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7th European Congress on Computational Methods in Applied Sciences and Engineering, ECCOMAS Congress 2016

作者： Lahnert, Michael Burstedde, Carsten Holm, Christian Mehl, Miriam Rempfer, Georg Weik, Florian Institute of Parallel and Distributed Systems University of Stuttgart Universitätsstraße 38 Stuttgart70569 Germany Institute for Numerical Simulation and Hausdorff Center for Mathematics University of Bonn Wegelerstraße 6 Bonn53115 Germany Institute for Computational Physics University of Stuttgart Allmandring 3 Stuttgart70569 Germany

ISBN: (纸本)9786188284401

We present the minimally-invasive exchange of the regular Cartesian grid in the lattice-Boltzmann solver of ESPResSo by a dynamically-adaptive octree grid. Octree grids are favoured by computer scientists over other grid types as they are very memory-efficient. In addition, they represent a natural generalisation of regular Cartesian grids, such that most discretisation details of a regular grid solver can be maintained. Optimised codes, however, require a special tree-oriented grid traversal, which typically conflicts with existing simulation codes using various iterators, some for only parts of the grid, e.g., boundaries. ESPResSo is a large software package developed for soft-matter simulations involving fluid flow, electrostatic, and electrokinetic effects, and molecular dynamics. The currently used regular Cartesian grid hinders the simulation of realistic domain sizes and significant time periods, a problem that can be solved using grid adaptivity. In a first step, we focus on the lattice-Boltzmann flow solver in ESPResSo. p4est is a grid framework, that already provides dynamically adaptive quadtree and octree grids together with high-level interfaces for flexible grid traversals with direct neighbour access in all grid components. In this paper, we first describe extensions of p4est that were necessary to fulfill certain application requirements. The second part of our work consists of the minimally-invasive changes in ESPResSo preserving the expertise accumulated in the software's implementation over years. Our numerical results demonstrate physical correctness of the implementation, good parallel scalability and low overhead of the dynamical grid adaptivity. These are prerequisites to actually profit from grid adaptivity in terms of being able to simulate larger domains over longer time periods with limited computational resources. Thus, the current status forms a solid basis for further steps such as the development of refinement criteria, the setup of mo

关键词： Molecular dynamics

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Coupled simulations and parameter inversion for neural system and electrophysiological muscle models

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GAMM Mitteilungen 2024年第3期47卷

作者： Homs-Pons, Carme Lautenschlager, Robin Schmid, Laura Ernst, Jennifer Göddeke, Dominik Röhrle, Oliver Schulte, Miriam Institute for Parallel and Distributed Systems University of Stuttgart Stuttgart Germany Institute of Applied Analysis and Numerical Simulation University of Stuttgart Stuttgart Germany Institute for Modeling and Simulation of Biomechanical Systems University of Stuttgart Stuttgart Germany Department of Trauma Surgery Hannover Medical School Hannover Germany Stuttgart Center for Simulation Science University of Stuttgart Stuttgart Germany

The functioning of the neuromuscular system is an important factor for quality of life. With the aim of restoring neuromuscular function after limb amputation, novel clinical techniques such as the agonist-antagonist myoneural interface (AMI) are being developed. In this technique, the residual muscles of an agonist-antagonist pair are (re-)connected via a tendon in order to restore their mechanical and neural interaction. Due to the complexity of the system, the AMI can substantially profit from in silico analysis, in particular to determine the prestretch of the residual muscles that is applied during the procedure and determines the range of motion of the residual muscle pair. We present our computational approach to facilitate this. We extend a detailed multi-X model for single muscles to the AMI setup, that is, a two-muscle-one-tendon system. The model considers subcellular processes as well as 3D muscle and tendon mechanics and is prepared for neural process simulation. It is solved on high performance computing systems. We present simulation results that show (i) the performance of our numerical coupling between muscles and tendon and (ii) a qualitatively correct dependence of the range of motion of muscles on their prestretch. Simultaneously, we pursue a Bayesian parameter inference approach to invert for parameters of interest. Our approach is independent of the underlying muscle model and represents a first step toward parameter optimization, for instance, finding the prestretch, to be applied during surgery, that maximizes the resulting range of motion. Since our multi-X fine-grained model is computationally expensive, we present inversion results for reduced Hill-type models. Our numerical results for cases with known ground truth show the convergence and robustness of our approach. © 2024 The Authors. GAMM - Mitteilungen published by Wiley-VCH GmbH.

关键词： Muscle

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A cots simulation package emulator (CSPE) for investigating cots simulation package interoperability

A cots simulation package emulator (CSPE) for investigating ...

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2005 Winter simulation Conference

作者： Wang, Xiaoguang Turner, Stephen John Taylor, Simon J. E. Low, Malcolm Yoke Hean Gan, Boon Ping Parallel and Distributed Computing Centre School of Computer Engineering Nanyang Technological University 639798 Singapore Singapore Centre for Applied Simulation Modeling School of Information Systems Computing and Mathematics Brunel University Uxbridge UB8 3PH United Kingdom D-SIMLAB Programme Singapore Institute of Manufacturing Technology 71 Nanyang Drive 638075 Singapore Singapore

ISBN: (纸本)0780395204

Commercial Off-The-Shelf (COTS) simulation Packages (CSPs) are widely used to facilitate the creation of simulation models using some kind of visual interactive interface. CSPs have "evolved" over the years and are well used to support modeling demands in different market niches and domains. However, in terms of distributed simulation, there is almost a complete lack of support for interoperability. The advent of the High Level Architecture (HLA) standard makes it possible to connect distributed model components together. The model components can be developed using specific CSPs best suited to the application area. In this paper, a CSP Emulator (CSPE) is proposed to investigate the interfaces between the CSPs and the HLA Runtime Infrastructure. In addition to support for standalone models as provided by current CSPs, the CSPE has some new features needed for building distributed models. An evaluation is conducted between CSPE and Simul8, one of the popular CSPs.

关键词： Electronics packaging

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PerSival: Neural-network-based visualisation for pervasive continuum-mechanical simulations in musculoskeletal biomechanics

arXiv

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arXiv 2023年

作者： Rosin, David Kässinger, Johannes Yu, Xingyao Avci, Okan Bleiler, Christian Röhrle, Oliver Institute for Modelling and Simulation of Biomechanical Systems University of Stuttgart Germany Institute for Parallel and Distributed Systems University of Stuttgart Germany Visualization Research Center VISUS University of Stuttgart Germany Biomechatronic Systems Fraunhofer IPA Stuttgart Germany University of Stuttgart Germany

This paper presents a novel neural network architecture for the purpose of pervasive visualisation of a 3D human upper limb musculoskeletal system model. Bringing simulation capabilities to resource-poor systems like mobile devices is of growing interest across many research fields, to widen applicability of methods and results. Until recently, this goal was thought to be out of reach for realistic continuum-mechanical simulations of musculoskeletal systems, due to prohibitive computational cost. Within this work we use a sparse grid surrogate to capture the surface deformation of the m. biceps brachii in order to train a deep learning model, used for real-time visualisation of the same muscle. Both these surrogate models take 5 muscle activation levels as input and output Cartesian coordinate vectors for each mesh node on the muscle’s surface. Thus, the neural network architecture features a significantly lower input than output dimension. 5 muscle activation levels were sufficient to achieve an average error of 0.97 ± 0.16 mm, or 0.57 ± 0.10 % for the 2809 mesh node positions of the biceps. The model achieved evaluation times of 9.88 ms per predicted deformation state on CPU only and 3.48 ms with GPU-support, leading to theoretical frame rates of 101 fps and 287 fps respectively. Deep learning surrogates thus provide a way to make continuum-mechanical simulations accessible for visual real-time applications. © 2023, CC BY-NC-ND.

关键词： Muscle

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Interoperating autosched AP using the high level architecture

Interoperating autosched AP using the high level architectur...

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2005 Winter simulation Conference

作者： Gan, Boon Ping Lendermann, Peter Low, Malcolm Yoke Hean Turner, Stephen J. Wang, Xiaoguang Taylor, Simon J. E. D-SIMLAB Programme Singapore Institute of Manufacturing Technology 71 Nanyang Drive Singapore 638075 Singapore Parallel and Distributed Computing Centre Nanyang Technological University Block N4 Nanyang Avenue Singapore 639798 Singapore Centre for Applied Simulation Modeling School of Information Systems Computing and Mathematics Brunel University Uxbridge UB8 3PH United Kingdom

ISBN: (纸本)0780395204

The High Level Architecture (HLA) is an IEEE standard for interoperating simulation federates. In this paper, we describe a set of requirements that simulation packages need to satisfy in order to be made interoperable using the HLA standard. AutoSched AP, a commercial off-the-shelf simulation package (CSP) which is widely used in the semiconductor industry, was used as a case study for this interoperation exercise. We demonstrated that a straight-forward customization of the CSP through a middleware that provides standard functions for interoperation may not provide a satisfactory solution. A specially optimized time synchronization mechanism needs to be installed to ensure good execution efficiency. Experimental results using a Borderless Fab model that comprises of two factory models show that an optimized time synchronization mechanism results in an execution time that is ten times better than a straightforward application of the HLA Runtime Infrastructure's time synchronization mechanism.

关键词： Computer architecture

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Partitioned fluid–structure–acoustics interaction on distributed data: Numerical results and visualization

Partitioned fluid–structure–acoustics interaction on distr...

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International Conference on Software for Exascale Computing, SPPEXA 2015

作者： Blom, David Ertl, Thomas Fernandes, Oliver Frey, Steffen Klimach, Harald Krupp, Verena Mehl, Miriam Roller, Sabine Sternel, Dörte C. Uekermann, Benjamin Winter, Tilo van Zuijlen, Alexander Aerospace Engineering Delft University of Technology Delft Netherlands Scientific Computing in Computer Science Technical University of Munich München Germany Simulation Techniques and Scientific Computing University of Siegen Siegen Germany Institute for Parallel and Distributed Systems University of Stuttgart Stuttgart Germany VISUS University of Stuttgart Stuttgart Germany Institut for Scientific Computing TU Darmstadt Darmstadt Germany Institute of Numerical Methods in Mechanical Engineering TU Darmstadt Darmstadt Germany

ISBN: (纸本)9783319405261

We present a coupled simulation approach for fluid–structure–acoustic interactions (FSAI) as an example for strongly surface coupled multi-physics problems. In addition to the multi-physics character, FSAI feature multi-scale properties as a further challenge. In our partitioned approach, the problem is split into spatially separated subdomains interacting via coupling surfaces. Within each subdomain, scalable, single-physics solvers are used to solve the respective equation systems. The surface coupling between them is realized with the scalable open-source coupling tool preCICE described in the "Partitioned Fluid–Structure– Acoustics Interaction on distributed Data: Coupling via preCICE". We show how this approach enables the use of existing solvers and present the overall scaling behavior for a three-dimensional test case with a bending tower generating acoustic *** run this simulation with different solvers demonstrating the performance of various solvers and the flexibility of the partitioned approach with the coupling tool preCICE. An efficient and scalable in-situ visualization reducing the amount of data in place at the simulation processors before sending them over the network or to a file system completes the simulation environment. © Springer International Publishing Switzerland 2016.

关键词： Data visualization

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Towards realistic HPC models of the neuromuscular system

arXiv

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arXiv 2018年

作者： Bradley, Chris Emamy, Nehzat Ertl, Thomas Göddeke, Dominik Hessenthaler, Andreas Klotz, Thomas Krämer, Aaron Krone, Michael Maier, Benjamin Mehl, Miriam Rau, Tobias Röhrle, Oliver SimTech Research Group on Continuum Biomechanics and Mechanobiology University of Stuttgart Institute for Applied Analysis and Numerical Simulation University of Stuttgart Institute for Parallel and Distributed Systems University of Stuttgart University of Stuttgart Stuttgart Centre for Simulation Sciences University of Stuttgart Germany Auckland Bioengineering Institute University of Auckland New Zealand

Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow for a high flexibility and generality in model development. Flexibility and model development, however, are often a limiting factor for large-scale simulations. Therefore, new models are typically tested and run on small-scale compute facilities. By using a detailed biophysics-based, chemo-electromechanical skeletal muscle model and the international open-source software library OpenCMISS as an example, we present an approach to upgrade an existing muscle simulation framework from a moderately parallel version towards a massively parallel one that scales both in terms of problem size and in terms of the number of parallel processes. For this purpose, we investigate different modeling, algorithmic and implementational aspects. We present improvements addressing both numerical and parallel scalability. In addition, our approach includes a novel visualization environment, which is based on the MegaMol environment capable of handling large amounts of simulated data. It offers a platform for fast visualization prototyping, distributed rendering, and advanced visualization techniques. We present results of a variety of scaling studies at the Tier-1 supercomputer HazelHen at the High Performance Computing Center Stuttgart (HLRS). We improve the overall runtime by a factor of up to 2.6 and achieved good scalability on up to 768 cores, where the previous implementation used only 4 *** Codes 65L99, 65M99 Copyright © 2018, The Authors. All rights reserved.

关键词： Scalability

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Interoperating AutoSched AP using the High Level Architecture 05

Interoperating AutoSched AP using the High Level Architectur...

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simulation Winter Conference

作者： Boon Ping Gan P. Lendermann M. Yoke Hean Low S.J. Turner Xiaoguang Wang S.J.E. Taylor D-SIMLAB Programme Singapore Institute of Manufacturing Technology Singapore Singapore Parallel and Distributed Computing Centre Nanyang Technological University Singapore Singapore Centre for Applied Simulation Modeling School of Information Systems Computing and Mathematics Brunei University Uxbridge UK

ISBN: (纸本)9780780395190

The high Level Architecture (HLA) is an IEEE standard for interoperating simulation federates. In this paper, we describe a set of requirements that simulation packages need to satisfy in order to be made interoperable using the HLA standard. AutoSched AP, a commercial off-the-shelf simulation package (CSP) which is widely used in the semiconductor industry, was used as a case study for this interoperation exercise. We demonstrated that a straightforward customization of the CSP through a middleware that provides standard functions for interoperation may not provide a satisfactory solution. A specially optimized time synchronization mechanism needs to be installed to ensure good execution efficiency. Experimental results using a Borderless Fab model that comprises of two factory models show that an optimized time synchronization mechanism results in an execution time that is ten times better than a straightforward application of the HLA runtime infrastructure's time synchronization mechanism.

关键词： Chip scale packaging Business Gallium nitride Standards development Standards organizations Communication standards Computational modeling Semiconductor device packaging Electronics industry Production facilities

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Guidelines for commercial off-the-shelf simulation Package interoperability 08

Guidelines for commercial off-the-shelf Simulation Package i...

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simulation Winter Conference

作者： Simon J.E. Taylor Stephen J. Turner Steffen Strassburger Centre for Applied Simulation Modelling School of Information Systems Computing & Maths Brunei University Uxbridge Middlesex UK Parallel & Distributed Computing Centre School of Computer Engineering Nanyang Technological University Singapore School of Economic Sciences Technical University Ilmenau Ilmenau Germany

ISBN: (纸本)9781424427086

Commercial-off-the-shelf (COTS) simulation Packages (CSPs) are widely used visual interactive modeling environments such as Arena™, Anylogic™, Flexsim™, Simul8™, Witness™, etc. CSP Interoperability (or distributed simulation) is a technique that allows a simulation to be executed over several computers or for several simulations running on different computers to run together. This also relates to simulation languages such as SLX™ and GPSS/H™. There have been various attempts to interoperate these CSPs, some with the IEEE 1516 high level architecture (HLA). These can be quite complex and it is easy to loose track of exactly what is occurring between interoperating CSPs and their models. This paper introduces a set of interoperability reference models (IRMs), or design patters for CSP Interoperability, that can be used as guidelines to simplify the interoperability process.

关键词： Guidelines Computational modeling Computer simulation Discrete event simulation distributed computing Chip scale packaging Production facilities Concurrent computing Computer architecture Logistics

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Commercial-Off-The-Shelf simulation Package interoperability: Issues and futures 09

Commercial-Off-The-Shelf Simulation Package interoperability...

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simulation Winter Conference

作者： Simon J. E. Taylor Navonil Mustafee Stephen J. Turner Ke Pan Steffen Strassburger Centre of Applied Simulation Modelling School of Information Systems Computing & Maths Brunei University Uxbridge Middlesex UK Parallel & Distributed Computing Centre School of Computer Engineering Nanyang Technological University Singapore Singapore School of Economic Sciences Technical University Ilmenau Ilmenau Germany

ISBN: (纸本)9781424457717

Commercial-Off-The-Shelf simulation Packages (CSPs) are widely used in industry to simulate discrete-event models. Interoperability of CSPs requires the use of distributed simulation techniques. Literature presents us with many examples of achieving CSP interoperability using bespoke solutions. However, for the wider adoption of CSP-based distributed simulation it is essential that, first and foremost, a standard for CSP interoperability be created, and secondly, these standards are adhered to by the CSP vendors. This advanced tutorial is on an emerging standard relating to CSP interoperability. It gives an overview of this standard and presents case studies that implement some of the proposed standards. Furthermore, interoperability is discussed in relation to large and complex models developed using CSPs that require large amount of computing resources. It is hoped that this tutorial will inform the simulation community of the issues associated with CSP interoperability, the importance of these standards and its future.

关键词： Computational modeling Context modeling Computer simulation Chip scale packaging distributed computing Concurrent computing Logistics Computer languages Grid computing Information systems

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