Lorena A. Barba group

2011-2012

View all publications as a chronological list

All Publications

  • "GPU@BU—GPU computing at Boston University", L. A. Barba. (29 November 2012). 10.6084/m9.figshare.98875

    A short history of GPU computing at Boston University, made into a handout for the BU booth at the Supercomputing Conference, Salt Lake City, November 2012. Published on figshare under CC-BY.

  • "Hierarchical N-body simulations with auto-tuning for heterogeneous systems", Rio Yokota, L. A. Barba. Computing in Science and Engineering (CiSE), 14(3):30–39 (May/June 2012). 10.1109/MCSE.2012.1 // Preprint arXiv:1108.5815

    IEEE Computer Society (online 3 Jan. 2012)

  • "A tuned and scalable fast multipole method as a preeminent algorithm for exascale systems", Rio Yokota, L. A. Barba. Int. J. High-Perf. Comput., 26(4):337–346 (November 2012). 10.1177/1094342011429952 // Preprint arXiv:1106.2176 // Journal website

    Published online 24 Jan. 2012

  • Invited: "Protein electrostatics on a desktop using GPU hardware and multipole algorithms", L. A. Barba. The Society for Mathematical Biology Annual Meeting and Conference (25–28 July 2012), Knoxville, TN.

    minisymposium on “Electrostatics: numerical algorithms and biological applications”, organized by Yongcheng Zhou (Colorado State University) and Weihua Geng (University of Alabama)

  • "Efficient boundary element method on Python using GPUs", Christopher D. Cooper, L. A. Barba. World Congress on Computational Mechanics (WCCM) (8–13 July 2012), Sao Paulo, Brazil.
  • "Projection-based immersed boundary method in CUDA", Anush Krishnan, L. A. Barba. World Congress on Computational Mechanics (WCCM) (8–13 July 2012), Sao Paulo, Brazil.
  • "Aerodynamics of flying snakes using an immersed boundary method", Anush Krishnan, L. A. Barba. 24th International Conference on Parallel Computational Fluid Dynamics, ParCFD’12 (21–25 May 2012).
  • Invited: "The success of multipole methods: Are we there yet?", L. A. Barba. Scalable Hierarchical Algorithms for eXtreme Computing (SHAX-C) organized by King Abdullah University of Science and Technology (KAUST) (28-30 April 2012), Thuwal, Saudi Arabia.
  • Invited: "The success of multipole methods: Are we there yet?", L. A. Barba. New England Numerical Analysis Day (NENAD) organized by University of Massachusetts (21 April 2012), Amherst, MA.
  • "Digital Pedagogy in Three Parts: Screencasting, Course Blog, Remote Guests", L. A. Barba. BU CEIT 4th Annual Instructional Innovation Conference organized by Boston University (2 August 2012), Boston, MA. 10.6084/m9.figshare.94016 // Screencast of the talk on You Tube // Course videos on iTunes U

    Presentation at BU’s Fourth Annual Instructional Innovation Conference, March 1st, 2012. Published 02 Aug 2012 on figshare under CC-BY.

  • Invited: "Hierarchical N-body algorithms: A pattern likely to lead at extreme scales", L. A. Barba. ICERM workshop on Synchronization-reducing Algorithms and Programming Models for Large-Scale Simulations organized by Brown University (9–13 January 2012), Providence, RI. // Streaming video
  • "Validation of the cuIBM code for Navier-Stokes equations with immersed boundary methods", Anush Krishnan, L. A. Barba. (6 July 2012). 10.6084/m9.figshare.92789 // Code repository

    Technical report published on figshare under CC-BY-NC.

  • "Weak scaling of parallel FMM vs. FFT up to 4096 processes", Rio Yokota, L. A. Barba. (18 June 2012). 10.6084/m9.figshare.92425 // exaFMM webpage

    Figure, data and plotting script published on figshare under CC-BY

  • "ExaFMM: An open source library for Fast Multipole Methods", L. A. Barba, Rio Yokota. (18 June 2012). 10.6084/m9.figshare.92426

    Trifold brochure, distributed with the exaFMM poster, published on figshare under CC-BY

  • "ExaFMM: An open source library for Fast Multipole Methods aimed towards Exascale systems", L. A. Barba, Rio Yokota. (31 May 2012). 10.6084/m9.figshare.92166

    Poster, published on figshare under CC-BY

  • "Illustration of the flow of an FMM calculation (fast multipole method)", Rio Yokota, L. A. Barba. (17 Mar 2012). 10.6084/m9.figshare.91441

    Figure published on figshare under CC-BY

  • "Hierarchical subdivision of space in FMM (fast multipole method)", Rio Yokota, L. A. Barba. (17 March 2012). 10.6084/m9.figshare.91440

    Figure published on figshare under CC-BY

  • "Digital inking and lecture screencasts", L. A. Barba. 1st Annual Instructional Innovation Conference organized by Center for Excellence and Innovation in Teaching, Boston University (12 October 2012), Boston, MA. 10.6084/m9.figshare.94015

    Presentation at BU’s First Annual Instructional Innovation Conference, held March 27, 2009. Published on figshare under CC-BY

  • "Reproducibility PI Manifesto", L. A. Barba. (13 December 2012). 10.6084/m9.figshare.104539

    Presentation for a talk given at the ICERM workshop “Reproducibility in Computational and Experimental Mathematics”. Published on figshare under CC-BY.

  • "Open, Blended, Flipped, Social—courses in Mechanical Engineering", L.A. Barba. (12 October 2012). 10.6084/m9.figshare.96414

    Poster presented at the NAE Frontiers of Engineering Education Symposium, and uploaded to figshare under CC-BY.

  • "Application for the NAE Frontiers of Engineering Education Symposium 2012", L. A. Barba. (12 October 2012). 10.6084/m9.figshare.96413

    Application essay for the NAE FOEE symposium, submitted July 2012. Published on figshare under CC-BY.

  • "Scalable Fast Multipole Methods for Vortex Element Methods", Qi Hu, Nail A. Gumerov, Rio Yokota, Lorena Barba, Ramani Duraiswami. The International Conference for High-Performance Computing, Networking, Storage and Analysis organized by ACM (Nov. 10–16 2012), Salt Lake City, Utah.. 10.1109/SC.Companion.2012.221 // IEEE Explore (Abstract)

    Supercomputing Conference SC12

  • "How to obtain efficient GPU kernels: an illustration using FMM & FGT", Felipe A. Cruz, Simon K. Layton, L. A. Barba. Comput. Phys. Commun., 182(10):2084–2098 (October 2011). 10.1016/j.cpc.2011.05.002 // Preprint arXiv:1009.3457
  • "Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns", Rio Yokota, J. P. Bardhan, M. G. Knepley, L. A. Barba, T. Hamada. Comput. Phys. Commun., 182(6):1271–1283 (June 2011). 10.1016/j.cpc.2011.02.013 // Preprint arXiv:1007.4591
  • "Comparing the treecode with FMM on GPUs for vortex particle simulations of a leapfrogging vortex ring", Rio Yokota, L. A. Barba. Computers & Fluids, 45(1):155–161 (June 2011). 10.1016/j.compfluid.2010.11.029
  • "Treecode and fast multipole method for N-body simulation with CUDA", Rio Yokota, L. A. Barba. (2011). 10.1016/B978-0-12-384988-5.00009-7 // Preprint arXiv:1010.1482

    Ch. 9 in GPU Computing Gems Emerald Edition, Wen-mei Hwu, ed.; Morgan Kaufmann/Elsevier (2011) pp. 113–132. ISBN: 978-0-12-384988-5

  • "Parameter tuning of a hybrid treecode-FMM on GPUs", Rio Yokota, L. A. Barba. (31 May–4 June 2011).

    In CACHES’11: Characterizing Applications for Heterogeneous Exascale Systems, at the 25th International Conference on Supercomputing (ACM/SIGARCH), Tucson, Arizona

  • "Fast multipole method vs. spectral methods for the simulation of isotropic turbulence on GPUs", Rio Yokota, L. A. Barba. 23rd International Conference on Parallel Computational Fluid Dynamics, ParCFD’11 (16–20 May 2011), Barcelona, Spain.
  • "cuIBM—A GPU accelerated immersed boundary method", Simon K. Layton, Anush Krishnan, L. A. Barba. 23rd International Conference on Parallel Computational Fluid Dynamics, ParCFD’11 (16–20 May 2011), Barcelona, Spain. // Code repository //
  • Invited: "Dare to think about exascale CFD — a research agenda", L. A. Barba. 23rd International Conference on Parallel Computational Fluid Dynamics, ParCFD’11 (16–20 May 2011), Barcelona, Spain.

    Plenary lecture

  • Invited: "The basis and perspectives of an exascale algorithm: our ExaFMM project", L. A. Barba. Workshop on Manycore and Accelerator-based High-performance Scientific Computing organized by International Center for Computational Science (ICCS), UC Berkeley (26–28 January 2011), Berkeley, CA.
  • Invited: "The basis and perspectives of an exascale algorithm: our ExaFMM project", L. A. Barba. IMA workshop on High-performance Computing and Emerging Architectures organized by University of Minnesota (10–14 January 2011). // Slides and video on the IMA site
  • "PetFMM–A dynamically load-balancing parallel fast multipole library", Felipe A. Cruz, Matthew G. Knepley, L. A. Barba. Int. J. Num. Meth. Eng., 85(4):403–428 (January 2011). 10.1002/nme.2972 // Preprint arXiv:0905.2637

Refereed Journal Articles

  • "Hierarchical N-body simulations with auto-tuning for heterogeneous systems", Rio Yokota, L. A. Barba. Computing in Science and Engineering (CiSE), 14(3):30–39 (May/June 2012). 10.1109/MCSE.2012.1 // Preprint arXiv:1108.5815

    IEEE Computer Society (online 3 Jan. 2012)

  • "A tuned and scalable fast multipole method as a preeminent algorithm for exascale systems", Rio Yokota, L. A. Barba. Int. J. High-Perf. Comput., 26(4):337–346 (November 2012). 10.1177/1094342011429952 // Preprint arXiv:1106.2176 // Journal website

    Published online 24 Jan. 2012

  • "How to obtain efficient GPU kernels: an illustration using FMM & FGT", Felipe A. Cruz, Simon K. Layton, L. A. Barba. Comput. Phys. Commun., 182(10):2084–2098 (October 2011). 10.1016/j.cpc.2011.05.002 // Preprint arXiv:1009.3457
  • "Biomolecular electrostatics using a fast multipole BEM on up to 512 GPUs and a billion unknowns", Rio Yokota, J. P. Bardhan, M. G. Knepley, L. A. Barba, T. Hamada. Comput. Phys. Commun., 182(6):1271–1283 (June 2011). 10.1016/j.cpc.2011.02.013 // Preprint arXiv:1007.4591
  • "Comparing the treecode with FMM on GPUs for vortex particle simulations of a leapfrogging vortex ring", Rio Yokota, L. A. Barba. Computers & Fluids, 45(1):155–161 (June 2011). 10.1016/j.compfluid.2010.11.029
  • "PetFMM–A dynamically load-balancing parallel fast multipole library", Felipe A. Cruz, Matthew G. Knepley, L. A. Barba. Int. J. Num. Meth. Eng., 85(4):403–428 (January 2011). 10.1002/nme.2972 // Preprint arXiv:0905.2637

Book Chapters

Refereed Conference Papers

  • "Parameter tuning of a hybrid treecode-FMM on GPUs", Rio Yokota, L. A. Barba. (31 May–4 June 2011).

    In CACHES’11: Characterizing Applications for Heterogeneous Exascale Systems, at the 25th International Conference on Supercomputing (ACM/SIGARCH), Tucson, Arizona

Open Research

  • "GPU@BU—GPU computing at Boston University", L. A. Barba. (29 November 2012). 10.6084/m9.figshare.98875

    A short history of GPU computing at Boston University, made into a handout for the BU booth at the Supercomputing Conference, Salt Lake City, November 2012. Published on figshare under CC-BY.

  • "Digital Pedagogy in Three Parts: Screencasting, Course Blog, Remote Guests", L. A. Barba. BU CEIT 4th Annual Instructional Innovation Conference organized by Boston University (2 August 2012), Boston, MA. 10.6084/m9.figshare.94016 // Screencast of the talk on You Tube // Course videos on iTunes U

    Presentation at BU’s Fourth Annual Instructional Innovation Conference, March 1st, 2012. Published 02 Aug 2012 on figshare under CC-BY.

  • "Validation of the cuIBM code for Navier-Stokes equations with immersed boundary methods", Anush Krishnan, L. A. Barba. (6 July 2012). 10.6084/m9.figshare.92789 // Code repository

    Technical report published on figshare under CC-BY-NC.

  • "Weak scaling of parallel FMM vs. FFT up to 4096 processes", Rio Yokota, L. A. Barba. (18 June 2012). 10.6084/m9.figshare.92425 // exaFMM webpage

    Figure, data and plotting script published on figshare under CC-BY

  • "ExaFMM: An open source library for Fast Multipole Methods", L. A. Barba, Rio Yokota. (18 June 2012). 10.6084/m9.figshare.92426

    Trifold brochure, distributed with the exaFMM poster, published on figshare under CC-BY

  • "ExaFMM: An open source library for Fast Multipole Methods aimed towards Exascale systems", L. A. Barba, Rio Yokota. (31 May 2012). 10.6084/m9.figshare.92166

    Poster, published on figshare under CC-BY

  • "Illustration of the flow of an FMM calculation (fast multipole method)", Rio Yokota, L. A. Barba. (17 Mar 2012). 10.6084/m9.figshare.91441

    Figure published on figshare under CC-BY

  • "Hierarchical subdivision of space in FMM (fast multipole method)", Rio Yokota, L. A. Barba. (17 March 2012). 10.6084/m9.figshare.91440

    Figure published on figshare under CC-BY

  • "Digital inking and lecture screencasts", L. A. Barba. 1st Annual Instructional Innovation Conference organized by Center for Excellence and Innovation in Teaching, Boston University (12 October 2012), Boston, MA. 10.6084/m9.figshare.94015

    Presentation at BU’s First Annual Instructional Innovation Conference, held March 27, 2009. Published on figshare under CC-BY

  • "Reproducibility PI Manifesto", L. A. Barba. (13 December 2012). 10.6084/m9.figshare.104539

    Presentation for a talk given at the ICERM workshop “Reproducibility in Computational and Experimental Mathematics”. Published on figshare under CC-BY.

  • "Open, Blended, Flipped, Social—courses in Mechanical Engineering", L.A. Barba. (12 October 2012). 10.6084/m9.figshare.96414

    Poster presented at the NAE Frontiers of Engineering Education Symposium, and uploaded to figshare under CC-BY.

  • "Application for the NAE Frontiers of Engineering Education Symposium 2012", L. A. Barba. (12 October 2012). 10.6084/m9.figshare.96413

    Application essay for the NAE FOEE symposium, submitted July 2012. Published on figshare under CC-BY.

Conference Presentations

  • Invited: "Protein electrostatics on a desktop using GPU hardware and multipole algorithms", L. A. Barba. The Society for Mathematical Biology Annual Meeting and Conference (25–28 July 2012), Knoxville, TN.

    minisymposium on “Electrostatics: numerical algorithms and biological applications”, organized by Yongcheng Zhou (Colorado State University) and Weihua Geng (University of Alabama)

  • "Efficient boundary element method on Python using GPUs", Christopher D. Cooper, L. A. Barba. World Congress on Computational Mechanics (WCCM) (8–13 July 2012), Sao Paulo, Brazil.
  • "Projection-based immersed boundary method in CUDA", Anush Krishnan, L. A. Barba. World Congress on Computational Mechanics (WCCM) (8–13 July 2012), Sao Paulo, Brazil.
  • "Aerodynamics of flying snakes using an immersed boundary method", Anush Krishnan, L. A. Barba. 24th International Conference on Parallel Computational Fluid Dynamics, ParCFD’12 (21–25 May 2012).
  • Invited: "The success of multipole methods: Are we there yet?", L. A. Barba. Scalable Hierarchical Algorithms for eXtreme Computing (SHAX-C) organized by King Abdullah University of Science and Technology (KAUST) (28-30 April 2012), Thuwal, Saudi Arabia.
  • Invited: "The success of multipole methods: Are we there yet?", L. A. Barba. New England Numerical Analysis Day (NENAD) organized by University of Massachusetts (21 April 2012), Amherst, MA.
  • Invited: "Hierarchical N-body algorithms: A pattern likely to lead at extreme scales", L. A. Barba. ICERM workshop on Synchronization-reducing Algorithms and Programming Models for Large-Scale Simulations organized by Brown University (9–13 January 2012), Providence, RI. // Streaming video
  • "Fast multipole method vs. spectral methods for the simulation of isotropic turbulence on GPUs", Rio Yokota, L. A. Barba. 23rd International Conference on Parallel Computational Fluid Dynamics, ParCFD’11 (16–20 May 2011), Barcelona, Spain.
  • "cuIBM—A GPU accelerated immersed boundary method", Simon K. Layton, Anush Krishnan, L. A. Barba. 23rd International Conference on Parallel Computational Fluid Dynamics, ParCFD’11 (16–20 May 2011), Barcelona, Spain. // Code repository //
  • Invited: "Dare to think about exascale CFD — a research agenda", L. A. Barba. 23rd International Conference on Parallel Computational Fluid Dynamics, ParCFD’11 (16–20 May 2011), Barcelona, Spain.

    Plenary lecture

  • Invited: "The basis and perspectives of an exascale algorithm: our ExaFMM project", L. A. Barba. Workshop on Manycore and Accelerator-based High-performance Scientific Computing organized by International Center for Computational Science (ICCS), UC Berkeley (26–28 January 2011), Berkeley, CA.
  • Invited: "The basis and perspectives of an exascale algorithm: our ExaFMM project", L. A. Barba. IMA workshop on High-performance Computing and Emerging Architectures organized by University of Minnesota (10–14 January 2011). // Slides and video on the IMA site

Posters