Grand challenges less challenging: new possibilities provided by Graphics Processing Units

• Autorzy: Kuna D. , Makowski M. , Mazura G. , Russek P. , Janiszewski M. , Wiatr K.
• Języki publikacji: EN

Abstrakty

EN

The specific features of general-purpose computing on graphics processing units (GPGPU) in the area of scientific computing are highlighted. The hardware and software resources provided by CYFRONET are presented and selected benchmark calculations are briefly introduced.

Słowa kluczowe

EN

GPGPU; molecular modelling; molecular mechanics; quantum chemistry

• Wydawca: Uniwersytet Jagielloński - Collegium Medicum ; Index Copernicus Sp. z o.o.
• Czasopismo: Bio-Algorithms and Med-Systems
• Rocznik: 2011
• Tom: Vol. 7, no. 4
• Strony: 23--27
• Opis fizyczny: Bibliogr. 12 poz., rys.

Twórcy

autor

Kuna D.

• ACC CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Makowski M.

• ACC CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland
• Department of Theoretical Chemistry, Jagiellonian University, Ingardena 3, Kraków, 30-060, Poland

autor

Mazura G.

• ACC CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland
• Department of Computational Methods in Chemistry, Jagiellonian University, Ingardena 3, Kraków, 30-060, Poland

autor

Russek P.

• ACC CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Janiszewski M.

• ACC CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

autor

Wiatr K.

• ACC CYFRONET AGH, Nawojki 11, 30-950 Kraków, Poland

Bibliografia

• [1] Walters J. P., Balu V., Kompalli S., Chaudhary V.: Evaluating the use of GPUs in Liver Image Segmentation and HMMER Database Searches. Proceedings of the 2009 IEEE International Symposium on Parallel & Distributed Processing, 2009, pp.1-12.
• [2] Stone, J. E., Hardy, D. J., Ufimtsev, I. S., Schulten, K.: GPU-accelerated molecular modeling coming of age. Journal of Molecular Graphics and Modelling 2010, 29: 116-125.
• [3] Vouzis, P. D., Sahinidis, N. V.: GPU-BLAST: using graphics processors to accelerate protein sequence alignment. Bioinformatics 2001, 27, 2: 182-188.
• [4] Yongchao, L., Maskell, D. L., Schmidt, B.: CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units. BMC Research Notes 2009, 2 (73). Retrieved 16 august 2011 from http://www.biomedcentral.com/1756-0500/2/73.
• [5] Ufimtsev, I. S., Martinez, T. J.: Graphical Processing Units for Quantum Chemistry. Computing in Science & Engineering 2008, 10, 6: 26-34.
• [6] Guochun, S., Kindratenko, V., Ufimtsev, I., Martinez, T.: Direct self-consistent field computations on GPU clusters, Parallel & Distributed Processing (IPDPS). 2010 IEEE International Symposium, 19-23 April 2010, pp.1-8.
• [7] Toukmaji, A. Y., Board, J. A. Jr.: Ewald Summation Techniques in Perspective: A Survey. Computer Physics Communications 1996, 95: 73-92 .
• [8] Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kale, L., Schulten, K.: Scalable molecular dynamics with NAMD. Journal of Computational Chemistry 2005, 26: 1781-1802.
• [9] Ufimtsev, I. S., Martinez, T. J.: Quantum Chemistry on Graphical Processing Units. 3. Analytical Energy Gradients and First Principles Molecular Dynamics. Journal Chemical Theory and Computations 2009, 5: 2619.
• [10] Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K. A., Su, S., Windus, T. L., Dupuis, M., Montgomery, J. A.: General Atomic and Molecular Electronic Structure System. Journal of Computational Chemistry 1993, 14: 1347-1363.
• [11] Mazur, G., Makowski, M.: Development and Optimization of Computational Chemistry Algorithms. Computing and Informatics 2009, 28: 115-125.
• [12] www.wielkiewyzwania.pl.