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Triangulating molecular surfaces on multiple GPUs

Published: 15 September 2013 Publication History

Abstract

Current GPU-based workstations are inadequate to triangulate and rendering large molecular datasets with thousands and hundreds of thousands, not to say millions, of atoms. The problem is not so the lack of processing power, but the memory limitations of current GPU graphics cards. For example, the NVidia GeForce GTX 590 graphics card comes with two 1.5GB GPUs. We tackle here this problem using a OpenMP-CUDA solution that runs on a loosely-coupled GPU cluster. Basically, we propose a fast, scalable, parallel triangulation algorithm for molecular surfaces that takes advantage of multicore processors of CPUs and GPUs of modern hardware architectures, where each CPU core works as the master of a single GPU, being the processing burden distributed over the CPU cores available in a single computer or a cluster. As much as we know, this is the first marching cubes algorithm that triangulates molecular surfaces on multiple GPUs using CUDA and OpenMP.

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Cited By

View all
  • (2017)Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A SurveyComputer Graphics Forum10.1111/cgf.1315836:8(643-683)Online publication date: Jun-2017
  • (2015)Triangulating molecular surfaces over a LAN of GPU-enabled computersParallel Computing10.1016/j.parco.2014.09.00942:C(35-47)Online publication date: 1-Feb-2015
  • (2014)Triangulating Gaussian-Like Surfaces of Molecules with Millions of AtomsComputational Electrostatics for Biological Applications10.1007/978-3-319-12211-3_9(177-198)Online publication date: 30-Nov-2014

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cover image ACM Other conferences
EuroMPI '13: Proceedings of the 20th European MPI Users' Group Meeting
September 2013
289 pages
ISBN:9781450319034
DOI:10.1145/2488551
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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  • ARCOS: Computer Architecture and Technology Area, Universidad Carlos III de Madrid

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Association for Computing Machinery

New York, NY, United States

Publication History

Published: 15 September 2013

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Author Tags

  1. GPU
  2. Gaussian surfaces
  3. molecular surfaces
  4. triangulations

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  • Research-article

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EuroMPI '13
Sponsor:
  • ARCOS
EuroMPI '13: 20th European MPI Users's Group Meeting
September 15 - 18, 2013
Madrid, Spain

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EuroMPI '13 Paper Acceptance Rate 22 of 47 submissions, 47%;
Overall Acceptance Rate 66 of 139 submissions, 47%

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Cited By

View all
  • (2017)Geometric Detection Algorithms for Cavities on Protein Surfaces in Molecular Graphics: A SurveyComputer Graphics Forum10.1111/cgf.1315836:8(643-683)Online publication date: Jun-2017
  • (2015)Triangulating molecular surfaces over a LAN of GPU-enabled computersParallel Computing10.1016/j.parco.2014.09.00942:C(35-47)Online publication date: 1-Feb-2015
  • (2014)Triangulating Gaussian-Like Surfaces of Molecules with Millions of AtomsComputational Electrostatics for Biological Applications10.1007/978-3-319-12211-3_9(177-198)Online publication date: 30-Nov-2014

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