High performance computation and display of molecular orbitals on and multi-core cpus

John E. Stone; Jan Saam; David J. Hardy; Kirby L. Vandivort; Wen Mei W. Hwu; Klaus Schulten

doi:10.1145/1513895.1513897

High performance computation and display of molecular orbitals on and multi-core cpus

John E. Stone, Jan Saam, David J. Hardy, Kirby L. Vandivort, Wen Mei W. Hwu, Klaus Schulten

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Abstract

The visualization of molecular orbitals (MOs) is important for analyzing the results of quantum chemistry simulations. The functions describing the MOs are computed on a threedimensional lattice, and the resulting data can then be used for plotting isocontours or isosurfaces for visualization as well as for other types of analyses. Existing software packages that render MOs perform calculations on the CPU and require runtimes of tens to hundreds of seconds depending on the complexity of the molecular system. We present novel data-parallel algorithms for computing lattices of MOs on modern graphics processing units (GPUs) and multi-core CPUs. The fastest GPU algorithm achieves up to a 125-fold speedup over an optimized CPU implementation running on one CPU core. We also demonstrate possible benefits of dynamic GPU kernel generation and just-intime compilation for MO calculation. We have implemented these algorithms within the popular molecular visualization program VMD, which can now produce high quality MO renderings for large systems in less than a second, and achieves the first-ever interactive animations of quantum chemistry simulation trajectories using only on-the-y calculation.

Original language	English (US)
Title of host publication	Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2
Pages	9
Number of pages	1
DOIs	https://doi.org/10.1145/1513895.1513897
State	Published - 2009
Event	2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2 - Washington, D.C., United States Duration: Mar 8 2009 → Mar 8 2009

Publication series

Name	Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2

Other

Other	2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2
Country/Territory	United States
City	Washington, D.C.
Period	3/8/09 → 3/8/09

Keywords

Algorithms
CUDA
Design
GPGPU
Molecular orbital
Performance GPU computing

ASJC Scopus subject areas

Computer Graphics and Computer-Aided Design
Hardware and Architecture
Software

Online availability

10.1145/1513895.1513897

Library availability

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Cite this

Stone, J. E., Saam, J., Hardy, D. J., Vandivort, K. L., Hwu, W. M. W., & Schulten, K. (2009). High performance computation and display of molecular orbitals on and multi-core cpus. In Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2 (pp. 9). (Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2). https://doi.org/10.1145/1513895.1513897

High performance computation and display of molecular orbitals on and multi-core cpus. / Stone, John E.; Saam, Jan; Hardy, David J. et al.
Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2. 2009. p. 9 (Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2).

Research output: Chapter in Book/Report/Conference proceeding › Conference contribution

Stone, JE, Saam, J, Hardy, DJ, Vandivort, KL, Hwu, WMW & Schulten, K 2009, High performance computation and display of molecular orbitals on and multi-core cpus. in Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2. Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2, pp. 9, 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2, Washington, D.C., United States, 3/8/09. https://doi.org/10.1145/1513895.1513897

Stone JE, Saam J, Hardy DJ, Vandivort KL, Hwu WMW, Schulten K. High performance computation and display of molecular orbitals on and multi-core cpus. In Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2. 2009. p. 9. (Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units, GPGPU-2). doi: 10.1145/1513895.1513897

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AB - The visualization of molecular orbitals (MOs) is important for analyzing the results of quantum chemistry simulations. The functions describing the MOs are computed on a threedimensional lattice, and the resulting data can then be used for plotting isocontours or isosurfaces for visualization as well as for other types of analyses. Existing software packages that render MOs perform calculations on the CPU and require runtimes of tens to hundreds of seconds depending on the complexity of the molecular system. We present novel data-parallel algorithms for computing lattices of MOs on modern graphics processing units (GPUs) and multi-core CPUs. The fastest GPU algorithm achieves up to a 125-fold speedup over an optimized CPU implementation running on one CPU core. We also demonstrate possible benefits of dynamic GPU kernel generation and just-intime compilation for MO calculation. We have implemented these algorithms within the popular molecular visualization program VMD, which can now produce high quality MO renderings for large systems in less than a second, and achieves the first-ever interactive animations of quantum chemistry simulation trajectories using only on-the-y calculation.

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High performance computation and display of molecular orbitals on and multi-core cpus

Abstract

Publication series

Other

Keywords

ASJC Scopus subject areas

Online availability

Library availability

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