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  • 251. Sanders, Kate
    et al.
    Boustedt, Jonas
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    McCartney, Robert
    Moström, Jan Erik
    Thomas, Lynda
    Zander, Carol
    Threshold concepts and threshold skills in computing2012In: Proc. 8th International Computing Education Research Conference, New York: ACM Press, 2012, p. 23-30Conference paper (Refereed)
  • 252. Sanders, Kate
    et al.
    Boustedt, Jonas
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    McCartney, Robert
    Zander, Carol
    Folk Pedagogy: Nobody doesn't like active learning2017In: Proc. 13th International Computing Education Research Conference, New York: ACM Press, 2017, p. 145-154Conference paper (Refereed)
  • 253. Sanders, Kate
    et al.
    Sheard, Judy
    Becker, Brett A.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hamouda, Sally
    Simon,
    Inferential statistics in computing education research: A methodological review2019In: Proc. 15th International Computing Education Research Conference, New York: ACM Press, 2019, p. 177-185Conference paper (Refereed)
  • 254. Schulte, Carsten
    et al.
    Hornung, Malte
    Sentance, Sue
    Dagiene, Valentina
    Jevsikova, Tatjana
    Thota, Neena
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Peters, Anne-Kathrin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Computer Science at School / CS Teacher Education: Koli working-group report on CS at school2012In: Proc. 12th International Conference on Computing Education Research: Koli Calling, New York: ACM Press, 2012, p. 29-38Conference paper (Refereed)
  • 255. Senek, Aleksandar
    et al.
    Engblom, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Multiscale stochastic neuron modeling – with applications in deep brain stimulation2017In: Proc. Summer Simulation Multiconference: 2017, San Diego, CA: Society for Computer Simulation International , 2017, p. 38:1-5, article id 38Conference paper (Refereed)
  • 256. Sheard, Judy
    et al.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Kinnunen, Päivi
    Malmi, Lauri
    Nylén, Aletta
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Thota, Neena
    MOOCs and their impact on academics2014In: Proc. 14th International Conference on Computing Education Research: Koli Calling, New York: ACM Press, 2014, p. 137-145Conference paper (Refereed)
  • 257.
    Singh, Prashant
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Claeys, Tim
    Vandenbosch, Guy A. E.
    Pissoort, Davy
    Automated line-based sequential sampling and modeling algorithm for EMC near-field scanning2017In: IEEE transactions on electromagnetic compatibility (Print), ISSN 0018-9375, E-ISSN 1558-187X, Vol. 59, p. 704-709Article in journal (Refereed)
  • 258.
    Singh, Prashant
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Couckuyt, Ivo
    Elsayed, Khairy
    Deschrijver, Dirk
    Dhaene, Tom
    Multi-objective geometry optimization of a gas cyclone using triple-fidelity co-Kriging surrogate models2017In: Journal of Optimization Theory and Applications, ISSN 0022-3239, E-ISSN 1573-2878, Vol. 175, p. 172-193Article in journal (Refereed)
  • 259.
    Singh, Prashant
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hyperparameter optimization for approximate Bayesian computation2018In: Proc. 50th Winter Simulation Conference, Piscataway, NJ: IEEE, 2018, p. 1718-1729Conference paper (Refereed)
  • 260.
    Singh, Prashant
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Multi-objective optimization driven construction of uniform priors for likelihood-free parameter inference2018In: Proc. 32nd European Simulation and Modelling Conference, EUROSIS , 2018, p. 22-27Conference paper (Refereed)
  • 261.
    Singh, Prashant
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Surrogate assisted model reduction for stochastic biochemical reaction networks2017In: Proc. 49th Winter Simulation Conference, Piscataway, NJ: IEEE, 2017, p. 1773-1783Conference paper (Refereed)
  • 262.
    Singh, Prashant
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Rossi, Marco
    Couckuyt, Ivo
    Deschrijver, Dirk
    Rogier, Hendrik
    Dhaene, Tom
    Constrained multi-objective antenna design optimization using surrogates2017In: International journal of numerical modelling, ISSN 0894-3370, E-ISSN 1099-1204, Vol. 30, p. e2248:1-5, article id e2248Article in journal (Refereed)
  • 263.
    Stegeby, Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Kowalewski, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Piszczatowski, Konrad
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Karlsson, Hans O.
    Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - Ångström, Theoretical Chemistry.
    Wave packet simulations of antiproton scattering on molecular hydrogen2015In: Journal of Physics B: Atomic, Molecular and Optical Physics, ISSN 0953-4075, E-ISSN 1361-6455, Vol. 48, no 19, p. 195204:1-7, article id 195204Article in journal (Refereed)
  • 264. Suwelack, Stefan
    et al.
    Lukarski, Dimitar
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Heuveline, Vincent
    Dillmann, Rüdiger
    Speidel, Stefanie
    Accurate surface embedding for higher order finite elements2013In: Proc. 12th ACM SIGGRAPH/Eurographics Symposium on Computer Animation, New York: ACM Press, 2013, p. 187-192Conference paper (Refereed)
  • 265. Thallmair, Sebastian
    et al.
    Kowalewski, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Fingerhut, Benjamin P.
    Sailer, Christian F.
    de Vivie-Riedle, Regina
    Molecular wave packet dynamics decelerated by solvent environment: A theoretical approach2013In: Proc. 18th International Conference on Ultrafast Phenomena, EDP Sciences, 2013, p. 05043:1-3Conference paper (Refereed)
  • 266. Thomas, Lynda
    et al.
    Boustedt, Jonas
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    McCartney, Robert
    Moström, Jan Erik
    Sanders, Kate
    Zander, Carol
    A broader threshold: Including skills as well as concepts in computing education2014In: Threshold Concepts: From personal practice to communities of practice, Cork, Ireland: NAIRTL , 2014, p. 154-158Conference paper (Refereed)
  • 267. Thomas, Lynda
    et al.
    Boustedt, Jonas
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    McCartney, Robert
    Moström, Jan Erik
    Sanders, Kate
    Zander, Carol
    In the liminal space: Software design as a threshold skill2017In: Practice and Evidence of the Scholarship of Teaching and Learning in Higher Education, ISSN 1750-8428, E-ISSN 1750-8428, Vol. 12, p. 333-351Article in journal (Refereed)
  • 268. Thomas, Lynda
    et al.
    Boustedt, Jonas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    McCartney, Robert
    Moström, Jan Erik
    Sanders, Kate
    Zander, Carol
    Threshold Concepts in Computer Science: an ongoing empirical investigation2010In: Threshold Concepts and Transformational Learning, Rotterdam, The Netherlands: Sense Publishers , 2010, p. 241-258Chapter in book (Refereed)
  • 269. Thomas, Lynda
    et al.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    McCartney, Robert
    Moström, Jan Erik
    Sanders, Kate
    Zander, Carol
    Graduating students' designs — through a phenomenographic lens2014In: Proc. 10th International Computing Education Research Conference, New York: ACM Press, 2014, p. 91-98Conference paper (Refereed)
  • 270. Thomas, Lynda
    et al.
    Zander, Carol
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Harnessing Surprise: Tales from students' transformational biographies2010In: Proc. 41st ACM Technical Symposium on Computer Science Education, New York: ACM Press , 2010, p. 300-304Conference paper (Refereed)
  • 271. Thomas, Lynda
    et al.
    Zander, Carol
    Loftus, Chris
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Student software designs at the undergraduate midpoint2017In: Proc. 22nd Conference on Innovation and Technology in Computer Science Education, New York: ACM Press, 2017, p. 34-39Conference paper (Refereed)
  • 272.
    Thuné, Michael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Analysis of students’ learning of computer programming in a computer laboratory context2019In: European Journal of Engineering Education, ISSN 0304-3797, E-ISSN 1469-5898, Vol. 44, p. 769-786Article in journal (Refereed)
  • 273.
    Thuné, Michael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Students’ Conceptions of Computer Programming2010Report (Other academic)
    Abstract [en]

    The present work has its focus on university level engineering education students that do not intend to major in computer science but still have to take a mandatory programming course. Phenomenography is applied to empirical data in the form of semi-structured interviews with students who had recently taken an introductory programming course. A phenomenographic outcome space is presented, with five qualitatively different categories of description of students' ways of seeing computer programming.

  • 274.
    Thuné, Michael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Variation theory applied to students' conceptions of computer programming2009In: European Journal of Engineering Education, ISSN 0304-3797, E-ISSN 1469-5898, Vol. 34, p. 339-347Article in journal (Refereed)
  • 275.
    Tillenius, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Leveraging multicore processors for scientific computing2012Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis deals with how to develop scientific computing software that runs efficiently on multicore processors. The goal is to find building blocks and programming models that increase the productivity and reduce the probability of programming errors when developing parallel software.

    In our search for new building blocks, we evaluate the use of hardware transactional memory for constructing atomic floating point operations. Using benchmark applications from scientific computing, we show in which situations this achieves better performance than other approaches.

    Driven by the needs of scientific computing applications, we develop a programming model and implement it as a reusable library. The library provides a run-time system for executing tasks on multicore architectures, with efficient and user-friendly management of dependencies. Our results from scientific computing benchmarks show excellent scaling up to at least 64 cores. We also investigate how the execution time depend on the task granularity, and build a model for the performance of the task library.

    List of papers
    1. Using hardware transactional memory for high-performance computing
    Open this publication in new window or tab >>Using hardware transactional memory for high-performance computing
    Show others...
    2011 (English)In: Proc. 25th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum, Piscataway, NJ: IEEE , 2011, p. 1660-1667Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE, 2011
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-158551 (URN)10.1109/IPDPS.2011.322 (DOI)978-1-61284-425-1 (ISBN)
    Conference
    IPDPS Workshop on Multi-Threaded Architectures and Applications
    Projects
    eSSENCEUPMARC
    Available from: 2011-09-01 Created: 2011-09-10 Last updated: 2018-01-12Bibliographically approved
    2. An efficient task-based approach for solving the n-body problem on multicore architectures
    Open this publication in new window or tab >>An efficient task-based approach for solving the n-body problem on multicore architectures
    2010 (English)Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Reykjavík: University of Iceland, 2010
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-135981 (URN)
    Conference
    PARA 2010: State of the Art in Scientific and Parallel Computing
    Projects
    eSSENCEUPMARC
    Available from: 2010-06-07 Created: 2010-12-09 Last updated: 2018-01-12Bibliographically approved
    3. A simple model for tuning tasks
    Open this publication in new window or tab >>A simple model for tuning tasks
    2011 (English)In: Proc. 4th Swedish Workshop on Multi-Core Computing, Linköping, Sweden: Linköping University , 2011, p. 45-49Conference paper, Published paper (Other academic)
    Place, publisher, year, edition, pages
    Linköping, Sweden: Linköping University, 2011
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-162609 (URN)
    Conference
    MCC11
    Projects
    UPMARCeSSENCE
    Available from: 2011-11-24 Created: 2011-12-02 Last updated: 2018-01-12Bibliographically approved
  • 276.
    Tillenius, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Scientific Computing on Multicore Architectures2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Computer simulations are an indispensable tool for scientists to gain new insights about nature. Simulations of natural phenomena are usually large, and limited by the available computer resources. By using the computer resources more efficiently, larger and more detailed simulations can be performed, and more information can be extracted to help advance human knowledge.

    The topic of this thesis is how to make best use of modern computers for scientific computations. The challenge here is the high level of parallelism that is required to fully utilize the multicore processors in these systems.

    Starting from the basics, the primitives for synchronizing between threads are investigated. Hardware transactional memory is a new construct for this, which is evaluated for a new use of importance for scientific software: atomic updates of floating point values. The evaluation includes experiments on real hardware and comparisons against standard methods.

    Higher level programming models for shared memory parallelism are then considered. The state of the art for efficient use of multicore systems is dynamically scheduled task-based systems, where tasks can depend on data. In such systems, the software is divided up into many small tasks that are scheduled asynchronously according to their data dependencies. This enables a high level of parallelism, and avoids global barriers.

    A new system for managing task dependencies is developed in this thesis, based on data versioning. The system is implemented as a reusable software library, and shown to be as efficient or more efficient than other shared-memory task-based systems in experimental comparisons.

    The developed runtime system is then extended to distributed memory machines, and used for implementing a parallel version of a software for global climate simulations. By running the optimized and parallelized version on eight servers, an equally sized problem can be solved over 100 times faster than in the original sequential version. The parallel version also allowed significantly larger problems to be solved, previously unreachable due to memory constraints.

    List of papers
    1. Using hardware transactional memory for high-performance computing
    Open this publication in new window or tab >>Using hardware transactional memory for high-performance computing
    Show others...
    2011 (English)In: Proc. 25th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum, Piscataway, NJ: IEEE , 2011, p. 1660-1667Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE, 2011
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-158551 (URN)10.1109/IPDPS.2011.322 (DOI)978-1-61284-425-1 (ISBN)
    Conference
    IPDPS Workshop on Multi-Threaded Architectures and Applications
    Projects
    eSSENCEUPMARC
    Available from: 2011-09-01 Created: 2011-09-10 Last updated: 2018-01-12Bibliographically approved
    2. SuperGlue: A shared memory framework using data versioning for dependency-aware task-based parallelization
    Open this publication in new window or tab >>SuperGlue: A shared memory framework using data versioning for dependency-aware task-based parallelization
    2014 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2014-010
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-221155 (URN)
    Projects
    UPMARCeSSENCE
    Available from: 2014-04-03 Created: 2014-03-25 Last updated: 2018-01-11Bibliographically approved
    3. Resource-aware task scheduling
    Open this publication in new window or tab >>Resource-aware task scheduling
    2015 (English)In: ACM Transactions on Embedded Computing Systems, ISSN 1539-9087, E-ISSN 1558-3465, Vol. 14, no 1, p. 5:1-25, article id 5Article in journal (Refereed) Published
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-216287 (URN)10.1145/2638554 (DOI)000349302200005 ()
    Projects
    UPMARCeSSENCE
    Available from: 2015-01-21 Created: 2014-01-20 Last updated: 2018-01-11Bibliographically approved
    4. A task parallel implementation of an RBF-generated finite difference method for the shallow water equations on the sphere
    Open this publication in new window or tab >>A task parallel implementation of an RBF-generated finite difference method for the shallow water equations on the sphere
    2014 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2014-011
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-221156 (URN)
    Projects
    eSSENCEUPMARC
    Available from: 2014-04-03 Created: 2014-03-25 Last updated: 2018-01-11Bibliographically approved
    5. Programming models based on data versioning for dependency-aware task-based parallelisation
    Open this publication in new window or tab >>Programming models based on data versioning for dependency-aware task-based parallelisation
    2012 (English)In: Proc. 15th International Conference on Computational Science and Engineering, Los Alamitos, CA: IEEE Computer Society, 2012, p. 275-280Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2012
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-187446 (URN)10.1109/ICCSE.2012.45 (DOI)000317475000038 ()978-1-4673-5165-2 (ISBN)
    Conference
    CSE 2012
    Projects
    eSSENCEUPMARC
    Available from: 2013-01-24 Created: 2012-12-06 Last updated: 2018-01-16Bibliographically approved
  • 277.
    Tillenius, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    SuperGlue: A shared memory framework using data versioning for dependency-aware task-based parallelization2015In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 37, p. C617-C642Article in journal (Refereed)
  • 278.
    Tillenius, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    SuperGlue: A shared memory framework using data versioning for dependency-aware task-based parallelization2014Report (Other academic)
  • 279.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    An efficient task-based approach for solving the n-body problem on multicore architectures2010Conference paper (Refereed)
  • 280.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Badia, Rosa M.
    Martorell, Xavier
    Resource-aware task scheduling2013In: 4th Workshop on Parallel Programming and Run-Time Management Techniques for Many-core Architectures (PARMA), Germany: Tech. Univ. Berlin , 2013, p. 6-Conference paper (Other academic)
  • 281.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Badia, Rosa M.
    Martorell, Xavier
    Resource-aware task scheduling2015In: ACM Transactions on Embedded Computing Systems, ISSN 1539-9087, E-ISSN 1558-3465, Vol. 14, no 1, p. 5:1-25, article id 5Article in journal (Refereed)
  • 282.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Lehto, Erik
    Flyer, Natasha
    A scalable RBF–FD method for atmospheric flow2015In: Journal of Computational Physics, ISSN 0021-9991, E-ISSN 1090-2716, Vol. 298, p. 406-422Article in journal (Refereed)
  • 283.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Lehto, Erik
    Flyer, Natasha
    A task parallel implementation of a scattered node stencil-based solver for the shallow water equations2013In: Proc. 6th Swedish Workshop on Multi-Core Computing, Halmstad, Sweden: Halmstad University , 2013, p. 33-36Conference paper (Other academic)
  • 284.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Lehto, Erik
    Flyer, Natasha
    A task parallel implementation of an RBF-generated finite difference method for the shallow water equations on the sphere2014Report (Other academic)
  • 285.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Managing applications and data in distributed computing infrastructures2010Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Over the last few decades, the needs of computational power and data storage by collaborative, distributed scientific communities have increased very rapidly. Distributed computing infrastructures such as computing and storage grids provide means to connect geographically distributed resources and helps in addressing the needs of these communities. Much progress has been made in developing and operating grids, but several issues still need further attention. This thesis discusses three different aspects of managing large-scale scientific applications in grids:

    • Using large-scale scientific applications is often in itself a complex task, and to set them up and run experiments in a distributed environment adds another level of complexity. It is important to design general purpose and application specific frameworks that enhance the overall productivity for the scientists. The thesis present further development of a general purpose framework where existing portal technology is combined with tools for robust and middleware independent job management. Also, a pilot implementation of a domain-specific problem solving environment based on a grid-enabled R solution is presented.

    • Many current and future applications will need large-scale storage systems. Centralized systems are eventually not scalable enough to handle huge data volumes and also have can have additional problems with security and availability. An alternative is a reliable and efficient distributed storage system. In the thesis the architecture of a self-healing, grid-aware distributed storage cloud, Chelonia, is described and performance results for a pilot implementation are presented.

    • In a distributed computing infrastructure it is very important to manage and utilize the available resources efficiently. The thesis presents a review of different resource brokering techniques and how they are implemented in different production level middlewares. Also, a modified resource allocation model for the Advanced Resource Connector (ARC) middleware is described and performance experiments are presented.

  • 286.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Lindberg, Mathias
    Fällman, Ingemar
    Vallin, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Mohill, Olof
    Freyhult, Pontus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Nilsson, Linus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Agback, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology.
    Viklund, Lars
    Zazzi, Henric
    Spjuth, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Capuccini, Marco
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Möller, Joakim
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Murtagh, Donal
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    SNIC Science Cloud (SSC): A national-scale cloud infrastructure for Swedish academia2017In: Proc. 13th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2017, p. 219-227Conference paper (Refereed)
  • 287.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Cameron, David
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Case-study for different models of resource brokering in grid systems2010Report (Other academic)
  • 288.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Sabesan, Manivasakan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Risch, Tore
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    A scalable architecture for e-Science data management2011In: Proc. 7th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2011, p. 210-217Conference paper (Refereed)
  • 289.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Töebbicke, Rainer
    Zotes Resines, Maitane
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Investigating an open source cloud storage infrastructure for CERN-specific data analysis2012In: Proc. 7th International Conference on Networking, Architecture, and Storage, Los Alamitos, CA: IEEE Computer Society, 2012, p. 84-88Conference paper (Refereed)
  • 290.
    Toor, Salman Zubair
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Managing Applications and Data in Distributed Computing Infrastructures2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    During the last decades the demand for large-scale computational and storage resources in science has increased dramatically. New computational infrastructures enable scientists to enter a new mode of science, e-science, which complements traditional theory and experiments. E-science is inherently interdisciplinary, involving researchers from several disciplines, and also opens up for large-scale collaborative efforts where physically distributed groups of scientists share software tools and data to make scientific progress. Within the field of e-science, new challenges are emerging in managing large-scale distributed computing efforts and distributed data sets. Different models, e.g. grids and clouds, have been introduced over the years, but new solutions built on these models are needed to enable easy and flexible use of distributed computing infrastructures by application scientists.

    In the first part of the thesis, application execution environments are studied. The goal is to hide technical details of the underlying distributed computing infrastructure and expose secure and user-friendly environments to the end users. First, a general-purpose solution using portal technology is described, enabling transparent and easy usage of a variety of grid systems. Then a problem-solving environment for genetic analysis is presented. Here the statistical software R is used as a workflow engine, enhanced with grid-enabled routines for performing the computationally demanding parts of the analysis. Finally, the issue of resource allocation in grid system is briefly studied and certain modifications in the distributed resource-brokering model for the ARC middleware are proposed.

    The second part of the thesis presents solutions for managing and analyzing scientific data using distributed storage resources. First, a new reliable and secure file-oriented distributed storage system, Chelonia, is presented. The architectural design of the system is described and implementation issues are considered. Also, the stability and scalable performance of Chelonia is verified using several test scenarios. Then, tools for providing an efficient and easy-to-use platform for data analysis built on Chelonia are presented. Here, a database driven approach is explored. An extended architecture where Chelonia is combined with the Web-Service MEDiator (WSMED) system is implemented, providing web service tools to query data without any further programming. This approach is then developed further and Chelonia is combined with SciSPARQL, a query language that extends SPARQL to queries over numeric scientific data. This results in a system that is capable of interactive analysis of distributed data sets. Writing customized modules in Java, Python or C can fulfill advanced application-specific analysis requirements. The viability of the approach is demonstrated by applying the system to data produced by URDME, a computational environment in systems biology and results for sample queries expressed in SciSPARQL are presented.

    Finally, the use of an open source storage cloud, Openstack – SWIFT, for analysis of data from CERN experiments is considered. Here, a pilot implementation for the ROOT data analysis framework is presented together with a performance evaluation.

    List of papers
    1. Empowering a flexible application portal with a SOA-based grid job management framework
    Open this publication in new window or tab >>Empowering a flexible application portal with a SOA-based grid job management framework
    Show others...
    2008 (English)Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Trondheim, Norway: Norwegian University of Science and Technology, 2008
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-173381 (URN)
    Conference
    PARA 2008: State of the Art in Scientific and Parallel Computing
    Available from: 2012-04-23 Created: 2012-04-23 Last updated: 2018-01-12Bibliographically approved
    2. A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Open this publication in new window or tab >>A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Show others...
    2010 (English)In: Proc. 2nd International Conference on Bioinformatics and Computational Biology, Cary, NC: ISCA , 2010, p. 202-209Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Cary, NC: ISCA, 2010
    National Category
    Software Engineering Genetics
    Identifiers
    urn:nbn:se:uu:diva-111594 (URN)978-1-880843-76-5 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
    3. Chelonia — a self-healing storage cloud
    Open this publication in new window or tab >>Chelonia — a self-healing storage cloud
    2010 (English)In: Proc. 9th Cracow Grid Workshop, Kraków, Poland: ACC Cyfronet AGH , 2010, p. 5-12Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Kraków, Poland: ACC Cyfronet AGH, 2010
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-129188 (URN)978-83-61433-01-9 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-03-01 Created: 2010-08-06 Last updated: 2018-01-12Bibliographically approved
    4. Chelonia: A self-healing, replicated storage system
    Open this publication in new window or tab >>Chelonia: A self-healing, replicated storage system
    2011 (English)In: Computing in High Energy and Nuclear Physics: CHEP 2010, Bristol, UK: Institute of Physics Publishing (IOPP), 2011, p. 062019:1-6Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Bristol, UK: Institute of Physics Publishing (IOPP), 2011
    Series
    Journal of Physics: Conference Series ; 331
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-173392 (URN)10.1088/1742-6596/331/6/062019 (DOI)000301120500019 ()
    Projects
    eSSENCE
    Available from: 2011-12-23 Created: 2012-04-23 Last updated: 2018-01-12Bibliographically approved
    5. Performance and stability of the Chelonia storage system
    Open this publication in new window or tab >>Performance and stability of the Chelonia storage system
    Show others...
    2012 (English)In: Proc. International Symposium on Grids and Clouds 2012, Trieste, Italy: SISSA , 2012, p. 009:1-14Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Trieste, Italy: SISSA, 2012
    Series
    Proceedings of Science, ISSN 1824-8039 ; 153
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-129189 (URN)
    Conference
    ISGC 2012
    Projects
    eSSENCE
    Available from: 2012-03-01 Created: 2010-08-06 Last updated: 2018-01-12Bibliographically approved
    6. A scalable architecture for e-Science data management
    Open this publication in new window or tab >>A scalable architecture for e-Science data management
    2011 (English)In: Proc. 7th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2011, p. 210-217Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2011
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-166258 (URN)10.1109/eScience.2011.37 (DOI)978-1-4577-2163-2 (ISBN)
    Projects
    eSSENCE
    Available from: 2012-01-09 Created: 2012-01-11 Last updated: 2018-01-12Bibliographically approved
    7. Scientific analysis by queries in extended SPARQL over a scalable e-Science data store
    Open this publication in new window or tab >>Scientific analysis by queries in extended SPARQL over a scalable e-Science data store
    Show others...
    2013 (English)In: Proc. 9th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2013, p. 98-106Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2013
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-173448 (URN)10.1109/eScience.2013.19 (DOI)000330195500012 ()978-0-7695-5083-1 (ISBN)
    Projects
    eSSENCE
    Available from: 2013-10-25 Created: 2012-04-24 Last updated: 2018-01-12Bibliographically approved
    8. Investigating an open source cloud storage infrastructure for CERN-specific data analysis
    Open this publication in new window or tab >>Investigating an open source cloud storage infrastructure for CERN-specific data analysis
    2012 (English)In: Proc. 7th International Conference on Networking, Architecture, and Storage, Los Alamitos, CA: IEEE Computer Society, 2012, p. 84-88Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2012
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-173388 (URN)10.1109/NAS.2012.14 (DOI)978-1-4673-1889-1 (ISBN)
    Conference
    NAS 2012
    Projects
    eSSENCE
    Available from: 2012-09-24 Created: 2012-04-23 Last updated: 2018-01-12Bibliographically approved
  • 291.
    Torabi Moghadam, Behrooz
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Alvarsson, Jonathan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Holm, Marcus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Eklund, Martin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences.
    Carlsson, Lars
    Spjuth, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Pharmaceutical Biosciences. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Scaling predictive modeling in drug development with cloud computing2015In: Journal of Chemical Information and Modeling, ISSN 1549-9596, Vol. 55, p. 19-25Article in journal (Refereed)
  • 292. Torruangwatthana, Preechakorn
    et al.
    Wieslander, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Blamey, Ben
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    HarmonicIO: Scalable data stream processing for scientific datasets2018In: Proc. 11th International Conference on Cloud Computing, Los Alamitos, CA: IEEE Computer Society, 2018, p. 879-882Conference paper (Refereed)
  • 293.
    Trost, Nico
    et al.
    KIT, Inst Neutron Phys & Reactor Technol INR, Hermann von Helmholtz Pl 1,Geb 521, D-76344 Eggenstein Leopoldshafen, Germany..
    Jimenez, Javier
    KIT, Inst Neutron Phys & Reactor Technol INR, Hermann von Helmholtz Pl 1,Geb 521, D-76344 Eggenstein Leopoldshafen, Germany..
    Lukarski, Dimitar
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science. Uppsala Univ, Dept Informat Technol, Div Sci Comp, Lagerhyddsvagen 2, S-75237 Uppsala, Sweden..
    Sanchez, Victor
    KIT, Inst Neutron Phys & Reactor Technol INR, Hermann von Helmholtz Pl 1,Geb 521, D-76344 Eggenstein Leopoldshafen, Germany..
    Accelerating COBAYA3 on multi-core CPU and GPU systems using PARALUTION2016In: SNA + MC 2013 - Joint International Conference On Supercomputing In Nuclear Applications + Monte Carlo / [ed] Caruge, D Calvin, C Diop, CM Malvagi, F Trama, JC, 2016, article id UNSP 04108Conference paper (Refereed)
    Abstract [en]

    COBAYA3 is a multi-physics system of codes which includes two 3D multi-group neutron diffusion codes, ANDES and COBAYA3-PBP, coupled with COBRA-TF, COBRA-IIIc and SUBCHANFLOW sub-channel thermal-hydraulic codes, for the simulation of LWR core transients. The 3D multi-group neutron diffusion equations are expressed in terms of a sparse linear system which can be solved using different iterative Krylov subspace solvers. The mathematical SPARSKIT library has been used for these purposes as it implements among others, external GMRES, PGMRES and BiCGStab solvers. Multi-core CPUs and graphical processing units (GPUs) provide high performance capabilities which are able to accelerate many scientific computations. To take advantage of these new hardware features in daily use computer codes, the integration of the PARALUTION library to solve sparse systems of linear equations is a good choice. It features several types of iterative solvers and preconditioners which can run on both multi-core CPUs and GPU devices without any modification from the interface point of view. This feature is due to the great portability obtained by the modular and flexible design of the library. By exploring this technology, namely the implementation of the PARALUTION library in COBAYA3, we are able to decrease the solution time of the sparse linear systems by a factor 5.15x on GPU and 2.56x on multi-core CPU using standard hardware. These obtained speedup factors in addition to the implementation details are discussed in this paper.

  • 294. Trost, Nico
    et al.
    Jiménez, Javier
    Lukarski, Dimitar
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Sanchez, Victor
    Accelerating COBAYA3 on multi-core CPU and GPU systems using PARALUTION2015In: Annals of Nuclear Energy, ISSN 0306-4549, E-ISSN 1873-2100, Vol. 82, p. 252-259Article in journal (Refereed)
  • 295. Trost, Nico
    et al.
    Jiménez, Javier
    Lukarski, Dimitar
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Sanchez, Victor
    Accelerating COBAYA3 on multi-core CPU and GPU systems using PARALUTION2013In: Proc. 2nd Joint International Conference on Supercomputing in Nuclear Applications and Monte Carlo, Paris, France: La Société Française d'Energie Nucléaire , 2013Conference paper (Other academic)
  • 296.
    Ullman, Gustaf
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Walldén, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Marklund, Erik G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mahmutovic, Anel
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Razinkov, Ivan
    Elf, Johan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Computational and Systems Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking2013In: Philosophical Transactions of the Royal Society of London. Biological Sciences, ISSN 0962-8436, E-ISSN 1471-2970, Vol. 368, no 1611, p. 20120025:1-8Article in journal (Refereed)
  • 297.
    von Hausswolff, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hands-on in computer programming education2017In: Proc. 13th International Computing Education Research Conference, New York: ACM Press, 2017, p. 279-280Conference paper (Refereed)
  • 298.
    von Hausswolff, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Practical thinking in programming education2017In: Proc. 17th International Conference on Computing Education Research: Koli Calling, New York: ACM Press, 2017, p. 203-204Conference paper (Refereed)
  • 299.
    von Hausswolff, Kristina
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Practical thinking while programming: A Deweyan approach to knowledge in Computer Science2018In: Proc. 14th International Computing Education Research Conference, New York: ACM Press, 2018, p. 268-269Conference paper (Refereed)
  • 300.
    von Hausswolff, Kristina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Measuring programming knowledge in a research context2018In: Proc. 48th ASEE/IEEE Frontiers in Education Conference, Piscataway, NJ: IEEE Press, 2018Conference paper (Refereed)
34567 251 - 300 of 325
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