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A general symbolic PDE solver generator: Beyond explicit schemes

Scientific programming 2003年第3期11卷 225-235页

作者： Sheshadri, K. Fritzson, Peter Programming Environment Laboratory Department of Computer Science Linköping University S-581 83 Linköping Sweden

This paper presents an extension of our Mathematica- and MathCode-based symbolic-numeric framework for solving a variety of partial differential equation (PDE) problems. The main features of our earlier work, which implemented explicit finite-difference schemes, include the ability to handle (1) arbitrary number of dependent variables, (2) arbitrary dimensionality, and (3) arbitrary geometry, as well as (4) developing finite-difference schemes to any desired order of approximation. In the present paper, extensions of this framework to implicit schemes and the method of lines are discussed. While C++ code is generated, using the MathCode system for the implicit method, Modelica code is generated for the method of lines. The latter provides a preliminary PDE support for the Modelica language. Examples illustrating the various aspects of the solver generator are presented.

关键词： Computer programming

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Compilation of modelica array computations into single assignment C for efficient execution on CUDA-enabled GPUs

Compilation of modelica array computations into single assig...

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3rd International Workshop on Equation-Based Object-Oriented Modeling Languages and Tools, EOOLT 2010 - In Conjunction with the MODELS 2010 Conference

作者： Stavåker, Kristian Rolls, Daniel Guo, Jing Fritzson, Peter Scholz, Sven-Bodo School of Computer Science University of Hertfordshire United Kingdom Programming Environment Laboratory Department of Computer Science Linköping University Sweden

Mathematical models, derived for example from discretisation of partial differential equations, often contain operations over large arrays. In this work we investigate the possibility of compiling array operations from models in the equation-based language Modelica into Single Assignment C (SAC). The SAC2C SAC compiler can generate highly efficient code that, for instance, can be executed on CUDAenabled GPUs. We plan to enhance the open-source Modelica compiler OpenModelica, with capabilities to detect and compile data parallel Modelica for-equations/arrayequations into SAC WITH-loops. As a first step we demonstrate the feasibility of this approach by manually inserting calls to SAC array operations in the code generated from OpenModelica and show how capabilities and runtimes can be extended. As a second step we demostrate the feasibility of rewriting parts of the OpenModelica simulation runtime system in SAC. Finally, we discuss SAC2C's switchable target architectures and demonstrate one by harnessing a CUDA-enabled GPU to improve runtimes. To the best of our knowledge, compilation of Modelica array operations for execution on CUDA-enabled GPUs is a new research area.

关键词： Graphics processing unit

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From castaways to discoveries: unveiling treasures in skin RNAseq using a novel multidimensional data processing workflow including infection-host dynamics

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Physiological Genomics 2025年第5期57卷 343-356页

作者： Bhargava, Disha Labadie, Alec Hanson-Rios-stutz, Rebecca L. Goodyke, Austin Moses, Ella M. Das, Akansha S. Vanderweele, Sophie Lemon, Janelle V. Cook, Taylor W. Pearson, David Redinger, Joseph M. Caulfield, Adam J. Olivero, Rosemary Foster, Kate Ashack, Kurt Rajasekaran, Surender Bupp, Caleb P. Triche, Timothy J. Krawczyk, Connie M. Chesla, Dave Sims, Matthew D. Hartog, Nicholas L. Prokop, Jeremy W. College of Human Medicine Michigan State University Grand Rapids MI United States Office of Research Corewell Health Grand Rapids MI United States Department of Biology Washington and Jefferson College Washington PA United States Department of Pharmacology and Toxicology Michigan State University East Lansing MI United States Department of Large Animal Clinical Sciences College of Veterinary Medicine Michigan State University East Lansing MI United States School for Environment and Sustainability University of Michigan Ann Arbor MI United States Regional Laboratory Corewell Health Grand Rapids MI United States Infectious Disease Helen DeVos Children’s Hospital Grand Rapids MI United States Dermatology Helen DeVos Children’s Hospital Corewell Health Grand Rapids MI United States Dermatology Associates of West Michigan Grand Rapids MI United States Pediatric Intensive Care Unit Helen DeVos Children’s Hospital Corewell Health Grand Rapids MI United States Medical Genetics Corewell Health Grand Rapids MI United States Center for Epigenetics Van Andel Research Institute Grand Rapids MI United States Department of Metabolism and Nutritional Programming Van Andel Institute Grand Rapids MI United States Section of Infectious Diseases Corewell Health Royal Oak MI United States Allergy and Immunology Corewell Health Grand Rapids MI United States

Defining physiology and methods to measure biological mechanisms is essential. Extensive datasets such as RNA sequencing are used with little analysis of the knowledge gained from the various methodologies. Within this work, we have processed publicly available NCBI RNAseq datasets using a combination of bioinformatics tools for the largest physiological organ, the skin. In many datasets, we identify the quality of the sample, human transcript mapping, the sex of each sample, foreign RNA from bacteria/viruses/protists, and the presence of B/T-cell immune repertoire. Processing 8,274 samples from 132 different experiments for skin samples identifies common flora of skin with elevation of protists (such as Leishmania), bacteria (Staphylococcus, Cutibacterium acnes), and viruses [Human alpha-herpesvirus (HSV), Human papillomavirus (HPV)] that may be involved in physiological differences. We observed samples with the Heilongjiang tick virus, human T-cell leukemia virus type I, and equine infectious anemia virus that likely play pathological roles in physi-ology. Integrating the various biomarkers identified five ideal datasets for skin pathologies that elucidated a novel correlation between the normal skin flora bacterium Bacillus megaterium with major histocompatibility complex (MHC) regulation and the immune repertoire clonal expansion, particularly in patients with hidradenitis suppurativa. Finally, we show that in multiple independent experiments, biological sex is associated with multiple sex chromosome gene differences, highlighting the importance of future work in studying sex differences in skin. Data integrations and multidimensional data mapping are critical for physiological omics advancements, and this work highlights the exciting ability to apply these tools to skin physiology. NEW & NOTEWORTHY Complex bioinformatics mapping to skin RNA sequencing datasets can simultaneously map biological sex, skin-specific genes, bacteria, viruses, protists, and the acqui

关键词： bacteria immune repertoire RNA skin virus

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Modelica — A cyber-physical modeling language and the OpenModelica environment

Modelica — A cyber-physical modeling language and the OpenM...

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International Wireless Communications and Mobile Computing Conference, IWCMC

作者： Peter Fritzson PELAB-Programming Environment Laboratory Department Computer Science Linköping University Linkoping Sweden

Modelica is a modern, strongly typed, declarative, equation-based, and object-oriented (EOO) language for modeling and simulation of complex cyber-physical systems. Major features are: ease of use, visual design of models with combination of lego-like predefined model building blocks, ability to define model libraries with reusable components, support for modeling and simulation of complex applications involving parts from several application domains, and many more useful facilities. This paper gives an overview of some aspects of the Modelica language and the OpenModelica environment - the most complete Modelica open-source tool for modeling, simulation, and development of Modelica applications. Special features are MetaModeling for efficient model transformations, the ModelicaML profile for UML-Modelica cyber-physical hardware-software modeling, as well as generation of parallel code for multi-core architectures.

关键词： Mathematical model Unified modeling language Object oriented modeling Equations Computational modeling Rabbits Software

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Modelica - a general object-oriented language for continuous and discrete-event system modeling and simulation

Modelica - a general object-oriented language for continuous...

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Annual Symposium on Simulation

作者： P. Fritzson P. Bunus PELAB-Programming Environment Laboratory Department of Computer and Information Science Linköping University Linkoping Sweden

Modelica is a general equation-based object-oriented language for continuous and discrete-event modeling of physical systems for the purpose of efficient simulation. The language unifies and generalizes previous object-oriented modeling languages. It is bringing about a revolution in this area, based on its ease of use, visual design of models with combination of Lego-like predefined model building blocks, its ability to define model libraries with re-usable components and its support for modeling and simulation of complex applications involving parts from several application domains. In this paper we present the Modelica language with emphasis on its language features and one of the associated simulation environments. Simulation models can be developed in an integrated problem-solving environment by using a graphical editor for connection diagrams. Connections are established just by drawing lines between objects picked from a class library. The principles of object oriented physical systems modeling and the multi-domain capabilities of the language are presented in the paper by several examples.

关键词： Object oriented modeling Discrete event systems Electrical capacitance tomography Equations Biological system modeling Mathematical model Computer simulation Thermodynamics Application software Computational modeling

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Rθ-signature: A new signature based on Radon Transform and its application in buildings extraction

Rθ-signature: A new signature based on Radon Transform and ...

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IEEE International Symposium on Signal Processing and Information Technology (ISSPIT)

作者： Hmida Rojbani Ines Elouedi Atef Hamouda Laboratory of Computing in Programming Algorithmic and Heuristic/Image City and Environment Faculty of Sciences of Tunis Tunis Tunisia

Object recognition has been a topic of research for decades, it operates by making decisions based on the values of several shape properties measured from an image of the object. In this paper, a new exploitation of the Radon Transform (RT) is proposed to extract only one projection according to a single angle. This projection is chosen in way that contains the necessary information to recognize an object (a shape descriptor). This descriptor (called Rθ-signature) provides global information of a binary shape regardless its form. After that, we use this signature in an extraction method of buildings from very high-resolution satellite imagery.

关键词： Buildings Image segmentation Shape Transforms Satellites Image edge detection Feature extraction

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Biochemical mathematical modeling with Modelica and the BioChem library 6

Biochemical mathematical modeling with Modelica and the BioC...

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6th International Conference APLIMAT 2007

作者： Fritzson, Peter Ulfhielm, Erik Belic, Ales Fransson, Martin Grèen, Henrik PELAB - Programming Environment Lab. Dept. of Computer and Information Science Linköpings Universitet LinköpingSE-581 83 Sweden Laboratory for Modeling Simulation and Control Faculty of Electrical Engineering University of Ljubljana LjubljanaSI-1000 Slovenia Clinical Pharmacology Dept. of Medicine and Care Linköpings Universitet LinköpingSE-581 85 Sweden

ISBN: (纸本)9788096956265

Considering the large amounts of data that is nowadays produced in the biochemistry (functional genomics) it is difficult to extract the information from the measurements. There is currently also a great interest in the development of novel analytical technologies for rapid screening of disease symptoms in pharmaceutical and clinical applications. Modeling and simulation can provide a useful help in understanding the relations of the measured substances and to minimize the need for measurements. The BioChem library presented here is the first free Modelica library available for mathematical modeling of biochemical processes. Three examples are shown to illustrate the library. First, a simple insulin model is presented. Then a simplified model of cholesterol together with simulations are shown. Next, a simple drug model together with parameter estimation in NONMEN are presented. The BioChem library allows for fast and end-user friendly modeling of biomedical systems. The graphical user interface provides graphics similar to that used in the description of metabolic pathways in biochemistry.

关键词： Cholesterol

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Building the next generation of high performance computing researchers in engineering and science: the NCSA/ARL MSRC PET summer internship program

Building the next generation of high performance computing r...

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Frontiers in Education (FIE) Conference

作者： M.B. Walker E.C. Grove V.A. To National Center for Supercomputing Applications University of Illinois Urbana-Champaign Urbana IL USA Major Shared Resource Command Programming Environment and Training Program Army Research Laboratory Aberdeen MD USA

The National Center for Supercomputing Applications (NCSA) at the University of Illinois at Urbana-Champaign (UIUC) is lead academic institution for the Army Research laboratory Major Shared Resource Center programming environment and Training Program (ARL MSRC PET). This program is part of the Department of Defense (DoD) high performance computing modernization program. ARL MSRC PET has a scientific advancement, outreach and training mission. With US-wide faculty and ARL engineers and scientists, the ARL MSRC PET training team offered its summer intern program in high performance computing (HPC) in 1998, 1999, and will again in 2000. It encourages young Americans to consider computer science and engineering careers in DoD and elsewhere. A program focus is outreach to under-represented minorities and women. Mentors and program administrators play a crucial role. The paper discusses the development of this innovative government-university collaborative education program and lessons learned for those wishing to establish similar programs to introduce young Americans to real-life HPC research and applications.

关键词： High performance computing Positron emission tomography programming environments Application software Military computing Computer science Computer science education Educational programs Laboratories Computational fluid dynamics

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OpenModelica - A free open-source environment for system modeling, simulation, and teaching

OpenModelica - A free open-source environment for system mod...

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IEEE International Conference on Computer-Aided Design

作者： Peter Fritzson Peter Aronsson Adrian Pop Hakan Lundvall Kaj Nystrom Levon Saldamli David Broman Anders Sandholm PELAB-Programming Environment Laboratory Department Computer Science Linköping University Linkoping Sweden MathCore Engineering AB Teknikringen 1B SE-583 30 Linköping Sweden EPACT AB Linköping Sweden

Modelica is a modern, strongly typed, declarative, and object-oriented language for modeling and simulation of complex systems. This paper gives a quick overview of some aspects of the OpenModelica environment - an open-source environment for modeling, simulation, and development of Modelica applications. An introduction of the objectives of the environment is given, an overview of the architecture is outlined and a number of examples are illustrated.

关键词： Open source software Education Load modeling Protection Equations Control systems System testing Packaging Connectors

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Including gap junctions into distributed neuronal network simulations 1

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2nd International Workshop on Brain-Inspired Computing, BrainComp 2015

作者： Hahne, Jan Helias, Moritz Kunkel, Susanne Igarashi, Jun Kitayama, Itaru Wylie, Brian Bolten, Matthias Frommer, Andreas Diesmann, Markus School of Mathematics and Natural Sciences University of Wuppertal Wuppertal Germany and JARA BRAIN Institute I Jülich Research Centre Jülich Germany RIKEN Advanced Institute for Computational Science Programming Environment Research Team Kobe Japan Department of Computational Science and Technology School of Computer Science and Communication KTH Royal Institute of Technology Stockholm Sweden Simulation Laboratory Neuroscience Bernstein Facility for Simulation and Database Technology Institute for Advanced Simulation Jülich Aachen Research Alliance Jülich Research Centre Jülich Germany Okinawa Institute of Science and Technology Neural Computation Unit Okinawa Japan Laboratory for Neural Circuit Theory RIKEN Brain Science Institute Wako Japan HPC Usability Research Team RIKEN Advanced Institute for Computational Science Kobe Japan Jülich Supercomputing Centre Jülich Research Centre Jülich Germany Institut für Mathematik Universität Kassel Kassel Germany Department of Psychiatry Psychotherapy and Psychosomatics Medical Faculty RWTH Aachen University Aachen Germany Department of Physics Faculty 1 RWTH Aachen University Aachen Germany

ISBN: (数字)9783319508627

ISBN: (纸本)9783319508610

Contemporary simulation technology for neuronal networks enables the simulation of brain-scale networks using neuron models with a single or a few compartments. However, distributed simulations at full cell density are still lacking the electrical coupling between cells via so called gap junctions. This is due to the absence of efficient algorithms to simulate gap junctions on large parallel computers. The difficulty is that gap junctions require an instantaneous interaction between the coupled neurons, whereas the efficiency of simulation codes for spiking neurons relies on delayed communication. In a recent paper [15] we describe a technology to overcome this obstacle. Here, we give an overview of the challenges to include gap junctions into a distributed simulation scheme for neuronal networks and present an implementation of the new technology available in the NEural Simulation Tool (NEST 2.10.0). Subsequently we introduce the usage of gap junctions in model scripts as well as benchmarks assessing the performance and overhead of the technology on the supercomputers JUQUEEN and K computer. © Springer International Publishing AG 2016.

关键词： Supercomputers

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