Citation: BAO Jian-Zhang, FENG Xin-Tian, YU Jian-Guo. GPU Triggered Revolution in Computational Chemistry[J]. Acta Physico-Chimica Sinica, ;2011, 27(09): 2019-2026. doi: 10.3866/PKU.WHXB20110830 shu

GPU Triggered Revolution in Computational Chemistry

1.
1. Department of Systems Science, School of Management, Beijing Normal University, Beijing 100875, P. R. China;
2. College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China

Received Date: 15 April 2011
Available Online: 24 June 2011
Fund Project: 国家自然科学基金(20733002, 20873008, 21073014)资助项目 (20733002, 20873008, 21073014)

Over the last 3 years, the use of graphics processing units (GPU) in general purpose computing has been increasing because of the development of GPU hardware and programming tools such as CUDA (compute unified device architecture). Here, we summarize the progress in al rithms and the corresponding software with regard to computational chemistry using GPU including quantum chemistry and molecular dynamics simulations in detail. We introduce and explore the newly developed TeraChem program, which is unique quantum chemical software and we discuss the al rithms, implementations, and functionality of the program. Finally, we give an optimistic outlook for the use of GPU in computational chemistry.
- GPU,
- CUDA,
- Computational chemistry,
- Molecular dynamics,
- TeraChem
1. [1]
  (1) NVIDIA CUDA.Compute Unified Device Architecture Programming Guide Version 3.0.http://www.nvidia.com/object/cuda_develop.html (accessed March 6, 2010).
2. [2]
  (2) Comparison of Nvidia Graphics Processing Units.http://en.wikipedia.org/wiki/Comparison_of_Nvidia_graphics_processing_units (accessed March 6, 2010).
3. [3]
  (3) Lengyel, J.; Reichert, M.; Donald, B.R.; Greenberg, D.P.Comput.Graph.1990, 24, 327.
4. [4]
  (4) Bohn, C.A.Joint Conference on Intelligent Systems 1999 (JCIS' 98) 1998, 2, 64.
5. [5]
  (5) Hoff, K.E., II.; Culver, T.; Keyser, J.; Ming, L.; Manocha, D.Fast Computation of Generalized Voronoi Diagrams Using Graphics hardware.In Proceeding of SIGGRAPH 99, Danvers, August 8-13, 1999; Assison-Wssley Publishing Company, 1999, 277-286.
6. [6]
  (6) Yang, J.;Wang, Y.; Chen, Y.J.Comput.Phys.2007, 221, 799.
7. [7]
  (7) Anderson, A.G.; ddard,W.A., III.; Schroder, P.Comput. Phys.Commun.2007, 177, 265.
8. [8]
  (8) ATI Stream Technology, http://www.amd.com/US/PRODUCTS/TECHNOLOGIES/STREAM-TECHNOLOGY/Pages/stream-technology.aspx (Accessed April 13, 2011).
9. [9]
  (9) CUDA: Santa Clara, CA.http://www.nvidia.com/object/cuda_home_new.html (accessed April 13, 2011).
10. [10]
  (10) NVIDIA: Santa Clara, CA, CUFFT Library.http://developer.download.nvidia.com/compute/cuda/2_3/toolkit/docs/CUFFT_Library_2.3.pdf (accessed March 6, 2010).
11. [11]
  (11) NVIDIA: Santa Clara, CA, CUBLAS Library 2.0.http://developer.download.nvidia.com/compute/cuda/2_0/docs/CUBLAS_Library_2.0.pdf (accessed March 6, 2010).
12. [12]
  (12) Innovative Computing Laboratory, University of Tennessee, Matrix Algebra on GPU and Multicore Architectures.http://icl.cs.utk.edu/magma (accessed March 6, 2010).
13. [13]
  (13) Yasuda, K.J.Comput.Chem.2008, 29, 334.
14. [14]
  (14) Frisch, M.J.; Trucks, G.W.; Schlegel, H.B.; et al.Gaussian 03, Revision B.01; Gaussian Inc.: Pittsburgh, PA, 2003.
15. [15]
  (15) Asadchev, A.; Allada, V.; Felder, J.; Bode, B.M.; rdon, M.S.; Windus, T.L.J.Chem.Theory Comput.2010, 6 (3), 696.
16. [16]
  (16) (a) Schmidt, M.W.; Baldridge, K.K.; Boatz, J.A.; Elbert, S.T.; rdon, M.S.; Jensen, J.H.; Koseki, S.; Matsunaga, N.; Nguyen, K.A.; Su, S.;Windus, T.L.; Dupuis, M.; Mont mery, J.A.J.Comput.Chem.1993, 14, 1347. (b) rdon, M.S.; Schmidt, M.W.Advances in Electronic Structure Theory: In Theory and Applications of Computational Chemistry: the First Forty Years; Dykstra, C.E., Frenking, G., Kim, K.S., Scuseria, G.E., Eds.; Elsevier: Amsterdam, 2005; p 1167.
17. [17]
  (17) Yasuda, K.J.Chem.Theory Comput.2008, 4, 1230.
18. [18]
  (18) Kermes, S.; Olivares-Amaya, R.; Vogt, L.; Shao, Y.; Amador-Bedolla, C.; Aspuru-Guzik, A.J.Phys.Chem.A 2008, 112, 2049.
19. [19]
  (19) Olivares-Amaya, R.;Watson, M.A.; Edgar, R.G.; Vogt, L.; Shao, Y.; Aspuru-Guzik, A.J.Chem.Theory Comput.2010, 6, 135.
20. [20]
  (20) Shao, Y.H.; Fusti-Molnar, L.; Jung, Y.S.et al.Phys.Chem. Chem.Phys.2006, 8, 3172.
21. [21]
  (21) Genovese, L.; Ospici, M.; Deutsch, T.; Mehaut, J.F.; Neelov, A.; edecker, S.J.Chem.Phys.2009, 131, 34103.
22. [22]
  (22) Granovsky, A.A.Firefly version 7.1.G.http://classic.chem.msu.su/gran/firefly/index.html (accessed April 4, 2011).
23. [23]
  (23) http://classic.chem.msu.su/gran/gamess/cuding.html (accessed April 4, 2011).
24. [24]
  (24) Gan, Z.; Shao, Y.; Kong, J.; Olivares-Amaya, R.; Aspuru-Guzik, A.http://www.nvidia.com/content/GTC/documents/1050_GTC09.pdf (accessed April 4, 2011).
25. [25]
  (25) Wolf, L.Chemical and Engineering News 2010, 88, 27.
26. [26]
  (26) Ufimtsev, I.S.; Martinez, T.J.J.Chem.Theory Comput.2009, 5, 2619.
27. [27]
  (27) TeraChem.http://www.petachem.com (accessed March 6, 2010).
28. [28]
  (28) Ufimtsev, I.S.; Martinez, T.J.J.Chem.Theory Comput.2008, 4, 222.
29. [29]
  (29) Ufimtsev, I.S.; Martinez, T.J.J.Chem.Theory Comput.2009, 5, 1004.
30. [30]
  (30) Ceperley, D.; Alder, B.Quantum Monte Carlo.Science 1986, 231, 555.
31. [31]
  (31) Meredith, J.S.; Alvarez, G.; Maier, T.A.; Schulthess, T.C.; Vette, J.S.Parallel Comput.2009, 35, 151.
32. [32]
  (32) McCammon, J.A.; Gelin, B.R.; Karplus, M.Nature 1977, 267, 585
33. [33]
  (33) Susukita, R.; Ebisuzaki, T.; Elmegreen, B.G.; Furusawa, H.; Kato, K.; Kawai, A.; Kobayashi, Y.; Koishi, T.; McNiven, G.D.; Narumi, T.; Yasuoka, K.Comput.Phys.Commun.2003, 155, 115.
34. [34]
  (34) Narumi, T.; Ohno, Y.; Noriyuk, F.; Okimoto, N.; Suenaga, A.; Yanai, R.; Taiji, M.In From Computational Biophysics to Systems Biology: MDGRAPE-3; Meinke, J., Zimmermann, O., Mohanty, S., Hansmann, U.H.E.Eds.; J.von Neumann Institute for Computing: Jülich, 2006; p 29.
35. [35]
  (35) Liu,W.; Schmidt, B.; Voss, G.; Müller-Wittig,W.In High Performance Computing-HiPC 2007: Lecture Notes in Computer Science; Aluru, S., Parashar, M., Badrinath, R., Prasanna, V.K.Eds.; Springer, Berlin/Heidelberg, 2007; Vol.4873, p 185.
36. [36]
  (36) Stone, J.E.; Phillips, J.C.; Freddolino, P.L.; Hardy, D.J.; Trabuco, L.G.; Schulten, K.J.Comput.Chem.2007, 28, 2618.
37. [37]
  (37) Phillips, J.C.; Stone, J.E.; Schulten, K.Adapting a Message-Driven Parallel Application to GPU Accelerated Clusters.In SC '08: Proceedings of the 2008 ACM/IEEE conference on Super Computing, 1-9, IEEE Press, Piscataway, NJ, USA, 2008.
38. [38]
  (38) van Meel, J.A.; Arnold, A.; Frenkel, D.; Portegies Zwart, S.F.; Belleman, R.G.Mol.Simulat.2008, 34, 259.
39. [39]
  (39) Rapaport, D.C.Comput.Phys.Commun.2011, 182, 926.
40. [40]
  (40) Anderson, J.A.; Lorenz, C.D.; Travesset, A.J.Comput.Phys. 2008, 227, 5342.
41. [41]
  (41) HOOMD: General Purpose Molecular Dynamics on Multiple GPUs Implemented Using CUDA Joshua A.Anderson Path to Petascale: Adapting GEO/CHEM/ASTRO Applications for Accelerators and Accelerator Clusters, April 2009.http://www.ncsa.uiuc.edu/Conferences/accelerators/agenda.html (accessed April 4, 2011).
42. [42]
  (42) Harvey, M.J.; Giupponi, G.; De Fabritiis, G.J.Chem.Theory Comput.2009, 5, 1632.
43. [43]
  (43) Friedrichs, M.S.; Eastman, P.; Vaidyanathan, V.; Houston, M.; Le Grand, S.; Beberg, A.L.; Ensign, D.L.; Bruns, C.M.; Pande, V.S.J.Comput.Chem.2009, 30, 864.
44. [44]
  (44) Eastman, P.; Pande, V.S.J.Comput.Chem.2010, 31, 1268.
45. [45]
  (45) GROMACS http://www.gromacs.org (accessed April 4, 2011).
46. [46]
  (46) Pearlman, D.A.; Case, D.A.; Caldwell, J.W.; Ross,W.S.; Cheatham, T.E., III.; DeBolt, S., Ferguson, D.; Seibel, G.; Kollman, P.Comp.Phys.Commun.2005, 91, 1.
47. [47]
  (47) Cornell,W.D.; Cieplak, P.; Bayly, C.I.; uld, I.R.; Merz, K.M., Jr.; Ferguson, D.M.; Spellmeyer, D.C.; Fox, T.; Caldwell, J.W.; Kollman, P.A.J.Am.Chem.Soc.1995, 117, 5179.
48. [48]
  (48) Case, D.A.; Darden, T.A.; Cheatham, T.E., III.; Simmerling, C.L.;Wang, J.; Duke, R.E.; Luo, R.;Walker, R.C.; Zhang,W.; Merz, K.M.; Roberts, B.;Wang, B.; Hayik, S.; Roitberg, A.; Seabra, G.; Kolossváry, I.;Wong, K.F.; Paesani, F.; Vanicek, J.; Liu, J.;Wu, X.; Brozell, S.R.; Steinbrecher, T.; hlke, H.; Cai, Q.; Ye, X.;Wang, J.; Hsieh, M.J.; Cui, G.; Roe, D.R.; Mathews, D.H.; Seetin, M.G.; Sagui, C.; Babin, V.; Luchko, T.; Gusarov, S.; Kovalenko, A.; Kollman, P.A.AMBER 11; University of California: San Francisco.
49. [49]
  (49) Götz, A.W.;Wölfle, T.;Walker, R.C.Annual Reports in Computational Chemistry; Elsevier: Amsterdam, 2010; Vol.6, p 21.
50. [50]
  (50) Xu, D.;Williamson, M.J.;Walker, R.C.Annual Reports in Computational Chemistry; Elsevier: Amsterdam, 2010; Vol.6, p 1
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