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High performance computation and interactive display of molecular orbitals on GPUs and multi-core CPUs

Published: 08 March 2009 Publication History

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 three-dimensional 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-in-time 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-fly calculation.

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  • (2023)VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical SimulationsJournal of Chemical Information and Modeling10.1021/acs.jcim.3c0065863:15(4664-4678)Online publication date: 28-Jul-2023
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cover image ACM Other conferences
GPGPU-2: Proceedings of 2nd Workshop on General Purpose Processing on Graphics Processing Units
March 2009
107 pages
ISBN:9781605585178
DOI:10.1145/1513895
Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Publication History

Published: 08 March 2009

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Author Tags

  1. CUDA
  2. GPGPU
  3. GPU computing
  4. molecular orbital

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GPGPU '09

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Cited By

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  • (2024)A Vision for the Future of Multiscale ModelingACS Physical Chemistry Au10.1021/acsphyschemau.3c000804:3(202-225)Online publication date: 4-Mar-2024
  • (2023)Application Experiences on a GPU-Accelerated Arm-based HPC TestbedProceedings of the HPC Asia 2023 Workshops10.1145/3581576.3581621(35-49)Online publication date: 27-Feb-2023
  • (2023)VMD as a Platform for Interactive Small Molecule Preparation and Visualization in Quantum and Classical SimulationsJournal of Chemical Information and Modeling10.1021/acs.jcim.3c0065863:15(4664-4678)Online publication date: 28-Jul-2023
  • (2022)Level of Detail Exploration of Electronic Transition Ensembles using Hierarchical ClusteringComputer Graphics Forum10.1111/cgf.1454441:3(333-344)Online publication date: 12-Aug-2022
  • (2021)Visual Analysis of Electronic Densities and Transitions in MoleculesComputer Graphics Forum10.1111/cgf.1430740:3(287-298)Online publication date: 29-Jun-2021
  • (2020)On Evaluating Runtime Performance of Interactive VisualizationsIEEE Transactions on Visualization and Computer Graphics10.1109/TVCG.2019.289843526:9(2848-2862)Online publication date: 1-Sep-2020
  • (2019)Computation Efficiency Analysis of Multiple GPUs and Multiple CPUs Based Cluster Computing EnvironmentsAdvances in Computer Science and Ubiquitous Computing10.1007/978-981-13-9341-9_71(410-415)Online publication date: 4-Dec-2019
  • (2017)Performance Evaluations of Multiple GPUs based on MPI EnvironmentsProceedings of the International Conference on Research in Adaptive and Convergent Systems10.1145/3129676.3129716(303-304)Online publication date: 20-Sep-2017
  • (2017)Application case study—molecular visualization and analysisProgramming Massively Parallel Processors10.1016/B978-0-12-811986-0.00015-7(331-344)Online publication date: 2017
  • (2016)GPU ScalingWeb-Based Services10.4018/978-1-4666-9466-8.ch105(2373-2384)Online publication date: 2016
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