Literature DB >> 26589024

Generating Efficient Quantum Chemistry Codes for Novel Architectures.

Alexey V Titov1,2, Ivan S Ufimtsev2, Nathan Luehr2, Todd J Martinez2.   

Abstract

We describe an extension of our graphics processing unit (GPU) electronic structure program TeraChem to include atom-centered Gaussian basis sets with d angular momentum functions. This was made possible by a "meta-programming" strategy that leverages computer algebra systems for the derivation of equations and their transformation to correct code. We generate a multitude of code fragments that are formally mathematically equivalent, but differ in their memory and floating-point operation footprints. We then select between different code fragments using empirical testing to find the highest performing code variant. This leads to an optimal balance of floating-point operations and memory bandwidth for a given target architecture without laborious manual tuning. We show that this approach is capable of similar performance compared to our hand-tuned GPU kernels for basis sets with s and p angular momenta. We also demonstrate that mixed precision schemes (using both single and double precision) remain stable and accurate for molecules with d functions. We provide benchmarks of the execution time of entire self-consistent field (SCF) calculations using our GPU code and compare to mature CPU based codes, showing the benefits of the GPU architecture for electronic structure theory with appropriately redesigned algorithms. We suggest that the meta-programming and empirical performance optimization approach may be important in future computational chemistry applications, especially in the face of quickly evolving computer architectures.

Year:  2012        PMID: 26589024     DOI: 10.1021/ct300321a

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


  35 in total

1.  Driving torsion scans with wavefront propagation.

Authors:  Yudong Qiu; Daniel G A Smith; Chaya D Stern; Mudong Feng; Hyesu Jang; Lee-Ping Wang
Journal:  J Chem Phys       Date:  2020-06-28       Impact factor: 3.488

2.  Hole Hopping Across a Protein-Protein Interface.

Authors:  Kana Takematsu; Petr Pospíšil; Martin Pižl; Michael Towrie; Jan Heyda; Stanislav Záliš; Jens T Kaiser; Jay R Winkler; Harry B Gray; Antonín Vlček
Journal:  J Phys Chem B       Date:  2019-02-06       Impact factor: 2.991

3.  Solving the scalability issue in quantum-based refinement: Q|R#1.

Authors:  Min Zheng; Nigel W Moriarty; Yanting Xu; Jeffrey R Reimers; Pavel V Afonine; Mark P Waller
Journal:  Acta Crystallogr D Struct Biol       Date:  2017-11-30       Impact factor: 7.652

4.  Robustness and Efficiency of Poisson-Boltzmann Modeling on Graphics Processing Units.

Authors:  Ruxi Qi; Ray Luo
Journal:  J Chem Inf Model       Date:  2018-12-31       Impact factor: 4.956

5.  TeraChem: Accelerating electronic structure and ab initio molecular dynamics with graphical processing units.

Authors:  Stefan Seritan; Christoph Bannwarth; B Scott Fales; Edward G Hohenstein; Sara I L Kokkila-Schumacher; Nathan Luehr; James W Snyder; Chenchen Song; Alexey V Titov; Ivan S Ufimtsev; Todd J Martínez
Journal:  J Chem Phys       Date:  2020-06-14       Impact factor: 3.488

6.  Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units.

Authors:  Ruxi Qi; Wesley M Botello-Smith; Ray Luo
Journal:  J Chem Theory Comput       Date:  2017-06-07       Impact factor: 6.006

7.  Photoinduced hole hopping through tryptophans in proteins.

Authors:  Stanislav Záliš; Jan Heyda; Filip Šebesta; Jay R Winkler; Harry B Gray; Antonín Vlček
Journal:  Proc Natl Acad Sci U S A       Date:  2021-03-16       Impact factor: 11.205

8.  Development of Vibrational Frequency Maps for Nucleobases.

Authors:  Yaoyukun Jiang; Lu Wang
Journal:  J Phys Chem B       Date:  2019-07-01       Impact factor: 2.991

9.  Combining Machine Learning and Computational Chemistry for Predictive Insights Into Chemical Systems.

Authors:  John A Keith; Valentin Vassilev-Galindo; Bingqing Cheng; Stefan Chmiela; Michael Gastegger; Klaus-Robert Müller; Alexandre Tkatchenko
Journal:  Chem Rev       Date:  2021-07-07       Impact factor: 60.622

10.  Insights Into Chemical Reactions at the Beginning of the Universe: From HeH+ to H3.

Authors:  Soumya Ranjan Dash; Tamal Das; Kumar Vanka
Journal:  Front Chem       Date:  2021-06-18       Impact factor: 5.221

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