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  • 101.
    Norrby, Elias
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing.
    Investigation and Implementation of a Log Management and Analysis Framework for the Treatment Planning System RayStation2018Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The purpose of this thesis is to investigate and implement a framework for log management and analysis tailored to the treatment planning system (TPS) RayStation. A TPS is a highly advanced software package used in radiation oncology clinics, and the complexity of the software makes writing robust code challenging. Although the product is tested rigorously during development, bugs are present in released software. The purpose of the the framework is to allow the RayStation development team insight into errors encountered in clinics by centralizing log file data recorded at clinics around the world.

    A framework based on the Elastic stack, a suite of open-source products, is proposed, addressing a set of known issues described as the access problem, the processing problem, and the analysis problem. Firstly, log files are stored locally on each machine running RayStation, some of which may not be connected to the Internet. Gaining access to the data is further complicated by legal frameworks such as HIPAA and GDPR that put constraints on how clinic data can be handled. The framework allows for access to the files while respecting these constraints. Secondly, log files are written in several different formats. The framework is flexible enough to process files of multiple different formats and consistently extracts relevant information. Thirdly, the framework offers comprehensive tools for analyzing the collected data. Deployed in-house on a set of 38 machines used by the RayStation development team, the framework was demonstrated to offer solutions to each of the listed problems.

  • 102.
    Olsson, Peter
    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 parallel computing with distributed memory1997Licentiate thesis, monograph (Other academic)
  • 103.
    Olsson, Peter
    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.
    Rantakokko, Jarmo
    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.
    Software tools for parallel CFD on composite grids1996In: Parallel Computational Fluid Dynamics: Implementations and Results Using Parallel Computers, Amsterdam, The Netherlands: Elsevier Science , 1996, p. 725-732Conference paper (Refereed)
  • 104.
    Otto, Kurt
    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.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Numerical Analysis.
    A flexible solver of the Helmholtz equation for layered media2006In: Proc. ECCOMAS CFD Conference 2006, The Netherlands: Tech. Univ. Delft , 2006, p. 8-Conference paper (Refereed)
  • 105.
    Panda, Anmol
    et al.
    BITS Pilani KK Birla Goa Campus, Dept Comp Sci & Informat Syst, Sancoale, Goa, India..
    Rümmer, Philipp
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Goveas, Neena
    BITS Pilani KK Birla Goa Campus, Dept Comp Sci & Informat Syst, Sancoale, Goa, India..
    A Comparative Study of GPUVerify and GKLEE2016In: 2016 Fourth International Conference On Parallel, Distributed And Grid Computing (PDGC) / [ed] Kumar, P Singh, AK, IEEE , 2016, p. 112-117Conference paper (Refereed)
    Abstract [en]

    Use of Graphics Processing Unit (CPU) software is increasing due to the need for data intensive operations and availability of GPUs. This has led to a need for effective GPU software verification tools. These tools have to satisfy requirements such as accuracy, reliability and ease of use. In this work, we have considered two such tools: GPUVerify and GKLEE. Our objectives were to learn about the common challenges developers faced in GPU programming, to understand the specific bugs that these two tools report and compare their scope and scalability aspects. We have also considered usability and learnability aspects. In order to test the software, twenty-six benchmarks were selected from open-source applications. These benchmarks were then verified using the tools and the results documented and analysed. The conclusions have been included in the final section.

  • 106.
    Paçacı, Görkem
    et al.
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media.
    Hamfelt, Andreas
    Uppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media, Information Systems.
    Towards a visual compositional relational programming methodology2012In: Diagrams 2012: Graduate Student Symposium, 2012, p. 17-19Conference paper (Refereed)
    Abstract [en]

    We present a new visual programming method, based on Combilog, a compositional relational programming language. In this paper we focus on the compositional aspect of Combilog, the make operator, visually implementing it via a modification of Higraph diagrams, in an attempt to overcome the obscurity and complexity in the textual representation of this operator.

  • 107.
    Peters, Anne-Kathrin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Hussain, Waqar
    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.
    Clear, Tony
    Daniels, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computer Systems.
    Preparing the global software engineer2015In: Proc. 10th International Conference on Global Software Engineering, Los Alamitos, CA: IEEE Computer Society, 2015, p. 61-70Conference paper (Refereed)
  • 108.
    Rantakokko, Jarmo
    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.
    Data Partitioning Methods and Parallel Block-Oriented PDE Solvers1998Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Data partitioning methods for block-structured problems within scientific computing have been studied. The applications are variational data assimilation in meteorology, ocean modeling, and airflow simulation with multiblock grids. Parallel computers offer in a cost efficient way the computational power and memory that is needed for these kinds of applications. An appropriate data partitioning is then necessary to get a high parallel efficiency and utilization of the parallel computer.

    In the meteorological and oceanographical applications the problem with an irregular workload distribution is treated. In meteorological data assimilation, weather observations are merged together with the dynamical flow model in order to compute an initial state of the atmosphere at a given time. Here, the observations are irregularly distributed in space and time. In ocean modeling the workload varies due to sea depth and ice conditions. New data partitioning methods have been developed for these applications. The new methods are better adapted to the problems and thus give higher efficiency than previous data partitioning methods.

    In the multiblock applications an additional difficulty is the irregular data dependencies. The blocks in a multiblock grid are usually of different sizes and irregularly coupled. This makes the data partitioning non-trivial. New methods have been developed and different strategies have been investigated - both experimentally and theoretically - using a compressible Navier-Stokes solver as a model problem. The behavior of the different strategies depends very much on the number of subgrids and their sizes as well as the number of processors.

    Moreover, software tools for block-oriented PDE solvers have been constructed. The tools are written in Fortran 90 with an object-oriented design and support explicit finite difference methods and multiblock grids. Programs using the tools run on parallel computers and the proposed data partitioning methods are utilized.

  • 109.
    Rantakokko, Jarmo
    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 composite-grid methods on parallel computers1995Licentiate thesis, monograph (Other academic)
  • 110.
    Rantakokko, Jarmo
    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.
    Software tools for partitioning block-structured applications1998In: Computing in Object-Oriented Parallel Environments, Berlin: Springer-Verlag , 1998, p. 83-94Conference paper (Refereed)
  • 111.
    Rubensson, Emanuel H.
    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.
    Rudberg, Elias
    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.
    Chunks and Tasks: A programming model for parallelization of dynamic algorithms2014In: Parallel Computing, ISSN 0167-8191, E-ISSN 1872-7336, Vol. 40, p. 328-343Article in journal (Refereed)
  • 112.
    Rudberg, Elias
    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.
    Rubensson, Emanuel H.
    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.
    Salek, Pawel
    Kruchinina, Anastasia
    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.
    Ergo: An open-source program for linear-scaling electronic structure calculations2018In: SoftwareX, E-ISSN 2352-7110, Vol. 7, p. 107-111Article in journal (Refereed)
  • 113.
    Ryeznik, Yevgen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Mathematics.
    Sverdlov, Oleksandr
    EMD Serono Inc, R&D Global Biostat, Billerica, MA 01821 USA..
    Wong, Weng Kee
    Univ Calif Los Angeles, Fielding Sch Publ Hlth, Dept Biostat, Los Angeles, CA 90095 USA..
    RARtool: A MATLAB Software Package for Designing Response-Adaptive Randomized Clinical Trials with Time-to-Event Outcomes2015In: Journal of Statistical Software, ISSN 1548-7660, E-ISSN 1548-7660, Vol. 66, no 1Article in journal (Refereed)
    Abstract [en]

    Response-adaptive randomization designs are becoming increasingly popular in clinical trial practice. In this paper, we present RARtool, a user interface software developed in MATLAB for designing response-adaptive randomized comparative clinical trials with censored time-to-event outcomes. The RARtool software can compute different types of optimal treatment allocation designs, and it can simulate response-adaptive randomization procedures targeting selected optimal allocations. Through simulations, an investigator can assess design characteristics under a variety of experimental scenarios and select the best procedure for practical implementation. We illustrate the utility of our RARtool software by redesigning a survival trial from the literature.

  • 114. Senek, Aleksandar
    et al.
    Engblom, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Multiscale stochastic neuron modeling – with applications in deep brain stimulation2017In: Proc. Summer Simulation Multiconference: 2017, San Diego, CA: Society for Computer Simulation International , 2017, p. 38:1-5, article id 38Conference paper (Refereed)
  • 115.
    Smite, Darja
    et al.
    Blekinge Tekniska Högskola.
    Moe, Nils BredeSINTEF.Ågerfalk, PärUppsala University, Disciplinary Domain of Humanities and Social Sciences, Faculty of Social Sciences, Department of Informatics and Media.
    Agility Across Time and Space: Implementing Agile Methods in Global Software Projects2010Collection (editor) (Other academic)
    Abstract [en]

    Rather than deciding whether or not to get involved in global sourcing, many companies are facing decisions about whether or not to apply agile methods in their distributed projects. These companies are often motivated by the opportunities to solve the coordination and communication difficulties associated with global software development. Yet while agile principles prescribe close interaction and co-location, the very nature of distributed software development does not support these prerequisites. Šmite, Moe, and Ågerfalk structured the book into five parts. In "Motivation" the editors introduce the fundamentals of agile distributed software development and explain the rationale behind the application of agile practices in globally distributed software projects. "Transition" describes implementation strategies, adoption of particular agile practices for distributed projects, and general concepts of agility. "Management" details practical implications for project planning, time management, and customer and subcontractor interaction. "Teams" discusses agile distributed team configuration, effective communication and knowledge transfer, and allocation of roles and responsibilities. Finally, in the "Epilogue" the editors summarize all contributions and present future trends for research and practice in agile distributed development. This book is primarily targeted at researchers, lecturers, and students in empirical software engineering, and at practitioners involved in globally distributed software projects. The contributions are based on sound empirical research and identify gaps and commonalities in both the existing state of the art and state of the practice. In addition, they also offer practical advice through many hints, checklists, and experience reports. Questions answered in this book include: What should companies expect from merging agile and distributed strategies? What are the stumbling blocks that prevent companies from realizing the benefits of the agile approach in distributed environments, and how can we recognize infeasible strategies and unfavorable circumstances? What helps managers cope with the challenges of implementing agile approaches in distributed software development projects? How can distributed teams survive the decisions taken by management and become efficient through the application of agile approaches?

  • 116.
    Steensland, Johan
    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.
    Domain-based partitioning for parallel SAMR applications2001Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis presents a study of domain-based partitioning techniques for dynamic structured grid hierarchies, occuring in structured adaptive mesh refinement (SAMR) methods. Such methods for obtaining the numerical solution to partial differential equations yield highly advantageous ratios for cost/accuracy as compared to methods based upon static uniform approximations. Distributed implementations of these techniques have the potential for enabling realistic simulations of complex systems. These implementations however, present significant challenges in dynamic data-distribution and load balancing. That is, when SAMR is executed on a parallel computer, the work load will change dynamically. Thus, there is need for dynamic load balancing in order to efficiently utilize the resourses of the parallel computer. Inverse space-filling curve partitioning (ISP) is appealing for load balancing in parallel SAMR, because of its speed. In this work, ISP is considered as part of a partitioning approach, which combines structured and unstructured techniques.

    Various design decisions for the structured partitioning are considered. Different design choices lead to graphs with different properties. One objective is to investigate how these differences affect the behavior of ISP. This thesis contributes by identifying certain design choices as being advantageous, and by presenting four new partitioning algorithms that correspond to these design decisions.

    An experimental comparison of dynamic partitioning techniques for blockwise parallel structured adaptive mesh refinement applications is presented. It is shown that an ISP-based technique can compete with other approaches for certain classes of applications. Moreover, an extended experimental characterization of dynamic partitioning/load-balancing techniques for general adaptive grid hierarchies is presented. Techniques studied include newly proposed as well as existing approaches. It was found that two of the proposed algorithms were particularly useful: pBD-ISP for the more communication dominated applications, and G-MISP+SP for the computation dominated applications.

    Policies for the automatic selection of partitioner based on application and system state are outlined. Recommendations for appropriate partitioning techniques, given application and system state, are given. The overall motivation is the formulation of policies required to drive a dynamically adaptive meta-partitioner for SAMR grid hierarchies capable of selecting the most appropriate partitioning strategy at runtime, based on current application and system state. Such a partitioner may significantly decrease application execution time.

  • 117.
    Steensland, Johan
    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.
    Efficient Partitioning of Dynamic Structured Grid Hierarchies2002Doctoral thesis, monograph (Other academic)
    Abstract [en]

    This thesis aims at decreasing execution time for large-scale structured adaptive mesh refinement (SAMR) applications executing on general parallel computers. The key contributions are (1) A conceptual dynamically adaptive meta-partitioner able to select and configure an appropriate partitioning technique, based on application and computer state, and (2) A characterization of new and existing domain-based partitioners, enabling a mapping from application and computer state onto appropriate partitioners, and (3) Sketched scalable solutions, expressed in terms of natural regions and expert algorithms, for the problem to efficiently partition large-scale SAMR applications with deep grid hierarchies executing on general parallel computers, and (4) A software partitioning tool Nature+Fable, implementing the greater parts of these sketched scalable solutions and engineered as part of the meta-partitioner.

    Both in academia and industry, computer simulations of physical phenomena are becoming increasingly popular as they constitute an important complement to real-life testing. In many cases, such simulations are based on solving partial differential equations by numerical methods. Adaptive methods are crucial to efficiently utilize computer resources such as memory and CPU. But even with adaption, the simulations are computationally demanding and yield huge data sets. Thus, parallelization is a necessity, demanding the next level of wise resource utilization --- the partitioning of data. Adaption causes the workload to change dynamically, calling for dynamic (re-) partitioning to maintain efficient resource utilization.

    The primary motivation for the present work is twofold, viz. (1) No single partitioning technique performs the best for all applications and computer systems, and (2) No established partitioning technique copes efficiently with large-scale SAMR applications with deep grid hierarchies executing on general parallel computers.

    The conclusions are that the execution time for large-scale SAMR applications can be decreased by the meta-partitioner, and that our proposed scalable solutions exhibit promising properties and behave as expected or better. Consequently, this thesis takes a step towards decreasing the execution times for large-scale SAMR applications.

  • 118.
    Stoica, Anca-Juliana
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Demonstrating early value in software system projects using software and system cost models2011In: Proc. 26th International Forum on Systems/Software Cost Modeling, Los Angeles, CA: University of Southern California , 2011Conference paper (Refereed)
  • 119.
    Stoica, Anca-Juliana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Babu, Prabhu
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    Stoica, Peter
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    Quantitative framework for managing software life cycle2011In: The Open Software Engineering Journal, ISSN 1874-107X, E-ISSN 1874-107X, Vol. 5, p. 1-18Article in journal (Refereed)
  • 120.
    Stoica, Anca-Juliana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Islam, Shareeful
    Concurrent view modeling for software risk management at early development stage2012In: Proc. 1st International Conference on Theory and Practice in Modern Computing, IADIS Press, 2012, p. 35-44Conference paper (Refereed)
  • 121.
    Stoica, Anca-Juliana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Islam, Shareeful
    Educational methods for software and systems development2012In: Proc. 15th International Conference on Interactive Collaborative Learning, Piscataway, NJ: IEEE , 2012, p. 8-Conference paper (Refereed)
  • 122.
    Stoica, Anca-Juliana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Islam, Shareeful
    Integrative educational approach oriented towards software and system development2013In: International Journal of Engineering Pedagogy, ISSN 2192-4880, Vol. 3, no 1, p. 36-43Article in journal (Refereed)
  • 123.
    Stoica, Anca-Juliana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Islam, Shareeful
    Teaching information and software security courses in regular and distance learning programs: Education theory and practice, framework, and examples2013In: Proc. 4th Global Engineering Education Conference, Piscataway, NJ: IEEE , 2013, p. 44-49Conference paper (Refereed)
  • 124.
    Stoica, Anca-Juliana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Nael, Margus
    Agile software development and ISO-IEC software quality standards: Measuring economic benefits and calculating quantitative yields2010In: Proc. 25th International Forum on Systems/Software Cost Modeling, Los Angeles, CA: University of Southern California , 2010Conference paper (Refereed)
  • 125.
    Stoica, Anca-Juliana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Pelckmans, Kristiaan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Systems and Control. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Automatic control.
    Rowe, William
    System components of a general theory of software engineering2015In: Science of Computer Programming, ISSN 0167-6423, E-ISSN 1872-7964, Vol. 101, p. 42-65Article in journal (Refereed)
    Abstract [en]

    The contribution of this paper to a general theory of software engineering is twofold: it presents the model system concept, and it integrates the software engineering design process into a decision making theory and a value-based decision-under-risk process. The model system concept is defined as a collection of interconnected and consistent components that work together for defining, developing, and delivering a software system. This model system concept is used to represent the multiple facets of a software engineering project such as stakeholders and models related to domain/environment, success, decision, product, process, and property. The model system concept is derived from software development practices in the industry and academia. The theoretical decision framework acts as a central governance component for a given software engineering project. Applying this decision framework allows for effectively managing risks and uncertainties related to success in the project building stage. Especially, this puts the design process in an economic perspective, where concepts such as value-of-waiting, value-of-information and possible outcomes can be coped with explicitly. In practice, the decision framework allows for the optimal control of modern adaptive software development. In particular, one can use dynamic programming to find the optimal sequence of decisions to be made considering a defined time horizon. In this way we can relate our contribution to a theory of software engineering to the well-studied areas of automatic control, optimization, decision theory and Bayesian analysis.

  • 126.
    Sundvall, Tomas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing.
    Simplifying Functional TestAutomation For Electronic TradingPlatforms at Nasdaq: Model Design And Proof of ConceptImplementation2015Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Noways the majority of all trading with financial assets are committed via electronictrading platforms (ETP). Nasdaq is a major ETP provider and powers over 100markets worldwide. Because operational disruptions and software bugs can causesignificant economic losses, software testing is a key part of Nasdaqs operations. Thefirst part of this project was to analyze how Nasdaq works with software testing of itsETP called Genium Inet Trading. Based on this analysis a system aimed at simplifyingand streamlining the process of automating functional tests was developed. Functionaltests are a vital part of Nasdaqs quality assurance efforts.

    The project resulted in a overall conceptual model and a ”proof of concept”implementation called Scenario Runner. The conceptual model describes howfunctional tests specifications can be represented in an abstract level that isindependent of which techniques that are used for implementation. Scenario Runnerwas developed as a plugin to Nasdaqs internal ETP testing software called NeXTWorkstation and uses MS Excel as input format for the functional test specifications.Scenario Runner reads and executes tests in the MS Excel document and presents theresults both in the NeXT Workstation GUI and as an output MS Excel file. Theproject was successful and Scenario Runner can be used to run simple functionaltests, but more importantly, to demonstrate how the conceptual model can be usedfor automating functional tests in practice.

  • 127.
    Söderman, Anton
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    How to improve value towards third-party developers: An analysis of the open data platform Trafiklab2016Independent thesis Advanced level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    This thesis studies the open dataplatform Trafiklab, which provides openaccess to data regarding public transportin Sweden. The study is from the perspective ofthird-party developersand deals with the question of how theyvalue creating mechanisms towards themcan be improved. It is based on twodifferent surveys and severalinterviews conducted with third-partydevelopers using Trafiklab. The resultsshow that Trafiklab needs to improvetheir documentation, communication,initial use, and change theirperspective and role towards thedevelopers using Trafiklab. To improveopen data, in general, a greater focus ontransparency rather then transparency issuggested.

  • 128. Thomas, Lynda
    et al.
    Zander, Carol
    Loftus, Chris
    Eckerdal, Anna
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Student software designs at the undergraduate midpoint2017In: Proc. 22nd Conference on Innovation and Technology in Computer Science Education, New York: ACM Press, 2017, p. 34-39Conference paper (Refereed)
  • 129.
    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.
    A software package for stability analysis of difference methods1984In: PDE Software: Modules, Interfaces and Systems, Amsterdam, The Netherlands: Elsevier Science , 1984, p. 89-102Conference paper (Refereed)
  • 130.
    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.
    Automatic GKS stability analysis1986In: SIAM Journal on Scientific and Statistical Computing, ISSN 0196-5204, Vol. 7, p. 959-977Article in journal (Refereed)
  • 131.
    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 parallel PDE solvers1996In: Wuhan University Journal of Natural Sciences, ISSN 1007-1202, Vol. 1, p. 420-429Article in journal (Refereed)
  • 132.
    Thuné, Michael
    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.
    Mossberg, Eva
    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.
    Olsson, Peter
    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.
    Rantakokko, Jarmo
    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.
    Åhlander, Krister
    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.
    Object-Oriented Construction of Parallel PDE Solvers1997In: Modern Software Tools for Scientific Computing, Boston, MA: Birkhäuser , 1997, p. 203-226Chapter in book (Refereed)
  • 133.
    Thuné, Michael
    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.
    Åhlander, Krister
    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.
    Towards an expressive language for PDE solvers1996In: Programming Languages and Systems, Berlin: Springer-Verlag , 1996, p. 373-386Conference paper (Refereed)
  • 134.
    Thuné, Michael
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, 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.
    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.
    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.
    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.
    Rantakokko, Jarmo
    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.
    Object-oriented modeling of parallel PDE solvers2001In: The Architecture of Scientific Software, Norwell, MA: Kluwer Academic Publishers , 2001, p. 159-174Conference paper (Refereed)
  • 135.
    Tillenius, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Leveraging multicore processors for scientific computing2012Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

    List of papers
    1. Using hardware transactional memory for high-performance computing
    Open this publication in new window or tab >>Using hardware transactional memory for high-performance computing
    Show others...
    2011 (English)In: Proc. 25th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum, Piscataway, NJ: IEEE , 2011, p. 1660-1667Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE, 2011
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-158551 (URN)10.1109/IPDPS.2011.322 (DOI)978-1-61284-425-1 (ISBN)
    Conference
    IPDPS Workshop on Multi-Threaded Architectures and Applications
    Projects
    eSSENCEUPMARC
    Available from: 2011-09-01 Created: 2011-09-10 Last updated: 2018-01-12Bibliographically approved
    2. An efficient task-based approach for solving the n-body problem on multicore architectures
    Open this publication in new window or tab >>An efficient task-based approach for solving the n-body problem on multicore architectures
    2010 (English)Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Reykjavík: University of Iceland, 2010
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-135981 (URN)
    Conference
    PARA 2010: State of the Art in Scientific and Parallel Computing
    Projects
    eSSENCEUPMARC
    Available from: 2010-06-07 Created: 2010-12-09 Last updated: 2018-01-12Bibliographically approved
    3. A simple model for tuning tasks
    Open this publication in new window or tab >>A simple model for tuning tasks
    2011 (English)In: Proc. 4th Swedish Workshop on Multi-Core Computing, Linköping, Sweden: Linköping University , 2011, p. 45-49Conference paper, Published paper (Other academic)
    Place, publisher, year, edition, pages
    Linköping, Sweden: Linköping University, 2011
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-162609 (URN)
    Conference
    MCC11
    Projects
    UPMARCeSSENCE
    Available from: 2011-11-24 Created: 2011-12-02 Last updated: 2018-01-12Bibliographically approved
  • 136.
    Tillenius, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Scientific Computing on Multicore Architectures2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

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

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

    List of papers
    1. Using hardware transactional memory for high-performance computing
    Open this publication in new window or tab >>Using hardware transactional memory for high-performance computing
    Show others...
    2011 (English)In: Proc. 25th International Symposium on Parallel and Distributed Processing Workshops and PhD Forum, Piscataway, NJ: IEEE , 2011, p. 1660-1667Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Piscataway, NJ: IEEE, 2011
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-158551 (URN)10.1109/IPDPS.2011.322 (DOI)978-1-61284-425-1 (ISBN)
    Conference
    IPDPS Workshop on Multi-Threaded Architectures and Applications
    Projects
    eSSENCEUPMARC
    Available from: 2011-09-01 Created: 2011-09-10 Last updated: 2018-01-12Bibliographically approved
    2. SuperGlue: A shared memory framework using data versioning for dependency-aware task-based parallelization
    Open this publication in new window or tab >>SuperGlue: A shared memory framework using data versioning for dependency-aware task-based parallelization
    2014 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2014-010
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-221155 (URN)
    Projects
    UPMARCeSSENCE
    Available from: 2014-04-03 Created: 2014-03-25 Last updated: 2018-01-11Bibliographically approved
    3. Resource-aware task scheduling
    Open this publication in new window or tab >>Resource-aware task scheduling
    2015 (English)In: ACM Transactions on Embedded Computing Systems, ISSN 1539-9087, E-ISSN 1558-3465, Vol. 14, no 1, p. 5:1-25, article id 5Article in journal (Refereed) Published
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-216287 (URN)10.1145/2638554 (DOI)000349302200005 ()
    Projects
    UPMARCeSSENCE
    Available from: 2015-01-21 Created: 2014-01-20 Last updated: 2018-01-11Bibliographically approved
    4. A task parallel implementation of an RBF-generated finite difference method for the shallow water equations on the sphere
    Open this publication in new window or tab >>A task parallel implementation of an RBF-generated finite difference method for the shallow water equations on the sphere
    2014 (English)Report (Other academic)
    Series
    Technical report / Department of Information Technology, Uppsala University, ISSN 1404-3203 ; 2014-011
    National Category
    Computer Sciences Computational Mathematics
    Identifiers
    urn:nbn:se:uu:diva-221156 (URN)
    Projects
    eSSENCEUPMARC
    Available from: 2014-04-03 Created: 2014-03-25 Last updated: 2018-01-11Bibliographically approved
    5. Programming models based on data versioning for dependency-aware task-based parallelisation
    Open this publication in new window or tab >>Programming models based on data versioning for dependency-aware task-based parallelisation
    2012 (English)In: Proc. 15th International Conference on Computational Science and Engineering, Los Alamitos, CA: IEEE Computer Society, 2012, p. 275-280Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2012
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-187446 (URN)10.1109/ICCSE.2012.45 (DOI)000317475000038 ()978-1-4673-5165-2 (ISBN)
    Conference
    CSE 2012
    Projects
    eSSENCEUPMARC
    Available from: 2013-01-24 Created: 2012-12-06 Last updated: 2018-01-16Bibliographically approved
  • 137.
    Tillenius, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    SuperGlue: A shared memory framework using data versioning for dependency-aware task-based parallelization2015In: SIAM Journal on Scientific Computing, ISSN 1064-8275, E-ISSN 1095-7197, Vol. 37, p. C617-C642Article in journal (Refereed)
  • 138.
    Tillenius, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    SuperGlue: A shared memory framework using data versioning for dependency-aware task-based parallelization2014Report (Other academic)
  • 139.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    An efficient task-based approach for solving the n-body problem on multicore architectures2010Conference paper (Refereed)
  • 140.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Badia, Rosa M.
    Martorell, Xavier
    Resource-aware task scheduling2013In: 4th Workshop on Parallel Programming and Run-Time Management Techniques for Many-core Architectures (PARMA), Germany: Tech. Univ. Berlin , 2013, p. 6-Conference paper (Other academic)
  • 141.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Badia, Rosa M.
    Martorell, Xavier
    Resource-aware task scheduling2015In: ACM Transactions on Embedded Computing Systems, ISSN 1539-9087, E-ISSN 1558-3465, Vol. 14, no 1, p. 5:1-25, article id 5Article in journal (Refereed)
  • 142.
    Tillenius, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Larsson, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Lehto, Erik
    Flyer, Natasha
    A task parallel implementation of a scattered node stencil-based solver for the shallow water equations2013In: Proc. 6th Swedish Workshop on Multi-Core Computing, Halmstad, Sweden: Halmstad University , 2013, p. 33-36Conference paper (Other academic)
  • 143.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Managing applications and data in distributed computing infrastructures2010Licentiate thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

  • 144.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Mohn, Bjarte
    Uppsala University, Disciplinary Domain of Science and Technology, Physics, Department of Physics and Astronomy, High Energy Physics.
    Cameron, David
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Case-study for different models of resource brokering in grid systems2010Report (Other academic)
  • 145.
    Toor, Salman
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Töebbicke, Rainer
    Zotes Resines, Maitane
    Holmgren, Sverker
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Investigating an open source cloud storage infrastructure for CERN-specific data analysis2012In: Proc. 7th International Conference on Networking, Architecture, and Storage, Los Alamitos, CA: IEEE Computer Society, 2012, p. 84-88Conference paper (Refereed)
  • 146.
    Toor, Salman Zubair
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Managing Applications and Data in Distributed Computing Infrastructures2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

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

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

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

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

    List of papers
    1. Empowering a flexible application portal with a SOA-based grid job management framework
    Open this publication in new window or tab >>Empowering a flexible application portal with a SOA-based grid job management framework
    Show others...
    2008 (English)Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Trondheim, Norway: Norwegian University of Science and Technology, 2008
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-173381 (URN)
    Conference
    PARA 2008: State of the Art in Scientific and Parallel Computing
    Available from: 2012-04-23 Created: 2012-04-23 Last updated: 2018-01-12Bibliographically approved
    2. A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Open this publication in new window or tab >>A Grid-Enabled Problem Solving Environment for QTL Analysis in R
    Show others...
    2010 (English)In: Proc. 2nd International Conference on Bioinformatics and Computational Biology, Cary, NC: ISCA , 2010, p. 202-209Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Cary, NC: ISCA, 2010
    National Category
    Software Engineering Genetics
    Identifiers
    urn:nbn:se:uu:diva-111594 (URN)978-1-880843-76-5 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-01-12 Created: 2009-12-17 Last updated: 2018-01-12Bibliographically approved
    3. Chelonia — a self-healing storage cloud
    Open this publication in new window or tab >>Chelonia — a self-healing storage cloud
    2010 (English)In: Proc. 9th Cracow Grid Workshop, Kraków, Poland: ACC Cyfronet AGH , 2010, p. 5-12Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Kraków, Poland: ACC Cyfronet AGH, 2010
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-129188 (URN)978-83-61433-01-9 (ISBN)
    Projects
    eSSENCE
    Available from: 2010-03-01 Created: 2010-08-06 Last updated: 2018-01-12Bibliographically approved
    4. Chelonia: A self-healing, replicated storage system
    Open this publication in new window or tab >>Chelonia: A self-healing, replicated storage system
    2011 (English)In: Computing in High Energy and Nuclear Physics: CHEP 2010, Bristol, UK: Institute of Physics Publishing (IOPP), 2011, p. 062019:1-6Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Bristol, UK: Institute of Physics Publishing (IOPP), 2011
    Series
    Journal of Physics: Conference Series ; 331
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-173392 (URN)10.1088/1742-6596/331/6/062019 (DOI)000301120500019 ()
    Projects
    eSSENCE
    Available from: 2011-12-23 Created: 2012-04-23 Last updated: 2018-01-12Bibliographically approved
    5. Performance and stability of the Chelonia storage system
    Open this publication in new window or tab >>Performance and stability of the Chelonia storage system
    Show others...
    2012 (English)In: Proc. International Symposium on Grids and Clouds 2012, Trieste, Italy: SISSA , 2012, p. 009:1-14Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Trieste, Italy: SISSA, 2012
    Series
    Proceedings of Science, ISSN 1824-8039 ; 153
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-129189 (URN)
    Conference
    ISGC 2012
    Projects
    eSSENCE
    Available from: 2012-03-01 Created: 2010-08-06 Last updated: 2018-01-12Bibliographically approved
    6. A scalable architecture for e-Science data management
    Open this publication in new window or tab >>A scalable architecture for e-Science data management
    2011 (English)In: Proc. 7th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2011, p. 210-217Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2011
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-166258 (URN)10.1109/eScience.2011.37 (DOI)978-1-4577-2163-2 (ISBN)
    Projects
    eSSENCE
    Available from: 2012-01-09 Created: 2012-01-11 Last updated: 2018-01-12Bibliographically approved
    7. Scientific analysis by queries in extended SPARQL over a scalable e-Science data store
    Open this publication in new window or tab >>Scientific analysis by queries in extended SPARQL over a scalable e-Science data store
    Show others...
    2013 (English)In: Proc. 9th International Conference on e-Science, Los Alamitos, CA: IEEE Computer Society, 2013, p. 98-106Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2013
    National Category
    Computer Sciences
    Identifiers
    urn:nbn:se:uu:diva-173448 (URN)10.1109/eScience.2013.19 (DOI)000330195500012 ()978-0-7695-5083-1 (ISBN)
    Projects
    eSSENCE
    Available from: 2013-10-25 Created: 2012-04-24 Last updated: 2018-01-12Bibliographically approved
    8. Investigating an open source cloud storage infrastructure for CERN-specific data analysis
    Open this publication in new window or tab >>Investigating an open source cloud storage infrastructure for CERN-specific data analysis
    2012 (English)In: Proc. 7th International Conference on Networking, Architecture, and Storage, Los Alamitos, CA: IEEE Computer Society, 2012, p. 84-88Conference paper, Published paper (Refereed)
    Place, publisher, year, edition, pages
    Los Alamitos, CA: IEEE Computer Society, 2012
    National Category
    Software Engineering
    Identifiers
    urn:nbn:se:uu:diva-173388 (URN)10.1109/NAS.2012.14 (DOI)978-1-4673-1889-1 (ISBN)
    Conference
    NAS 2012
    Projects
    eSSENCE
    Available from: 2012-09-24 Created: 2012-04-23 Last updated: 2018-01-12Bibliographically approved
  • 147. Torruangwatthana, Preechakorn
    et al.
    Wieslander, Håkan
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Visual Information and Interaction.
    Blamey, Ben
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Hellander, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    Toor, Salman
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Division of Scientific Computing. Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computational Science.
    HarmonicIO: Scalable data stream processing for scientific datasets2018In: Proc. 11th International Conference on Cloud Computing, Los Alamitos, CA: IEEE Computer Society, 2018, p. 879-882Conference paper (Refereed)
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    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science. Natl Tech Univ Athens, Athens, Greece.
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    Baker, Robert
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    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Li, Huiqing
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    Roukounaki, Katerina
    Natl Tech Univ Athens, Athens, Greece.
    Tsiouris, Yiannis
    Natl Tech Univ Athens, Athens, Greece.
    Winblad, Kjell
    Uppsala University, Disciplinary Domain of Science and Technology, Mathematics and Computer Science, Department of Information Technology, Computing Science.
    Scaling Reliably: Improving the scalability of the Erlang distributed actor platform2017In: ACM Transactions on Programming Languages and Systems, ISSN 0164-0925, E-ISSN 1558-4593, Vol. 39, no 4, article id 17Article in journal (Refereed)
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    Sanchez, Victor
    Accelerating COBAYA3 on multi-core CPU and GPU systems using PARALUTION2015In: Annals of Nuclear Energy, ISSN 0306-4549, E-ISSN 1873-2100, Vol. 82, p. 252-259Article in journal (Refereed)
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    Sanchez, Victor
    Accelerating COBAYA3 on multi-core CPU and GPU systems using PARALUTION2013In: Proc. 2nd Joint International Conference on Supercomputing in Nuclear Applications and Monte Carlo, Paris, France: La Société Française d'Energie Nucléaire , 2013Conference paper (Other academic)
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