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X-Ray Laser Imaging of Biomolecules Using Multiple GPUs

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Parallel Processing and Applied Mathematics (PPAM 2013)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 8384))

Abstract

Extremely bright X-ray lasers are becoming a promising tool for 3D imaging of biomolecules. By hitting a beam of streaming particles with a very short burst of a high energy X-ray and collecting the resulting scattering pattern, the 3D structure of the particles can be deduced. The computational complexity associated with transforming the data thus collected into a 3D intensity map is very high and calls for efficient data-parallel implementations.

We present ongoing work in accelerating this application using multiple GPU nodes. In particular, we look at the scaling properties of the application and give predictions as to the computational viability of this imaging technique.

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Acknowledgment

This work was financially supported by the Swedish Research Council, the Röntgen Ångström Cluster, the Knut och Alice Wallenbergs Stiftelse, the European Research Council (JL), and by the Swedish Research Council within the UPMARC Linnaeus center of Excellence (SE, JL).

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Authors and Affiliations

  1. Division of Scientific Computing, Department of Information Technology, Uppsala University, 751 05, Uppsala, Sweden

    Stefan Engblom & Jing Liu

  2. Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, 751 24, Uppsala, Sweden

    Jing Liu

Authors
  1. Stefan Engblom
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  2. Jing Liu
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Corresponding author

Correspondence to Jing Liu .

Editor information

Editors and Affiliations

  1. Institute of Computer and Information Science, Czestochowa University of Technology, Czestochowa, Poland

    Roman Wyrzykowski

  2. University of Tennessee, Department of Computer Science, Knoxville, Tennessee, USA

    Jack Dongarra

  3. Institute of Computer and Information Science, Czestochowa University of Technology, Czestochowa, Poland

    Konrad Karczewski

  4. Technical University of Denmark Informatics and Mathematical Modelling, Kongens Lyngby, Denmark

    Jerzy Waśniewski

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Engblom, S., Liu, J. (2014). X-Ray Laser Imaging of Biomolecules Using Multiple GPUs. In: Wyrzykowski, R., Dongarra, J., Karczewski, K., Waśniewski, J. (eds) Parallel Processing and Applied Mathematics. PPAM 2013. Lecture Notes in Computer Science(), vol 8384. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-55224-3_45

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  • DOI: https://doi.org/10.1007/978-3-642-55224-3_45

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-55223-6

  • Online ISBN: 978-3-642-55224-3

  • eBook Packages: Computer ScienceComputer Science (R0)

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