsev, I. S.; Martinez, T. J. J. Chem. Theory Comput. 2009, 5, 2619-2628
13. Vogt, L.; Olivares-Amaya, R.; Kermes, S.; Shao, Y.; Amador-Bedolla, C.; Aspuru-Guzik, A. J. Phys. Chem. A 2008, 112, 2049-2057
14. DePrince, A. E.; Hammond, J. R. J. Chem. Theory Comput. 2011, 7, 1287-1295
15. Ma, W.; Krishnamoorthy, S.; Villa, O.; Kowalski, K. J. Chem. Theory Comput. 2011, 7, 1316-1327
16. Ye, D.; Titov, A.; Kindratenko, V.; Ufimtsev, I.; Martinez, T. Porting Optimized GPU Kernels to a Multi-core CPU: Computational Quantum Chemistry Application Example. In Proceedings of the 2011 Symposium on Application Accelerators in High-Performance Computing, Knoxville, TN, July 19-21, 2011; IEEE Press: New York, 2011; pp 72-75.
17. Levine, B. G.; Stone, J. E.; Kohlmeyer, A. J. Comput. Phys. 2011, 230, 3556-3569
18. Uejima, Y.; Terashima, T.; Maezono, R. Y. O. J. Comput. Chem. 2011, 32, 2264-2272
19. Wilkinson, K. A.; Sherwood, P.; Guest, M. F.; Naidoo, K. J. J. Comput. Chem. 2011, 32, 2313-2318
20. Watson, M.; Olivares-Amaya, R.; Edgar, R. G.; Aspuru-Guzik, A. Comput. Sci. Eng. 2010, 12, 40-51
21. Gotz, A. W.; Wolfle, T.; Walker, R. C. Annu. Rep. Comput. Chem. 2010, 6, 21-35
22. Harvey, M. J.; De Fabritiis, G. WIREs Comput Mol Sci. 2012, DOI: http://dx.doi.org/10.1002/wcms.1101.
23. Cruz, F. A.; Layton, S. K.; Barba, L. A. Comput. Phys. Commun. 2011, 182, 2084-2098
24. Stewart, J. J. P. MOPAC; Stewart Computational Chemistry: Colorado Springs, CO, 2012. http://www.openmopac.net (accessed August 2012).
25. Bakowies, D.; Thiel, W. J. Am. Chem. Soc. 1991, 113, 3704-3714
26. Green, D.; Boston, I.; Thiel, W. Parallelisation in quantum chemistry: the MNDO code. In Lect. Notes Comput. Sc.; Hertzberger, B.; Serazzi, G., Eds.; Springer-Verlag: Berlin, Germany, 1995; Vol. 919, pp 880-885.
27. Thiel, W.; Green, D. G. In Methods and Techniques in Computational Chemistry: METECC-95; Clementi, E.; Corongiu, G., Eds.; STEF: Cagliari, Italy, 1995; pp 141-168.
28. Thiel, W. In Modern Methods and Algorithms of Quantum Chemistry; Grotendorst, J., Eds.; John von Neumann Institute for Computing, NIC Series: Jülich, Germany, 2000; Vol 3, pp 261-283.
29. Baldridge, K. K. J. Math. Chem. 1996, 19, 87-109
30. Früchtl, H. A.; Nobes, R. H.; Bliznyuk, A. THEOCHEM 2000, 506, 87-97
31. Rendell, A. P.; Bliznyuk, A.; Huber, T.; Nobes, R. H.; Akhmatskaya, E. V.; Früchtl, H. A.; Kung, P. W.C.; Milman, V.; Lung, H. Parallel Comput. 2000, 26, 887-911
32. Berzigiyarov, P. K.; Zayets, V. A.; Ginzburg, I. Y.; Razumov, V. F.; Sheka, E. F. Int. J. Quantum Chem. 2002, 88, 449-462
33. Lin, T. H. Parallelizing Legacy Applications Using Message Passing Programming Model and The Example of MOPAC; Syracuse University: Syracuse, NY, 2000.
34. Lin, T. H.; Tomasz, T. L.; Geo, H.; Fox, C. Parallelizing MOPAC on Distributed Computing Systems within AVS Framework; Syracuse University: Syracuse, NY, 2000.
35. Mangueira, C. P., Jr.; Maia, J. D. C.; Cabral, L. A. F.; Rocha, G. B. Accelerating semiempirical quantum chemistry calculations using sparse linear algebra GPU libraries for large systems. Presented at XVI Simpósio Brasileiro de Química Teórica; Ouro Preto, Minas Gerais, Brazil, November 20-24, 2011. http://www.sbqt.net/resumos/412.pdf (accessed July 25, 2012).
36. Wu, X.; Koslowski, A.; Thiel, W. J. Chem. Theory Comput. 2012, 8, 2272-2281
37. Zalesny, R.; Mezey, P. G.; Papadopoulos, M. G.; Leszczynski, J. Linear-Scaling Techniques in Computational Chemistry and Physics; Springer: Dordrecht, The Netherlands, 2011.
38. Fedorov, D.; Kitaura, K. The Fragment Molecular Orbital Method-Practical Applications to Large Molecular Systems; CRC Press: Boca Raton, FL, 2009.
39. Fukushima, K.; Wada, M.; Sakurai, M. Proteins 2008, 71, 1940-1954
40. Dewar, M. J. S.; Zoebisch, E. G.; Healy, E. F.; Stewart, J. J. P. J. Am. Chem. Soc. 1985, 107, 3902-3909
41. Stewart, J. J. P. Int. J. Quantum Chem. 1996, 58, 133-146
42. Anderson, E.; Bai, Z.; Bischof, C.; Blackford, L. S.; Demmel, J.; Dongarra, J.; Croz, J.; Du; Greenbaum, A.; Hammarling, S.; McKenney, A.; Sorensen, D. LAPACK Users' Guide, 3rd ed.; SIAM: Philadelphia, PA, 1999.
43. Stewart, J. J. P.; Császár, P.; Pulay, P. J. Comput. Chem. 1982, 3, 227-228
44. HyperChem Professional, version 8.0; Hypercube, Inc.: Gainesville, FL, 2012.
45. Rocha, G. B.; Freire, R. O.; Simas, A. M.; Stewart, J. J. P. J. Comput. Chem. 2006, 27, 1101-1111
46. Allada, V.; Benjegerdes, T.; Bode, B. In Proceedings of 2009 IEEE International Conference on Cluster Computing and Workshops, New Orleans, Louisiana, USA, Aug 31-Sep. 4, 2009; IEEE: New York, 2009; pp 1-9.
47. Olivares-Amaya, R.; Watson, M. A.; Edgar, R. G.; Vogt, L.; Shao, Y.; Aspuru-Guzik, A. J. Chem. Theory Comput. 2010, 6, 135-144
48. Tomov, S.; Nath, R.; Du, P.; Dongarra, J. Matrix Algebra on GPU and Multicore Architectures (MAGMA), Version 1.0.0, Users' Guide. Technical Report; Innovative Computing Laboratory, University of Tennessee, Knoxville: Knoxville, TN, 2011.
49. Park, B.; Levitt, M. J. Mol. Biol. 1996, 258, 367-92
50. Lazaridis, T. Curr. Opin. Struc. Biol. 2000, 10, 139-145
51. Wollacott, A. M.; Merz, K. M. J. Chem. Theory Comput. 2007, 3, 1609-1619
52. Gogonea, V.; Merz, K. M. J. Phys. Chem. A 1999, 103, 5171-5188
53. Korth, M. J. Chem. Theory Comput. 2010, 6, 3808-3816
54. Klamt, A.; Schüürmann, G. J. Chem. Soc., Perkin Trans. 2 1993, 5, 799-805
55. McConkey, B. J.; Sobolev, V.; Edelman, M. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 3215-3220
56. Case, D. A.; Darden, T. A.; Cheatham, T. E.; Simmerling, C. L.; Wang, J.; Duke, R. E.; Luo, R.; Walker, R. C.; Zhang, W.; Merz, K. M.; Roberts, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Swails, J.; Goetz, A. W.; Kolossvai, I.; Wong, K. F.; Paesani, F.; Vanicek, J.; Wolf, R. M.; Liu, J.; Wu, X.; Brozell, S. R.; Steinbrecher, T.; Gohlke, H.; Cai, Q.; Ye, X.; Wang, J.; Hsieh, M.-J.; Cui, G.; Roe, D. R.; Mathews, D. H.; Seetin, M. G.; Salomon-Ferrer, R.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P. A. Amber 11; University of California, San Francisco: San Francisco, CA, 2010.
57. Hornak, V.; Abel, R.; Okur, A.; Strockbine, B.; Roitberg, A.; Simmerling, C. Proteins 2006, 65, 712-725