Authors

Xin Wu, Axel Koslowski, Walter Thiel

Abstract

In this work, we demonstrate that semiempirical quantum chemical calculations can be accelerated significantly by leveraging the graphics processing unit (GPU) as a coprocessor on a hybrid multicore CPU-GPU computing platform. Semiempirical calculations using the MNDO, AM1, PM3, OM1, OM2, and OM3 model Hamiltonians were systematically profiled for three types of test systems (fullerenes, water clusters, and solvated crambin) to identify the most time-consuming sections of the code. The corresponding routines were ported to the GPU and optimized employing both existing library functions and a GPU kernel that carries out a sequence of noniterative Jacobi transformations during pseudodiagonalization. The overall computation times for single-point energy calculations and geometry optimizations of large molecules were reduced by one order of magnitude for all methods, as compared to runs on a single CPU core.

Citation

  • Journal: Journal of Chemical Theory and Computation
  • Year: 2012
  • Volume: 8
  • Issue: 7
  • Pages: 2272–2281
  • Publisher: American Chemical Society (ACS)
  • DOI: 10.1021/ct3001798

BibTeX

@article{Wu_2012,
  title={{Semiempirical Quantum Chemical Calculations Accelerated on a Hybrid Multicore CPU–GPU Computing Platform}},
  volume={8},
  ISSN={1549-9626},
  DOI={10.1021/ct3001798},
  number={7},
  journal={Journal of Chemical Theory and Computation},
  publisher={American Chemical Society (ACS)},
  author={Wu, Xin and Koslowski, Axel and Thiel, Walter},
  year={2012},
  pages={2272--2281}
}

Download the bib file

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