GPU Linear Algebra Libraries and GPGPU Programming for Accelerating MOPAC Semiempirical Quantum Chemistry Calculations

Journal of Chemical Theory and Computation - Tập 8 Số 9 - Trang 3072-3081 - 2012
Julio D. C. Maia1, Gabriel A. Urquiza‐Carvalho2, Carlos Peixoto Mangueira1, Sidney R. Santana2, Lucídio A. F. Cabral1, Gerd B. Rocha2
1Centro de Informática, Universidade Federal da Paraíba, CEP: 58051-900, João Pessoa/PB, Brazil
2Departamento de Química, CCEN, Universidade Federal da Paraíba, Caixa Postal: 5093, CEP: 58051-970, João Pessoa/PB, Brazil

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Tài liệu tham khảo

De Jong W. A., 2010, Phys. Chem. Chem. Phys., 12, 6896, 10.1039/c002859b

Seeger R., 1981, J. Comput. Chem., 2, 168, 10.1002/jcc.540020206

Hwu W. W., 2011, GPU Computing Gems Emerald, 1

Stone J. E., 2010, J. Mol. Graphics Modell., 29, 116, 10.1016/j.jmgm.2010.06.010

Xu D., 2010, Annu. Rep. Comput. Chem., 6, 1

Anderson J., 2008, J. Comput. Phys., 227, 5342, 10.1016/j.jcp.2008.01.047

Friedrichs M. S., 2009, J. Comput. Chem., 30, 864, 10.1002/jcc.21209

Brown P., 2010, J. Comput. Chem., 31, 2008, 10.1002/jcc.21485

Ufimtsev I. S., 2009, J. Chem. Theory Comput., 5, 3138, 10.1021/ct900433g

Luehr N., 2011, J. Chem. Theory Comput., 7, 949, 10.1021/ct100701w

Kindratenko V., 2010, Comput. Sci. Eng., 12, 12, 10.1109/MCSE.2010.88

Ufimtsev I. S., 2009, J. Chem. Theory Comput., 5, 2619, 10.1021/ct9003004

Vogt L., 2008, J. Phys. Chem. A, 112, 2049, 10.1021/jp0776762

DePrince A. E., 2011, J. Chem. Theory Comput., 7, 1287, 10.1021/ct100584w

Ma W., 2011, J. Chem. Theory Comput., 7, 1316, 10.1021/ct1007247

Ye D., 2011, Proceedings of the 2011 Symposium on Application Accelerators in High-Performance Computing, 72, 10.1109/SAAHPC.2011.8

Levine B. G., 2011, J. Comput. Phys., 230, 3556, 10.1016/j.jcp.2011.01.048

Uejima Y., 2011, J. Comput. Chem., 32, 2264, 10.1002/jcc.21809

Wilkinson K. A., 2011, J. Comput. Chem., 32, 2313, 10.1002/jcc.21815

Watson M., 2010, Comput. Sci. Eng., 12, 40, 10.1109/MCSE.2010.29

Gotz A. W., 2010, Annu. Rep. Comput. Chem., 6, 21, 10.1016/S1574-1400(10)06002-0

Harvey M. J., 2012, WIREs Comput Mol Sci.

Cruz F. A., 2011, Comput. Phys. Commun., 182, 2084, 10.1016/j.cpc.2011.05.002

Stewart J. J. P., 2012, MOPAC

Bakowies D., 1991, J. Am. Chem. Soc., 113, 3704, 10.1021/ja00010a012

Green D., 1995, Lect. Notes Comput. Sc., 919, 880

Thiel, W.; Green, D. G.InMethods and Techniques in Computational Chemistry: METECC-95;Clementi, E.; Corongiu, G., Eds.STEF:Cagliari, Italy, 1995; pp141–168.

Thiel, W.InModern Methods and Algorithms of Quantum Chemistry;Grotendorst, J., Eds.John von Neumann Institute for Computing, NIC Series:Jülich, Germany, 2000; Vol3, pp261–283.

Baldridge K. K., 1996, J. Math. Chem., 19, 87, 10.1007/BF01165133

Früchtl H. A., 2000, THEOCHEM, 506, 87, 10.1016/S0166-1280(00)00404-8

Rendell A. P., 2000, Parallel Comput., 26, 887, 10.1016/S0167-8191(00)00017-X

Berzigiyarov P. K., 2002, Int. J. Quantum Chem., 88, 449, 10.1002/qua.10193

Lin T. H., 2000, Parallelizing Legacy Applications Using Message Passing Programming Model and The Example of MOPAC

Lin T. H., 2000, Parallelizing MOPAC on Distributed Computing Systems within AVS Framework

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) .

Wu X., 2012, J. Chem. Theory Comput., 8, 2272, 10.1021/ct3001798

Zalesny R., 2011, Linear-Scaling Techniques in Computational Chemistry and Physics, 10.1007/978-90-481-2853-2

Fedorov D., 2009, The Fragment Molecular Orbital Method - Practical Applications to Large Molecular Systems, 10.1201/9781420078497

Fukushima K., 2008, Proteins, 71, 1940, 10.1002/prot.21865

Dewar M. J. S., 1985, J. Am. Chem. Soc., 107, 3902, 10.1021/ja00299a024

Stewart J. J. P., 1996, Int. J. Quantum Chem., 58, 133, 10.1002/(SICI)1097-461X(1996)58:2<133::AID-QUA2>3.0.CO;2-Z

Anderson E., 1999, LAPACK Users’ Guide, 3, 10.1137/1.9780898719604

Stewart J. J. P., 1982, J. Comput. Chem., 3, 227, 10.1002/jcc.540030214

2012, HyperChem Professional

Rocha G. B., 2006, J. Comput. Chem., 27, 1101, 10.1002/jcc.20425

Allada, V.; Benjegerdes, T.; Bode, B.InProceedings of 2009 IEEE International Conference on Cluster Computing and Workshops, New Orleans, Louisiana, USA, Aug 31–Sep. 4, 2009;IEEE:New York, 2009; pp1–9.

Olivares-Amaya R., 2010, J. Chem. Theory Comput., 6, 135, 10.1021/ct900543q

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.

Park B., 1996, J. Mol. Biol., 258, 367, 10.1006/jmbi.1996.0256

Lazaridis T., 2000, Curr. Opin. Struc. Biol., 10, 139, 10.1016/S0959-440X(00)00063-4

Wollacott A. M., 2007, J. Chem. Theory Comput., 3, 1609, 10.1021/ct600325q

Gogonea V., 1999, J. Phys. Chem. A, 103, 5171, 10.1021/jp990266w

Korth M., 2010, J. Chem. Theory Comput., 6, 3808, 10.1021/ct100408b

Klamt A., 1993, J. Chem. Soc., Perkin Trans. 2, 5, 799, 10.1039/P29930000799

McConkey B. J., 2003, Proc. Natl. Acad. Sci. U.S.A., 100, 3215, 10.1073/pnas.0535768100

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.

Hornak V., 2006, Proteins, 65, 712, 10.1002/prot.21123