Literature DB >> 26614326

Accelerating Correlated Quantum Chemistry Calculations Using Graphical Processing Units and a Mixed Precision Matrix Multiplication Library.

Roberto Olivares-Amaya1, Mark A Watson1, Richard G Edgar1, Leslie Vogt1, Yihan Shao1, Alán Aspuru-Guzik1.   

Abstract

Two new tools for the acceleration of computational chemistry codes using graphical processing units (GPUs) are presented. First, we propose a general black-box approach for the efficient GPU acceleration of matrix-matrix multiplications where the matrix size is too large for the whole computation to be held in the GPU's onboard memory. Second, we show how to improve the accuracy of matrix multiplications when using only single-precision GPU devices by proposing a heterogeneous computing model, whereby single- and double-precision operations are evaluated in a mixed fashion on the GPU and central processing unit, respectively. The utility of the library is illustrated for quantum chemistry with application to the acceleration of resolution-of-the-identity second-order Møller-Plesset perturbation theory calculations for molecules, which we were previously unable to treat. In particular, for the 168-atom valinomycin molecule in a cc-pVDZ basis set, we observed speedups of 13.8, 7.8, and 10.1 times for single-, double- and mixed-precision general matrix multiply (SGEMM, DGEMM, and MGEMM), respectively. The corresponding errors in the correlation energy were reduced from -10.0 to -1.2 kcal mol(-1) for SGEMM and MGEMM, respectively, while higher accuracy can be easily achieved with a different choice of cutoff parameter.

Entities:  

Year:  2010        PMID: 26614326     DOI: 10.1021/ct900543q

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  6 in total

1.  GPU-accelerated molecular modeling coming of age.

Authors:  John E Stone; David J Hardy; Ivan S Ufimtsev; Klaus Schulten
Journal:  J Mol Graph Model       Date:  2010-07-08       Impact factor: 2.518

2.  Fast Analysis of Molecular Dynamics Trajectories with Graphics Processing Units-Radial Distribution Function Histogramming.

Authors:  Benjamin G Levine; John E Stone; Axel Kohlmeyer
Journal:  J Comput Phys       Date:  2011-05-01       Impact factor: 3.553

3.  Excited-State Electronic Structure with Configuration Interaction Singles and Tamm-Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units.

Authors:  Christine M Isborn; Nathan Luehr; Ivan S Ufimtsev; Todd J Martínez
Journal:  J Chem Theory Comput       Date:  2011-05-12       Impact factor: 6.006

4.  From macromolecules to electrons-grand challenges in theoretical and computational chemistry.

Authors:  Thomas S Hofer
Journal:  Front Chem       Date:  2013-05-27       Impact factor: 5.221

Review 5.  Mathematical and computational modeling in biology at multiple scales.

Authors:  Jack A Tuszynski; Philip Winter; Diana White; Chih-Yuan Tseng; Kamlesh K Sahu; Francesco Gentile; Ivana Spasevska; Sara Ibrahim Omar; Niloofar Nayebi; Cassandra Dm Churchill; Mariusz Klobukowski; Rabab M Abou El-Magd
Journal:  Theor Biol Med Model       Date:  2014-12-27       Impact factor: 2.432

6.  Quantum chemical approach to estimating the thermodynamics of metabolic reactions.

Authors:  Adrian Jinich; Dmitrij Rappoport; Ian Dunn; Benjamin Sanchez-Lengeling; Roberto Olivares-Amaya; Elad Noor; Arren Bar Even; Alán Aspuru-Guzik
Journal:  Sci Rep       Date:  2014-11-12       Impact factor: 4.379

  6 in total

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