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
1. [1]
  Shule Liu . Application of SPC/E Water Model in Molecular Dynamics Teaching Experiments. University Chemistry, 2024, 39(4): 338-342. doi: 10.3866/PKU.DXHX202310029
2. [2]
  Yiying Yang , Dongju Zhang . Elucidating the Concepts of Thermodynamic Control and Kinetic Control in Chemical Reactions through Theoretical Chemistry Calculations: A Computational Chemistry Experiment on the Diels-Alder Reaction. University Chemistry, 2024, 39(3): 327-335. doi: 10.3866/PKU.DXHX202309074
3. [3]
  Qian Huang , Zhaowei Li , Jianing Zhao , Ao Yu . Quantum Chemical Calculations Reveal the Details Below the Experimental Phenomenon. University Chemistry, 2024, 39(3): 395-400. doi: 10.3866/PKU.DXHX202309018
4. [4]
  Congying Lu , Fei Zhong , Zhenyu Yuan , Shuaibing Li , Jiayao Li , Jiewen Liu , Xianyang Hu , Liqun Sun , Rui Li , Meijuan Hu . Experimental Improvement of Surfactant Interface Chemistry: An Integrated Design for the Fusion of Experiment and Simulation. University Chemistry, 2024, 39(3): 283-293. doi: 10.3866/PKU.DXHX202308097
5. [5]
  Xiaochen Zhang , Fei Yu , Jie Ma . 多角度数理模拟在电容去离子中的前沿应用. Acta Physico-Chimica Sinica, 2024, 40(11): 2311026-. doi: 10.3866/PKU.WHXB202311026
6. [6]
  Xuyang Wang , Jiapei Zhang , Lirui Zhao , Xiaowen Xu , Guizheng Zou , Bin Zhang . Theoretical Study on the Structure and Stability of Copper-Ammonia Coordination Ions. University Chemistry, 2024, 39(3): 384-389. doi: 10.3866/PKU.DXHX202309065
7. [7]
  Jinfu Ma , Hui Lu , Jiandong Wu , Zhongli Zou . Teaching Design of Electrochemical Principles Course Based on “Cognitive Laws”: Kinetics of Electron Transfer Steps. University Chemistry, 2024, 39(3): 174-177. doi: 10.3866/PKU.DXHX202309052
8. [8]
  Yeyun Zhang , Ling Fan , Yanmei Wang , Zhenfeng Shang . Development and Application of Kinetic Reaction Flasks in Physical Chemistry Experimental Teaching. University Chemistry, 2024, 39(4): 100-106. doi: 10.3866/PKU.DXHX202308044
9. [9]
  Dexin Tan , Limin Liang , Baoyi Lv , Huiwen Guan , Haicheng Chen , Yanli Wang . Exploring Reverse Teaching Practices in Physical Chemistry Experiment Courses: A Case Study on Chemical Reaction Kinetics. University Chemistry, 2024, 39(11): 79-86. doi: 10.12461/PKU.DXHX202403048
10. [10]
  Xuzhen Wang , Xinkui Wang , Dongxu Tian , Wei Liu . Enhancing the Comprehensive Quality and Innovation Abilities of Graduate Students through a “Student-Centered, Dual Integration and Dual Drive” Teaching Model: A Case Study in the Course of Chemical Reaction Kinetics. University Chemistry, 2024, 39(6): 160-165. doi: 10.3866/PKU.DXHX202401074
11. [11]
  Yue Wu , Jun Li , Bo Zhang , Yan Yang , Haibo Li , Xian-Xi Zhang . Research on Kinetic and Thermodynamic Transformations of Organic-Inorganic Hybrid Materials for Fluorescent Anti-Counterfeiting Application information: Introducing a Comprehensive Chemistry Experiment. University Chemistry, 2024, 39(6): 390-399. doi: 10.3866/PKU.DXHX202403028
12. [12]
  Yan Li , Xinze Wang , Xue Yao , Shouyun Yu . Kinetic Resolution Enabled by Photoexcited Chiral Copper Complex-Mediated Alkene E→Z Isomerization: A Comprehensive Chemistry Experiment for Undergraduate Students. University Chemistry, 2024, 39(5): 1-10. doi: 10.3866/PKU.DXHX202309053
13. [13]
  Yaling Chen . Basic Theory and Competitive Exam Analysis of Dynamic Isotope Effect. University Chemistry, 2024, 39(8): 403-410. doi: 10.3866/PKU.DXHX202311093
14. [14]
  Jia Zhou . Constructing Potential Energy Surface of Water Molecule by Quantum Chemistry and Machine Learning: Introduction to a Comprehensive Computational Chemistry Experiment. University Chemistry, 2024, 39(3): 351-358. doi: 10.3866/PKU.DXHX202309060
15. [15]
  You Wu , Chang Cheng , Kezhen Qi , Bei Cheng , Jianjun Zhang , Jiaguo Yu , Liuyang Zhang . ZnO/D-A共轭聚合物S型异质结高效光催化产H₂O₂及其电荷转移动力学研究. Acta Physico-Chimica Sinica, 2024, 40(11): 2406027-. doi: 10.3866/PKU.WHXB202406027
16. [16]
  Hua Hou , Baoshan Wang . Course Ideology and Politics Education in Theoretical and Computational Chemistry. University Chemistry, 2024, 39(2): 307-313. doi: 10.3866/PKU.DXHX202309045
17. [17]
  Ling Fan , Meili Pang , Yeyun Zhang , Yanmei Wang , Zhenfeng Shang . Quantum Chemistry Calculation Research on the Diels-Alder Reaction of Anthracene and Maleic Anhydride: Introduction to a Computational Chemistry Experiment. University Chemistry, 2024, 39(4): 133-139. doi: 10.3866/PKU.DXHX202309024
18. [18]
  Tingbo Wang , Yao Luo , Bingyan Hu , Ruiyuan Liu , Jing Miao , Huizhe Lu . Quantitative Computational Study on the Claisen Rearrangement Reaction of Allyl Phenyl Ethers: An Introduction to a Computational Chemistry Experiment. University Chemistry, 2024, 39(11): 278-285. doi: 10.12461/PKU.DXHX202403082
19. [19]
  Hongyi Zhang , Zhihong Shi , Zhijun Zhang . A New Strategy for “De-formulized” Calculation of Dynamic Buffer Capacity in Analytical Chemistry Education. University Chemistry, 2024, 39(3): 390-394. doi: 10.3866/PKU.DXHX202309030
20. [20]
  Pingping Zhu , Yongjun Xie , Yuanping Yi , Yu Huang , Qiang Zhou , Shiyan Xiao , Haiyang Yang , Pingsheng He . Excavation and Extraction of Ideological and Political Elements for the Virtual Simulation Experiments at Molecular Level: Taking the Project “the Simulation and Computation of Conformation, Morphology and Dimensions of Polymer Chains” as an Example. University Chemistry, 2024, 39(2): 83-88. doi: 10.3866/PKU.DXHX202309063

Get Citation

PDF

XML

Metrics

PDF Downloads(2009)
Abstract views(3731)
HTML views(14)

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142