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  • 51.
    Jayawardena, Mahen
    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.
    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.
    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.
    Computational and visualization tools for genetic analysis of complex traits2010Report (Other academic)
  • 52. Jiménez, Miguel
    et al.
    Lindahl, Tobias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    A language for specifying type contracts in Erlang and its interaction with success typings2007In: Proc. 6th ACM SIGPLAN Workshop on ERLANG, New York: ACM Press , 2007, p. 11-17Conference paper (Refereed)
  • 53.
    Johansson, Henrik
    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.
    A Meta-Partitioner for run-time selection and evaluation of multiple partitioning algorithms for SAMR grid hierarchies2009Report (Other academic)
  • 54.
    Johansson, Henrik
    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.
    Autonomic Management of Partitioners for SAMR Grid Hierarchies2009Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Parallel structured adaptive mesh refinement methods decrease the execution time and memory usage of partial differential equation solvers by adaptively assigning computational resources to regions with large solution errors. These methods result in a dynamic grid hierarchy. To get good parallel performance, the grid hierarchy is frequently re-partitioned and distributed over the processors. Optimally, the partitioner should minimize all performance-inhibiting factors like load imbalance, communication volumes, synchronization delays, and data migration. No single partitioner performs well for all hierarchies and parallel computers. Because the partitioning conditions change during run-time, dynamically selecting a partitioner is non-trivial.

    In this thesis, we present the Meta-Partitioner: a partitioning framework that autonomously selects, configures, invokes, and evaluates partitioning algorithms during run-time. For the implementation, we use component-based software-engineering. We predict the performance of the candidate partitioning algorithms with historical performance data for grid hierarchies similar to the current hierarchy. We focus the partitioning effort on the most performance-inhibiting factors — the load imbalance and the synchronization delays. At re-partitioning, a user-specified number of partitioning algorithms is selected and invoked. The performance of each partitioning is evaluated during run-time and the best one is selected.

    The performance of the selected partitioning algorithms was compared both to the average performance of 768 algorithms and the global minimum at each re-partitioning. The results showed huge improvements both for the load imbalance and the synchronization delays. Compared to the average partitioning, the load imbalance was decreased by 28.2%. The synchronization delays were decreased by 21.5%. Compared to the global optimum, the load imbalance was increased by only 11.5%. For the synchronization delays, the increase was 13.6%. Often, the Meta-Partitioner selected the best algorithm among all candidate algorithms.

    List of papers
    1. A performance characterization of load balancing algorithms for parallel SAMR applications
    Open this publication in new window or tab >>A performance characterization of load balancing algorithms for parallel SAMR applications
    2006 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2006-047
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-83321 (URN)
    Available from: 2008-02-19 Created: 2008-02-19 Last updated: 2018-01-13Bibliographically approved
    2. Design and implementation of a dynamic and adaptive meta-partitioner for parallel SAMR grid hierarchies
    Open this publication in new window or tab >>Design and implementation of a dynamic and adaptive meta-partitioner for parallel SAMR grid hierarchies
    2008 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2008-017
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-17508 (URN)
    Available from: 2008-06-29 Created: 2008-06-29 Last updated: 2018-01-12Bibliographically approved
    3. A patch-based partitioner for parallel SAMR applications
    Open this publication in new window or tab >>A patch-based partitioner for parallel SAMR applications
    2008 (English)In: Proc. Parallel and Distributed Computing and Systems: 2008, Calgary, Canada: ACTA Press , 2008, p. 53-58Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Calgary, Canada: ACTA Press, 2008
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-99354 (URN)978-0-88986-773-4 (ISBN)
    Available from: 2009-03-12 Created: 2009-03-12 Last updated: 2018-01-13Bibliographically approved
    4. Component infrastructure for managing performance data and runtime adaptation of parallel applications
    Open this publication in new window or tab >>Component infrastructure for managing performance data and runtime adaptation of parallel applications
    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-99358 (URN)
    Conference
    PARA 2008: State of the Art in Scientific and Parallel Computing
    Available from: 2009-03-12 Created: 2009-03-12 Last updated: 2018-01-13Bibliographically approved
    5. Run-time selection of partitioning algorithms for parallel SAMR applications
    Open this publication in new window or tab >>Run-time selection of partitioning algorithms for parallel SAMR applications
    2009 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2009-007
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-99186 (URN)
    Available from: 2009-03-10 Created: 2009-03-10 Last updated: 2018-01-13Bibliographically approved
    6. A Meta-Partitioner for run-time selection and evaluation of multiple partitioning algorithms for SAMR grid hierarchies
    Open this publication in new window or tab >>A Meta-Partitioner for run-time selection and evaluation of multiple partitioning algorithms for SAMR grid hierarchies
    2009 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2009-008
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-99359 (URN)
    Available from: 2009-03-12 Created: 2009-03-12 Last updated: 2018-01-13Bibliographically approved
  • 55.
    Johansson, Henrik
    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.
    Design and implementation of a dynamic and adaptive meta-partitioner for parallel SAMR grid hierarchies2008Report (Other academic)
  • 56.
    Johansson, Henrik
    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.
    Performance characterization and evaluation of parallel PDE solvers2006Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Computer simulations that solve partial differential equations (PDEs) are common in many fields of science and engineering. To decrease the execution time of the simulations, the PDEs can be solved on parallel computers. For efficient parallel implementations, the characteristics of both the hardware and the PDE solver must be taken into account. In this thesis, we explore two ways to increase the efficiency of parallel PDE solvers.

    First, we use full-system simulation of a parallel computer to get detailed knowledge about cache memory usage for three parallel PDE solvers. The results reveal cases of bad cache memory locality. This insight can be used to improve the performance of the PDE solvers.

    Second, we study the adaptive mesh refinement (AMR) partitioning problem. Using AMR, computational resources are dynamically concentrated to areas in need of a high accuracy. Because of the dynamic resource allocation, the workload must repeatedly be partitioned and distributed over the processors. We perform two comprehensive characterizations of partitioning algorithms for AMR on structured grids. For an efficient parallel AMR implementation, the partitioning algorithm must be dynamically selected at run-time with regard to both the application and computer state. We prove the viability of dynamic algorithm selection and present performance data that show the benefits of using a large number of complementing partitioning algorithms. Finally, we discuss how our characterizations can be used in an algorithm selection framework.

  • 57. Johnson, David
    et al.
    McKeever, Steve
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media.
    Deisboeck, Thomas S.
    Wang, Zhihui
    Connecting digital cancer model repositories with markup: introducing TumorML version 1.02013In: ACM SIGBioinformatics Record, ISSN 2331-9291, Vol. 3, no 3, p. 5-11Article in journal (Refereed)
    Abstract [en]

    The cancer research community requires a standardized way of describing mathematical and computational models to enable interoperation between systems, repositories, and between the models themselves. In this paper we describe a new markup language, TumorML, for describing computational models that fall within the domain of cancer. TumorML is an XML-based markup language that wraps existing cancer model implementations with metadata for model curation, parametric interface description, implementation description, and compound model linking.

    In this paper we first introduce the rationale for a new markup language for computational cancer model description based on our experiences and requirements from the European Commission's 'Transatlantic Tumor Model Repositories' project. The aim of the project is to develop a European-based digital cancer model repository to link and interoperate with a similar established repository based in the United States. TumorML was developed to enable this interoperation between repositories. We introduce the language and describe the main features of the specification and go on to describe a real application of TumorML where a molecular pathway model has been packaged using the new markup language.

  • 58.
    Kallas, Konstantinos
    et al.
    Univ Penn, Philadelphia, PA 19104 USA.
    Sagonas, Konstantinos
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    HiPErJiT: A Profile-Driven Just-in-Time Compiler for Erlang2018In: Proceedings of the 30th Symposium on Implementation and Application ff Functional Languages (IFL 2018) / [ed] Cimini, M, Association for Computing Machinery (ACM), 2018, p. 25-36Conference paper (Refereed)
    Abstract [en]

    We introduce HiPErJiT, a profile-driven Just-in-Time compiler for the BEAM ecosystem based on HiPE, the High Performance Erlang compiler. HiPErJiT uses runtime profiling to decide which modules to compile to native code and which of their functions to inline and type-specialize. HiPErJiT is integrated with the runtime system of Erlang/OTP and preserves aspects of Erlang's compilation which are crucial for its applications: most notably, tail-call optimization and hot code loading at the module level. We present HiPErJiT's architecture, describe the optimizations that it performs, and compare its performance with BEAM, HiPE, and Pyrlang. HiPErJiT offers performance which is about two times faster than BEAM and almost as fast as HiPE, despite the profiling and compilation overhead that it has to pay compared to an ahead-of-time native code compiler. But there also exist programs for which HiPErJiT's profile-driven optimizations allow it to surpass HiPE's performance.

  • 59.
    Kronbichler, 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, Numerical Analysis.
    Computational Techniques for Coupled Flow-Transport Problems2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents numerical techniques for solving problems of incompressible flow coupled to scalar transport equations using finite element discretizations in space. The two applications considered in this thesis are multi-phase flow, modeled by level set or phase field methods, and planetary mantle convection based on the Boussinesq approximation.

    A systematic numerical study of approximation errors in evaluating the surface tension in finite element models for two-phase flow is presented. Forces constructed from a gradient in the same discrete function space as used for the pressure are shown to give the best performance. Moreover, two approaches for introducing contact line dynamics into level set methods are proposed. Firstly, a multiscale approach extracts a slip velocity from a micro simulation based on the phase field method and imposes it as a boundary condition in the macro model. This multiscale method is shown to provide an efficient model for the simulation of contact-line driven flow. The second approach combines a level set method based on a smoothed color function with a the phase field method in different parts of the domain. Away from contact lines, the additional information in phase field models is not necessary and it is disabled from the equations by a switch function. An in-depth convergence study is performed in order to quantify the benefits from this combination. Also, the resulting hybrid method is shown to satisfy an a priori energy estimate.

    For the simulation of mantle convection, an implementation framework based on modern finite element and solver packages is presented. The framework is capable of running on today's large computing clusters with thousands of processors. All parts in the solution chain, from mesh adaptation over assembly to the solution of linear systems, are done in a fully distributed way. These tools are used for a parallel solver that combines higher order time and space discretizations. For treating the convection-dominated temperature equation, an advanced stabilization technique based on an artificial viscosity is used.

    For more efficient evaluation of finite element operators in iterative methods, a matrix-free implementation built on cell-based quadrature is proposed. We obtain remarkable speedups over sparse matrix-vector products for many finite elements which are of practical interest. Our approach is particularly efficient for systems of differential equations.

    List of papers
    1. Spurious currents in finite element based level set methods for two-phase flow
    Open this publication in new window or tab >>Spurious currents in finite element based level set methods for two-phase flow
    2012 (English)In: International Journal for Numerical Methods in Fluids, ISSN 0271-2091, E-ISSN 1097-0363, Vol. 69, p. 1433-1456Article in journal (Refereed) Published
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-156454 (URN)10.1002/fld.2643 (DOI)000305450000001 ()
    Projects
    eSSENCE
    Available from: 2011-07-19 Created: 2011-07-22 Last updated: 2018-01-12Bibliographically approved
    2. Multiscale modeling of capillary-driven contact line dynamics
    Open this publication in new window or tab >>Multiscale modeling of capillary-driven contact line dynamics
    2011 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2011-024
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-162211 (URN)
    Available from: 2011-11-27 Created: 2011-11-27 Last updated: 2018-01-12Bibliographically approved
    3. A hybrid level-set-phase-field method for two-phase flow with contact lines
    Open this publication in new window or tab >>A hybrid level-set-phase-field method for two-phase flow with contact lines
    2011 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2011-026
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-162212 (URN)
    Available from: 2011-11-27 Created: 2011-11-27 Last updated: 2018-01-12Bibliographically approved
    4. High accuracy mantle convection simulation through modern numerical methods
    Open this publication in new window or tab >>High accuracy mantle convection simulation through modern numerical methods
    2012 (English)In: Geophysical Journal International, ISSN 0956-540X, E-ISSN 1365-246X, Vol. 191, p. 12-29Article in journal (Refereed) Published
    National Category
    Computational Mathematics Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-162213 (URN)10.1111/j.1365-246X.2012.05609.x (DOI)000308636800002 ()
    Available from: 2012-08-21 Created: 2011-11-27 Last updated: 2018-01-12Bibliographically approved
    5. Algorithms and data structures for massively parallel generic adaptive finite element codes
    Open this publication in new window or tab >>Algorithms and data structures for massively parallel generic adaptive finite element codes
    2011 (English)In: ACM Transactions on Mathematical Software, ISSN 0098-3500, E-ISSN 1557-7295, Vol. 38, no 2, p. 14:1-28Article in journal (Refereed) Published
    National Category
    Software Engineering Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-161398 (URN)10.1145/2049673.2049678 (DOI)000298638200005 ()
    Available from: 2011-11-11 Created: 2011-11-11 Last updated: 2018-01-12Bibliographically approved
    6. A generic interface for parallel cell-based finite element operator application
    Open this publication in new window or tab >>A generic interface for parallel cell-based finite element operator application
    2011 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2011-025
    National Category
    Computational Mathematics Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-162214 (URN)
    Projects
    eSSENCE
    Available from: 2011-11-27 Created: 2011-11-27 Last updated: 2018-01-12Bibliographically approved
  • 60.
    Kronbichler, 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, Numerical Analysis.
    Kormann, Katharina
    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.
    A generic interface for parallel cell-based finite element operator application2011Report (Other academic)
  • 61.
    Kronbichler, 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, Numerical Analysis.
    Kormann, Katharina
    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.
    A generic interface for parallel cell-based finite element operator application2012In: Computers & Fluids, ISSN 0045-7930, E-ISSN 1879-0747, Vol. 63, p. 135-147Article in journal (Refereed)
  • 62. Krusche, Stephan
    et al.
    Scharlau, Bruce
    Cajander, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computerized Image Analysis and Human-Computer Interaction.
    Hughes, Janet
    50 years of software engineering: Challenges, results, and opportunities in its education2018In: Proc. 23rd Conference on Innovation and Technology in Computer Science Education, New York: ACM Press, 2018, p. 362-363Conference paper (Refereed)
  • 63.
    Källén, Malin
    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.
    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.
    Hvannberg, Ebba þóra
    Impact of code refactoring using object-oriented methodology on a scientific computing application2014In: Proc. 14th International Working Conference on Source Code Analysis and Manipulation, Los Alamitos, CA: IEEE Computer Society, 2014, p. 125-134Conference paper (Refereed)
  • 64.
    Larsson, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Computer Systems. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Applying configuration management techniques to component-based systems2000Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Building software from components, rather than writing the code from scratch has several advantages, including reduced time to market and more efficient resource usage. However, component-based development without consideration of all the risks and limitations involved may give unpredictable results, such as the failure of a system when a component is used in an environment for which it was not originally designed.

    One of the basic problems when developing component-based systems is that it is difficult to keep track of components and their interrelationships. This is particularly problematic when upgrading components. One way to maintain control over upgrades is to use component identification and dependency analysis. These are well known techniques for managing system configurations during development, but are rarely applied in managing run-time dependencies. The main contribution of this thesis is to show how Configuration Management (CM) principles and methods can be applied to component-based systems.

    This thesis presents a method for analysing dependencies between components. The method predicts the influence of a component update by identifying the components in a system and constructing a graph describing their dependencies. Knowledge of the possible influences of an update is important, since it can be used to limit the scope of testing and be a basis for evaluating the potential damage of the update. The dependency graphs can also be used to facilitate maintenance by identifying differences between configurations, e.g., making it possible to recognise any deviations from a functioning reference configuration.

    For evaluation of the method, a prototype tool which explores dependencies and stores them under version control has been developed. The prototype has been used for partial analysis of the Windows 2000 platform, for which it has been important to remain aware of dynamic dependencies. Preliminary experiments indicate that most components have only a few dependencies. The method has thus given an indication that the analysis of the effects of component updates may not be as difficult as might be expected.

  • 65.
    Leetmaa, Mikael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory.
    Skorodumova, Natalia V.
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Materials Theory. KTH Royal Inst Technol, Sch Ind Engn & Management, Multiscale Mat Modelling Mat Sci & Engn, S-10044 Stockholm, Sweden..
    KMCLib 1.1: Extended random number support and technical updates to the KMCLib general framework for kinetic Monte-Carlo simulations2015In: Computer Physics Communications, ISSN 0010-4655, E-ISSN 1879-2944, Vol. 196, p. 611-613Article in journal (Refereed)
    Abstract [en]

    We here present a revised version, v1.1, of the KMCLib general framework for kinetic Monte-Carlo (KMC) simulations. The generation of random numbers in KMCLib now relies on the C++11 standard library implementation, and support has been added for the user to choose from a set of C++11 implemented random number generators. The Mersenne-twister, the 24 and 48 bit RANLUX and a 'minimal-standard' PRNG are supported. We have also included the possibility to use true random numbers via the C++11 std::random_device generator. This release also includes technical updates to support the use of an extended range of operating systems and compilers. New version program summary Program title: KMCLib v1.1 Catalogue identifier: AESZ_v1_1 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AESZ_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License, version 3 No. of lines in distributed program, including test data, etc.: 49,398 No. of bytes in distributed program, including test data, etc.: 1,536,855 Distribution format: tar.gz Programming language: Python and C++. Computer: Any computer that can run a C++11 compatible C++ compiler and a Python 2.7 interpreter. Operating system: Tested on Ubuntu 14.4 LTS, Ubuntu 12.4 LTS, CentOS 6.6, Mac OSX 10.10.3, Mac OSX 10.9.5 and Mac OSX 10.8.2 but should run on any system that can have a C++11 compatible C++ compiler and a Python 2.7 interpreter. Has the code been vectorized or parallelized?: Yes, with MPI. From one to hundreds of processors may be used depending on the type of input and simulation. RAM: From a few megabytes to several gigabytes depending on input parameters and the size of the system to simulate. Catalogue identifier of previous version: AESZ_v1_0 Journal reference of previous version: Comput. Phys. Comm. 185 (2014) 2340 Classification: 4.13, 16.13. External routines: To run the serial version of KMCLib no external libraries are needed other than the standard C++ runtime library and a Python 2.7 interpreter with support for numpy. For running the parallel version an MPI implementation is needed, such as e.g. MPICH from http://www.mpich.org or Open-MPI from http://www.open-mpi.org. SWIG (obtainable from http://www.swig.org/) and CMake (obtainable from http://www.cmake.org/) are both needed for building the backend module, while Sphinx (obtainable from http://sphinx-doc.org) is needed for building the documentation. CPPUNIT (obtainable from http://sourceforge.net/projects/cppuniti, also included in the KMCLib distribution) is needed for building the C++ unit tests Does the new version supersede the previous version?: Yes Nature of problem: Atomic scale simulation of slowly evolving dynamics is a great challenge in many areas of computational materials science and catalysis. When the rare-events dynamics of interest is orders of magnitude slower than the typical atomic vibrational frequencies a straight-forward propagation of the equations of motions for the particles in the simulation cannot reach time scales of relevance for modeling the slow dynamics. Solution method: KMCLib provides an implementation of the kinetic Monte Carlo (KMC) method that solves the slow dynamics problem by utilizing the separation of time scales between fast vibrational motion and the slowly evolving rare-events dynamics. Only the latter is treated explicitly and the system is simulated as jumping between fully equilibrated local energy minima on the slow-dynamics potential energy surface. Reasons for new version: The v1.1 revision increases the reliability and flexibility of the random number generation options in KMCLib, which is a central part of the KMC algorithm. The new release also comes with extended support for additional compilers and updates to the build system to simplify the installation procedure on some widely used platforms. Summary of revisions: Enough time has passed since the introduction of the < random > header in the C++ standard runtime library with the C++11 standard, that most installed compilers today have support to enable the use of C++11 specific language features in C+++. The < random > standard header comes with a set of well-defined pseudo random number generators (PRNG). Using standard library routines in favor of custom implementations has the obvious advantage of being more reliable and with guaranteed support over a longer time. From the v1.1 revision, KMCLib therefore relies on the C++11 standard library < random > header to produce pseudo-random numbers. This also makes it easier to enable support for several different PRNG:s for the user to choose from. From previously only supporting a Mersenne-twister implementation, KMCLib now has support for using the Mersenne-twister [1], the 24 and 48-bit RANLUX [2] generators, as well as a 'minimal-standard' PRNG [3]. For machines with a random device installed, KMCLib v1.1 can run simulations with true random numbers, This is enabled by using the std::random_device generator in C++. If the random device is properly installed the true random numbers are available to KMCLib out of the box and the user only needs to specify the use of the random device with an input flag in the same way as she chooses any of the available PRNG:s. The v1.1 revision includes major updates to the build system. The build system has no effect on the outcome of the simulations, but has a great impact on how easy it is to install the program. The Intel compiler is widely available on super computer clusters and support for this compiler widely extends the number of systems where KMCLib can be easily setup and run. The popularity of the Mac platform also makes smooth installation and compilation with clang desirable. With version v1.1 the make system for KMClib now includes support for the clang compiler on Mac and support for both the Intel compiler and the gee compiler on Linux. See the reference manual for details of which versions of the operating systems and compilers have been tested. Restrictions: KMCLib implements the lattice KMC method and is as such, restricted to geometries that can be expressed on a grid in space. See the original paper describing KMCLib [4] for further details. Unusual features: KMCLib has been designed to be easily customized, to allow for user-defined functionality and integration with other codes. The user can define her own on-the-fly rate calculator via a Python API, so that site-specific elementary process rates, or rates depending on long-range interactions or complex geometrical features can easily be included. KMCLib also allows for on-the-fly analysis with user-defined analysis modules. KMCLib can keep track of individual particle movements and includes tools for mean square displacement analysis based on the algorithm described in Ref. [5], and is therefore particularly well suited for studying diffusion processes at surfaces and in solids. With the release of v1.1 KMCLib now supports several different pseudo random number generators, but can also, if a random device is installed on the machine, use true random numbers via the std::random_device generator. Additional comments: The full documentation of the program is distributed with the code and can also be found online at http://leetmaa.github.io/KMCLibimanual-v1.1/. Running time: From a few seconds to several days depending on the type of simulation and input parameters.

  • 66. Li, Li
    et al.
    Norris, Boyana
    Johansson, Henrik
    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.
    Curfman McInnes, Lois
    Ray, Jaideep
    Component infrastructure for managing performance data and runtime adaptation of parallel applications2008Conference paper (Refereed)
  • 67. Liu, Shudong
    et al.
    Song, Miao
    Tan, Kok Choon
    Zhang, Changyong
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics, Analysis and Probability Theory.
    Multi-class dynamic inventory rationing with stochastic demands and backordering2015In: European Journal of Operational Research, ISSN 0377-2217, E-ISSN 1872-6860, Vol. 244, no 1, p. 153-163Article in journal (Refereed)
    Abstract [en]

    Dynamic inventory rationing is considered for systems with multiple demand classes, stationary stochastic demands, and backordering. In the literature, dynamic programming has been often applied to address this type of problems. However, due to the curse of dimensionality, computation is a critical challenge for dynamic programming. In this paper, an innovative two-step approach is proposed based on an idea similar to the certainty equivalence principle. First the deterministic inventory rationing problem is studied, where the future demands are set to be the expectation of the stochastic demand processes. The important properties obtained from solving the problem with the KKT conditions are then used to develop effective dynamic rationing policies for stochastic demands, which gives closed-form expressions for dynamic rationing thresholds. These expressions are easy to calculate and are applicable to any number of demand classes. Numerical results show that the expressions are close to and provide a lower bound for the optimal dynamic thresholds. They also shed light on important managerial insights, for example, the relation between different parameters and the rationing thresholds.

  • 68.
    Ljungberg, Malin
    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.
    Composable difference operators for coordinate invariant partial differential equations2007Report (Other academic)
  • 69.
    Ljungberg, Malin
    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.
    Curvilinear coordinates in a PDE solver framework: Analysis2004Report (Other academic)
  • 70.
    Ljungberg, Malin
    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.
    Design of High Performance Computing Software for Genericity and Variability2007Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Computer simulations have emerged as a cost efficient complement to laboratory experiments, as computers have become increasingly powerful.

    The aim of the present work is to explore the ideas of some state of the art software development practices, and ways in which these can be useful for developing high performance research codes.

    The introduction of these practices, and the modular designs that they give rise to, raises issues regarding a potential conflict between runtime efficiency on one hand and development efficiency on the other. Flexible software modules, based on mathematical abstractions, will provide support for convenient implementation and modification of numerical operators. Questions still remain about whether such modules will provide the efficiency which is required for high performance applications.

    To answer these questions, investigations were performed within two different problem domains. The first domain consisted of modular frameworks for the numerical solution of Partial Differential Equations. Such frameworks proved a suitable setting, since several of my research questions revolved around the issue of modularity.

    The second problem domain was that of symmetry exploiting algorithms. These algorithms are based on group theory, and make ample use of mathematical abstractions from that field. The domain of symmetry exploiting algorithms gave us opportunities to investigate difficulties in combining modularity based on high level abstractions with low level optimizations using data layout and parallelization.

    In conclusion, my investigation of software development practices for the area of high performance computing has proved very fruitful indeed. I have found that none of the concerns that were raised should lead us to refrain from the use of the practices that I have considered. On the contrary, in the two case studies presented here, these practices lead to designs that perform well in terms of usability as well as runtime efficiency.

    List of papers
    1. Mixed C++/Fortran 90 implementation of parallel flow solvers
    Open this publication in new window or tab >>Mixed C++/Fortran 90 implementation of parallel flow solvers
    2001 (English)In: Parallel Computational Fluid Dynamics: Trends and Applications, Amsterdam, The Netherlands: Elsevier Science , 2001, p. 233-240Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Amsterdam, The Netherlands: Elsevier Science, 2001
    National Category
    Software Engineering Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-40570 (URN)10.1016/B978-044450673-3/50097-X (DOI)0-444-50673-X (ISBN)
    Available from: 2006-05-15 Created: 2006-05-15 Last updated: 2018-01-11Bibliographically approved
    2. High performance generative programming with a Fortran 95 application
    Open this publication in new window or tab >>High performance generative programming with a Fortran 95 application
    2005 (English)Conference paper, Published paper (Other academic)
    Place, publisher, year, edition, pages
    Glasgow, Scotland: , 2005
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-95625 (URN)
    Conference
    5th Workshop on Parallel/High-Performance Object-Oriented Scientific Computing
    Available from: 2007-03-30 Created: 2007-03-30 Last updated: 2018-01-13Bibliographically approved
    3. Design and usability of a PDE solver framework for curvilinear coordinates
    Open this publication in new window or tab >>Design and usability of a PDE solver framework for curvilinear coordinates
    2006 (English)In: Advances in Engineering Software, ISSN 0965-9978, E-ISSN 1873-5339, Vol. 37, p. 814-825Article in journal (Refereed) Published
    National Category
    Software Engineering Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-81926 (URN)10.1016/j.advengsoft.2006.04.005 (DOI)000241177900005 ()
    Projects
    TENGO
    Available from: 2008-02-15 Created: 2008-02-15 Last updated: 2018-01-13Bibliographically approved
    4. Composable difference operators for coordinate invariant partial differential equations
    Open this publication in new window or tab >>Composable difference operators for coordinate invariant partial differential equations
    2007 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2007-007
    National Category
    Software Engineering Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-10383 (URN)
    Available from: 2007-03-20 Created: 2007-03-20 Last updated: 2018-01-12Bibliographically approved
    5. Generic programming aspects of symmetry exploiting numerical software
    Open this publication in new window or tab >>Generic programming aspects of symmetry exploiting numerical software
    2004 (English)In: Proc. ECCOMAS Congress 2004, Jyväskylä, Finland, 2004, p. 20-Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Jyväskylä, Finland: , 2004
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-67888 (URN)
    Available from: 2007-03-11 Created: 2007-03-11 Last updated: 2018-01-10Bibliographically approved
    6. Designing for geometrical symmetry exploitation
    Open this publication in new window or tab >>Designing for geometrical symmetry exploitation
    2006 (English)In: Scientific Programming, ISSN 1058-9244, E-ISSN 1875-919X, Vol. 14, p. 61-80Article in journal (Refereed) Published
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-10685 (URN)
    Available from: 2008-02-08 Created: 2008-02-08 Last updated: 2018-01-12Bibliographically approved
  • 71.
    Ljungberg, Malin
    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.
    Handling of curvilinear coordinates in a PDE solver framework2003Licentiate thesis, monograph (Other academic)
    Abstract [en]

    By the use of object-oriented analysis and design combined with variability modeling a highly flexible software model for the metrics handling functionality of a PDE solver framework was obtained. This new model was evaluated in terms of usability, particularly with respect to efficiency and flexibility. The efficiency of a pilot implementation is similar to, or even higher than that of a pre-existing application-specific reference code. With regards to flexibility it is shown that the new software model performs well for a set of four change scenarios selected by an expert user group.

  • 72.
    Ljungberg, Malin
    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.
    High performance generative programming with a Fortran 95 application2005Conference paper (Other academic)
  • 73.
    Ljungberg, Malin
    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, Numerical Analysis.
    Otto, Kurt
    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.
    Curvilinear coordinates in a PDE solver framework: Validation2004Report (Other academic)
  • 74.
    Ljungberg, Malin
    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, Numerical Analysis.
    Otto, Kurt
    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.
    Thuné, Michael
    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.
    Design and usability of a PDE solver framework for curvilinear coordinates2006In: Advances in Engineering Software, ISSN 0965-9978, E-ISSN 1873-5339, Vol. 37, p. 814-825Article in journal (Refereed)
  • 75.
    Ljungberg, Malin
    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, Numerical Analysis.
    Thuné, Michael
    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.
    Mixed C++/Fortran 90 implementation of parallel flow solvers2001In: Parallel Computational Fluid Dynamics: Trends and Applications, Amsterdam, The Netherlands: Elsevier Science , 2001, p. 233-240Conference paper (Refereed)
  • 76.
    Ljungberg, Malin
    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, Numerical Analysis.
    Åhlander, Krister
    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.
    Generic programming aspects of symmetry exploiting numerical software2004In: Proc. ECCOMAS Congress 2004, Jyväskylä, Finland, 2004, p. 20-Conference paper (Refereed)
  • 77.
    Ljungberg, Malin
    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, Numerical Analysis.
    Åhlander, Krister
    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.
    Generic programming aspects of symmetry exploiting numerical software2004Report (Other academic)
  • 78.
    Llerena Herrera, Isbel
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, Applied Nuclear Physics.
    An automated software for analysis of experimental data on decay heat from spent nuclear fuel2012Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The Swedish Nuclear Fuel and Waste Management Company (SKB) has developed a method for final disposal of spent nuclear fuel. This technique requires accurate measurement of the residual decay heat of every assembly. For this purpose, depletion codes as well as calorimetric and gamma-ray spectroscopy experimental methods have been developed and evaluated.

    In this work a prototype analysis tool has been developed to automate the analysis of both calorimetric and gamma-ray spectroscopy measurements. The performance of the analysis tool has been investigated by comparing its output with earlier results and calculations. Parallel to the software development, new measurements on 73 BWR assemblies were performed.

    The results obtained for the determination of the residual decay heat are presented. Finally, suggestions for further development are outlined and discussed.

  • 79. Lv, Mingsong
    et al.
    Guan, Nan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Deng, Qingxu
    Yu, Ge
    Yi, Wang
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    McAiT — a timing analyzer for multicore real-time software2011In: Automated Technology for Verification and Analysis, Berlin: Springer-Verlag , 2011, p. 414-417Conference paper (Refereed)
  • 80.
    Löf, Henrik
    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.
    Iterative and Adaptive PDE Solvers for Shared Memory Architectures2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Scientific computing is used frequently in an increasing number of disciplines to accelerate scientific discovery. Many such computing problems involve the numerical solution of partial differential equations (PDE). In this thesis we explore and develop methodology for high-performance implementations of PDE solvers for shared-memory multiprocessor architectures.

    We consider three realistic PDE settings: solution of the Maxwell equations in 3D using an unstructured grid and the method of conjugate gradients, solution of the Poisson equation in 3D using a geometric multigrid method, and solution of an advection equation in 2D using structured adaptive mesh refinement. We apply software optimization techniques to increase both parallel efficiency and the degree of data locality.

    In our evaluation we use several different shared-memory architectures ranging from symmetric multiprocessors and distributed shared-memory architectures to chip-multiprocessors. For distributed shared-memory systems we explore methods of data distribution to increase the amount of geographical locality. We evaluate automatic and transparent page migration based on runtime sampling, user-initiated page migration using a directive with an affinity-on-next-touch semantic, and algorithmic optimizations for page-placement policies.

    Our results show that page migration increases the amount of geographical locality and that the parallel overhead related to page migration can be amortized over the iterations needed to reach convergence. This is especially true for the affinity-on-next-touch methodology whereby page migration can be initiated at an early stage in the algorithms.

    We also develop and explore methodology for other forms of data locality and conclude that the effect on performance is significant and that this effect will increase for future shared-memory architectures. Our overall conclusion is that, if the involved locality issues are addressed, the shared-memory programming model provides an efficient and productive environment for solving many important PDE problems.

    List of papers
    1. Improving Geographical Locality of Data for Shared Memory Implementations of PDE Solvers
    Open this publication in new window or tab >>Improving Geographical Locality of Data for Shared Memory Implementations of PDE Solvers
    2004 (English)In: Computational Science – ICCS 2004, Berlin: Springer-Verlag , 2004, p. 9-16Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2004
    Series
    Lecture Notes in Computer Science ; 3037
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-71098 (URN)10.1007/b97988 (DOI)
    Available from: 2007-03-11 Created: 2007-03-11 Last updated: 2018-01-10Bibliographically approved
    2. affinity-on-next-touch: Increasing the Performance of an Industrial PDE Solver on a cc-NUMA System
    Open this publication in new window or tab >>affinity-on-next-touch: Increasing the Performance of an Industrial PDE Solver on a cc-NUMA System
    2005 (English)In: Proc. 19th ACM International Conference on Supercomputing, New York: ACM Press , 2005, p. 387-392Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    New York: ACM Press, 2005
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-80041 (URN)10.1145/1088149.1088201 (DOI)1-59593-167-8 (ISBN)
    Available from: 2006-05-19 Created: 2009-01-19 Last updated: 2018-01-13Bibliographically approved
    3. Algorithmic optimizations of a conjugate gradient solver on shared memory architectures
    Open this publication in new window or tab >>Algorithmic optimizations of a conjugate gradient solver on shared memory architectures
    2006 (English)In: International Journal of Parallel, Emergent and Distributed Systems, ISSN 1744-5760, E-ISSN 1744-5779, Vol. 21, p. 345-363Article in journal (Refereed) Published
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-80937 (URN)10.1080/17445760600568139 (DOI)
    Available from: 2006-06-29 Created: 2006-06-29 Last updated: 2018-01-13Bibliographically approved
    4. Multigrid and Gauss-Seidel smoothers revisited: Parallelization on chip multiprocessors
    Open this publication in new window or tab >>Multigrid and Gauss-Seidel smoothers revisited: Parallelization on chip multiprocessors
    2006 (English)In: Proc. 20th ACM International Conference on Supercomputing, New York: ACM Press , 2006, p. 145-155Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    New York: ACM Press, 2006
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-19810 (URN)10.1145/1183401.1183423 (DOI)1-59593-282-8 (ISBN)
    Available from: 2008-02-08 Created: 2008-02-08 Last updated: 2018-01-12Bibliographically approved
    5. Geographical locality and dynamic data migration for OpenMP implementations of adaptive PDE solvers
    Open this publication in new window or tab >>Geographical locality and dynamic data migration for OpenMP implementations of adaptive PDE solvers
    2008 (English)In: OpenMP Shared Memory Parallel Programming, Berlin: Springer-Verlag , 2008, p. 382-393Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2008
    Series
    Lecture Notes in Computer Science ; 4315
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-17844 (URN)10.1007/978-3-540-68555-5_31 (DOI)000256573200031 ()978-3-540-68554-8 (ISBN)
    Projects
    UPMARC
    Available from: 2008-09-05 Created: 2008-09-05 Last updated: 2018-01-12Bibliographically approved
  • 81.
    Löf, Henrik
    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.
    Parallelizing the Method of Conjugate Gradients for Shared Memory Architectures2004Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    Solving Partial Differential Equations (PDEs) is an important problem in many fields of science and engineering. For most real-world problems modeled by PDEs, we can only approximate the solution using numerical methods. Many of these numerical methods result in very large systems of linear equations. A common way of solving these systems is to use an iterative solver such as the method of conjugate gradients. Furthermore, due to the size of these systems we often need parallel computers to be able to solve them in a reasonable amount of time.

    Shared memory architectures represent a class of parallel computer systems commonly used both in commercial applications and in scientific computing. To be able to provide cost-efficient computing solutions, shared memory architectures come in a large variety of configurations and sizes. From a programming point of view, we do not want to spend a lot of effort optimizing an application for a specific computer architecture. We want to find methods and principles of optimizing our programs that are generally applicable to a large class of architectures.

    In this thesis, we investigate how to implement the method of conjugate gradients efficiently on shared memory architectures. We seek algorithmic optimizations that result in efficient programs for a variety of architectures. To study this problem, we have implemented the method of conjugate gradients using OpenMP and we have measured the runtime performance of this solver on a variety of both uniform and non-uniform shared memory architectures. The input data used in the experiments come from a Finite-Element discretization of the Maxwell equations in three dimensions of a fighter-jet geometry.

    Our results show that, for all architectures studied, optimizations targeting the memory hierarchy exhibited the largest performance increase. Improving the load balance, by balancing the arithmetical work and minimizing the number of global barriers showed to be of lesser importance. Overall, bandwidth minimization of the iteration matrix showed to be the most efficient optimization.

    On non-uniform architectures, proper data distribution showed to be very important. In our experiments we used page migration to improve the data distribution during runtime. Our results indicate that page migration can be very efficient if we can keep the migration cost low. Furthermore, we believe that page migration can be introduced in a portable way into OpenMP in the form of a directive with a affinity-on-next-touch semantic.

  • 82.
    Lövheim, Jona
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    VadÄrVar: -en organisationsapp2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [sv]

    Arbetet utforskar möjligheten att skapa en iOS-applikation och undersöker Apples

    programmeringsspråk Swift. Appen syftar till att ge föräldrar en möjlighet att

    organisera undanlagda barnkläder och skor genom att lägga in dem i ett register.

    Slutprodukten är en app där användaren lägger in föremål som definieras av fem

    kategorier. Appen sorterar föremålen och presenterar en trädvy som visar de

    gemensamma kategorierna.Data i appen sparas permanent som JSON-filer.

  • 83.
    Mahjani, Behrang
    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.
    Global optimization algorithm PruneDIRECT as an R package2016Report (Other academic)
  • 84.
    Mahjani, Behrang
    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.
    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.
    Software as a service in analysis of quantitative trait loci2016Report (Other academic)
  • 85.
    Mahjani, Behrang
    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.
    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.
    Nettelblad, Carl
    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.
    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.
    QTL as a service: PruneDIRECT for multi-dimensional QTL scans in cloud settings2016In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811Article in journal (Other academic)
  • 86.
    Mathur, Parul
    et al.
    Amrita Vishwa Vidyapeetham, RF & Wireless Syst Lab, Dept Elect & Commun Engn, Sch Engn, Bengaluru, India.
    Perez, Mauricio D.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Augustine, Robin
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Solid State Electronics.
    Kurup, Dhanesh G.
    Amrita Vishwa Vidyapeetham, RF & Wireless Syst Lab, Dept Elect & Commun Engn, Sch Engn, Bengaluru, India.
    NDECOAX: A software package for nondestructive evaluation of stratified dielectric media2019In: SoftwareX, E-ISSN 2352-7110, Vol. 9, p. 187-192Article in journal (Refereed)
    Abstract [en]

    This article presents a software package based on the C++ language for accurate computation of material properties of a stratified media using an open ended coaxial probe (OECP). Since OECP is one of the most commonly used sensors for evaluation of materials today, the program developed can be customized for real time nondestructive evaluation of materials. The main contribution of this article is a computationally efficient software for solving an infinite domain integral with multiple singularities based on plane wave spectrum theory. The computed results for aperture admittance of the coaxial probe using the developed software show good agreement with both measurements and results from a commercial solver using the finite element method (FEM). It is also proved that, the execution time per frequency point of the developed code is much faster than FEM. (C) 2019 The Authors. Published by Elsevier B.V.

  • 87.
    Monette, Jean-Noël
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Flener, Pierre
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Pearson, Justin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Towards solver-independent propagators2012In: Principles and Practice of Constraint Programming: CP 2012 / [ed] Milano, Michela, Springer Berlin/Heidelberg, 2012, p. 544-560Conference paper (Refereed)
  • 88.
    Mossberg, Eva
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Otto, Kurt
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Thuné, Michael
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    Object-oriented software tools for the construction of preconditioners1997In: Scientific Programming, ISSN 1058-9244, E-ISSN 1875-919X, Vol. 6, p. 285-295Article in journal (Refereed)
  • 89.
    Mukha, Timofey
    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.
    Turbulucid: A Python package for post-processing of fluid flow simulations2018In: Journal of Open Research Software, E-ISSN 2049-9647, Vol. 6, article id 23Article in journal (Refereed)
  • 90.
    Munasinghe, Kalyani
    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.
    On using mobile agents for load balancing in high performance computing2002Licentiate thesis, monograph (Other academic)
    Abstract [en]

    One recent advance in software technology is the development of software agents that can adapt to changes in their environment and can cooperate and coordinate their activities to complete a given task. Such agents can be distributed over a network.

    Advances in hardware technology have meant that clusters of workstations can be used to create parallel virtual machines that bring the power of parallel computing to a much wider research and development community. Many software packages are now being developed to utilise such cluster environments.

    In a cluster, each processor will be multitasking and running other jobs simultaneously with a distributed application that uses a message passing environment such as MPI. A typical application might be a large scale mesh-based computation, such as a finite element code, in which load balancing is equivalent to mesh partitioning. When the load is varying between processors within the cluster, distributing the computation in equal amounts may not deliver the optimum performance. Some machines may be very heavily loaded by other users while other processors may have no such additional load. It may be beneficial to measure current system information and use this information when balancing the load within a single distributed application program.

    This thesis presents one approach to distributing workload more efficiently in a multi-user distributed environment by using mobile agents to collect system information which is then transmitted to all the MPI tasks. The thesis contains a review of software agents and mesh partitioning together with some numerical experiments and a paper.

  • 91.
    Naumanen, Hampus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Malmgård, Torsten
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Waade, Eystein
    Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences.
    Analytics tool for radar data2018Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Analytics tool for radar data was a project that started when radar specialists at Saab needed to modernize their tools that analyzes binary encoded radar data. Today, the analysis is accomplished using inadequate and ineffective applications not designed for that purpose, and consequently this makes the analysis tedious and more difficult compared to using an appropriate interface. The applications had limitations regarding different radar systems too, which restricted their usage significantly. The solution was to design a new software that imports, translates and visualizes the data independent of the radar system.

    The software was developed with several parts that communicates with each other to translate a binary file. A binary file consists of a series of bytes containing the information of the targets and markers separating the revolutions of the radar. The byte stream is split according to the ASTERIX protocol that defines the length of each Data Item and the extracted positional values are stored in arrays. The code is then designed to convert the positional values to cartesian coordinates and plot them on the screen. The software has implemented features such as play, pause, reverse and a plotting history that allows the user to analyze the data in a simple and user-friendly manner.

    There are also numerous ways the software could be extended. The code is constructed in such a way that new features can be implemented for additional analytical abilities without affecting the components already designed.

  • 92.
    Nettelblad, Carl
    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.
    Two Optimization Problems in Genetics: Multi-dimensional QTL Analysis and Haplotype Inference2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The existence of new technologies, implemented in efficient platforms and workflows has made massive genotyping available to all fields of biology and medicine. Genetic analyses are no longer dominated by experimental work in laboratories, but rather the interpretation of the resulting data. When billions of data points representing thousands of individuals are available, efficient computational tools are required. The focus of this thesis is on developing models, methods and implementations for such tools.

    The first theme of the thesis is multi-dimensional scans for quantitative trait loci (QTL) in experimental crosses. By mating individuals from different lines, it is possible to gather data that can be used to pinpoint the genetic variation that influences specific traits to specific genome loci. However, it is natural to expect multiple genes influencing a single trait to interact. The thesis discusses model structure and model selection, giving new insight regarding under what conditions orthogonal models can be devised. The thesis also presents a new optimization method for efficiently and accurately locating QTL, and performing the permuted data searches needed for significance testing. This method has been implemented in a software package that can seamlessly perform the searches on grid computing infrastructures.

    The other theme in the thesis is the development of adapted optimization schemes for using hidden Markov models in tracing allele inheritance pathways, and specifically inferring haplotypes. The advances presented form the basis for more accurate and non-biased line origin probabilities in experimental crosses, especially multi-generational ones. We show that the new tools are able to reconstruct haplotypes and even genotypes in founder individuals and offspring alike, based on only unordered offspring genotypes. The tools can also handle larger populations than competing methods, resolving inheritance pathways and phase in much larger and more complex populations. Finally, the methods presented are also applicable to datasets where individual relationships are not known, which is frequently the case in human genetics studies. One immediate application for this would be improved accuracy for imputation of SNP markers within genome-wide association studies (GWAS).

    List of papers
    1. Coherent estimates of genetic effects with missing information
    Open this publication in new window or tab >>Coherent estimates of genetic effects with missing information
    2012 (English)In: Open Journal of Genetics, ISSN 2162-4453, E-ISSN 2162-4461, Vol. 2, p. 31-38Article in journal (Refereed) Published
    Keywords
    genetic effects, missing genotypes, orthogonal estimation, QTL analysis
    National Category
    Bioinformatics and Systems Biology Genetics Probability Theory and Statistics Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-180915 (URN)10.4236/ojgen.2012.21003 (DOI)
    Projects
    eSSENCE
    Available from: 2012-03-02 Created: 2012-09-12 Last updated: 2017-12-07Bibliographically approved
    2. Fast and accurate detection of multiple quantitative trait loci
    Open this publication in new window or tab >>Fast and accurate detection of multiple quantitative trait loci
    2013 (English)In: Journal of Computational Biology, ISSN 1066-5277, E-ISSN 1557-8666, Vol. 20, p. 687-702Article in journal (Refereed) Published
    National Category
    Bioinformatics and Systems Biology Genetics Computational Mathematics Probability Theory and Statistics
    Identifiers
    urn:nbn:se:uu:diva-180916 (URN)10.1089/cmb.2012.0242 (DOI)000323822000006 ()
    Projects
    eSSENCE
    Available from: 2013-08-06 Created: 2012-09-13 Last updated: 2017-12-07Bibliographically approved
    3. 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
    4. cnF2freq: Efficient determination of genotype and haplotype probabilities in outbred populations using Markov models
    Open this publication in new window or tab >>cnF2freq: Efficient determination of genotype and haplotype probabilities in outbred populations using Markov models
    2009 (English)In: Bioinformatics and Computational Biology, Berlin: Springer-Verlag , 2009, p. 307-319Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2009
    Series
    Lecture Notes in Computer Science ; 5462
    National Category
    Computational Mathematics Genetics
    Identifiers
    urn:nbn:se:uu:diva-103916 (URN)10.1007/978-3-642-00727-9_29 (DOI)000265785800029 ()978-3-642-00726-2 (ISBN)
    Available from: 2009-05-25 Created: 2009-05-25 Last updated: 2017-01-25Bibliographically approved
    5. An improved method for estimating chromosomal line origin in QTL analysis of crosses between outbred lines
    Open this publication in new window or tab >>An improved method for estimating chromosomal line origin in QTL analysis of crosses between outbred lines
    2011 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 1, p. 57-64Article in journal (Refereed) Published
    National Category
    Computational Mathematics Genetics
    Identifiers
    urn:nbn:se:uu:diva-156197 (URN)10.1534/g3.111.000109 (DOI)000312405400007 ()
    Projects
    eSSENCE
    Available from: 2011-06-01 Created: 2011-07-15 Last updated: 2017-12-08Bibliographically approved
    6. MAPfastR: Quantitative trait loci mapping in outbred line crosses
    Open this publication in new window or tab >>MAPfastR: Quantitative trait loci mapping in outbred line crosses
    Show others...
    2013 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, p. 2147-2149Article in journal (Refereed) Published
    National Category
    Computational Mathematics Genetics Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-180917 (URN)10.1534/g3.113.008623 (DOI)000328334500005 ()
    Projects
    eSSENCE
    Available from: 2013-10-11 Created: 2012-09-13 Last updated: 2017-12-07Bibliographically approved
    7. Haplotype inference based on hidden Markov models in the QTL–MAS 2010 multigenerational dataset
    Open this publication in new window or tab >>Haplotype inference based on hidden Markov models in the QTL–MAS 2010 multigenerational dataset
    2011 (English)In: Proc. 14th European Workshop on QTL Mapping and Marker Assisted Selection, London: BioMed Central , 2011, p. S10:1-7Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    London: BioMed Central, 2011
    Series
    BMC Proceedings, ISSN 1753-6561 ; 5:3
    National Category
    Computational Mathematics Genetics
    Identifiers
    urn:nbn:se:uu:diva-153449 (URN)10.1186/1753-6561-5-S3-S10 (DOI)
    Projects
    eSSENCE
    Available from: 2010-05-17 Created: 2011-05-12 Last updated: 2017-01-25Bibliographically approved
    8. Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data
    Open this publication in new window or tab >>Inferring haplotypes and parental genotypes in larger full sib-ships and other pedigrees with missing or erroneous genotype data
    2012 (English)In: BMC Genetics, ISSN 1471-2156, E-ISSN 1471-2156, Vol. 13, p. 85:1-13Article in journal (Refereed) Published
    Keywords
    haplotyping, phasing, genotype inference, nuclear family data, hidden Markov models
    National Category
    Probability Theory and Statistics Computational Mathematics Genetics Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-182488 (URN)10.1186/1471-2156-13-85 (DOI)000314354600001 ()
    Projects
    eSSENCE
    Available from: 2012-10-10 Created: 2012-10-10 Last updated: 2017-12-07Bibliographically approved
    9. Breakdown of methods for phasing and imputation in the presence of double genotype sharing
    Open this publication in new window or tab >>Breakdown of methods for phasing and imputation in the presence of double genotype sharing
    2012 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2012-027
    National Category
    Probability Theory and Statistics Computational Mathematics Genetics Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-181598 (URN)
    Projects
    eSSENCE
    Available from: 2012-09-25 Created: 2012-09-26 Last updated: 2017-01-25Bibliographically approved
  • 93.
    Nettelblad, Carl
    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.
    Using Markov models and a stochastic Lipschitz condition for genetic analyses2010Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    A proper understanding of biological processes requires an understanding of genetics and evolutionary mechanisms. The vast amounts of genetical information that can routinely be extracted with modern technology have so far not been accompanied by an equally extended understanding of the corresponding processes.

    The relationship between a single gene and the resulting properties, phenotype of an individual is rarely clear. This thesis addresses several computational challenges regarding identifying and assessing the effects of quantitative trait loci (QTL), genomic positions where variation is affecting a trait. The genetic information available for each individual is rarely complete, meaning that the unknown variable of the genotype in the loci modelled also needs to be addressed. This thesis contains the presentation of new tools for employing the information that is available in a way that maximizes the information used, by using hidden Markov models (HMMs), resulting in a change in algorithm runtime complexity from exponential to log-linear, in terms of the number of markers. It also proposes the introduction of inferred haplotypes to further increase the power to assess these unknown variables for pedigrees of related genetically diverse individuals. Modelling consequences of partial genetic information are also treated.

    Furthermore, genes are not directly affecting traits, but are rather expressed in the environment of and in concordance with other genes. Therefore, significant interactions can be expected within genes, where some combination of genetic variation gives a pronounced, or even opposite, effect, compared to when occurring separately. This thesis addresses how to perform efficient scans for multiple interacting loci, as well as how to derive highly accurate empirical significance tests in these settings. This is done by analyzing the mathematical properties of the objective function describing the quality of model fits, and reformulating it through a simple transformation. Combined with the presented prototype of a problem-solving environment, these developments can make multi-dimensional searches for QTL routine, allowing the pursuit of new biological insight.

  • 94. Nilsen, Jon K.
    et al.
    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.
    Nagy, Zsombor
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Chelonia — a self-healing storage cloud2010In: Proc. 9th Cracow Grid Workshop, Kraków, Poland: ACC Cyfronet AGH , 2010, p. 5-12Conference paper (Refereed)
  • 95. Nilsen, Jon Kerr
    et al.
    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.
    Nagy, Zsombor
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Read, Alex
    Performance and stability of the Chelonia storage system2012In: Proc. International Symposium on Grids and Clouds 2012, Trieste, Italy: SISSA , 2012, p. 009:1-14Conference paper (Refereed)
  • 96. Nilsen, Jon Kerr
    et al.
    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.
    Nagy, Zsombor
    Read, Alex
    Chelonia: A self-healing, replicated storage system2011In: Computing in High Energy and Nuclear Physics: CHEP 2010, Bristol, UK: Institute of Physics Publishing (IOPP), 2011, p. 062019:1-6Conference paper (Refereed)
  • 97.
    Nordén, 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, Numerical Analysis.
    Multithreaded PDE Solvers on Non-Uniform Memory Architectures2006Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    A trend in parallel computer architecture is that systems with a large shared memory are becoming more and more popular. A shared memory system can be either a uniform memory architecture (UMA) or a cache coherent non-uniform memory architecture (cc-NUMA).

    In the present thesis, the performance of parallel PDE solvers on cc-NUMA computers is studied. In particular, we consider the shared namespace programming model, represented by OpenMP. Since the main memory is physically, or geographically distributed over several multi-processor nodes, the latency for local memory accesses is smaller than for remote accesses. Therefore, the geographical locality of the data becomes important.

    The focus of the present thesis is to study multithreaded PDE solvers on cc-NUMA systems, in particular their memory access pattern with respect to geographical locality. The questions posed are: (1) How large is the influence on performance of the non-uniformity of the memory system? (2) How should a program be written in order to reduce this influence? (3) Is it possible to introduce optimizations in the computer system for this purpose?

    The main conclusion is that geographical locality is important for performance on cc-NUMA systems. This is shown experimentally for a broad range of PDE solvers as well as theoretically using a model involving characteristics of computer systems and applications.

    Geographical locality can be achieved through migration directives that are inserted by the programmer or — possibly in the future — automatically by the compiler. On some systems, it can also be accomplished by means of transparent, hardware initiated migration and replication. However, a necessary condition that must be fulfilled if migration is to be effective is that the memory access pattern must not be "speckled", i.e. as few threads as possible shall make accesses to each memory page.

    We also conclude that OpenMP is competitive with MPI on cc-NUMA systems if care is taken to get a favourable data distribution.

    List of papers
    1. OpenMP versus MPI for PDE solvers based on regular sparse numerical operators
    Open this publication in new window or tab >>OpenMP versus MPI for PDE solvers based on regular sparse numerical operators
    2006 (English)In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 22, p. 194-203Article in journal (Refereed) Published
    National Category
    Software Engineering Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-47210 (URN)10.1016/j.future.2003.09.004 (DOI)000234408800016 ()
    Available from: 2006-05-23 Created: 2006-05-23 Last updated: 2018-01-11Bibliographically approved
    2. Performance of PDE solvers on a self-optimizing NUMA architecture
    Open this publication in new window or tab >>Performance of PDE solvers on a self-optimizing NUMA architecture
    2002 (English)In: Parallel Algorithms and Applications, ISSN 1063-7192, E-ISSN 1029-032X, Vol. 17, p. 285-299Article in journal (Refereed) Published
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-66909 (URN)10.1080/01495730208941445 (DOI)
    Available from: 2006-05-22 Created: 2006-05-22 Last updated: 2018-01-10Bibliographically approved
    3. Improving Geographical Locality of Data for Shared Memory Implementations of PDE Solvers
    Open this publication in new window or tab >>Improving Geographical Locality of Data for Shared Memory Implementations of PDE Solvers
    2004 (English)In: Computational Science – ICCS 2004, Berlin: Springer-Verlag , 2004, p. 9-16Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2004
    Series
    Lecture Notes in Computer Science ; 3037
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-71098 (URN)10.1007/b97988 (DOI)
    Available from: 2007-03-11 Created: 2007-03-11 Last updated: 2018-01-10Bibliographically approved
    4. Geographical locality and dynamic data migration for OpenMP implementations of adaptive PDE solvers
    Open this publication in new window or tab >>Geographical locality and dynamic data migration for OpenMP implementations of adaptive PDE solvers
    2008 (English)In: OpenMP Shared Memory Parallel Programming, Berlin: Springer-Verlag , 2008, p. 382-393Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Berlin: Springer-Verlag, 2008
    Series
    Lecture Notes in Computer Science ; 4315
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-17844 (URN)10.1007/978-3-540-68555-5_31 (DOI)000256573200031 ()978-3-540-68554-8 (ISBN)
    Projects
    UPMARC
    Available from: 2008-09-05 Created: 2008-09-05 Last updated: 2018-01-12Bibliographically approved
    5. Performance modelling for parallel PDE solvers on NUMA-systems
    Open this publication in new window or tab >>Performance modelling for parallel PDE solvers on NUMA-systems
    2006 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2006-041
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-81930 (URN)
    Available from: 2008-02-19 Created: 2008-02-19 Last updated: 2018-01-13Bibliographically approved
  • 98.
    Nordén, 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, Numerical Analysis.
    Parallel PDE Solvers on cc-NUMA Systems2004Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    The current trend in parallel computers is that systems with a large shared memory are becoming more and more popular. A shared memory system can be either a uniform memory architecture (UMA) or a cache coherent non-uniform memory architecture (cc-NUMA).

    In the present thesis, the performance of parallel PDE solvers on cc-NUMA computers is studied. In particular, we consider the shared namespace programming model, represented by OpenMP. Since the main memory is physically, or geographically distributed over several multi-processor nodes, the latency for local memory accesses is smaller than for remote accesses. Therefore, the geographical locality of the data becomes important.

    The questions posed in this thesis are: (1) How large is the influence on performance of the non-uniformity of the memory system? (2) How should a program be written in order to reduce this influence? (3) Is it possible to introduce optimizations in the computer system for this purpose?

    Most of the application codes studied address the Euler equations using a finite difference method and a finite volume method respectively and are parallelized with OpenMP. Comparisons are made with an alternative implementation using MPI and with PDE solvers implemented with OpenMP that solve other equations using different numerical methods.

    The main conclusion is that geographical locality is important for performance on cc-NUMA systems. This can be achieved through self optimization provided in the system or through migrate-on-next-touch directives that could be inserted automatically by the compiler.

    We also conclude that OpenMP is competitive with MPI on cc-NUMA systems if care is taken to get a favourable data distribution.

  • 99.
    Nordén, Markus
    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, Numerical Analysis.
    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, Numerical Analysis.
    Thuné, Michael
    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.
    OpenMP versus MPI for PDE solvers based on regular sparse numerical operators2002In: Computational Science – ICCS 2002, Berlin: Springer-Verlag , 2002, p. 681-690Conference paper (Other academic)
  • 100.
    Nordén, Markus
    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, Numerical Analysis.
    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, Numerical Analysis.
    Thuné, Michael
    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.
    OpenMP versus MPI for PDE solvers based on regular sparse numerical operators2006In: Future generations computer systems, ISSN 0167-739X, E-ISSN 1872-7115, Vol. 22, p. 194-203Article in journal (Refereed)
1234 51 - 100 of 173
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