3D multiphysics modeling of superconducting cavities with a massively parallel simulation suite
Directory of Open Access Journals (Sweden)
Oleksiy Kononenko
2017-10-01
Full Text Available Radiofrequency cavities based on superconducting technology are widely used in particle accelerators for various applications. The cavities usually have high quality factors and hence narrow bandwidths, so the field stability is sensitive to detuning from the Lorentz force and external loads, including vibrations and helium pressure variations. If not properly controlled, the detuning can result in a serious performance degradation of a superconducting accelerator, so an understanding of the underlying detuning mechanisms can be very helpful. Recent advances in the simulation suite ace3p have enabled realistic multiphysics characterization of such complex accelerator systems on supercomputers. In this paper, we present the new capabilities in ace3p for large-scale 3D multiphysics modeling of superconducting cavities, in particular, a parallel eigensolver for determining mechanical resonances, a parallel harmonic response solver to calculate the response of a cavity to external vibrations, and a numerical procedure to decompose mechanical loads, such as from the Lorentz force or piezoactuators, into the corresponding mechanical modes. These capabilities have been used to do an extensive rf-mechanical analysis of dressed TESLA-type superconducting cavities. The simulation results and their implications for the operational stability of the Linac Coherent Light Source-II are discussed.
Massive hybrid parallelism for fully implicit multiphysics
International Nuclear Information System (INIS)
Gaston, D. R.; Permann, C. J.; Andrs, D.; Peterson, J. W.
2013-01-01
As hardware advances continue to modify the supercomputing landscape, traditional scientific software development practices will become more outdated, ineffective, and inefficient. The process of rewriting/retooling existing software for new architectures is a Sisyphean task, and results in substantial hours of development time, effort, and money. Software libraries which provide an abstraction of the resources provided by such architectures are therefore essential if the computational engineering and science communities are to continue to flourish in this modern computing environment. The Multiphysics Object Oriented Simulation Environment (MOOSE) framework enables complex multiphysics analysis tools to be built rapidly by scientists, engineers, and domain specialists, while also allowing them to both take advantage of current HPC architectures, and efficiently prepare for future supercomputer designs. MOOSE employs a hybrid shared-memory and distributed-memory parallel model and provides a complete and consistent interface for creating multiphysics analysis tools. In this paper, a brief discussion of the mathematical algorithms underlying the framework and the internal object-oriented hybrid parallel design are given. Representative massively parallel results from several applications areas are presented, and a brief discussion of future areas of research for the framework are provided. (authors)
Massive hybrid parallelism for fully implicit multiphysics
Energy Technology Data Exchange (ETDEWEB)
Gaston, D. R.; Permann, C. J.; Andrs, D.; Peterson, J. W. [Idaho National Laboratory, 2525 N. Fremont Ave., Idaho Falls, ID 83415 (United States)
2013-07-01
As hardware advances continue to modify the supercomputing landscape, traditional scientific software development practices will become more outdated, ineffective, and inefficient. The process of rewriting/retooling existing software for new architectures is a Sisyphean task, and results in substantial hours of development time, effort, and money. Software libraries which provide an abstraction of the resources provided by such architectures are therefore essential if the computational engineering and science communities are to continue to flourish in this modern computing environment. The Multiphysics Object Oriented Simulation Environment (MOOSE) framework enables complex multiphysics analysis tools to be built rapidly by scientists, engineers, and domain specialists, while also allowing them to both take advantage of current HPC architectures, and efficiently prepare for future supercomputer designs. MOOSE employs a hybrid shared-memory and distributed-memory parallel model and provides a complete and consistent interface for creating multiphysics analysis tools. In this paper, a brief discussion of the mathematical algorithms underlying the framework and the internal object-oriented hybrid parallel design are given. Representative massively parallel results from several applications areas are presented, and a brief discussion of future areas of research for the framework are provided. (authors)
MASSIVE HYBRID PARALLELISM FOR FULLY IMPLICIT MULTIPHYSICS
Energy Technology Data Exchange (ETDEWEB)
Cody J. Permann; David Andrs; John W. Peterson; Derek R. Gaston
2013-05-01
As hardware advances continue to modify the supercomputing landscape, traditional scientific software development practices will become more outdated, ineffective, and inefficient. The process of rewriting/retooling existing software for new architectures is a Sisyphean task, and results in substantial hours of development time, effort, and money. Software libraries which provide an abstraction of the resources provided by such architectures are therefore essential if the computational engineering and science communities are to continue to flourish in this modern computing environment. The Multiphysics Object Oriented Simulation Environment (MOOSE) framework enables complex multiphysics analysis tools to be built rapidly by scientists, engineers, and domain specialists, while also allowing them to both take advantage of current HPC architectures, and efficiently prepare for future supercomputer designs. MOOSE employs a hybrid shared-memory and distributed-memory parallel model and provides a complete and consistent interface for creating multiphysics analysis tools. In this paper, a brief discussion of the mathematical algorithms underlying the framework and the internal object-oriented hybrid parallel design are given. Representative massively parallel results from several applications areas are presented, and a brief discussion of future areas of research for the framework are provided.
Poulet, Thomas; Paesold, Martin; Veveakis, Manolis
2017-03-01
Faults play a major role in many economically and environmentally important geological systems, ranging from impermeable seals in petroleum reservoirs to fluid pathways in ore-forming hydrothermal systems. Their behavior is therefore widely studied and fault mechanics is particularly focused on the mechanisms explaining their transient evolution. Single faults can change in time from seals to open channels as they become seismically active and various models have recently been presented to explain the driving forces responsible for such transitions. A model of particular interest is the multi-physics oscillator of Alevizos et al. (J Geophys Res Solid Earth 119(6), 4558-4582, 2014) which extends the traditional rate and state friction approach to rate and temperature-dependent ductile rocks, and has been successfully applied to explain spatial features of exposed thrusts as well as temporal evolutions of current subduction zones. In this contribution we implement that model in REDBACK, a parallel open-source multi-physics simulator developed to solve such geological instabilities in three dimensions. The resolution of the underlying system of equations in a tightly coupled manner allows REDBACK to capture appropriately the various theoretical regimes of the system, including the periodic and non-periodic instabilities. REDBACK can then be used to simulate the drastic permeability evolution in time of such systems, where nominally impermeable faults can sporadically become fluid pathways, with permeability increases of several orders of magnitude.
Parallel multiphysics algorithms and software for computational nuclear engineering
International Nuclear Information System (INIS)
Gaston, D; Hansen, G; Kadioglu, S; Knoll, D A; Newman, C; Park, H; Permann, C; Taitano, W
2009-01-01
There is a growing trend in nuclear reactor simulation to consider multiphysics problems. This can be seen in reactor analysis where analysts are interested in coupled flow, heat transfer and neutronics, and in fuel performance simulation where analysts are interested in thermomechanics with contact coupled to species transport and chemistry. These more ambitious simulations usually motivate some level of parallel computing. Many of the coupling efforts to date utilize simple code coupling or first-order operator splitting, often referred to as loose coupling. While these approaches can produce answers, they usually leave questions of accuracy and stability unanswered. Additionally, the different physics often reside on separate grids which are coupled via simple interpolation, again leaving open questions of stability and accuracy. Utilizing state of the art mathematics and software development techniques we are deploying next generation tools for nuclear engineering applications. The Jacobian-free Newton-Krylov (JFNK) method combined with physics-based preconditioning provide the underlying mathematical structure for our tools. JFNK is understood to be a modern multiphysics algorithm, but we are also utilizing its unique properties as a scale bridging algorithm. To facilitate rapid development of multiphysics applications we have developed the Multiphysics Object-Oriented Simulation Environment (MOOSE). Examples from two MOOSE-based applications: PRONGHORN, our multiphysics gas cooled reactor simulation tool and BISON, our multiphysics, multiscale fuel performance simulation tool will be presented.
Multiphysics simulations: Challenges and opportunities
Keyes, David E.; McInnes, Lois Curfman; Woodward, Carol S.; Gropp, William D.; Myra, Eric S.; Pernice, Michael; Bell, John B.; Brown, Jed; Clo, Alain M.; Connors, Jeffrey Mark; Constantinescu, Emil M.; Estep, Donald J.; Evans, Katherine J.; Farhat, Charbel H.; Hakim, Ammar H.; Hammond, Glenn E.; Hansen, Glen A.; Hill, Judith C.; Isaac, Tobin; Jiao, Xiangmin; Jordan, Kirk E.; Kaushik, Dinesh K.; Kaxiras, Efthimios; Koniges, Alice E.; Lee, Kihwan; Lott, Aaron; Lu, Qiming; Magerlein, John H.; Maxwell, Reed M.; McCourt, Michael J.; Mehl, Miriam; Pawlowski, Roger P.; Randles, Amanda Peters; Reynolds, Daniel R.; Riviè re, Bé atrice M.; Rü de, Ulrich; Scheibe, Timothy D.; Shadid, John N.; Sheehan, Brendan; Shephard, Mark S.; Siegel, Andrew R.; Smith, Barry F.; Tang, Xianzhu; Wilson, Cian R G; Wohlmuth, Barbara Ian
2013-01-01
We consider multiphysics applications from algorithmic and architectural perspectives, where "algorithmic" includes both mathematical analysis and computational complexity, and "architectural" includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities. © The Author(s) 2012.
Multiphysics simulations: Challenges and opportunities
Keyes, David E.
2013-02-01
We consider multiphysics applications from algorithmic and architectural perspectives, where "algorithmic" includes both mathematical analysis and computational complexity, and "architectural" includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities. © The Author(s) 2012.
Multiphysics simulations: challenges and opportunities.
Energy Technology Data Exchange (ETDEWEB)
Keyes, D.; McInnes, L. C.; Woodward, C.; Gropp, W.; Myra, E.; Pernice, M. (Mathematics and Computer Science); (KAUST and Columbia Univ.); (Lawrence Livermore National Laboratory); (Univ. of Illinois at Urbana-Champaign); (Univ. of Mich.); (Idaho National Lab.)
2012-11-29
This report is an outcome of the workshop Multiphysics Simulations: Challenges and Opportunities, sponsored by the Institute of Computing in Science (ICiS). Additional information about the workshop, including relevant reading and presentations on multiphysics issues in applications, algorithms, and software, is available via https://sites.google.com/site/icismultiphysics2011/. We consider multiphysics applications from algorithmic and architectural perspectives, where 'algorithmic' includes both mathematical analysis and computational complexity and 'architectural' includes both software and hardware environments. Many diverse multiphysics applications can be reduced, en route to their computational simulation, to a common algebraic coupling paradigm. Mathematical analysis of multiphysics coupling in this form is not always practical for realistic applications, but model problems representative of applications discussed herein can provide insight. A variety of software frameworks for multiphysics applications have been constructed and refined within disciplinary communities and executed on leading-edge computer systems. We examine several of these, expose some commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities. We also initiate a modest suite of test problems encompassing features present in many applications.
National Aeronautics and Space Administration — In this proposal, researchers from Cascade Technologies and Stanford University outline a multi-year research plan to develop large-eddy simulation (LES) tools to...
The Fluxgate Magnetometer Simulation in Comsol Multiphysics
Directory of Open Access Journals (Sweden)
Kolomeytsev Andrey
2018-01-01
Full Text Available This article describes the fluxgate magnetometer simulation in Comsol Multiphysics software package. The simulation results coincide with the experiment described earlier. Decomposition of the output signal by the Fourier coefficients shows a frequency doubling.
The Fluxgate Magnetometer Simulation in Comsol Multiphysics
Kolomeytsev Andrey; Baranov Pavel; Zatonov Ivan
2018-01-01
This article describes the fluxgate magnetometer simulation in Comsol Multiphysics software package. The simulation results coincide with the experiment described earlier. Decomposition of the output signal by the Fourier coefficients shows a frequency doubling.
Multiphysics simulation electromechanical system applications and optimization
Dede, Ercan M; Nomura, Tsuyoshi
2014-01-01
This book highlights a unique combination of numerical tools and strategies for handling the challenges of multiphysics simulation, with a specific focus on electromechanical systems as the target application. Features: introduces the concept of design via simulation, along with the role of multiphysics simulation in today's engineering environment; discusses the importance of structural optimization techniques in the design and development of electromechanical systems; provides an overview of the physics commonly involved with electromechanical systems for applications such as electronics, ma
Coupled multi-physics simulation frameworks for reactor simulation: A bottom-up approach
International Nuclear Information System (INIS)
Tautges, Timothy J.; Caceres, Alvaro; Jain, Rajeev; Kim, Hong-Jun; Kraftcheck, Jason A.; Smith, Brandon M.
2011-01-01
A 'bottom-up' approach to multi-physics frameworks is described, where first common interfaces to simulation data are developed, then existing physics modules are adapted to communicate through those interfaces. Physics modules read and write data through those common interfaces, which also provide access to common simulation services like parallel IO, mesh partitioning, etc.. Multi-physics codes are assembled as a combination of physics modules, services, interface implementations, and driver code which coordinates calling these various pieces. Examples of various physics modules and services connected to this framework are given. (author)
Concurrent, parallel, multiphysics coupling in the FACETS project
Energy Technology Data Exchange (ETDEWEB)
Cary, J R; Carlsson, J A; Hakim, A H; Kruger, S E; Miah, M; Pletzer, A; Shasharina, S [Tech-X Corporation, 5621 Arapahoe Avenue, Suite A, Boulder, CO 80303 (United States); Candy, J; Groebner, R J [General Atomics (United States); Cobb, J; Fahey, M R [Oak Ridge National Laboratory (United States); Cohen, R H; Epperly, T [Lawrence Livermore National Laboratory (United States); Estep, D J [Colorado State University (United States); Krasheninnikov, S [University of California at San Diego (United States); Malony, A D [ParaTools, Inc (United States); McCune, D C [Princeton Plasma Physics Laboratory (United States); McInnes, L; Balay, S [Argonne National Laboratory (United States); Pankin, A, E-mail: cary@txcorp.co [Lehigh University (United States)
2009-07-01
FACETS (Framework Application for Core-Edge Transport Simulations), is now in its third year. The FACETS team has developed a framework for concurrent coupling of parallel computational physics for use on Leadership Class Facilities (LCFs). In the course of the last year, FACETS has tackled many of the difficult problems of moving to parallel, integrated modeling by developing algorithms for coupled systems, extracting legacy applications as components, modifying them to run on LCFs, and improving the performance of all components. The development of FACETS abides by rigorous engineering standards, including cross platform build and test systems, with the latter covering regression, performance, and visualization. In addition, FACETS has demonstrated the ability to incorporate full turbulence computations for the highest fidelity transport computations. Early indications are that the framework, using such computations, scales to multiple tens of thousands of processors. These accomplishments were a result of an interdisciplinary collaboration among computational physics, computer scientists and applied mathematicians on the team.
Multiphysics Modelling and Simulation for Systems Design Conference
Abbes, Mohamed; Choley, Jean-Yves; Boukharouba, Taoufik; Elnady, Tamer; Kanaev, Andrei; Amar, Mounir; Chaari, Fakher
2015-01-01
This book reports on the state of the art in the field of multiphysics systems. It consists of accurately reviewed contributions to the MMSSD’2014 conference, which was held from December 17 to 19, 2004 in Hammamet, Tunisia. The different chapters, covering new theories, methods and a number of case studies, provide readers with an up-to-date picture of multiphysics modeling and simulation. They highlight the role played by high-performance computing and newly available software in promoting the study of multiphysics coupling effects, and show how these technologies can be practically implemented to bring about significant improvements in the field of design, control and monitoring of machines. In addition to providing a detailed description of the methods and their applications, the book also identifies new research issues, challenges and opportunities, thus providing researchers and practitioners with both technical information to support their daily work and a new source of inspiration for their future...
The Integrated Plasma Simulator: A Flexible Python Framework for Coupled Multiphysics Simulation
Energy Technology Data Exchange (ETDEWEB)
Foley, Samantha S [ORNL; Elwasif, Wael R [ORNL; Bernholdt, David E [ORNL
2011-11-01
High-fidelity coupled multiphysics simulations are an increasingly important aspect of computational science. In many domains, however, there has been very limited experience with simulations of this sort, therefore research in coupled multiphysics often requires computational frameworks with significant flexibility to respond to the changing directions of the physics and mathematics. This paper presents the Integrated Plasma Simulator (IPS), a framework designed for loosely coupled simulations of fusion plasmas. The IPS provides users with a simple component architecture into which a wide range of existing plasma physics codes can be inserted as components. Simulations can take advantage of multiple levels of parallelism supported in the IPS, and can be controlled by a high-level ``driver'' component, or by other coordination mechanisms, such as an asynchronous event service. We describe the requirements and design of the framework, and how they were implemented in the Python language. We also illustrate the flexibility of the framework by providing examples of different types of simulations that utilize various features of the IPS.
International Nuclear Information System (INIS)
Gaston, Derek; Guo, Luanjing; Hansen, Glen; Huang, Hai; Johnson, Richard; Park, HyeongKae; Podgorney, Robert; Tonks, Michael; Williamson, Richard
2012-01-01
There is a growing trend within energy and environmental simulation to consider tightly coupled solutions to multiphysics problems. This can be seen in nuclear reactor analysis where analysts are interested in coupled flow, heat transfer and neutronics, and in nuclear fuel performance simulation where analysts are interested in thermomechanics with contact coupled to species transport and chemistry. In energy and environmental applications, energy extraction involves geomechanics, flow through porous media and fractured formations, adding heat transport for enhanced oil recovery and geothermal applications, and adding reactive transport in the case of applications modeling the underground flow of contaminants. These more ambitious simulations usually motivate some level of parallel computing. Many of the physics coupling efforts to date utilize simple code coupling or first-order operator splitting, often referred to as loose coupling. While these approaches can produce answers, they usually leave questions of accuracy and stability unanswered. Additionally, the different physics often reside on distinct meshes and data are coupled via simple interpolation, again leaving open questions of stability and accuracy.
Quench Simulation of Superconducting Magnets with Commercial Multiphysics Software
AUTHOR|(SzGeCERN)751171; Auchmann, Bernhard; Jarkko, Niiranen; Maciejewski, Michal
The simulation of quenches in superconducting magnets is a multiphysics problem of highest complexity. Operated at 1.9 K above absolute zero, the material properties of superconductors and superfluid helium vary by several orders of magnitude over a range of only 10 K. The heat transfer from metal to helium goes through different transfer and boiling regimes as a function of temperature, heat flux, and transferred energy. Electrical, magnetic, thermal, and fluid dynamic effects are intimately coupled, yet live on vastly different time and spatial scales. While the physical models may be the same in all cases, it is an open debate whether the user should opt for commercial multiphysics software like ANSYS or COMSOL, write customized models based on general purpose network solvers like SPICE, or implement the physics models and numerical solvers entirely in custom software like the QP3, THEA, and ROXIE codes currently in use at the European Organisation for Nuclear Research (CERN). Each approach has its strengt...
A MULTIDIMENSIONAL AND MULTIPHYSICS APPROACH TO NUCLEAR FUEL BEHAVIOR SIMULATION
Energy Technology Data Exchange (ETDEWEB)
R. L. Williamson; J. D. Hales; S. R. Novascone; M. R. Tonks; D. R. Gaston; C. J. Permann; D. Andrs; R. C. Martineau
2012-04-01
Important aspects of fuel rod behavior, for example pellet-clad mechanical interaction (PCMI), fuel fracture, oxide formation, non-axisymmetric cooling, and response to fuel manufacturing defects, are inherently multidimensional in addition to being complicated multiphysics problems. Many current modeling tools are strictly 2D axisymmetric or even 1.5D. This paper outlines the capabilities of a new fuel modeling tool able to analyze either 2D axisymmetric or fully 3D models. These capabilities include temperature-dependent thermal conductivity of fuel; swelling and densification; fuel creep; pellet fracture; fission gas release; cladding creep; irradiation growth; and gap mechanics (contact and gap heat transfer). The need for multiphysics, multidimensional modeling is then demonstrated through a discussion of results for a set of example problems. The first, a 10-pellet rodlet, demonstrates the viability of the solution method employed. This example highlights the effect of our smeared cracking model and also shows the multidimensional nature of discrete fuel pellet modeling. The second example relies on our the multidimensional, multiphysics approach to analyze a missing pellet surface problem. As a final example, we show a lower-length-scale simulation coupled to a continuum-scale simulation.
IMPETUS - Interactive MultiPhysics Environment for Unified Simulations.
Ha, Vi Q; Lykotrafitis, George
2016-12-08
We introduce IMPETUS - Interactive MultiPhysics Environment for Unified Simulations, an object oriented, easy-to-use, high performance, C++ program for three-dimensional simulations of complex physical systems that can benefit a large variety of research areas, especially in cell mechanics. The program implements cross-communication between locally interacting particles and continuum models residing in the same physical space while a network facilitates long-range particle interactions. Message Passing Interface is used for inter-processor communication for all simulations. Copyright © 2016 Elsevier Ltd. All rights reserved.
Practical integrated simulation systems for coupled numerical simulations in parallel
Energy Technology Data Exchange (ETDEWEB)
Osamu, Hazama; Zhihong, Guo [Japan Atomic Energy Research Inst., Centre for Promotion of Computational Science and Engineering, Tokyo (Japan)
2003-07-01
In order for the numerical simulations to reflect 'real-world' phenomena and occurrences, incorporation of multidisciplinary and multi-physics simulations considering various physical models and factors are becoming essential. However, there still exist many obstacles which inhibit such numerical simulations. For example, it is still difficult in many instances to develop satisfactory software packages which allow for such coupled simulations and such simulations will require more computational resources. A precise multi-physics simulation today will require parallel processing which again makes it a complicated process. Under the international cooperative efforts between CCSE/JAERI and Fraunhofer SCAI, a German institute, a library called the MpCCI, or Mesh-based Parallel Code Coupling Interface, has been implemented together with a library called STAMPI to couple two existing codes to develop an 'integrated numerical simulation system' intended for meta-computing environments. (authors)
High-Fidelity Space-Time Adaptive Multiphysics Simulations in Nuclear Engineering
Energy Technology Data Exchange (ETDEWEB)
Solin, Pavel [Univ. of Reno, NV (United States); Ragusa, Jean [Texas A & M Univ., College Station, TX (United States)
2014-03-09
We delivered a series of fundamentally new computational technologies that have the potential to significantly advance the state-of-the-art of computer simulations of transient multiphysics nuclear reactor processes. These methods were implemented in the form of a C++ library, and applied to a number of multiphysics coupled problems relevant to nuclear reactor simulations.
High-Fidelity Space-Time Adaptive Multiphysics Simulations in Nuclear Engineering
International Nuclear Information System (INIS)
Solin, Pavel; Ragusa, Jean
2014-01-01
We delivered a series of fundamentally new computational technologies that have the potential to significantly advance the state-of-the-art of computer simulations of transient multiphysics nuclear reactor processes. These methods were implemented in the form of a C++ library, and applied to a number of multiphysics coupled problems relevant to nuclear reactor simulations.
An approach for coupled-code multiphysics core simulations from a common input
International Nuclear Information System (INIS)
Schmidt, Rodney; Belcourt, Kenneth; Hooper, Russell; Pawlowski, Roger; Clarno, Kevin; Simunovic, Srdjan; Slattery, Stuart; Turner, John; Palmtag, Scott
2015-01-01
Highlights: • We describe an approach for coupled-code multiphysics reactor core simulations. • The approach can enable tight coupling of distinct physics codes with a common input. • Multi-code multiphysics coupling and parallel data transfer issues are explained. • The common input approach and how the information is processed is described. • Capabilities are demonstrated on an eigenvalue and power distribution calculation. - Abstract: This paper describes an approach for coupled-code multiphysics reactor core simulations that is being developed by the Virtual Environment for Reactor Applications (VERA) project in the Consortium for Advanced Simulation of Light-Water Reactors (CASL). In this approach a user creates a single problem description, called the “VERAIn” common input file, to define and setup the desired coupled-code reactor core simulation. A preprocessing step accepts the VERAIn file and generates a set of fully consistent input files for the different physics codes being coupled. The problem is then solved using a single-executable coupled-code simulation tool applicable to the problem, which is built using VERA infrastructure software tools and the set of physics codes required for the problem of interest. The approach is demonstrated by performing an eigenvalue and power distribution calculation of a typical three-dimensional 17 × 17 assembly with thermal–hydraulic and fuel temperature feedback. All neutronics aspects of the problem (cross-section calculation, neutron transport, power release) are solved using the Insilico code suite and are fully coupled to a thermal–hydraulic analysis calculated by the Cobra-TF (CTF) code. The single-executable coupled-code (Insilico-CTF) simulation tool is created using several VERA tools, including LIME (Lightweight Integrating Multiphysics Environment for coupling codes), DTK (Data Transfer Kit), Trilinos, and TriBITS. Parallel calculations are performed on the Titan supercomputer at Oak
Parallel discrete event simulation
Overeinder, B.J.; Hertzberger, L.O.; Sloot, P.M.A.; Withagen, W.J.
1991-01-01
In simulating applications for execution on specific computing systems, the simulation performance figures must be known in a short period of time. One basic approach to the problem of reducing the required simulation time is the exploitation of parallelism. However, in parallelizing the simulation
Parallel Atomistic Simulations
Energy Technology Data Exchange (ETDEWEB)
HEFFELFINGER,GRANT S.
2000-01-18
Algorithms developed to enable the use of atomistic molecular simulation methods with parallel computers are reviewed. Methods appropriate for bonded as well as non-bonded (and charged) interactions are included. While strategies for obtaining parallel molecular simulations have been developed for the full variety of atomistic simulation methods, molecular dynamics and Monte Carlo have received the most attention. Three main types of parallel molecular dynamics simulations have been developed, the replicated data decomposition, the spatial decomposition, and the force decomposition. For Monte Carlo simulations, parallel algorithms have been developed which can be divided into two categories, those which require a modified Markov chain and those which do not. Parallel algorithms developed for other simulation methods such as Gibbs ensemble Monte Carlo, grand canonical molecular dynamics, and Monte Carlo methods for protein structure determination are also reviewed and issues such as how to measure parallel efficiency, especially in the case of parallel Monte Carlo algorithms with modified Markov chains are discussed.
Parallel reservoir simulator computations
International Nuclear Information System (INIS)
Hemanth-Kumar, K.; Young, L.C.
1995-01-01
The adaptation of a reservoir simulator for parallel computations is described. The simulator was originally designed for vector processors. It performs approximately 99% of its calculations in vector/parallel mode and relative to scalar calculations it achieves speedups of 65 and 81 for black oil and EOS simulations, respectively on the CRAY C-90
International Nuclear Information System (INIS)
Salko, Robert K.; Schmidt, Rodney C.; Avramova, Maria N.
2015-01-01
Highlights: • COBRA-TF was adopted by the Consortium for Advanced Simulation of LWRs. • We have improved code performance to support running large-scale LWR simulations. • Code optimization has led to reductions in execution time and memory usage. • An MPI parallelization has reduced full-core simulation time from days to minutes. - Abstract: This paper describes major improvements to the computational infrastructure of the CTF subchannel code so that full-core, pincell-resolved (i.e., one computational subchannel per real bundle flow channel) simulations can now be performed in much shorter run-times, either in stand-alone mode or as part of coupled-code multi-physics calculations. These improvements support the goals of the Department Of Energy Consortium for Advanced Simulation of Light Water Reactors (CASL) Energy Innovation Hub to develop high fidelity multi-physics simulation tools for nuclear energy design and analysis. A set of serial code optimizations—including fixing computational inefficiencies, optimizing the numerical approach, and making smarter data storage choices—are first described and shown to reduce both execution time and memory usage by about a factor of ten. Next, a “single program multiple data” parallelization strategy targeting distributed memory “multiple instruction multiple data” platforms utilizing domain decomposition is presented. In this approach, data communication between processors is accomplished by inserting standard Message-Passing Interface (MPI) calls at strategic points in the code. The domain decomposition approach implemented assigns one MPI process to each fuel assembly, with each domain being represented by its own CTF input file. The creation of CTF input files, both for serial and parallel runs, is also fully automated through use of a pressurized water reactor (PWR) pre-processor utility that uses a greatly simplified set of user input compared with the traditional CTF input. To run CTF in
Multiphysics simulation of thermal phenomena in direct laser metal powder deposition
CSIR Research Space (South Africa)
Pityana, SL
2016-11-01
Full Text Available presents on two dimensional multi-physics models to describe the physical mechanism of heat transfer, melting and solidification that take place during and post laser-powder interaction. The simulated transient temperature profile, the geometrical features...
Multi-Physics Simulation of TREAT Kinetics using MAMMOTH
Energy Technology Data Exchange (ETDEWEB)
DeHart, Mark; Gleicher, Frederick; Ortensi, Javier; Alberti, Anthony; Palmer, Todd
2015-11-01
With the advent of next generation reactor systems and new fuel designs, the U.S. Department of Energy (DOE) has identified the need for the resumption of transient testing of nuclear fuels. DOE has decided that the Transient Reactor Test Facility (TREAT) at Idaho National Laboratory (INL) is best suited for future testing. TREAT is a thermal neutron spectrum nuclear test facility that is designed to test nuclear fuels in transient scenarios. These specific fuels transient tests range from simple temperature transients to full fuel melt accidents. The current TREAT core is driven by highly enriched uranium (HEU) dispersed in a graphite matrix (1:10000 U-235/C atom ratio). At the center of the core, fuel is removed allowing for the insertion of an experimental test vehicle. TREAT’s design provides experimental flexibility and inherent safety during neutron pulsing. This safety stems from the graphite in the driver fuel having a strong negative temperature coefficient of reactivity resulting from a thermal Maxwellian shift with increased leakage, as well as graphite acting as a temperature sink. Air cooling is available, but is generally used post-transient for heat removal. DOE and INL have expressed a desire to develop a simulation capability that will accurately model the experiments before they are irradiated at the facility, with an emphasis on effective and safe operation while minimizing experimental time and cost. At INL, the Multi-physics Object Oriented Simulation Environment (MOOSE) has been selected as the model development framework for this work. This paper describes the results of preliminary simulations of a TREAT fuel element under transient conditions using the MOOSE-based MAMMOTH reactor physics tool.
Massively parallel multicanonical simulations
Gross, Jonathan; Zierenberg, Johannes; Weigel, Martin; Janke, Wolfhard
2018-03-01
Generalized-ensemble Monte Carlo simulations such as the multicanonical method and similar techniques are among the most efficient approaches for simulations of systems undergoing discontinuous phase transitions or with rugged free-energy landscapes. As Markov chain methods, they are inherently serial computationally. It was demonstrated recently, however, that a combination of independent simulations that communicate weight updates at variable intervals allows for the efficient utilization of parallel computational resources for multicanonical simulations. Implementing this approach for the many-thread architecture provided by current generations of graphics processing units (GPUs), we show how it can be efficiently employed with of the order of 104 parallel walkers and beyond, thus constituting a versatile tool for Monte Carlo simulations in the era of massively parallel computing. We provide the fully documented source code for the approach applied to the paradigmatic example of the two-dimensional Ising model as starting point and reference for practitioners in the field.
An introduction to LIME 1.0 and its use in coupling codes for multiphysics simulations.
Energy Technology Data Exchange (ETDEWEB)
Belcourt, Noel; Pawlowski, Roger Patrick; Schmidt, Rodney Cannon; Hooper, Russell Warren
2011-11-01
LIME is a small software package for creating multiphysics simulation codes. The name was formed as an acronym denoting 'Lightweight Integrating Multiphysics Environment for coupling codes.' LIME is intended to be especially useful when separate computer codes (which may be written in any standard computer language) already exist to solve different parts of a multiphysics problem. LIME provides the key high-level software (written in C++), a well defined approach (with example templates), and interface requirements to enable the assembly of multiple physics codes into a single coupled-multiphysics simulation code. In this report we introduce important software design characteristics of LIME, describe key components of a typical multiphysics application that might be created using LIME, and provide basic examples of its use - including the customized software that must be written by a user. We also describe the types of modifications that may be needed to individual physics codes in order for them to be incorporated into a LIME-based multiphysics application.
Xyce parallel electronic simulator.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Rankin, Eric Lamont; Schiek, Richard Louis; Thornquist, Heidi K.; Fixel, Deborah A.; Coffey, Todd S; Pawlowski, Roger P; Santarelli, Keith R.
2010-05-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide.
Energy Technology Data Exchange (ETDEWEB)
Matthew Ellis; Derek Gaston; Benoit Forget; Kord Smith
2011-07-01
In recent years the use of Monte Carlo methods for modeling reactors has become feasible due to the increasing availability of massively parallel computer systems. One of the primary challenges yet to be fully resolved, however, is the efficient and accurate inclusion of multiphysics feedback in Monte Carlo simulations. The research in this paper presents a preliminary coupling of the open source Monte Carlo code OpenMC with the open source Multiphysics Object-Oriented Simulation Environment (MOOSE). The coupling of OpenMC and MOOSE will be used to investigate efficient and accurate numerical methods needed to include multiphysics feedback in Monte Carlo codes. An investigation into the sensitivity of Doppler feedback to fuel temperature approximations using a two dimensional 17x17 PWR fuel assembly is presented in this paper. The results show a functioning multiphysics coupling between OpenMC and MOOSE. The coupling utilizes Functional Expansion Tallies to accurately and efficiently transfer pin power distributions tallied in OpenMC to unstructured finite element meshes used in MOOSE. The two dimensional PWR fuel assembly case also demonstrates that for a simplified model the pin-by-pin doppler feedback can be adequately replicated by scaling a representative pin based on pin relative powers.
Nuclear reactor multi-physics simulations with coupled MCNP5 and STAR-CCM+
International Nuclear Information System (INIS)
Cardoni, Jeffrey Neil; Rizwan-uddin
2011-01-01
The MCNP5 Monte Carlo particle transport code has been coupled to the computational fluid dynamics code, STAR-CCM+, to provide a high fidelity multi-physics simulation tool for pressurized water nuclear reactors. The codes are executed separately and coupled externally through a Perl script. The Perl script automates the exchange of temperature, density, and volumetric heating information between the codes using ASCII text data files. Fortran90 and Java utility programs assist job automation with data post-processing and file management. The MCNP5 utility code, MAKXSF, pre-generates temperature dependent cross section libraries for the thermal feedback calculations. The MCNP5–STAR-CCM+ coupled simulation tool, dubbed MULTINUKE, was applied to a steady state, PWR cell model to demonstrate its usage and capabilities. The demonstration calculation showed reasonable results that agree with PWR values typically reported in literature. Temperature and fission reaction rate distributions were realistic and intuitive. Reactivity coefficients were also deemed reasonable in comparison to historically reported data. The demonstration problem consisted of 9,984 CFD cells and 7,489 neutronic cells. MCNP5 tallied fission energy deposition over 3,328 UO_2 cells. The coupled solution converged within eight hours and in three MULTINUKE iterations. The simulation was carried out on a 64 bit, quad core, Intel 2.8 GHz microprocessor with 1 GB RAM. The simulations on a quad core machine indicated that a massively parallelized implementation of MULTINUKE can be used to assess larger multi-million cell models. (author)
Multiphysics simulation by design for electrical machines, power electronics and drives
Rosu, Marius; Lin, Dingsheng; Ionel, Dan M; Popescu, Mircea; Blaabjerg, Frede; Rallabandi, Vandana; Staton, David
2018-01-01
This book combines the knowledge of experts from both academia and the software industry to present theories of multiphysics simulation by design for electrical machines, power electronics, and drives. The comprehensive design approach described within supports new applications required by technologies sustaining high drive efficiency. The highlighted framework considers the electric machine at the heart of the entire electric drive. The book also emphasizes the simulation by design concept--a concept that frames the entire highlighted design methodology, which is described and illustrated by various advanced simulation technologies. Multiphysics Simulation by Design for Electrical Machines, Power Electronics and Drives begins with the basics of electrical machine design and manufacturing tolerances. It also discusses fundamental aspects of the state of the art design process and includes examples from industrial practice. It explains FEM-based analysis techniques for electrical machine design--providing deta...
International Nuclear Information System (INIS)
Mo Zeyao
2004-11-01
Multiphysics parallel numerical simulations are usually essential to simplify researches on complex physical phenomena in which several physics are tightly coupled. It is very important on how to concatenate those coupled physics for fully scalable parallel simulation. Meanwhile, three objectives should be balanced, the first is efficient data transfer among simulations, the second and the third are efficient parallel executions and simultaneously developments of those simulation codes. Two concatenating algorithms for multiphysics parallel numerical simulations coupling radiation hydrodynamics with neutron transport on unstructured grid are presented. The first algorithm, Fully Loosely Concatenation (FLC), focuses on the independence of code development and the independence running with optimal performance of code. The second algorithm. Two Level Tightly Concatenation (TLTC), focuses on the optimal tradeoffs among above three objectives. Theoretical analyses for communicational complexity and parallel numerical experiments on hundreds of processors on two parallel machines have showed that these two algorithms are efficient and can be generalized to other multiphysics parallel numerical simulations. In especial, algorithm TLTC is linearly scalable and has achieved the optimal parallel performance. (authors)
Multiphysical Simulation of PT-CT Contact with Outer Boundary Condition
Energy Technology Data Exchange (ETDEWEB)
Chang, Se-Myong [Kunsan National Univ., Gunsan (Korea, Republic of); Kim, Hyoung Tae [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)
2016-10-15
The present study is about preliminary calculation results for these ICSP activity works, where the COMSOL Multiphysics code is used to simulate plastic deformation of a pressure tube as a result of the interaction of stress and temperature. It is shown that the thermal stress model of COMSOL is compatible to simulate the multiple heat transfers (including the radiation heat transfer and heat conduction) and stress strain in the simplified 2-D problem. The benchmark test result for radiation heat transfer is in good agreement with the analytical solution for the concentric configuration of PT(pressure tube) and CT(calandria tube). In this paper, the authors did an open computation of these multi-physical phenomena by changing the outer boundary condition of CT according to the experimental result of ICSP. A series of simulation has been done based on the benchmark test proposed by IAEA/ICSP. The unsteady multi-physics was treated some numerical models with COMSOL. The comparison with CATHENA code is verified as a good agreement as we increase the accuracy of numerical method, Gaussian quadrature. The open computation for the validation of this numerical code is still on-going, and the temperature inside and outside the PT shows a very good agreement.
Multiphysical Simulation of PT-CT Contact with Outer Boundary Condition
International Nuclear Information System (INIS)
Chang, Se-Myong; Kim, Hyoung Tae
2016-01-01
The present study is about preliminary calculation results for these ICSP activity works, where the COMSOL Multiphysics code is used to simulate plastic deformation of a pressure tube as a result of the interaction of stress and temperature. It is shown that the thermal stress model of COMSOL is compatible to simulate the multiple heat transfers (including the radiation heat transfer and heat conduction) and stress strain in the simplified 2-D problem. The benchmark test result for radiation heat transfer is in good agreement with the analytical solution for the concentric configuration of PT(pressure tube) and CT(calandria tube). In this paper, the authors did an open computation of these multi-physical phenomena by changing the outer boundary condition of CT according to the experimental result of ICSP. A series of simulation has been done based on the benchmark test proposed by IAEA/ICSP. The unsteady multi-physics was treated some numerical models with COMSOL. The comparison with CATHENA code is verified as a good agreement as we increase the accuracy of numerical method, Gaussian quadrature. The open computation for the validation of this numerical code is still on-going, and the temperature inside and outside the PT shows a very good agreement
An Undergraduate Course in Modeling and Simulation of Multiphysics Systems
Ortiz-Rodriguez, Estanislao; Vazquez-Arenas, Jorge; Ricardez-Sandoval, Luis A.
2010-01-01
An overview of a course on modeling and simulation offered at the Nanotechnology Engineering undergraduate program at the University of Waterloo. The motivation for having this course in the undergraduate nanotechnology curriculum, the course structure, and its learning objectives are discussed. Further, one of the computational laboratories…
Full Core Multiphysics Simulation with Offline Mesh Deformation
Energy Technology Data Exchange (ETDEWEB)
Merzari, E. [Argonne National Lab. (ANL), Argonne, IL (United States); Shemon, E. R. [Argonne National Lab. (ANL), Argonne, IL (United States); Yu, Y. [Argonne National Lab. (ANL), Argonne, IL (United States); Thomas, J. W. [Argonne National Lab. (ANL), Argonne, IL (United States); Obabko, A. [Argonne National Lab. (ANL), Argonne, IL (United States); Jain, Rajeev [Argonne National Lab. (ANL), Argonne, IL (United States); Mahadevan, Vijay [Argonne National Lab. (ANL), Argonne, IL (United States); Solberg, Jerome [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ferencz, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Whitesides, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-12-21
In this report, building on previous reports issued in FY13 we describe our continued efforts to integrate thermal/hydraulics, neutronics, and structural mechanics modeling codes to perform coupled analysis of a representative fast sodium-cooled reactor core. The focus of the present report is a full core simulation with off-line mesh deformation.
Ventilation Structure Improvement of Induction Motor Using Multiphysics Simulations
Directory of Open Access Journals (Sweden)
Tao Huang
2012-09-01
Full Text Available Temperature rise analysis has significant impact in the design of air-cooled asynchronous induction motor. However, the affection cannot be accurately evaluated by using traditional empirical curves method due to the complexity of the inductor architecture. Considering Joules losses in stator windings and the induced eddy current in squirrel cages, and heat dissipation by air convection and solid conduction, in this paper a 3-D coupled-field finite-element method (FEM is investigated to demonstrate the temperature distribution. The Joules losses calculated by 3-D eddy- current field analysis are used as the input for the thermal field analysis, which is deeply dependent on accurate air fluid field analysis. A novel multi-component fluid model is employed to deal with the influence of rotor rotation upon the air convection. The simulation results show the fatal influence of the ventilation structure and the effectiveness of the proposed cooling improvement way.
Advanced graphical user interface for multi-physics simulations using AMST
Hoffmann, Florian; Vogel, Frank
2017-07-01
Numerical modelling of particulate matter has gained much popularity in recent decades. Advanced Multi-physics Simulation Technology (AMST) is a state-of-the-art three dimensional numerical modelling technique combining the eX-tended Discrete Element Method (XDEM) with Computational Fluid Dynamics (CFD) and Finite Element Analysis (FEA) [1]. One major limitation of this code is the lack of a graphical user interface (GUI) meaning that all pre-processing has to be made directly in a HDF5-file. This contribution presents the first graphical pre-processor developed for AMST.
Massively parallel quantum computer simulator
De Raedt, K.; Michielsen, K.; De Raedt, H.; Trieu, B.; Arnold, G.; Richter, M.; Lippert, Th.; Watanabe, H.; Ito, N.
2007-01-01
We describe portable software to simulate universal quantum computers on massive parallel Computers. We illustrate the use of the simulation software by running various quantum algorithms on different computer architectures, such as a IBM BlueGene/L, a IBM Regatta p690+, a Hitachi SR11000/J1, a Cray
A Multi-Physics simulation of the Reactor Core using CUPID/MASTER
International Nuclear Information System (INIS)
Lee, Jae Ryong; Cho, Hyoung Kyu; Yoon, Han Young; Cho, Jin Young; Jeong, Jae Jun
2011-01-01
KAERI has been developing a component-scale thermal hydraulics code, CUPID. The aim of the code is for multi-dimensional, multi-physics and multi-scale thermal hydraulics analysis. In our previous papers, the CUPID code has proved to be able to reproduce multidimensional thermal hydraulic analysis by validated with various conceptual problems and experimental data. For the numerical closure, it adopts a three dimensional, transient, two-phase and three-field model, and includes physical models and correlations of the interfacial mass, momentum, and energy transfer. For the multi-scale analysis, the CUPID is on progress to merge into system-scale thermal hydraulic code, MARS. In the present paper, a multi-physics simulation was performed by coupling the CUPID with three dimensional neutron kinetics code, MASTER. The MASTER is merged into the CUPID as a dynamic link library (DLL). The APR1400 reactor core during control rod drop/ejection accident was simulated as an example by adopting a porous media approach to employ fuel assembly. The following sections present the numerical modeling for the reactor core, coupling of the kinetics code, and the simulation results
Multi-Physics Demonstration Problem with the SHARP Reactor Simulation Toolkit
Energy Technology Data Exchange (ETDEWEB)
Merzari, E. [Argonne National Lab. (ANL), Argonne, IL (United States); Shemon, E. R. [Argonne National Lab. (ANL), Argonne, IL (United States); Yu, Y. Q. [Argonne National Lab. (ANL), Argonne, IL (United States); Thomas, J. W. [Argonne National Lab. (ANL), Argonne, IL (United States); Obabko, A. [Argonne National Lab. (ANL), Argonne, IL (United States); Jain, Rajeev [Argonne National Lab. (ANL), Argonne, IL (United States); Mahadevan, Vijay [Argonne National Lab. (ANL), Argonne, IL (United States); Tautges, Timothy [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Solberg, Jerome [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Ferencz, Robert Mark [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Whitesides, R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-12-21
This report describes to employ SHARP to perform a first-of-a-kind analysis of the core radial expansion phenomenon in an SFR. This effort required significant advances in the framework Multi-Physics Demonstration Problem with the SHARP Reactor Simulation Toolkit used to drive the coupled simulations, manipulate the mesh in response to the deformation of the geometry, and generate the necessary modified mesh files. Furthermore, the model geometry is fairly complex, and consistent mesh generation for the three physics modules required significant effort. Fully-integrated simulations of a 7-assembly mini-core test problem have been performed, and the results are presented here. Physics models of a full-core model of the Advanced Burner Test Reactor have also been developed for each of the three physics modules. Standalone results of each of the three physics modules for the ABTR are presented here, which provides a demonstration of the feasibility of the fully-integrated simulation.
Multi-physic simulations of irradiation experiments in a technological irradiation reactor
International Nuclear Information System (INIS)
Bonaccorsi, Th.
2007-09-01
A Material Testing Reactor (MTR) makes it possible to irradiate material samples under intense neutron and photonic fluxes. These experiments are carried out in experimental devices localised in the reactor core or in periphery (reflector). Available physics simulation tools only treat, most of the time, one physics field in a very precise way. Multi-physic simulations of irradiation experiments therefore require a sequential use of several calculation codes and data exchanges between these codes: this corresponds to problems coupling. In order to facilitate multi-physic simulations, this thesis sets up a data model based on data-processing objects, called Technological Entities. This data model is common to all of the physics fields. It permits defining the geometry of an irradiation device in a parametric way and to associate information about materials to it. Numerical simulations are encapsulated into interfaces providing the ability to call specific functionalities with the same command (to initialize data, to launch calculations, to post-treat, to get results,... ). Thus, once encapsulated, numerical simulations can be re-used for various studies. This data model is developed in a SALOME platform component. The first application case made it possible to perform neutronic simulations (OSIRIS reactor and RJH) coupled with fuel behavior simulations. In a next step, thermal hydraulics could also be taken into account. In addition to the improvement of the calculation accuracy due to the physical phenomena coupling, the time spent in the development phase of the simulation is largely reduced and the possibilities of uncertainty treatment are under consideration. (author)
Energy Technology Data Exchange (ETDEWEB)
Kim, Seung Jun [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Buechler, Cynthia Eileen [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
2017-07-17
The current study aims to predict the steady state power of a generic solution vessel and to develop a corresponding heat transfer coefficient correlation for a Moly99 production facility by conducting a fully coupled multi-physics simulation. A prediction of steady state power for the current application is inherently interconnected between thermal hydraulic characteristics (i.e. Multiphase computational fluid dynamics solved by ANSYS-Fluent 17.2) and the corresponding neutronic behavior (i.e. particle transport solved by MCNP6.2) in the solution vessel. Thus, the development of a coupling methodology is vital to understand the system behavior at a variety of system design and postulated operating scenarios. In this study, we report on the k-effective (keff) calculation for the baseline solution vessel configuration with a selected solution concentration using MCNP K-code modeling. The associated correlation of thermal properties (e.g. density, viscosity, thermal conductivity, specific heat) at the selected solution concentration are developed based on existing experimental measurements in the open literature. The numerical coupling methodology between multiphase CFD and MCNP is successfully demonstrated, and the detailed coupling procedure is documented. In addition, improved coupling methods capturing realistic physics in the solution vessel thermal-neutronic dynamics are proposed and tested further (i.e. dynamic height adjustment, mull-cell approach). As a key outcome of the current study, a multi-physics coupling methodology between MCFD and MCNP is demonstrated and tested for four different operating conditions. Those different operating conditions are determined based on the neutron source strength at a fixed geometry condition. The steady state powers for the generic solution vessel at various operating conditions are reported, and a generalized correlation of the heat transfer coefficient for the current application is discussed. The assessment of multi-physics
Parallel PDE-Based Simulations Using the Common Component Architecture
International Nuclear Information System (INIS)
McInnes, Lois C.; Allan, Benjamin A.; Armstrong, Robert; Benson, Steven J.; Bernholdt, David E.; Dahlgren, Tamara L.; Diachin, Lori; Krishnan, Manoj Kumar; Kohl, James A.; Larson, J. Walter; Lefantzi, Sophia; Nieplocha, Jarek; Norris, Boyana; Parker, Steven G.; Ray, Jaideep; Zhou, Shujia
2006-01-01
The complexity of parallel PDE-based simulations continues to increase as multimodel, multiphysics, and multi-institutional projects become widespread. A goal of component based software engineering in such large-scale simulations is to help manage this complexity by enabling better interoperability among various codes that have been independently developed by different groups. The Common Component Architecture (CCA) Forum is defining a component architecture specification to address the challenges of high-performance scientific computing. In addition, several execution frameworks, supporting infrastructure, and general purpose components are being developed. Furthermore, this group is collaborating with others in the high-performance computing community to design suites of domain-specific component interface specifications and underlying implementations. This chapter discusses recent work on leveraging these CCA efforts in parallel PDE-based simulations involving accelerator design, climate modeling, combustion, and accidental fires and explosions. We explain how component technology helps to address the different challenges posed by each of these applications, and we highlight how component interfaces built on existing parallel toolkits facilitate the reuse of software for parallel mesh manipulation, discretization, linear algebra, integration, optimization, and parallel data redistribution. We also present performance data to demonstrate the suitability of this approach, and we discuss strategies for applying component technologies to both new and existing applications
International Nuclear Information System (INIS)
Yue Liyang; Wang Zengbo; Li Lin
2012-01-01
Light could interact differently with thin-film contaminants and particle contaminates because of their different surface morphologies. In the case of dry laser cleaning of small transparent particles, it is well known that particles could function like mini-lenses, causing a localized near-field hot spot effect on the cleaning process. This paper looks into a special, yet important, phenomenon of dry laser cleaning of particles trapped in micro-sized slots. The effects of slot size, particle size and particle aggregate states in the cleaning process have been theoretically investigated, based on a coupled electromagnetic-thermal-mechanical multiphysics modelling and simulation approach. The study is important for the development and optimization of laser cleaning processes for contamination removal from cracks and slots. (paper)
Xyce parallel electronic simulator design.
Energy Technology Data Exchange (ETDEWEB)
Thornquist, Heidi K.; Rankin, Eric Lamont; Mei, Ting; Schiek, Richard Louis; Keiter, Eric Richard; Russo, Thomas V.
2010-09-01
This document is the Xyce Circuit Simulator developer guide. Xyce has been designed from the 'ground up' to be a SPICE-compatible, distributed memory parallel circuit simulator. While it is in many respects a research code, Xyce is intended to be a production simulator. As such, having software quality engineering (SQE) procedures in place to insure a high level of code quality and robustness are essential. Version control, issue tracking customer support, C++ style guildlines and the Xyce release process are all described. The Xyce Parallel Electronic Simulator has been under development at Sandia since 1999. Historically, Xyce has mostly been funded by ASC, the original focus of Xyce development has primarily been related to circuits for nuclear weapons. However, this has not been the only focus and it is expected that the project will diversify. Like many ASC projects, Xyce is a group development effort, which involves a number of researchers, engineers, scientists, mathmaticians and computer scientists. In addition to diversity of background, it is to be expected on long term projects for there to be a certain amount of staff turnover, as people move on to different projects. As a result, it is very important that the project maintain high software quality standards. The point of this document is to formally document a number of the software quality practices followed by the Xyce team in one place. Also, it is hoped that this document will be a good source of information for new developers.
Synchronization Techniques in Parallel Discrete Event Simulation
Lindén, Jonatan
2018-01-01
Discrete event simulation is an important tool for evaluating system models in many fields of science and engineering. To improve the performance of large-scale discrete event simulations, several techniques to parallelize discrete event simulation have been developed. In parallel discrete event simulation, the work of a single discrete event simulation is distributed over multiple processing elements. A key challenge in parallel discrete event simulation is to ensure that causally dependent ...
Zhang, Jingyi
Ferroelectric (FE) and closely related antiferroelectric (AFE) materials have unique electromechanical properties that promote various applications in the area of capacitors, sensors, generators (FE) and high density energy storage (AFE). These smart materials with extensive applications have drawn wide interest in the industrial and scientific world because of their reliability and tunable property. However, reliability issues changes its paradigms and requires guidance from detailed mechanism theory as the materials applications are pushed for better performance. A host of modeling work were dedicated to study the macro-structural behavior and microstructural evolution in FE and AFE material under various conditions. This thesis is focused on direct observation of domain evolution under multiphysics loading for both FE and AFE material. Landau-Devonshire time-dependent phase field models were built for both materials, and were simulated in finite element software Comsol. In FE model, dagger-shape 90 degree switched domain was observed at preexisting crack tip under pure mechanical loading. Polycrystal structure was tested under same condition, and blocking effect of the growth of dagger-shape switched domain from grain orientation difference and/or grain boundary was directly observed. AFE ceramic model was developed using two sublattice theory, this model was used to investigate the mechanism of energy efficiency increase with self-confined loading in experimental tests. Consistent results was found in simulation and careful investigation of calculation results gave confirmation that origin of energy density increase is from three aspects: self-confinement induced inner compression field as the cause of increase of critical field, fringe leak as the source of elevated saturation polarization and uneven defects distribution as the reason for critical field shifting and phase transition speed. Another important affecting aspect in polycrystalline materials is the
The Cea multi-scale and multi-physics simulation project for nuclear applications
International Nuclear Information System (INIS)
Ledermann, P.; Chauliac, C.; Thomas, J.B.
2005-01-01
Full text of publication follows. Today numerical modelling is everywhere recognized as an essential tool of capitalization, integration and share of knowledge. For this reason, it becomes the central tool of research. Until now, the Cea developed a set of scientific software allowing to model, in each situation, the operation of whole or part of a nuclear installation and these codes are largely used in nuclear industry. However, for the future, it is essential to aim for a better accuracy, a better control of uncertainties and better performance in computing times. The objective is to obtain validated models allowing accurate predictive calculations for actual complex nuclear problems such as fuel behaviour in accidental situation. This demands to master a large and interactive set of phenomena ranging from nuclear reaction to heat transfer. To this end, Cea, with industrial partners (EDF, Framatome-ANP, ANDRA) has designed an integrated platform of calculation, devoted to the study of nuclear systems, and intended at the same time for industries and scientists. The development of this platform is under way with the start in 2005 of the integrated project NURESIM, with 18 European partners. Improvement is coming not only through a multi-scale description of all phenomena but also through an innovative design approach requiring deep functional analysis which is upstream from the development of the simulation platform itself. In addition, the studies of future nuclear systems are increasingly multidisciplinary (simultaneous modelling of core physics, thermal-hydraulics and fuel behaviour). These multi-physics and multi-scale aspects make mandatory to pay very careful attention to software architecture issues. A global platform is thus developed integrating dedicated specialized platforms: DESCARTES for core physics, NEPTUNE for thermal-hydraulics, PLEIADES for fuel behaviour, SINERGY for materials behaviour under irradiation, ALLIANCES for the performance
Li, Hua; Wang, Xiaogui; Yan, Guoping; Lam, K. Y.; Cheng, Sixue; Zou, Tao; Zhuo, Renxi
2005-03-01
In this paper, a novel multiphysic mathematical model is developed for simulation of swelling equilibrium of ionized temperature sensitive hydrogels with the volume phase transition, and it is termed the multi-effect-coupling thermal-stimulus (MECtherm) model. This model consists of the steady-state Nernst-Planck equation, Poisson equation and swelling equilibrium governing equation based on the Flory's mean field theory, in which two types of polymer-solvent interaction parameters, as the functions of temperature and polymer-network volume fraction, are specified with or without consideration of the hydrogen bond interaction. In order to examine the MECtherm model consisting of nonlinear partial differential equations, a meshless Hermite-Cloud method is used for numerical solution of one-dimensional swelling equilibrium of thermal-stimulus responsive hydrogels immersed in a bathing solution. The computed results are in very good agreements with experimental data for the variation of volume swelling ratio with temperature. The influences of the salt concentration and initial fixed-charge density are discussed in detail on the variations of volume swelling ratio of hydrogels, mobile ion concentrations and electric potential of both interior hydrogels and exterior bathing solution.
Atomistic to Continuum Multiscale and Multiphysics Simulation of NiTi Shape Memory Alloy
Gur, Sourav
(transformation temperature, phase fraction evolution kinetics due to temperature) are also demonstrated herein. Next, to couple and transfer the statistical information of length scale dependent phase transformation process, multiscale/ multiphysics methods are used. Here, the computational difficulty from the fact that the representative governing equations (i.e. different sub-methods such as molecular dynamics simulations, phase field simulations and continuum level constitutive/ material models) are only valid or can be implemented over a range of spatiotemporal scales. Therefore, in the present study, a wavelet based multiscale coupling method is used, where simulation results (phase fraction evolution kinetics) from different sub-methods are linked via concurrent multiscale coupling fashion. Finally, these multiscale/ multiphysics simulation results are used to develop/ modify the macro/ continuum scale thermo-mechanical constitutive relations for NiTi SMA. Finally, the improved material model is used to model new devices, such as thermal diodes and smart dampers.
Synchronization Of Parallel Discrete Event Simulations
Steinman, Jeffrey S.
1992-01-01
Adaptive, parallel, discrete-event-simulation-synchronization algorithm, Breathing Time Buckets, developed in Synchronous Parallel Environment for Emulation and Discrete Event Simulation (SPEEDES) operating system. Algorithm allows parallel simulations to process events optimistically in fluctuating time cycles that naturally adapt while simulation in progress. Combines best of optimistic and conservative synchronization strategies while avoiding major disadvantages. Algorithm processes events optimistically in time cycles adapting while simulation in progress. Well suited for modeling communication networks, for large-scale war games, for simulated flights of aircraft, for simulations of computer equipment, for mathematical modeling, for interactive engineering simulations, and for depictions of flows of information.
Parallel Computing for Brain Simulation.
Pastur-Romay, L A; Porto-Pazos, A B; Cedron, F; Pazos, A
2017-01-01
The human brain is the most complex system in the known universe, it is therefore one of the greatest mysteries. It provides human beings with extraordinary abilities. However, until now it has not been understood yet how and why most of these abilities are produced. For decades, researchers have been trying to make computers reproduce these abilities, focusing on both understanding the nervous system and, on processing data in a more efficient way than before. Their aim is to make computers process information similarly to the brain. Important technological developments and vast multidisciplinary projects have allowed creating the first simulation with a number of neurons similar to that of a human brain. This paper presents an up-to-date review about the main research projects that are trying to simulate and/or emulate the human brain. They employ different types of computational models using parallel computing: digital models, analog models and hybrid models. This review includes the current applications of these works, as well as future trends. It is focused on various works that look for advanced progress in Neuroscience and still others which seek new discoveries in Computer Science (neuromorphic hardware, machine learning techniques). Their most outstanding characteristics are summarized and the latest advances and future plans are presented. In addition, this review points out the importance of considering not only neurons: Computational models of the brain should also include glial cells, given the proven importance of astrocytes in information processing. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.
Parallelization of quantum molecular dynamics simulation code
International Nuclear Information System (INIS)
Kato, Kaori; Kunugi, Tomoaki; Shibahara, Masahiko; Kotake, Susumu
1998-02-01
A quantum molecular dynamics simulation code has been developed for the analysis of the thermalization of photon energies in the molecule or materials in Kansai Research Establishment. The simulation code is parallelized for both Scalar massively parallel computer (Intel Paragon XP/S75) and Vector parallel computer (Fujitsu VPP300/12). Scalable speed-up has been obtained with a distribution to processor units by division of particle group in both parallel computers. As a result of distribution to processor units not only by particle group but also by the particles calculation that is constructed with fine calculations, highly parallelization performance is achieved in Intel Paragon XP/S75. (author)
Suzuki, Yuma; Shimizu, Tetsuhide; Yang, Ming
2017-01-01
The quantitative evaluation of the biomolecules transport with multi-physics in nano/micro scale is demanded in order to optimize the design of microfluidics device for the biomolecules detection with high detection sensitivity and rapid diagnosis. This paper aimed to investigate the effectivity of the computational simulation using the numerical model of the biomolecules transport with multi-physics near a microchannel surface on the development of biomolecules-detection devices. The biomolecules transport with fluid drag force, electric double layer (EDL) force, and van der Waals force was modeled by Newtonian Equation of motion. The model validity was verified in the influence of ion strength and flow velocity on biomolecules distribution near the surface compared with experimental results of previous studies. The influence of acting forces on its distribution near the surface was investigated by the simulation. The trend of its distribution to ion strength and flow velocity was agreement with the experimental result by the combination of all acting forces. Furthermore, EDL force dominantly influenced its distribution near its surface compared with fluid drag force except for the case of high velocity and low ion strength. The knowledges from the simulation might be useful for the design of biomolecules-detection devices and the simulation can be expected to be applied on its development as the design tool for high detection sensitivity and rapid diagnosis in the future.
Massmann, J.; Nagel, T.; Bilke, L.; Böttcher, N.; Heusermann, S.; Fischer, T.; Kumar, V.; Schäfers, A.; Shao, H.; Vogel, P.; Wang, W.; Watanabe, N.; Ziefle, G.; Kolditz, O.
2016-12-01
As part of the German site selection process for a high-level nuclear waste repository, different repository concepts in the geological candidate formations rock salt, clay stone and crystalline rock are being discussed. An open assessment of these concepts using numerical simulations requires physical models capturing the individual particularities of each rock type and associated geotechnical barrier concept to a comparable level of sophistication. In a joint work group of the Helmholtz Centre for Environmental Research (UFZ) and the German Federal Institute for Geosciences and Natural Resources (BGR), scientists of the UFZ are developing and implementing multiphysical process models while BGR scientists apply them to large scale analyses. The advances in simulation methods for waste repositories are incorporated into the open-source code OpenGeoSys. Here, recent application-driven progress in this context is highlighted. A robust implementation of visco-plasticity with temperature-dependent properties into a framework for the thermo-mechanical analysis of rock salt will be shown. The model enables the simulation of heat transport along with its consequences on the elastic response as well as on primary and secondary creep or the occurrence of dilatancy in the repository near field. Transverse isotropy, non-isothermal hydraulic processes and their coupling to mechanical stresses are taken into account for the analysis of repositories in clay stone. These processes are also considered in the near field analyses of engineered barrier systems, including the swelling/shrinkage of the bentonite material. The temperature-dependent saturation evolution around the heat-emitting waste container is described by different multiphase flow formulations. For all mentioned applications, we illustrate the workflow from model development and implementation, over verification and validation, to repository-scale application simulations using methods of high performance computing.
Konishi, Toshifumi; Yamane, Daisuke; Matsushima, Takaaki; Masu, Kazuya; Machida, Katsuyuki; Toshiyoshi, Hiroshi
2014-01-01
This paper reports the design and evaluation results of a capacitive CMOS-MEMS sensor that consists of the proposed sensor circuit and a capacitive MEMS device implemented on the circuit. To design a capacitive CMOS-MEMS sensor, a multi-physics simulation of the electromechanical behavior of both the MEMS structure and the sensing LSI was carried out simultaneously. In order to verify the validity of the design, we applied the capacitive CMOS-MEMS sensor to a MEMS accelerometer implemented by the post-CMOS process onto a 0.35-µm CMOS circuit. The experimental results of the CMOS-MEMS accelerometer exhibited good agreement with the simulation results within the input acceleration range between 0.5 and 6 G (1 G = 9.8 m/s2), corresponding to the output voltages between 908.6 and 915.4 mV, respectively. Therefore, we have confirmed that our capacitive CMOS-MEMS sensor and the multi-physics simulation will be beneficial method to realize integrated CMOS-MEMS technology.
Building a parallel file system simulator
International Nuclear Information System (INIS)
Molina-Estolano, E; Maltzahn, C; Brandt, S A; Bent, J
2009-01-01
Parallel file systems are gaining in popularity in high-end computing centers as well as commercial data centers. High-end computing systems are expected to scale exponentially and to pose new challenges to their storage scalability in terms of cost and power. To address these challenges scientists and file system designers will need a thorough understanding of the design space of parallel file systems. Yet there exist few systematic studies of parallel file system behavior at petabyte- and exabyte scale. An important reason is the significant cost of getting access to large-scale hardware to test parallel file systems. To contribute to this understanding we are building a parallel file system simulator that can simulate parallel file systems at very large scale. Our goal is to simulate petabyte-scale parallel file systems on a small cluster or even a single machine in reasonable time and fidelity. With this simulator, file system experts will be able to tune existing file systems for specific workloads, scientists and file system deployment engineers will be able to better communicate workload requirements, file system designers and researchers will be able to try out design alternatives and innovations at scale, and instructors will be able to study very large-scale parallel file system behavior in the class room. In this paper we describe our approach and provide preliminary results that are encouraging both in terms of fidelity and simulation scalability.
Structured building model reduction toward parallel simulation
Energy Technology Data Exchange (ETDEWEB)
Dobbs, Justin R. [Cornell University; Hencey, Brondon M. [Cornell University
2013-08-26
Building energy model reduction exchanges accuracy for improved simulation speed by reducing the number of dynamical equations. Parallel computing aims to improve simulation times without loss of accuracy but is poorly utilized by contemporary simulators and is inherently limited by inter-processor communication. This paper bridges these disparate techniques to implement efficient parallel building thermal simulation. We begin with a survey of three structured reduction approaches that compares their performance to a leading unstructured method. We then use structured model reduction to find thermal clusters in the building energy model and allocate processing resources. Experimental results demonstrate faster simulation and low error without any interprocessor communication.
Energy Technology Data Exchange (ETDEWEB)
Campbell, Michael T. [Illinois Rocstar LLC, Champaign, IL (United States); Safdari, Masoud [Illinois Rocstar LLC, Champaign, IL (United States); Kress, Jessica E. [Illinois Rocstar LLC, Champaign, IL (United States); Anderson, Michael J. [Illinois Rocstar LLC, Champaign, IL (United States); Horvath, Samantha [Illinois Rocstar LLC, Champaign, IL (United States); Brandyberry, Mark D. [Illinois Rocstar LLC, Champaign, IL (United States); Kim, Woohyun [Illinois Rocstar LLC, Champaign, IL (United States); Sarwal, Neil [Illinois Rocstar LLC, Champaign, IL (United States); Weisberg, Brian [Illinois Rocstar LLC, Champaign, IL (United States)
2016-10-15
The project described in this report constructed and exercised an innovative multiphysics coupling toolkit called the Illinois Rocstar MultiPhysics Application Coupling Toolkit (IMPACT). IMPACT is an open source, flexible, natively parallel infrastructure for coupling multiple uniphysics simulation codes into multiphysics computational systems. IMPACT works with codes written in several high-performance-computing (HPC) programming languages, and is designed from the beginning for HPC multiphysics code development. It is designed to be minimally invasive to the individual physics codes being integrated, and has few requirements on those physics codes for integration. The goal of IMPACT is to provide the support needed to enable coupling existing tools together in unique and innovative ways to produce powerful new multiphysics technologies without extensive modification and rewrite of the physics packages being integrated. There are three major outcomes from this project: 1) construction, testing, application, and open-source release of the IMPACT infrastructure, 2) production of example open-source multiphysics tools using IMPACT, and 3) identification and engagement of interested organizations in the tools and applications resulting from the project. This last outcome represents the incipient development of a user community and application echosystem being built using IMPACT. Multiphysics coupling standardization can only come from organizations working together to define needs and processes that span the space of necessary multiphysics outcomes, which Illinois Rocstar plans to continue driving toward. The IMPACT system, including source code, documentation, and test problems are all now available through the public gitHUB.org system to anyone interested in multiphysics code coupling. Many of the basic documents explaining use and architecture of IMPACT are also attached as appendices to this document. Online HTML documentation is available through the gitHUB site
Program For Parallel Discrete-Event Simulation
Beckman, Brian C.; Blume, Leo R.; Geiselman, John S.; Presley, Matthew T.; Wedel, John J., Jr.; Bellenot, Steven F.; Diloreto, Michael; Hontalas, Philip J.; Reiher, Peter L.; Weiland, Frederick P.
1991-01-01
User does not have to add any special logic to aid in synchronization. Time Warp Operating System (TWOS) computer program is special-purpose operating system designed to support parallel discrete-event simulation. Complete implementation of Time Warp mechanism. Supports only simulations and other computations designed for virtual time. Time Warp Simulator (TWSIM) subdirectory contains sequential simulation engine interface-compatible with TWOS. TWOS and TWSIM written in, and support simulations in, C programming language.
Data parallel sorting for particle simulation
Dagum, Leonardo
1992-01-01
Sorting on a parallel architecture is a communications intensive event which can incur a high penalty in applications where it is required. In the case of particle simulation, only integer sorting is necessary, and sequential implementations easily attain the minimum performance bound of O (N) for N particles. Parallel implementations, however, have to cope with the parallel sorting problem which, in addition to incurring a heavy communications cost, can make the minimun performance bound difficult to attain. This paper demonstrates how the sorting problem in a particle simulation can be reduced to a merging problem, and describes an efficient data parallel algorithm to solve this merging problem in a particle simulation. The new algorithm is shown to be optimal under conditions usual for particle simulation, and its fieldwise implementation on the Connection Machine is analyzed in detail. The new algorithm is about four times faster than a fieldwise implementation of radix sort on the Connection Machine.
Parallel Monte Carlo simulation of aerosol dynamics
Zhou, K.; He, Z.; Xiao, M.; Zhang, Z.
2014-01-01
is simulated with a stochastic method (Marcus-Lushnikov stochastic process). Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallelized using the Message Passing Interface (MPI
Acoustic simulation in architecture with parallel algorithm
Li, Xiaohong; Zhang, Xinrong; Li, Dan
2004-03-01
In allusion to complexity of architecture environment and Real-time simulation of architecture acoustics, a parallel radiosity algorithm was developed. The distribution of sound energy in scene is solved with this method. And then the impulse response between sources and receivers at frequency segment, which are calculated with multi-process, are combined into whole frequency response. The numerical experiment shows that parallel arithmetic can improve the acoustic simulating efficiency of complex scene.
Using a Linux Cluster for Parallel Simulations of an Active Magnetic Regenerator Refrigerator
DEFF Research Database (Denmark)
Petersen, T.F.; Pryds, N.; Smith, A.
2006-01-01
This paper describes the implementation of a Comsol Multiphysics model on a Linux computer Cluster. The Magnetic Refrigerator (MR) is a special type of refrigerator with potential to reduce the energy consumption of household refrigeration by a factor of two or more. To conduct numerical analysis....... The coupled set of equations and the transient convergence towards the final steady state means that the model has an excessive solution time. To make parametric studies practical, the developed model was implemented on a Cluster to allow parallel simulations, which has decreased the solution time...
Simulation Exploration through Immersive Parallel Planes: Preprint
Energy Technology Data Exchange (ETDEWEB)
Brunhart-Lupo, Nicholas; Bush, Brian W.; Gruchalla, Kenny; Smith, Steve
2016-03-01
We present a visualization-driven simulation system that tightly couples systems dynamics simulations with an immersive virtual environment to allow analysts to rapidly develop and test hypotheses in a high-dimensional parameter space. To accomplish this, we generalize the two-dimensional parallel-coordinates statistical graphic as an immersive 'parallel-planes' visualization for multivariate time series emitted by simulations running in parallel with the visualization. In contrast to traditional parallel coordinate's mapping the multivariate dimensions onto coordinate axes represented by a series of parallel lines, we map pairs of the multivariate dimensions onto a series of parallel rectangles. As in the case of parallel coordinates, each individual observation in the dataset is mapped to a polyline whose vertices coincide with its coordinate values. Regions of the rectangles can be 'brushed' to highlight and select observations of interest: a 'slider' control allows the user to filter the observations by their time coordinate. In an immersive virtual environment, users interact with the parallel planes using a joystick that can select regions on the planes, manipulate selection, and filter time. The brushing and selection actions are used to both explore existing data as well as to launch additional simulations corresponding to the visually selected portions of the input parameter space. As soon as the new simulations complete, their resulting observations are displayed in the virtual environment. This tight feedback loop between simulation and immersive analytics accelerates users' realization of insights about the simulation and its output.
Simulation Exploration through Immersive Parallel Planes
Energy Technology Data Exchange (ETDEWEB)
Brunhart-Lupo, Nicholas J [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Bush, Brian W [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Gruchalla, Kenny M [National Renewable Energy Laboratory (NREL), Golden, CO (United States); Smith, Steve [Los Alamos Visualization Associates
2017-05-25
We present a visualization-driven simulation system that tightly couples systems dynamics simulations with an immersive virtual environment to allow analysts to rapidly develop and test hypotheses in a high-dimensional parameter space. To accomplish this, we generalize the two-dimensional parallel-coordinates statistical graphic as an immersive 'parallel-planes' visualization for multivariate time series emitted by simulations running in parallel with the visualization. In contrast to traditional parallel coordinate's mapping the multivariate dimensions onto coordinate axes represented by a series of parallel lines, we map pairs of the multivariate dimensions onto a series of parallel rectangles. As in the case of parallel coordinates, each individual observation in the dataset is mapped to a polyline whose vertices coincide with its coordinate values. Regions of the rectangles can be 'brushed' to highlight and select observations of interest: a 'slider' control allows the user to filter the observations by their time coordinate. In an immersive virtual environment, users interact with the parallel planes using a joystick that can select regions on the planes, manipulate selection, and filter time. The brushing and selection actions are used to both explore existing data as well as to launch additional simulations corresponding to the visually selected portions of the input parameter space. As soon as the new simulations complete, their resulting observations are displayed in the virtual environment. This tight feedback loop between simulation and immersive analytics accelerates users' realization of insights about the simulation and its output.
Pawar, Sumedh; Sharma, Atul
2018-01-01
This work presents mathematical model and solution methodology for a multiphysics engineering problem on arc formation during welding and inside a nozzle. A general-purpose commercial CFD solver ANSYS FLUENT 13.0.0 is used in this work. Arc formation involves strongly coupled gas dynamics and electro-dynamics, simulated by solution of coupled Navier-Stoke equations, Maxwell's equations and radiation heat-transfer equation. Validation of the present numerical methodology is demonstrated with an excellent agreement with the published results. The developed mathematical model and the user defined functions (UDFs) are independent of the geometry and are applicable to any system that involves arc-formation, in 2D axisymmetric coordinates system. The high-pressure flow of SF6 gas in the nozzle-arc system resembles arc chamber of SF6 gas circuit breaker; thus, this methodology can be extended to simulate arcing phenomenon during current interruption.
Advanced multi-physics simulation capability for very high temperature reactors
International Nuclear Information System (INIS)
Lee, Hyun Chul; Tak, Nam Il; Jo Chang Keun; Noh, Jae Man; Cho, Bong Hyun; Cho, Jin Woung; Hong, Ser Gi
2012-01-01
The purpose of this research is to develop methodologies and computer code for high-fidelity multi-physics analysis of very high temperature gas-cooled reactors(VHTRs). The research project was performed through Korea-US I-NERI program. The main research topic was development of methodologies for high-fidelity 3-D whole core transport calculation, development of DeCART code for VHTR reactor physics analysis, generation of VHTR specific 190-group cross-section library for DeCART code, development of DeCART/CORONA coupled code system for neutronics/thermo-fluid multi-physics analysis, and benchmark analysis against various benchmark problems derived from PMR200 reactor. The methodologies and the code systems will be utilized a key technologies in the Nuclear Hydrogen Development and Demonstration program. Export of code system is expected in the near future and the code systems developed in this project are expected to contribute to development and export of nuclear hydrogen production system
Parallel programming with Easy Java Simulations
Esquembre, F.; Christian, W.; Belloni, M.
2018-01-01
Nearly all of today's processors are multicore, and ideally programming and algorithm development utilizing the entire processor should be introduced early in the computational physics curriculum. Parallel programming is often not introduced because it requires a new programming environment and uses constructs that are unfamiliar to many teachers. We describe how we decrease the barrier to parallel programming by using a java-based programming environment to treat problems in the usual undergraduate curriculum. We use the easy java simulations programming and authoring tool to create the program's graphical user interface together with objects based on those developed by Kaminsky [Building Parallel Programs (Course Technology, Boston, 2010)] to handle common parallel programming tasks. Shared-memory parallel implementations of physics problems, such as time evolution of the Schrödinger equation, are available as source code and as ready-to-run programs from the AAPT-ComPADRE digital library.
Parallel and Distributed System Simulation
Dongarra, Jack
1998-01-01
This exploratory study initiated our research into the software infrastructure necessary to support the modeling and simulation techniques that are most appropriate for the Information Power Grid. Such computational power grids will use high-performance networking to connect hardware, software, instruments, databases, and people into a seamless web that supports a new generation of computation-rich problem solving environments for scientists and engineers. In this context we looked at evaluating the NetSolve software environment for network computing that leverages the potential of such systems while addressing their complexities. NetSolve's main purpose is to enable the creation of complex applications that harness the immense power of the grid, yet are simple to use and easy to deploy. NetSolve uses a modular, client-agent-server architecture to create a system that is very easy to use. Moreover, it is designed to be highly composable in that it readily permits new resources to be added by anyone willing to do so. In these respects NetSolve is to the Grid what the World Wide Web is to the Internet. But like the Web, the design that makes these wonderful features possible can also impose significant limitations on the performance and robustness of a NetSolve system. This project explored the design innovations that push the performance and robustness of the NetSolve paradigm as far as possible without sacrificing the Web-like ease of use and composability that make it so powerful.
Xyce parallel electronic simulator release notes.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R; Hoekstra, Robert John; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Rankin, Eric Lamont; Coffey, Todd S; Pawlowski, Roger P; Santarelli, Keith R.
2010-05-01
The Xyce Parallel Electronic Simulator has been written to support, in a rigorous manner, the simulation needs of the Sandia National Laboratories electrical designers. Specific requirements include, among others, the ability to solve extremely large circuit problems by supporting large-scale parallel computing platforms, improved numerical performance and object-oriented code design and implementation. The Xyce release notes describe: Hardware and software requirements New features and enhancements Any defects fixed since the last release Current known defects and defect workarounds For up-to-date information not available at the time these notes were produced, please visit the Xyce web page at http://www.cs.sandia.gov/xyce.
Parallel Monte Carlo simulation of aerosol dynamics
Zhou, K.
2014-01-01
A highly efficient Monte Carlo (MC) algorithm is developed for the numerical simulation of aerosol dynamics, that is, nucleation, surface growth, and coagulation. Nucleation and surface growth are handled with deterministic means, while coagulation is simulated with a stochastic method (Marcus-Lushnikov stochastic process). Operator splitting techniques are used to synthesize the deterministic and stochastic parts in the algorithm. The algorithm is parallelized using the Message Passing Interface (MPI). The parallel computing efficiency is investigated through numerical examples. Near 60% parallel efficiency is achieved for the maximum testing case with 3.7 million MC particles running on 93 parallel computing nodes. The algorithm is verified through simulating various testing cases and comparing the simulation results with available analytical and/or other numerical solutions. Generally, it is found that only small number (hundreds or thousands) of MC particles is necessary to accurately predict the aerosol particle number density, volume fraction, and so forth, that is, low order moments of the Particle Size Distribution (PSD) function. Accurately predicting the high order moments of the PSD needs to dramatically increase the number of MC particles. 2014 Kun Zhou et al.
Parallel discrete event simulation using shared memory
Reed, Daniel A.; Malony, Allen D.; Mccredie, Bradley D.
1988-01-01
With traditional event-list techniques, evaluating a detailed discrete-event simulation-model can often require hours or even days of computation time. By eliminating the event list and maintaining only sufficient synchronization to ensure causality, parallel simulation can potentially provide speedups that are linear in the numbers of processors. A set of shared-memory experiments, using the Chandy-Misra distributed-simulation algorithm, to simulate networks of queues is presented. Parameters of the study include queueing network topology and routing probabilities, number of processors, and assignment of network nodes to processors. These experiments show that Chandy-Misra distributed simulation is a questionable alternative to sequential-simulation of most queueing network models.
Parallel adaptive simulations on unstructured meshes
International Nuclear Information System (INIS)
Shephard, M S; Jansen, K E; Sahni, O; Diachin, L A
2007-01-01
This paper discusses methods being developed by the ITAPS center to support the execution of parallel adaptive simulations on unstructured meshes. The paper first outlines the ITAPS approach to the development of interoperable mesh, geometry and field services to support the needs of SciDAC application in these areas. The paper then demonstrates the ability of unstructured adaptive meshing methods built on such interoperable services to effectively solve important physics problems. Attention is then focused on ITAPs' developing ability to solve adaptive unstructured mesh problems on massively parallel computers
Xyce parallel electronic simulator : reference guide.
Energy Technology Data Exchange (ETDEWEB)
Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Warrender, Christina E.; Keiter, Eric Richard; Pawlowski, Roger Patrick
2011-05-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide. The Xyce Parallel Electronic Simulator has been written to support, in a rigorous manner, the simulation needs of the Sandia National Laboratories electrical designers. It is targeted specifically to run on large-scale parallel computing platforms but also runs well on a variety of architectures including single processor workstations. It also aims to support a variety of devices and models specific to Sandia needs. This document is intended to complement the Xyce Users Guide. It contains comprehensive, detailed information about a number of topics pertinent to the usage of Xyce. Included in this document is a netlist reference for the input-file commands and elements supported within Xyce; a command line reference, which describes the available command line arguments for Xyce; and quick-references for users of other circuit codes, such as Orcad's PSpice and Sandia's ChileSPICE.
Li, Yingkun; Chen, Xiong; Xu, Jinsheng; Zhou, Changsheng; Musa, Omer
2018-05-01
In this paper, numerical investigation of ignition transient in a dual pulse solid rocket motor has been conducted. An in-house code has been developed in order to solve multi-physics governing equations, including unsteady compressible flow, heat conduction and structural dynamic. The simplified numerical models for solid propellant ignition and combustion have been added. The conventional serial staggered algorithm is adopted to simulate the fluid structure interaction problems in a loosely-coupled manner. The accuracy of the coupling procedure is validated by the behavior of a cantilever panel subjected to a shock wave. Then, the detailed flow field development, flame propagation characteristics, pressure evolution in the combustion chamber, and the structural response of metal diaphragm are analyzed carefully. The burst-time and burst-pressure of the metal diaphragm are also obtained. The individual effects of the igniter's mass flow rate, metal diaphragm thickness and diameter on the ignition transient have been systemically compared. The numerical results show that the evolution of the flow field in the combustion chamber, the temperature distribution on the propellant surface and the pressure loading on the metal diaphragm surface present a strong three-dimensional behavior during the initial ignition stage. The rupture of metal diaphragm is not only related to the magnitude of pressure loading on the diaphragm surface, but also to the history of pressure loading. The metal diaphragm thickness and diameter have a significant effect on the burst-time and burst-pressure of metal diaphragm.
A program code generator for multiphysics biological simulation using markup languages.
Amano, Akira; Kawabata, Masanari; Yamashita, Yoshiharu; Rusty Punzalan, Florencio; Shimayoshi, Takao; Kuwabara, Hiroaki; Kunieda, Yoshitoshi
2012-01-01
To cope with the complexity of the biological function simulation models, model representation with description language is becoming popular. However, simulation software itself becomes complex in these environment, thus, it is difficult to modify the simulation conditions, target computation resources or calculation methods. In the complex biological function simulation software, there are 1) model equations, 2) boundary conditions and 3) calculation schemes. Use of description model file is useful for first point and partly second point, however, third point is difficult to handle for various calculation schemes which is required for simulation models constructed from two or more elementary models. We introduce a simulation software generation system which use description language based description of coupling calculation scheme together with cell model description file. By using this software, we can easily generate biological simulation code with variety of coupling calculation schemes. To show the efficiency of our system, example of coupling calculation scheme with three elementary models are shown.
Parallel beam dynamics simulation of linear accelerators
International Nuclear Information System (INIS)
Qiang, Ji; Ryne, Robert D.
2002-01-01
In this paper we describe parallel particle-in-cell methods for the large scale simulation of beam dynamics in linear accelerators. These techniques have been implemented in the IMPACT (Integrated Map and Particle Accelerator Tracking) code. IMPACT is being used to study the behavior of intense charged particle beams and as a tool for the design of next-generation linear accelerators. As examples, we present applications of the code to the study of emittance exchange in high intensity beams and to the study of beam transport in a proposed accelerator for the development of accelerator-driven waste transmutation technologies
Multibus-based parallel processor for simulation
Ogrady, E. P.; Wang, C.-H.
1983-01-01
A Multibus-based parallel processor simulation system is described. The system is intended to serve as a vehicle for gaining hands-on experience, testing system and application software, and evaluating parallel processor performance during development of a larger system based on the horizontal/vertical-bus interprocessor communication mechanism. The prototype system consists of up to seven Intel iSBC 86/12A single-board computers which serve as processing elements, a multiple transmission controller (MTC) designed to support system operation, and an Intel Model 225 Microcomputer Development System which serves as the user interface and input/output processor. All components are interconnected by a Multibus/IEEE 796 bus. An important characteristic of the system is that it provides a mechanism for a processing element to broadcast data to other selected processing elements. This parallel transfer capability is provided through the design of the MTC and a minor modification to the iSBC 86/12A board. The operation of the MTC, the basic hardware-level operation of the system, and pertinent details about the iSBC 86/12A and the Multibus are described.
Energy Technology Data Exchange (ETDEWEB)
S. R. Novascone; B. W. Spencer; D. Andrs; R. L. Williamson; J. D. Hales; D. M. Perez
2013-05-01
The behavior of nuclear fuel in the reactor environment is affected by multiple physics, most notably heat conduction and solid mechanics, which can have a strong influence on each other. To provide credible solutions, a fuel performance simulation code must have the ability to obtain solutions for each of the physics, including coupling between them. Solution strategies for solving systems of coupled equations can be categorized as loosely-coupled, where the individual physics are solved separately, keeping the solutions for the other physics fixed at each iteration, or tightly coupled, where the nonlinear solver simultaneously drives down the residual for each physics, taking into account the coupling between the physics in each nonlinear iteration. In this paper, we compare the performance of loosely and tightly coupled solution algorithms for thermomechanical problems involving coupled thermal and mechanical contact, which is a primary source of interdependence between thermal and mechanical solutions in fuel performance models. The results indicate that loosely-coupled simulations require significantly more nonlinear iterations, and may lead to convergence trouble when the thermal conductivity of the gap is too small. We also apply the tightly coupled solution strategy to a nuclear fuel simulation of an experiment in a test reactor. Studying the results from these simulations indicates that perhaps convergence for either approach may be problem dependent, i.e., there may be problems for which a loose coupled approach converges, where tightly coupled won’t converge and vice versa.
International Nuclear Information System (INIS)
Novascone, S. R.; Spencer, B. W.; Andrs, D.; Williamson, R. L.; Hales, J. D.; Perez, D. M.
2013-01-01
The behavior of nuclear fuel in the reactor environment is affected by multiple physics, most notably heat conduction and solid mechanics, which can have a strong influence on each other. To provide credible solutions, a fuel performance simulation code must have the ability to obtain solutions for each of the physics, including coupling between them. Solution strategies for solving systems of coupled equations can be categorized as loosely-coupled, where the individual physics are solved separately, keeping the solutions for the other physics fixed at each iteration, or tightly coupled, where the nonlinear solver simultaneously drives down the residual for each physics, taking into account the coupling between the physics in each nonlinear iteration. In this paper, we compare the performance of loosely and tightly coupled solution algorithms for thermomechanical problems involving coupled thermal and mechanical contact, which is a primary source of interdependence between thermal and mechanical solutions in fuel performance models. The results indicate that loosely-coupled simulations require significantly more nonlinear iterations, and may lead to convergence trouble when the thermal conductivity of the gap is too small. We also apply the tightly coupled solution strategy to a nuclear fuel simulation of an experiment in a test reactor. Studying the results from these simulations indicates that perhaps convergence for either approach may be problem dependent, i.e., there may be problems for which a loose coupled approach converges, where tightly coupled won't converge and vice versa. (authors)
Multi-scale and multi-physics simulations using the multi-fluid plasma model
2017-04-25
small The simulation uses 512 second-order elements Bz = 1.0, Te = Ti = 0.01, ui = ue = 0 ne = ni = 1.0 + e−10(x−6) 2 Baboolal, Math . and Comp. Sim. 55...DISTRIBUTION Clearance No. 17211 23 / 31 SUMMARY The blended finite element method (BFEM) is presented DG spatial discretization with explicit Runge...Kutta (i+, n) CG spatial discretization with implicit Crank-Nicolson (e−, fileds) DG captures shocks and discontinuities CG is efficient and robust for
Modeling and simulation of multi-physics multi-scale transport phenomenain bio-medical applications
International Nuclear Information System (INIS)
Kenjereš, Saša
2014-01-01
We present a short overview of some of our most recent work that combines the mathematical modeling, advanced computer simulations and state-of-the-art experimental techniques of physical transport phenomena in various bio-medical applications. In the first example, we tackle predictions of complex blood flow patterns in the patient-specific vascular system (carotid artery bifurcation) and transfer of the so-called 'bad' cholesterol (low-density lipoprotein, LDL) within the multi-layered artery wall. This two-way coupling between the blood flow and corresponding mass transfer of LDL within the artery wall is essential for predictions of regions where atherosclerosis can develop. It is demonstrated that a recently developed mathematical model, which takes into account the complex multi-layer arterial-wall structure, produced LDL profiles within the artery wall in good agreement with in-vivo experiments in rabbits, and it can be used for predictions of locations where the initial stage of development of atherosclerosis may take place. The second example includes a combination of pulsating blood flow and medical drug delivery and deposition controlled by external magnetic field gradients in the patient specific carotid artery bifurcation. The results of numerical simulations are compared with own PIV (Particle Image Velocimetry) and MRI (Magnetic Resonance Imaging) in the PDMS (silicon-based organic polymer) phantom. A very good agreement between simulations and experiments is obtained for different stages of the pulsating cycle. Application of the magnetic drug targeting resulted in an increase of up to ten fold in the efficiency of local deposition of the medical drug at desired locations. Finally, the LES (Large Eddy Simulation) of the aerosol distribution within the human respiratory system that includes up to eight bronchial generations is performed. A very good agreement between simulations and MRV (Magnetic Resonance Velocimetry) measurements is
Modeling and simulation of multi-physics multi-scale transport phenomenain bio-medical applications
Kenjereš, Saša
2014-08-01
We present a short overview of some of our most recent work that combines the mathematical modeling, advanced computer simulations and state-of-the-art experimental techniques of physical transport phenomena in various bio-medical applications. In the first example, we tackle predictions of complex blood flow patterns in the patient-specific vascular system (carotid artery bifurcation) and transfer of the so-called "bad" cholesterol (low-density lipoprotein, LDL) within the multi-layered artery wall. This two-way coupling between the blood flow and corresponding mass transfer of LDL within the artery wall is essential for predictions of regions where atherosclerosis can develop. It is demonstrated that a recently developed mathematical model, which takes into account the complex multi-layer arterial-wall structure, produced LDL profiles within the artery wall in good agreement with in-vivo experiments in rabbits, and it can be used for predictions of locations where the initial stage of development of atherosclerosis may take place. The second example includes a combination of pulsating blood flow and medical drug delivery and deposition controlled by external magnetic field gradients in the patient specific carotid artery bifurcation. The results of numerical simulations are compared with own PIV (Particle Image Velocimetry) and MRI (Magnetic Resonance Imaging) in the PDMS (silicon-based organic polymer) phantom. A very good agreement between simulations and experiments is obtained for different stages of the pulsating cycle. Application of the magnetic drug targeting resulted in an increase of up to ten fold in the efficiency of local deposition of the medical drug at desired locations. Finally, the LES (Large Eddy Simulation) of the aerosol distribution within the human respiratory system that includes up to eight bronchial generations is performed. A very good agreement between simulations and MRV (Magnetic Resonance Velocimetry) measurements is obtained
International Nuclear Information System (INIS)
Gomez Torres, Armando Miguel
2011-01-01
This doctoral thesis describes the methodological development of coupled neutron-kinetics/thermal-hydraulics codes for the design and safety analysis of reactor systems taking into account the feedback mechanisms on the fuel rod level, according to different approaches. A central part of this thesis is the development and validation of a high fidelity simulation tool, DYNSUB, which results from the ''two-way-coupling'' of DYN3D-SP3 and SUBCHANFLOW. It allows the determination of local safety parameters through a detailed description of the core behavior under stationary and transient conditions at fuel rod level.
International Nuclear Information System (INIS)
Miyamoto, Akira; Sato, Etsuko; Sato, Ryo; Inaba, Kenji; Hatakeyama, Nozomu
2014-01-01
In collaboration with experimental experts we have reported in the present conference (Hatakeyama, N. et al., “Experiment-integrated multi-scale, multi-physics computational chemistry simulation applied to corrosion behaviour of BWR structural materials”) the results of multi-scale multi-physics computational chemistry simulations applied to the corrosion behaviour of BWR structural materials. In macro-scale, a macroscopic simulator of anode polarization curve was developed to solve the spatially one-dimensional electrochemical equations on the material surface in continuum level in order to understand the corrosion behaviour of typical BWR structural material, SUS304. The experimental anode polarization behaviours of each pure metal were reproduced by fitting all the rates of electrochemical reactions and then the anode polarization curve of SUS304 was calculated by using the same parameters and found to reproduce the experimental behaviour successfully. In meso-scale, a kinetic Monte Carlo (KMC) simulator was applied to an actual-time simulation of the morphological corrosion behaviour under the influence of an applied voltage. In micro-scale, an ultra-accelerated quantum chemical molecular dynamics (UA-QCMD) code was applied to various metallic oxide surfaces of Fe 2 O 3 , Fe 3 O 4 , Cr 2 O 3 modelled as same as water molecules and dissolved metallic ions on the surfaces, then the dissolution and segregation behaviours were successfully simulated dynamically by using UA-QCMD. In this paper we describe details of the multi-scale, multi-physics computational chemistry method especially the UA-QCMD method. This method is approximately 10,000,000 times faster than conventional first-principles molecular dynamics methods based on density-functional theory (DFT), and the accuracy was also validated for various metals and metal oxides compared with DFT results. To assure multi-scale multi-physics computational chemistry simulation based on the UA-QCMD method for
Empirical study of parallel LRU simulation algorithms
Carr, Eric; Nicol, David M.
1994-01-01
This paper reports on the performance of five parallel algorithms for simulating a fully associative cache operating under the LRU (Least-Recently-Used) replacement policy. Three of the algorithms are SIMD, and are implemented on the MasPar MP-2 architecture. Two other algorithms are parallelizations of an efficient serial algorithm on the Intel Paragon. One SIMD algorithm is quite simple, but its cost is linear in the cache size. The two other SIMD algorithm are more complex, but have costs that are independent on the cache size. Both the second and third SIMD algorithms compute all stack distances; the second SIMD algorithm is completely general, whereas the third SIMD algorithm presumes and takes advantage of bounds on the range of reference tags. Both MIMD algorithm implemented on the Paragon are general and compute all stack distances; they differ in one step that may affect their respective scalability. We assess the strengths and weaknesses of these algorithms as a function of problem size and characteristics, and compare their performance on traces derived from execution of three SPEC benchmark programs.
Parallel Numerical Simulations of Water Reservoirs
Torres, Pedro; Mangiavacchi, Norberto
2010-11-01
The study of the water flow and scalar transport in water reservoirs is important for the determination of the water quality during the initial stages of the reservoir filling and during the life of the reservoir. For this scope, a parallel 2D finite element code for solving the incompressible Navier-Stokes equations coupled with scalar transport was implemented using the message-passing programming model, in order to perform simulations of hidropower water reservoirs in a computer cluster environment. The spatial discretization is based on the MINI element that satisfies the Babuska-Brezzi (BB) condition, which provides sufficient conditions for a stable mixed formulation. All the distributed data structures needed in the different stages of the code, such as preprocessing, solving and post processing, were implemented using the PETSc library. The resulting linear systems for the velocity and the pressure fields were solved using the projection method, implemented by an approximate block LU factorization. In order to increase the parallel performance in the solution of the linear systems, we employ the static condensation method for solving the intermediate velocity at vertex and centroid nodes separately. We compare performance results of the static condensation method with the approach of solving the complete system. In our tests the static condensation method shows better performance for large problems, at the cost of an increased memory usage. Performance results for other intensive parts of the code in a computer cluster are also presented.
Kaltenbacher, Manfred
2015-01-01
Like the previous editions also the third edition of this book combines the detailed physical modeling of mechatronic systems and their precise numerical simulation using the Finite Element (FE) method. Thereby, the basic chapter concerning the Finite Element (FE) method is enhanced, provides now also a description of higher order finite elements (both for nodal and edge finite elements) and a detailed discussion of non-conforming mesh techniques. The author enhances and improves many discussions on principles and methods. In particular, more emphasis is put on the description of single fields by adding the flow field. Corresponding to these field, the book is augmented with the new chapter about coupled flow-structural mechanical systems. Thereby, the discussion of computational aeroacoustics is extended towards perturbation approaches, which allows a decomposition of flow and acoustic quantities within the flow region. Last but not least, applications are updated and restructured so that the book meets mode...
Energy Technology Data Exchange (ETDEWEB)
Aldemir, Tunc [The Ohio State Univ., Columbus, OH (United States); Denning, Richard [The Ohio State Univ., Columbus, OH (United States); Catalyurek, Umit [The Ohio State Univ., Columbus, OH (United States); Unwin, Stephen [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)
2015-01-23
Reduction in safety margin can be expected as passive structures and components undergo degradation with time. Limitations in the traditional probabilistic risk assessment (PRA) methodology constrain its value as an effective tool to address the impact of aging effects on risk and for quantifying the impact of aging management strategies in maintaining safety margins. A methodology has been developed to address multiple aging mechanisms involving large numbers of components (with possibly statistically dependent failures) within the PRA framework in a computationally feasible manner when the sequencing of events is conditioned on the physical conditions predicted in a simulation environment, such as the New Generation System Code (NGSC) concept. Both epistemic and aleatory uncertainties can be accounted for within the same phenomenological framework and maintenance can be accounted for in a coherent fashion. The framework accommodates the prospective impacts of various intervention strategies such as testing, maintenance, and refurbishment. The methodology is illustrated with several examples.
International Nuclear Information System (INIS)
Aldemir, Tunc; Denning, Richard; Catalyurek, Umit; Unwin, Stephen
2015-01-01
Reduction in safety margin can be expected as passive structures and components undergo degradation with time. Limitations in the traditional probabilistic risk assessment (PRA) methodology constrain its value as an effective tool to address the impact of aging effects on risk and for quantifying the impact of aging management strategies in maintaining safety margins. A methodology has been developed to address multiple aging mechanisms involving large numbers of components (with possibly statistically dependent failures) within the PRA framework in a computationally feasible manner when the sequencing of events is conditioned on the physical conditions predicted in a simulation environment, such as the New Generation System Code (NGSC) concept. Both epistemic and aleatory uncertainties can be accounted for within the same phenomenological framework and maintenance can be accounted for in a coherent fashion. The framework accommodates the prospective impacts of various intervention strategies such as testing, maintenance, and refurbishment. The methodology is illustrated with several examples.
Multiphysical simulation analysis of the dislocation structure in germanium single crystals
Podkopaev, O. I.; Artemyev, V. V.; Smirnov, A. D.; Mamedov, V. M.; Sid'ko, A. P.; Kalaev, V. V.; Kravtsova, E. D.; Shimanskii, A. F.
2016-09-01
To grow high-quality germanium crystals is one of the most important problems of growth industry. The dislocation density is an important parameter of the quality of single crystals. The dislocation densities in germanium crystals 100 mm in diameter, which have various shapes of the side surface and are grown by the Czochralski technique, are experimentally measured. The crystal growth is numerically simulated using heat-transfer and hydrodynamics models and the Alexander-Haasen dislocation model in terms of the CGSim software package. A comparison of the experimental and calculated dislocation densities shows that the dislocation model can be applied to study lattice defects in germanium crystals and to improve their quality.
Multi-physics modeling and numerical simulation of weld pool in GTA welding
International Nuclear Information System (INIS)
Nguyen, Minh-Chien
2015-01-01
In this work, we develop a 3D physical and numerical model of the GTA (Gas Tungsten Arc) welding process in order to predict, for given welding parameters, useful quantities for the designer of welded assembly: weld bead shape, fluid flow in the weld pool as well as thermal distribution in the work piece. The model is developed in the Cast3M (http://www-cast3m.cea.fr/) finite element software and takes into account the main physical phenomena acting in the work piece and particularly in the weld pool, subject to source terms modeling the arc part of the welding process. A steady solution of this model is thought for and involves the coupling of the nonlinear thermohydraulics and electromagnetic equations together with the displacement of the deformable free surface of the weld pool. A first step in the development consisted in modeling the electromagnetic phenomena with two different numerical methods, in comparing the numerical results obtained with those of the literature and in quantifying the importance of the Lorentz force and the Joule effect compared to the other mechanical and thermal sources by computing power balances. Then, in order to assess the predictive capability of the model, simulations of various welding configurations are performed: variation in the chemical composition of the material, of the welding speed, of the prescribed arc pressure and of the welding positions, which is a focus of this work, are studied. A good agreement is obtained between the results of our model and other experimental and numerical results of the literature. Eventually, a model accounting for metal filling is proposed and its results are discussed. Thus, our complete model can be seen as a solid foundation towards future totally-coupled 3D welding models including the arc and it will be included in WPROCESS the in-house CEA software dedicated to the numerical simulation of welding. (author) [fr
Extreme scale multi-physics simulations of the tsunamigenic 2004 Sumatra megathrust earthquake
Ulrich, T.; Gabriel, A. A.; Madden, E. H.; Wollherr, S.; Uphoff, C.; Rettenberger, S.; Bader, M.
2017-12-01
SeisSol (www.seissol.org) is an open-source software package based on an arbitrary high-order derivative Discontinuous Galerkin method (ADER-DG). It solves spontaneous dynamic rupture propagation on pre-existing fault interfaces according to non-linear friction laws, coupled to seismic wave propagation with high-order accuracy in space and time (minimal dispersion errors). SeisSol exploits unstructured meshes to account for complex geometries, e.g. high resolution topography and bathymetry, 3D subsurface structure, and fault networks. We present the up-to-date largest (1500 km of faults) and longest (500 s) dynamic rupture simulation modeling the 2004 Sumatra-Andaman earthquake. We demonstrate the need for end-to-end-optimization and petascale performance of scientific software to realize realistic simulations on the extreme scales of subduction zone earthquakes: Considering the full complexity of subduction zone geometries leads inevitably to huge differences in element sizes. The main code improvements include a cache-aware wave propagation scheme and optimizations of the dynamic rupture kernels using code generation. In addition, a novel clustered local-time-stepping scheme for dynamic rupture has been established. Finally, asynchronous output has been implemented to overlap I/O and compute time. We resolve the frictional sliding process on the curved mega-thrust and a system of splay faults, as well as the seismic wave field and seafloor displacement with frequency content up to 2.2 Hz. We validate the scenario by geodetic, seismological and tsunami observations. The resulting rupture dynamics shed new light on the activation and importance of splay faults.
Parallel multiscale simulations of a brain aneurysm
Energy Technology Data Exchange (ETDEWEB)
Grinberg, Leopold [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States); Fedosov, Dmitry A. [Institute of Complex Systems and Institute for Advanced Simulation, Forschungszentrum Jülich, Jülich 52425 (Germany); Karniadakis, George Em, E-mail: george_karniadakis@brown.edu [Division of Applied Mathematics, Brown University, Providence, RI 02912 (United States)
2013-07-01
Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in
Parallel multiscale simulations of a brain aneurysm
International Nuclear Information System (INIS)
Grinberg, Leopold; Fedosov, Dmitry A.; Karniadakis, George Em
2013-01-01
Cardiovascular pathologies, such as a brain aneurysm, are affected by the global blood circulation as well as by the local microrheology. Hence, developing computational models for such cases requires the coupling of disparate spatial and temporal scales often governed by diverse mathematical descriptions, e.g., by partial differential equations (continuum) and ordinary differential equations for discrete particles (atomistic). However, interfacing atomistic-based with continuum-based domain discretizations is a challenging problem that requires both mathematical and computational advances. We present here a hybrid methodology that enabled us to perform the first multiscale simulations of platelet depositions on the wall of a brain aneurysm. The large scale flow features in the intracranial network are accurately resolved by using the high-order spectral element Navier–Stokes solver NεκTαr. The blood rheology inside the aneurysm is modeled using a coarse-grained stochastic molecular dynamics approach (the dissipative particle dynamics method) implemented in the parallel code LAMMPS. The continuum and atomistic domains overlap with interface conditions provided by effective forces computed adaptively to ensure continuity of states across the interface boundary. A two-way interaction is allowed with the time-evolving boundary of the (deposited) platelet clusters tracked by an immersed boundary method. The corresponding heterogeneous solvers (NεκTαr and LAMMPS) are linked together by a computational multilevel message passing interface that facilitates modularity and high parallel efficiency. Results of multiscale simulations of clot formation inside the aneurysm in a patient-specific arterial tree are presented. We also discuss the computational challenges involved and present scalability results of our coupled solver on up to 300 K computer processors. Validation of such coupled atomistic-continuum models is a main open issue that has to be addressed in
A multiphysics-viscoplastic cap model for simulating blast response of cemented tailings backfill
Directory of Open Access Journals (Sweden)
Gongda Lu
2017-06-01
Full Text Available Although a large number of previous researches have significantly contributed to the understanding of the quasi-static mechanical behavior of cemented tailings backfill, an evolutive porous medium used in underground mine cavities, very few efforts have been made to improve the knowledge on its response under sudden dynamic loading during the curing process. In fact, there is a great need for such information given that cemented backfill structures are often subjected to blast loadings due to mine exploitations. In this study, a coupled thermo-hydro-mechanical-chemical (THMC-viscoplastic cap model is developed to describe the behavior of cementing mine backfill material under blast loading. A THMC model for cemented backfill is adopted to evaluate its behavior and evolution of its properties in curing processes with coupled thermal, hydraulic, mechanical and chemical factors. Then, the model is coupled to a Perzyna type of viscoplastic model with a modified smooth surface cap envelope and a variable bulk modulus, in order to reasonably capture the nonlinear and rate-dependent behaviors of the cemented tailings backfill under blast loading. All of the parameters required for the variable-modulus viscoplastic cap model were obtained by applying the THMC model to reproducing evolution of cemented paste backfill (CPB properties in the curing process. Thus, the behavior of hydrating cemented backfill under high-rate impacts can be evaluated under any curing time of concern. The validation results of the proposed model indicate a good agreement between the experimental and the simulated results. The authors believe that the proposed model will contribute to a better understanding of the performance of hydrating cemented backfill under blasting, and also to practical risk management of backfill structures associated with such a dynamic condition.
Directory of Open Access Journals (Sweden)
Sulin Garro Acón
2012-11-01
Full Text Available En este estudio se analizó la transferencia de calor en tres disipadores de calor utilizados para enfriar los procesadores de computadoras de escritorio. El objetivo de estos disipadores es evitar el sobrecalentamiento de la unidad de procesamiento y la consecuente reducción de la vida útil del computador. Los disipadores de calor se modelaron usando COMSOL Multiphysics con las dimensiones reales de los dispositivos y la generación de calor se modeló con una fuente puntual. Luego se modificaron los diseños de los disipadores para lograr una temperatura más baja en la zona más caliente del procesador. El resultado fue una reducción en la temperatura en el rango de 5-78 grados Kelvin, al rediseñarse el disipador de calor con variaciones feasibles como la reducción del grosor de las placas de intercambio de calor y el aumento de su número. Esto demuestra la posibilidad de desarrollar diseños optimizados para disipadores de calor que no requieran más materiales sino una mejor ingeniería. El trabajo se inició como parte del curso CM-4101 Modelización y Simulación.In this study, the heat transfer of three desktop- computer heat sinks was analyzed. The objective of using these heat sinks is to avoid overheating of the computer’s processing unit and in turn reduce the corresponding loss in the unit’s service time. The heat sinks were modeled using COMSOL Multiphysics with the actual dimensions of the devices, and heat generation was modeled with a point source. In the next step, the heat sink designs were modified to achieve a lower temperature in the higher temperature location on the heat sink. The results were temperature reductions in the range of 5-78 degrees Kelvin, by making feasible variations in design such as reducing the thickness of the heat exchanger fins and increasing their number. This paper demonstrates that there is room to develop improved designs that do not require more materials but rather a better engineering
Parallel magnetic field perturbations in gyrokinetic simulations
International Nuclear Information System (INIS)
Joiner, N.; Hirose, A.; Dorland, W.
2010-01-01
At low β it is common to neglect parallel magnetic field perturbations on the basis that they are of order β 2 . This is only true if effects of order β are canceled by a term in the ∇B drift also of order β[H. L. Berk and R. R. Dominguez, J. Plasma Phys. 18, 31 (1977)]. To our knowledge this has not been rigorously tested with modern gyrokinetic codes. In this work we use the gyrokinetic code GS2[Kotschenreuther et al., Comput. Phys. Commun. 88, 128 (1995)] to investigate whether the compressional magnetic field perturbation B || is required for accurate gyrokinetic simulations at low β for microinstabilities commonly found in tokamaks. The kinetic ballooning mode (KBM) demonstrates the principle described by Berk and Dominguez strongly, as does the trapped electron mode, in a less dramatic way. The ion and electron temperature gradient (ETG) driven modes do not typically exhibit this behavior; the effects of B || are found to depend on the pressure gradients. The terms which are seen to cancel at long wavelength in KBM calculations can be cumulative in the ion temperature gradient case and increase with η e . The effect of B || on the ETG instability is shown to depend on the normalized pressure gradient β ' at constant β.
Energy Technology Data Exchange (ETDEWEB)
Bonaccorsi, Th
2007-09-15
A Material Testing Reactor (MTR) makes it possible to irradiate material samples under intense neutron and photonic fluxes. These experiments are carried out in experimental devices localised in the reactor core or in periphery (reflector). Available physics simulation tools only treat, most of the time, one physics field in a very precise way. Multi-physic simulations of irradiation experiments therefore require a sequential use of several calculation codes and data exchanges between these codes: this corresponds to problems coupling. In order to facilitate multi-physic simulations, this thesis sets up a data model based on data-processing objects, called Technological Entities. This data model is common to all of the physics fields. It permits defining the geometry of an irradiation device in a parametric way and to associate information about materials to it. Numerical simulations are encapsulated into interfaces providing the ability to call specific functionalities with the same command (to initialize data, to launch calculations, to post-treat, to get results,... ). Thus, once encapsulated, numerical simulations can be re-used for various studies. This data model is developed in a SALOME platform component. The first application case made it possible to perform neutronic simulations (OSIRIS reactor and RJH) coupled with fuel behavior simulations. In a next step, thermal hydraulics could also be taken into account. In addition to the improvement of the calculation accuracy due to the physical phenomena coupling, the time spent in the development phase of the simulation is largely reduced and the possibilities of uncertainty treatment are under consideration. (author)
International Nuclear Information System (INIS)
Chauliac, Christian; Bestion, Dominique; Crouzet, Nicolas; Aragones, Jose-Maria; Cacuci, Dan Gabriel; Weiss, Frank-Peter; Zimmermann, Martin A.
2010-01-01
The NURESIM project, the numerical simulation platform, is developed in the frame of the NURISP European Collaborative Project (FP7), which includes 22 organizations from 14 European countries. NURESIM intends to be a reference platform providing high quality software tools, physical models, generic functions and assessment results. The NURESIM platform provides an accurate representation of the physical phenomena by promoting and incorporating the latest advances in core physics, two-phase thermal-hydraulics and fuel modelling. It includes multi-scale and multi-physics features, especially for coupling core physics and thermal-hydraulics models for reactor safety. Easy coupling of the different codes and solvers is provided through the use of a common data structure and generic functions (e.g., for interpolation between non-conforming meshes). More generally, the platform includes generic pre-processing, post-processing and supervision functions through the open-source SALOME software, in order to make the codes more user-friendly. The platform also provides the informatics environment for testing and comparing different codes. The contribution summarizes the achievements and ongoing developments of the simulation platform in core physics, thermal-hydraulics, multi-physics, uncertainties and code integration
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp
2012-06-01
We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm as well as parallel execution of the hybrid simulation. We describe the implementational concept of the tool and its parallel extensions. We particularly focus on the parallel execution of particle insertions into dense molecular systems and propose a respective parallel algorithm. Our implementations are validated for serial and parallel setups in two and three dimensions. © 2012 IEEE.
Parallel sparse direct solver for integrated circuit simulation
Chen, Xiaoming; Yang, Huazhong
2017-01-01
This book describes algorithmic methods and parallelization techniques to design a parallel sparse direct solver which is specifically targeted at integrated circuit simulation problems. The authors describe a complete flow and detailed parallel algorithms of the sparse direct solver. They also show how to improve the performance by simple but effective numerical techniques. The sparse direct solver techniques described can be applied to any SPICE-like integrated circuit simulator and have been proven to be high-performance in actual circuit simulation. Readers will benefit from the state-of-the-art parallel integrated circuit simulation techniques described in this book, especially the latest parallel sparse matrix solution techniques. · Introduces complicated algorithms of sparse linear solvers, using concise principles and simple examples, without complex theory or lengthy derivations; · Describes a parallel sparse direct solver that can be adopted to accelerate any SPICE-like integrated circuit simulato...
Parallelization and automatic data distribution for nuclear reactor simulations
Energy Technology Data Exchange (ETDEWEB)
Liebrock, L.M. [Liebrock-Hicks Research, Calumet, MI (United States)
1997-07-01
Detailed attempts at realistic nuclear reactor simulations currently take many times real time to execute on high performance workstations. Even the fastest sequential machine can not run these simulations fast enough to ensure that the best corrective measure is used during a nuclear accident to prevent a minor malfunction from becoming a major catastrophe. Since sequential computers have nearly reached the speed of light barrier, these simulations will have to be run in parallel to make significant improvements in speed. In physical reactor plants, parallelism abounds. Fluids flow, controls change, and reactions occur in parallel with only adjacent components directly affecting each other. These do not occur in the sequentialized manner, with global instantaneous effects, that is often used in simulators. Development of parallel algorithms that more closely approximate the real-world operation of a reactor may, in addition to speeding up the simulations, actually improve the accuracy and reliability of the predictions generated. Three types of parallel architecture (shared memory machines, distributed memory multicomputers, and distributed networks) are briefly reviewed as targets for parallelization of nuclear reactor simulation. Various parallelization models (loop-based model, shared memory model, functional model, data parallel model, and a combined functional and data parallel model) are discussed along with their advantages and disadvantages for nuclear reactor simulation. A variety of tools are introduced for each of the models. Emphasis is placed on the data parallel model as the primary focus for two-phase flow simulation. Tools to support data parallel programming for multiple component applications and special parallelization considerations are also discussed.
Parallelization and automatic data distribution for nuclear reactor simulations
International Nuclear Information System (INIS)
Liebrock, L.M.
1997-01-01
Detailed attempts at realistic nuclear reactor simulations currently take many times real time to execute on high performance workstations. Even the fastest sequential machine can not run these simulations fast enough to ensure that the best corrective measure is used during a nuclear accident to prevent a minor malfunction from becoming a major catastrophe. Since sequential computers have nearly reached the speed of light barrier, these simulations will have to be run in parallel to make significant improvements in speed. In physical reactor plants, parallelism abounds. Fluids flow, controls change, and reactions occur in parallel with only adjacent components directly affecting each other. These do not occur in the sequentialized manner, with global instantaneous effects, that is often used in simulators. Development of parallel algorithms that more closely approximate the real-world operation of a reactor may, in addition to speeding up the simulations, actually improve the accuracy and reliability of the predictions generated. Three types of parallel architecture (shared memory machines, distributed memory multicomputers, and distributed networks) are briefly reviewed as targets for parallelization of nuclear reactor simulation. Various parallelization models (loop-based model, shared memory model, functional model, data parallel model, and a combined functional and data parallel model) are discussed along with their advantages and disadvantages for nuclear reactor simulation. A variety of tools are introduced for each of the models. Emphasis is placed on the data parallel model as the primary focus for two-phase flow simulation. Tools to support data parallel programming for multiple component applications and special parallelization considerations are also discussed
Scalable Adaptive Multilevel Solvers for Multiphysics Problems
Energy Technology Data Exchange (ETDEWEB)
Xu, Jinchao [Pennsylvania State Univ., University Park, PA (United States). Dept. of Mathematics
2014-11-26
In this project, we carried out many studies on adaptive and parallel multilevel methods for numerical modeling for various applications, including Magnetohydrodynamics (MHD) and complex fluids. We have made significant efforts and advances in adaptive multilevel methods of the multiphysics problems: multigrid methods, adaptive finite element methods, and applications.
Parallel and vector implementation of APROS simulator code
International Nuclear Information System (INIS)
Niemi, J.; Tommiska, J.
1990-01-01
In this paper the vector and parallel processing implementation of a general purpose simulator code is discussed. In this code the utilization of vector processing is straightforward. In addition to the loop level parallel processing, the functional decomposition and the domain decomposition have been considered. Results represented for a PWR-plant simulation illustrate the potential speed-up factors of the alternatives. It turns out that the loop level parallelism and the domain decomposition are the most promising alternative to employ the parallel processing. (author)
A compositional reservoir simulator on distributed memory parallel computers
International Nuclear Information System (INIS)
Rame, M.; Delshad, M.
1995-01-01
This paper presents the application of distributed memory parallel computes to field scale reservoir simulations using a parallel version of UTCHEM, The University of Texas Chemical Flooding Simulator. The model is a general purpose highly vectorized chemical compositional simulator that can simulate a wide range of displacement processes at both field and laboratory scales. The original simulator was modified to run on both distributed memory parallel machines (Intel iPSC/960 and Delta, Connection Machine 5, Kendall Square 1 and 2, and CRAY T3D) and a cluster of workstations. A domain decomposition approach has been taken towards parallelization of the code. A portion of the discrete reservoir model is assigned to each processor by a set-up routine that attempts a data layout as even as possible from the load-balance standpoint. Each of these subdomains is extended so that data can be shared between adjacent processors for stencil computation. The added routines that make parallel execution possible are written in a modular fashion that makes the porting to new parallel platforms straight forward. Results of the distributed memory computing performance of Parallel simulator are presented for field scale applications such as tracer flood and polymer flood. A comparison of the wall-clock times for same problems on a vector supercomputer is also presented
Parallel-Processing Test Bed For Simulation Software
Blech, Richard; Cole, Gary; Townsend, Scott
1996-01-01
Second-generation Hypercluster computing system is multiprocessor test bed for research on parallel algorithms for simulation in fluid dynamics, electromagnetics, chemistry, and other fields with large computational requirements but relatively low input/output requirements. Built from standard, off-shelf hardware readily upgraded as improved technology becomes available. System used for experiments with such parallel-processing concepts as message-passing algorithms, debugging software tools, and computational steering. First-generation Hypercluster system described in "Hypercluster Parallel Processor" (LEW-15283).
Parallel simulated annealing algorithms for cell placement on hypercube multiprocessors
Banerjee, Prithviraj; Jones, Mark Howard; Sargent, Jeff S.
1990-01-01
Two parallel algorithms for standard cell placement using simulated annealing are developed to run on distributed-memory message-passing hypercube multiprocessors. The cells can be mapped in a two-dimensional area of a chip onto processors in an n-dimensional hypercube in two ways, such that both small and large cell exchange and displacement moves can be applied. The computation of the cost function in parallel among all the processors in the hypercube is described, along with a distributed data structure that needs to be stored in the hypercube to support the parallel cost evaluation. A novel tree broadcasting strategy is used extensively for updating cell locations in the parallel environment. A dynamic parallel annealing schedule estimates the errors due to interacting parallel moves and adapts the rate of synchronization automatically. Two novel approaches in controlling error in parallel algorithms are described: heuristic cell coloring and adaptive sequence control.
Prototyping and Simulating Parallel, Distributed Computations with VISA
National Research Council Canada - National Science Library
Demeure, Isabelle M; Nutt, Gary J
1989-01-01
...] to support the design, prototyping, and simulation of parallel, distributed computations. In particular, VISA is meant to guide the choice of partitioning and communication strategies for such computations, based on their performance...
Visual Interfaces for Parallel Simulations (VIPS), Phase I
National Aeronautics and Space Administration — Configuring the 3D geometry and physics of large scale parallel physics simulations is increasingly complex. Given the investment in time and effort to run these...
Parallel discrete-event simulation of FCFS stochastic queueing networks
Nicol, David M.
1988-01-01
Physical systems are inherently parallel. Intuition suggests that simulations of these systems may be amenable to parallel execution. The parallel execution of a discrete-event simulation requires careful synchronization of processes in order to ensure the execution's correctness; this synchronization can degrade performance. Largely negative results were recently reported in a study which used a well-known synchronization method on queueing network simulations. Discussed here is a synchronization method (appointments), which has proven itself to be effective on simulations of FCFS queueing networks. The key concept behind appointments is the provision of lookahead. Lookahead is a prediction on a processor's future behavior, based on an analysis of the processor's simulation state. It is shown how lookahead can be computed for FCFS queueing network simulations, give performance data that demonstrates the method's effectiveness under moderate to heavy loads, and discuss performance tradeoffs between the quality of lookahead, and the cost of computing lookahead.
Xyce parallel electronic simulator : users' guide.
Energy Technology Data Exchange (ETDEWEB)
Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Warrender, Christina E.; Keiter, Eric Richard; Pawlowski, Roger Patrick
2011-05-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers; (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only); and (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is
Running Parallel Discrete Event Simulators on Sierra
Energy Technology Data Exchange (ETDEWEB)
Barnes, P. D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Jefferson, D. R. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
2015-12-03
In this proposal we consider porting the ROSS/Charm++ simulator and the discrete event models that run under its control so that they run on the Sierra architecture and make efficient use of the Volta GPUs.
Parallel pic plasma simulation through particle decomposition techniques
International Nuclear Information System (INIS)
Briguglio, S.; Vlad, G.; Di Martino, B.; Naples, Univ. 'Federico II'
1998-02-01
Particle-in-cell (PIC) codes are among the major candidates to yield a satisfactory description of the detail of kinetic effects, such as the resonant wave-particle interaction, relevant in determining the transport mechanism in magnetically confined plasmas. A significant improvement of the simulation performance of such codes con be expected from parallelization, e.g., by distributing the particle population among several parallel processors. Parallelization of a hybrid magnetohydrodynamic-gyrokinetic code has been accomplished within the High Performance Fortran (HPF) framework, and tested on the IBM SP2 parallel system, using a 'particle decomposition' technique. The adopted technique requires a moderate effort in porting the code in parallel form and results in intrinsic load balancing and modest inter processor communication. The performance tests obtained confirm the hypothesis of high effectiveness of the strategy, if targeted towards moderately parallel architectures. Optimal use of resources is also discussed with reference to a specific physics problem [it
Derkevorkian, Armen; Peterson, Lee; Kolaini, Ali R.; Hendricks, Terry J.; Nesmith, Bill J.
2016-01-01
An analytic approach is demonstrated to reveal potential pyroshock -driven dynamic effects causing power losses in the Thermo -Electric (TE) module bars of the Mars Science Laboratory (MSL) Multi -Mission Radioisotope Thermoelectric Generator (MMRTG). This study utilizes high- fidelity finite element analysis with SIERRA/PRESTO codes to estimate wave propagation effects due to large -amplitude suddenly -applied pyro shock loads in the MMRTG. A high fidelity model of the TE module bar was created with approximately 30 million degrees -of-freedom (DOF). First, a quasi -static preload was applied on top of the TE module bar, then transient tri- axial acceleration inputs were simultaneously applied on the preloaded module. The applied input acceleration signals were measured during MMRTG shock qualification tests performed at the Jet Propulsion Laboratory. An explicit finite element solver in the SIERRA/PRESTO computational environment, along with a 3000 processor parallel super -computing framework at NASA -AMES, was used for the simulation. The simulation results were investigated both qualitatively and quantitatively. The predicted shock wave propagation results provide detailed structural responses throughout the TE module bar, and key insights into the dynamic response (i.e., loads, displacements, accelerations) of critical internal spring/piston compression systems, TE materials, and internal component interfaces in the MMRTG TE module bar. They also provide confidence on the viability of this high -fidelity modeling scheme to accurately predict shock wave propagation patterns within complex structures. This analytic approach is envisioned for modeling shock sensitive hardware susceptible to intense shock environments positioned near shock separation devices in modern space vehicles and systems.
Parallel discrete event simulation: A shared memory approach
Reed, Daniel A.; Malony, Allen D.; Mccredie, Bradley D.
1987-01-01
With traditional event list techniques, evaluating a detailed discrete event simulation model can often require hours or even days of computation time. Parallel simulation mimics the interacting servers and queues of a real system by assigning each simulated entity to a processor. By eliminating the event list and maintaining only sufficient synchronization to insure causality, parallel simulation can potentially provide speedups that are linear in the number of processors. A set of shared memory experiments is presented using the Chandy-Misra distributed simulation algorithm to simulate networks of queues. Parameters include queueing network topology and routing probabilities, number of processors, and assignment of network nodes to processors. These experiments show that Chandy-Misra distributed simulation is a questionable alternative to sequential simulation of most queueing network models.
Bi, Linfeng
2009-01-01
The main challenges in modeling fluid flow through naturally-fractured carbonate karst reservoirs are how to address various flow physics in complex geological architectures due to the presence of vugs and caves which are connected via fracture networks at multiple scales. In this paper, we present a unified multi-physics model that adapts to the complex flow regime through naturally-fractured carbonate karst reservoirs. This approach generalizes Stokes-Brinkman model (Popov et al. 2007). The fracture networks provide the essential connection between the caves in carbonate karst reservoirs. It is thus very important to resolve the flow in fracture network and the interaction between fractures and caves to better understand the complex flow behavior. The idea is to use Stokes-Brinkman model to represent flow through rock matrix, void caves as well as intermediate flows in very high permeability regions and to use an idea similar to discrete fracture network model to represent flow in fracture network. Consequently, various numerical solution strategies can be efficiently applied to greatly improve the computational efficiency in flow simulations. We have applied this unified multi-physics model as a fine-scale flow solver in scale-up computations. Both local and global scale-up are considered. It is found that global scale-up has much more accurate than local scale-up. Global scale-up requires the solution of global flow problems on fine grid, which generally is computationally expensive. The proposed model has the ability to deal with large number of fractures and caves, which facilitate the application of Stokes-Brinkman model in global scale-up computation. The proposed model flexibly adapts to the different flow physics in naturally-fractured carbonate karst reservoirs in a simple and effective way. It certainly extends modeling and predicting capability in efficient development of this important type of reservoir.
CUBESIM, Hypercube and Denelcor Hep Parallel Computer Simulation
International Nuclear Information System (INIS)
Dunigan, T.H.
1988-01-01
1 - Description of program or function: CUBESIM is a set of subroutine libraries and programs for the simulation of message-passing parallel computers and shared-memory parallel computers. Subroutines are supplied to simulate the Intel hypercube and the Denelcor HEP parallel computers. The system permits a user to develop and test parallel programs written in C or FORTRAN on a single processor. The user may alter such hypercube parameters as message startup times, packet size, and the computation-to-communication ratio. The simulation generates a trace file that can be used for debugging, performance analysis, or graphical display. 2 - Method of solution: The CUBESIM simulator is linked with the user's parallel application routines to run as a single UNIX process. The simulator library provides a small operating system to perform process and message management. 3 - Restrictions on the complexity of the problem: Up to 128 processors can be simulated with a virtual memory limit of 6 million bytes. Up to 1000 processes can be simulated
Beam dynamics simulations using a parallel version of PARMILA
International Nuclear Information System (INIS)
Ryne, R.D.
1996-01-01
The computer code PARMILA has been the primary tool for the design of proton and ion linacs in the United States for nearly three decades. Previously it was sufficient to perform simulations with of order 10000 particles, but recently the need to perform high resolution halo studies for next-generation, high intensity linacs has made it necessary to perform simulations with of order 100 million particles. With the advent of massively parallel computers such simulations are now within reach. Parallel computers already make it possible, for example, to perform beam dynamics calculations with tens of millions of particles, requiring over 10 GByte of core memory, in just a few hours. Also, parallel computers are becoming easier to use thanks to the availability of mature, Fortran-like languages such as Connection Machine Fortran and High Performance Fortran. We will describe our experience developing a parallel version of PARMILA and the performance of the new code
Beam dynamics simulations using a parallel version of PARMILA
International Nuclear Information System (INIS)
Ryne, Robert
1996-01-01
The computer code PARMILA has been the primary tool for the design of proton and ion linacs in the United States for nearly three decades. Previously it was sufficient to perform simulations with of order 10000 particles, but recently the need to perform high resolution halo studies for next-generation, high intensity linacs has made it necessary to perform simulations with of order 100 million particles. With the advent of massively parallel computers such simulations are now within reach. Parallel computers already make it possible, for example, to perform beam dynamics calculations with tens of millions of particles, requiring over 10 GByte of core memory, in just a few hours. Also, parallel computers are becoming easier to use thanks to the availability of mature, Fortran-like languages such as Connection Machine Fortran and High Performance Fortran. We will describe our experience developing a parallel version of PARMILA and the performance of the new code. (author)
A path-level exact parallelization strategy for sequential simulation
Peredo, Oscar F.; Baeza, Daniel; Ortiz, Julián M.; Herrero, José R.
2018-01-01
Sequential Simulation is a well known method in geostatistical modelling. Following the Bayesian approach for simulation of conditionally dependent random events, Sequential Indicator Simulation (SIS) method draws simulated values for K categories (categorical case) or classes defined by K different thresholds (continuous case). Similarly, Sequential Gaussian Simulation (SGS) method draws simulated values from a multivariate Gaussian field. In this work, a path-level approach to parallelize SIS and SGS methods is presented. A first stage of re-arrangement of the simulation path is performed, followed by a second stage of parallel simulation for non-conflicting nodes. A key advantage of the proposed parallelization method is to generate identical realizations as with the original non-parallelized methods. Case studies are presented using two sequential simulation codes from GSLIB: SISIM and SGSIM. Execution time and speedup results are shown for large-scale domains, with many categories and maximum kriging neighbours in each case, achieving high speedup results in the best scenarios using 16 threads of execution in a single machine.
Ariane, Mostapha; Kassinos, Stavros; Velaga, Sitaram; Alexiadis, Alessio
2018-04-01
In this paper, the mass transfer coefficient (permeability) of boundary layers containing motile cilia is investigated by means of discrete multi-physics. The idea is to understand the main mechanisms of mass transport occurring in a ciliated-layer; one specific application being inhaled drugs in the respiratory epithelium. The effect of drug diffusivity, cilia beat frequency and cilia flexibility is studied. Our results show the existence of three mass transfer regimes. A low frequency regime, which we called shielding regime, where the presence of the cilia hinders mass transport; an intermediate frequency regime, which we have called diffusive regime, where diffusion is the controlling mechanism; and a high frequency regime, which we have called convective regime, where the degree of bending of the cilia seems to be the most important factor controlling mass transfer in the ciliated-layer. Since the flexibility of the cilia and the frequency of the beat changes with age and health conditions, the knowledge of these three regimes allows prediction of how mass transfer varies with these factors. Copyright © 2018 Elsevier Ltd. All rights reserved.
A Generic Mesh Data Structure with Parallel Applications
Cochran, William Kenneth, Jr.
2009-01-01
High performance, massively-parallel multi-physics simulations are built on efficient mesh data structures. Most data structures are designed from the bottom up, focusing on the implementation of linear algebra routines. In this thesis, we explore a top-down approach to design, evaluating the various needs of many aspects of simulation, not just…
Tutorial: Parallel Computing of Simulation Models for Risk Analysis.
Reilly, Allison C; Staid, Andrea; Gao, Michael; Guikema, Seth D
2016-10-01
Simulation models are widely used in risk analysis to study the effects of uncertainties on outcomes of interest in complex problems. Often, these models are computationally complex and time consuming to run. This latter point may be at odds with time-sensitive evaluations or may limit the number of parameters that are considered. In this article, we give an introductory tutorial focused on parallelizing simulation code to better leverage modern computing hardware, enabling risk analysts to better utilize simulation-based methods for quantifying uncertainty in practice. This article is aimed primarily at risk analysts who use simulation methods but do not yet utilize parallelization to decrease the computational burden of these models. The discussion is focused on conceptual aspects of embarrassingly parallel computer code and software considerations. Two complementary examples are shown using the languages MATLAB and R. A brief discussion of hardware considerations is located in the Appendix. © 2016 Society for Risk Analysis.
Parallelization of Rocket Engine Simulator Software (PRESS)
Cezzar, Ruknet
1998-01-01
We have outlined our work in the last half of the funding period. We have shown how a demo package for RESSAP using MPI can be done. However, we also mentioned the difficulties with the UNIX platform. We have reiterated some of the suggestions made during the presentation of the progress of the at Fourth Annual HBCU Conference. Although we have discussed, in some detail, how TURBDES/PUMPDES software can be run in parallel using MPI, at present, we are unable to experiment any further with either MPI or PVM. Due to X windows not being implemented, we are also not able to experiment further with XPVM, which it will be recalled, has a nice GUI interface. There are also some concerns, on our part, about MPI being an appropriate tool. The best thing about MPr is that it is public domain. Although and plenty of documentation exists for the intricacies of using MPI, little information is available on its actual implementations. Other than very typical, somewhat contrived examples, such as Jacobi algorithm for solving Laplace's equation, there are few examples which can readily be applied to real situations, such as in our case. In effect, the review of literature on both MPI and PVM, and there is a lot, indicate something similar to the enormous effort which was spent on LISP and LISP-like languages as tools for artificial intelligence research. During the development of a book on programming languages [12], when we searched the literature for very simple examples like taking averages, reading and writing records, multiplying matrices, etc., we could hardly find a any! Yet, so much was said and done on that topic in academic circles. It appears that we faced the same problem with MPI, where despite significant documentation, we could not find even a simple example which supports course-grain parallelism involving only a few processes. From the foregoing, it appears that a new direction may be required for more productive research during the extension period (10/19/98 - 10
Vlasov simulations of parallel potential drops
Directory of Open Access Journals (Sweden)
H. Gunell
2013-07-01
Full Text Available An auroral flux tube is modelled from the magnetospheric equator to the ionosphere using Vlasov simulations. Starting from an initial state, the evolution of the plasma on the flux tube is followed in time. It is found that when applying a voltage between the ends of the flux tube, about two thirds of the potential drop is concentrated in a thin double layer at approximately one Earth radius altitude. The remaining part is situated in an extended region 1–2 Earth radii above the double layer. Waves on the ion timescale develop above the double layer, and they move toward higher altitude at approximately the ion acoustic speed. These waves are seen both in the electric field and as perturbations of the ion and electron distributions, indicative of an instability. Electrons of magnetospheric origin become trapped between the magnetic mirror and the double layer during its formation. At low altitude, waves on electron timescales appear and are seen to be non-uniformly distributed in space. The temporal evolution of the potential profile and the total voltage affect the double layer altitude, which decreases with an increasing field aligned potential drop. A current–voltage relationship is found by running several simulations with different voltages over the system, and it agrees with the Knight relation reasonably well.
General-purpose parallel simulator for quantum computing
International Nuclear Information System (INIS)
Niwa, Jumpei; Matsumoto, Keiji; Imai, Hiroshi
2002-01-01
With current technologies, it seems to be very difficult to implement quantum computers with many qubits. It is therefore of importance to simulate quantum algorithms and circuits on the existing computers. However, for a large-size problem, the simulation often requires more computational power than is available from sequential processing. Therefore, simulation methods for parallel processors are required. We have developed a general-purpose simulator for quantum algorithms/circuits on the parallel computer (Sun Enterprise4500). It can simulate algorithms/circuits with up to 30 qubits. In order to test efficiency of our proposed methods, we have simulated Shor's factorization algorithm and Grover's database search, and we have analyzed robustness of the corresponding quantum circuits in the presence of both decoherence and operational errors. The corresponding results, statistics, and analyses are presented in this paper
A hybrid algorithm for parallel molecular dynamics simulations
Mangiardi, Chris M.; Meyer, R.
2017-10-01
This article describes algorithms for the hybrid parallelization and SIMD vectorization of molecular dynamics simulations with short-range forces. The parallelization method combines domain decomposition with a thread-based parallelization approach. The goal of the work is to enable efficient simulations of very large (tens of millions of atoms) and inhomogeneous systems on many-core processors with hundreds or thousands of cores and SIMD units with large vector sizes. In order to test the efficiency of the method, simulations of a variety of configurations with up to 74 million atoms have been performed. Results are shown that were obtained on multi-core systems with Sandy Bridge and Haswell processors as well as systems with Xeon Phi many-core processors.
A tool for simulating parallel branch-and-bound methods
Golubeva, Yana; Orlov, Yury; Posypkin, Mikhail
2016-01-01
The Branch-and-Bound method is known as one of the most powerful but very resource consuming global optimization methods. Parallel and distributed computing can efficiently cope with this issue. The major difficulty in parallel B&B method is the need for dynamic load redistribution. Therefore design and study of load balancing algorithms is a separate and very important research topic. This paper presents a tool for simulating parallel Branchand-Bound method. The simulator allows one to run load balancing algorithms with various numbers of processors, sizes of the search tree, the characteristics of the supercomputer's interconnect thereby fostering deep study of load distribution strategies. The process of resolution of the optimization problem by B&B method is replaced by a stochastic branching process. Data exchanges are modeled using the concept of logical time. The user friendly graphical interface to the simulator provides efficient visualization and convenient performance analysis.
Parallel alternating direction preconditioner for isogeometric simulations of explicit dynamics
Łoś, Marcin
2015-04-27
In this paper we present a parallel implementation of the alternating direction preconditioner for isogeometric simulations of explicit dynamics. The Alternating Direction Implicit (ADI) algorithm, belongs to the category of matrix-splitting iterative methods, was proposed almost six decades ago for solving parabolic and elliptic partial differential equations, see [1–4]. The new version of this algorithm has been recently developed for isogeometric simulations of two dimensional explicit dynamics [5] and steady-state diffusion equations with orthotropic heterogenous coefficients [6]. In this paper we present a parallel version of the alternating direction implicit algorithm for three dimensional simulations. The algorithm has been incorporated as a part of PETIGA an isogeometric framework [7] build on top of PETSc [8]. We show the scalability of the parallel algorithm on STAMPEDE linux cluster up to 10,000 processors, as well as the convergence rate of the PCG solver with ADI algorithm as preconditioner.
Engineering-Based Thermal CFD Simulations on Massive Parallel Systems
Frisch, Jérôme
2015-05-22
The development of parallel Computational Fluid Dynamics (CFD) codes is a challenging task that entails efficient parallelization concepts and strategies in order to achieve good scalability values when running those codes on modern supercomputers with several thousands to millions of cores. In this paper, we present a hierarchical data structure for massive parallel computations that supports the coupling of a Navier–Stokes-based fluid flow code with the Boussinesq approximation in order to address complex thermal scenarios for energy-related assessments. The newly designed data structure is specifically designed with the idea of interactive data exploration and visualization during runtime of the simulation code; a major shortcoming of traditional high-performance computing (HPC) simulation codes. We further show and discuss speed-up values obtained on one of Germany’s top-ranked supercomputers with up to 140,000 processes and present simulation results for different engineering-based thermal problems.
A tool for simulating parallel branch-and-bound methods
Directory of Open Access Journals (Sweden)
Golubeva Yana
2016-01-01
Full Text Available The Branch-and-Bound method is known as one of the most powerful but very resource consuming global optimization methods. Parallel and distributed computing can efficiently cope with this issue. The major difficulty in parallel B&B method is the need for dynamic load redistribution. Therefore design and study of load balancing algorithms is a separate and very important research topic. This paper presents a tool for simulating parallel Branchand-Bound method. The simulator allows one to run load balancing algorithms with various numbers of processors, sizes of the search tree, the characteristics of the supercomputer’s interconnect thereby fostering deep study of load distribution strategies. The process of resolution of the optimization problem by B&B method is replaced by a stochastic branching process. Data exchanges are modeled using the concept of logical time. The user friendly graphical interface to the simulator provides efficient visualization and convenient performance analysis.
A hybrid parallel framework for the cellular Potts model simulations
Energy Technology Data Exchange (ETDEWEB)
Jiang, Yi [Los Alamos National Laboratory; He, Kejing [SOUTH CHINA UNIV; Dong, Shoubin [SOUTH CHINA UNIV
2009-01-01
The Cellular Potts Model (CPM) has been widely used for biological simulations. However, most current implementations are either sequential or approximated, which can't be used for large scale complex 3D simulation. In this paper we present a hybrid parallel framework for CPM simulations. The time-consuming POE solving, cell division, and cell reaction operation are distributed to clusters using the Message Passing Interface (MPI). The Monte Carlo lattice update is parallelized on shared-memory SMP system using OpenMP. Because the Monte Carlo lattice update is much faster than the POE solving and SMP systems are more and more common, this hybrid approach achieves good performance and high accuracy at the same time. Based on the parallel Cellular Potts Model, we studied the avascular tumor growth using a multiscale model. The application and performance analysis show that the hybrid parallel framework is quite efficient. The hybrid parallel CPM can be used for the large scale simulation ({approx}10{sup 8} sites) of complex collective behavior of numerous cells ({approx}10{sup 6}).
Parallel simulation of radio-frequency plasma discharges
International Nuclear Information System (INIS)
Fivaz, M.; Howling, A.; Ruegsegger, L.; Schwarzenbach, W.; Baeumle, B.
1994-01-01
The 1D Particle-In-Cell and Monte Carlo collision code XPDP1 is used to model radio-frequency argon plasma discharges. The code runs faster on a single-user parallel system called MUSIC than on a CRAY-YMP. The low cost of the MUSIC system allows a 24-hours-per-day use and the simulation results are available one to two orders of magnitude quicker than with a super computer shared with other users. The parallelization strategy and its implementation are discussed. Very good agreement is found between simulation results and measurements done in an experimental argon discharge. (author) 2 figs., 3 refs
Multiphysics modeling of magnetorheological dampers
Directory of Open Access Journals (Sweden)
D Case
2016-09-01
Full Text Available The dynamics of a small scale magnetorheological damper were modeled and analyzed using multiphysics commercial finite element software to couple the electromagnetic field distribution with the non-Newtonian fluid flow. The magnetic flux lines and field intensity generated within the damper and cyclic fluid flow in the damper under harmonic motion were simulated with the AC/DC and CFD physics modules of COMSOL Multiphysics, respectively. Coupling of the physics is achieved through a modified Bingham plastic definition, relating the fluid's dynamic viscosity to the intensity of the induced magnetic field. Good agreement is confirmed between simulation results and experimentally observed resistance forces in the damper. This study was conducted to determine the feasibility of utilizing magnetorheological dampers in a medical orthosis for pathological tremor attenuation. The implemented models are thus dimensioned on a relatively small scale. The method used, however, is not specific to the damper's size or geometry and can be extended to larger-scale devices with little or no complication.
Parallelization of a Monte Carlo particle transport simulation code
Hadjidoukas, P.; Bousis, C.; Emfietzoglou, D.
2010-05-01
We have developed a high performance version of the Monte Carlo particle transport simulation code MC4. The original application code, developed in Visual Basic for Applications (VBA) for Microsoft Excel, was first rewritten in the C programming language for improving code portability. Several pseudo-random number generators have been also integrated and studied. The new MC4 version was then parallelized for shared and distributed-memory multiprocessor systems using the Message Passing Interface. Two parallel pseudo-random number generator libraries (SPRNG and DCMT) have been seamlessly integrated. The performance speedup of parallel MC4 has been studied on a variety of parallel computing architectures including an Intel Xeon server with 4 dual-core processors, a Sun cluster consisting of 16 nodes of 2 dual-core AMD Opteron processors and a 200 dual-processor HP cluster. For large problem size, which is limited only by the physical memory of the multiprocessor server, the speedup results are almost linear on all systems. We have validated the parallel implementation against the serial VBA and C implementations using the same random number generator. Our experimental results on the transport and energy loss of electrons in a water medium show that the serial and parallel codes are equivalent in accuracy. The present improvements allow for studying of higher particle energies with the use of more accurate physical models, and improve statistics as more particles tracks can be simulated in low response time.
Simulation of neutron transport equation using parallel Monte Carlo for deep penetration problems
International Nuclear Information System (INIS)
Bekar, K. K.; Tombakoglu, M.; Soekmen, C. N.
2001-01-01
Neutron transport equation is simulated using parallel Monte Carlo method for deep penetration neutron transport problem. Monte Carlo simulation is parallelized by using three different techniques; direct parallelization, domain decomposition and domain decomposition with load balancing, which are used with PVM (Parallel Virtual Machine) software on LAN (Local Area Network). The results of parallel simulation are given for various model problems. The performances of the parallelization techniques are compared with each other. Moreover, the effects of variance reduction techniques on parallelization are discussed
Parallelization of a numerical simulation code for isotropic turbulence
International Nuclear Information System (INIS)
Sato, Shigeru; Yokokawa, Mitsuo; Watanabe, Tadashi; Kaburaki, Hideo.
1996-03-01
A parallel pseudospectral code which solves the three-dimensional Navier-Stokes equation by direct numerical simulation is developed and execution time, parallelization efficiency, load balance and scalability are evaluated. A vector parallel supercomputer, Fujitsu VPP500 with up to 16 processors is used for this calculation for Fourier modes up to 256x256x256 using 16 processors. Good scalability for number of processors is achieved when number of Fourier mode is fixed. For small Fourier modes, calculation time of the program is proportional to NlogN which is ideal complexity of calculation for 3D-FFT on vector parallel processors. It is found that the calculation performance decreases as the increase of the Fourier modes. (author)
Enabling parallel simulation of large-scale HPC network systems
International Nuclear Information System (INIS)
Mubarak, Misbah; Carothers, Christopher D.; Ross, Robert B.; Carns, Philip
2016-01-01
Here, with the increasing complexity of today’s high-performance computing (HPC) architectures, simulation has become an indispensable tool for exploring the design space of HPC systems—in particular, networks. In order to make effective design decisions, simulations of these systems must possess the following properties: (1) have high accuracy and fidelity, (2) produce results in a timely manner, and (3) be able to analyze a broad range of network workloads. Most state-of-the-art HPC network simulation frameworks, however, are constrained in one or more of these areas. In this work, we present a simulation framework for modeling two important classes of networks used in today’s IBM and Cray supercomputers: torus and dragonfly networks. We use the Co-Design of Multi-layer Exascale Storage Architecture (CODES) simulation framework to simulate these network topologies at a flit-level detail using the Rensselaer Optimistic Simulation System (ROSS) for parallel discrete-event simulation. Our simulation framework meets all the requirements of a practical network simulation and can assist network designers in design space exploration. First, it uses validated and detailed flit-level network models to provide an accurate and high-fidelity network simulation. Second, instead of relying on serial time-stepped or traditional conservative discrete-event simulations that limit simulation scalability and efficiency, we use the optimistic event-scheduling capability of ROSS to achieve efficient and scalable HPC network simulations on today’s high-performance cluster systems. Third, our models give network designers a choice in simulating a broad range of network workloads, including HPC application workloads using detailed network traces, an ability that is rarely offered in parallel with high-fidelity network simulations
Treatment planning in radiosurgery: parallel Monte Carlo simulation software
Energy Technology Data Exchange (ETDEWEB)
Scielzo, G [Galliera Hospitals, Genova (Italy). Dept. of Hospital Physics; Grillo Ruggieri, F [Galliera Hospitals, Genova (Italy) Dept. for Radiation Therapy; Modesti, M; Felici, R [Electronic Data System, Rome (Italy); Surridge, M [University of South Hampton (United Kingdom). Parallel Apllication Centre
1995-12-01
The main objective of this research was to evaluate the possibility of direct Monte Carlo simulation for accurate dosimetry with short computation time. We made us of: graphics workstation, linear accelerator, water, PMMA and anthropomorphic phantoms, for validation purposes; ionometric, film and thermo-luminescent techniques, for dosimetry; treatment planning system for comparison. Benchmarking results suggest that short computing times can be obtained with use of the parallel version of EGS4 that was developed. Parallelism was obtained assigning simulation incident photons to separate processors, and the development of a parallel random number generator was necessary. Validation consisted in: phantom irradiation, comparison of predicted and measured values good agreement in PDD and dose profiles. Experiments on anthropomorphic phantoms (with inhomogeneities) were carried out, and these values are being compared with results obtained with the conventional treatment planning system.
Xyce parallel electronic simulator reference guide, version 6.1
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Sholander, Peter E.; Thornquist, Heidi K.; Verley, Jason C.; Baur, David Gregory
2014-03-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide [1] .
Xyce™ Parallel Electronic Simulator: Reference Guide, Version 5.1
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical and Microsystems Modeling; Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical and Microsystems Modeling; Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical and Microsystems Modeling; Rankin, Eric Lamont [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical and Microsystems Modeling; Schiek, Richard Louis [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical and Microsystems Modeling; Santarelli, Keith R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical and Microsystems Modeling; Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical and Microsystems Modeling; Fixel, Deborah A. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical and Microsystems Modeling; Coffey, Todd S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Applied Mathematics and Applications; Pawlowski, Roger P. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Applied Mathematics and Applications
2009-11-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users’ Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users’ Guide.
Xyce Parallel Electronic Simulator : reference guide, version 4.1.
Energy Technology Data Exchange (ETDEWEB)
Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick
2009-02-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide.
Xyce™ Parallel Electronic Simulator Reference Guide Version 6.8
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aadithya, Karthik Venkatraman [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2017-10-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide.
Xyce parallel electronic simulator reference guide, version 6.0.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Verley, Jason C.; Fixel, Deborah A.; Coffey, Todd S; Pawlowski, Roger P; Warrender, Christina E.; Baur, David Gregory.
2013-08-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide [1] .
Smoldyn on graphics processing units: massively parallel Brownian dynamics simulations.
Dematté, Lorenzo
2012-01-01
Space is a very important aspect in the simulation of biochemical systems; recently, the need for simulation algorithms able to cope with space is becoming more and more compelling. Complex and detailed models of biochemical systems need to deal with the movement of single molecules and particles, taking into consideration localized fluctuations, transportation phenomena, and diffusion. A common drawback of spatial models lies in their complexity: models can become very large, and their simulation could be time consuming, especially if we want to capture the systems behavior in a reliable way using stochastic methods in conjunction with a high spatial resolution. In order to deliver the promise done by systems biology to be able to understand a system as whole, we need to scale up the size of models we are able to simulate, moving from sequential to parallel simulation algorithms. In this paper, we analyze Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of Graphics Processing Units (GPUs). The implementation executes the most computational demanding steps (computation of diffusion, unimolecular, and bimolecular reaction, as well as the most common cases of molecule-surface interaction) on the GPU, computing them in parallel on each molecule of the system. The implementation offers good speed-ups and real time, high quality graphics output
May, Christian P; Kolokotroni, Eleni; Stamatakos, Georgios S; Büchler, Philippe
2011-10-01
Modeling of tumor growth has been performed according to various approaches addressing different biocomplexity levels and spatiotemporal scales. Mathematical treatments range from partial differential equation based diffusion models to rule-based cellular level simulators, aiming at both improving our quantitative understanding of the underlying biological processes and, in the mid- and long term, constructing reliable multi-scale predictive platforms to support patient-individualized treatment planning and optimization. The aim of this paper is to establish a multi-scale and multi-physics approach to tumor modeling taking into account both the cellular and the macroscopic mechanical level. Therefore, an already developed biomodel of clinical tumor growth and response to treatment is self-consistently coupled with a biomechanical model. Results are presented for the free growth case of the imageable component of an initially point-like glioblastoma multiforme tumor. The composite model leads to significant tumor shape corrections that are achieved through the utilization of environmental pressure information and the application of biomechanical principles. Using the ratio of smallest to largest moment of inertia of the tumor material to quantify the effect of our coupled approach, we have found a tumor shape correction of 20% by coupling biomechanics to the cellular simulator as compared to a cellular simulation without preferred growth directions. We conclude that the integration of the two models provides additional morphological insight into realistic tumor growth behavior. Therefore, it might be used for the development of an advanced oncosimulator focusing on tumor types for which morphology plays an important role in surgical and/or radio-therapeutic treatment planning. Copyright © 2011 Elsevier Ltd. All rights reserved.
An Advanced Simulation Framework for Parallel Discrete-Event Simulation
Li, P. P.; Tyrrell, R. Yeung D.; Adhami, N.; Li, T.; Henry, H.
1994-01-01
Discrete-event simulation (DEVS) users have long been faced with a three-way trade-off of balancing execution time, model fidelity, and number of objects simulated. Because of the limits of computer processing power the analyst is often forced to settle for less than desired performances in one or more of these areas.
Directory of Open Access Journals (Sweden)
Roger P. Pawlowski
2012-01-01
Full Text Available An approach for incorporating embedded simulation and analysis capabilities in complex simulation codes through template-based generic programming is presented. This approach relies on templating and operator overloading within the C++ language to transform a given calculation into one that can compute a variety of additional quantities that are necessary for many state-of-the-art simulation and analysis algorithms. An approach for incorporating these ideas into complex simulation codes through general graph-based assembly is also presented. These ideas have been implemented within a set of packages in the Trilinos framework and are demonstrated on a simple problem from chemical engineering.
A theory manual for multi-physics code coupling in LIME.
Energy Technology Data Exchange (ETDEWEB)
Belcourt, Noel; Bartlett, Roscoe Ainsworth; Pawlowski, Roger Patrick; Schmidt, Rodney Cannon; Hooper, Russell Warren
2011-03-01
The Lightweight Integrating Multi-physics Environment (LIME) is a software package for creating multi-physics simulation codes. Its primary application space is when computer codes are currently available to solve different parts of a multi-physics problem and now need to be coupled with other such codes. In this report we define a common domain language for discussing multi-physics coupling and describe the basic theory associated with multiphysics coupling algorithms that are to be supported in LIME. We provide an assessment of coupling techniques for both steady-state and time dependent coupled systems. Example couplings are also demonstrated.
Study and simulation of a parallel numerical processing machine
International Nuclear Information System (INIS)
Bel Hadj, Slaheddine
1981-12-01
This study has been carried out in the perspective of the implementation on a minicomputer of the NEPTUNIX package (software for the resolution of very large algebra-differential equation systems). Aiming at increasing the system performance, a previous research work has shown the necessity of reducing the execution time of certain numerical computation tasks, which are of frequent use. It has also demonstrated the feasibility of handling these tasks with efficient algorithms of parallel type. The present work deals with the study and simulation of a parallel architecture processor adapted to the fast execution of these algorithms. A minicomputer fitted with a connection to such a parallel processor, has a greatly extended computing power. Then the architecture of a parallel numerical processor, based on the use of VLSI microprocessors and co-processors, is described. Its design aims at the best cost / performance ratio. The last part deals with the simulation processor with the 'CHAMBOR' program. Results show an increasing factor of 30 in speed, in comparison with the execution on a MITRA 15 minicomputer. Moreover the conflicts importance, mainly at the level of access to a shared resource is evaluated. Although this implementation has been designed having in mind a dedicated application, other uses could be envisaged, particularly for the simulation of nuclear reactors: operator guiding system, the behavioural study under accidental circumstances, etc. (author) [fr
Efficient Parallel Algorithm For Direct Numerical Simulation of Turbulent Flows
Moitra, Stuti; Gatski, Thomas B.
1997-01-01
A distributed algorithm for a high-order-accurate finite-difference approach to the direct numerical simulation (DNS) of transition and turbulence in compressible flows is described. This work has two major objectives. The first objective is to demonstrate that parallel and distributed-memory machines can be successfully and efficiently used to solve computationally intensive and input/output intensive algorithms of the DNS class. The second objective is to show that the computational complexity involved in solving the tridiagonal systems inherent in the DNS algorithm can be reduced by algorithm innovations that obviate the need to use a parallelized tridiagonal solver.
Kinematics analysis and simulation of a new underactuated parallel robot
Directory of Open Access Journals (Sweden)
Wenxu YAN
2017-04-01
Full Text Available The number of degrees of freedom is equal to the number of the traditional robot driving motors, which causes defects such as low efficiency. To overcome that problem, based on the traditional parallel robot, a new underactuated parallel robot is presented. The structure characteristics and working principles of the underactuated parallel robot are analyzed. The forward and inverse solutions are derived by way of space analytic geometry and vector algebra. The kinematics model is established, and MATLAB is implied to verify the accuracy of forward and inverse solutions and identify the optimal work space. The simulation results show that the robot can realize the function of robot switch with three or four degrees of freedom when the number of driving motors is three, improving the efficiency of robot grasping, with the characteristics of large working space, high speed operation, high positioning accuracy, low manufacturing cost and so on, and it will have a wide range of industrial applications.
Parallel and distributed processing in power system simulation and control
Energy Technology Data Exchange (ETDEWEB)
Falcao, Djalma M [Universidade Federal, Rio de Janeiro, RJ (Brazil). Coordenacao dos Programas de Pos-graduacao de Engenharia
1994-12-31
Recent advances in computer technology will certainly have a great impact in the methodologies used in power system expansion and operational planning as well as in real-time control. Parallel and distributed processing are among the new technologies that present great potential for application in these areas. Parallel computers use multiple functional or processing units to speed up computation while distributed processing computer systems are collection of computers joined together by high speed communication networks having many objectives and advantages. The paper presents some ideas for the use of parallel and distributed processing in power system simulation and control. It also comments on some of the current research work in these topics and presents a summary of the work presently being developed at COPPE. (author) 53 refs., 2 figs.
The cost of conservative synchronization in parallel discrete event simulations
Nicol, David M.
1990-01-01
The performance of a synchronous conservative parallel discrete-event simulation protocol is analyzed. The class of simulation models considered is oriented around a physical domain and possesses a limited ability to predict future behavior. A stochastic model is used to show that as the volume of simulation activity in the model increases relative to a fixed architecture, the complexity of the average per-event overhead due to synchronization, event list manipulation, lookahead calculations, and processor idle time approach the complexity of the average per-event overhead of a serial simulation. The method is therefore within a constant factor of optimal. The analysis demonstrates that on large problems--those for which parallel processing is ideally suited--there is often enough parallel workload so that processors are not usually idle. The viability of the method is also demonstrated empirically, showing how good performance is achieved on large problems using a thirty-two node Intel iPSC/2 distributed memory multiprocessor.
Micro-mechanical Simulations of Soils using Massively Parallel Supercomputers
Directory of Open Access Journals (Sweden)
David W. Washington
2004-06-01
Full Text Available In this research a computer program, Trubal version 1.51, based on the Discrete Element Method was converted to run on a Connection Machine (CM-5,a massively parallel supercomputer with 512 nodes, to expedite the computational times of simulating Geotechnical boundary value problems. The dynamic memory algorithm in Trubal program did not perform efficiently in CM-2 machine with the Single Instruction Multiple Data (SIMD architecture. This was due to the communication overhead involving global array reductions, global array broadcast and random data movement. Therefore, a dynamic memory algorithm in Trubal program was converted to a static memory arrangement and Trubal program was successfully converted to run on CM-5 machines. The converted program was called "TRUBAL for Parallel Machines (TPM." Simulating two physical triaxial experiments and comparing simulation results with Trubal simulations validated the TPM program. With a 512 nodes CM-5 machine TPM produced a nine-fold speedup demonstrating the inherent parallelism within algorithms based on the Discrete Element Method.
Noise simulation in cone beam CT imaging with parallel computing
International Nuclear Information System (INIS)
Tu, S.-J.; Shaw, Chris C; Chen, Lingyun
2006-01-01
We developed a computer noise simulation model for cone beam computed tomography imaging using a general purpose PC cluster. This model uses a mono-energetic x-ray approximation and allows us to investigate three primary performance components, specifically quantum noise, detector blurring and additive system noise. A parallel random number generator based on the Weyl sequence was implemented in the noise simulation and a visualization technique was accordingly developed to validate the quality of the parallel random number generator. In our computer simulation model, three-dimensional (3D) phantoms were mathematically modelled and used to create 450 analytical projections, which were then sampled into digital image data. Quantum noise was simulated and added to the analytical projection image data, which were then filtered to incorporate flat panel detector blurring. Additive system noise was generated and added to form the final projection images. The Feldkamp algorithm was implemented and used to reconstruct the 3D images of the phantoms. A 24 dual-Xeon PC cluster was used to compute the projections and reconstructed images in parallel with each CPU processing 10 projection views for a total of 450 views. Based on this computer simulation system, simulated cone beam CT images were generated for various phantoms and technique settings. Noise power spectra for the flat panel x-ray detector and reconstructed images were then computed to characterize the noise properties. As an example among the potential applications of our noise simulation model, we showed that images of low contrast objects can be produced and used for image quality evaluation
Modularized Parallel Neutron Instrument Simulation on the TeraGrid
International Nuclear Information System (INIS)
Chen, Meili; Cobb, John W.; Hagen, Mark E.; Miller, Stephen D.; Lynch, Vickie E.
2007-01-01
In order to build a bridge between the TeraGrid (TG), a national scale cyberinfrastructure resource, and neutron science, the Neutron Science TeraGrid Gateway (NSTG) is focused on introducing productive HPC usage to the neutron science community, primarily the Spallation Neutron Source (SNS) at Oak Ridge National Laboratory (ORNL). Monte Carlo simulations are used as a powerful tool for instrument design and optimization at SNS. One of the successful efforts of a collaboration team composed of NSTG HPC experts and SNS instrument scientists is the development of a software facility named PSoNI, Parallelizing Simulations of Neutron Instruments. Parallelizing the traditional serial instrument simulation on TeraGrid resources, PSoNI quickly computes full instrument simulation at sufficient statistical levels in instrument de-sign. Upon SNS successful commissioning, to the end of 2007, three out of five commissioned instruments in SNS target station will be available for initial users. Advanced instrument study, proposal feasibility evaluation, and experiment planning are on the immediate schedule of SNS, which pose further requirements such as flexibility and high runtime efficiency on fast instrument simulation. PSoNI has been redesigned to meet the new challenges and a preliminary version is developed on TeraGrid. This paper explores the motivation and goals of the new design, and the improved software structure. Further, it describes the realized new features seen from MPI parallelized McStas running high resolution design simulations of the SEQUOIA and BSS instruments at SNS. A discussion regarding future work, which is targeted to do fast simulation for automated experiment adjustment and comparing models to data in analysis, is also presented
Fast robot kinematics modeling by using a parallel simulator (PSIM)
International Nuclear Information System (INIS)
El-Gazzar, H.M.; Ayad, N.M.A.
2002-01-01
High-speed computers are strongly needed not only for solving scientific and engineering problems, but also for numerous industrial applications. Such applications include computer-aided design, oil exploration, weather predication, space applications and safety of nuclear reactors. The rapid development in VLSI technology makes it possible to implement time consuming algorithms in real-time situations. Parallel processing approaches can now be used to reduce the processing-time for models of very high mathematical structure such as the kinematics molding of robot manipulator. This system is used to construct and evaluate the performance and cost effectiveness of several proposed methods to solve the Jacobian algorithm. Parallelism is introduced to the algorithms by using different task-allocations and dividing the whole job into sub tasks. Detailed analysis is performed and results are obtained for the case of six DOF (degree of freedom) robot arms (Stanford Arm). Execution times comparisons between Von Neumann (uni processor) and parallel processor architectures by using parallel simulator package (PSIM) are presented. The gained results are much in favour for the parallel techniques by at least fifty-percent improvements. Of course, further studies are needed to achieve the convenient and optimum number of processors has to be done
Fast robot kinematics modeling by using a parallel simulator (PSIM)
Energy Technology Data Exchange (ETDEWEB)
El-Gazzar, H M; Ayad, N M.A. [Atomic Energy Authority, Reactor Dept., Computer and Control Lab., P.O. Box no 13759 (Egypt)
2002-09-15
High-speed computers are strongly needed not only for solving scientific and engineering problems, but also for numerous industrial applications. Such applications include computer-aided design, oil exploration, weather predication, space applications and safety of nuclear reactors. The rapid development in VLSI technology makes it possible to implement time consuming algorithms in real-time situations. Parallel processing approaches can now be used to reduce the processing-time for models of very high mathematical structure such as the kinematics molding of robot manipulator. This system is used to construct and evaluate the performance and cost effectiveness of several proposed methods to solve the Jacobian algorithm. Parallelism is introduced to the algorithms by using different task-allocations and dividing the whole job into sub tasks. Detailed analysis is performed and results are obtained for the case of six DOF (degree of freedom) robot arms (Stanford Arm). Execution times comparisons between Von Neumann (uni processor) and parallel processor architectures by using parallel simulator package (PSIM) are presented. The gained results are much in favour for the parallel techniques by at least fifty-percent improvements. Of course, further studies are needed to achieve the convenient and optimum number of processors has to be done.
Parallel Stochastic discrete event simulation of calcium dynamics in neuron.
Ishlam Patoary, Mohammad Nazrul; Tropper, Carl; McDougal, Robert A; Zhongwei, Lin; Lytton, William W
2017-09-26
The intra-cellular calcium signaling pathways of a neuron depends on both biochemical reactions and diffusions. Some quasi-isolated compartments (e.g. spines) are so small and calcium concentrations are so low that one extra molecule diffusing in by chance can make a nontrivial difference in its concentration (percentage-wise). These rare events can affect dynamics discretely in such way that they cannot be evaluated by a deterministic simulation. Stochastic models of such a system provide a more detailed understanding of these systems than existing deterministic models because they capture their behavior at a molecular level. Our research focuses on the development of a high performance parallel discrete event simulation environment, Neuron Time Warp (NTW), which is intended for use in the parallel simulation of stochastic reaction-diffusion systems such as intra-calcium signaling. NTW is integrated with NEURON, a simulator which is widely used within the neuroscience community. We simulate two models, a calcium buffer and a calcium wave model. The calcium buffer model is employed in order to verify the correctness and performance of NTW by comparing it to a serial deterministic simulation in NEURON. We also derived a discrete event calcium wave model from a deterministic model using the stochastic IP3R structure.
Particle simulation on a distributed memory highly parallel processor
International Nuclear Information System (INIS)
Sato, Hiroyuki; Ikesaka, Morio
1990-01-01
This paper describes parallel molecular dynamics simulation of atoms governed by local force interaction. The space in the model is divided into cubic subspaces and mapped to the processor array of the CAP-256, a distributed memory, highly parallel processor developed at Fujitsu Labs. We developed a new technique to avoid redundant calculation of forces between atoms in different processors. Experiments showed the communication overhead was less than 5%, and the idle time due to load imbalance was less than 11% for two model problems which contain 11,532 and 46,128 argon atoms. From the software simulation, the CAP-II which is under development is estimated to be about 45 times faster than CAP-256 and will be able to run the same problem about 40 times faster than Fujitsu's M-380 mainframe when 256 processors are used. (author)
Parallel algorithms for simulating continuous time Markov chains
Nicol, David M.; Heidelberger, Philip
1992-01-01
We have previously shown that the mathematical technique of uniformization can serve as the basis of synchronization for the parallel simulation of continuous-time Markov chains. This paper reviews the basic method and compares five different methods based on uniformization, evaluating their strengths and weaknesses as a function of problem characteristics. The methods vary in their use of optimism, logical aggregation, communication management, and adaptivity. Performance evaluation is conducted on the Intel Touchstone Delta multiprocessor, using up to 256 processors.
cellGPU: Massively parallel simulations of dynamic vertex models
Sussman, Daniel M.
2017-10-01
Vertex models represent confluent tissue by polygonal or polyhedral tilings of space, with the individual cells interacting via force laws that depend on both the geometry of the cells and the topology of the tessellation. This dependence on the connectivity of the cellular network introduces several complications to performing molecular-dynamics-like simulations of vertex models, and in particular makes parallelizing the simulations difficult. cellGPU addresses this difficulty and lays the foundation for massively parallelized, GPU-based simulations of these models. This article discusses its implementation for a pair of two-dimensional models, and compares the typical performance that can be expected between running cellGPU entirely on the CPU versus its performance when running on a range of commercial and server-grade graphics cards. By implementing the calculation of topological changes and forces on cells in a highly parallelizable fashion, cellGPU enables researchers to simulate time- and length-scales previously inaccessible via existing single-threaded CPU implementations. Program Files doi:http://dx.doi.org/10.17632/6j2cj29t3r.1 Licensing provisions: MIT Programming language: CUDA/C++ Nature of problem: Simulations of off-lattice "vertex models" of cells, in which the interaction forces depend on both the geometry and the topology of the cellular aggregate. Solution method: Highly parallelized GPU-accelerated dynamical simulations in which the force calculations and the topological features can be handled on either the CPU or GPU. Additional comments: The code is hosted at https://gitlab.com/dmsussman/cellGPU, with documentation additionally maintained at http://dmsussman.gitlab.io/cellGPUdocumentation
Time parallelization of advanced operation scenario simulations of ITER plasma
International Nuclear Information System (INIS)
Samaddar, D; Casper, T A; Kim, S H; Houlberg, W A; Berry, L A; Elwasif, W R; Batchelor, D
2013-01-01
This work demonstrates that simulations of advanced burning plasma operation scenarios can be successfully parallelized in time using the parareal algorithm. CORSICA -an advanced operation scenario code for tokamak plasmas is used as a test case. This is a unique application since the parareal algorithm has so far been applied to relatively much simpler systems except for the case of turbulence. In the present application, a computational gain of an order of magnitude has been achieved which is extremely promising. A successful implementation of the Parareal algorithm to codes like CORSICA ushers in the possibility of time efficient simulations of ITER plasmas.
Xyce™ Parallel Electronic Simulator Reference Guide, Version 6.5
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Aadithya, Karthik V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Schiek, Richard L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Verley, Jason C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation
2016-06-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users’ Guide. The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users’ Guide. The information herein is subject to change without notice. Copyright © 2002-2016 Sandia Corporation. All rights reserved.
SPINET: A Parallel Computing Approach to Spine Simulations
Directory of Open Access Journals (Sweden)
Peter G. Kropf
1996-01-01
Full Text Available Research in scientitic programming enables us to realize more and more complex applications, and on the other hand, application-driven demands on computing methods and power are continuously growing. Therefore, interdisciplinary approaches become more widely used. The interdisciplinary SPINET project presented in this article applies modern scientific computing tools to biomechanical simulations: parallel computing and symbolic and modern functional programming. The target application is the human spine. Simulations of the spine help us to investigate and better understand the mechanisms of back pain and spinal injury. Two approaches have been used: the first uses the finite element method for high-performance simulations of static biomechanical models, and the second generates a simulation developmenttool for experimenting with different dynamic models. A finite element program for static analysis has been parallelized for the MUSIC machine. To solve the sparse system of linear equations, a conjugate gradient solver (iterative method and a frontal solver (direct method have been implemented. The preprocessor required for the frontal solver is written in the modern functional programming language SML, the solver itself in C, thus exploiting the characteristic advantages of both functional and imperative programming. The speedup analysis of both solvers show very satisfactory results for this irregular problem. A mixed symbolic-numeric environment for rigid body system simulations is presented. It automatically generates C code from a problem specification expressed by the Lagrange formalism using Maple.
Synchronous Parallel System for Emulation and Discrete Event Simulation
Steinman, Jeffrey S. (Inventor)
2001-01-01
A synchronous parallel system for emulation and discrete event simulation having parallel nodes responds to received messages at each node by generating event objects having individual time stamps, stores only the changes to the state variables of the simulation object attributable to the event object and produces corresponding messages. The system refrains from transmitting the messages and changing the state variables while it determines whether the changes are superseded, and then stores the unchanged state variables in the event object for later restoral to the simulation object if called for. This determination preferably includes sensing the time stamp of each new event object and determining which new event object has the earliest time stamp as the local event horizon, determining the earliest local event horizon of the nodes as the global event horizon, and ignoring events whose time stamps are less than the global event horizon. Host processing between the system and external terminals enables such a terminal to query, monitor, command or participate with a simulation object during the simulation process.
HPC parallel programming model for gyrokinetic MHD simulation
International Nuclear Information System (INIS)
Naitou, Hiroshi; Yamada, Yusuke; Tokuda, Shinji; Ishii, Yasutomo; Yagi, Masatoshi
2011-01-01
The 3-dimensional gyrokinetic PIC (particle-in-cell) code for MHD simulation, Gpic-MHD, was installed on SR16000 (“Plasma Simulator”), which is a scalar cluster system consisting of 8,192 logical cores. The Gpic-MHD code advances particle and field quantities in time. In order to distribute calculations over large number of logical cores, the total simulation domain in cylindrical geometry was broken up into N DD-r × N DD-z (number of radial decomposition times number of axial decomposition) small domains including approximately the same number of particles. The axial direction was uniformly decomposed, while the radial direction was non-uniformly decomposed. N RP replicas (copies) of each decomposed domain were used (“particle decomposition”). The hybrid parallelization model of multi-threads and multi-processes was employed: threads were parallelized by the auto-parallelization and N DD-r × N DD-z × N RP processes were parallelized by MPI (message-passing interface). The parallelization performance of Gpic-MHD was investigated for the medium size system of N r × N θ × N z = 1025 × 128 × 128 mesh with 4.196 or 8.192 billion particles. The highest speed for the fixed number of logical cores was obtained for two threads, the maximum number of N DD-z , and optimum combination of N DD-r and N RP . The observed optimum speeds demonstrated good scaling up to 8,192 logical cores. (author)
International Nuclear Information System (INIS)
Ivanov, A.; Sanchez, V.; Stieglitz, R.; Ivanov, K.
2014-01-01
Highlights: • The current paper focuses on a optimized method for performing coupled Monte-Carlo/thermal–hydraulics calculations. • Innovative on-the-fly method for supplying the temperature and density distributions is presented. • Convergence acceleration method is presented. It is proven applicable by generalizing the Robbins-Monro theorem. • Tallying is optimized by using collision probability estimator for the power profile estimation. - Abstract: In order to increase the accuracy and the degree of spatial and energy resolution of core design studies, coupled 3D neutronic (multi-group deterministic and continuous energy Monte-Carlo) and 3D thermal–hydraulic (CFD and subchannel) codes are being developed worldwide. At KIT, both deterministic and Monte-Carlo codes were coupled with subchannel codes and applied to predict the safety-related design parameters such as minimal critical power ratio (MCPR), maximal cladding and fuel temperature, departure from nuclide boiling ratio (DNBR). These coupling approaches were revised and considerably improved. Innovative method of internal on-the-fly thermal feedback interchange between the codes was implemented. It no longer relies on explicit material definitions and allows the modeling of temperature and density distributions based on the cell coordinates. In contrast to all existing coupled schemes, this method uses only standard MCNP geometry input and requires only proper definition of the geometrical dimensions. The initial material definition is arbitrary and is determined on-the-fly during the neutron transport by the thermal–hydraulic feedback. Another key issue addressed is the optimal application of parallel computing and the implementation of less time consuming tally estimators. Using multi-processor computer architectures and implementing collision density flux estimator, it is possible to reduce the Monte-Carlo running time and obtain converged results within reasonable time limit. The coupled
Parallel hyperbolic PDE simulation on clusters: Cell versus GPU
Rostrup, Scott; De Sterck, Hans
2010-12-01
Increasingly, high-performance computing is looking towards data-parallel computational devices to enhance computational performance. Two technologies that have received significant attention are IBM's Cell Processor and NVIDIA's CUDA programming model for graphics processing unit (GPU) computing. In this paper we investigate the acceleration of parallel hyperbolic partial differential equation simulation on structured grids with explicit time integration on clusters with Cell and GPU backends. The message passing interface (MPI) is used for communication between nodes at the coarsest level of parallelism. Optimizations of the simulation code at the several finer levels of parallelism that the data-parallel devices provide are described in terms of data layout, data flow and data-parallel instructions. Optimized Cell and GPU performance are compared with reference code performance on a single x86 central processing unit (CPU) core in single and double precision. We further compare the CPU, Cell and GPU platforms on a chip-to-chip basis, and compare performance on single cluster nodes with two CPUs, two Cell processors or two GPUs in a shared memory configuration (without MPI). We finally compare performance on clusters with 32 CPUs, 32 Cell processors, and 32 GPUs using MPI. Our GPU cluster results use NVIDIA Tesla GPUs with GT200 architecture, but some preliminary results on recently introduced NVIDIA GPUs with the next-generation Fermi architecture are also included. This paper provides computational scientists and engineers who are considering porting their codes to accelerator environments with insight into how structured grid based explicit algorithms can be optimized for clusters with Cell and GPU accelerators. It also provides insight into the speed-up that may be gained on current and future accelerator architectures for this class of applications. Program summaryProgram title: SWsolver Catalogue identifier: AEGY_v1_0 Program summary URL
An FPGA-Based Massively Parallel Neuromorphic Cortex Simulator.
Wang, Runchun M; Thakur, Chetan S; van Schaik, André
2018-01-01
This paper presents a massively parallel and scalable neuromorphic cortex simulator designed for simulating large and structurally connected spiking neural networks, such as complex models of various areas of the cortex. The main novelty of this work is the abstraction of a neuromorphic architecture into clusters represented by minicolumns and hypercolumns, analogously to the fundamental structural units observed in neurobiology. Without this approach, simulating large-scale fully connected networks needs prohibitively large memory to store look-up tables for point-to-point connections. Instead, we use a novel architecture, based on the structural connectivity in the neocortex, such that all the required parameters and connections can be stored in on-chip memory. The cortex simulator can be easily reconfigured for simulating different neural networks without any change in hardware structure by programming the memory. A hierarchical communication scheme allows one neuron to have a fan-out of up to 200 k neurons. As a proof-of-concept, an implementation on one Altera Stratix V FPGA was able to simulate 20 million to 2.6 billion leaky-integrate-and-fire (LIF) neurons in real time. We verified the system by emulating a simplified auditory cortex (with 100 million neurons). This cortex simulator achieved a low power dissipation of 1.62 μW per neuron. With the advent of commercially available FPGA boards, our system offers an accessible and scalable tool for the design, real-time simulation, and analysis of large-scale spiking neural networks.
Simulation and parallel connection of step-down piezoelectric transformers
International Nuclear Information System (INIS)
Thang, Vo Viet; Kim, In Sung; Jeong, Soon Jong; Kim, Min Soo; Song, Jae Sung
2012-01-01
Piezoelectric transformers have been used widely in electronic circuits due to advantages such as high efficiency, miniaturization and no flammability; however the output power has been limited. For overcoming this drawback, some research has recently been focused on connections between piezoelectric transformers. Based on these operations, the output power has been improved compared to the single operation. Parallel operation of step-down piezoelectric transformers is presented in this paper. An important factor affecting the parallel operation of piezoelectric transformer was the resonance frequency, and a small difference in resonance frequencies was obtained with transformers having the same dimensions and fabricating processes. The piezoelectric transformers were found to operate in first radial mode at a frequency of 68 kHz. An equivalent circuit was used to investigate parallel driving of piezoelectric transformers and then to compare the result with experimental observations. The electrical characteristics, including the output voltage, output power and efficient were measured at a matching resistive load. Effects of frequency on the step-down ratio and of the input voltage on the power properties in the simulation were similar to the experimental results. The output power of the parallel operation was 35 W at a load of 50 Ω and an input voltage of 100 V; the temperature rise was 30 .deg. C and the efficiency was 88%.
Parallel conjugate gradient algorithms for manipulator dynamic simulation
Fijany, Amir; Scheld, Robert E.
1989-01-01
Parallel conjugate gradient algorithms for the computation of multibody dynamics are developed for the specialized case of a robot manipulator. For an n-dimensional positive-definite linear system, the Classical Conjugate Gradient (CCG) algorithms are guaranteed to converge in n iterations, each with a computation cost of O(n); this leads to a total computational cost of O(n sq) on a serial processor. A conjugate gradient algorithms is presented that provide greater efficiency using a preconditioner, which reduces the number of iterations required, and by exploiting parallelism, which reduces the cost of each iteration. Two Preconditioned Conjugate Gradient (PCG) algorithms are proposed which respectively use a diagonal and a tridiagonal matrix, composed of the diagonal and tridiagonal elements of the mass matrix, as preconditioners. Parallel algorithms are developed to compute the preconditioners and their inversions in O(log sub 2 n) steps using n processors. A parallel algorithm is also presented which, on the same architecture, achieves the computational time of O(log sub 2 n) for each iteration. Simulation results for a seven degree-of-freedom manipulator are presented. Variants of the proposed algorithms are also developed which can be efficiently implemented on the Robot Mathematics Processor (RMP).
Directory of Open Access Journals (Sweden)
Roger P. Pawlowski
2012-01-01
Full Text Available A template-based generic programming approach was presented in Part I of this series of papers [Sci. Program. 20 (2012, 197–219] that separates the development effort of programming a physical model from that of computing additional quantities, such as derivatives, needed for embedded analysis algorithms. In this paper, we describe the implementation details for using the template-based generic programming approach for simulation and analysis of partial differential equations (PDEs. We detail several of the hurdles that we have encountered, and some of the software infrastructure developed to overcome them. We end with a demonstration where we present shape optimization and uncertainty quantification results for a 3D PDE application.
Capacity Analysis for Parallel Runway through Agent-Based Simulation
Directory of Open Access Journals (Sweden)
Yang Peng
2013-01-01
Full Text Available Parallel runway is the mainstream structure of China hub airport, runway is often the bottleneck of an airport, and the evaluation of its capacity is of great importance to airport management. This study outlines a model, multiagent architecture, implementation approach, and software prototype of a simulation system for evaluating runway capacity. Agent Unified Modeling Language (AUML is applied to illustrate the inbound and departing procedure of planes and design the agent-based model. The model is evaluated experimentally, and the quality is studied in comparison with models, created by SIMMOD and Arena. The results seem to be highly efficient, so the method can be applied to parallel runway capacity evaluation and the model propose favorable flexibility and extensibility.
Kumar, Mayank
2012-01-19
In this two-part paper, we describe the construction, validation, and application of a multiscale model of entrained flow gasification. The accuracy of the model is demonstrated by (1) rigorously constructing and validating the key constituent submodels against relevant canonical test cases from the literature and (2) validating the integrated model against experimental data from laboratory scale and commercial scale gasifiers. In part I, the flow solver and particle turbulent dispersion models are validated against experimental data from nonswirling flow and swirling flow test cases in an axisymmetric sudden expansion geometry and a two-phase flow test case in a cylindrical bluff body geometry. Results show that while the large eddy simulation (LES) performs best among all tested models in predicting both swirling and nonswirling flows, the shear stress transport (SST) k-ω model is the best choice among the commonly used Reynolds-averaged Navier-Stokes (RANS) models. The particle turbulent dispersion model is accurate enough in predicting particle trajectories in complex turbulent flows when the underlying turbulent flow is well predicted. Moreover, a commonly used modeling constant in the particle dispersion model is optimized on the basis of comparisons with particle-phase experimental data for the two-phase flow bluff body case. © 2011 American Chemical Society.
Xyce Parallel Electronic Simulator Users Guide Version 6.2.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R.; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Sholander, Peter E.; Thornquist, Heidi K.; Verley, Jason C.; Baur, David Gregory
2014-09-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. Trademarks The information herein is subject to change without notice. Copyright c 2002-2014 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are
Xyce Parallel Electronic Simulator Users Guide Version 6.4
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Baur, David Gregory [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2015-12-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. Trademarks The information herein is subject to change without notice. Copyright c 2002-2015 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are
CHOLLA: A NEW MASSIVELY PARALLEL HYDRODYNAMICS CODE FOR ASTROPHYSICAL SIMULATION
Energy Technology Data Exchange (ETDEWEB)
Schneider, Evan E.; Robertson, Brant E. [Steward Observatory, University of Arizona, 933 North Cherry Avenue, Tucson, AZ 85721 (United States)
2015-04-15
We present Computational Hydrodynamics On ParaLLel Architectures (Cholla ), a new three-dimensional hydrodynamics code that harnesses the power of graphics processing units (GPUs) to accelerate astrophysical simulations. Cholla models the Euler equations on a static mesh using state-of-the-art techniques, including the unsplit Corner Transport Upwind algorithm, a variety of exact and approximate Riemann solvers, and multiple spatial reconstruction techniques including the piecewise parabolic method (PPM). Using GPUs, Cholla evolves the fluid properties of thousands of cells simultaneously and can update over 10 million cells per GPU-second while using an exact Riemann solver and PPM reconstruction. Owing to the massively parallel architecture of GPUs and the design of the Cholla code, astrophysical simulations with physically interesting grid resolutions (≳256{sup 3}) can easily be computed on a single device. We use the Message Passing Interface library to extend calculations onto multiple devices and demonstrate nearly ideal scaling beyond 64 GPUs. A suite of test problems highlights the physical accuracy of our modeling and provides a useful comparison to other codes. We then use Cholla to simulate the interaction of a shock wave with a gas cloud in the interstellar medium, showing that the evolution of the cloud is highly dependent on its density structure. We reconcile the computed mixing time of a turbulent cloud with a realistic density distribution destroyed by a strong shock with the existing analytic theory for spherical cloud destruction by describing the system in terms of its median gas density.
CHOLLA: A NEW MASSIVELY PARALLEL HYDRODYNAMICS CODE FOR ASTROPHYSICAL SIMULATION
International Nuclear Information System (INIS)
Schneider, Evan E.; Robertson, Brant E.
2015-01-01
We present Computational Hydrodynamics On ParaLLel Architectures (Cholla ), a new three-dimensional hydrodynamics code that harnesses the power of graphics processing units (GPUs) to accelerate astrophysical simulations. Cholla models the Euler equations on a static mesh using state-of-the-art techniques, including the unsplit Corner Transport Upwind algorithm, a variety of exact and approximate Riemann solvers, and multiple spatial reconstruction techniques including the piecewise parabolic method (PPM). Using GPUs, Cholla evolves the fluid properties of thousands of cells simultaneously and can update over 10 million cells per GPU-second while using an exact Riemann solver and PPM reconstruction. Owing to the massively parallel architecture of GPUs and the design of the Cholla code, astrophysical simulations with physically interesting grid resolutions (≳256 3 ) can easily be computed on a single device. We use the Message Passing Interface library to extend calculations onto multiple devices and demonstrate nearly ideal scaling beyond 64 GPUs. A suite of test problems highlights the physical accuracy of our modeling and provides a useful comparison to other codes. We then use Cholla to simulate the interaction of a shock wave with a gas cloud in the interstellar medium, showing that the evolution of the cloud is highly dependent on its density structure. We reconcile the computed mixing time of a turbulent cloud with a realistic density distribution destroyed by a strong shock with the existing analytic theory for spherical cloud destruction by describing the system in terms of its median gas density
Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
International Nuclear Information System (INIS)
Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten
2017-01-01
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach and paper, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. Finally, these two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.
Scalable and fast heterogeneous molecular simulation with predictive parallelization schemes
Guzman, Horacio V.; Junghans, Christoph; Kremer, Kurt; Stuehn, Torsten
2017-11-01
Multiscale and inhomogeneous molecular systems are challenging topics in the field of molecular simulation. In particular, modeling biological systems in the context of multiscale simulations and exploring material properties are driving a permanent development of new simulation methods and optimization algorithms. In computational terms, those methods require parallelization schemes that make a productive use of computational resources for each simulation and from its genesis. Here, we introduce the heterogeneous domain decomposition approach, which is a combination of an heterogeneity-sensitive spatial domain decomposition with an a priori rearrangement of subdomain walls. Within this approach, the theoretical modeling and scaling laws for the force computation time are proposed and studied as a function of the number of particles and the spatial resolution ratio. We also show the new approach capabilities, by comparing it to both static domain decomposition algorithms and dynamic load-balancing schemes. Specifically, two representative molecular systems have been simulated and compared to the heterogeneous domain decomposition proposed in this work. These two systems comprise an adaptive resolution simulation of a biomolecule solvated in water and a phase-separated binary Lennard-Jones fluid.
Parallelization of ultrasonic field simulations for non destructive testing
International Nuclear Information System (INIS)
Lambert, Jason
2015-01-01
The Non Destructive Testing field increasingly uses simulation. It is used at every step of the whole control process of an industrial part, from speeding up control development to helping experts understand results. During this thesis, a fast ultrasonic field simulation tool dedicated to the computation of an ultrasonic field radiated by a phase array probe in an isotropic specimen has been developed. During this thesis, a simulation tool dedicated to the fast computation of an ultrasonic field radiated by a phased array probe in an isotropic specimen has been developed. Its performance enables an interactive usage. To benefit from the commonly available parallel architectures, a regular model (aimed at removing divergent branching) derived from the generic CIVA model has been developed. First, a reference implementation was developed to validate this model against CIVA results, and to analyze its performance behaviour before optimization. The resulting code has been optimized for three kinds of parallel architectures commonly available in workstations: general purpose processors (GPP), many-core co-processors (Intel MIC) and graphics processing units (nVidia GPU). On the GPP and the MIC, the algorithm was reorganized and implemented to benefit from both parallelism levels, multithreading and vector instructions. On the GPU, the multiple steps of field computing have been divided in multiple successive CUDA kernels. Moreover, libraries dedicated to each architecture were used to speedup Fast Fourier Transforms, Intel MKL on GPP and MIC and nVidia cuFFT on GPU. Performance and hardware adequation of the produced codes were thoroughly studied for each architecture. On multiple realistic control configurations, interactive performance was reached. Perspectives to address more complex configurations were drawn. Finally, the integration and the industrialization of this code in the commercial NDT platform CIVA is discussed. (author) [fr
Massively parallel algorithms for trace-driven cache simulations
Nicol, David M.; Greenberg, Albert G.; Lubachevsky, Boris D.
1991-01-01
Trace driven cache simulation is central to computer design. A trace is a very long sequence of reference lines from main memory. At the t(exp th) instant, reference x sub t is hashed into a set of cache locations, the contents of which are then compared with x sub t. If at the t sup th instant x sub t is not present in the cache, then it is said to be a miss, and is loaded into the cache set, possibly forcing the replacement of some other memory line, and making x sub t present for the (t+1) sup st instant. The problem of parallel simulation of a subtrace of N references directed to a C line cache set is considered, with the aim of determining which references are misses and related statistics. A simulation method is presented for the Least Recently Used (LRU) policy, which regradless of the set size C runs in time O(log N) using N processors on the exclusive read, exclusive write (EREW) parallel model. A simpler LRU simulation algorithm is given that runs in O(C log N) time using N/log N processors. Timings are presented of the second algorithm's implementation on the MasPar MP-1, a machine with 16384 processors. A broad class of reference based line replacement policies are considered, which includes LRU as well as the Least Frequently Used and Random replacement policies. A simulation method is presented for any such policy that on any trace of length N directed to a C line set runs in the O(C log N) time with high probability using N processors on the EREW model. The algorithms are simple, have very little space overhead, and are well suited for SIMD implementation.
Multiphysics modeling of a rail gun launcher
Directory of Open Access Journals (Sweden)
Y W Kwon
2016-03-01
Full Text Available A finite element based multiphysics modeling was conducted for a rail gunlauncher to predict the exit velocity of the launch object, and temperaturedistribution. For this modeling, electromagnetic field analysis, heat transferanalysis, thermal stress analysis, and dynamic analysis were conducted fora system consisting of two parallel rails and a moving armature. In particular,an emphasis was given to model the contact interface between rails andthe armature. A contact theory was used to estimate the electric as well asthermal conductivities at the interface. Using the developed model, aparametric study was conducted to understand effects of variousparameters on the exit velocity as well as the temperature distribution in therail gun launcher.
An FPGA-Based Massively Parallel Neuromorphic Cortex Simulator
Directory of Open Access Journals (Sweden)
Runchun M. Wang
2018-04-01
Full Text Available This paper presents a massively parallel and scalable neuromorphic cortex simulator designed for simulating large and structurally connected spiking neural networks, such as complex models of various areas of the cortex. The main novelty of this work is the abstraction of a neuromorphic architecture into clusters represented by minicolumns and hypercolumns, analogously to the fundamental structural units observed in neurobiology. Without this approach, simulating large-scale fully connected networks needs prohibitively large memory to store look-up tables for point-to-point connections. Instead, we use a novel architecture, based on the structural connectivity in the neocortex, such that all the required parameters and connections can be stored in on-chip memory. The cortex simulator can be easily reconfigured for simulating different neural networks without any change in hardware structure by programming the memory. A hierarchical communication scheme allows one neuron to have a fan-out of up to 200 k neurons. As a proof-of-concept, an implementation on one Altera Stratix V FPGA was able to simulate 20 million to 2.6 billion leaky-integrate-and-fire (LIF neurons in real time. We verified the system by emulating a simplified auditory cortex (with 100 million neurons. This cortex simulator achieved a low power dissipation of 1.62 μW per neuron. With the advent of commercially available FPGA boards, our system offers an accessible and scalable tool for the design, real-time simulation, and analysis of large-scale spiking neural networks.
Parallel Multiscale Algorithms for Astrophysical Fluid Dynamics Simulations
Norman, Michael L.
1997-01-01
Our goal is to develop software libraries and applications for astrophysical fluid dynamics simulations in multidimensions that will enable us to resolve the large spatial and temporal variations that inevitably arise due to gravity, fronts and microphysical phenomena. The software must run efficiently on parallel computers and be general enough to allow the incorporation of a wide variety of physics. Cosmological structure formation with realistic gas physics is the primary application driver in this work. Accurate simulations of e.g. galaxy formation require a spatial dynamic range (i.e., ratio of system scale to smallest resolved feature) of 104 or more in three dimensions in arbitrary topologies. We take this as our technical requirement. We have achieved, and in fact, surpassed these goals.
International Nuclear Information System (INIS)
Li Hanyu; Zhou Haijing; Dong Zhiwei; Liao Cheng; Chang Lei; Cao Xiaolin; Xiao Li
2010-01-01
A large-scale parallel electromagnetic field simulation program JEMS-FDTD(J Electromagnetic Solver-Finite Difference Time Domain) is designed and implemented on JASMIN (J parallel Adaptive Structured Mesh applications INfrastructure). This program can simulate propagation, radiation, couple of electromagnetic field by solving Maxwell equations on structured mesh explicitly with FDTD method. JEMS-FDTD is able to simulate billion-mesh-scale problems on thousands of processors. In this article, the program is verified by simulating the radiation of an electric dipole. A beam waveguide is simulated to demonstrate the capability of large scale parallel computation. A parallel performance test indicates that a high parallel efficiency is obtained. (authors)
Energy Technology Data Exchange (ETDEWEB)
Bonaccorsi, Th
2007-09-15
A Material Testing Reactor (MTR) makes it possible to irradiate material samples under intense neutron and photonic fluxes. These experiments are carried out in experimental devices localised in the reactor core or in periphery (reflector). Available physics simulation tools only treat, most of the time, one physics field in a very precise way. Multi-physic simulations of irradiation experiments therefore require a sequential use of several calculation codes and data exchanges between these codes: this corresponds to problems coupling. In order to facilitate multi-physic simulations, this thesis sets up a data model based on data-processing objects, called Technological Entities. This data model is common to all of the physics fields. It permits defining the geometry of an irradiation device in a parametric way and to associate information about materials to it. Numerical simulations are encapsulated into interfaces providing the ability to call specific functionalities with the same command (to initialize data, to launch calculations, to post-treat, to get results,... ). Thus, once encapsulated, numerical simulations can be re-used for various studies. This data model is developed in a SALOME platform component. The first application case made it possible to perform neutronic simulations (OSIRIS reactor and RJH) coupled with fuel behavior simulations. In a next step, thermal hydraulics could also be taken into account. In addition to the improvement of the calculation accuracy due to the physical phenomena coupling, the time spent in the development phase of the simulation is largely reduced and the possibilities of uncertainty treatment are under consideration. (author)
Direct numerical simulation of bubbles with parallelized adaptive mesh refinement
International Nuclear Information System (INIS)
Talpaert, A.
2015-01-01
The study of two-phase Thermal-Hydraulics is a major topic for Nuclear Engineering for both security and efficiency of nuclear facilities. In addition to experiments, numerical modeling helps to knowing precisely where bubbles appear and how they behave, in the core as well as in the steam generators. This work presents the finest scale of representation of two-phase flows, Direct Numerical Simulation of bubbles. We use the 'Di-phasic Low Mach Number' equation model. It is particularly adapted to low-Mach number flows, that is to say flows which velocity is much slower than the speed of sound; this is very typical of nuclear thermal-hydraulics conditions. Because we study bubbles, we capture the front between vapor and liquid phases thanks to a downward flux limiting numerical scheme. The specific discrete analysis technique this work introduces is well-balanced parallel Adaptive Mesh Refinement (AMR). With AMR, we refined the coarse grid on a batch of patches in order to locally increase precision in areas which matter more, and capture fine changes in the front location and its topology. We show that patch-based AMR is very adapted for parallel computing. We use a variety of physical examples: forced advection, heat transfer, phase changes represented by a Stefan model, as well as the combination of all those models. We will present the results of those numerical simulations, as well as the speed up compared to equivalent non-AMR simulation and to serial computation of the same problems. This document is made up of an abstract and the slides of the presentation. (author)
International Nuclear Information System (INIS)
Yoshimura, Shinobu; Kawai, Hiroshi; Sugimoto, Shin'ichiro; Hori, Muneo; Nakajima, Norihiro; Kobayashi, Kei
2010-01-01
Recently importance of nuclear energy has been recognized again due to serious concerns of global warming and energy security. In parallel, it is one of critical issues to verify safety capability of ageing nuclear power plants (NPPs) subjected to strong earthquake. Since 2007, we have been developing the multi-scale and multi-physics based numerical simulator for quantitatively predicting actual quake-proof capability of ageing NPPs under operation or just after plant trip subjected to strong earthquake. In this paper, we describe an overview of the simulator with some preliminary results. (author)
Massive parallel 3D PIC simulation of negative ion extraction
Revel, Adrien; Mochalskyy, Serhiy; Montellano, Ivar Mauricio; Wünderlich, Dirk; Fantz, Ursel; Minea, Tiberiu
2017-09-01
The 3D PIC-MCC code ONIX is dedicated to modeling Negative hydrogen/deuterium Ion (NI) extraction and co-extraction of electrons from radio-frequency driven, low pressure plasma sources. It provides valuable insight on the complex phenomena involved in the extraction process. In previous calculations, a mesh size larger than the Debye length was used, implying numerical electron heating. Important steps have been achieved in terms of computation performance and parallelization efficiency allowing successful massive parallel calculations (4096 cores), imperative to resolve the Debye length. In addition, the numerical algorithms have been improved in terms of grid treatment, i.e., the electric field near the complex geometry boundaries (plasma grid) is calculated more accurately. The revised model preserves the full 3D treatment, but can take advantage of a highly refined mesh. ONIX was used to investigate the role of the mesh size, the re-injection scheme for lost particles (extracted or wall absorbed), and the electron thermalization process on the calculated extracted current and plasma characteristics. It is demonstrated that all numerical schemes give the same NI current distribution for extracted ions. Concerning the electrons, the pair-injection technique is found well-adapted to simulate the sheath in front of the plasma grid.
Xyce Parallel Electronic Simulator Reference Guide Version 6.7.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aadithya, Karthik Venkatraman [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2017-05-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] . The information herein is subject to change without notice. Copyright c 2002-2017 Sandia Corporation. All rights reserved. Trademarks Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. All other trademarks are property of their respective owners. Contacts World Wide Web http://xyce.sandia.gov https://info.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only) Bug Reports (Sandia only) http://joseki-vm.sandia.gov/bugzilla http://morannon.sandia.gov/bugzilla
A parallel algorithm for switch-level timing simulation on a hypercube multiprocessor
Rao, Hariprasad Nannapaneni
1989-01-01
The parallel approach to speeding up simulation is studied, specifically the simulation of digital LSI MOS circuitry on the Intel iPSC/2 hypercube. The simulation algorithm is based on RSIM, an event driven switch-level simulator that incorporates a linear transistor model for simulating digital MOS circuits. Parallel processing techniques based on the concepts of Virtual Time and rollback are utilized so that portions of the circuit may be simulated on separate processors, in parallel for as large an increase in speed as possible. A partitioning algorithm is also developed in order to subdivide the circuit for parallel processing.
Out-of-order parallel discrete event simulation for electronic system-level design
Chen, Weiwei
2014-01-01
This book offers readers a set of new approaches and tools a set of tools and techniques for facing challenges in parallelization with design of embedded systems.? It provides an advanced parallel simulation infrastructure for efficient and effective system-level model validation and development so as to build better products in less time.? Since parallel discrete event simulation (PDES) has the potential to exploit the underlying parallel computational capability in today's multi-core simulation hosts, the author begins by reviewing the parallelization of discrete event simulation, identifyin
A parallel adaptive finite difference algorithm for petroleum reservoir simulation
Energy Technology Data Exchange (ETDEWEB)
Hoang, Hai Minh
2005-07-01
Adaptive finite differential for problems arising in simulation of flow in porous medium applications are considered. Such methods have been proven useful for overcoming limitations of computational resources and improving the resolution of the numerical solutions to a wide range of problems. By local refinement of the computational mesh where it is needed to improve the accuracy of solutions, yields better solution resolution representing more efficient use of computational resources than is possible with traditional fixed-grid approaches. In this thesis, we propose a parallel adaptive cell-centered finite difference (PAFD) method for black-oil reservoir simulation models. This is an extension of the adaptive mesh refinement (AMR) methodology first developed by Berger and Oliger (1984) for the hyperbolic problem. Our algorithm is fully adaptive in time and space through the use of subcycling, in which finer grids are advanced at smaller time steps than the coarser ones. When coarse and fine grids reach the same advanced time level, they are synchronized to ensure that the global solution is conservative and satisfy the divergence constraint across all levels of refinement. The material in this thesis is subdivided in to three overall parts. First we explain the methodology and intricacies of AFD scheme. Then we extend a finite differential cell-centered approximation discretization to a multilevel hierarchy of refined grids, and finally we are employing the algorithm on parallel computer. The results in this work show that the approach presented is robust, and stable, thus demonstrating the increased solution accuracy due to local refinement and reduced computing resource consumption. (Author)
Tightly Coupled Multiphysics Algorithm for Pebble Bed Reactors
International Nuclear Information System (INIS)
Park, HyeongKae; Knoll, Dana; Gaston, Derek; Martineau, Richard
2010-01-01
We have developed a tightly coupled multiphysics simulation tool for the pebble-bed reactor (PBR) concept, a type of Very High-Temperature gas-cooled Reactor (VHTR). The simulation tool, PRONGHORN, takes advantages of the Multiphysics Object-Oriented Simulation Environment library, and is capable of solving multidimensional thermal-fluid and neutronics problems implicitly with a Newton-based approach. Expensive Jacobian matrix formation is alleviated via the Jacobian-free Newton-Krylov method, and physics-based preconditioning is applied to minimize Krylov iterations. Motivation for the work is provided via analysis and numerical experiments on simpler multiphysics reactor models. We then provide detail of the physical models and numerical methods in PRONGHORN. Finally, PRONGHORN's algorithmic capability is demonstrated on a number of PBR test cases.
Engineering Multiphysics Research
Directory of Open Access Journals (Sweden)
Tom Eppes
2011-05-01
Full Text Available This paper describes an engineering undergraduate course that covers the methods and techniques of multiphysics modeling. Students become active participants in analysis and discovery by being challenged to solve a sequence of problems related to high priority technology areas. Projects range from power systems and thermal control of habitats to autonomous flight systems and harsh environment electronics. Working in a cooperative learning environment, teams encounter a series of assignments that build on existing skills while gradually expanding their knowledge and expertise in disciplines outside of their own. This project-based approach employs a scaffolding structure with assignments organized in progressively challenging modules supported by mentoring. Each project begins with a problem definition which requires consideration of factors and influences beyond a single discipline. Solution development then moves to setting material properties, boundary constraints and including the necessary physics engines. For many students, this is the first in depth exposure to problems with specialized terminologies, driving equations and limiting conditions. Lastly, solving and post processing are addressed exploring steady state, time-variant, frequency response, optimization and sensitivity methods. The paper discusses the teaching and learning strategies, course structure, outcome assessment and project examples.
Parallel continuous simulated tempering and its applications in large-scale molecular simulations
Energy Technology Data Exchange (ETDEWEB)
Zang, Tianwu; Yu, Linglin; Zhang, Chong [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Ma, Jianpeng, E-mail: jpma@bcm.tmc.edu [Applied Physics Program and Department of Bioengineering, Rice University, Houston, Texas 77005 (United States); Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, One Baylor Plaza, BCM-125, Houston, Texas 77030 (United States)
2014-07-28
In this paper, we introduce a parallel continuous simulated tempering (PCST) method for enhanced sampling in studying large complex systems. It mainly inherits the continuous simulated tempering (CST) method in our previous studies [C. Zhang and J. Ma, J. Chem. Phys. 130, 194112 (2009); C. Zhang and J. Ma, J. Chem. Phys. 132, 244101 (2010)], while adopts the spirit of parallel tempering (PT), or replica exchange method, by employing multiple copies with different temperature distributions. Differing from conventional PT methods, despite the large stride of total temperature range, the PCST method requires very few copies of simulations, typically 2–3 copies, yet it is still capable of maintaining a high rate of exchange between neighboring copies. Furthermore, in PCST method, the size of the system does not dramatically affect the number of copy needed because the exchange rate is independent of total potential energy, thus providing an enormous advantage over conventional PT methods in studying very large systems. The sampling efficiency of PCST was tested in two-dimensional Ising model, Lennard-Jones liquid and all-atom folding simulation of a small globular protein trp-cage in explicit solvent. The results demonstrate that the PCST method significantly improves sampling efficiency compared with other methods and it is particularly effective in simulating systems with long relaxation time or correlation time. We expect the PCST method to be a good alternative to parallel tempering methods in simulating large systems such as phase transition and dynamics of macromolecules in explicit solvent.
Engineering-Based Thermal CFD Simulations on Massive Parallel Systems
Frisch, Jé rô me; Mundani, Ralf-Peter; Rank, Ernst; van Treeck, Christoph
2015-01-01
The development of parallel Computational Fluid Dynamics (CFD) codes is a challenging task that entails efficient parallelization concepts and strategies in order to achieve good scalability values when running those codes on modern supercomputers
Parallelization of simulation code for liquid-gas model of lattice-gas fluid
International Nuclear Information System (INIS)
Kawai, Wataru; Ebihara, Kenichi; Kume, Etsuo; Watanabe, Tadashi
2000-03-01
A simulation code for hydrodynamical phenomena which is based on the liquid-gas model of lattice-gas fluid is parallelized by using MPI (Message Passing Interface) library. The parallelized code can be applied to the larger size of the simulations than the non-parallelized code. The calculation times of the parallelized code on VPP500 (Vector-Parallel super computer with dispersed memory units), AP3000 (Scalar-parallel server with dispersed memory units), and a workstation cluster decreased in inverse proportion to the number of processors. (author)
Xyce Parallel Electronic Simulator Reference Guide Version 6.4
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Baur, David Gregory [Raytheon, Albuquerque, NM (United States)
2015-12-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] . Trademarks The information herein is subject to change without notice. Copyright c 2002-2015 Sandia Corporation. All rights reserved. Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Portions of the Xyce TM code are: Copyright c 2002, The Regents of the University of California. Produced at the Lawrence Livermore National Laboratory. Written by Alan Hindmarsh, Allan Taylor, Radu Serban. UCRL-CODE-2002-59 All rights reserved. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of Amtec Engineering, Inc. Xyce 's expression library is based on that inside Spice 3F5 developed by the EECS Department at the University of California. The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. All other trademarks are property of their respective owners. Contacts Bug Reports (Sandia only) http://joseki.sandia.gov/bugzilla http://charleston.sandia.gov/bugzilla World Wide Web http://xyce.sandia.gov http://charleston.sandia.gov/xyce (Sandia only) Email xyce@sandia.gov (outside Sandia) xyce-sandia@sandia.gov (Sandia only)
Multiphysics modelling of the spray forming process
International Nuclear Information System (INIS)
Mi, J.; Grant, P.S.; Fritsching, U.; Belkessam, O.; Garmendia, I.; Landaberea, A.
2008-01-01
An integrated, multiphysics numerical model has been developed through the joint efforts of the University of Oxford (UK), University of Bremen (Germany) and Inasmet (Spain) to simulate the spray forming process. The integrated model consisted of four sub-models: (1) an atomization model simulating the fragmentation of a continuous liquid metal stream into droplet spray during gas atomization; (2) a droplet spray model simulating the droplet spray mass and enthalpy evolution in the gas flow field prior to deposition; (3) a droplet deposition model simulating droplet deposition, splashing and re-deposition behavior and the resulting preform shape and heat flow; and (4) a porosity model simulating the porosity distribution inside a spray formed ring preform. The model has been validated against experiments of the spray forming of large diameter IN718 Ni superalloy rings. The modelled preform shape, surface temperature and final porosity distribution showed good agreement with experimental measurements
Parallel linear solvers for simulations of reactor thermal hydraulics
International Nuclear Information System (INIS)
Yan, Y.; Antal, S.P.; Edge, B.; Keyes, D.E.; Shaver, D.; Bolotnov, I.A.; Podowski, M.Z.
2011-01-01
The state-of-the-art multiphase fluid dynamics code, NPHASE-CMFD, performs multiphase flow simulations in complex domains using implicit nonlinear treatment of the governing equations and in parallel, which is a very challenging environment for the linear solver. The present work illustrates how the Portable, Extensible Toolkit for Scientific Computation (PETSc) and scalable Algebraic Multigrid (AMG) preconditioner from Hypre can be utilized to construct robust and scalable linear solvers for the Newton correction equation obtained from the discretized system of governing conservation equations in NPHASE-CMFD. The overall long-tem objective of this work is to extend the NPHASE-CMFD code into a fully-scalable solver of multiphase flow and heat transfer problems, applicable to both steady-state and stiff time-dependent phenomena in complete fuel assemblies of nuclear reactors and, eventually, the entire reactor core (such as the Virtual Reactor concept envisioned by CASL). This campaign appropriately begins with the linear algebraic equation solver, which is traditionally a bottleneck to scalability in PDE-based codes. The computational complexity of the solver is usually superlinear in problem size, whereas the rest of the code, the “physics” portion, usually has its complexity linear in the problem size. (author)
Visualizing Network Traffic to Understand the Performance of Massively Parallel Simulations
Landge, A. G.
2012-12-01
The performance of massively parallel applications is often heavily impacted by the cost of communication among compute nodes. However, determining how to best use the network is a formidable task, made challenging by the ever increasing size and complexity of modern supercomputers. This paper applies visualization techniques to aid parallel application developers in understanding the network activity by enabling a detailed exploration of the flow of packets through the hardware interconnect. In order to visualize this large and complex data, we employ two linked views of the hardware network. The first is a 2D view, that represents the network structure as one of several simplified planar projections. This view is designed to allow a user to easily identify trends and patterns in the network traffic. The second is a 3D view that augments the 2D view by preserving the physical network topology and providing a context that is familiar to the application developers. Using the massively parallel multi-physics code pF3D as a case study, we demonstrate that our tool provides valuable insight that we use to explain and optimize pF3D-s performance on an IBM Blue Gene/P system. © 1995-2012 IEEE.
Parallel-Architecture Simulator Development Using Hardware Transactional Memory
Armejach Sanosa, Adrià
2009-01-01
To address the need for a simpler parallel programming model, Transactional Memory (TM) has been developed and promises good parallel performance with easy-to-write parallel code. Unlike lock-based approaches, with TM, programmers do not need to explicitly specify and manage the synchronization among threads. However, programmers simply mark code segments as transactions, and the TM system manages the concurrency control for them. TM can be implemented either in software (STM) or hardware (HT...
Hsieh, Shang-Hsien
1993-01-01
The principal objective of this research is to develop, test, and implement coarse-grained, parallel-processing strategies for nonlinear dynamic simulations of practical structural problems. There are contributions to four main areas: finite element modeling and analysis of rotational dynamics, numerical algorithms for parallel nonlinear solutions, automatic partitioning techniques to effect load-balancing among processors, and an integrated parallel analysis system.
Xyce Parallel Electronic Simulator Reference Guide Version 6.6.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aadithya, Karthik Venkatraman [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2016-11-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users' Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce . This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users' Guide [1] . The information herein is subject to change without notice. Copyright c 2002-2016 Sandia Corporation. All rights reserved. Acknowledgements The BSIM Group at the University of California, Berkeley developed the BSIM3, BSIM4, BSIM6, BSIM-CMG and BSIM-SOI models. The BSIM3 is Copyright c 1999, Regents of the University of California. The BSIM4 is Copyright c 2006, Regents of the University of California. The BSIM6 is Copyright c 2015, Regents of the University of California. The BSIM-CMG is Copyright c 2012 and 2016, Regents of the University of California. The BSIM-SOI is Copyright c 1990, Regents of the University of California. All rights reserved. The Mextram model has been developed by NXP Semiconductors until 2007, Delft University of Technology from 2007 to 2014, and Auburn University since April 2015. Copyrights c of Mextram are with Delft University of Technology, NXP Semiconductors and Auburn University. The MIT VS Model Research Group developed the MIT Virtual Source (MVS) model. Copyright c 2013 Massachusetts Institute of Technology (MIT). The EKV3 MOSFET model was developed by the EKV Team of the Electronics Laboratory-TUC of the Technical University of Crete. Trademarks Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and Tec
Design and multi-physics optimization of rotary MRF brakes
Topcu, Okan; Taşcıoğlu, Yiğit; Konukseven, Erhan İlhan
2018-03-01
Particle swarm optimization (PSO) is a popular method to solve the optimization problems. However, calculations for each particle will be excessive when the number of particles and complexity of the problem increases. As a result, the execution speed will be too slow to achieve the optimized solution. Thus, this paper proposes an automated design and optimization method for rotary MRF brakes and similar multi-physics problems. A modified PSO algorithm is developed for solving multi-physics engineering optimization problems. The difference between the proposed method and the conventional PSO is to split up the original single population into several subpopulations according to the division of labor. The distribution of tasks and the transfer of information to the next party have been inspired by behaviors of a hunting party. Simulation results show that the proposed modified PSO algorithm can overcome the problem of heavy computational burden of multi-physics problems while improving the accuracy. Wire type, MR fluid type, magnetic core material, and ideal current inputs have been determined by the optimization process. To the best of the authors' knowledge, this multi-physics approach is novel for optimizing rotary MRF brakes and the developed PSO algorithm is capable of solving other multi-physics engineering optimization problems. The proposed method has showed both better performance compared to the conventional PSO and also has provided small, lightweight, high impedance rotary MRF brake designs.
Optimized Parallel Discrete Event Simulation (PDES) for High Performance Computing (HPC) Clusters
National Research Council Canada - National Science Library
Abu-Ghazaleh, Nael
2005-01-01
The aim of this project was to study the communication subsystem performance of state of the art optimistic simulator Synchronous Parallel Environment for Emulation and Discrete-Event Simulation (SPEEDES...
Parallelized FDTD simulation for flat-plate bounded wave EMP simulator with lumped terminator
International Nuclear Information System (INIS)
Zhu Xiangqin; Chen Weiqing; Chen Zaigao; Cai Libing; Wang Jianguo
2013-01-01
A parallelized finite-difference time-domain(FDTD) method for simulating the bounded wave electromagnetic pulse (EMP) simulator with lumped terminator and parallel plate is presented. The effects of several model-parameters on the simulator to the fields in the working volume are simulated and analyzed. The results show that if the width of the lower PEC plate is(or is bigger than)1.5 times that of the upper plate of working volume, the projection length of front transitional section does not have a significant effect on the rise-times of electric fields at the points near the front transitional section, and the rise-times of electric fields at the points near the working volume center decrease as the projection length increases, but the decrement of rise-time decreases. The rise-times of E z at all points also decrease as the lower PEC plate's width increases, but the decrements of rise-time decreases. If the projection length of the front transitional section is fixed, the good results can not be obtained by increasing or decreasing the height of the simulator only, however, which has an optimal value. (authors)
The Data Transfer Kit: A geometric rendezvous-based tool for multiphysics data transfer
International Nuclear Information System (INIS)
Slattery, S. R.; Wilson, P. P. H.; Pawlowski, R. P.
2013-01-01
The Data Transfer Kit (DTK) is a software library designed to provide parallel data transfer services for arbitrary physics components based on the concept of geometric rendezvous. The rendezvous algorithm provides a means to geometrically correlate two geometric domains that may be arbitrarily decomposed in a parallel simulation. By repartitioning both domains such that they have the same geometric domain on each parallel process, efficient and load balanced search operations and data transfer can be performed at a desirable algorithmic time complexity with low communication overhead relative to other types of mapping algorithms. With the increased development efforts in multiphysics simulation and other multiple mesh and geometry problems, generating parallel topology maps for transferring fields and other data between geometric domains is a common operation. The algorithms used to generate parallel topology maps based on the concept of geometric rendezvous as implemented in DTK are described with an example using a conjugate heat transfer calculation and thermal coupling with a neutronics code. In addition, we provide the results of initial scaling studies performed on the Jaguar Cray XK6 system at Oak Ridge National Laboratory for a worse-case-scenario problem in terms of algorithmic complexity that shows good scaling on 0(1 x 104) cores for topology map generation and excellent scaling on 0(1 x 105) cores for the data transfer operation with meshes of O(1 x 109) elements. (authors)
The Data Transfer Kit: A geometric rendezvous-based tool for multiphysics data transfer
Energy Technology Data Exchange (ETDEWEB)
Slattery, S. R.; Wilson, P. P. H. [Department of Engineering Physics, University of Wisconsin - Madison, 1500 Engineering Dr., Madison, WI 53706 (United States); Pawlowski, R. P. [Sandia National Laboratories, P.O. Box 5800, Albuquerque, NM 87185 (United States)
2013-07-01
The Data Transfer Kit (DTK) is a software library designed to provide parallel data transfer services for arbitrary physics components based on the concept of geometric rendezvous. The rendezvous algorithm provides a means to geometrically correlate two geometric domains that may be arbitrarily decomposed in a parallel simulation. By repartitioning both domains such that they have the same geometric domain on each parallel process, efficient and load balanced search operations and data transfer can be performed at a desirable algorithmic time complexity with low communication overhead relative to other types of mapping algorithms. With the increased development efforts in multiphysics simulation and other multiple mesh and geometry problems, generating parallel topology maps for transferring fields and other data between geometric domains is a common operation. The algorithms used to generate parallel topology maps based on the concept of geometric rendezvous as implemented in DTK are described with an example using a conjugate heat transfer calculation and thermal coupling with a neutronics code. In addition, we provide the results of initial scaling studies performed on the Jaguar Cray XK6 system at Oak Ridge National Laboratory for a worse-case-scenario problem in terms of algorithmic complexity that shows good scaling on 0(1 x 104) cores for topology map generation and excellent scaling on 0(1 x 105) cores for the data transfer operation with meshes of O(1 x 109) elements. (authors)
Adaptive hybrid mesh refinement for multiphysics applications
International Nuclear Information System (INIS)
Khamayseh, Ahmed; Almeida, Valmor de
2007-01-01
The accuracy and convergence of computational solutions of mesh-based methods is strongly dependent on the quality of the mesh used. We have developed methods for optimizing meshes that are comprised of elements of arbitrary polygonal and polyhedral type. We present in this research the development of r-h hybrid adaptive meshing technology tailored to application areas relevant to multi-physics modeling and simulation. Solution-based adaptation methods are used to reposition mesh nodes (r-adaptation) or to refine the mesh cells (h-adaptation) to minimize solution error. The numerical methods perform either the r-adaptive mesh optimization or the h-adaptive mesh refinement method on the initial isotropic or anisotropic meshes to equidistribute weighted geometric and/or solution error function. We have successfully introduced r-h adaptivity to a least-squares method with spherical harmonics basis functions for the solution of the spherical shallow atmosphere model used in climate modeling. In addition, application of this technology also covers a wide range of disciplines in computational sciences, most notably, time-dependent multi-physics, multi-scale modeling and simulation
Kinematics and dynamics analysis of a novel serial-parallel dynamic simulator
Energy Technology Data Exchange (ETDEWEB)
Hu, Bo; Zhang, Lian Dong; Yu, Jingjing [Parallel Robot and Mechatronic System Laboratory of Hebei Province, Yanshan University, Qinhuangdao, Hebei (China)
2016-11-15
A serial-parallel dynamics simulator based on serial-parallel manipulator is proposed. According to the dynamics simulator motion requirement, the proposed serial-parallel dynamics simulator formed by 3-RRS (active revolute joint-revolute joint-spherical joint) and 3-SPR (Spherical joint-active prismatic joint-revolute joint) PMs adopts the outer and inner layout. By integrating the kinematics, constraint and coupling information of the 3-RRS and 3-SPR PMs into the serial-parallel manipulator, the inverse Jacobian matrix, velocity, and acceleration of the serial-parallel dynamics simulator are studied. Based on the principle of virtual work and the kinematics model, the inverse dynamic model is established. Finally, the workspace of the (3-RRS)+(3-SPR) dynamics simulator is constructed.
Kinematics and dynamics analysis of a novel serial-parallel dynamic simulator
International Nuclear Information System (INIS)
Hu, Bo; Zhang, Lian Dong; Yu, Jingjing
2016-01-01
A serial-parallel dynamics simulator based on serial-parallel manipulator is proposed. According to the dynamics simulator motion requirement, the proposed serial-parallel dynamics simulator formed by 3-RRS (active revolute joint-revolute joint-spherical joint) and 3-SPR (Spherical joint-active prismatic joint-revolute joint) PMs adopts the outer and inner layout. By integrating the kinematics, constraint and coupling information of the 3-RRS and 3-SPR PMs into the serial-parallel manipulator, the inverse Jacobian matrix, velocity, and acceleration of the serial-parallel dynamics simulator are studied. Based on the principle of virtual work and the kinematics model, the inverse dynamic model is established. Finally, the workspace of the (3-RRS)+(3-SPR) dynamics simulator is constructed
Implementation of Parallel Dynamic Simulation on Shared-Memory vs. Distributed-Memory Environments
Energy Technology Data Exchange (ETDEWEB)
Jin, Shuangshuang; Chen, Yousu; Wu, Di; Diao, Ruisheng; Huang, Zhenyu
2015-12-09
Power system dynamic simulation computes the system response to a sequence of large disturbance, such as sudden changes in generation or load, or a network short circuit followed by protective branch switching operation. It consists of a large set of differential and algebraic equations, which is computational intensive and challenging to solve using single-processor based dynamic simulation solution. High-performance computing (HPC) based parallel computing is a very promising technology to speed up the computation and facilitate the simulation process. This paper presents two different parallel implementations of power grid dynamic simulation using Open Multi-processing (OpenMP) on shared-memory platform, and Message Passing Interface (MPI) on distributed-memory clusters, respectively. The difference of the parallel simulation algorithms and architectures of the two HPC technologies are illustrated, and their performances for running parallel dynamic simulation are compared and demonstrated.
Lithium-Ion Battery Safety Study Using Multi-Physics Internal Short-Circuit Model (Presentation)
Energy Technology Data Exchange (ETDEWEB)
Kim, G-.H.; Smith, K.; Pesaran, A.
2009-06-01
This presentation outlines NREL's multi-physics simulation study to characterize an internal short by linking and integrating electrochemical cell, electro-thermal, and abuse reaction kinetics models.
Numerical simulation of Vlasov equation with parallel tools
International Nuclear Information System (INIS)
Peyroux, J.
2005-11-01
This project aims to make even more powerful the resolution of Vlasov codes through the various parallelization tools (MPI, OpenMP...). A simplified test case served as a base for constructing the parallel codes for obtaining a data-processing skeleton which, thereafter, could be re-used for increasingly complex models (more than four variables of phase space). This will thus make it possible to treat more realistic situations linked, for example, to the injection of ultra short and ultra intense impulses in inertial fusion plasmas, or the study of the instability of trapped ions now taken as being responsible for the generation of turbulence in tokamak plasmas. (author)
ANNarchy: a code generation approach to neural simulations on parallel hardware
Vitay, Julien; Dinkelbach, Helge Ü.; Hamker, Fred H.
2015-01-01
Many modern neural simulators focus on the simulation of networks of spiking neurons on parallel hardware. Another important framework in computational neuroscience, rate-coded neural networks, is mostly difficult or impossible to implement using these simulators. We present here the ANNarchy (Artificial Neural Networks architect) neural simulator, which allows to easily define and simulate rate-coded and spiking networks, as well as combinations of both. The interface in Python has been designed to be close to the PyNN interface, while the definition of neuron and synapse models can be specified using an equation-oriented mathematical description similar to the Brian neural simulator. This information is used to generate C++ code that will efficiently perform the simulation on the chosen parallel hardware (multi-core system or graphical processing unit). Several numerical methods are available to transform ordinary differential equations into an efficient C++code. We compare the parallel performance of the simulator to existing solutions. PMID:26283957
Parallel alternating direction preconditioner for isogeometric simulations of explicit dynamics
Łoś, Marcin; Woźniak, Maciej; Paszyński, Maciej; Dalcin, Lisandro; Calo, Victor M.
2015-01-01
incorporated as a part of PETIGA an isogeometric framework [7] build on top of PETSc [8]. We show the scalability of the parallel algorithm on STAMPEDE linux cluster up to 10,000 processors, as well as the convergence rate of the PCG solver
Efficient Simulation of Population Overflow in Parallel Queues
Nicola, V.F.; Zaburnenko, T.S.
2006-01-01
In this paper we propose a state-dependent importance sampling heuristic to estimate the probability of population overﬂow in networks of parallel queues. This heuristic approximates the “optimal��? state-dependent change of measure without the need for dif��?cult mathematical analysis or costly
Efficient Heuristics for Simulating Population Overflow in Parallel Networks
Zaburnenko, T.S.; Nicola, V.F.
2006-01-01
In this paper we propose a state-dependent importance sampling heuristic to estimate the probability of population overflow in networks of parallel queues. This heuristic approximates the “optimal��? state-dependent change of measure without the need for costly optimization involved in other
Co-simulation of dynamic systems in parallel and serial model configurations
International Nuclear Information System (INIS)
Sweafford, Trevor; Yoon, Hwan Sik
2013-01-01
Recent advancement in simulation software and computation hardware make it realizable to simulate complex dynamic systems comprised of multiple submodels developed in different modeling languages. The so-called co-simulation enables one to study various aspects of a complex dynamic system with heterogeneous submodels in a cost-effective manner. Among several different model configurations for co-simulation, synchronized parallel configuration is regarded to expedite the simulation process by simulation multiple sub models concurrently on a multi core processor. In this paper, computational accuracies as well as computation time are studied for three different co-simulation frameworks : integrated, serial, and parallel. for this purpose, analytical evaluations of the three different methods are made using the explicit Euler method and then they are applied to two-DOF mass-spring systems. The result show that while the parallel simulation configuration produces the same accurate results as the integrated configuration, results of the serial configuration, results of the serial configuration show a slight deviation. it is also shown that the computation time can be reduced by running simulation in the parallel configuration. Therefore, it can be concluded that the synchronized parallel simulation methodology is the best for both simulation accuracy and time efficiency.
Parallelizing an electron transport Monte Carlo simulator (MOCASIN 2.0)
International Nuclear Information System (INIS)
Schwetman, H.; Burdick, S.
1988-01-01
Electron transport simulators are tools for studying electrical properties of semiconducting materials and devices. As demands for modeling more complex devices and new materials have emerged, so have demands for more processing power. This paper documents a project to convert an electron transport simulator (MOCASIN 2.0) to a parallel processing environment. In addition to describing the conversion, the paper presents PPL, a parallel programming version of C running on a Sequent multiprocessor system. In timing tests, models that simulated the movement of 2,000 particles for 100 time steps were executed on ten processors, with a parallel efficiency of over 97%
Static and dynamic load-balancing strategies for parallel reservoir simulation
International Nuclear Information System (INIS)
Anguille, L.; Killough, J.E.; Li, T.M.C.; Toepfer, J.L.
1995-01-01
Accurate simulation of the complex phenomena that occur in flow in porous media can tax even the most powerful serial computers. Emergence of new parallel computer architectures as a future efficient tool in reservoir simulation may overcome this difficulty. Unfortunately, major problems remain to be solved before using parallel computers commercially: production serial programs must be rewritten to be efficient in parallel environments and load balancing methods must be explored to evenly distribute the workload on each processor during the simulation. This study implements both a static load-balancing algorithm and a receiver-initiated dynamic load-sharing algorithm to achieve high parallel efficiencies on both the IBM SP2 and Intel IPSC/860 parallel computers. Significant speedup improvement was recorded for both methods. Further optimization of these algorithms yielded a technique with efficiencies as high as 90% and 70% on 8 and 32 nodes, respectively. The increased performance was the result of the minimization of message-passing overhead
Parallel Motion Simulation of Large-Scale Real-Time Crowd in a Hierarchical Environmental Model
Directory of Open Access Journals (Sweden)
Xin Wang
2012-01-01
Full Text Available This paper presents a parallel real-time crowd simulation method based on a hierarchical environmental model. A dynamical model of the complex environment should be constructed to simulate the state transition and propagation of individual motions. By modeling of a virtual environment where virtual crowds reside, we employ different parallel methods on a topological layer, a path layer and a perceptual layer. We propose a parallel motion path matching method based on the path layer and a parallel crowd simulation method based on the perceptual layer. The large-scale real-time crowd simulation becomes possible with these methods. Numerical experiments are carried out to demonstrate the methods and results.
Building Blocks for the Rapid Development of Parallel Simulations, Phase I
National Aeronautics and Space Administration — Scientists need to be able to quickly develop and run parallel simulations without paying the high price of writing low-level message passing codes using compiled...
Kinetic-Monte-Carlo-Based Parallel Evolution Simulation Algorithm of Dust Particles
Directory of Open Access Journals (Sweden)
Xiaomei Hu
2014-01-01
Full Text Available The evolution simulation of dust particles provides an important way to analyze the impact of dust on the environment. KMC-based parallel algorithm is proposed to simulate the evolution of dust particles. In the parallel evolution simulation algorithm of dust particles, data distribution way and communication optimizing strategy are raised to balance the load of every process and reduce the communication expense among processes. The experimental results show that the simulation of diffusion, sediment, and resuspension of dust particles in virtual campus is realized and the simulation time is shortened by parallel algorithm, which makes up for the shortage of serial computing and makes the simulation of large-scale virtual environment possible.
Analysis for Parallel Execution without Performing Hardware/Software Co-simulation
Muhammad Rashid
2014-01-01
Hardware/software co-simulation improves the performance of embedded applications by executing the applications on a virtual platform before the actual hardware is available in silicon. However, the virtual platform of the target architecture is often not available during early stages of the embedded design flow. Consequently, analysis for parallel execution without performing hardware/software co-simulation is required. This article presents an analysis methodology for parallel execution of ...
Xyce parallel electronic simulator : users' guide. Version 5.1.
Energy Technology Data Exchange (ETDEWEB)
Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick
2009-11-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is a
Xyce Parallel Electronic Simulator : users' guide, version 4.1.
Energy Technology Data Exchange (ETDEWEB)
Mei, Ting; Rankin, Eric Lamont; Thornquist, Heidi K.; Santarelli, Keith R.; Fixel, Deborah A.; Coffey, Todd Stirling; Russo, Thomas V.; Schiek, Richard Louis; Keiter, Eric Richard; Pawlowski, Roger Patrick
2009-02-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) Device models which are specifically tailored to meet Sandia's needs, including some radiation-aware devices (for Sandia users only). (4) Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing parallel implementation - which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The development of Xyce provides a platform for computational research and development aimed specifically at the needs of the Laboratory. With Xyce, Sandia has an 'in-house' capability with which both new electrical (e.g., device model development) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms) research and development can be performed. As a result, Xyce is a
Energy Technology Data Exchange (ETDEWEB)
Yu, Y. Q. [Argonne National Lab. (ANL), Argonne, IL (United States); Shemon, E. R. [Argonne National Lab. (ANL), Argonne, IL (United States); Mahadevan, Vijay S. [Argonne National Lab. (ANL), Argonne, IL (United States); Rahaman, Ronald O. [Argonne National Lab. (ANL), Argonne, IL (United States)
2016-02-29
SHARP, developed under the NEAMS Reactor Product Line, is an advanced modeling and simulation toolkit for the analysis of advanced nuclear reactors. SHARP is comprised of three physics modules currently including neutronics, thermal hydraulics, and structural mechanics. SHARP empowers designers to produce accurate results for modeling physical phenomena that have been identified as important for nuclear reactor analysis. SHARP can use existing physics codes and take advantage of existing infrastructure capabilities in the MOAB framework and the coupling driver/solver library, the Coupled Physics Environment (CouPE), which utilizes the widely used, scalable PETSc library. This report aims at identifying the coupled-physics simulation capability of SHARP by introducing the demonstration example called sahex in advance of the SHARP release expected by Mar 2016. sahex consists of 6 fuel pins with cladding, 1 control rod, sodium coolant and an outer duct wall that encloses all the other components. This example is carefully chosen to demonstrate the proof of concept for solving more complex demonstration examples such as EBR II assembly and ABTR full core. The workflow of preparing the input files, running the case and analyzing the results is demonstrated in this report. Moreover, an extension of the sahex model called sahex_core, which adds six homogenized neighboring assemblies to the full heterogeneous sahex model, is presented to test homogenization capabilities in both Nek5000 and PROTEUS. Some primary information on the configuration and build aspects for the SHARP toolkit, which includes capability to auto-download dependencies and configure/install with optimal flags in an architecture-aware fashion, is also covered by this report. A step-by-step instruction is provided to help users to create their cases. Details on these processes will be provided in the SHARP user manual that will accompany the first release.
International Nuclear Information System (INIS)
Yu, Y. Q.; Shemon, E. R.; Mahadevan, Vijay S.; Rahaman, Ronald O.
2016-01-01
SHARP, developed under the NEAMS Reactor Product Line, is an advanced modeling and simulation toolkit for the analysis of advanced nuclear reactors. SHARP is comprised of three physics modules currently including neutronics, thermal hydraulics, and structural mechanics. SHARP empowers designers to produce accurate results for modeling physical phenomena that have been identified as important for nuclear reactor analysis. SHARP can use existing physics codes and take advantage of existing infrastructure capabilities in the MOAB framework and the coupling driver/solver library, the Coupled Physics Environment (CouPE), which utilizes the widely used, scalable PETSc library. This report aims at identifying the coupled-physics simulation capability of SHARP by introducing the demonstration example called sahex in advance of the SHARP release expected by Mar 2016. sahex consists of 6 fuel pins with cladding, 1 control rod, sodium coolant and an outer duct wall that encloses all the other components. This example is carefully chosen to demonstrate the proof of concept for solving more complex demonstration examples such as EBR II assembly and ABTR full core. The workflow of preparing the input files, running the case and analyzing the results is demonstrated in this report. Moreover, an extension of the sahex model called sahex c ore, which adds six homogenized neighboring assemblies to the full heterogeneous sahex model, is presented to test homogenization capabilities in both Nek5000 and PROTEUS. Some primary information on the configuration and build aspects for the SHARP toolkit, which includes capability to auto-download dependencies and configure/install with optimal flags in an architecture-aware fashion, is also covered by this report. A step-by-step instruction is provided to help users to create their cases. Details on these processes will be provided in the SHARP user manual that will accompany the first release.
Valasek, Lukas; Glasa, Jan
2017-12-01
Current fire simulation systems are capable to utilize advantages of high-performance computer (HPC) platforms available and to model fires efficiently in parallel. In this paper, efficiency of a corridor fire simulation on a HPC computer cluster is discussed. The parallel MPI version of Fire Dynamics Simulator is used for testing efficiency of selected strategies of allocation of computational resources of the cluster using a greater number of computational cores. Simulation results indicate that if the number of cores used is not equal to a multiple of the total number of cluster node cores there are allocation strategies which provide more efficient calculations.
Molecular Dynamic Simulations of Nanostructured Ceramic Materials on Parallel Computers
International Nuclear Information System (INIS)
Vashishta, Priya; Kalia, Rajiv
2005-01-01
Large-scale molecular-dynamics (MD) simulations have been performed to gain insight into: (1) sintering, structure, and mechanical behavior of nanophase SiC and SiO2; (2) effects of dynamic charge transfers on the sintering of nanophase TiO2; (3) high-pressure structural transformation in bulk SiC and GaAs nanocrystals; (4) nanoindentation in Si3N4; and (5) lattice mismatched InAs/GaAs nanomesas. In addition, we have designed a multiscale simulation approach that seamlessly embeds MD and quantum-mechanical (QM) simulations in a continuum simulation. The above research activities have involved strong interactions with researchers at various universities, government laboratories, and industries. 33 papers have been published and 22 talks have been given based on the work described in this report
A Coupling Tool for Parallel Molecular Dynamics-Continuum Simulations
Neumann, Philipp; Tchipev, Nikola
2012-01-01
We present a tool for coupling Molecular Dynamics and continuum solvers. It is written in C++ and is meant to support the developers of hybrid molecular - continuum simulations in terms of both realisation of the respective coupling algorithm
Migrating to a real-time distributed parallel simulator architecture
CSIR Research Space (South Africa)
Duvenhage, B
2007-07-01
Full Text Available A legacy non-distributed logical time simulator is migrated to a distributed architecture to parallelise execution. The existing Discrete Time System Specification (DTSS) modelling formalism is retained to simplify the reuse of existing models...
Parallel Earthquake Simulations on Large-Scale Multicore Supercomputers
Wu, Xingfu; Duan, Benchun; Taylor, Valerie
2011-01-01
, such as California and Japan, scientists have been using numerical simulations to study earthquake rupture propagation along faults and seismic wave propagation in the surrounding media on ever-advancing modern computers over past several decades. In particular
Xyce parallel electronic simulator users guide, version 6.0.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Verley, Jason C.; Fixel, Deborah A.; Coffey, Todd S; Pawlowski, Roger P; Warrender, Christina E.; Baur, David Gregory.
2013-08-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandias needs, including some radiationaware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase a message passing parallel implementation which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.
Xyce parallel electronic simulator users' guide, Version 6.0.1.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Verley, Jason C.; Fixel, Deborah A.; Coffey, Todd S; Pawlowski, Roger P; Warrender, Christina E.; Baur, David Gregory.
2014-01-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandias needs, including some radiationaware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase a message passing parallel implementation which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.
Xyce parallel electronic simulator users guide, version 6.1
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Sholander, Peter E.; Thornquist, Heidi K.; Verley, Jason C.; Baur, David Gregory
2014-03-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas; Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers; A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models; Device models that are specifically tailored to meet Sandia's needs, including some radiationaware devices (for Sandia users only); and Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase-a message passing parallel implementation-which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.
Xyce™ Parallel Electronic Simulator Users' Guide, Version 6.5.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Aadithya, Karthik V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Schiek, Richard L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation; Verley, Jason C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States). Electrical Models and Simulation
2016-06-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The information herein is subject to change without notice. Copyright © 2002-2016 Sandia Corporation. All rights reserved.
Xyce Parallel Electronic Simulator Users' Guide Version 6.8
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aadithya, Karthik Venkatraman [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard L. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason C. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2017-10-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase$-$ a message passing parallel implementation $-$ which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows.
Event Based Simulator for Parallel Computing over the Wide Area Network for Real Time Visualization
Sundararajan, Elankovan; Harwood, Aaron; Kotagiri, Ramamohanarao; Satria Prabuwono, Anton
As the computational requirement of applications in computational science continues to grow tremendously, the use of computational resources distributed across the Wide Area Network (WAN) becomes advantageous. However, not all applications can be executed over the WAN due to communication overhead that can drastically slowdown the computation. In this paper, we introduce an event based simulator to investigate the performance of parallel algorithms executed over the WAN. The event based simulator known as SIMPAR (SIMulator for PARallel computation), simulates the actual computations and communications involved in parallel computation over the WAN using time stamps. Visualization of real time applications require steady stream of processed data flow for visualization purposes. Hence, SIMPAR may prove to be a valuable tool to investigate types of applications and computing resource requirements to provide uninterrupted flow of processed data for real time visualization purposes. The results obtained from the simulation show concurrence with the expected performance using the L-BSP model.
Simulation of partially coherent light propagation using parallel computing devices
Magalhães, Tiago C.; Rebordão, José M.
2017-08-01
Light acquires or loses coherence and coherence is one of the few optical observables. Spectra can be derived from coherence functions and understanding any interferometric experiment is also relying upon coherence functions. Beyond the two limiting cases (full coherence or incoherence) the coherence of light is always partial and it changes with propagation. We have implemented a code to compute the propagation of partially coherent light from the source plane to the observation plane using parallel computing devices (PCDs). In this paper, we restrict the propagation in free space only. To this end, we used the Open Computing Language (OpenCL) and the open-source toolkit PyOpenCL, which gives access to OpenCL parallel computation through Python. To test our code, we chose two coherence source models: an incoherent source and a Gaussian Schell-model source. In the former case, we divided into two different source shapes: circular and rectangular. The results were compared to the theoretical values. Our implemented code allows one to choose between the PyOpenCL implementation and a standard one, i.e using the CPU only. To test the computation time for each implementation (PyOpenCL and standard), we used several computer systems with different CPUs and GPUs. We used powers of two for the dimensions of the cross-spectral density matrix (e.g. 324, 644) and a significant speed increase is observed in the PyOpenCL implementation when compared to the standard one. This can be an important tool for studying new source models.
Random number generators for large-scale parallel Monte Carlo simulations on FPGA
Lin, Y.; Wang, F.; Liu, B.
2018-05-01
Through parallelization, field programmable gate array (FPGA) can achieve unprecedented speeds in large-scale parallel Monte Carlo (LPMC) simulations. FPGA presents both new constraints and new opportunities for the implementations of random number generators (RNGs), which are key elements of any Monte Carlo (MC) simulation system. Using empirical and application based tests, this study evaluates all of the four RNGs used in previous FPGA based MC studies and newly proposed FPGA implementations for two well-known high-quality RNGs that are suitable for LPMC studies on FPGA. One of the newly proposed FPGA implementations: a parallel version of additive lagged Fibonacci generator (Parallel ALFG) is found to be the best among the evaluated RNGs in fulfilling the needs of LPMC simulations on FPGA.
Development of parallel benchmark code by sheet metal forming simulator 'ITAS'
International Nuclear Information System (INIS)
Watanabe, Hiroshi; Suzuki, Shintaro; Minami, Kazuo
1999-03-01
This report describes the development of parallel benchmark code by sheet metal forming simulator 'ITAS'. ITAS is a nonlinear elasto-plastic analysis program by the finite element method for the purpose of the simulation of sheet metal forming. ITAS adopts the dynamic analysis method that computes displacement of sheet metal at every time unit and utilizes the implicit method with the direct linear equation solver. Therefore the simulator is very robust. However, it requires a lot of computational time and memory capacity. In the development of the parallel benchmark code, we designed the code by MPI programming to reduce the computational time. In numerical experiments on the five kinds of parallel super computers at CCSE JAERI, i.e., SP2, SR2201, SX-4, T94 and VPP300, good performances are observed. The result will be shown to the public through WWW so that the benchmark results may become a guideline of research and development of the parallel program. (author)
Modular high-temperature gas-cooled reactor simulation using parallel processors
International Nuclear Information System (INIS)
Ball, S.J.; Conklin, J.C.
1989-01-01
The MHPP (Modular HTGR Parallel Processor) code has been developed to simulate modular high-temperature gas-cooled reactor (MHTGR) transients and accidents. MHPP incorporates a very detailed model for predicting the dynamics of the reactor core, vessel, and cooling systems over a wide variety of scenarios ranging from expected transients to very-low-probability severe accidents. The simulations routines, which had originally been developed entirely as serial code, were readily adapted to parallel processing Fortran. The resulting parallelized simulation speed was enhanced significantly. Workstation interfaces are being developed to provide for user (operator) interaction. In this paper the benefits realized by adapting previous MHTGR codes to run on a parallel processor are discussed, along with results of typical accident analyses
Predictive modeling of coupled multi-physics systems: I. Theory
International Nuclear Information System (INIS)
Cacuci, Dan Gabriel
2014-01-01
Highlights: • We developed “predictive modeling of coupled multi-physics systems (PMCMPS)”. • PMCMPS reduces predicted uncertainties in predicted model responses and parameters. • PMCMPS treats efficiently very large coupled systems. - Abstract: This work presents an innovative mathematical methodology for “predictive modeling of coupled multi-physics systems (PMCMPS).” This methodology takes into account fully the coupling terms between the systems but requires only the computational resources that would be needed to perform predictive modeling on each system separately. The PMCMPS methodology uses the maximum entropy principle to construct an optimal approximation of the unknown a priori distribution based on a priori known mean values and uncertainties characterizing the parameters and responses for both multi-physics models. This “maximum entropy”-approximate a priori distribution is combined, using Bayes’ theorem, with the “likelihood” provided by the multi-physics simulation models. Subsequently, the posterior distribution thus obtained is evaluated using the saddle-point method to obtain analytical expressions for the optimally predicted values for the multi-physics models parameters and responses along with corresponding reduced uncertainties. Noteworthy, the predictive modeling methodology for the coupled systems is constructed such that the systems can be considered sequentially rather than simultaneously, while preserving exactly the same results as if the systems were treated simultaneously. Consequently, very large coupled systems, which could perhaps exceed available computational resources if treated simultaneously, can be treated with the PMCMPS methodology presented in this work sequentially and without any loss of generality or information, requiring just the resources that would be needed if the systems were treated sequentially
Directory of Open Access Journals (Sweden)
Zhiteng Wang
2014-01-01
Full Text Available Service oriented modeling and simulation are hot issues in the field of modeling and simulation, and there is need to call service resources when simulation task workflow is running. How to optimize the service resource allocation to ensure that the task is complete effectively is an important issue in this area. In military modeling and simulation field, it is important to improve the probability of success and timeliness in simulation task workflow. Therefore, this paper proposes an optimization algorithm for multipath service resource parallel allocation, in which multipath service resource parallel allocation model is built and multiple chains coding scheme quantum optimization algorithm is used for optimization and solution. The multiple chains coding scheme quantum optimization algorithm is to extend parallel search space to improve search efficiency. Through the simulation experiment, this paper investigates the effect for the probability of success in simulation task workflow from different optimization algorithm, service allocation strategy, and path number, and the simulation result shows that the optimization algorithm for multipath service resource parallel allocation is an effective method to improve the probability of success and timeliness in simulation task workflow.
Long-range interactions and parallel scalability in molecular simulations
Patra, M.; Hyvönen, M.T.; Falck, E.; Sabouri-Ghomi, M.; Vattulainen, I.; Karttunen, M.E.J.
2007-01-01
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform
Nardi, Albert; Idiart, Andrés; Trinchero, Paolo; de Vries, Luis Manuel; Molinero, Jorge
2014-08-01
This paper presents the development, verification and application of an efficient interface, denoted as iCP, which couples two standalone simulation programs: the general purpose Finite Element framework COMSOL Multiphysics® and the geochemical simulator PHREEQC. The main goal of the interface is to maximize the synergies between the aforementioned codes, providing a numerical platform that can efficiently simulate a wide number of multiphysics problems coupled with geochemistry. iCP is written in Java and uses the IPhreeqc C++ dynamic library and the COMSOL Java-API. Given the large computational requirements of the aforementioned coupled models, special emphasis has been placed on numerical robustness and efficiency. To this end, the geochemical reactions are solved in parallel by balancing the computational load over multiple threads. First, a benchmark exercise is used to test the reliability of iCP regarding flow and reactive transport. Then, a large scale thermo-hydro-chemical (THC) problem is solved to show the code capabilities. The results of the verification exercise are successfully compared with those obtained using PHREEQC and the application case demonstrates the scalability of a large scale model, at least up to 32 threads.
Böddeker, B.; Teichler, H.
The MD simulation program TABB is motivated by the need of long time simulations for the investigation of slow processes near the glass transition of glass forming alloys. TABB is written in C++ with a high degree of flexibility: TABB allows the use of any short ranged pair potentials or EAM potentials, by generating and using a spline representation of all functions and their derivatives. TABB supports several numerical integration algorithms like the Runge-Kotta or the modified Gear-predictor-corrector algorithm of order five. The boundary conditions can be chosen to resemble the geometry of bulk materials or films. The simulation box length or the pressure can be fixed for each dimension separately. TABB may be used in isokinetic, isoenergeric or canonic (with random forces) mode. TABB contains a simple instruction interpreter to easily control the parameters and options during the simulation. The same source code can be compiled either for workstations or for parallel computers. The main optimization goal of TABB is to allow long time simulations of medium or small sized systems. To make this possible, much attention is spent on the optimized communication between the nodes. TABB uses a domain decomposition procedure. To use many nodes with a small system, the domain size has to be small compared to the range of particle interactions. In the limit of many nodes for only few atoms, the bottle neck of communication is the latency time. TABB minimizes the number of pairs of domains containing atoms that interact between these domains. This procedure minimizes the need of communication calls between pairs of nodes. TABB decides automatically, to how many, and to which directions the decomposition shall be applied. E.g., in the case of one dimensional domain decomposition, the simulation box is only split into "slabs" along a selected direction. The three dimensional domain decomposition is best with respect to the number of interacting domains only for simulations
Parallel Reservoir Simulations with Sparse Grid Techniques and Applications to Wormhole Propagation
Wu, Yuanqing
2015-09-08
In this work, two topics of reservoir simulations are discussed. The first topic is the two-phase compositional flow simulation in hydrocarbon reservoir. The major obstacle that impedes the applicability of the simulation code is the long run time of the simulation procedure, and thus speeding up the simulation code is necessary. Two means are demonstrated to address the problem: parallelism in physical space and the application of sparse grids in parameter space. The parallel code can gain satisfactory scalability, and the sparse grids can remove the bottleneck of flash calculations. Instead of carrying out the flash calculation in each time step of the simulation, a sparse grid approximation of all possible results of the flash calculation is generated before the simulation. Then the constructed surrogate model is evaluated to approximate the flash calculation results during the simulation. The second topic is the wormhole propagation simulation in carbonate reservoir. In this work, different from the traditional simulation technique relying on the Darcy framework, we propose a new framework called Darcy-Brinkman-Forchheimer framework to simulate wormhole propagation. Furthermore, to process the large quantity of cells in the simulation grid and shorten the long simulation time of the traditional serial code, standard domain-based parallelism is employed, using the Hypre multigrid library. In addition to that, a new technique called “experimenting field approach” to set coefficients in the model equations is introduced. In the 2D dissolution experiments, different configurations of wormholes and a series of properties simulated by both frameworks are compared. We conclude that the numerical results of the DBF framework are more like wormholes and more stable than the Darcy framework, which is a demonstration of the advantages of the DBF framework. The scalability of the parallel code is also evaluated, and good scalability can be achieved. Finally, a mixed
International Nuclear Information System (INIS)
Anderson, D.V.; Shumaker, D.E.
1993-01-01
From a computational standpoint, particle simulation calculations for plasmas have not adapted well to the transitions from scalar to vector processing nor from serial to parallel environments. They have suffered from inordinate and excessive accessing of computer memory and have been hobbled by relatively inefficient gather-scatter constructs resulting from the use of indirect indexing. Lastly, the many-to-one mapping characteristic of the deposition phase has made it difficult to perform this in parallel. The authors' code sorts and reorders the particles in a spatial order. This allows them to greatly reduce the memory references, to run in directly indexed vector mode, and to employ domain decomposition to achieve parallelization. In this hybrid simulation the electrons are modeled as a fluid and the field equations solved are obtained from the electron momentum equation together with the pre-Maxwell equations (displacement current neglected). Either zero or finite electron mass can be used in the electron model. The resulting field equations are solved with an iteratively explicit procedure which is thus trivial to parallelize. Likewise, the field interpolations and the particle pushing is simple to parallelize. The deposition, sorting, and reordering phases are less simple and it is for these that the authors present detailed algorithms. They have now successfully tested the parallel version of HOPS in serial mode and it is now being readied for parallel execution on the Cray C-90. They will then port HOPS to a massively parallel computer, in the next year
Efficient parallel simulation of CO2 geologic sequestration in saline aquifers
International Nuclear Information System (INIS)
Zhang, Keni; Doughty, Christine; Wu, Yu-Shu; Pruess, Karsten
2007-01-01
An efficient parallel simulator for large-scale, long-term CO2 geologic sequestration in saline aquifers has been developed. The parallel simulator is a three-dimensional, fully implicit model that solves large, sparse linear systems arising from discretization of the partial differential equations for mass and energy balance in porous and fractured media. The simulator is based on the ECO2N module of the TOUGH2code and inherits all the process capabilities of the single-CPU TOUGH2code, including a comprehensive description of the thermodynamics and thermophysical properties of H2O-NaCl- CO2 mixtures, modeling single and/or two-phase isothermal or non-isothermal flow processes, two-phase mixtures, fluid phases appearing or disappearing, as well as salt precipitation or dissolution. The new parallel simulator uses MPI for parallel implementation, the METIS software package for simulation domain partitioning, and the iterative parallel linear solver package Aztec for solving linear equations by multiple processors. In addition, the parallel simulator has been implemented with an efficient communication scheme. Test examples show that a linear or super-linear speedup can be obtained on Linux clusters as well as on supercomputers. Because of the significant improvement in both simulation time and memory requirement, the new simulator provides a powerful tool for tackling larger scale and more complex problems than can be solved by single-CPU codes. A high-resolution simulation example is presented that models buoyant convection, induced by a small increase in brine density caused by dissolution of CO2
Monte Carlo simulations of quantum systems on massively parallel supercomputers
International Nuclear Information System (INIS)
Ding, H.Q.
1993-01-01
A large class of quantum physics applications uses operator representations that are discrete integers by nature. This class includes magnetic properties of solids, interacting bosons modeling superfluids and Cooper pairs in superconductors, and Hubbard models for strongly correlated electrons systems. This kind of application typically uses integer data representations and the resulting algorithms are dominated entirely by integer operations. The authors implemented an efficient algorithm for one such application on the Intel Touchstone Delta and iPSC/860. The algorithm uses a multispin coding technique which allows significant data compactification and efficient vectorization of Monte Carlo updates. The algorithm regularly switches between two data decompositions, corresponding naturally to different Monte Carlo updating processes and observable measurements such that only nearest-neighbor communications are needed within a given decomposition. On 128 nodes of Intel Delta, this algorithm updates 183 million spins per second (compared to 21 million on CM-2 and 6.2 million on a Cray Y-MP). A systematic performance analysis shows a better than 90% efficiency in the parallel implementation
Cluster Optimization and Parallelization of Simulations with Dynamically Adaptive Grids
Schreiber, Martin; Weinzierl, Tobias; Bungartz, Hans-Joachim
2013-01-01
The present paper studies solvers for partial differential equations that work on dynamically adaptive grids stemming from spacetrees. Due to the underlying tree formalism, such grids efficiently can be decomposed into connected grid regions (clusters) on-the-fly. A graph on those clusters classified according to their grid invariancy, workload, multi-core affinity, and further meta data represents the inter-cluster communication. While stationary clusters already can be handled more efficiently than their dynamic counterparts, we propose to treat them as atomic grid entities and introduce a skip mechanism that allows the grid traversal to omit those regions completely. The communication graph ensures that the cluster data nevertheless are kept consistent, and several shared memory parallelization strategies are feasible. A hyperbolic benchmark that has to remesh selected mesh regions iteratively to preserve conforming tessellations acts as benchmark for the present work. We discuss runtime improvements resulting from the skip mechanism and the implications on shared memory performance and load balancing. © 2013 Springer-Verlag.
Parallel Performance Optimizations on Unstructured Mesh-based Simulations
Energy Technology Data Exchange (ETDEWEB)
Sarje, Abhinav; Song, Sukhyun; Jacobsen, Douglas; Huck, Kevin; Hollingsworth, Jeffrey; Malony, Allen; Williams, Samuel; Oliker, Leonid
2015-01-01
© The Authors. Published by Elsevier B.V. This paper addresses two key parallelization challenges the unstructured mesh-based ocean modeling code, MPAS-Ocean, which uses a mesh based on Voronoi tessellations: (1) load imbalance across processes, and (2) unstructured data access patterns, that inhibit intra- and inter-node performance. Our work analyzes the load imbalance due to naive partitioning of the mesh, and develops methods to generate mesh partitioning with better load balance and reduced communication. Furthermore, we present methods that minimize both inter- and intranode data movement and maximize data reuse. Our techniques include predictive ordering of data elements for higher cache efficiency, as well as communication reduction approaches. We present detailed performance data when running on thousands of cores using the Cray XC30 supercomputer and show that our optimization strategies can exceed the original performance by over 2×. Additionally, many of these solutions can be broadly applied to a wide variety of unstructured grid-based computations.
Parallel Earthquake Simulations on Large-Scale Multicore Supercomputers
Wu, Xingfu
2011-01-01
Earthquakes are one of the most destructive natural hazards on our planet Earth. Hugh earthquakes striking offshore may cause devastating tsunamis, as evidenced by the 11 March 2011 Japan (moment magnitude Mw9.0) and the 26 December 2004 Sumatra (Mw9.1) earthquakes. Earthquake prediction (in terms of the precise time, place, and magnitude of a coming earthquake) is arguably unfeasible in the foreseeable future. To mitigate seismic hazards from future earthquakes in earthquake-prone areas, such as California and Japan, scientists have been using numerical simulations to study earthquake rupture propagation along faults and seismic wave propagation in the surrounding media on ever-advancing modern computers over past several decades. In particular, ground motion simulations for past and future (possible) significant earthquakes have been performed to understand factors that affect ground shaking in populated areas, and to provide ground shaking characteristics and synthetic seismograms for emergency preparation and design of earthquake-resistant structures. These simulation results can guide the development of more rational seismic provisions for leading to safer, more efficient, and economical50pt]Please provide V. Taylor author e-mail ID. structures in earthquake-prone regions.
DEFF Research Database (Denmark)
Ferraris, Chiara F; Geiker, Mette Rica; Martys, Nicos S
2007-01-01
inapplicable here. This paper presents the analysis of a modified parallel plate rheometer for measuring cement mortar and propose a methodology for calibration using standard oils and numerical simulation of the flow. A lattice Boltzmann method was used to simulate the flow in the modified rheometer, thus...
Parallel-plate rheometer calibration using oil and lattice Boltzmann simulation
DEFF Research Database (Denmark)
Ferraris, Chiara F; Geiker, Mette Rica; Martys, Nicos S.
2007-01-01
compute the viscosity. This paper presents a modified parallel plate rheometer, and proposes means of calibration using standard oils and numerical simulation of the flow. A lattice Boltzmann method was used to simulate the flow in the modified rheometer, thus using an accurate numerical solution in place...
Acceleration of Radiance for Lighting Simulation by Using Parallel Computing with OpenCL
Energy Technology Data Exchange (ETDEWEB)
Zuo, Wangda; McNeil, Andrew; Wetter, Michael; Lee, Eleanor
2011-09-06
We report on the acceleration of annual daylighting simulations for fenestration systems in the Radiance ray-tracing program. The algorithm was optimized to reduce both the redundant data input/output operations and the floating-point operations. To further accelerate the simulation speed, the calculation for matrix multiplications was implemented using parallel computing on a graphics processing unit. We used OpenCL, which is a cross-platform parallel programming language. Numerical experiments show that the combination of the above measures can speed up the annual daylighting simulations 101.7 times or 28.6 times when the sky vector has 146 or 2306 elements, respectively.
Characterization of parallel-hole collimator using Monte Carlo Simulation
International Nuclear Information System (INIS)
Pandey, Anil Kumar; Sharma, Sanjay Kumar; Karunanithi, Sellam; Kumar, Praveen; Bal, Chandrasekhar; Kumar, Rakesh
2015-01-01
Accuracy of in vivo activity quantification improves after the correction of penetrated and scattered photons. However, accurate assessment is not possible with physical experiment. We have used Monte Carlo Simulation to accurately assess the contribution of penetrated and scattered photons in the photopeak window. Simulations were performed with Simulation of Imaging Nuclear Detectors Monte Carlo Code. The simulations were set up in such a way that it provides geometric, penetration, and scatter components after each simulation and writes binary images to a data file. These components were analyzed graphically using Microsoft Excel (Microsoft Corporation, USA). Each binary image was imported in software (ImageJ) and logarithmic transformation was applied for visual assessment of image quality, plotting profile across the center of the images and calculating full width at half maximum (FWHM) in horizontal and vertical directions. The geometric, penetration, and scatter at 140 keV for low-energy general-purpose were 93.20%, 4.13%, 2.67% respectively. Similarly, geometric, penetration, and scatter at 140 keV for low-energy high-resolution (LEHR), medium-energy general-purpose (MEGP), and high-energy general-purpose (HEGP) collimator were (94.06%, 3.39%, 2.55%), (96.42%, 1.52%, 2.06%), and (96.70%, 1.45%, 1.85%), respectively. For MEGP collimator at 245 keV photon and for HEGP collimator at 364 keV were 89.10%, 7.08%, 3.82% and 67.78%, 18.63%, 13.59%, respectively. Low-energy general-purpose and LEHR collimator is best to image 140 keV photon. HEGP can be used for 245 keV and 364 keV; however, correction for penetration and scatter must be applied if one is interested to quantify the in vivo activity of energy 364 keV. Due to heavy penetration and scattering, 511 keV photons should not be imaged with HEGP collimator
Gyrokinetic simulation of finite-β plasmas on parallel architectures
International Nuclear Information System (INIS)
Reynders, J.V.W.
1993-01-01
Much research exists on the linear and non-linear properties of plasma microinstabilities induced by density and temperature gradients. There has been an interest in the electromagnetic or finite-β effects on these microinstabilities. This thesis focuses on the finite-β modification of an ion temperature gradient (ITG) driven microinstability in a two-dimensional shearless and sheared-slab geometries. A gyrokinetic model is employed in the numerical and analytic studies of this instability. Chapter 1 introduces the electromagnetic gyrokinetic model employed in the numerical and analytic studies of the ITG instability. Some discussion of the Klimontovich particle representation of the gyrokinetic Vlasov equation and a multiple scale model of the background plasma gradient is presented. Chapter 2 details the computational issues facing an electromagnetic gyrokinetic particle simulation of the ITG mode. An electromagnetic extension of the partially linearized algorithm is presented with a comparison of quiet particle initialization routines. Chapter 3 presents and compares algorithms for the gyrokinetic particle simulation technique on SIMD and MIMD computing platforms. Chapter 4 discusses electromagnetic gyrokinetic fluctuation theory and provides a comparison of analytic and numerical results. Chapter 5 contains a linear and a non-linear three-wave coupling analysis of the finite-β modified ITG mode in a shearless slab geometry. Comparisons are made with linear and partially linearized gyrokinetic simulation results. Chapter 6 presents results from a finite-β modified ITG mode in a sheared slab geometry. The linear dispersion relation is derived and results from an integral eigenvalue code are presented. Comparisons are made with the gyrokinetic particle code in a variety of limits with both adiabatic and non-adiabatic electrons. Evidence of ITG driven microtearing is presented
International Nuclear Information System (INIS)
Apisit, Patchimpattapong; Alireza, Haghighat; Shedlock, D.
2003-01-01
An expert system for generating an effective mesh distribution for the SN particle transport simulation has been developed. This expert system consists of two main parts: 1) an algorithm for generating an effective mesh distribution in a serial environment, and 2) an algorithm for inference of an effective domain decomposition strategy for parallel computing. For the first part, the algorithm prepares an effective mesh distribution considering problem physics and the spatial differencing scheme. For the second part, the algorithm determines a parallel-performance-index (PPI), which is defined as the ratio of the granularity to the degree-of-coupling. The parallel-performance-index provides expected performance of an algorithm depending on computing environment and resources. A large index indicates a high granularity algorithm with relatively low coupling among processors. This expert system has been successfully tested within the PENTRAN (Parallel Environment Neutral-Particle Transport) code system for simulating real-life shielding problems. (authors)
Energy Technology Data Exchange (ETDEWEB)
Apisit, Patchimpattapong [Electricity Generating Authority of Thailand, Office of Corporate Planning, Bangkruai, Nonthaburi (Thailand); Alireza, Haghighat; Shedlock, D. [Florida Univ., Department of Nuclear and Radiological Engineering, Gainesville, FL (United States)
2003-07-01
An expert system for generating an effective mesh distribution for the SN particle transport simulation has been developed. This expert system consists of two main parts: 1) an algorithm for generating an effective mesh distribution in a serial environment, and 2) an algorithm for inference of an effective domain decomposition strategy for parallel computing. For the first part, the algorithm prepares an effective mesh distribution considering problem physics and the spatial differencing scheme. For the second part, the algorithm determines a parallel-performance-index (PPI), which is defined as the ratio of the granularity to the degree-of-coupling. The parallel-performance-index provides expected performance of an algorithm depending on computing environment and resources. A large index indicates a high granularity algorithm with relatively low coupling among processors. This expert system has been successfully tested within the PENTRAN (Parallel Environment Neutral-Particle Transport) code system for simulating real-life shielding problems. (authors)
SPEEDES - A multiple-synchronization environment for parallel discrete-event simulation
Steinman, Jeff S.
1992-01-01
Synchronous Parallel Environment for Emulation and Discrete-Event Simulation (SPEEDES) is a unified parallel simulation environment. It supports multiple-synchronization protocols without requiring users to recompile their code. When a SPEEDES simulation runs on one node, all the extra parallel overhead is removed automatically at run time. When the same executable runs in parallel, the user preselects the synchronization algorithm from a list of options. SPEEDES currently runs on UNIX networks and on the California Institute of Technology/Jet Propulsion Laboratory Mark III Hypercube. SPEEDES also supports interactive simulations. Featured in the SPEEDES environment is a new parallel synchronization approach called Breathing Time Buckets. This algorithm uses some of the conservative techniques found in Time Bucket synchronization, along with the optimism that characterizes the Time Warp approach. A mathematical model derived from first principles predicts the performance of Breathing Time Buckets. Along with the Breathing Time Buckets algorithm, this paper discusses the rules for processing events in SPEEDES, describes the implementation of various other synchronization protocols supported by SPEEDES, describes some new ones for the future, discusses interactive simulations, and then gives some performance results.
Xyce Parallel Electronic Simulator - User's Guide, Version 1.0
Energy Technology Data Exchange (ETDEWEB)
HUTCHINSON, SCOTT A; KEITER, ERIC R.; HOEKSTRA, ROBERT J.; WATERS, LON J.; RUSSO, THOMAS V.; RANKIN, ERIC LAMONT; WIX, STEVEN D.
2002-11-01
This manual describes the use of the Xyce Parallel Electronic Simulator code for simulating electrical circuits at a variety of abstraction levels. The Xyce Parallel Electronic Simulator has been written to support,in a rigorous manner, the simulation needs of the Sandia National Laboratories electrical designers. As such, the development has focused on improving the capability over the current state-of-the-art in the following areas: (1) Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. (2) Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. (3) A client-server or multi-tiered operating model wherein the numerical kernel can operate independently of the graphical user interface (GUI). (4) Object-oriented code design and implementation using modern coding-practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. The code is a parallel code in the most general sense of the phrase--a message passing parallel implementation--which allows it to run efficiently on the widest possible number of computing platforms. These include serial, shared-memory and distributed-memory parallel as well as heterogeneous platforms. Furthermore, careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved even as the number of processors grows. Another feature required by designers is the ability to add device models, many specific to the needs of Sandia, to the code. To this end, the device package in the Xyce Parallel Electronic Simulator is designed to support a variety of device model inputs. These input formats include standard analytical models, behavioral models
An Evaluation of Parallel Synchronous and Conservative Asynchronous Logic-Level Simulations
Directory of Open Access Journals (Sweden)
Ausif Mahmood
1996-01-01
a circuit remain fixed during the entire simulation. We remove this limitation and, by extending the analyses to multi-input, multi-output circuits with an arbitrary number of input events, show that the conservative asynchronous simulation extracts more parallelism and executes faster than synchronous simulation in general. Our conclusions are supported by a comparison of the idealized execution times of synchronous and conservative asynchronous algorithms on ISCAS combinational and sequential benchmark circuits.
Parallel treatment of simulation particles in particle-in-cell codes on SUPRENUM
International Nuclear Information System (INIS)
Seldner, D.
1990-02-01
This report contains the program documentation and description of the program package 2D-PLAS, which has been developed at the Nuclear Research Center Karlsruhe in the Institute for Data Processing in Technology (IDT) under the auspices of the BMFT. 2D-PLAS is a parallel program version of the treatment of the simulation particles of the two-dimensional stationary particle-in-cell code BFCPIC which has been developed at the Nuclear Research Center Karlsruhe. This parallel version has been designed for the parallel computer SUPRENUM. (orig.) [de
A parallel algorithm for transient solid dynamics simulations with contact detection
International Nuclear Information System (INIS)
Attaway, S.; Hendrickson, B.; Plimpton, S.; Gardner, D.; Vaughan, C.; Heinstein, M.; Peery, J.
1996-01-01
Solid dynamics simulations with Lagrangian finite elements are used to model a wide variety of problems, such as the calculation of impact damage to shipping containers for nuclear waste and the analysis of vehicular crashes. Using parallel computers for these simulations has been hindered by the difficulty of searching efficiently for material surface contacts in parallel. A new parallel algorithm for calculation of arbitrary material contacts in finite element simulations has been developed and implemented in the PRONTO3D transient solid dynamics code. This paper will explore some of the issues involved in developing efficient, portable, parallel finite element models for nonlinear transient solid dynamics simulations. The contact-detection problem poses interesting challenges for efficient implementation of a solid dynamics simulation on a parallel computer. The finite element mesh is typically partitioned so that each processor owns a localized region of the finite element mesh. This mesh partitioning is optimal for the finite element portion of the calculation since each processor must communicate only with the few connected neighboring processors that share boundaries with the decomposed mesh. However, contacts can occur between surfaces that may be owned by any two arbitrary processors. Hence, a global search across all processors is required at every time step to search for these contacts. Load-imbalance can become a problem since the finite element decomposition divides the volumetric mesh evenly across processors but typically leaves the surface elements unevenly distributed. In practice, these complications have been limiting factors in the performance and scalability of transient solid dynamics on massively parallel computers. In this paper the authors present a new parallel algorithm for contact detection that overcomes many of these limitations
Robust large-scale parallel nonlinear solvers for simulations.
Energy Technology Data Exchange (ETDEWEB)
Bader, Brett William; Pawlowski, Roger Patrick; Kolda, Tamara Gibson (Sandia National Laboratories, Livermore, CA)
2005-11-01
This report documents research to develop robust and efficient solution techniques for solving large-scale systems of nonlinear equations. The most widely used method for solving systems of nonlinear equations is Newton's method. While much research has been devoted to augmenting Newton-based solvers (usually with globalization techniques), little has been devoted to exploring the application of different models. Our research has been directed at evaluating techniques using different models than Newton's method: a lower order model, Broyden's method, and a higher order model, the tensor method. We have developed large-scale versions of each of these models and have demonstrated their use in important applications at Sandia. Broyden's method replaces the Jacobian with an approximation, allowing codes that cannot evaluate a Jacobian or have an inaccurate Jacobian to converge to a solution. Limited-memory methods, which have been successful in optimization, allow us to extend this approach to large-scale problems. We compare the robustness and efficiency of Newton's method, modified Newton's method, Jacobian-free Newton-Krylov method, and our limited-memory Broyden method. Comparisons are carried out for large-scale applications of fluid flow simulations and electronic circuit simulations. Results show that, in cases where the Jacobian was inaccurate or could not be computed, Broyden's method converged in some cases where Newton's method failed to converge. We identify conditions where Broyden's method can be more efficient than Newton's method. We also present modifications to a large-scale tensor method, originally proposed by Bouaricha, for greater efficiency, better robustness, and wider applicability. Tensor methods are an alternative to Newton-based methods and are based on computing a step based on a local quadratic model rather than a linear model. The advantage of Bouaricha's method is that it can use any
Simulation of reflooding on two parallel heated channel by TRACE
Energy Technology Data Exchange (ETDEWEB)
Zakir, Md. Ghulam [Department of Nuclear Engineering, Chalmers University of Technology, Gothenburg (Sweden)
2016-07-12
In case of Loss-Of-Coolant accident (LOCA) in a Boiling Water Reactor (BWR), heat generated in the nuclear fuel is not adequately removed because of the decrease of the coolant mass flow rate in the reactor core. This fact leads to an increase of the fuel temperature that can cause damage to the core and leakage of the radioactive fission products. In order to reflood the core and to discontinue the increase of temperature, an Emergency Core Cooling System (ECCS) delivers water under this kind of conditions. This study is an investigation of how the power distribution between two channels can affect the process of reflooding when the emergency water is injected from the top of the channels. The peak cladding temperature (PCT) on LOCA transient for different axial level is determined as well. A thermal-hydraulic system code TRACE has been used. A TRACE model of the two heated channels has been developed, and three hypothetical cases with different power distributions have been studied. Later, a comparison between a simulated and experimental data has been shown as well.
Multiphysics Integrated Coupling Environment (MICE) User Manual
Energy Technology Data Exchange (ETDEWEB)
Varija Agarwal; Donna Post Guillen
2013-08-01
The complex, multi-part nature of waste glass melters used in nuclear waste vitrification poses significant modeling challenges. The focus of this project has been to couple a 1D MATLAB model of the cold cap region within a melter with a 3D STAR-CCM+ model of the melter itself. The Multiphysics Integrated Coupling Environment (MICE) has been developed to create a cohesive simulation of a waste glass melter that accurately represents the cold cap. The one-dimensional mathematical model of the cold cap uses material properties, axial heat, and mass fluxes to obtain a temperature profile for the cold cap, the region where feed-to-glass conversion occurs. The results from Matlab are used to update simulation data in the three-dimensional STAR-CCM+ model so that the cold cap is appropriately incorporated into the 3D simulation. The two processes are linked through ModelCenter integration software using time steps that are specified for each process. Data is to be exchanged circularly between the two models, as the inputs and outputs of each model depend on the other.
Xyce Parallel Electronic Simulator : users' guide, version 2.0.
Energy Technology Data Exchange (ETDEWEB)
Hoekstra, Robert John; Waters, Lon J.; Rankin, Eric Lamont; Fixel, Deborah A.; Russo, Thomas V.; Keiter, Eric Richard; Hutchinson, Scott Alan; Pawlowski, Roger Patrick; Wix, Steven D.
2004-06-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator capable of simulating electrical circuits at a variety of abstraction levels. Primarily, Xyce has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability the current state-of-the-art in the following areas: {sm_bullet} Capability to solve extremely large circuit problems by supporting large-scale parallel computing platforms (up to thousands of processors). Note that this includes support for most popular parallel and serial computers. {sm_bullet} Improved performance for all numerical kernels (e.g., time integrator, nonlinear and linear solvers) through state-of-the-art algorithms and novel techniques. {sm_bullet} Device models which are specifically tailored to meet Sandia's needs, including many radiation-aware devices. {sm_bullet} A client-server or multi-tiered operating model wherein the numerical kernel can operate independently of the graphical user interface (GUI). {sm_bullet} Object-oriented code design and implementation using modern coding practices that ensure that the Xyce Parallel Electronic Simulator will be maintainable and extensible far into the future. Xyce is a parallel code in the most general sense of the phrase - a message passing of computing platforms. These include serial, shared-memory and distributed-memory parallel implementation - which allows it to run efficiently on the widest possible number parallel as well as heterogeneous platforms. Careful attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. One feature required by designers is the ability to add device models, many specific to the needs of Sandia, to the code. To this end, the device package in the Xyce
International Nuclear Information System (INIS)
Tome, Carlos N.; Caro, J.A.; Lebensohn, R.A.; Unal, Cetin; Arsenlis, A.; Marian, J.; Pasamehmetoglu, K.
2010-01-01
Advancing the performance of Light Water Reactors, Advanced Nuclear Fuel Cycles, and Advanced Reactors, such as the Next Generation Nuclear Power Plants, requires enhancing our fundamental understanding of fuel and materials behavior under irradiation. The capability to accurately model the nuclear fuel systems to develop predictive tools is critical. Not only are fabrication and performance models needed to understand specific aspects of the nuclear fuel, fully coupled fuel simulation codes are required to achieve licensing of specific nuclear fuel designs for operation. The backbone of these codes, models, and simulations is a fundamental understanding and predictive capability for simulating the phase and microstructural behavior of the nuclear fuel system materials and matrices. In this paper we review the current status of the advanced modeling and simulation of nuclear reactor cladding, with emphasis on what is available and what is to be developed in each scale of the project, how we propose to pass information from one scale to the next, and what experimental information is required for benchmarking and advancing the modeling at each scale level.
Massively parallel simulator of optical coherence tomography of inhomogeneous turbid media.
Malektaji, Siavash; Lima, Ivan T; Escobar I, Mauricio R; Sherif, Sherif S
2017-10-01
An accurate and practical simulator for Optical Coherence Tomography (OCT) could be an important tool to study the underlying physical phenomena in OCT such as multiple light scattering. Recently, many researchers have investigated simulation of OCT of turbid media, e.g., tissue, using Monte Carlo methods. The main drawback of these earlier simulators is the long computational time required to produce accurate results. We developed a massively parallel simulator of OCT of inhomogeneous turbid media that obtains both Class I diffusive reflectivity, due to ballistic and quasi-ballistic scattered photons, and Class II diffusive reflectivity due to multiply scattered photons. This Monte Carlo-based simulator is implemented on graphic processing units (GPUs), using the Compute Unified Device Architecture (CUDA) platform and programming model, to exploit the parallel nature of propagation of photons in tissue. It models an arbitrary shaped sample medium as a tetrahedron-based mesh and uses an advanced importance sampling scheme. This new simulator speeds up simulations of OCT of inhomogeneous turbid media by about two orders of magnitude. To demonstrate this result, we have compared the computation times of our new parallel simulator and its serial counterpart using two samples of inhomogeneous turbid media. We have shown that our parallel implementation reduced simulation time of OCT of the first sample medium from 407 min to 92 min by using a single GPU card, to 12 min by using 8 GPU cards and to 7 min by using 16 GPU cards. For the second sample medium, the OCT simulation time was reduced from 209 h to 35.6 h by using a single GPU card, and to 4.65 h by using 8 GPU cards, and to only 2 h by using 16 GPU cards. Therefore our new parallel simulator is considerably more practical to use than its central processing unit (CPU)-based counterpart. Our new parallel OCT simulator could be a practical tool to study the different physical phenomena underlying OCT
Parallel simulation of tsunami inundation on a large-scale supercomputer
Oishi, Y.; Imamura, F.; Sugawara, D.
2013-12-01
An accurate prediction of tsunami inundation is important for disaster mitigation purposes. One approach is to approximate the tsunami wave source through an instant inversion analysis using real-time observation data (e.g., Tsushima et al., 2009) and then use the resulting wave source data in an instant tsunami inundation simulation. However, a bottleneck of this approach is the large computational cost of the non-linear inundation simulation and the computational power of recent massively parallel supercomputers is helpful to enable faster than real-time execution of a tsunami inundation simulation. Parallel computers have become approximately 1000 times faster in 10 years (www.top500.org), and so it is expected that very fast parallel computers will be more and more prevalent in the near future. Therefore, it is important to investigate how to efficiently conduct a tsunami simulation on parallel computers. In this study, we are targeting very fast tsunami inundation simulations on the K computer, currently the fastest Japanese supercomputer, which has a theoretical peak performance of 11.2 PFLOPS. One computing node of the K computer consists of 1 CPU with 8 cores that share memory, and the nodes are connected through a high-performance torus-mesh network. The K computer is designed for distributed-memory parallel computation, so we have developed a parallel tsunami model. Our model is based on TUNAMI-N2 model of Tohoku University, which is based on a leap-frog finite difference method. A grid nesting scheme is employed to apply high-resolution grids only at the coastal regions. To balance the computation load of each CPU in the parallelization, CPUs are first allocated to each nested layer in proportion to the number of grid points of the nested layer. Using CPUs allocated to each layer, 1-D domain decomposition is performed on each layer. In the parallel computation, three types of communication are necessary: (1) communication to adjacent neighbours for the
Parallelization of a beam dynamics code and first large scale radio frequency quadrupole simulations
Directory of Open Access Journals (Sweden)
J. Xu
2007-01-01
Full Text Available The design and operation support of hadron (proton and heavy-ion linear accelerators require substantial use of beam dynamics simulation tools. The beam dynamics code TRACK has been originally developed at Argonne National Laboratory (ANL to fulfill the special requirements of the rare isotope accelerator (RIA accelerator systems. From the beginning, the code has been developed to make it useful in the three stages of a linear accelerator project, namely, the design, commissioning, and operation of the machine. To realize this concept, the code has unique features such as end-to-end simulations from the ion source to the final beam destination and automatic procedures for tuning of a multiple charge state heavy-ion beam. The TRACK code has become a general beam dynamics code for hadron linacs and has found wide applications worldwide. Until recently, the code has remained serial except for a simple parallelization used for the simulation of multiple seeds to study the machine errors. To speed up computation, the TRACK Poisson solver has been parallelized. This paper discusses different parallel models for solving the Poisson equation with the primary goal to extend the scalability of the code onto 1024 and more processors of the new generation of supercomputers known as BlueGene (BG/L. Domain decomposition techniques have been adapted and incorporated into the parallel version of the TRACK code. To demonstrate the new capabilities of the parallelized TRACK code, the dynamics of a 45 mA proton beam represented by 10^{8} particles has been simulated through the 325 MHz radio frequency quadrupole and initial accelerator section of the proposed FNAL proton driver. The results show the benefits and advantages of large-scale parallel computing in beam dynamics simulations.
A parallel simulated annealing algorithm for standard cell placement on a hypercube computer
Jones, Mark Howard
1987-01-01
A parallel version of a simulated annealing algorithm is presented which is targeted to run on a hypercube computer. A strategy for mapping the cells in a two dimensional area of a chip onto processors in an n-dimensional hypercube is proposed such that both small and large distance moves can be applied. Two types of moves are allowed: cell exchanges and cell displacements. The computation of the cost function in parallel among all the processors in the hypercube is described along with a distributed data structure that needs to be stored in the hypercube to support parallel cost evaluation. A novel tree broadcasting strategy is used extensively in the algorithm for updating cell locations in the parallel environment. Studies on the performance of the algorithm on example industrial circuits show that it is faster and gives better final placement results than the uniprocessor simulated annealing algorithms. An improved uniprocessor algorithm is proposed which is based on the improved results obtained from parallelization of the simulated annealing algorithm.
Parallel electric fields in a simulation of magnetotail reconnection and plasmoid evolution
International Nuclear Information System (INIS)
Hesse, M.; Birn, J.
1990-01-01
Properties of the electric field component parallel to the magnetic field are investigate in a 3D MHD simulation of plasmoid formation and evolution in the magnetotail, in the presence of a net dawn-dusk magnetic field component. The spatial localization of E-parallel, and the concept of a diffusion zone and the role of E-parallel in accelerating electrons are discussed. A localization of the region of enhanced E-parallel in all space directions is found, with a strong concentration in the z direction. This region is identified as the diffusion zone, which plays a crucial role in reconnection theory through the local break-down of magnetic flux conservation. 12 refs
International Nuclear Information System (INIS)
Al-Hallaq, A.; Amin, S.
1998-01-01
This paper introduces a new parallel algorithm and its simulation on a hypercube simulator for the low pass digital image filtering using a systolic array. This new algorithm is faster than the old one (Amin, 1988). This is due to the the fact that the old algorithm carries out the addition operations in a sequential mode. But in our new design these addition operations are divided into tow groups, which can be performed in parallel. One group will be performed on one half of the systolic array and the other on the second half, that is, by folding. This parallelism reduces the time required for the whole process by almost quarter the time of the old algorithm.(authors). 18 refs., 3 figs
STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB
Klingbeil, G.
2011-02-25
Motivation: The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. Results: The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user\\'s models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. © The Author 2011. Published by Oxford University Press. All rights reserved.
Xyce parallel electronic simulator reference guide, Version 6.0.1.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R; Mei, Ting; Russo, Thomas V.; Schiek, Richard Louis; Thornquist, Heidi K.; Verley, Jason C.; Fixel, Deborah A.; Coffey, Todd S; Pawlowski, Roger P; Warrender, Christina E.; Baur, David Gregory.
2014-01-01
This document is a reference guide to the Xyce Parallel Electronic Simulator, and is a companion document to the Xyce Users Guide [1] . The focus of this document is (to the extent possible) exhaustively list device parameters, solver options, parser options, and other usage details of Xyce. This document is not intended to be a tutorial. Users who are new to circuit simulation are better served by the Xyce Users Guide [1] .
Parallel shooting methods for finding steady state solutions to engine simulation models
DEFF Research Database (Denmark)
Andersen, Stig Kildegård; Thomsen, Per Grove; Carlsen, Henrik
2007-01-01
Parallel single- and multiple shooting methods were tested for finding periodic steady state solutions to a Stirling engine model. The model was used to illustrate features of the methods and possibilities for optimisations. Performance was measured using simulation of an experimental data set...
MaMiCo: Software design for parallel molecular-continuum flow simulations
Neumann, Philipp; Flohr, Hanno; Arora, Rahul; Jarmatz, Piet; Tchipev, Nikola; Bungartz, Hans-Joachim
2015-01-01
The macro-micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum simulations, retaining sequential and parallel performance. We demonstrate the functionality and performance of MaMiCo by coupling
Simulating streamer discharges in 3D with the parallel adaptive Afivo framework
H.J. Teunissen (Jannis); U. M. Ebert (Ute)
2017-01-01
htmlabstractWe present an open-source plasma fluid code for 2D, cylindrical and 3D simulations of streamer discharges, based on the Afivo framework that features adaptive mesh refinement, geometric multigrid methods for Poisson's equation, and OpenMP parallelism. We describe the numerical
A software framework for the portable parallelization of particle-mesh simulations
DEFF Research Database (Denmark)
Sbalzarini, I.F.; Walther, Jens Honore; Polasek, B.
2006-01-01
Abstract: We present a software framework for the transparent and portable parallelization of simulations using particle-mesh methods. Particles are used to transport physical properties and a mesh is required in order to reinitialize the distorted particle locations, ensuring the convergence...
Generation of Random Numbers and Parallel Random Number Streams for Monte Carlo Simulations
Directory of Open Access Journals (Sweden)
L. Yu. Barash
2012-01-01
Full Text Available Modern methods and libraries for high quality pseudorandom number generation and for generation of parallel random number streams for Monte Carlo simulations are considered. The probability equidistribution property and the parameters when the property holds at dimensions up to logarithm of mesh size are considered for Multiple Recursive Generators.
Towards an efficient multiphysics model for nuclear reactor dynamics
Directory of Open Access Journals (Sweden)
Obaidurrahman K.
2015-01-01
Full Text Available Availability of fast computer resources nowadays has facilitated more in-depth modeling of complex engineering systems which involve strong multiphysics interactions. This multiphysics modeling is an important necessity in nuclear reactor safety studies where efforts are being made worldwide to combine the knowledge from all associated disciplines at one place to accomplish the most realistic simulation of involved phenomenon. On these lines coupled modeling of nuclear reactor neutron kinetics, fuel heat transfer and coolant transport is a regular practice nowadays for transient analysis of reactor core. However optimization between modeling accuracy and computational economy has always been a challenging task to ensure the adequate degree of reliability in such extensive numerical exercises. Complex reactor core modeling involves estimation of evolving 3-D core thermal state, which in turn demands an expensive multichannel based detailed core thermal hydraulics model. A novel approach of power weighted coupling between core neutronics and thermal hydraulics presented in this work aims to reduce the bulk of core thermal calculations in core dynamics modeling to a significant extent without compromising accuracy of computation. Coupled core model has been validated against a series of international benchmarks. Accuracy and computational efficiency of the proposed multiphysics model has been demonstrated by analyzing a reactivity initiated transient.
Review of multi-physics temporal coupling methods for analysis of nuclear reactors
International Nuclear Information System (INIS)
Zerkak, Omar; Kozlowski, Tomasz; Gajev, Ivan
2015-01-01
Highlights: • Review of the numerical methods used for the multi-physics temporal coupling. • Review of high-order improvements to the Operator Splitting coupling method. • Analysis of truncation error due to the temporal coupling. • Recommendations on best-practice approaches for multi-physics temporal coupling. - Abstract: The advanced numerical simulation of a realistic physical system typically involves multi-physics problem. For example, analysis of a LWR core involves the intricate simulation of neutron production and transport, heat transfer throughout the structures of the system and the flowing, possibly two-phase, coolant. Such analysis involves the dynamic coupling of multiple simulation codes, each one devoted to the solving of one of the coupled physics. Multiple temporal coupling methods exist, yet the accuracy of such coupling is generally driven by the least accurate numerical scheme. The goal of this paper is to review in detail the approaches and numerical methods that can be used for the multi-physics temporal coupling, including a comprehensive discussion of the issues associated with the temporal coupling, and define approaches that can be used to perform multi-physics analysis. The paper is not limited to any particular multi-physics process or situation, but is intended to provide a generic description of multi-physics temporal coupling schemes for any development stage of the individual (single-physics) tools and methods. This includes a wide spectrum of situation, where the individual (single-physics) solvers are based on pre-existing computation codes embedded as individual components, or a new development where the temporal coupling can be developed and implemented as a part of code development. The discussed coupling methods are demonstrated in the framework of LWR core analysis
Parallel spatial direct numerical simulations on the Intel iPSC/860 hypercube
Joslin, Ronald D.; Zubair, Mohammad
1993-01-01
The implementation and performance of a parallel spatial direct numerical simulation (PSDNS) approach on the Intel iPSC/860 hypercube is documented. The direct numerical simulation approach is used to compute spatially evolving disturbances associated with the laminar-to-turbulent transition in boundary-layer flows. The feasibility of using the PSDNS on the hypercube to perform transition studies is examined. The results indicate that the direct numerical simulation approach can effectively be parallelized on a distributed-memory parallel machine. By increasing the number of processors nearly ideal linear speedups are achieved with nonoptimized routines; slower than linear speedups are achieved with optimized (machine dependent library) routines. This slower than linear speedup results because the Fast Fourier Transform (FFT) routine dominates the computational cost and because the routine indicates less than ideal speedups. However with the machine-dependent routines the total computational cost decreases by a factor of 4 to 5 compared with standard FORTRAN routines. The computational cost increases linearly with spanwise wall-normal and streamwise grid refinements. The hypercube with 32 processors was estimated to require approximately twice the amount of Cray supercomputer single processor time to complete a comparable simulation; however it is estimated that a subgrid-scale model which reduces the required number of grid points and becomes a large-eddy simulation (PSLES) would reduce the computational cost and memory requirements by a factor of 10 over the PSDNS. This PSLES implementation would enable transition simulations on the hypercube at a reasonable computational cost.
Massive Parallelism of Monte-Carlo Simulation on Low-End Hardware using Graphic Processing Units
Energy Technology Data Exchange (ETDEWEB)
Mburu, Joe Mwangi; Hah, Chang Joo Hah [KEPCO International Nuclear Graduate School, Ulsan (Korea, Republic of)
2014-05-15
Within the past decade, research has been done on utilizing GPU massive parallelization in core simulation with impressive results but unfortunately, not much commercial application has been done in the nuclear field especially in reactor core simulation. The purpose of this paper is to give an introductory concept on the topic and illustrate the potential of exploiting the massive parallel nature of GPU computing on a simple monte-carlo simulation with very minimal hardware specifications. To do a comparative analysis, a simple two dimension monte-carlo simulation is implemented for both the CPU and GPU in order to evaluate performance gain based on the computing devices. The heterogeneous platform utilized in this analysis is done on a slow notebook with only 1GHz processor. The end results are quite surprising whereby high speedups obtained are almost a factor of 10. In this work, we have utilized heterogeneous computing in a GPU-based approach in applying potential high arithmetic intensive calculation. By applying a complex monte-carlo simulation on GPU platform, we have speed up the computational process by almost a factor of 10 based on one million neutrons. This shows how easy, cheap and efficient it is in using GPU in accelerating scientific computing and the results should encourage in exploring further this avenue especially in nuclear reactor physics simulation where deterministic and stochastic calculations are quite favourable in parallelization.
Massive Parallelism of Monte-Carlo Simulation on Low-End Hardware using Graphic Processing Units
International Nuclear Information System (INIS)
Mburu, Joe Mwangi; Hah, Chang Joo Hah
2014-01-01
Within the past decade, research has been done on utilizing GPU massive parallelization in core simulation with impressive results but unfortunately, not much commercial application has been done in the nuclear field especially in reactor core simulation. The purpose of this paper is to give an introductory concept on the topic and illustrate the potential of exploiting the massive parallel nature of GPU computing on a simple monte-carlo simulation with very minimal hardware specifications. To do a comparative analysis, a simple two dimension monte-carlo simulation is implemented for both the CPU and GPU in order to evaluate performance gain based on the computing devices. The heterogeneous platform utilized in this analysis is done on a slow notebook with only 1GHz processor. The end results are quite surprising whereby high speedups obtained are almost a factor of 10. In this work, we have utilized heterogeneous computing in a GPU-based approach in applying potential high arithmetic intensive calculation. By applying a complex monte-carlo simulation on GPU platform, we have speed up the computational process by almost a factor of 10 based on one million neutrons. This shows how easy, cheap and efficient it is in using GPU in accelerating scientific computing and the results should encourage in exploring further this avenue especially in nuclear reactor physics simulation where deterministic and stochastic calculations are quite favourable in parallelization
AC losses in horizontally parallel HTS tapes for possible wireless power transfer applications
Shen, Boyang; Geng, Jianzhao; Zhang, Xiuchang; Fu, Lin; Li, Chao; Zhang, Heng; Dong, Qihuan; Ma, Jun; Gawith, James; Coombs, T. A.
2017-12-01
This paper presents the concept of using horizontally parallel HTS tapes with AC loss study, and the investigation on possible wireless power transfer (WPT) applications. An example of three parallel HTS tapes was proposed, whose AC loss study was carried out both from experiment using electrical method; and simulation using 2D H-formulation on the FEM platform of COMSOL Multiphysics. The electromagnetic induction around the three parallel tapes was monitored using COMSOL simulation. The electromagnetic induction and AC losses generated by a conventional three turn coil was simulated as well, and then compared to the case of three parallel tapes with the same AC transport current. The analysis demonstrates that HTS parallel tapes could be potentially used into wireless power transfer systems, which could have lower total AC losses than conventional HTS coils.
Sohbatzadeh, F.; Soltani, H.
2018-04-01
The results of time-dependent one-dimensional modelling of a dielectric barrier discharge (DBD) in a nitrogen-oxygen-water vapor mixture at atmospheric pressure are presented. The voltage-current characteristics curves and the production of active species are studied. The discharge is driven by a sinusoidal alternating high voltage-power supply at 30 kV with frequency of 27 kHz. The electrodes and the dielectric are assumed to be copper and quartz, respectively. The current discharge consists of an electrical breakdown that occurs in each half-period. A detailed description of the electron attachment and detachment processes, surface charge accumulation, charged species recombination, conversion of negative and positive ions, ion production and losses, excitations and dissociations of molecules are taken into account. Time-dependent one-dimensional electron density, electric field, electric potential, electron temperature, densities of reactive oxygen species (ROS) and reactive nitrogen species (RNS) such as: O, O-, O+, {O}2^{ - } , {O}2^{ + } , O3, {N}, {N}2^{ + } , N2s and {N}2^{ - } are simulated versus time across the gas gap. The results of this work could be used in plasma-based pollutant degradation devices.
Simulation of a parallel processor on a serial processor: The neutron diffusion equation
International Nuclear Information System (INIS)
Honeck, H.C.
1981-01-01
Parallel processors could provide the nuclear industry with very high computing power at a very moderate cost. Will we be able to make effective use of this power. This paper explores the use of a very simple parallel processor for solving the neutron diffusion equation to predict power distributions in a nuclear reactor. We first describe a simple parallel processor and estimate its theoretical performance based on the current hardware technology. Next, we show how the parallel processor could be used to solve the neutron diffusion equation. We then present the results of some simulations of a parallel processor run on a serial processor and measure some of the expected inefficiencies. Finally we extrapolate the results to estimate how actual design codes would perform. We find that the standard numerical methods for solving the neutron diffusion equation are still applicable when used on a parallel processor. However, some simple modifications to these methods will be necessary if we are to achieve the full power of these new computers. (orig.) [de
Parallel Simulation of Three-Dimensional Free Surface Fluid Flow Problems
International Nuclear Information System (INIS)
BAER, THOMAS A.; SACKINGER, PHILIP A.; SUBIA, SAMUEL R.
1999-01-01
Simulation of viscous three-dimensional fluid flow typically involves a large number of unknowns. When free surfaces are included, the number of unknowns increases dramatically. Consequently, this class of problem is an obvious application of parallel high performance computing. We describe parallel computation of viscous, incompressible, free surface, Newtonian fluid flow problems that include dynamic contact fines. The Galerkin finite element method was used to discretize the fully-coupled governing conservation equations and a ''pseudo-solid'' mesh mapping approach was used to determine the shape of the free surface. In this approach, the finite element mesh is allowed to deform to satisfy quasi-static solid mechanics equations subject to geometric or kinematic constraints on the boundaries. As a result, nodal displacements must be included in the set of unknowns. Other issues discussed are the proper constraints appearing along the dynamic contact line in three dimensions. Issues affecting efficient parallel simulations include problem decomposition to equally distribute computational work among a SPMD computer and determination of robust, scalable preconditioners for the distributed matrix systems that must be solved. Solution continuation strategies important for serial simulations have an enhanced relevance in a parallel coquting environment due to the difficulty of solving large scale systems. Parallel computations will be demonstrated on an example taken from the coating flow industry: flow in the vicinity of a slot coater edge. This is a three dimensional free surface problem possessing a contact line that advances at the web speed in one region but transitions to static behavior in another region. As such, a significant fraction of the computational time is devoted to processing boundary data. Discussion focuses on parallel speed ups for fixed problem size, a class of problems of immediate practical importance
A 3D gyrokinetic particle-in-cell simulation of fusion plasma microturbulence on parallel computers
Williams, T. J.
1992-12-01
One of the grand challenge problems now supported by HPCC is the Numerical Tokamak Project. A goal of this project is the study of low-frequency micro-instabilities in tokamak plasmas, which are believed to cause energy loss via turbulent thermal transport across the magnetic field lines. An important tool in this study is gyrokinetic particle-in-cell (PIC) simulation. Gyrokinetic, as opposed to fully-kinetic, methods are particularly well suited to the task because they are optimized to study the frequency and wavelength domain of the microinstabilities. Furthermore, many researchers now employ low-noise delta(f) methods to greatly reduce statistical noise by modelling only the perturbation of the gyrokinetic distribution function from a fixed background, not the entire distribution function. In spite of the increased efficiency of these improved algorithms over conventional PIC algorithms, gyrokinetic PIC simulations of tokamak micro-turbulence are still highly demanding of computer power--even fully-vectorized codes on vector supercomputers. For this reason, we have worked for several years to redevelop these codes on massively parallel computers. We have developed 3D gyrokinetic PIC simulation codes for SIMD and MIMD parallel processors, using control-parallel, data-parallel, and domain-decomposition message-passing (DDMP) programming paradigms. This poster summarizes our earlier work on codes for the Connection Machine and BBN TC2000 and our development of a generic DDMP code for distributed-memory parallel machines. We discuss the memory-access issues which are of key importance in writing parallel PIC codes, with special emphasis on issues peculiar to gyrokinetic PIC. We outline the domain decompositions in our new DDMP code and discuss the interplay of different domain decompositions suited for the particle-pushing and field-solution components of the PIC algorithm.
Simulated parallel annealing within a neighborhood for optimization of biomechanical systems.
Higginson, J S; Neptune, R R; Anderson, F C
2005-09-01
Optimization problems for biomechanical systems have become extremely complex. Simulated annealing (SA) algorithms have performed well in a variety of test problems and biomechanical applications; however, despite advances in computer speed, convergence to optimal solutions for systems of even moderate complexity has remained prohibitive. The objective of this study was to develop a portable parallel version of a SA algorithm for solving optimization problems in biomechanics. The algorithm for simulated parallel annealing within a neighborhood (SPAN) was designed to minimize interprocessor communication time and closely retain the heuristics of the serial SA algorithm. The computational speed of the SPAN algorithm scaled linearly with the number of processors on different computer platforms for a simple quadratic test problem and for a more complex forward dynamic simulation of human pedaling.
International Nuclear Information System (INIS)
Rios, Paulo R; Assis, Weslley L S; Ribeiro, Tatiana C S; Villa, Elena
2012-01-01
In a classical paper, Cahn derived expressions for the kinetics of transformations nucleated on random planes and lines. He used those as a model for nucleation on the boundaries, edges and vertices of a polycrystal consisting of equiaxed grains. In this paper it is demonstrated that Cahn's expression for random planes may be used in situations beyond the scope envisaged in Cahn's original paper. For instance, we derived an expression for the kinetics of transformations nucleated on random parallel planes that is identical to that formerly obtained by Cahn considering random planes. Computer simulation of transformations nucleated on random parallel planes is carried out. It is shown that there is excellent agreement between simulated results and analytical solutions. Such an agreement is to be expected if both the simulation and the analytical solution are correct. (paper)
Simulating Growth Kinetics in a Data-Parallel 3D Lattice Photobioreactor
Directory of Open Access Journals (Sweden)
A. V. Husselmann
2013-01-01
Full Text Available Though there have been many attempts to address growth kinetics in algal photobioreactors, surprisingly little have attempted an agent-based modelling (ABM approach. ABM has been heralded as a method of practical scientific inquiry into systems of a complex nature and has been applied liberally in a range of disciplines including ecology, physics, social science, and microbiology with special emphasis on pathogenic bacterial growth. We bring together agent-based simulation with the Photosynthetic Factory (PSF model, as well as certain key bioreactor characteristics in a visual 3D, parallel computing fashion. Despite being at small scale, the simulation gives excellent visual cues on the dynamics of such a reactor, and we further investigate the model in a variety of ways. Our parallel implementation on graphical processing units of the simulation provides key advantages, which we also briefly discuss. We also provide some performance data, along with particular effort in visualisation, using volumetric and isosurface rendering.
Application of parallel computing to seismic damage process simulation of an arch dam
International Nuclear Information System (INIS)
Zhong Hong; Lin Gao; Li Jianbo
2010-01-01
The simulation of damage process of high arch dam subjected to strong earthquake shocks is significant to the evaluation of its performance and seismic safety, considering the catastrophic effect of dam failure. However, such numerical simulation requires rigorous computational capacity. Conventional serial computing falls short of that and parallel computing is a fairly promising solution to this problem. The parallel finite element code PDPAD was developed for the damage prediction of arch dams utilizing the damage model with inheterogeneity of concrete considered. Developed with programming language Fortran, the code uses a master/slave mode for programming, domain decomposition method for allocation of tasks, MPI (Message Passing Interface) for communication and solvers from AZTEC library for solution of large-scale equations. Speedup test showed that the performance of PDPAD was quite satisfactory. The code was employed to study the damage process of a being-built arch dam on a 4-node PC Cluster, with more than one million degrees of freedom considered. The obtained damage mode was quite similar to that of shaking table test, indicating that the proposed procedure and parallel code PDPAD has a good potential in simulating seismic damage mode of arch dams. With the rapidly growing need for massive computation emerged from engineering problems, parallel computing will find more and more applications in pertinent areas.
Parallel Monte Carlo simulations on an ARC-enabled computing grid
International Nuclear Information System (INIS)
Nilsen, Jon K; Samset, Bjørn H
2011-01-01
Grid computing opens new possibilities for running heavy Monte Carlo simulations of physical systems in parallel. The presentation gives an overview of GaMPI, a system for running an MPI-based random walker simulation on grid resources. Integrating the ARC middleware and the new storage system Chelonia with the Ganga grid job submission and control system, we show that MPI jobs can be run on a world-wide computing grid with good performance and promising scaling properties. Results for relatively communication-heavy Monte Carlo simulations run on multiple heterogeneous, ARC-enabled computing clusters in several countries are presented.
A method for data handling numerical results in parallel OpenFOAM simulations
International Nuclear Information System (INIS)
nd Vasile Pârvan Ave., 300223, TM Timişoara, Romania, alin.anton@cs.upt.ro (Romania))" data-affiliation=" (Faculty of Automatic Control and Computing, Politehnica University of Timişoara, 2nd Vasile Pârvan Ave., 300223, TM Timişoara, Romania, alin.anton@cs.upt.ro (Romania))" >Anton, Alin; th Mihai Viteazu Ave., 300221, TM Timişoara (Romania))" data-affiliation=" (Center for Advanced Research in Engineering Science, Romanian Academy – Timişoara Branch, 24th Mihai Viteazu Ave., 300221, TM Timişoara (Romania))" >Muntean, Sebastian
2015-01-01
Parallel computational fluid dynamics simulations produce vast amount of numerical result data. This paper introduces a method for reducing the size of the data by replaying the interprocessor traffic. The results are recovered only in certain regions of interest configured by the user. A known test case is used for several mesh partitioning scenarios using the OpenFOAM toolkit ® [1]. The space savings obtained with classic algorithms remain constant for more than 60 Gb of floating point data. Our method is most efficient on large simulation meshes and is much better suited for compressing large scale simulation results than the regular algorithms
A method for data handling numerical results in parallel OpenFOAM simulations
Energy Technology Data Exchange (ETDEWEB)
Anton, Alin [Faculty of Automatic Control and Computing, Politehnica University of Timişoara, 2" n" d Vasile Pârvan Ave., 300223, TM Timişoara, Romania, alin.anton@cs.upt.ro (Romania); Muntean, Sebastian [Center for Advanced Research in Engineering Science, Romanian Academy – Timişoara Branch, 24" t" h Mihai Viteazu Ave., 300221, TM Timişoara (Romania)
2015-12-31
Parallel computational fluid dynamics simulations produce vast amount of numerical result data. This paper introduces a method for reducing the size of the data by replaying the interprocessor traffic. The results are recovered only in certain regions of interest configured by the user. A known test case is used for several mesh partitioning scenarios using the OpenFOAM toolkit{sup ®}[1]. The space savings obtained with classic algorithms remain constant for more than 60 Gb of floating point data. Our method is most efficient on large simulation meshes and is much better suited for compressing large scale simulation results than the regular algorithms.
Application of parallel computing techniques to a large-scale reservoir simulation
International Nuclear Information System (INIS)
Zhang, Keni; Wu, Yu-Shu; Ding, Chris; Pruess, Karsten
2001-01-01
Even with the continual advances made in both computational algorithms and computer hardware used in reservoir modeling studies, large-scale simulation of fluid and heat flow in heterogeneous reservoirs remains a challenge. The problem commonly arises from intensive computational requirement for detailed modeling investigations of real-world reservoirs. This paper presents the application of a massive parallel-computing version of the TOUGH2 code developed for performing large-scale field simulations. As an application example, the parallelized TOUGH2 code is applied to develop a three-dimensional unsaturated-zone numerical model simulating flow of moisture, gas, and heat in the unsaturated zone of Yucca Mountain, Nevada, a potential repository for high-level radioactive waste. The modeling approach employs refined spatial discretization to represent the heterogeneous fractured tuffs of the system, using more than a million 3-D gridblocks. The problem of two-phase flow and heat transfer within the model domain leads to a total of 3,226,566 linear equations to be solved per Newton iteration. The simulation is conducted on a Cray T3E-900, a distributed-memory massively parallel computer. Simulation results indicate that the parallel computing technique, as implemented in the TOUGH2 code, is very efficient. The reliability and accuracy of the model results have been demonstrated by comparing them to those of small-scale (coarse-grid) models. These comparisons show that simulation results obtained with the refined grid provide more detailed predictions of the future flow conditions at the site, aiding in the assessment of proposed repository performance
Design of a real-time wind turbine simulator using a custom parallel architecture
Hoffman, John A.; Gluck, R.; Sridhar, S.
1995-01-01
The design of a new parallel-processing digital simulator is described. The new simulator has been developed specifically for analysis of wind energy systems in real time. The new processor has been named: the Wind Energy System Time-domain simulator, version 3 (WEST-3). Like previous WEST versions, WEST-3 performs many computations in parallel. The modules in WEST-3 are pure digital processors, however. These digital processors can be programmed individually and operated in concert to achieve real-time simulation of wind turbine systems. Because of this programmability, WEST-3 is very much more flexible and general than its two predecessors. The design features of WEST-3 are described to show how the system produces high-speed solutions of nonlinear time-domain equations. WEST-3 has two very fast Computational Units (CU's) that use minicomputer technology plus special architectural features that make them many times faster than a microcomputer. These CU's are needed to perform the complex computations associated with the wind turbine rotor system in real time. The parallel architecture of the CU causes several tasks to be done in each cycle, including an IO operation and the combination of a multiply, add, and store. The WEST-3 simulator can be expanded at any time for additional computational power. This is possible because the CU's interfaced to each other and to other portions of the simulation using special serial buses. These buses can be 'patched' together in essentially any configuration (in a manner very similar to the programming methods used in analog computation) to balance the input/ output requirements. CU's can be added in any number to share a given computational load. This flexible bus feature is very different from many other parallel processors which usually have a throughput limit because of rigid bus architecture.
Coupling methods for parallel running RELAPSim codes in nuclear power plant simulation
Energy Technology Data Exchange (ETDEWEB)
Li, Yankai; Lin, Meng, E-mail: linmeng@sjtu.edu.cn; Yang, Yanhua
2016-02-15
When the plant is modeled detailedly for high precision, it is hard to achieve real-time calculation for one single RELAP5 in a large-scale simulation. To improve the speed and ensure the precision of simulation at the same time, coupling methods for parallel running RELAPSim codes were proposed in this study. Explicit coupling method via coupling boundaries was realized based on a data-exchange and procedure-control environment. Compromise of synchronization frequency was well considered to improve the precision of simulation and guarantee the real-time simulation at the same time. The coupling methods were assessed using both single-phase flow models and two-phase flow models and good agreements were obtained between the splitting–coupling models and the integrated model. The mitigation of SGTR was performed as an integral application of the coupling models. A large-scope NPP simulator was developed adopting six splitting–coupling models of RELAPSim and other simulation codes. The coupling models could improve the speed of simulation significantly and make it possible for real-time calculation. In this paper, the coupling of the models in the engineering simulator is taken as an example to expound the coupling methods, i.e., coupling between parallel running RELAPSim codes, and coupling between RELAPSim code and other types of simulation codes. However, the coupling methods are also referable in other simulator, for example, a simulator employing ATHLETE instead of RELAP5, other logic code instead of SIMULINK. It is believed the coupling method is commonly used for NPP simulator regardless of the specific codes chosen in this paper.
Xyce Parallel Electronic Simulator Users' Guide Version 6.7.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aadithya, Karthik Venkatraman [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2017-05-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been designed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The information herein is subject to change without notice. Copyright c 2002-2017 Sandia Corporation. All rights reserved. Trademarks Xyce TM Electronic Simulator and Xyce TM are trademarks of Sandia Corporation. Orcad, Orcad Capture, PSpice and Probe are registered trademarks of Cadence Design Systems, Inc. Microsoft, Windows and Windows 7 are registered trademarks of Microsoft Corporation. Medici, DaVinci and Taurus are registered trademarks of Synopsys Corporation. Amtec and TecPlot are trademarks of
Parallel computing simulation of fluid flow in the unsaturated zone of Yucca Mountain, Nevada
International Nuclear Information System (INIS)
Zhang, Keni; Wu, Yu-Shu; Bodvarsson, G.S.
2001-01-01
This paper presents the application of parallel computing techniques to large-scale modeling of fluid flow in the unsaturated zone (UZ) at Yucca Mountain, Nevada. In this study, parallel computing techniques, as implemented into the TOUGH2 code, are applied in large-scale numerical simulations on a distributed-memory parallel computer. The modeling study has been conducted using an over-one-million-cell three-dimensional numerical model, which incorporates a wide variety of field data for the highly heterogeneous fractured formation at Yucca Mountain. The objective of this study is to analyze the impact of various surface infiltration scenarios (under current and possible future climates) on flow through the UZ system, using various hydrogeological conceptual models with refined grids. The results indicate that the one-million-cell models produce better resolution results and reveal some flow patterns that cannot be obtained using coarse-grid modeling models
Concurrent particle-in-cell plasma simulation on a multi-transputer parallel computer
International Nuclear Information System (INIS)
Khare, A.N.; Jethra, A.; Patel, Kartik
1992-01-01
This report describes the parallelization of a Particle-in-Cell (PIC) plasma simulation code on a multi-transputer parallel computer. The algorithm used in the parallelization of the PIC method is described. The decomposition schemes related to the distribution of the particles among the processors are discussed. The implementation of the algorithm on a transputer network connected as a torus is presented. The solutions of the problems related to global communication of data are presented in the form of a set of generalized communication functions. The performance of the program as a function of data size and the number of transputers show that the implementation is scalable and represents an effective way of achieving high performance at acceptable cost. (author). 11 refs., 4 figs., 2 tabs., appendices
Applications of parallel computer architectures to the real-time simulation of nuclear power systems
International Nuclear Information System (INIS)
Doster, J.M.; Sills, E.D.
1988-01-01
In this paper the authors report on efforts to utilize parallel computer architectures for the thermal-hydraulic simulation of nuclear power systems and current research efforts toward the development of advanced reactor operator aids and control systems based on this new technology. Many aspects of reactor thermal-hydraulic calculations are inherently parallel, and the computationally intensive portions of these calculations can be effectively implemented on modern computers. Timing studies indicate faster-than-real-time, high-fidelity physics models can be developed when the computational algorithms are designed to take advantage of the computer's architecture. These capabilities allow for the development of novel control systems and advanced reactor operator aids. Coupled with an integral real-time data acquisition system, evolving parallel computer architectures can provide operators and control room designers improved control and protection capabilities. Current research efforts are currently under way in this area
Rodrigues, Manuel J.; Fernandes, David E.; Silveirinha, Mário G.; Falcão, Gabriel
2018-01-01
This work introduces a parallel computing framework to characterize the propagation of electron waves in graphene-based nanostructures. The electron wave dynamics is modeled using both "microscopic" and effective medium formalisms and the numerical solution of the two-dimensional massless Dirac equation is determined using a Finite-Difference Time-Domain scheme. The propagation of electron waves in graphene superlattices with localized scattering centers is studied, and the role of the symmetry of the microscopic potential in the electron velocity is discussed. The computational methodologies target the parallel capabilities of heterogeneous multi-core CPU and multi-GPU environments and are built with the OpenCL parallel programming framework which provides a portable, vendor agnostic and high throughput-performance solution. The proposed heterogeneous multi-GPU implementation achieves speedup ratios up to 75x when compared to multi-thread and multi-core CPU execution, reducing simulation times from several hours to a couple of minutes.
GROMACS 4.5: A high-throughput and highly parallel open source molecular simulation toolkit
Energy Technology Data Exchange (ETDEWEB)
Pronk, Sander [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Pall, Szilard [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Schulz, Roland [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Larsson, Per [Univ. of Virginia, Charlottesville, VA (United States); Bjelkmar, Par [Science for Life Lab., Stockholm (Sweden); Stockholm Univ., Stockholm (Sweden); Apostolov, Rossen [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Shirts, Michael R. [Univ. of Virginia, Charlottesville, VA (United States); Smith, Jeremy C. [Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Kasson, Peter M. [Univ. of Virginia, Charlottesville, VA (United States); van der Spoel, David [Science for Life Lab., Stockholm (Sweden); Uppsala Univ., Uppsala (Sweden); Hess, Berk [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Lindahl, Erik [Science for Life Lab., Stockholm (Sweden); KTH Royal Institute of Technology, Stockholm (Sweden); Stockholm Univ., Stockholm (Sweden)
2013-02-13
In this study, molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. As a result, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations.
A conceptual design of multidisciplinary-integrated C.F.D. simulation on parallel computers
International Nuclear Information System (INIS)
Onishi, Ryoichi; Ohta, Takashi; Kimura, Toshiya.
1996-11-01
A design of a parallel aeroelastic code for aircraft integrated simulations is conducted. The method for integrating aerodynamics and structural dynamics software on parallel computers is devised by using the Euler/Navier-Stokes equations coupled with wing-box finite element structures. A synthesis of modern aircraft requires the optimizations of aerodynamics, structures, controls, operabilities, or other design disciplines, and the R and D efforts to implement Multidisciplinary Design Optimization environments using high performance computers are made especially among the U.S. aerospace industries. This report describes a Multiple Program Multiple Data (MPMD) parallelization of aerodynamics and structural dynamics codes with a dynamic deformation grid. A three-dimensional computation of a flowfield with dynamic deformation caused by a structural deformation is performed, and a pressure data calculated is used for a computation of the structural deformation which is input again to a fluid dynamics code. This process is repeated exchanging the computed data of pressures and deformations between flowfield grids and structural elements. It enables to simulate the structure movements which take into account of the interaction of fluid and structure. The conceptual design for achieving the aforementioned various functions is reported. Also the future extensions to incorporate control systems, which enable to simulate a realistic aircraft configuration to be a major tool for Aircraft Integrated Simulation, are investigated. (author)
Recent progress in 3D EM/EM-PIC simulation with ARGUS and parallel ARGUS
International Nuclear Information System (INIS)
Mankofsky, A.; Petillo, J.; Krueger, W.; Mondelli, A.; McNamara, B.; Philp, R.
1994-01-01
ARGUS is an integrated, 3-D, volumetric simulation model for systems involving electric and magnetic fields and charged particles, including materials embedded in the simulation region. The code offers the capability to carry out time domain and frequency domain electromagnetic simulations of complex physical systems. ARGUS offers a boolean solid model structure input capability that can include essentially arbitrary structures on the computational domain, and a modular architecture that allows multiple physics packages to access the same data structure and to share common code utilities. Physics modules are in place to compute electrostatic and electromagnetic fields, the normal modes of RF structures, and self-consistent particle-in-cell (PIC) simulation in either a time dependent mode or a steady state mode. The PIC modules include multiple particle species, the Lorentz equations of motion, and algorithms for the creation of particles by emission from material surfaces, injection onto the grid, and ionization. In this paper, we present an updated overview of ARGUS, with particular emphasis given in recent algorithmic and computational advances. These include a completely rewritten frequency domain solver which efficiently treats lossy materials and periodic structures, a parallel version of ARGUS with support for both shared memory parallel vector (i.e. CRAY) machines and distributed memory massively parallel MIMD systems, and numerous new applications of the code
GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.
Pronk, Sander; Páll, Szilárd; Schulz, Roland; Larsson, Per; Bjelkmar, Pär; Apostolov, Rossen; Shirts, Michael R; Smith, Jeremy C; Kasson, Peter M; van der Spoel, David; Hess, Berk; Lindahl, Erik
2013-04-01
Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. GROMACS is an open source and free software available from http://www.gromacs.org. Supplementary data are available at Bioinformatics online.
Fast Simulation of Large-Scale Floods Based on GPU Parallel Computing
Directory of Open Access Journals (Sweden)
Qiang Liu
2018-05-01
Full Text Available Computing speed is a significant issue of large-scale flood simulations for real-time response to disaster prevention and mitigation. Even today, most of the large-scale flood simulations are generally run on supercomputers due to the massive amounts of data and computations necessary. In this work, a two-dimensional shallow water model based on an unstructured Godunov-type finite volume scheme was proposed for flood simulation. To realize a fast simulation of large-scale floods on a personal computer, a Graphics Processing Unit (GPU-based, high-performance computing method using the OpenACC application was adopted to parallelize the shallow water model. An unstructured data management method was presented to control the data transportation between the GPU and CPU (Central Processing Unit with minimum overhead, and then both computation and data were offloaded from the CPU to the GPU, which exploited the computational capability of the GPU as much as possible. The parallel model was validated using various benchmarks and real-world case studies. The results demonstrate that speed-ups of up to one order of magnitude can be achieved in comparison with the serial model. The proposed parallel model provides a fast and reliable tool with which to quickly assess flood hazards in large-scale areas and, thus, has a bright application prospect for dynamic inundation risk identification and disaster assessment.
An efficient parallel stochastic simulation method for analysis of nonviral gene delivery systems
Kuwahara, Hiroyuki
2011-01-01
Gene therapy has a great potential to become an effective treatment for a wide variety of diseases. One of the main challenges to make gene therapy practical in clinical settings is the development of efficient and safe mechanisms to deliver foreign DNA molecules into the nucleus of target cells. Several computational and experimental studies have shown that the design process of synthetic gene transfer vectors can be greatly enhanced by computational modeling and simulation. This paper proposes a novel, effective parallelization of the stochastic simulation algorithm (SSA) for pharmacokinetic models that characterize the rate-limiting, multi-step processes of intracellular gene delivery. While efficient parallelizations of the SSA are still an open problem in a general setting, the proposed parallel simulation method is able to substantially accelerate the next reaction selection scheme and the reaction update scheme in the SSA by exploiting and decomposing the structures of stochastic gene delivery models. This, thus, makes computationally intensive analysis such as parameter optimizations and gene dosage control for specific cell types, gene vectors, and transgene expression stability substantially more practical than that could otherwise be with the standard SSA. Here, we translated the nonviral gene delivery model based on mass-action kinetics by Varga et al. [Molecular Therapy, 4(5), 2001] into a more realistic model that captures intracellular fluctuations based on stochastic chemical kinetics, and as a case study we applied our parallel simulation to this stochastic model. Our results show that our simulation method is able to increase the efficiency of statistical analysis by at least 50% in various settings. © 2011 ACM.
Long-time atomistic simulations with the Parallel Replica Dynamics method
Perez, Danny
Molecular Dynamics (MD) -- the numerical integration of atomistic equations of motion -- is a workhorse of computational materials science. Indeed, MD can in principle be used to obtain any thermodynamic or kinetic quantity, without introducing any approximation or assumptions beyond the adequacy of the interaction potential. It is therefore an extremely powerful and flexible tool to study materials with atomistic spatio-temporal resolution. These enviable qualities however come at a steep computational price, hence limiting the system sizes and simulation times that can be achieved in practice. While the size limitation can be efficiently addressed with massively parallel implementations of MD based on spatial decomposition strategies, allowing for the simulation of trillions of atoms, the same approach usually cannot extend the timescales much beyond microseconds. In this article, we discuss an alternative parallel-in-time approach, the Parallel Replica Dynamics (ParRep) method, that aims at addressing the timescale limitation of MD for systems that evolve through rare state-to-state transitions. We review the formal underpinnings of the method and demonstrate that it can provide arbitrarily accurate results for any definition of the states. When an adequate definition of the states is available, ParRep can simulate trajectories with a parallel speedup approaching the number of replicas used. We demonstrate the usefulness of ParRep by presenting different examples of materials simulations where access to long timescales was essential to access the physical regime of interest and discuss practical considerations that must be addressed to carry out these simulations. Work supported by the United States Department of Energy (U.S. DOE), Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division.
Visual Data-Analytics of Large-Scale Parallel Discrete-Event Simulations
Energy Technology Data Exchange (ETDEWEB)
Ross, Caitlin; Carothers, Christopher D.; Mubarak, Misbah; Carns, Philip; Ross, Robert; Li, Jianping Kelvin; Ma, Kwan-Liu
2016-11-13
Parallel discrete-event simulation (PDES) is an important tool in the codesign of extreme-scale systems because PDES provides a cost-effective way to evaluate designs of highperformance computing systems. Optimistic synchronization algorithms for PDES, such as Time Warp, allow events to be processed without global synchronization among the processing elements. A rollback mechanism is provided when events are processed out of timestamp order. Although optimistic synchronization protocols enable the scalability of large-scale PDES, the performance of the simulations must be tuned to reduce the number of rollbacks and provide an improved simulation runtime. To enable efficient large-scale optimistic simulations, one has to gain insight into the factors that affect the rollback behavior and simulation performance. We developed a tool for ROSS model developers that gives them detailed metrics on the performance of their large-scale optimistic simulations at varying levels of simulation granularity. Model developers can use this information for parameter tuning of optimistic simulations in order to achieve better runtime and fewer rollbacks. In this work, we instrument the ROSS optimistic PDES framework to gather detailed statistics about the simulation engine. We have also developed an interactive visualization interface that uses the data collected by the ROSS instrumentation to understand the underlying behavior of the simulation engine. The interface connects real time to virtual time in the simulation and provides the ability to view simulation data at different granularities. We demonstrate the usefulness of our framework by performing a visual analysis of the dragonfly network topology model provided by the CODES simulation framework built on top of ROSS. The instrumentation needs to minimize overhead in order to accurately collect data about the simulation performance. To ensure that the instrumentation does not introduce unnecessary overhead, we perform a
Parallel-vector algorithms for particle simulations on shared-memory multiprocessors
International Nuclear Information System (INIS)
Nishiura, Daisuke; Sakaguchi, Hide
2011-01-01
Over the last few decades, the computational demands of massive particle-based simulations for both scientific and industrial purposes have been continuously increasing. Hence, considerable efforts are being made to develop parallel computing techniques on various platforms. In such simulations, particles freely move within a given space, and so on a distributed-memory system, load balancing, i.e., assigning an equal number of particles to each processor, is not guaranteed. However, shared-memory systems achieve better load balancing for particle models, but suffer from the intrinsic drawback of memory access competition, particularly during (1) paring of contact candidates from among neighboring particles and (2) force summation for each particle. Here, novel algorithms are proposed to overcome these two problems. For the first problem, the key is a pre-conditioning process during which particle labels are sorted by a cell label in the domain to which the particles belong. Then, a list of contact candidates is constructed by pairing the sorted particle labels. For the latter problem, a table comprising the list indexes of the contact candidate pairs is created and used to sum the contact forces acting on each particle for all contacts according to Newton's third law. With just these methods, memory access competition is avoided without additional redundant procedures. The parallel efficiency and compatibility of these two algorithms were evaluated in discrete element method (DEM) simulations on four types of shared-memory parallel computers: a multicore multiprocessor computer, scalar supercomputer, vector supercomputer, and graphics processing unit. The computational efficiency of a DEM code was found to be drastically improved with our algorithms on all but the scalar supercomputer. Thus, the developed parallel algorithms are useful on shared-memory parallel computers with sufficient memory bandwidth.
3-D electromagnetic plasma particle simulations on the Intel Delta parallel computer
International Nuclear Information System (INIS)
Wang, J.; Liewer, P.C.
1994-01-01
A three-dimensional electromagnetic PIC code has been developed on the 512 node Intel Touchstone Delta MIMD parallel computer. This code is based on the General Concurrent PIC algorithm which uses a domain decomposition to divide the computation among the processors. The 3D simulation domain can be partitioned into 1-, 2-, or 3-dimensional sub-domains. Particles must be exchanged between processors as they move among the subdomains. The Intel Delta allows one to use this code for very-large-scale simulations (i.e. over 10 8 particles and 10 6 grid cells). The parallel efficiency of this code is measured, and the overall code performance on the Delta is compared with that on Cray supercomputers. It is shown that their code runs with a high parallel efficiency of ≥ 95% for large size problems. The particle push time achieved is 115 nsecs/particle/time step for 162 million particles on 512 nodes. Comparing with the performance on a single processor Cray C90, this represents a factor of 58 speedup. The code uses a finite-difference leap frog method for field solve which is significantly more efficient than fast fourier transforms on parallel computers. The performance of this code on the 128 node Cray T3D will also be discussed
International Nuclear Information System (INIS)
Schleier, W.; Besold, G.; Heinz, K.
1992-01-01
The authors study the applicability of parallelized/vectorized Monte Carlo (MC) algorithms to the simulation of domain growth in two-dimensional lattice gas models undergoing an ordering process after a rapid quench below an order-disorder transition temperature. As examples they consider models with 2 x 1 and c(2 x 2) equilibrium superstructures on the square and rectangular lattices, respectively. They also study the case of phase separation ('1 x 1' islands) on the square lattice. A generalized parallel checkerboard algorithm for Kawasaki dynamics is shown to give rise to artificial spatial correlations in all three models. However, only if superstructure domains evolve do these correlations modify the kinetics by influencing the nucleation process and result in a reduced growth exponent compared to the value from the conventional heat bath algorithm with random single-site updates. In order to overcome these artificial modifications, two MC algorithms with a reduced degree of parallelism ('hybrid' and 'mask' algorithms, respectively) are presented and applied. As the results indicate, these algorithms are suitable for the simulation of superstructure domain growth on parallel/vector computers. 60 refs., 10 figs., 1 tab
A multi-transputer system for parallel Monte Carlo simulations of extensive air showers
International Nuclear Information System (INIS)
Gils, H.J.; Heck, D.; Oehlschlaeger, J.; Schatz, G.; Thouw, T.
1989-01-01
A multiprocessor computer system has been brought into operation at the Kernforschungszentrum Karlsruhe. It is dedicated to Monte Carlo simulations of extensive air showers induced by ultra-high energy cosmic rays. The architecture consists of two independently working VMEbus systems each with a 68020 microprocessor as host computer and twelve T800 transputers for parallel processing. The two systems are linked via Ethernet for data exchange. The T800 transputers are equipped with 4 Mbyte RAM each, sufficient to run rather large codes. The host computers are operated under UNIX 5.3. On the transputers compilers for PARALLEL FORTRAN, C, and PASCAL are available. The simple modular architecture of this parallel computer reflects the single purpose for which it is intended. The hardware of the multiprocessor computer is described as well as the way how the user software is handled and distributed to the 24 working processors. The performance of the parallel computer is demonstrated by well-known benchmarks and by realistic Monte Carlo simulations of air showers. Comparisons with other types of microprocessors and with large universal computers are made. It is demonstrated that a cost reduction by more than a factor of 20 is achieved by this system as compared to universal computer. (orig.)
A Parallel, Finite-Volume Algorithm for Large-Eddy Simulation of Turbulent Flows
Bui, Trong T.
1999-01-01
A parallel, finite-volume algorithm has been developed for large-eddy simulation (LES) of compressible turbulent flows. This algorithm includes piecewise linear least-square reconstruction, trilinear finite-element interpolation, Roe flux-difference splitting, and second-order MacCormack time marching. Parallel implementation is done using the message-passing programming model. In this paper, the numerical algorithm is described. To validate the numerical method for turbulence simulation, LES of fully developed turbulent flow in a square duct is performed for a Reynolds number of 320 based on the average friction velocity and the hydraulic diameter of the duct. Direct numerical simulation (DNS) results are available for this test case, and the accuracy of this algorithm for turbulence simulations can be ascertained by comparing the LES solutions with the DNS results. The effects of grid resolution, upwind numerical dissipation, and subgrid-scale dissipation on the accuracy of the LES are examined. Comparison with DNS results shows that the standard Roe flux-difference splitting dissipation adversely affects the accuracy of the turbulence simulation. For accurate turbulence simulations, only 3-5 percent of the standard Roe flux-difference splitting dissipation is needed.
Parallel simulation of wormhole propagation with the Darcy-Brinkman-Forchheimer framework
Wu, Yuanqing
2015-07-09
The acid treatment of carbonate reservoirs is a widely practiced oil and gas well stimulation technique. The injected acid dissolves the material near the wellbore and creates flow channels that establish a good connectivity between the reservoir and the well. Such flow channels are called wormholes. Different from the traditional simulation technology relying on Darcy framework, the new Darcy-Brinkman-Forchheimer (DBF) framework is introduced to simulate the wormhole forming procedure. The DBF framework considers both large and small porosity conditions and should output better simulation results than the Darcy framework. To process the huge quantity of cells in the simulation grid and shorten the long simulation time of the traditional serial code, a parallel code with FORTRAN 90 and MPI was developed. The experimenting field approach to set coefficients in the model equations was also introduced. Moreover, a procedure to fill in the coefficient matrix in the linear system in the solver was described. After this, 2D dissolution experiments were carried out. In the experiments, different configurations of wormholes and a series of properties simulated by both frameworks were compared. We conclude that the numerical results of the DBF framework are more like wormholes and more stable than the Darcy framework, which is a demonstration of the advantages of the DBF framework. Finally, the scalability of the parallel code was evaluated, and we conclude that superlinear scalability can be achieved. © 2015 Elsevier Ltd.
Large scale simulations of lattice QCD thermodynamics on Columbia Parallel Supercomputers
International Nuclear Information System (INIS)
Ohta, Shigemi
1989-01-01
The Columbia Parallel Supercomputer project aims at the construction of a parallel processing, multi-gigaflop computer optimized for numerical simulations of lattice QCD. The project has three stages; 16-node, 1/4GF machine completed in April 1985, 64-node, 1GF machine completed in August 1987, and 256-node, 16GF machine now under construction. The machines all share a common architecture; a two dimensional torus formed from a rectangular array of N 1 x N 2 independent and identical processors. A processor is capable of operating in a multi-instruction multi-data mode, except for periods of synchronous interprocessor communication with its four nearest neighbors. Here the thermodynamics simulations on the two working machines are reported. (orig./HSI)
International Nuclear Information System (INIS)
Paćko, P; Bielak, T; Staszewski, W J; Uhl, T; Spencer, A B; Worden, K
2012-01-01
This paper demonstrates new parallel computation technology and an implementation for Lamb wave propagation modelling in complex structures. A graphical processing unit (GPU) and computer unified device architecture (CUDA), available in low-cost graphical cards in standard PCs, are used for Lamb wave propagation numerical simulations. The local interaction simulation approach (LISA) wave propagation algorithm has been implemented as an example. Other algorithms suitable for parallel discretization can also be used in practice. The method is illustrated using examples related to damage detection. The results demonstrate good accuracy and effective computational performance of very large models. The wave propagation modelling presented in the paper can be used in many practical applications of science and engineering. (paper)
Energy Technology Data Exchange (ETDEWEB)
Hepburn, I.; De Schutter, E., E-mail: erik@oist.jp [Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495 (Japan); Theoretical Neurobiology & Neuroengineering, University of Antwerp, Antwerp 2610 (Belgium); Chen, W. [Computational Neuroscience Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa 904 0495 (Japan)
2016-08-07
Spatial stochastic molecular simulations in biology are limited by the intense computation required to track molecules in space either in a discrete time or discrete space framework, which has led to the development of parallel methods that can take advantage of the power of modern supercomputers in recent years. We systematically test suggested components of stochastic reaction-diffusion operator splitting in the literature and discuss their effects on accuracy. We introduce an operator splitting implementation for irregular meshes that enhances accuracy with minimal performance cost. We test a range of models in small-scale MPI simulations from simple diffusion models to realistic biological models and find that multi-dimensional geometry partitioning is an important consideration for optimum performance. We demonstrate performance gains of 1-3 orders of magnitude in the parallel implementation, with peak performance strongly dependent on model specification.
Yu, Leiming; Nina-Paravecino, Fanny; Kaeli, David; Fang, Qianqian
2018-01-01
We present a highly scalable Monte Carlo (MC) three-dimensional photon transport simulation platform designed for heterogeneous computing systems. Through the development of a massively parallel MC algorithm using the Open Computing Language framework, this research extends our existing graphics processing unit (GPU)-accelerated MC technique to a highly scalable vendor-independent heterogeneous computing environment, achieving significantly improved performance and software portability. A number of parallel computing techniques are investigated to achieve portable performance over a wide range of computing hardware. Furthermore, multiple thread-level and device-level load-balancing strategies are developed to obtain efficient simulations using multiple central processing units and GPUs. (2018) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE).
Object-Oriented Parallel Particle-in-Cell Code for Beam Dynamics Simulation in Linear Accelerators
International Nuclear Information System (INIS)
Qiang, J.; Ryne, R.D.; Habib, S.; Decky, V.
1999-01-01
In this paper, we present an object-oriented three-dimensional parallel particle-in-cell code for beam dynamics simulation in linear accelerators. A two-dimensional parallel domain decomposition approach is employed within a message passing programming paradigm along with a dynamic load balancing. Implementing object-oriented software design provides the code with better maintainability, reusability, and extensibility compared with conventional structure based code. This also helps to encapsulate the details of communications syntax. Performance tests on SGI/Cray T3E-900 and SGI Origin 2000 machines show good scalability of the object-oriented code. Some important features of this code also include employing symplectic integration with linear maps of external focusing elements and using z as the independent variable, typical in accelerators. A successful application was done to simulate beam transport through three superconducting sections in the APT linac design
Yang, Sheng-Chun; Lu, Zhong-Yuan; Qian, Hu-Jun; Wang, Yong-Lei; Han, Jie-Ping
2017-11-01
In this work, we upgraded the electrostatic interaction method of CU-ENUF (Yang, et al., 2016) which first applied CUNFFT (nonequispaced Fourier transforms based on CUDA) to the reciprocal-space electrostatic computation and made the computation of electrostatic interaction done thoroughly in GPU. The upgraded edition of CU-ENUF runs concurrently in a hybrid parallel way that enables the computation parallelizing on multiple computer nodes firstly, then further on the installed GPU in each computer. By this parallel strategy, the size of simulation system will be never restricted to the throughput of a single CPU or GPU. The most critical technical problem is how to parallelize a CUNFFT in the parallel strategy, which is conquered effectively by deep-seated research of basic principles and some algorithm skills. Furthermore, the upgraded method is capable of computing electrostatic interactions for both the atomistic molecular dynamics (MD) and the dissipative particle dynamics (DPD). Finally, the benchmarks conducted for validation and performance indicate that the upgraded method is able to not only present a good precision when setting suitable parameters, but also give an efficient way to compute electrostatic interactions for huge simulation systems. Program Files doi:http://dx.doi.org/10.17632/zncf24fhpv.1 Licensing provisions: GNU General Public License 3 (GPL) Programming language: C, C++, and CUDA C Supplementary material: The program is designed for effective electrostatic interactions of large-scale simulation systems, which runs on particular computers equipped with NVIDIA GPUs. It has been tested on (a) single computer node with Intel(R) Core(TM) i7-3770@ 3.40 GHz (CPU) and GTX 980 Ti (GPU), and (b) MPI parallel computer nodes with the same configurations. Nature of problem: For molecular dynamics simulation, the electrostatic interaction is the most time-consuming computation because of its long-range feature and slow convergence in simulation space
An efficient numerical scheme for the simulation of parallel-plate active magnetic regenerators
DEFF Research Database (Denmark)
Torregrosa-Jaime, Bárbara; Corberán, José M.; Payá, Jorge
2015-01-01
A one-dimensional model of a parallel-plate active magnetic regenerator (AMR) is presented in this work. The model is based on an efficient numerical scheme which has been developed after analysing the heat transfer mechanisms in the regenerator bed. The new finite difference scheme optimally com...... to the fully implicit scheme, the proposed scheme achieves more accurate results, prevents numerical errors and requires less computational effort. In AMR simulations the new scheme can reduce the computational time by 88%....
Steinman, Jeffrey S. (Inventor)
1998-01-01
The present invention is embodied in a method of performing object-oriented simulation and a system having inter-connected processor nodes operating in parallel to simulate mutual interactions of a set of discrete simulation objects distributed among the nodes as a sequence of discrete events changing state variables of respective simulation objects so as to generate new event-defining messages addressed to respective ones of the nodes. The object-oriented simulation is performed at each one of the nodes by assigning passive self-contained simulation objects to each one of the nodes, responding to messages received at one node by generating corresponding active event objects having user-defined inherent capabilities and individual time stamps and corresponding to respective events affecting one of the passive self-contained simulation objects of the one node, restricting the respective passive self-contained simulation objects to only providing and receiving information from die respective active event objects, requesting information and changing variables within a passive self-contained simulation object by the active event object, and producing corresponding messages specifying events resulting therefrom by the active event objects.
Directory of Open Access Journals (Sweden)
Zhang Bin Loo
2017-01-01
Full Text Available Current network simulators abstract out wireless propagation models due to the high computation requirements for realistic modeling. As such, there is still a large gap between the results obtained from simulators and real world scenario. In this paper, we present a framework for improved path loss simulation built on top of an existing network simulation software, NS-3. Different from the conventional disk model, the proposed simulation also considers the diffraction loss computed using Epstein and Peterson’s model through the use of actual terrain elevation data to give an accurate estimate of path loss between a transmitter and a receiver. The drawback of high computation requirements is relaxed by offloading the computationally intensive components onto an inexpensive off-the-shelf parallel coprocessor, which is a NVIDIA GPU. Experiments are performed using actual terrain elevation data provided from United States Geological Survey. As compared to the conventional CPU architecture, the experimental result shows that a speedup of 20x to 42x is achieved by exploiting the parallel processing of GPU to compute the path loss between two nodes using terrain elevation data. The result shows that the path losses between two nodes are greatly affected by the terrain profile between these two nodes. Besides this, the result also suggests that the common strategy to place the transmitter in the highest position may not always work.
A parallel code named NEPTUNE for 3D fully electromagnetic and pic simulations
International Nuclear Information System (INIS)
Dong Ye; Yang Wenyuan; Chen Jun; Zhao Qiang; Xia Fang; Ma Yan; Xiao Li; Sun Huifang; Chen Hong; Zhou Haijing; Mao Zeyao; Dong Zhiwei
2010-01-01
A parallel code named NEPTUNE for 3D fully electromagnetic and particle-in-cell (PIC) simulations is introduced, which could run on the Linux system with hundreds to thousand CPUs. NEPTUNE is suitable to simulate entire 3D HPM devices; many HPM devices are simulated and designed by using it. In NEPTUNE code, the electromagnetic fields are updated by using the finite-difference in time domain (FDTD) method of solving Maxwell equations and the particles are moved by using Buneman-Boris advance method of solving relativistic Newton-Lorentz equation. Electromagnetic fields and particles are coupled by using liner weighing interpolation PIC method, and the electric filed components are corrected by using Boris method of solve Poisson equation in order to ensure charge-conservation. NEPTUNE code could construct many complicated geometric structures, such as arbitrary axial-symmetric structures, plane transforming structures, slow-wave-structures, coupling holes, foils, and so on. The boundary conditions used in NEPTUNE code are introduced in brief, including perfectly electric conductor boundary, external wave boundary, and particle boundary. Finally, some typical HPM devices are simulated and test by using NEPTUNE code, including MILO, RBWO, VCO, and RKA. The simulation results are with correct and credible physical images, and the parallel efficiencies are also given. (authors)
Directory of Open Access Journals (Sweden)
Xiaoliang Yin
2015-03-01
Full Text Available Complex electromechanical system is usually composed of multiple components from different domains, including mechanical, electronic, hydraulic, control, and so on. Modeling and simulation for electromechanical system on a unified platform is one of the research hotspots in system engineering at present. It is also the development trend of the design for complex electromechanical system. The unified modeling techniques and tools based on Modelica language provide a satisfactory solution. To meet with the requirements of collaborative modeling, simulation, and parallel computing for complex electromechanical systems based on Modelica, a general web-based modeling and simulation prototype environment, namely, WebMWorks, is designed and implemented. Based on the rich Internet application technologies, an interactive graphic user interface for modeling and post-processing on web browser was implemented; with the collaborative design module, the environment supports top-down, concurrent modeling and team cooperation; additionally, service-oriented architecture–based architecture was applied to supply compiling and solving services which run on cloud-like servers, so the environment can manage and dispatch large-scale simulation tasks in parallel on multiple computing servers simultaneously. An engineering application about pure electric vehicle is tested on WebMWorks. The results of simulation and parametric experiment demonstrate that the tested web-based environment can effectively shorten the design cycle of the complex electromechanical system.
Schnek: A C++ library for the development of parallel simulation codes on regular grids
Schmitz, Holger
2018-05-01
A large number of algorithms across the field of computational physics are formulated on grids with a regular topology. We present Schnek, a library that enables fast development of parallel simulations on regular grids. Schnek contains a number of easy-to-use modules that greatly reduce the amount of administrative code for large-scale simulation codes. The library provides an interface for reading simulation setup files with a hierarchical structure. The structure of the setup file is translated into a hierarchy of simulation modules that the developer can specify. The reader parses and evaluates mathematical expressions and initialises variables or grid data. This enables developers to write modular and flexible simulation codes with minimal effort. Regular grids of arbitrary dimension are defined as well as mechanisms for defining physical domain sizes, grid staggering, and ghost cells on these grids. Ghost cells can be exchanged between neighbouring processes using MPI with a simple interface. The grid data can easily be written into HDF5 files using serial or parallel I/O.
International Nuclear Information System (INIS)
Pic, Marc Michel
1995-01-01
Parallel programming covers task-parallelism and data-parallelism. Many problems need both parallelisms. Multi-SIMD computers allow hierarchical approach of these parallelisms. The T++ language, based on C++, is dedicated to exploit Multi-SIMD computers using a programming paradigm which is an extension of array-programming to tasks managing. Our language introduced array of independent tasks to achieve separately (MIMD), on subsets of processors of identical behaviour (SIMD), in order to translate the hierarchical inclusion of data-parallelism in task-parallelism. To manipulate in a symmetrical way tasks and data we propose meta-operations which have the same behaviour on tasks arrays and on data arrays. We explain how to implement this language on our parallel computer SYMPHONIE in order to profit by the locally-shared memory, by the hardware virtualization, and by the multiplicity of communications networks. We analyse simultaneously a typical application of such architecture. Finite elements scheme for Fluid mechanic needs powerful parallel computers and requires large floating points abilities. Lattice gases is an alternative to such simulations. Boolean lattice bases are simple, stable, modular, need to floating point computation, but include numerical noise. Boltzmann lattice gases present large precision of computation, but needs floating points and are only locally stable. We propose a new scheme, called multi-bit, who keeps the advantages of each boolean model to which it is applied, with large numerical precision and reduced noise. Experiments on viscosity, physical behaviour, noise reduction and spurious invariants are shown and implementation techniques for parallel Multi-SIMD computers detailed. (author) [fr
Real-time simulation of MHD/steam power plants by digital parallel processors
International Nuclear Information System (INIS)
Johnson, R.M.; Rudberg, D.A.
1981-01-01
Attention is given to a large FORTRAN coded program which simulates the dynamic response of the MHD/steam plant on either a SEL 32/55 or VAX 11/780 computer. The code realizes a detailed first-principle model of the plant. Quite recently, in addition to the VAX 11/780, an AD-10 has been installed for usage as a real-time simulation facility. The parallel processor AD-10 is capable of simulating the MHD/steam plant at several times real-time rates. This is desirable in order to develop rapidly a large data base of varied plant operating conditions. The combined-cycle MHD/steam plant model is discussed, taking into account a number of disadvantages. The disadvantages can be overcome with the aid of an array processor used as an adjunct to the unit processor. The conversion of some computations for real-time simulation is considered
Directory of Open Access Journals (Sweden)
Mondry Adrian
2004-08-01
Full Text Available Abstract Background Many arrhythmias are triggered by abnormal electrical activity at the ionic channel and cell level, and then evolve spatio-temporally within the heart. To understand arrhythmias better and to diagnose them more precisely by their ECG waveforms, a whole-heart model is required to explore the association between the massively parallel activities at the channel/cell level and the integrative electrophysiological phenomena at organ level. Methods We have developed a method to build large-scale electrophysiological models by using extended cellular automata, and to run such models on a cluster of shared memory machines. We describe here the method, including the extension of a language-based cellular automaton to implement quantitative computing, the building of a whole-heart model with Visible Human Project data, the parallelization of the model on a cluster of shared memory computers with OpenMP and MPI hybrid programming, and a simulation algorithm that links cellular activity with the ECG. Results We demonstrate that electrical activities at channel, cell, and organ levels can be traced and captured conveniently in our extended cellular automaton system. Examples of some ECG waveforms simulated with a 2-D slice are given to support the ECG simulation algorithm. A performance evaluation of the 3-D model on a four-node cluster is also given. Conclusions Quantitative multicellular modeling with extended cellular automata is a highly efficient and widely applicable method to weave experimental data at different levels into computational models. This process can be used to investigate complex and collective biological activities that can be described neither by their governing differentiation equations nor by discrete parallel computation. Transparent cluster computing is a convenient and effective method to make time-consuming simulation feasible. Arrhythmias, as a typical case, can be effectively simulated with the methods
Xyce Parallel Electronic Simulator - Users' Guide Version 2.1.
Energy Technology Data Exchange (ETDEWEB)
Hutchinson, Scott A; Hoekstra, Robert J.; Russo, Thomas V.; Rankin, Eric; Pawlowski, Roger P.; Fixel, Deborah A; Schiek, Richard; Bogdan, Carolyn W.; Shirley, David N.; Campbell, Phillip M.; Keiter, Eric R.
2005-06-01
This manual describes the use of theXyceParallel Electronic Simulator.Xycehasbeen designed as a SPICE-compatible, high-performance analog circuit simulator, andhas been written to support the simulation needs of the Sandia National Laboratorieselectrical designers. This development has focused on improving capability over thecurrent state-of-the-art in the following areas:%04Capability to solve extremely large circuit problems by supporting large-scale par-allel computing platforms (up to thousands of processors). Note that this includessupport for most popular parallel and serial computers.%04Improved performance for all numerical kernels (e.g., time integrator, nonlinearand linear solvers) through state-of-the-art algorithms and novel techniques.%04Device models which are specifically tailored to meet Sandia's needs, includingmany radiation-aware devices.3 XyceTMUsers' Guide%04Object-oriented code design and implementation using modern coding practicesthat ensure that theXyceParallel Electronic Simulator will be maintainable andextensible far into the future.Xyceis a parallel code in the most general sense of the phrase - a message passingparallel implementation - which allows it to run efficiently on the widest possible numberof computing platforms. These include serial, shared-memory and distributed-memoryparallel as well as heterogeneous platforms. Careful attention has been paid to thespecific nature of circuit-simulation problems to ensure that optimal parallel efficiencyis achieved as the number of processors grows.The development ofXyceprovides a platform for computational research and de-velopment aimed specifically at the needs of the Laboratory. WithXyce, Sandia hasan %22in-house%22 capability with which both new electrical (e.g., device model develop-ment) and algorithmic (e.g., faster time-integration methods, parallel solver algorithms)research and development can be performed. As a result,Xyceis a unique electricalsimulation capability
Massively parallel Monte Carlo for many-particle simulations on GPUs
Energy Technology Data Exchange (ETDEWEB)
Anderson, Joshua A.; Jankowski, Eric [Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Grubb, Thomas L. [Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Engel, Michael [Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Glotzer, Sharon C., E-mail: sglotzer@umich.edu [Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109 (United States); Department of Materials Science and Engineering, University of Michigan, Ann Arbor, MI 48109 (United States)
2013-12-01
Current trends in parallel processors call for the design of efficient massively parallel algorithms for scientific computing. Parallel algorithms for Monte Carlo simulations of thermodynamic ensembles of particles have received little attention because of the inherent serial nature of the statistical sampling. In this paper, we present a massively parallel method that obeys detailed balance and implement it for a system of hard disks on the GPU. We reproduce results of serial high-precision Monte Carlo runs to verify the method. This is a good test case because the hard disk equation of state over the range where the liquid transforms into the solid is particularly sensitive to small deviations away from the balance conditions. On a Tesla K20, our GPU implementation executes over one billion trial moves per second, which is 148 times faster than on a single Intel Xeon E5540 CPU core, enables 27 times better performance per dollar, and cuts energy usage by a factor of 13. With this improved performance we are able to calculate the equation of state for systems of up to one million hard disks. These large system sizes are required in order to probe the nature of the melting transition, which has been debated for the last forty years. In this paper we present the details of our computational method, and discuss the thermodynamics of hard disks separately in a companion paper.
Moon, Hongsik
What is the impact of multicore and associated advanced technologies on computational software for science? Most researchers and students have multicore laptops or desktops for their research and they need computing power to run computational software packages. Computing power was initially derived from Central Processing Unit (CPU) clock speed. That changed when increases in clock speed became constrained by power requirements. Chip manufacturers turned to multicore CPU architectures and associated technological advancements to create the CPUs for the future. Most software applications benefited by the increased computing power the same way that increases in clock speed helped applications run faster. However, for Computational ElectroMagnetics (CEM) software developers, this change was not an obvious benefit - it appeared to be a detriment. Developers were challenged to find a way to correctly utilize the advancements in hardware so that their codes could benefit. The solution was parallelization and this dissertation details the investigation to address these challenges. Prior to multicore CPUs, advanced computer technologies were compared with the performance using benchmark software and the metric was FLoting-point Operations Per Seconds (FLOPS) which indicates system performance for scientific applications that make heavy use of floating-point calculations. Is FLOPS an effective metric for parallelized CEM simulation tools on new multicore system? Parallel CEM software needs to be benchmarked not only by FLOPS but also by the performance of other parameters related to type and utilization of the hardware, such as CPU, Random Access Memory (RAM), hard disk, network, etc. The codes need to be optimized for more than just FLOPs and new parameters must be included in benchmarking. In this dissertation, the parallel CEM software named High Order Basis Based Integral Equation Solver (HOBBIES) is introduced. This code was developed to address the needs of the
Use of Parallel Micro-Platform for the Simulation the Space Exploration
Velasco Herrera, Victor Manuel; Velasco Herrera, Graciela; Rosano, Felipe Lara; Rodriguez Lozano, Salvador; Lucero Roldan Serrato, Karen
The purpose of this work is to create a parallel micro-platform, that simulates the virtual movements of a space exploration in 3D. One of the innovations presented in this design consists of the application of a lever mechanism for the transmission of the movement. The development of such a robot is a challenging task very different of the industrial manipulators due to a totally different target system of requirements. This work presents the study and simulation, aided by computer, of the movement of this parallel manipulator. The development of this model has been developed using the platform of computer aided design Unigraphics, in which it was done the geometric modeled of each one of the components and end assembly (CAD), the generation of files for the computer aided manufacture (CAM) of each one of the pieces and the kinematics simulation of the system evaluating different driving schemes. We used the toolbox (MATLAB) of aerospace and create an adaptive control module to simulate the system.
H5Part A Portable High Performance Parallel Data Interface for Particle Simulations
Adelmann, Andreas; Shalf, John M; Siegerist, Cristina
2005-01-01
Largest parallel particle simulations, in six dimensional phase space generate wast amont of data. It is also desirable to share data and data analysis tools such as ParViT (Particle Visualization Toolkit) among other groups who are working on particle-based accelerator simulations. We define a very simple file schema built on top of HDF5 (Hierarchical Data Format version 5) as well as an API that simplifies the reading/writing of the data to the HDF5 file format. HDF5 offers a self-describing machine-independent binary file format that supports scalable parallel I/O performance for MPI codes on a variety of supercomputing systems and works equally well on laptop computers. The API is available for C, C++, and Fortran codes. The file format will enable disparate research groups with very different simulation implementations to share data transparently and share data analysis tools. For instance, the common file format will enable groups that depend on completely different simulation implementations to share c...
STOCHSIMGPU: parallel stochastic simulation for the Systems Biology Toolbox 2 for MATLAB.
Klingbeil, Guido; Erban, Radek; Giles, Mike; Maini, Philip K
2011-04-15
The importance of stochasticity in biological systems is becoming increasingly recognized and the computational cost of biologically realistic stochastic simulations urgently requires development of efficient software. We present a new software tool STOCHSIMGPU that exploits graphics processing units (GPUs) for parallel stochastic simulations of biological/chemical reaction systems and show that significant gains in efficiency can be made. It is integrated into MATLAB and works with the Systems Biology Toolbox 2 (SBTOOLBOX2) for MATLAB. The GPU-based parallel implementation of the Gillespie stochastic simulation algorithm (SSA), the logarithmic direct method (LDM) and the next reaction method (NRM) is approximately 85 times faster than the sequential implementation of the NRM on a central processing unit (CPU). Using our software does not require any changes to the user's models, since it acts as a direct replacement of the stochastic simulation software of the SBTOOLBOX2. The software is open source under the GPL v3 and available at http://www.maths.ox.ac.uk/cmb/STOCHSIMGPU. The web site also contains supplementary information. klingbeil@maths.ox.ac.uk Supplementary data are available at Bioinformatics online.
Nishiura, Daisuke; Furuichi, Mikito; Sakaguchi, Hide
2015-09-01
The computational performance of a smoothed particle hydrodynamics (SPH) simulation is investigated for three types of current shared-memory parallel computer devices: many integrated core (MIC) processors, graphics processing units (GPUs), and multi-core CPUs. We are especially interested in efficient shared-memory allocation methods for each chipset, because the efficient data access patterns differ between compute unified device architecture (CUDA) programming for GPUs and OpenMP programming for MIC processors and multi-core CPUs. We first introduce several parallel implementation techniques for the SPH code, and then examine these on our target computer architectures to determine the most effective algorithms for each processor unit. In addition, we evaluate the effective computing performance and power efficiency of the SPH simulation on each architecture, as these are critical metrics for overall performance in a multi-device environment. In our benchmark test, the GPU is found to produce the best arithmetic performance as a standalone device unit, and gives the most efficient power consumption. The multi-core CPU obtains the most effective computing performance. The computational speed of the MIC processor on Xeon Phi approached that of two Xeon CPUs. This indicates that using MICs is an attractive choice for existing SPH codes on multi-core CPUs parallelized by OpenMP, as it gains computational acceleration without the need for significant changes to the source code.
Shen, Yanfeng; Cesnik, Carlos E. S.
2016-04-01
This paper presents a parallelized modeling technique for the efficient simulation of nonlinear ultrasonics introduced by the wave interaction with fatigue cracks. The elastodynamic wave equations with contact effects are formulated using an explicit Local Interaction Simulation Approach (LISA). The LISA formulation is extended to capture the contact-impact phenomena during the wave damage interaction based on the penalty method. A Coulomb friction model is integrated into the computation procedure to capture the stick-slip contact shear motion. The LISA procedure is coded using the Compute Unified Device Architecture (CUDA), which enables the highly parallelized supercomputing on powerful graphic cards. Both the explicit contact formulation and the parallel feature facilitates LISA's superb computational efficiency over the conventional finite element method (FEM). The theoretical formulations based on the penalty method is introduced and a guideline for the proper choice of the contact stiffness is given. The convergence behavior of the solution under various contact stiffness values is examined. A numerical benchmark problem is used to investigate the new LISA formulation and results are compared with a conventional contact finite element solution. Various nonlinear ultrasonic phenomena are successfully captured using this contact LISA formulation, including the generation of nonlinear higher harmonic responses. Nonlinear mode conversion of guided waves at fatigue cracks is also studied.
International Nuclear Information System (INIS)
Adelmann, Andreas; Gsell, Achim; Oswald, Benedikt; Schietinger, Thomas; Bethel, Wes; Shalf, John; Siegerist, Cristina; Stockinger, Kurt
2007-01-01
Significant problems facing all experimental and computational sciences arise from growing data size and complexity. Common to all these problems is the need to perform efficient data I/O on diverse computer architectures. In our scientific application, the largest parallel particle simulations generate vast quantities of six-dimensional data. Such a simulation run produces data for an aggregate data size up to several TB per run. Motivated by the need to address data I/O and access challenges, we have implemented H5Part, an open source data I/O API that simplifies the use of the Hierarchical Data Format v5 library (HDF5). HDF5 is an industry standard for high performance, cross-platform data storage and retrieval that runs on all contemporary architectures from large parallel supercomputers to laptops. H5Part, which is oriented to the needs of the particle physics and cosmology communities, provides support for parallel storage and retrieval of particles, structured and in the future unstructured meshes. In this paper, we describe recent work focusing on I/O support for particles and structured meshes and provide data showing performance on modern supercomputer architectures like the IBM POWER 5
International Nuclear Information System (INIS)
Trinitis, C; Schulz, M
2006-01-01
In today's world, the use of parallel programming and architectures is essential for simulating practical problems in engineering and related disciplines. Remarkable progress in CPU architecture, system scalability, and interconnect technology continues to provide new opportunities, as well as new challenges for both system architects and software developers. These trends are paralleled by progress in parallel algorithms, simulation techniques, and software integration from multiple disciplines. ParSim brings together researchers from both application disciplines and computer science and aims at fostering closer cooperation between these fields. Since its successful introduction in 2002, ParSim has established itself as an integral part of the EuroPVM/MPI conference series. In contrast to traditional conferences, emphasis is put on the presentation of up-to-date results with a short turn-around time. This offers a unique opportunity to present new aspects in this dynamic field and discuss them with a wide, interdisciplinary audience. The EuroPVM/MPI conference series, as one of the prime events in parallel computation, serves as an ideal surrounding for ParSim. This combination enables the participants to present and discuss their work within the scope of both the session and the host conference. This year, eleven papers from authors in nine countries were submitted to ParSim, and we selected five of them. They cover a wide range of different application fields including gas flow simulations, thermo-mechanical processes in nuclear waste storage, and cosmological simulations. At the same time, the selected contributions also address the computer science side of their codes and discuss different parallelization strategies, programming models and languages, as well as the use nonblocking collective operations in MPI. We are confident that this provides an attractive program and that ParSim will be an informal setting for lively discussions and for fostering new
International Nuclear Information System (INIS)
Pang, Kar Mun; Ng, Hoon Kiat; Gan, Suyin
2012-01-01
Highlights: ► A performance benchmarking exercise is conducted for diesel combustion simulations. ► The reduced chemical mechanism shows its advantages over base and skeletal models. ► High efficiency and great reduction of CPU runtime are achieved through 4-node solver. ► Increasing ISAT memory from 0.1 to 2 GB reduces the CPU runtime by almost 35%. ► Combustion and soot processes are predicted well with minimal computational cost. - Abstract: In the present study, in-cylinder diesel combustion simulation was performed with parallel processing on an Intel Xeon Quad-Core platform to allow both fluid dynamics and chemical kinetics of the surrogate diesel fuel model to be solved simultaneously on multiple processors. Here, Cartesian Z-Coordinate was selected as the most appropriate partitioning algorithm since it computationally bisects the domain such that the dynamic load associated with fuel particle tracking was evenly distributed during parallel computations. Other variables examined included number of compute nodes, chemistry sizes and in situ adaptive tabulation (ISAT) parameters. Based on the performance benchmarking test conducted, parallel configuration of 4-compute node was found to reduce the computational runtime most efficiently whereby a parallel efficiency of up to 75.4% was achieved. The simulation results also indicated that accuracy level was insensitive to the number of partitions or the partitioning algorithms. The effect of reducing the number of species on computational runtime was observed to be more significant than reducing the number of reactions. Besides, the study showed that an increase in the ISAT maximum storage of up to 2 GB reduced the computational runtime by 50%. Also, the ISAT error tolerance of 10 −3 was chosen to strike a balance between results accuracy and computational runtime. The optimised parameters in parallel processing and ISAT, as well as the use of the in-house reduced chemistry model allowed accurate
De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers
Energy Technology Data Exchange (ETDEWEB)
Nakano, A; Kalia, R K; Nomura, K; Sharma, A; Vashishta, P; Shimojo, F; van Duin, A; Goddard, III, W A; Biswas, R; Srivastava, D; Yang, L H
2006-09-04
We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and geographically distributed clusters. In this framework, high-end chemically reactive and non-reactive molecular dynamics (MD) simulations explore a wide solution space to discover microscopic mechanisms that govern macroscopic material properties, into which highly accurate quantum mechanical (QM) simulations are embedded to validate the discovered mechanisms and quantify the uncertainty of the solution. The framework includes an embedded divide-and-conquer (EDC) algorithmic framework for the design of linear-scaling simulation algorithms with minimal bandwidth complexity and tight error control. The EDC framework also enables adaptive hierarchical simulation with automated model transitioning assisted by graph-based event tracking. A tunable hierarchical cellular decomposition parallelization framework then maps the O(N) EDC algorithms onto Petaflops computers, while achieving performance tunability through a hierarchy of parameterized cell data/computation structures, as well as its implementation using hybrid Grid remote procedure call + message passing + threads programming. High-end computing platforms such as IBM BlueGene/L, SGI Altix 3000 and the NSF TeraGrid provide an excellent test grounds for the framework. On these platforms, we have achieved unprecedented scales of quantum-mechanically accurate and well validated, chemically reactive atomistic simulations--1.06 billion-atom fast reactive force-field MD and 11.8 million-atom (1.04 trillion grid points) quantum-mechanical MD in the framework of the EDC density functional theory on adaptive multigrids--in addition to 134 billion-atom non-reactive space-time multiresolution MD, with the parallel efficiency as high as 0.998 on 65,536 dual-processor BlueGene/L nodes. We have also achieved an automated execution of hierarchical QM
Directory of Open Access Journals (Sweden)
Mark James Abraham
2015-09-01
Full Text Available GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules. It provides a rich set of calculation types, preparation and analysis tools. Several advanced techniques for free-energy calculations are supported. In version 5, it reaches new performance heights, through several new and enhanced parallelization algorithms. These work on every level; SIMD registers inside cores, multithreading, heterogeneous CPU–GPU acceleration, state-of-the-art 3D domain decomposition, and ensemble-level parallelization through built-in replica exchange and the separate Copernicus framework. The latest best-in-class compressed trajectory storage format is supported.
Parallel Beam Dynamics Simulation Tools for Future Light Source Linac Modeling
International Nuclear Information System (INIS)
Qiang, Ji; Pogorelov, Ilya v.; Ryne, Robert D.
2007-01-01
Large-scale modeling on parallel computers is playing an increasingly important role in the design of future light sources. Such modeling provides a means to accurately and efficiently explore issues such as limits to beam brightness, emittance preservation, the growth of instabilities, etc. Recently the IMPACT codes suite was enhanced to be applicable to future light source design. Simulations with IMPACT-Z were performed using up to one billion simulation particles for the main linac of a future light source to study the microbunching instability. Combined with the time domain code IMPACT-T, it is now possible to perform large-scale start-to-end linac simulations for future light sources, including the injector, main linac, chicanes, and transfer lines. In this paper we provide an overview of the IMPACT code suite, its key capabilities, and recent enhancements pertinent to accelerator modeling for future linac-based light sources
Xyce parallel electronic simulator design : mathematical formulation, version 2.0.
Energy Technology Data Exchange (ETDEWEB)
Hoekstra, Robert John; Waters, Lon J.; Hutchinson, Scott Alan; Keiter, Eric Richard; Russo, Thomas V.
2004-06-01
This document is intended to contain a detailed description of the mathematical formulation of Xyce, a massively parallel SPICE-style circuit simulator developed at Sandia National Laboratories. The target audience of this document are people in the role of 'service provider'. An example of such a person would be a linear solver expert who is spending a small fraction of his time developing solver algorithms for Xyce. Such a person probably is not an expert in circuit simulation, and would benefit from an description of the equations solved by Xyce. In this document, modified nodal analysis (MNA) is described in detail, with a number of examples. Issues that are unique to circuit simulation, such as voltage limiting, are also described in detail.
Multiphysics pore-scale model for the rehydration of porous foods
Sman, van der R.G.M.; Vergeldt, F.J.; As, van H.; Dalen, van G.; Voda, A.; Duynhoven, van J.P.M.
2014-01-01
In this paper we present a pore-scale model describing the multiphysics occurring during the rehydration of freeze-dried vegetables. This pore-scale model is part of a multiscale simulation model, which should explain the effect of microstructure and pre-treatments on the rehydration rate.
Validation of a 3D multi-physics model for unidirectional silicon solidification
Simons, P.; Lankhorst, A.M.; Habraken, A.; Faber, A.J.; Tiuleanu, D.; Pingel, R.
2012-01-01
A model for transient movements of solidification fronts has been added to X-stream, an existing multi-physics simulation program for high temperature processes with flow and chemical reactions. The implementation uses an enthalpy formulation and works on fixed grids. First we show the results of a
Xyce Parallel Electronic Simulator Users' Guide Version 6.6.
Energy Technology Data Exchange (ETDEWEB)
Keiter, Eric R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Aadithya, Karthik Venkatraman [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Mei, Ting [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Russo, Thomas V. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Schiek, Richard [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Sholander, Peter E. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Thornquist, Heidi K. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Verley, Jason [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)
2016-11-01
This manual describes the use of the Xyce Parallel Electronic Simulator. Xyce has been de- signed as a SPICE-compatible, high-performance analog circuit simulator, and has been written to support the simulation needs of the Sandia National Laboratories electrical designers. This development has focused on improving capability over the current state-of-the-art in the following areas: Capability to solve extremely large circuit problems by supporting large-scale parallel com- puting platforms (up to thousands of processors). This includes support for most popular parallel and serial computers. A differential-algebraic-equation (DAE) formulation, which better isolates the device model package from solver algorithms. This allows one to develop new types of analysis without requiring the implementation of analysis-specific device models. Device models that are specifically tailored to meet Sandia's needs, including some radiation- aware devices (for Sandia users only). Object-oriented code design and implementation using modern coding practices. Xyce is a parallel code in the most general sense of the phrase -- a message passing parallel implementation -- which allows it to run efficiently a wide range of computing platforms. These include serial, shared-memory and distributed-memory parallel platforms. Attention has been paid to the specific nature of circuit-simulation problems to ensure that optimal parallel efficiency is achieved as the number of processors grows. The information herein is subject to change without notice. Copyright c 2002-2016 Sandia Corporation. All rights reserved. Acknowledgements The BSIM Group at the University of California, Berkeley developed the BSIM3, BSIM4, BSIM6, BSIM-CMG and BSIM-SOI models. The BSIM3 is Copyright c 1999, Regents of the University of California. The BSIM4 is Copyright c 2006, Regents of the University of California. The BSIM6 is Copyright c 2015, Regents of the University of California. The BSIM-CMG is Copyright c
International Nuclear Information System (INIS)
Yeh, M.; Kim, J.; Khan, F.S.
1995-01-01
We present a parallel decomposition of the tight-binding fictitious Lagrangian algorithm for the Intel iPSC/860 and the Intel Paragon parallel computers. We show that it is possible to perform long simulations, of the order of 10 000 time steps, on semiconducting clusters consisting of as many as 512 atoms, on a time scale of the order of 20 h or less. We have made a very careful timing analysis of all parts of our code, and have identified the bottlenecks. We have also derived formulas which can predict the timing of our code, based on the number of processors, message passing bandwidth, floating point performance of each node, and the set up time for message passing, appropriate to the machine being used. The time of the simulation scales as the square of the number of particles, if the number of processors is made to scale linearly with the number of particles. We show that for a system as large as 512 atoms, the main bottleneck of the computation is the orthogonalization of the wave functions, which consumes about 90% of the total time of the simulation
An efficient parallel simulation of unsteady blood flows in patient-specific pulmonary artery.
Kong, Fande; Kheyfets, Vitaly; Finol, Ender; Cai, Xiao-Chuan
2018-04-01
Simulation of blood flows in the pulmonary artery provides some insight into certain diseases by examining the relationship between some continuum metrics, eg, the wall shear stress acting on the vascular endothelium, which responds to flow-induced mechanical forces by releasing vasodilators/constrictors. V. Kheyfets, in his previous work, studies numerically a patient-specific pulmonary circulation to show that decreasing wall shear stress is correlated with increasing pulmonary vascular impedance. In this paper, we develop a scalable parallel algorithm based on domain decomposition methods to investigate an unsteady model with patient-specific pulsatile waveforms as the inlet boundary condition. The unsteady model offers tremendously more information about the dynamic behavior of the flow field, but computationally speaking, the simulation is a lot more expensive since a problem which is similar to the steady-state problem has to be solved many times, and therefore, the traditional sequential approach is not suitable anymore. We show computationally that simulations using the proposed parallel approach with up to 10 000 processor cores can be obtained with much reduced compute time. This makes the technology potentially usable for the routine study of the dynamic behavior of blood flows in the pulmonary artery, in particular, the changes of the blood flows and the wall shear stress in the spatial and temporal dimensions. Copyright © 2017 John Wiley & Sons, Ltd.
A general parallelization strategy for random path based geostatistical simulation methods
Mariethoz, Grégoire
2010-07-01
The size of simulation grids used for numerical models has increased by many orders of magnitude in the past years, and this trend is likely to continue. Efficient pixel-based geostatistical simulation algorithms have been developed, but for very large grids and complex spatial models, the computational burden remains heavy. As cluster computers become widely available, using parallel strategies is a natural step for increasing the usable grid size and the complexity of the models. These strategies must profit from of the possibilities offered by machines with a large number of processors. On such machines, the bottleneck is often the communication time between processors. We present a strategy distributing grid nodes among all available processors while minimizing communication and latency times. It consists in centralizing the simulation on a master processor that calls other slave processors as if they were functions simulating one node every time. The key is to decouple the sending and the receiving operations to avoid synchronization. Centralization allows having a conflict management system ensuring that nodes being simulated simultaneously do not interfere in terms of neighborhood. The strategy is computationally efficient and is versatile enough to be applicable to all random path based simulation methods.
3-D Hybrid Simulation of Quasi-Parallel Bow Shock and Its Effects on the Magnetosphere
International Nuclear Information System (INIS)
Lin, Y.; Wang, X.Y.
2005-01-01
A three-dimensional (3-D) global-scale hybrid simulation is carried out for the structure of the quasi-parallel bow shock, in particular the foreshock waves and pressure pulses. The wave evolution and interaction with the dayside magnetosphere are discussed. It is shown that diamagnetic cavities are generated in the turbulent foreshock due to the ion beam plasma interaction, and these compressional pulses lead to strong surface perturbations at the magnetopause and Alfven waves/field line resonance in the magnetosphere
Forced-convection boiling tests performed in parallel simulated LMR fuel assemblies
International Nuclear Information System (INIS)
Rose, S.D.; Carbajo, J.J.; Levin, A.E.; Lloyd, D.B.; Montgomery, B.H.; Wantland, J.L.
1985-01-01
Forced-convection tests have been carried out using parallel simulated Liquid Metal Reactor fuel assemblies in an engineering-scale sodium loop, the Thermal-Hydraulic Out-of-Reactor Safety facility. The tests, performed under single- and two-phase conditions, have shown that for low forced-convection flow there is significant flow augmentation by thermal convection, an important phenomenon under degraded shutdown heat removal conditions in an LMR. The power and flows required for boiling and dryout to occur are much higher than decay heat levels. The experimental evidence supports analytical results that heat removal from an LMR is possible with a degraded shutdown heat removal system
Analysis of IDR(s Family of Solvers for Reservoir Simulations on Different Parallel Architectures
Directory of Open Access Journals (Sweden)
Seignole Vincent
2016-09-01
Full Text Available The present contribution consists in providing a detailed analysis of several realizations of the IDR(s family of solvers, under different facets: robustness, performance and implementation on different parallel environments in regards of sequential IDR(s resolution implementation tested through several industrial geologically and structurally coherent 3D-field case reservoir models. This work is the result of continuous efforts towards time-response improvement of Storengy’s reservoir three-dimensional simulator named Multi, dedicated to gas-storage applications.
International Nuclear Information System (INIS)
Spencer, VN
2001-01-01
An investigation has been conducted regarding the ability of clustered personal computers to improve the performance of executing software simulations for solving engineering problems. The power and utility of personal computers continues to grow exponentially through advances in computing capabilities such as newer microprocessors, advances in microchip technologies, electronic packaging, and cost effective gigabyte-size hard drive capacity. Many engineering problems require significant computing power. Therefore, the computation has to be done by high-performance computer systems that cost millions of dollars and need gigabytes of memory to complete the task. Alternately, it is feasible to provide adequate computing in the form of clustered personal computers. This method cuts the cost and size by linking (clustering) personal computers together across a network. Clusters also have the advantage that they can be used as stand-alone computers when they are not operating as a parallel computer. Parallel computing software to exploit clusters is available for computer operating systems like Unix, Windows NT, or Linux. This project concentrates on the use of Windows NT, and the Parallel Virtual Machine (PVM) system to solve an engineering dynamics problem in Fortran
Directory of Open Access Journals (Sweden)
Helio Yochihiro Fuchigami
2014-08-01
Full Text Available This article addresses the problem of minimizing makespan on two parallel flow shops with proportional processing and setup times. The setup times are separated and sequence-independent. The parallel flow shop scheduling problem is a specific case of well-known hybrid flow shop, characterized by a multistage production system with more than one machine working in parallel at each stage. This situation is very common in various kinds of companies like chemical, electronics, automotive, pharmaceutical and food industries. This work aimed to propose six Simulated Annealing algorithms, their perturbation schemes and an algorithm for initial sequence generation. This study can be classified as “applied research” regarding the nature, “exploratory” about the objectives and “experimental” as to procedures, besides the “quantitative” approach. The proposed algorithms were effective regarding the solution and computationally efficient. Results of Analysis of Variance (ANOVA revealed no significant difference between the schemes in terms of makespan. It’s suggested the use of PS4 scheme, which moves a subsequence of jobs, for providing the best percentage of success. It was also found that there is a significant difference between the results of the algorithms for each value of the proportionality factor of the processing and setup times of flow shops.
COMSOL Multiphysics Model for HLW Canister Filling
Energy Technology Data Exchange (ETDEWEB)
Kesterson, M. R. [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)
2016-04-11
The U.S. Department of Energy (DOE) is building a Tank Waste Treatment and Immobilization Plant (WTP) at the Hanford Site in Washington to remediate 55 million gallons of radioactive waste that is being temporarily stored in 177 underground tanks. Efforts are being made to increase the loading of Hanford tank wastes in glass while meeting melter lifetime expectancies and process, regulatory, and product quality requirements. Wastes containing high concentrations of Al_{2}O_{3} and Na_{2}O can contribute to nepheline (generally NaAlSiO_{4}) crystallization, which can sharply reduce the chemical durability of high level waste (HLW) glass. Nepheline crystallization can occur during slow cooling of the glass within the stainless steel canister. The purpose of this work was to develop a model that can be used to predict temperatures of the glass in a WTP HLW canister during filling and cooling. The intent of the model is to support scoping work in the laboratory. It is not intended to provide precise predictions of temperature profiles, but rather to provide a simplified representation of glass cooling profiles within a full scale, WTP HLW canister under various glass pouring rates. These data will be used to support laboratory studies for an improved understanding of the mechanisms of nepheline crystallization. The model was created using COMSOL Multiphysics, a commercially available software. The model results were compared to available experimental data, TRR-PLT-080, and were found to yield sufficient results for the scoping nature of the study. The simulated temperatures were within 60 ºC for the centerline, 0.0762m (3 inch) from centerline, and 0.2286m (9 inch) from centerline thermocouples once the thermocouples were covered with glass. The temperature difference between the experimental and simulated values reduced to 40 ºC, 4 hours after the thermocouple was covered, and down to 20 ºC, 6 hours after the thermocouple was covered
Directory of Open Access Journals (Sweden)
Lorenzo L. Pesce
2013-01-01
Full Text Available Our limited understanding of the relationship between the behavior of individual neurons and large neuronal networks is an important limitation in current epilepsy research and may be one of the main causes of our inadequate ability to treat it. Addressing this problem directly via experiments is impossibly complex; thus, we have been developing and studying medium-large-scale simulations of detailed neuronal networks to guide us. Flexibility in the connection schemas and a complete description of the cortical tissue seem necessary for this purpose. In this paper we examine some of the basic issues encountered in these multiscale simulations. We have determined the detailed behavior of two such simulators on parallel computer systems. The observed memory and computation-time scaling behavior for a distributed memory implementation were very good over the range studied, both in terms of network sizes (2,000 to 400,000 neurons and processor pool sizes (1 to 256 processors. Our simulations required between a few megabytes and about 150 gigabytes of RAM and lasted between a few minutes and about a week, well within the capability of most multinode clusters. Therefore, simulations of epileptic seizures on networks with millions of cells should be feasible on current supercomputers.
Co-simulation of Six DOF Wire Driven Parallel Mechanism Based on ADAMS and Matlab
Directory of Open Access Journals (Sweden)
Tang Aofei
2015-01-01
Full Text Available The dynamic model of the 6 DOF Wire Driven Parallel Mechanism (WDPM system is introduced. Based on MATLAB system, the simulation of the inverse dynamic model is achieved. According to the simulation result, the mechanical model for the WDPM system is reasonable. Using ADAMS system, the dynamic model of the virtual prototype is verified by the simulation analysis. The combined control model based on ADAMS/Simulink is derived. The WDPM control system is designed with MATLAB/Simulink. The torque control method is selected for the outer ring and the PD control method for the inner ring. Combined with the ADAMS control model and control law design, the interactive simulation analysis of the WDPM system is completed. According to the simulation results of the spatial circle tracking and line tracking at the end of the moving platform, the tracking error can be reduced by the designed control algorithm. The minimum tracking error is 0.2 mm to 0.3 mm. Therefore, the theoretical foundation for designing hardware systems of the WDPM control system is established.
Pesce, Lorenzo L; Lee, Hyong C; Hereld, Mark; Visser, Sid; Stevens, Rick L; Wildeman, Albert; van Drongelen, Wim
2013-01-01
Our limited understanding of the relationship between the behavior of individual neurons and large neuronal networks is an important limitation in current epilepsy research and may be one of the main causes of our inadequate ability to treat it. Addressing this problem directly via experiments is impossibly complex; thus, we have been developing and studying medium-large-scale simulations of detailed neuronal networks to guide us. Flexibility in the connection schemas and a complete description of the cortical tissue seem necessary for this purpose. In this paper we examine some of the basic issues encountered in these multiscale simulations. We have determined the detailed behavior of two such simulators on parallel computer systems. The observed memory and computation-time scaling behavior for a distributed memory implementation were very good over the range studied, both in terms of network sizes (2,000 to 400,000 neurons) and processor pool sizes (1 to 256 processors). Our simulations required between a few megabytes and about 150 gigabytes of RAM and lasted between a few minutes and about a week, well within the capability of most multinode clusters. Therefore, simulations of epileptic seizures on networks with millions of cells should be feasible on current supercomputers.
A PARALLEL MONTE CARLO CODE FOR SIMULATING COLLISIONAL N-BODY SYSTEMS
Energy Technology Data Exchange (ETDEWEB)
Pattabiraman, Bharath; Umbreit, Stefan; Liao, Wei-keng; Choudhary, Alok; Kalogera, Vassiliki; Memik, Gokhan; Rasio, Frederic A., E-mail: bharath@u.northwestern.edu [Center for Interdisciplinary Exploration and Research in Astrophysics, Northwestern University, Evanston, IL (United States)
2013-02-15
We present a new parallel code for computing the dynamical evolution of collisional N-body systems with up to N {approx} 10{sup 7} particles. Our code is based on the Henon Monte Carlo method for solving the Fokker-Planck equation, and makes assumptions of spherical symmetry and dynamical equilibrium. The principal algorithmic developments involve optimizing data structures and the introduction of a parallel random number generation scheme as well as a parallel sorting algorithm required to find nearest neighbors for interactions and to compute the gravitational potential. The new algorithms we introduce along with our choice of decomposition scheme minimize communication costs and ensure optimal distribution of data and workload among the processing units. Our implementation uses the Message Passing Interface library for communication, which makes it portable to many different supercomputing architectures. We validate the code by calculating the evolution of clusters with initial Plummer distribution functions up to core collapse with the number of stars, N, spanning three orders of magnitude from 10{sup 5} to 10{sup 7}. We find that our results are in good agreement with self-similar core-collapse solutions, and the core-collapse times generally agree with expectations from the literature. Also, we observe good total energy conservation, within {approx}< 0.04% throughout all simulations. We analyze the performance of the code, and demonstrate near-linear scaling of the runtime with the number of processors up to 64 processors for N = 10{sup 5}, 128 for N = 10{sup 6} and 256 for N = 10{sup 7}. The runtime reaches saturation with the addition of processors beyond these limits, which is a characteristic of the parallel sorting algorithm. The resulting maximum speedups we achieve are approximately 60 Multiplication-Sign , 100 Multiplication-Sign , and 220 Multiplication-Sign , respectively.
Parallel 3-D numerical simulation of dielectric barrier discharge plasma actuators
Houba, Tomas
Dielectric barrier discharge plasma actuators have shown promise in a range of applications including flow control, sterilization and ozone generation. Developing numerical models of plasma actuators is of great importance, because a high-fidelity parallel numerical model allows new design configurations to be tested rapidly. Additionally, it provides a better understanding of the plasma actuator physics which is useful for further innovation. The physics of plasma actuators is studied numerically. A loosely coupled approach is utilized for the coupling of the plasma to the neutral fluid. The state of the art in numerical plasma modeling is advanced by the development of a parallel, three-dimensional, first-principles model with detailed air chemistry. The model incorporates 7 charged species and 18 reactions, along with a solution of the electron energy equation. To the author's knowledge, a parallel three-dimensional model of a gas discharge with a detailed air chemistry model and the solution of electron energy is unique. Three representative geometries are studied using the gas discharge model. The discharge of gas between two parallel electrodes is used to validate the air chemistry model developed for the gas discharge code. The gas discharge model is then applied to the discharge produced by placing a dc powered wire and grounded plate electrodes in a channel. Finally, a three-dimensional simulation of gas discharge produced by electrodes placed inside a riblet is carried out. The body force calculated with the gas discharge model is loosely coupled with a fluid model to predict the induced flow inside the riblet.
A Pipelined and Parallel Architecture for Quantum Monte Carlo Simulations on FPGAs
Directory of Open Access Journals (Sweden)
Akila Gothandaraman
2010-01-01
Full Text Available Recent advances in Field-Programmable Gate Array (FPGA technology make reconfigurable computing using FPGAs an attractive platform for accelerating scientific applications. We develop a deeply pipelined and parallel architecture for Quantum Monte Carlo simulations using FPGAs. Quantum Monte Carlo simulations enable us to obtain the structural and energetic properties of atomic clusters. We experiment with different pipeline structures for each component of the design and develop a deeply pipelined architecture that provides the best performance in terms of achievable clock rate, while at the same time has a modest use of the FPGA resources. We discuss the details of the pipelined and generic architecture that is used to obtain the potential energy and wave function of a cluster of atoms.
Directory of Open Access Journals (Sweden)
Ravil’ Kudermetov
2018-02-01
Full Text Available Nowadays multi-core processors are installed almost in each modern workstation, but the question of these computational resources effective utilization is still a topical one. In this paper the four-point block one-step integration method is considered, the parallel algorithm of this method is proposed and the Java programmatic implementation of this algorithm is discussed. The effectiveness of the proposed algorithm is demonstrated by way of spacecraft attitude motion simulation. The results of this work can be used for practical simulation of dynamic systems that are described by ordinary differential equations. The results are also applicable to the development and debugging of computer programs that integrate the dynamic and kinematic equations of the angular motion of a rigid body.
An Optimized Parallel FDTD Topology for Challenging Electromagnetic Simulations on Supercomputers
Directory of Open Access Journals (Sweden)
Shugang Jiang
2015-01-01
Full Text Available It may not be a challenge to run a Finite-Difference Time-Domain (FDTD code for electromagnetic simulations on a supercomputer with more than 10 thousands of CPU cores; however, to make FDTD code work with the highest efficiency is a challenge. In this paper, the performance of parallel FDTD is optimized through MPI (message passing interface virtual topology, based on which a communication model is established. The general rules of optimal topology are presented according to the model. The performance of the method is tested and analyzed on three high performance computing platforms with different architectures in China. Simulations including an airplane with a 700-wavelength wingspan, and a complex microstrip antenna array with nearly 2000 elements are performed very efficiently using a maximum of 10240 CPU cores.
Parallel Beam-Beam Simulation Incorporating Multiple Bunches and Multiple Interaction Regions
Jones, F W; Pieloni, T
2007-01-01
The simulation code COMBI has been developed to enable the study of coherent beam-beam effects in the full collision scenario of the LHC, with multiple bunches interacting at multiple crossing points over many turns. The program structure and input are conceived in a general way which allows arbitrary numbers and placements of bunches and interaction points (IP's), together with procedural options for head-on and parasitic collisions (in the strong-strong sense), beam transport, statistics gathering, harmonic analysis, and periodic output of simulation data. The scale of this problem, once we go beyond the simplest case of a pair of bunches interacting once per turn, quickly escalates into the parallel computing arena, and herein we will describe the construction of an MPI-based version of COMBI able to utilize arbitrary numbers of processors to support efficient calculation of multi-bunch multi-IP interactions and transport. Implementing the parallel version did not require extensive disruption of the basic ...
Directory of Open Access Journals (Sweden)
Jiang Lei
2015-01-01
Full Text Available Direct numerical simulation (DNS of a round jet in crossflow based on lattice Boltzmann method (LBM is carried out on multi-GPU cluster. Data parallel SIMT (single instruction multiple thread characteristic of GPU matches the parallelism of LBM well, which leads to the high efficiency of GPU on the LBM solver. With present GPU settings (6 Nvidia Tesla K20M, the present DNS simulation can be completed in several hours. A grid system of 1.5 × 108 is adopted and largest jet Reynolds number reaches 3000. The jet-to-free-stream velocity ratio is set as 3.3. The jet is orthogonal to the mainstream flow direction. The validated code shows good agreement with experiments. Vortical structures of CRVP, shear-layer vortices and horseshoe vortices, are presented and analyzed based on velocity fields and vorticity distributions. Turbulent statistical quantities of Reynolds stress are also displayed. Coherent structures are revealed in a very fine resolution based on the second invariant of the velocity gradients.
Parallel Simulation of HGMS of Weakly Magnetic Nanoparticles in Irrotational Flow of Inviscid Fluid
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Kanok Hournkumnuard
2014-01-01
Full Text Available The process of high gradient magnetic separation (HGMS using a microferromagnetic wire for capturing weakly magnetic nanoparticles in the irrotational flow of inviscid fluid is simulated by using parallel algorithm developed based on openMP. The two-dimensional problem of particle transport under the influences of magnetic force and fluid flow is considered in an annular domain surrounding the wire with inner radius equal to that of the wire and outer radius equal to various multiples of wire radius. The differential equations governing particle transport are solved numerically as an initial and boundary values problem by using the finite-difference method. Concentration distribution of the particles around the wire is investigated and compared with some previously reported results and shows the good agreement between them. The results show the feasibility of accumulating weakly magnetic nanoparticles in specific regions on the wire surface which is useful for applications in biomedical and environmental works. The speedup of parallel simulation ranges from 1.8 to 21 depending on the number of threads and the domain problem size as well as the number of iterations. With the nature of computing in the application and current multicore technology, it is observed that 4–8 threads are sufficient to obtain the optimized speedup.
International Nuclear Information System (INIS)
Zhang, B.; Li, G.; Wang, W.; Shangguan, D.; Deng, L.
2015-01-01
This paper introduces the Strategy of multilevel hybrid parallelism of JCOGIN Infrastructure on Monte Carlo Particle Transport for the large-scale full-core pin-by-pin simulations. The particle parallelism, domain decomposition parallelism and MPI/OpenMP parallelism are designed and implemented. By the testing, JMCT presents the parallel scalability of JCOGIN, which reaches the parallel efficiency 80% on 120,000 cores for the pin-by-pin computation of the BEAVRS benchmark. (author)
Parallel 3D Simulation of Seismic Wave Propagation in the Structure of Nobi Plain, Central Japan
Kotani, A.; Furumura, T.; Hirahara, K.
2003-12-01
We performed large-scale parallel simulations of the seismic wave propagation to understand the complex wave behavior in the 3D basin structure of the Nobi Plain, which is one of the high population cities in central Japan. In this area, many large earthquakes occurred in the past, such as the 1891 Nobi earthquake (M8.0), the 1944 Tonankai earthquake (M7.9) and the 1945 Mikawa earthquake (M6.8). In order to mitigate the potential disasters for future earthquakes, 3D subsurface structure of Nobi Plain has recently been investigated by local governments. We referred to this model together with bouguer anomaly data to construct a detail 3D basin structure model for Nobi plain, and conducted computer simulations of ground motions. We first evaluated the ground motions for two small earthquakes (M4~5); one occurred just beneath the basin edge at west, and the other occurred at south. The ground motions from these earthquakes were well recorded by the strong motion networks; K-net, Kik-net, and seismic intensity instruments operated by local governments. We compare the observed seismograms with simulations to validate the 3D model. For the 3D simulation we sliced the 3D model into a number of layers to assign to many processors for concurrent computing. The equation of motions are solved using a high order (32nd) staggered-grid FDM in horizontal directions, and a conventional (4th-order) FDM in vertical direction with the MPI inter-processor communications between neighbor region. The simulation model is 128km by 128km by 43km, which is discritized at variable grid size of 62.5-125m in horizontal directions and of 31.25-62.5m in vertical direction. We assigned a minimum shear wave velocity is Vs=0.4km/s, at the top of the sedimentary basin. The seismic sources for the small events are approximated by double-couple point source and we simulate the seismic wave propagation at maximum frequency of 2Hz. We used the Earth Simulator (JAMSTEC, Yokohama Inst) to conduct such
Induction Heating Process Design Using COMSOL Multiphysics Software
Directory of Open Access Journals (Sweden)
Andy Triwinarko
2011-08-01
Full Text Available Induction heating is clean environmental heating process due to a non-contact heating process. There is lots of the induction heating type that be used in the home appliance but it is still new technology in Indonesia. The main interesting area of the induction heating design is the efficiency of the usage of energy and choice of the plate material. COMSOL Multiphysics Software can be used to simulate and estimate the induction heating process. Therefore, the software can be used to design the induction heating process that will have a optimum efficiency. The properties of the induction heating design were also simulated and analyzed such as effect of inductors width, inductors distance, and conductive plate material. The result was shown that the good design of induction heating must have a short width and distance inductor and used silicon carbide as material plate with high frequency controller.
Multiphysics/multiscale multifluid computations
International Nuclear Information System (INIS)
Yadigaroglu, George
2014-01-01
Regarding experimentation, interesting examples of multi-scale approaches are found: the small-scale experiments to understand the mechanisms of counter-current flow limitations (CCFL) such as the growth of instabilities on films, droplet entrainment, etc; meso-scale experiments to quantify the CCFL conditions in typical geometries such as tubes and gaps between parallel plates, and finally full-scale experimentation in a typical reactor geometry - the UPTF tests. Another example is the mixing of the atmosphere produced by plumes and jets in a reactor containment: one needs first basic turbulence information that can be obtained at the microscopic level; follow medium-scale experiments to understand the behaviour of jets and plumes; finally reactor-scale tests can be conducted in facilities such as PANDA at PSI, in Switzerland to study the phenomena at large scale
International Nuclear Information System (INIS)
Kiviniemi, T.
2001-01-01
One of the principal problems en route to a fusion reactor is that of insufficient plasma confinement, which has lead to both theoretical and experimental research into transport processes in the parameter range relevant for fusion energy production. The neoclassical theory of tokamak transport is well-established unlike the theory of turbulence driven anomalous transport in which extensive progress has been made during last few years. So far, anomalous transport has been dominant in experiments, but transport may be reduced to the neoclassical level in advanced tokamak scenarios. This thesis reports a numerical study of neoclassical fluxes, parallel viscosity, and neoclassical radial current balance in tokamaks. Neoclassical parallel viscosity and particle fluxes are simulated over a wide range of collisionalities, using the fully kinetic five-dimensional neoclassical orbit-following Monte Carlo code ASCOT. The qualitative behavior of parallel viscosity derived in earlier analytic models is shown to be incorrect for high poloidal Mach numbers. This is because the poloidal dependence of density was neglected. However, in high Mach number regime, it is the convection and compression terms, rather than the parallel viscosity term, that are shown to dominate the momentum balance. For fluxes, a reasonable agreement between numerical and analytical results is found in the collisional parameter regime. Neoclassical particle fluxes are additionally studied in the banana regime using the three-dimensional Fokker-Planck code DEPORA, which solves the drift-kinetic equation with finite differencing. Limitations of the small inverse aspect ratio approximation adopted in the analytic theory are addressed. Assuming that the anomalous transport is ambipolar, the radial electric field and its shear at the tokamak plasma edge can be solved from the neoclassical radial current balance. This is performed both for JET and ASDEX Upgrade tokamaks using the ASCOT code. It is shown that
Multiphysical Testing of Soils and Shales
Ferrari, Alessio
2013-01-01
Significant advancements in the experimental analysis of soils and shales have been achieved during the last few decades. Outstanding progress in the field has led to the theoretical development of geomechanical theories and important engineering applications. This book provides the reader with an overview of recent advances in a variety of advanced experimental techniques and results for the analysis of the behaviour of geomaterials under multiphysical testing conditions. Modern trends in experimental geomechanics for soils and shales are discussed, including testing materials in variably saturated conditions, non-isothermal experiments, micro-scale investigations and image analysis techniques. Six theme papers from leading researchers in experimental geomechanics are also included. This book is intended for postgraduate students, researchers and practitioners in fields where multiphysical testing of soils and shales plays a fundamental role, such as unsaturated soil and rock mechanics, petroleum engineering...
Investigating Darcy-scale assumptions by means of a multiphysics algorithm
Tomin, Pavel; Lunati, Ivan
2016-09-01
Multiphysics (or hybrid) algorithms, which couple Darcy and pore-scale descriptions of flow through porous media in a single numerical framework, are usually employed to decrease the computational cost of full pore-scale simulations or to increase the accuracy of pure Darcy-scale simulations when a simple macroscopic description breaks down. Despite the massive increase in available computational power, the application of these techniques remains limited to core-size problems and upscaling remains crucial for practical large-scale applications. In this context, the Hybrid Multiscale Finite Volume (HMsFV) method, which constructs the macroscopic (Darcy-scale) problem directly by numerical averaging of pore-scale flow, offers not only a flexible framework to efficiently deal with multiphysics problems, but also a tool to investigate the assumptions used to derive macroscopic models and to better understand the relationship between pore-scale quantities and the corresponding macroscale variables. Indeed, by direct comparison of the multiphysics solution with a reference pore-scale simulation, we can assess the validity of the closure assumptions inherent to the multiphysics algorithm and infer the consequences for macroscopic models at the Darcy scale. We show that the definition of the scale ratio based on the geometric properties of the porous medium is well justified only for single-phase flow, whereas in case of unstable multiphase flow the nonlinear interplay between different forces creates complex fluid patterns characterized by new spatial scales, which emerge dynamically and weaken the scale-separation assumption. In general, the multiphysics solution proves very robust even when the characteristic size of the fluid-distribution patterns is comparable with the observation length, provided that all relevant physical processes affecting the fluid distribution are considered. This suggests that macroscopic constitutive relationships (e.g., the relative
Integration of Advanced Probabilistic Analysis Techniques with Multi-Physics Models
Energy Technology Data Exchange (ETDEWEB)
Cetiner, Mustafa Sacit; none,; Flanagan, George F. [ORNL; Poore III, Willis P. [ORNL; Muhlheim, Michael David [ORNL
2014-07-30
An integrated simulation platform that couples probabilistic analysis-based tools with model-based simulation tools can provide valuable insights for reactive and proactive responses to plant operating conditions. The objective of this work is to demonstrate the benefits of a partial implementation of the Small Modular Reactor (SMR) Probabilistic Risk Assessment (PRA) Detailed Framework Specification through the coupling of advanced PRA capabilities and accurate multi-physics plant models. Coupling a probabilistic model with a multi-physics model will aid in design, operations, and safety by providing a more accurate understanding of plant behavior. This represents the first attempt at actually integrating these two types of analyses for a control system used for operations, on a faster than real-time basis. This report documents the development of the basic communication capability to exchange data with the probabilistic model using Reliability Workbench (RWB) and the multi-physics model using Dymola. The communication pathways from injecting a fault (i.e., failing a component) to the probabilistic and multi-physics models were successfully completed. This first version was tested with prototypic models represented in both RWB and Modelica. First, a simple event tree/fault tree (ET/FT) model was created to develop the software code to implement the communication capabilities between the dynamic-link library (dll) and RWB. A program, written in C#, successfully communicates faults to the probabilistic model through the dll. A systems model of the Advanced Liquid-Metal Reactor–Power Reactor Inherently Safe Module (ALMR-PRISM) design developed under another DOE project was upgraded using Dymola to include proper interfaces to allow data exchange with the control application (ConApp). A program, written in C+, successfully communicates faults to the multi-physics model. The results of the example simulation were successfully plotted.
Efficient graph-based dynamic load-balancing for parallel large-scale agent-based traffic simulation
Xu, Y.; Cai, W.; Aydt, H.; Lees, M.; Tolk, A.; Diallo, S.Y.; Ryzhov, I.O.; Yilmaz, L.; Buckley, S.; Miller, J.A.
2014-01-01
One of the issues of parallelizing large-scale agent-based traffic simulations is partitioning and load-balancing. Traffic simulations are dynamic applications where the distribution of workload in the spatial domain constantly changes. Dynamic load-balancing at run-time has shown better efficiency
Accelerating Dust Storm Simulation by Balancing Task Allocation in Parallel Computing Environment
Gui, Z.; Yang, C.; XIA, J.; Huang, Q.; YU, M.
2013-12-01
Dust storm has serious negative impacts on environment, human health, and assets. The continuing global climate change has increased the frequency and intensity of dust storm in the past decades. To better understand and predict the distribution, intensity and structure of dust storm, a series of dust storm models have been developed, such as Dust Regional Atmospheric Model (DREAM), the NMM meteorological module (NMM-dust) and Chinese Unified Atmospheric Chemistry Environment for Dust (CUACE/Dust). The developments and applications of these models have contributed significantly to both scientific research and our daily life. However, dust storm simulation is a data and computing intensive process. Normally, a simulation for a single dust storm event may take several days or hours to run. It seriously impacts the timeliness of prediction and potential applications. To speed up the process, high performance computing is widely adopted. By partitioning a large study area into small subdomains according to their geographic location and executing them on different computing nodes in a parallel fashion, the computing performance can be significantly improved. Since spatiotemporal correlations exist in the geophysical process of dust storm simulation, each subdomain allocated to a node need to communicate with other geographically adjacent subdomains to exchange data. Inappropriate allocations may introduce imbalance task loads and unnecessary communications among computing nodes. Therefore, task allocation method is the key factor, which may impact the feasibility of the paralleling. The allocation algorithm needs to carefully leverage the computing cost and communication cost for each computing node to minimize total execution time and reduce overall communication cost for the entire system. This presentation introduces two algorithms for such allocation and compares them with evenly distributed allocation method. Specifically, 1) In order to get optimized solutions, a
International Nuclear Information System (INIS)
Satake, Shinsuke; Okamoto, Masao; Nakajima, Noriyoshi; Takamaru, Hisanori
2005-11-01
A neoclassical transport simulation code (FORTEC-3D) applicable to three-dimensional configurations has been developed using High Performance Fortran (HPF). Adoption of computing techniques for parallelization and a hybrid simulation model to the δf Monte-Carlo method transport simulation, including non-local transport effects in three-dimensional configurations, makes it possible to simulate the dynamism of global, non-local transport phenomena with a self-consistent radial electric field within a reasonable computation time. In this paper, development of the transport code using HPF is reported. Optimization techniques in order to achieve both high vectorization and parallelization efficiency, adoption of a parallel random number generator, and also benchmark results, are shown. (author)
Romano, Paul Kollath
Monte Carlo particle transport methods are being considered as a viable option for high-fidelity simulation of nuclear reactors. While Monte Carlo methods offer several potential advantages over deterministic methods, there are a number of algorithmic shortcomings that would prevent their immediate adoption for full-core analyses. In this thesis, algorithms are proposed both to ameliorate the degradation in parallel efficiency typically observed for large numbers of processors and to offer a means of decomposing large tally data that will be needed for reactor analysis. A nearest-neighbor fission bank algorithm was proposed and subsequently implemented in the OpenMC Monte Carlo code. A theoretical analysis of the communication pattern shows that the expected cost is O( N ) whereas traditional fission bank algorithms are O(N) at best. The algorithm was tested on two supercomputers, the Intrepid Blue Gene/P and the Titan Cray XK7, and demonstrated nearly linear parallel scaling up to 163,840 processor cores on a full-core benchmark problem. An algorithm for reducing network communication arising from tally reduction was analyzed and implemented in OpenMC. The proposed algorithm groups only particle histories on a single processor into batches for tally purposes---in doing so it prevents all network communication for tallies until the very end of the simulation. The algorithm was tested, again on a full-core benchmark, and shown to reduce network communication substantially. A model was developed to predict the impact of load imbalances on the performance of domain decomposed simulations. The analysis demonstrated that load imbalances in domain decomposed simulations arise from two distinct phenomena: non-uniform particle densities and non-uniform spatial leakage. The dominant performance penalty for domain decomposition was shown to come from these physical effects rather than insufficient network bandwidth or high latency. The model predictions were verified with
A package of Linux scripts for the parallelization of Monte Carlo simulations
Badal, Andreu; Sempau, Josep
2006-09-01
Despite the fact that fast computers are nowadays available at low cost, there are many situations where obtaining a reasonably low statistical uncertainty in a Monte Carlo (MC) simulation involves a prohibitively large amount of time. This limitation can be overcome by having recourse to parallel computing. Most tools designed to facilitate this approach require modification of the source code and the installation of additional software, which may be inconvenient for some users. We present a set of tools, named clonEasy, that implement a parallelization scheme of a MC simulation that is free from these drawbacks. In clonEasy, which is designed to run under Linux, a set of "clone" CPUs is governed by a "master" computer by taking advantage of the capabilities of the Secure Shell (ssh) protocol. Any Linux computer on the Internet that can be ssh-accessed by the user can be used as a clone. A key ingredient for the parallel calculation to be reliable is the availability of an independent string of random numbers for each CPU. Many generators—such as RANLUX, RANECU or the Mersenne Twister—can readily produce these strings by initializing them appropriately and, hence, they are suitable to be used with clonEasy. This work was primarily motivated by the need to find a straightforward way to parallelize PENELOPE, a code for MC simulation of radiation transport that (in its current 2005 version) employs the generator RANECU, which uses a combination of two multiplicative linear congruential generators (MLCGs). Thus, this paper is focused on this class of generators and, in particular, we briefly present an extension of RANECU that increases its period up to ˜5×10 and we introduce seedsMLCG, a tool that provides the information necessary to initialize disjoint sequences of an MLCG to feed different CPUs. This program, in combination with clonEasy, allows to run PENELOPE in parallel easily, without requiring specific libraries or significant alterations of the
Hybrid parallel strategy for the simulation of fast transient accidental situations at reactor scale
International Nuclear Information System (INIS)
Faucher, V.; Galon, P.; Beccantini, A.; Crouzet, F.; Debaud, F.; Gautier, T.
2015-01-01
Highlights: • Reference accidental situations for current and future reactors are considered. • They require the modeling of complex fluid–structure systems at full reactor scale. • EPX software computes the non-linear transient solution with explicit time stepping. • Focus on the parallel hybrid solver specific to the proposed coupled equations. - Abstract: This contribution is dedicated to the latest methodological developments implemented in the fast transient dynamics software EUROPLEXUS (EPX) to simulate the mechanical response of fully coupled fluid–structure systems to accidental situations to be considered at reactor scale, among which the Loss of Coolant Accident, the Core Disruptive Accident and the Hydrogen Explosion. Time integration is explicit and the search for reference solutions within the safety framework prevents any simplification and approximations in the coupled algorithm: for instance, all kinematic constraints are dealt with using Lagrange Multipliers, yielding a complex flow chart when non-permanent constraints such as unilateral contact or immersed fluid–structure boundaries are considered. The parallel acceleration of the solution process is then achieved through a hybrid approach, based on a weighted domain decomposition for distributed memory computing and the use of the KAAPI library for self-balanced shared memory processing inside subdomains
Wang, Ting; Plecháč, Petr
2017-12-01
Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.
Hardware and software and machine-tool simulation with parallel structures mechanisms
Directory of Open Access Journals (Sweden)
Keba P.V.
2016-12-01
Full Text Available The usage spectrum of mechanisms with parallel structure is spreading all the time. The mechanisms of machine-tools and manipulators become more complicated and it is necessary to improve the program-controlled modules. Closed circuit mechanisms are mostly spread in robotic complexes, where manipulator performs complicated spatial movements by the given trajectory. The usage spectrum is very wide and the most popular are sorting, welding, assembling and others. However, the problem of designing the operating programs is still present even today. It is just because the developed post-processors are created for the equipment that we have for now. But new machine tool constructions appear every day and there is a necessity to control them. The problems associated with using of hardware and software of mechanisms with parallel structure in computer-aided simulation are considered. The program for inverse problem kinematics solving is designed. New method of designing the control programs is found. The kinematic analysis methods options and calculated data obtained by computer mathematics systems are shown with «Tools Glide» software taken as an example.
Wang, Ting; Plecháč, Petr
2017-12-21
Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.
Parallel Adjective High-Order CFD Simulations Characterizing SOFIA Cavity Acoustics
Barad, Michael F.; Brehm, Christoph; Kiris, Cetin C.; Biswas, Rupak
2016-01-01
This paper presents large-scale MPI-parallel computational uid dynamics simulations for the Stratospheric Observatory for Infrared Astronomy (SOFIA). SOFIA is an airborne, 2.5-meter infrared telescope mounted in an open cavity in the aft fuselage of a Boeing 747SP. These simulations focus on how the unsteady ow eld inside and over the cavity interferes with the optical path and mounting structure of the telescope. A temporally fourth-order accurate Runge-Kutta, and spatially fth-order accurate WENO- 5Z scheme was used to perform implicit large eddy simulations. An immersed boundary method provides automated gridding for complex geometries and natural coupling to a block-structured Cartesian adaptive mesh re nement framework. Strong scaling studies using NASA's Pleiades supercomputer with up to 32k CPU cores and 4 billion compu- tational cells shows excellent scaling. Dynamic load balancing based on execution time on individual AMR blocks addresses irregular numerical cost associated with blocks con- taining boundaries. Limits to scaling beyond 32k cores are identi ed, and targeted code optimizations are discussed.
Experiences with serial and parallel algorithms for channel routing using simulated annealing
Brouwer, Randall Jay
1988-01-01
Two algorithms for channel routing using simulated annealing are presented. Simulated annealing is an optimization methodology which allows the solution process to back up out of local minima that may be encountered by inappropriate selections. By properly controlling the annealing process, it is very likely that the optimal solution to an NP-complete problem such as channel routing may be found. The algorithm presented proposes very relaxed restrictions on the types of allowable transformations, including overlapping nets. By freeing that restriction and controlling overlap situations with an appropriate cost function, the algorithm becomes very flexible and can be applied to many extensions of channel routing. The selection of the transformation utilizes a number of heuristics, still retaining the pseudorandom nature of simulated annealing. The algorithm was implemented as a serial program for a workstation, and a parallel program designed for a hypercube computer. The details of the serial implementation are presented, including many of the heuristics used and some of the resulting solutions.
Yasuda, Shugo; Yamamoto, Ryoichi
2015-11-01
The Synchronized Molecular-Dynamics simulation which was recently proposed by authors is applied to the analysis of polymer lubrication between parallel plates. In the SMD method, the MD simulations are assigned to small fluid elements to calculate the local stresses and temperatures and are synchronized at certain time intervals to satisfy the macroscopic heat- and momentum-transport equations.The rheological properties and conformation of the polymer chains coupled with local viscous heating are investigated with a non-dimensional parameter, the Nahme-Griffith number, which is defined as the ratio of the viscous heating to the thermal conduction at the characteristic temperature required to sufficiently change the viscosity. The present simulation demonstrates that strong shear thinning and a transitional behavior of the conformation of the polymer chains are exhibited with a rapid temperature rise when the Nahme-Griffith number exceeds unity.The results also clarify that the reentrant transition of the linear stress-optical relation occurs for large shear stresses due to the coupling of the conformation of polymer chains with heat generation under shear flows. This study was financially supported by JSPS KAKENHI Grant Nos. 26790080 and 26247069.
Baumgärtel, M.; Ghanem, K.; Kiani, A.; Koch, E.; Pavarini, E.; Sims, H.; Zhang, G.
2017-07-01
We discuss the efficient implementation of general impurity solvers for dynamical mean-field theory. We show that both Lanczos and quantum Monte Carlo in different flavors (Hirsch-Fye, continuous-time hybridization- and interaction-expansion) exhibit excellent scaling on massively parallel supercomputers. We apply these algorithms to simulate realistic model Hamiltonians including the full Coulomb vertex, crystal-field splitting, and spin-orbit interaction. We discuss how to remove the sign problem in the presence of non-diagonal crystal-field and hybridization matrices. We show how to extract the physically observable quantities from imaginary time data, in particular correlation functions and susceptibilities. Finally, we present benchmarks and applications for representative correlated systems.
Parallel CFD simulation of flow in a 3D model of vibrating human vocal folds
Czech Academy of Sciences Publication Activity Database
Šidlof, Petr; Horáček, Jaromír; Řidký, V.
2013-01-01
Roč. 80, č. 1 (2013), s. 290-300 ISSN 0045-7930 R&D Projects: GA ČR(CZ) GAP101/11/0207 Institutional research plan: CEZ:AV0Z20760514 Keywords : numerical simulation * vocal folds * glottal airflow * inite volume method * parallel CFD Subject RIV: BI - Acoustics Impact factor: 1.532, year: 2013 http://www.sciencedirect.com/science?_ob=ArticleListURL&_method=list&_ArticleListID=-268060849&_sort=r&_st=13&view=c&_acct=C000034318&_version=1&_urlVersion=0&_userid=640952&md5=7c5b5539857ee9a02af5e690585b3126&searchtype=a
Hybrid parallel strategy for the simulation of fast transient accidental situations at reactor scale
International Nuclear Information System (INIS)
Faucher, V.; Galon, P.; Beccantini, A.; Crouzet, F.; Debaud, F.; Gautier, T.
2013-01-01
This contribution is dedicated to the latest methodological developments implemented in the fast transient dynamics software EUROPLEXUS (EPX) to simulate the mechanical response of fully coupled fluid-structure systems to accidental situations to be considered at reactor scale, among which the Loss of Coolant Accident, the Core Disruptive Accident and the Hydrogen Explosion. Time integration is explicit and the search for reference solutions within the safety framework prevents any simplification and approximations in the coupled algorithm: for instance, all kinematic constraints are dealt with using Lagrange Multipliers, yielding a complex flow chart when non-permanent constraints such as unilateral contact or immersed fluid-structure boundaries are considered. The parallel acceleration of the solution process is then achieved through a hybrid approach, based on a weighted domain decomposition for distributed memory computing and the use of the KAAPI library for self-balanced shared memory processing inside sub-domains. (authors)
Directory of Open Access Journals (Sweden)
Řidký Václav
2014-03-01
Full Text Available The work is devoted to 3D and 2D parallel numerical computation of pressure and velocity fields around an elastically supported airfoil self-oscillating due to interaction with the airflow. Numerical solution is computed in the OpenFOAM package, an open-source software package based on finite volume method. Movement of airfoil is described by translation and rotation, identified from experimental data. A new boundary condition for the 2DOF motion of the airfoil was implemented. The results of numerical simulations (velocity are compared with data measured in a wind tunnel, where a physical model of NACA0015 airfoil was mounted and tuned to exhibit the flutter instability. The experimental results were obtained previously in the Institute of Thermomechanics by interferographic measurements in a subsonic wind tunnel in Nový Knín.
Tirapu Azpiroz, Jaione; Burr, Geoffrey W.; Rosenbluth, Alan E.; Hibbs, Michael
2008-03-01
In the Hyper-NA immersion lithography regime, the electromagnetic response of the reticle is known to deviate in a complicated manner from the idealized Thin-Mask-like behavior. Already, this is driving certain RET choices, such as the use of polarized illumination and the customization of reticle film stacks. Unfortunately, full 3-D electromagnetic mask simulations are computationally intensive. And while OPC-compatible mask electromagnetic field (EMF) models can offer a reasonable tradeoff between speed and accuracy for full-chip OPC applications, full understanding of these complex physical effects demands higher accuracy. Our paper describes recent advances in leveraging High Performance Computing as a critical step towards lithographic modeling of the full manufacturing process. In this paper, highly accurate full 3-D electromagnetic simulation of very large mask layouts are conducted in parallel with reasonable turnaround time, using a Blue- Gene/L supercomputer and a Finite-Difference Time-Domain (FDTD) code developed internally within IBM. A 3-D simulation of a large 2-D layout spanning 5μm×5μm at the wafer plane (and thus (20μm×20μm×0.5μm at the mask) results in a simulation with roughly 12.5GB of memory (grid size of 10nm at the mask, single-precision computation, about 30 bytes/grid point). FDTD is flexible and easily parallelizable to enable full simulations of such large layout in approximately an hour using one BlueGene/L "midplane" containing 512 dual-processor nodes with 256MB of memory per processor. Our scaling studies on BlueGene/L demonstrate that simulations up to 100μm × 100μm at the mask can be computed in a few hours. Finally, we will show that the use of a subcell technique permits accurate simulation of features smaller than the grid discretization, thus improving on the tradeoff between computational complexity and simulation accuracy. We demonstrate the correlation of the real and quadrature components that comprise the
Directory of Open Access Journals (Sweden)
Gianni Castelli
2010-01-01
Full Text Available This paper presents results on the modelling, simulation and experimental tests of a cable-based parallel manipulator to be used as an aiding or guiding system for people with motion disabilities. There is a high level of motivation for people with a motion disability or the elderly to perform basic daily-living activities independently. Therefore, it is of great interest to design and implement safe and reliable motion assisting and guiding devices that are able to help end-users. In general, a robot for a medical application should be able to interact with a patient in safety conditions, i.e. it must not damage people or surroundings; it must be designed to guarantee high accuracy and low acceleration during the operation. Furthermore, it should not be too bulky and it should exert limited wrenches after close interaction with people. It can be advisable to have a portable system which can be easily brought into and assembled in a hospital or a domestic environment. Cable-based robotic structures can fulfil those requirements because of their main characteristics that make them light and intrinsically safe. In this paper, a reconfigurable four-cable-based parallel manipulator has been proposed as a motion assisting and guiding device to help people to accomplish a number of tasks, such as an aiding or guiding system to move the upper and lower limbs or the whole body. Modelling and simulation are presented in the ADAMS environment. Moreover, experimental tests are reported as based on an available laboratory prototype.
Unterkircher, A
2005-01-01
We propose methods for parallel assembling and iterative equation solving based on graph algorithms. The assembling technique is independent of dimension, element type and model shape. As a parallel solving technique we construct a multiplicative symmetric Schwarz preconditioner for the conjugate gradient method. Both methods have been incorporated into a non-linear FE code to simulate 3D metal extrusion processes. We illustrate the efficiency of these methods on shared memory computers by realistic examples.
International Nuclear Information System (INIS)
Hwang, F-N; Wei, Z-H; Huang, T-M; Wang Weichung
2010-01-01
We develop a parallel Jacobi-Davidson approach for finding a partial set of eigenpairs of large sparse polynomial eigenvalue problems with application in quantum dot simulation. A Jacobi-Davidson eigenvalue solver is implemented based on the Portable, Extensible Toolkit for Scientific Computation (PETSc). The eigensolver thus inherits PETSc's efficient and various parallel operations, linear solvers, preconditioning schemes, and easy usages. The parallel eigenvalue solver is then used to solve higher degree polynomial eigenvalue problems arising in numerical simulations of three dimensional quantum dots governed by Schroedinger's equations. We find that the parallel restricted additive Schwarz preconditioner in conjunction with a parallel Krylov subspace method (e.g. GMRES) can solve the correction equations, the most costly step in the Jacobi-Davidson algorithm, very efficiently in parallel. Besides, the overall performance is quite satisfactory. We have observed near perfect superlinear speedup by using up to 320 processors. The parallel eigensolver can find all target interior eigenpairs of a quintic polynomial eigenvalue problem with more than 32 million variables within 12 minutes by using 272 Intel 3.0 GHz processors.
Modular ORIGEN-S for multi-physics code systems
International Nuclear Information System (INIS)
Yesilyurt, Gokhan; Clarno, Kevin T.; Gauld, Ian C.; Galloway, Jack
2011-01-01
The ORIGEN-S code in the SCALE 6.0 nuclear analysis code suite is a well-validated tool to calculate the time-dependent concentrations of nuclides due to isotopic depletion, decay, and transmutation for many systems in a wide range of time scales. Application areas include nuclear reactor and spent fuel storage analyses, burnup credit evaluations, decay heat calculations, and environmental assessments. Although simple to use within the SCALE 6.0 code system, especially with the ORIGEN-ARP graphical user interface, it is generally complex to use as a component within an externally developed code suite because of its tight coupling within the infrastructure of the larger SCALE 6.0 system. The ORIGEN2 code, which has been widely integrated within other simulation suites, is no longer maintained by Oak Ridge National Laboratory (ORNL), has obsolete data, and has a relatively small validation database. Therefore, a modular version of the SCALE/ORIGEN-S code was developed to simplify its integration with other software packages to allow multi-physics nuclear code systems to easily incorporate the well-validated isotopic depletion, decay, and transmutation capability to perform realistic nuclear reactor and fuel simulations. SCALE/ORIGEN-S was extensively restructured to develop a modular version that allows direct access to the matrix solvers embedded in the code. Problem initialization and the solver were segregated to provide a simple application program interface and fewer input/output operations for the multi-physics nuclear code systems. Furthermore, new interfaces were implemented to access and modify the ORIGEN-S input variables and nuclear cross-section data through external drivers. Three example drivers were implemented, in the C, C++, and Fortran 90 programming languages, to demonstrate the modular use of the new capability. This modular version of SCALE/ORIGEN-S has been embedded within several multi-physics software development projects at ORNL, including
Modular ORIGEN-S for multi-physics code systems
Energy Technology Data Exchange (ETDEWEB)
Yesilyurt, Gokhan; Clarno, Kevin T.; Gauld, Ian C., E-mail: yesilyurtg@ornl.gov, E-mail: clarnokt@ornl.gov, E-mail: gauldi@ornl.gov [Oak Ridge National Laboratory, TN (United States); Galloway, Jack, E-mail: jack@galloways.net [Los Alamos National Laboratory, Los Alamos, NM (United States)
2011-07-01
The ORIGEN-S code in the SCALE 6.0 nuclear analysis code suite is a well-validated tool to calculate the time-dependent concentrations of nuclides due to isotopic depletion, decay, and transmutation for many systems in a wide range of time scales. Application areas include nuclear reactor and spent fuel storage analyses, burnup credit evaluations, decay heat calculations, and environmental assessments. Although simple to use within the SCALE 6.0 code system, especially with the ORIGEN-ARP graphical user interface, it is generally complex to use as a component within an externally developed code suite because of its tight coupling within the infrastructure of the larger SCALE 6.0 system. The ORIGEN2 code, which has been widely integrated within other simulation suites, is no longer maintained by Oak Ridge National Laboratory (ORNL), has obsolete data, and has a relatively small validation database. Therefore, a modular version of the SCALE/ORIGEN-S code was developed to simplify its integration with other software packages to allow multi-physics nuclear code systems to easily incorporate the well-validated isotopic depletion, decay, and transmutation capability to perform realistic nuclear reactor and fuel simulations. SCALE/ORIGEN-S was extensively restructured to develop a modular version that allows direct access to the matrix solvers embedded in the code. Problem initialization and the solver were segregated to provide a simple application program interface and fewer input/output operations for the multi-physics nuclear code systems. Furthermore, new interfaces were implemented to access and modify the ORIGEN-S input variables and nuclear cross-section data through external drivers. Three example drivers were implemented, in the C, C++, and Fortran 90 programming languages, to demonstrate the modular use of the new capability. This modular version of SCALE/ORIGEN-S has been embedded within several multi-physics software development projects at ORNL, including
Multiphysics Numerical Modeling of a Fin and Tube Heat Exchanger
DEFF Research Database (Denmark)
Singh, Shobhana; Sørensen, Kim; Condra, Thomas Joseph
2015-01-01
In the present research work, a modeling effort to predict the performance of a liquid-gas type fin and tube heat exchanger design is made. Three dimensional (3D) steady state numerical model is developed using commercial software COMSOL Multiphysics based on finite element method (FEM......). For the purposes here, only gas flowing over the fin side is simulated assuming constant inner tube wall temperature. The study couples conjugate heat transfer mechanism with turbulent flow in order to describe the temperature and velocity profile. In addition, performance characteristics of the heat exchanger...... design in terms of heat transfer and pressure loss are determined by parameters such as overall heat transfer coefficient, Colburn j-factor, flow resistance factor, and efficiency index. The model provides useful insights necessary for optimization of heat exchanger design....
Chang, Ouliang
The objective of this dissertation is to study the physics of whistler turbulence evolution and its role in energy transport and dissipation in the solar wind plasmas through computational and theoretical investigations. This dissertation presents the first fully three-dimensional (3D) particle-in-cell (PIC) simulations of whistler turbulence forward cascade in a homogeneous, collisionless plasma with a uniform background magnetic field B o, and the first 3D PIC simulation of whistler turbulence with both forward and inverse cascades. Such computationally demanding research is made possible through the use of massively parallel, high performance electromagnetic PIC simulations on state-of-the-art supercomputers. Simulations are carried out to study characteristic properties of whistler turbulence under variable solar wind fluctuation amplitude (epsilon e) and electron beta (betae), relative contributions to energy dissipation and electron heating in whistler turbulence from the quasilinear scenario and the intermittency scenario, and whistler turbulence preferential cascading direction and wavevector anisotropy. The 3D simulations of whistler turbulence exhibit a forward cascade of fluctuations into broadband, anisotropic, turbulent spectrum at shorter wavelengths with wavevectors preferentially quasi-perpendicular to B o. The overall electron heating yields T ∥ > T⊥ for all epsilone and betae values, indicating the primary linear wave-particle interaction is Landau damping. But linear wave-particle interactions play a minor role in shaping the wavevector spectrum, whereas nonlinear wave-wave interactions are overall stronger and faster processes, and ultimately determine the wavevector anisotropy. Simulated magnetic energy spectra as function of wavenumber show a spectral break to steeper slopes, which scales as k⊥lambda e ≃ 1 independent of betae values, where lambdae is electron inertial length, qualitatively similar to solar wind observations. Specific
Energy Technology Data Exchange (ETDEWEB)
Peyroux, J
2005-11-15
This project aims to make even more powerful the resolution of Vlasov codes through the various parallelization tools (MPI, OpenMP...). A simplified test case served as a base for constructing the parallel codes for obtaining a data-processing skeleton which, thereafter, could be re-used for increasingly complex models (more than four variables of phase space). This will thus make it possible to treat more realistic situations linked, for example, to the injection of ultra short and ultra intense impulses in inertial fusion plasmas, or the study of the instability of trapped ions now taken as being responsible for the generation of turbulence in tokamak plasmas. (author)
Energy Technology Data Exchange (ETDEWEB)
Peyroux, J
2005-11-15
This project aims to make even more powerful the resolution of Vlasov codes through the various parallelization tools (MPI, OpenMP...). A simplified test case served as a base for constructing the parallel codes for obtaining a data-processing skeleton which, thereafter, could be re-used for increasingly complex models (more than four variables of phase space). This will thus make it possible to treat more realistic situations linked, for example, to the injection of ultra short and ultra intense impulses in inertial fusion plasmas, or the study of the instability of trapped ions now taken as being responsible for the generation of turbulence in tokamak plasmas. (author)
A Global Sensitivity Analysis Methodology for Multi-physics Applications
Energy Technology Data Exchange (ETDEWEB)
Tong, C H; Graziani, F R
2007-02-02
Experiments are conducted to draw inferences about an entire ensemble based on a selected number of observations. This applies to both physical experiments as well as computer experiments, the latter of which are performed by running the simulation models at different input configurations and analyzing the output responses. Computer experiments are instrumental in enabling model analyses such as uncertainty quantification and sensitivity analysis. This report focuses on a global sensitivity analysis methodology that relies on a divide-and-conquer strategy and uses intelligent computer experiments. The objective is to assess qualitatively and/or quantitatively how the variabilities of simulation output responses can be accounted for by input variabilities. We address global sensitivity analysis in three aspects: methodology, sampling/analysis strategies, and an implementation framework. The methodology consists of three major steps: (1) construct credible input ranges; (2) perform a parameter screening study; and (3) perform a quantitative sensitivity analysis on a reduced set of parameters. Once identified, research effort should be directed to the most sensitive parameters to reduce their uncertainty bounds. This process is repeated with tightened uncertainty bounds for the sensitive parameters until the output uncertainties become acceptable. To accommodate the needs of multi-physics application, this methodology should be recursively applied to individual physics modules. The methodology is also distinguished by an efficient technique for computing parameter interactions. Details for each step will be given using simple examples. Numerical results on large scale multi-physics applications will be available in another report. Computational techniques targeted for this methodology have been implemented in a software package called PSUADE.
Byun, Hye Suk; El-Naggar, Mohamed Y.; Kalia, Rajiv K.; Nakano, Aiichiro; Vashishta, Priya
2017-10-01
Kinetic Monte Carlo (KMC) simulations are used to study long-time dynamics of a wide variety of systems. Unfortunately, the conventional KMC algorithm is not scalable to larger systems, since its time scale is inversely proportional to the simulated system size. A promising approach to resolving this issue is the synchronous parallel KMC (SPKMC) algorithm, which makes the time scale size-independent. This paper introduces a formal derivation of the SPKMC algorithm based on local transition-state and time-dependent Hartree approximations, as well as its scalable parallel implementation based on a dual linked-list cell method. The resulting algorithm has achieved a weak-scaling parallel efficiency of 0.935 on 1024 Intel Xeon processors for simulating biological electron transfer dynamics in a 4.2 billion-heme system, as well as decent strong-scaling parallel efficiency. The parallel code has been used to simulate a lattice of cytochrome complexes on a bacterial-membrane nanowire, and it is broadly applicable to other problems such as computational synthesis of new materials.
Borazjani, Iman; Ge, Liang; Le, Trung; Sotiropoulos, Fotis
2013-01-01
We develop an overset-curvilinear immersed boundary (overset-CURVIB) method in a general non-inertial frame of reference to simulate a wide range of challenging biological flow problems. The method incorporates overset-curvilinear grids to efficiently handle multi-connected geometries and increase the resolution locally near immersed boundaries. Complex bodies undergoing arbitrarily large deformations may be embedded within the overset-curvilinear background grid and treated as sharp interfaces using the curvilinear immersed boundary (CURVIB) method (Ge and Sotiropoulos, Journal of Computational Physics, 2007). The incompressible flow equations are formulated in a general non-inertial frame of reference to enhance the overall versatility and efficiency of the numerical approach. Efficient search algorithms to identify areas requiring blanking, donor cells, and interpolation coefficients for constructing the boundary conditions at grid interfaces of the overset grid are developed and implemented using efficient parallel computing communication strategies to transfer information among sub-domains. The governing equations are discretized using a second-order accurate finite-volume approach and integrated in time via an efficient fractional-step method. Various strategies for ensuring globally conservative interpolation at grid interfaces suitable for incompressible flow fractional step methods are implemented and evaluated. The method is verified and validated against experimental data, and its capabilities are demonstrated by simulating the flow past multiple aquatic swimmers and the systolic flow in an anatomic left ventricle with a mechanical heart valve implanted in the aortic position. PMID:23833331
A scalable fully implicit framework for reservoir simulation on parallel computers
Yang, Haijian
2017-11-10
The modeling of multiphase fluid flow in porous medium is of interest in the field of reservoir simulation. The promising numerical methods in the literature are mostly based on the explicit or semi-implicit approach, which both have certain stability restrictions on the time step size. In this work, we introduce and study a scalable fully implicit solver for the simulation of two-phase flow in a porous medium with capillarity, gravity and compressibility, which is free from the limitations of the conventional methods. In the fully implicit framework, a mixed finite element method is applied to discretize the model equations for the spatial terms, and the implicit Backward Euler scheme with adaptive time stepping is used for the temporal integration. The resultant nonlinear system arising at each time step is solved in a monolithic way by using a Newton–Krylov type method. The corresponding linear system from the Newton iteration is large sparse, nonsymmetric and ill-conditioned, consequently posing a significant challenge to the fully implicit solver. To address this issue, the family of additive Schwarz preconditioners is taken into account to accelerate the convergence of the linear system, and thereby improves the robustness of the outer Newton method. Several test cases in one, two and three dimensions are used to validate the correctness of the scheme and examine the performance of the newly developed algorithm on parallel computers.
Massively parallel Monte Carlo. Experiences running nuclear simulations on a large condor cluster
International Nuclear Information System (INIS)
Tickner, James; O'Dwyer, Joel; Roach, Greg; Uher, Josef; Hitchen, Greg
2010-01-01
The trivially-parallel nature of Monte Carlo (MC) simulations make them ideally suited for running on a distributed, heterogeneous computing environment. We report on the setup and operation of a large, cycle-harvesting Condor computer cluster, used to run MC simulations of nuclear instruments ('jobs') on approximately 4,500 desktop PCs. Successful operation must balance the competing goals of maximizing the availability of machines for running jobs whilst minimizing the impact on users' PC performance. This requires classification of jobs according to anticipated run-time and priority and careful optimization of the parameters used to control job allocation to host machines. To maximize use of a large Condor cluster, we have created a powerful suite of tools to handle job submission and analysis, as the manual creation, submission and evaluation of large numbers (hundred to thousands) of jobs would be too arduous. We describe some of the key aspects of this suite, which has been interfaced to the well-known MCNP and EGSnrc nuclear codes and our in-house PHOTON optical MC code. We report on our practical experiences of operating our Condor cluster and present examples of several large-scale instrument design problems that have been solved using this tool. (author)
Behrens, Jörg; Hanke, Moritz; Jahns, Thomas
2014-05-01
In this talk we present a way to facilitate efficient use of MPI communication for developers of climate models. Exploitation of the performance potential of today's highly parallel supercomputers with real world simulations is a complex task. This is partly caused by the low level nature of the MPI communication library which is the dominant communication tool at least for inter-node communication. In order to manage the complexity of the task, climate simulations with non-trivial communication patterns often use an internal abstraction layer above MPI without exploiting the benefits of communication aggregation or MPI-datatypes. The solution for the complexity and performance problem we propose is the communication library YAXT. This library is built on top of MPI and takes high level descriptions of arbitrary domain decompositions and automatically derives an efficient collective data exchange. Several exchanges can be aggregated in order to reduce latency costs. Examples are given which demonstrate the simplicity and the performance gains for selected climate applications.
Two-phase flow steam generator simulations on parallel computers using domain decomposition method
International Nuclear Information System (INIS)
Belliard, M.
2003-01-01
Within the framework of the Domain Decomposition Method (DDM), we present industrial steady state two-phase flow simulations of PWR Steam Generators (SG) using iteration-by-sub-domain methods: standard and Adaptive Dirichlet/Neumann methods (ADN). The averaged mixture balance equations are solved by a Fractional-Step algorithm, jointly with the Crank-Nicholson scheme and the Finite Element Method. The algorithm works with overlapping or non-overlapping sub-domains and with conforming or nonconforming meshing. Computations are run on PC networks or on massively parallel mainframe computers. A CEA code-linker and the PVM package are used (master-slave context). SG mock-up simulations, involving up to 32 sub-domains, highlight the efficiency (speed-up, scalability) and the robustness of the chosen approach. With the DDM, the computational problem size is easily increased to about 1,000,000 cells and the CPU time is significantly reduced. The difficulties related to industrial use are also discussed. (author)
A scalable fully implicit framework for reservoir simulation on parallel computers
Yang, Haijian; Sun, Shuyu; Li, Yiteng; Yang, Chao
2017-01-01
The modeling of multiphase fluid flow in porous medium is of interest in the field of reservoir simulation. The promising numerical methods in the literature are mostly based on the explicit or semi-implicit approach, which both have certain stability restrictions on the time step size. In this work, we introduce and study a scalable fully implicit solver for the simulation of two-phase flow in a porous medium with capillarity, gravity and compressibility, which is free from the limitations of the conventional methods. In the fully implicit framework, a mixed finite element method is applied to discretize the model equations for the spatial terms, and the implicit Backward Euler scheme with adaptive time stepping is used for the temporal integration. The resultant nonlinear system arising at each time step is solved in a monolithic way by using a Newton–Krylov type method. The corresponding linear system from the Newton iteration is large sparse, nonsymmetric and ill-conditioned, consequently posing a significant challenge to the fully implicit solver. To address this issue, the family of additive Schwarz preconditioners is taken into account to accelerate the convergence of the linear system, and thereby improves the robustness of the outer Newton method. Several test cases in one, two and three dimensions are used to validate the correctness of the scheme and examine the performance of the newly developed algorithm on parallel computers.
Automated integration of genomic physical mapping data via parallel simulated annealing
Energy Technology Data Exchange (ETDEWEB)
Slezak, T.
1994-06-01
The Human Genome Center at the Lawrence Livermore National Laboratory (LLNL) is nearing closure on a high-resolution physical map of human chromosome 19. We have build automated tools to assemble 15,000 fingerprinted cosmid clones into 800 contigs with minimal spanning paths identified. These islands are being ordered, oriented, and spanned by a variety of other techniques including: Fluorescence Insitu Hybridization (FISH) at 3 levels of resolution, ECO restriction fragment mapping across all contigs, and a multitude of different hybridization and PCR techniques to link cosmid, YAC, AC, PAC, and Pl clones. The FISH data provide us with partial order and distance data as well as orientation. We made the observation that map builders need a much rougher presentation of data than do map readers; the former wish to see raw data since these can expose errors or interesting biology. We further noted that by ignoring our length and distance data we could simplify our problem into one that could be readily attacked with optimization techniques. The data integration problem could then be seen as an M x N ordering of our N cosmid clones which ``intersect`` M larger objects by defining ``intersection`` to mean either contig/map membership or hybridization results. Clearly, the goal of making an integrated map is now to rearrange the N cosmid clone ``columns`` such that the number of gaps on the object ``rows`` are minimized. Our FISH partially-ordered cosmid clones provide us with a set of constraints that cannot be violated by the rearrangement process. We solved the optimization problem via simulated annealing performed on a network of 40+ Unix machines in parallel, using a server/client model built on explicit socket calls. For current maps we can create a map in about 4 hours on the parallel net versus 4+ days on a single workstation. Our biologists are now using this software on a daily basis to guide their efforts toward final closure.
3D streamers simulation in a pin to plane configuration using massively parallel computing
Plewa, J.-M.; Eichwald, O.; Ducasse, O.; Dessante, P.; Jacobs, C.; Renon, N.; Yousfi, M.
2018-03-01
This paper concerns the 3D simulation of corona discharge using high performance computing (HPC) managed with the message passing interface (MPI) library. In the field of finite volume methods applied on non-adaptive mesh grids and in the case of a specific 3D dynamic benchmark test devoted to streamer studies, the great efficiency of the iterative R&B SOR and BiCGSTAB methods versus the direct MUMPS method was clearly demonstrated in solving the Poisson equation using HPC resources. The optimization of the parallelization and the resulting scalability was undertaken as a function of the HPC architecture for a number of mesh cells ranging from 8 to 512 million and a number of cores ranging from 20 to 1600. The R&B SOR method remains at least about four times faster than the BiCGSTAB method and requires significantly less memory for all tested situations. The R&B SOR method was then implemented in a 3D MPI parallelized code that solves the classical first order model of an atmospheric pressure corona discharge in air. The 3D code capabilities were tested by following the development of one, two and four coplanar streamers generated by initial plasma spots for 6 ns. The preliminary results obtained allowed us to follow in detail the formation of the tree structure of a corona discharge and the effects of the mutual interactions between the streamers in terms of streamer velocity, trajectory and diameter. The computing time for 64 million of mesh cells distributed over 1000 cores using the MPI procedures is about 30 min ns-1, regardless of the number of streamers.
Revealing the Physics of Galactic Winds Through Massively-Parallel Hydrodynamics Simulations
Schneider, Evan Elizabeth
This thesis documents the hydrodynamics code Cholla and a numerical study of multiphase galactic winds. Cholla is a massively-parallel, GPU-based code designed for astrophysical simulations that is freely available to the astrophysics community. A static-mesh Eulerian code, Cholla is ideally suited to carrying out massive simulations (> 20483 cells) that require very high resolution. The code incorporates state-of-the-art hydrodynamics algorithms including third-order spatial reconstruction, exact and linearized Riemann solvers, and unsplit integration algorithms that account for transverse fluxes on multidimensional grids. Operator-split radiative cooling and a dual-energy formalism for high mach number flows are also included. An extensive test suite demonstrates Cholla's superior ability to model shocks and discontinuities, while the GPU-native design makes the code extremely computationally efficient - speeds of 5-10 million cell updates per GPU-second are typical on current hardware for 3D simulations with all of the aforementioned physics. The latter half of this work comprises a comprehensive study of the mixing between a hot, supernova-driven wind and cooler clouds representative of those observed in multiphase galactic winds. Both adiabatic and radiatively-cooling clouds are investigated. The analytic theory of cloud-crushing is applied to the problem, and adiabatic turbulent clouds are found to be mixed with the hot wind on similar timescales as the classic spherical case (4-5 t cc) with an appropriate rescaling of the cloud-crushing time. Radiatively cooling clouds survive considerably longer, and the differences in evolution between turbulent and spherical clouds cannot be reconciled with a simple rescaling. The rapid incorporation of low-density material into the hot wind implies efficient mass-loading of hot phases of galactic winds. At the same time, the extreme compression of high-density cloud material leads to long-lived but slow-moving clumps
Zaidi, H; Morel, Christian
1998-01-01
This paper describes the implementation of the Eidolon Monte Carlo program designed to simulate fully three-dimensional (3D) cylindrical positron tomographs on a MIMD parallel architecture. The original code was written in Objective-C and developed under the NeXTSTEP development environment. Different steps involved in porting the software on a parallel architecture based on PowerPC 604 processors running under AIX 4.1 are presented. Basic aspects and strategies of running Monte Carlo calculations on parallel computers are described. A linear decrease of the computing time was achieved with the number of computing nodes. The improved time performances resulting from parallelisation of the Monte Carlo calculations makes it an attractive tool for modelling photon transport in 3D positron tomography. The parallelisation paradigm used in this work is independent from the chosen parallel architecture
Scalability of Parallel Spatial Direct Numerical Simulations on Intel Hypercube and IBM SP1 and SP2
Joslin, Ronald D.; Hanebutte, Ulf R.; Zubair, Mohammad
1995-01-01
The implementation and performance of a parallel spatial direct numerical simulation (PSDNS) approach on the Intel iPSC/860 hypercube and IBM SP1 and SP2 parallel computers is documented. Spatially evolving disturbances associated with the laminar-to-turbulent transition in boundary-layer flows are computed with the PSDNS code. The feasibility of using the PSDNS to perform transition studies on these computers is examined. The results indicate that PSDNS approach can effectively be parallelized on a distributed-memory parallel machine by remapping the distributed data structure during the course of the calculation. Scalability information is provided to estimate computational costs to match the actual costs relative to changes in the number of grid points. By increasing the number of processors, slower than linear speedups are achieved with optimized (machine-dependent library) routines. This slower than linear speedup results because the computational cost is dominated by FFT routine, which yields less than ideal speedups. By using appropriate compile options and optimized library routines on the SP1, the serial code achieves 52-56 M ops on a single node of the SP1 (45 percent of theoretical peak performance). The actual performance of the PSDNS code on the SP1 is evaluated with a "real world" simulation that consists of 1.7 million grid points. One time step of this simulation is calculated on eight nodes of the SP1 in the same time as required by a Cray Y/MP supercomputer. For the same simulation, 32-nodes of the SP1 and SP2 are required to reach the performance of a Cray C-90. A 32 node SP1 (SP2) configuration is 2.9 (4.6) times faster than a Cray Y/MP for this simulation, while the hypercube is roughly 2 times slower than the Y/MP for this application. KEY WORDS: Spatial direct numerical simulations; incompressible viscous flows; spectral methods; finite differences; parallel computing.
International Nuclear Information System (INIS)
Liu, H.
1996-01-01
Computer simulations using the multi-particle code PARMELA with a three-dimensional point-by-point space charge algorithm have turned out to be very helpful in supporting injector commissioning and operations at Thomas Jefferson National Accelerator Facility (Jefferson Lab, formerly called CEBAF). However, this algorithm, which defines a typical N 2 problem in CPU time scaling, is very time-consuming when N, the number of macro-particles, is large. Therefore, it is attractive to use massively parallel processors (MPPs) to speed up the simulations. Motivated by this, the authors modified the space charge subroutine for using the MPPs of the Cray T3D. The techniques used to parallelize and optimize the code on the T3D are discussed in this paper. The performance of the code on the T3D is examined in comparison with a Parallel Vector Processing supercomputer of the Cray C90 and an HP 735/15 high-end workstation
NREL Multiphysics Modeling Tools and ISC Device for Designing Safer Li-Ion Batteries
Energy Technology Data Exchange (ETDEWEB)
Pesaran, Ahmad A.; Yang, Chuanbo
2016-03-24
The National Renewable Energy Laboratory has developed a portfolio of multiphysics modeling tools to aid battery designers better understand the response of lithium ion batteries to abusive conditions. We will discuss this portfolio, which includes coupled electrical, thermal, chemical, electrochemical, and mechanical modeling. These models can simulate the response of a cell to overheating, overcharge, mechanical deformation, nail penetration, and internal short circuit. Cell-to-cell thermal propagation modeling will be discussed.
Directory of Open Access Journals (Sweden)
Denis Becker
2016-05-01
Full Text Available Transaction level models of systems-on-chip in SystemC are commonly used in the industry to provide an early simulation environment. The SystemC standard imposes coroutine semantics for the scheduling of simulated processes, to ensure determinism and reproducibility of simulations. However, because of this, sequential implementations have, for a long time, been the only option available, and still now the reference implementation is sequential. With the increasing size and complexity of models, and the multiplication of computation cores on recent machines, the parallelization of SystemC simulations is a major research concern. There have been several proposals for SystemC parallelization, but most of them are limited to cycle-accurate models. In this paper we focus on loosely timed models, which are commonly used in the industry. We present an industrial context and show that, unfortunately, most of the existing approaches for SystemC parallelization can fundamentally not apply in this context. We support this claim with a set of measurements performed on a platform used in production at STMicroelectronics. This paper surveys existing techniques, presents a visualization and profiling tool and identifies unsolved challenges in the parallelization of SystemC models at transaction level.
Shen, Wenfeng; Wei, Daming; Xu, Weimin; Zhu, Xin; Yuan, Shizhong
2010-10-01
Biological computations like electrocardiological modelling and simulation usually require high-performance computing environments. This paper introduces an implementation of parallel computation for computer simulation of electrocardiograms (ECGs) in a personal computer environment with an Intel CPU of Core (TM) 2 Quad Q6600 and a GPU of Geforce 8800GT, with software support by OpenMP and CUDA. It was tested in three parallelization device setups: (a) a four-core CPU without a general-purpose GPU, (b) a general-purpose GPU plus 1 core of CPU, and (c) a four-core CPU plus a general-purpose GPU. To effectively take advantage of a multi-core CPU and a general-purpose GPU, an algorithm based on load-prediction dynamic scheduling was developed and applied to setting (c). In the simulation with 1600 time steps, the speedup of the parallel computation as compared to the serial computation was 3.9 in setting (a), 16.8 in setting (b), and 20.0 in setting (c). This study demonstrates that a current PC with a multi-core CPU and a general-purpose GPU provides a good environment for parallel computations in biological modelling and simulation studies. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.
A Parallel 2D Numerical Simulation of Tumor Cells Necrosis by Local Hyperthermia
International Nuclear Information System (INIS)
Reis, R F; Loureiro, F S; Lobosco, M
2014-01-01
Hyperthermia has been widely used in cancer treatment to destroy tumors. The main idea of the hyperthermia is to heat a specific region like a tumor so that above a threshold temperature the tumor cells are destroyed. This can be accomplished by many heat supply techniques and the use of magnetic nanoparticles that generate heat when an alternating magnetic field is applied has emerged as a promise technique. In the present paper, the Pennes bioheat transfer equation is adopted to model the thermal tumor ablation in the context of magnetic nanoparticles. Numerical simulations are carried out considering different injection sites for the nanoparticles in an attempt to achieve better hyperthermia conditions. Explicit finite difference method is employed to solve the equations. However, a large amount of computation is required for this purpose. Therefore, this work also presents an initial attempt to improve performance using OpenMP, a parallel programming API. Experimental results were quite encouraging: speedups around 35 were obtained on a 64-core machine
A parallel direct-forcing fictitious domain method for simulating microswimmers
Gao, Tong; Lin, Zhaowu
2017-11-01
We present a 3D parallel direct-forcing fictitious domain method for simulating swimming micro-organisms at small Reynolds numbers. We treat the motile micro-swimmers as spherical rigid particles using the ``Squirmer'' model. The particle dynamics are solved on the moving Larangian meshes that overlay upon a fixed Eulerian mesh for solving the fluid motion, and the momentum exchange between the two phases is resolved by distributing pseudo body-forces over the particle interior regions which constrain the background fictitious fluids to follow the particle movement. While the solid and fluid subproblems are solved separately, no inner-iterations are required to enforce numerical convergence. We demonstrate the accuracy and robustness of the method by comparing our results with the existing analytical and numerical studies for various cases of single particle dynamics and particle-particle interactions. We also perform a series of numerical explorations to obtain statistical and rheological measurements to characterize the dynamics and structures of Squirmer suspensions. NSF DMS 1619960.
Energy Technology Data Exchange (ETDEWEB)
Bylaska, Eric J., E-mail: Eric.Bylaska@pnnl.gov [Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352 (United States); Weare, Jonathan Q., E-mail: weare@uchicago.edu [Department of Mathematics, University of Chicago, Chicago, Illinois 60637 (United States); Weare, John H., E-mail: jweare@ucsd.edu [Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093 (United States)
2013-08-21
Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t{sub i} (trajectory positions and velocities x{sub i} = (r{sub i}, v{sub i})) to time t{sub i+1} (x{sub i+1}) by x{sub i+1} = f{sub i}(x{sub i}), the dynamics problem spanning an interval from t{sub 0}…t{sub M} can be transformed into a root finding problem, F(X) = [x{sub i} − f(x{sub (i−1})]{sub i} {sub =1,M} = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H{sub 2}O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up
International Nuclear Information System (INIS)
Bylaska, Eric J.; Weare, Jonathan Q.; Weare, John H.
2013-01-01
Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time t i (trajectory positions and velocities x i = (r i , v i )) to time t i+1 (x i+1 ) by x i+1 = f i (x i ), the dynamics problem spanning an interval from t 0 …t M can be transformed into a root finding problem, F(X) = [x i − f(x (i−1 )] i =1,M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H 2 O AIMD simulation at the MP2 level. The maximum speedup ((serial execution time)/(parallel execution time) ) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a
Design Process of IDT Aided by Multiphysics FE Analyses
Directory of Open Access Journals (Sweden)
A Martowicz
2016-09-01
Full Text Available Presented work is devoted to a design process performed for the interdigital transducer, which is a perspective application for the area of structural health monitoring. In order to obtain the desirable characteristic of the transducer fully coupled numerical analyses were performed in ANSYS Multiphysics software. Utilised finite element models considered both structural dynamics and properties of used piezoelectric material. The process of design improvement was preceded by the sensitivity analysis. In order to search for the best electrode pattern selected geometrical features of the transducer were assumed to vary within allowed ranges. The design parameters, which were taken into account, related to the efficiency of proposed transducer design for the emission of acoustic waves in the monitored structure. The search objectives considered the criteria related to the shape of the beampattern and amplitudes of generated Lamb waves. As a result of the optimization procedure, the simultaneous increase of anti-symmetric mode amplitude and the reduction of undesirable symmetric mode amplitude of generated Lamb waves in the direction perpendicular to the transducer fingers was expected. Another aim of the optimization was to minimize the main lobe width and undesirable contribution of both symmetric and anti-symmetric waves in the parallel direction to the transducer fingers. The response surface method and genetic algorithms were used for fast and effective search through the input design domain.
MaMiCo: Software design for parallel molecular-continuum flow simulations
Neumann, Philipp
2015-11-19
The macro-micro-coupling tool (MaMiCo) was developed to ease the development of and modularize molecular-continuum simulations, retaining sequential and parallel performance. We demonstrate the functionality and performance of MaMiCo by coupling the spatially adaptive Lattice Boltzmann framework waLBerla with four molecular dynamics (MD) codes: the light-weight Lennard-Jones-based implementation SimpleMD, the node-level optimized software ls1 mardyn, and the community codes ESPResSo and LAMMPS. We detail interface implementations to connect each solver with MaMiCo. The coupling for each waLBerla-MD setup is validated in three-dimensional channel flow simulations which are solved by means of a state-based coupling method. We provide sequential and strong scaling measurements for the four molecular-continuum simulations. The overhead of MaMiCo is found to come at 10%-20% of the total (MD) runtime. The measurements further show that scalability of the hybrid simulations is reached on up to 500 Intel SandyBridge, and more than 1000 AMD Bulldozer compute cores. Program summary: Program title: MaMiCo. Catalogue identifier: AEYW_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEYW_v1_0.html Program obtainable from: CPC Program Library, Queen\\'s University, Belfast, N. Ireland. Licensing provisions: BSD License. No. of lines in distributed program, including test data, etc.: 67905. No. of bytes in distributed program, including test data, etc.: 1757334. Distribution format: tar.gz. Programming language: C, C++II. Computer: Standard PCs, compute clusters. Operating system: Unix/Linux. RAM: Test cases consume ca. 30-50 MB. Classification: 7.7. External routines: Scons (http:www.scons.org), ESPResSo, LAMMPS, ls1 mardyn, waLBerla. Nature of problem: Coupled molecular-continuum simulation for multi-resolution fluid dynamics: parts of the domain are resolved by molecular dynamics whereas large parts are covered by a CFD solver, e.g. a lattice Boltzmann automaton
Curing of Thick Thermoset Composite Laminates: Multiphysics Modeling and Experiments
Anandan, S.; Dhaliwal, G. S.; Huo, Z.; Chandrashekhara, K.; Apetre, N.; Iyyer, N.
2017-11-01
Fiber reinforced polymer composites are used in high-performance aerospace applications as they are resistant to fatigue, corrosion free and possess high specific strength. The mechanical properties of these composite components depend on the degree of cure and residual stresses developed during the curing process. While these parameters are difficult to determine experimentally in large and complex parts, they can be simulated using numerical models in a cost-effective manner. These simulations can be used to develop cure cycles and change processing parameters to obtain high-quality parts. In the current work, a numerical model was built in Comsol MultiPhysics to simulate the cure behavior of a carbon/epoxy prepreg system (IM7/Cycom 5320-1). A thermal spike was observed in thick laminates when the recommended cure cycle was used. The cure cycle was modified to reduce the thermal spike and maintain the degree of cure at the laminate center. A parametric study was performed to evaluate the effect of air flow in the oven, post cure cycles and cure temperatures on the thermal spike and the resultant degree of cure in the laminate.
Parallelization of the preconditioned IDR solver for modern multicore computer systems
Bessonov, O. A.; Fedoseyev, A. I.
2012-10-01
This paper present the analysis, parallelization and optimization approach for the large sparse matrix solver CNSPACK for modern multicore microprocessors. CNSPACK is an advanced solver successfully used for coupled solution of stiff problems arising in multiphysics applications such as CFD, semiconductor transport, kinetic and quantum problems. It employs iterative IDR algorithm with ILU preconditioning (user chosen ILU preconditioning order). CNSPACK has been successfully used during last decade for solving problems in several application areas, including fluid dynamics and semiconductor device simulation. However, there was a dramatic change in processor architectures and computer system organization in recent years. Due to this, performance criteria and methods have been revisited, together with involving the parallelization of the solver and preconditioner using Open MP environment. Results of the successful implementation for efficient parallelization are presented for the most advances computer system (Intel Core i7-9xx or two-processor Xeon 55xx/56xx).
Reactive transport modeling of the ABM experiment with Comsol Multiphysics
International Nuclear Information System (INIS)
Pekala, Marek; Idiart, Andres; Arcos, David
2012-01-01
solution) in a stack of 30 bentonite blocks of 11 distinct initial compositions. In the model, ion diffusion is allowed between the individual bentonite blocks and between the bentonite blocks and a sand layer filling the bentonite-rock gap. The effective diffusion coefficient values for individual bentonite blocks were estimated based on the dry density of the bentonite, and the temperature-dependent evolution of the diffusion coefficients is approximated in the course of the simulation. In order to solve the problem, a set of non-linear algebraic equations (mass action law for the cation-exchange reactions, and charge and mass balance equations) have been coupled with Fickian diffusion equations. As mentioned above, the Finite Element code COMSOL Multiphysics has been used to carry out the simulations. Preliminary results for the studied problem indicate that the effect of diffusion for the studied cations and chloride is significant and has the potential to explain quantitatively the observed patterns of homogenisation in the chemical composition in the bentonite package. However, the work is currently in progress and further analyses, including a sensitivity study of variables such as diffusion coefficients and boundary conditions, are on-going. A model simulating coupled cation-exchange and diffusion of major ions in the Package 1 of the ABM field experiment has been developed. This work demonstrates the feasibility of implementing a reactive transport model directly into Comsol Multiphysics using conservation and mass action equations. Comsol offers an intuitive and at the same time powerful modelling environment for simulating coupled multiphase, multi-species reactive transport phenomena and mechanical effects in complex geometries. For this reason, Amphos 21 has been involved in work aiming to couple Comsol with other codes such as the geochemical code PHREEQC. Such code integration has the potential to provide tools uniquely suited to solving complicated reactive
Bylaska, Eric J; Weare, Jonathan Q; Weare, John H
2013-08-21
Parallel in time simulation algorithms are presented and applied to conventional molecular dynamics (MD) and ab initio molecular dynamics (AIMD) models of realistic complexity. Assuming that a forward time integrator, f (e.g., Verlet algorithm), is available to propagate the system from time ti (trajectory positions and velocities xi = (ri, vi)) to time ti + 1 (xi + 1) by xi + 1 = fi(xi), the dynamics problem spanning an interval from t0[ellipsis (horizontal)]tM can be transformed into a root finding problem, F(X) = [xi - f(x(i - 1)]i = 1, M = 0, for the trajectory variables. The root finding problem is solved using a variety of root finding techniques, including quasi-Newton and preconditioned quasi-Newton schemes that are all unconditionally convergent. The algorithms are parallelized by assigning a processor to each time-step entry in the columns of F(X). The relation of this approach to other recently proposed parallel in time methods is discussed, and the effectiveness of various approaches to solving the root finding problem is tested. We demonstrate that more efficient dynamical models based on simplified interactions or coarsening time-steps provide preconditioners for the root finding problem. However, for MD and AIMD simulations, such preconditioners are not required to obtain reasonable convergence and their cost must be considered in the performance of the algorithm. The parallel in time algorithms developed are tested by applying them to MD and AIMD simulations of size and complexity similar to those encountered in present day applications. These include a 1000 Si atom MD simulation using Stillinger-Weber potentials, and a HCl + 4H2O AIMD simulation at the MP2 level. The maximum speedup (serial execution/timeparallel execution time) obtained by parallelizing the Stillinger-Weber MD simulation was nearly 3.0. For the AIMD MP2 simulations, the algorithms achieved speedups of up to 14.3. The parallel in time algorithms can be implemented in a
Multiphysics modelling of manufacturing processes: A review
DEFF Research Database (Denmark)
Jabbari, Masoud; Baran, Ismet; Mohanty, Sankhya
2018-01-01
Numerical modelling is increasingly supporting the analysis and optimization of manufacturing processes in the production industry. Even if being mostly applied to multistep processes, single process steps may be so complex by nature that the needed models to describe them must include multiphysics...... the diversity in the field of modelling of manufacturing processes as regards process, materials, generic disciplines as well as length scales: (1) modelling of tape casting for thin ceramic layers, (2) modelling the flow of polymers in extrusion, (3) modelling the deformation process of flexible stamps...... for nanoimprint lithography, (4) modelling manufacturing of composite parts and (5) modelling the selective laser melting process. For all five examples, the emphasis is on modelling results as well as describing the models in brief mathematical details. Alongside with relevant references to the original work...
International Nuclear Information System (INIS)
Epelboin, Y.
1996-01-01
This paper presents a new algorithm for the integration of Takagi-Taupin equations taking into account the fact that X-ray diffraction is a parallel phenomenon. The diffraction equations show that the propagation of the waves is independent in each incidence plane. It is thus possible to compute in parallel the propagation of the waves in different planes. Two algorithms are presented: the first one for multiprocessor machines where the processors share a common memory, the second one for massively parallel computers. The program is written to achieve a high vectorization ratio and to make it as efficient as possible with modern superscalar and array processors. The simulation of the image of a defect has been divided into two independent parts. In the first one, one computes the derivatives of the deformation inside the crystal; in the second one, these results are used to simulate the image. This allows one rapidly to change the model for a defect, something that was not feasible in all previously written simulation programs since the computation of the deformation was part of the simulation. The study of stroboscopic images of the propagation of acoustic waves in piezoelectric devices is given as an example of the possibilities of this new program. (orig.)
Parallel real-time visualization system for large-scale simulation. Application to WSPEEDI
International Nuclear Information System (INIS)
Muramatsu, Kazuhiro; Otani, Takayuki; Kitabata, Hideyuki; Matsumoto, Hideki; Takei, Toshifumi; Doi, Shun
2000-01-01
The real-time visualization system, PATRAS (PArallel TRAcking Steering system) has been developed on parallel computing servers. The system performs almost all of the visualization tasks on a parallel computing server, and uses image data compression technique for efficient communication between the server and the client terminal. Therefore, the system realizes high performance concurrent visualization in an internet computing environment. The experience in applying PATRAS to WSPEEDI (Worldwide version of System for Prediction Environmental Emergency Dose Information) is reported. The application of PATRAS to WSPEEDI enables users to understand behaviours of radioactive tracers from different release points easily and quickly. (author)
Jung, Jaewoon; Mori, Takaharu; Kobayashi, Chigusa; Matsunaga, Yasuhiro; Yoda, Takao; Feig, Michael; Sugita, Yuji
2015-07-01
GENESIS (Generalized-Ensemble Simulation System) is a new software package for molecular dynamics (MD) simulations of macromolecules. It has two MD simulators, called ATDYN and SPDYN. ATDYN is parallelized based on an atomic decomposition algorithm for the simulations of all-atom force-field models as well as coarse-grained Go-like models. SPDYN is highly parallelized based on a domain decomposition scheme, allowing large-scale MD simulations on supercomputers. Hybrid schemes combining OpenMP and MPI are used in both simulators to target modern multicore computer architectures. Key advantages of GENESIS are (1) the highly parallel performance of SPDYN for very large biological systems consisting of more than one million atoms and (2) the availability of various REMD algorithms (T-REMD, REUS, multi-dimensional REMD for both all-atom and Go-like models under the NVT, NPT, NPAT, and NPγT ensembles). The former is achieved by a combination of the midpoint cell method and the efficient three-dimensional Fast Fourier Transform algorithm, where the domain decomposition space is shared in real-space and reciprocal-space calculations. Other features in SPDYN, such as avoiding concurrent memory access, reducing communication times, and usage of parallel input/output files, also contribute to the performance. We show the REMD simulation results of a mixed (POPC/DMPC) lipid bilayer as a real application using GENESIS. GENESIS is released as free software under the GPLv2 licence and can be easily modified for the development of new algorithms and molecular models. WIREs Comput Mol Sci 2015, 5:310-323. doi: 10.1002/wcms.1220.
Multiscale and Multiphysics Modeling of Additive Manufacturing of Advanced Materials
Liou, Frank; Newkirk, Joseph; Fan, Zhiqiang; Sparks, Todd; Chen, Xueyang; Fletcher, Kenneth; Zhang, Jingwei; Zhang, Yunlu; Kumar, Kannan Suresh; Karnati, Sreekar
2015-01-01
The objective of this proposed project is to research and develop a prediction tool for advanced additive manufacturing (AAM) processes for advanced materials and develop experimental methods to provide fundamental properties and establish validation data. Aircraft structures and engines demand materials that are stronger, useable at much higher temperatures, provide less acoustic transmission, and enable more aeroelastic tailoring than those currently used. Significant improvements in properties can only be achieved by processing the materials under nonequilibrium conditions, such as AAM processes. AAM processes encompass a class of processes that use a focused heat source to create a melt pool on a substrate. Examples include Electron Beam Freeform Fabrication and Direct Metal Deposition. These types of additive processes enable fabrication of parts directly from CAD drawings. To achieve the desired material properties and geometries of the final structure, assessing the impact of process parameters and predicting optimized conditions with numerical modeling as an effective prediction tool is necessary. The targets for the processing are multiple and at different spatial scales, and the physical phenomena associated occur in multiphysics and multiscale. In this project, the research work has been developed to model AAM processes in a multiscale and multiphysics approach. A macroscale model was developed to investigate the residual stresses and distortion in AAM processes. A sequentially coupled, thermomechanical, finite element model was developed and validated experimentally. The results showed the temperature distribution, residual stress, and deformation within the formed deposits and substrates. A mesoscale model was developed to include heat transfer, phase change with mushy zone, incompressible free surface flow, solute redistribution, and surface tension. Because of excessive computing time needed, a parallel computing approach was also tested. In addition
International Nuclear Information System (INIS)
Veerasingam, R.
1990-01-01
In fusion plasmas impurities such as carbon, oxygen or nickel can contaminate the plasma and cause degradation of the performance of a fusion device through radiation. However, impurities can also be used as diagnostics to obtain information about a plasma through spectroscopic experiments which can then be used in plasma modeling and simulations. In the past, serial algorithms have been described for either the time dependent or steady state problem. In this paper, we describe a parallel procedure adopted to solve the time-dependent problem. It can be shown that for the steady state problem a parallel procedure would not be a useful application of parallelization because a few seconds of the Central Processing Unit time on a CRAY-XMP or IBM 3090/600S would suffice to obtain the solution, while this is not the case for the time-dependent problem. In order to study the effects of low Z and high Z impurities on the final state of a plasma, time-dependent solutions are necessary. For purposes of diagnostics and comparisons with experiments, a fast turn around time of the simulations would be advantageous. We have implemented a parallel algorithm on and IBM 3090/600S and tested its performance for a typical set of fusion plasma parameters. 4 refs., 1 tab
Energy Technology Data Exchange (ETDEWEB)
Le Pallec, J. C.; Crouzet, N.; Bergeaud, V.; Delavaud, C. [CEA/DEN/DM2S, CEA/Saclay, 91191 Gif sur Yvette Cedex (France)
2012-07-01
The control of uncertainties in the field of reactor physics and their propagation in best-estimate modeling are a major issue in safety analysis. In this framework, the CEA develops a methodology to perform multi-physics simulations including uncertainties analysis. The present paper aims to present and apply this methodology for the analysis of an accidental situation such as REA (Rod Ejection Accident). This accident is characterized by a strong interaction between the different areas of the reactor physics (neutronic, fuel thermal and thermal hydraulic). The modeling is performed with CRONOS2 code. The uncertainties analysis has been conducted with the URANIE platform developed by the CEA: For each identified response from the modeling (output) and considering a set of key parameters with their uncertainties (input), a surrogate model in the form of a neural network has been produced. The set of neural networks is then used to carry out a sensitivity analysis which consists on a global variance analysis with the determination of the Sobol indices for all responses. The sensitivity indices are obtained for the input parameters by an approach based on the use of polynomial chaos. The present exercise helped to develop a methodological flow scheme, to consolidate the use of URANIE tool in the framework of parallel calculations. Finally, the use of polynomial chaos allowed computing high order sensitivity indices and thus highlighting and classifying the influence of identified uncertainties on each response of the analysis (single and interaction effects). (authors)
Parallel Reservoir Simulations with Sparse Grid Techniques and Applications to Wormhole Propagation
Wu, Yuanqing
2015-01-01
the traditional simulation technique relying on the Darcy framework, we propose a new framework called Darcy-Brinkman-Forchheimer framework to simulate wormhole propagation. Furthermore, to process the large quantity of cells in the simulation grid and shorten
A Massively Parallel Solver for the Mechanical Harmonic Analysis of Accelerator Cavities
International Nuclear Information System (INIS)
2015-01-01
ACE3P is a 3D massively parallel simulation suite that developed at SLAC National Accelerator Laboratory that can perform coupled electromagnetic, thermal and mechanical study. Effectively utilizing supercomputer resources, ACE3P has become a key simulation tool for particle accelerator R and D. A new frequency domain solver to perform mechanical harmonic response analysis of accelerator components is developed within the existing parallel framework. This solver is designed to determine the frequency response of the mechanical system to external harmonic excitations for time-efficient accurate analysis of the large-scale problems. Coupled with the ACE3P electromagnetic modules, this capability complements a set of multi-physics tools for a comprehensive study of microphonics in superconducting accelerating cavities in order to understand the RF response and feedback requirements for the operational reliability of a particle accelerator. (auth)
International Nuclear Information System (INIS)
Takei, Toshifumi; Doi, Shun; Matsumoto, Hideki; Muramatsu, Kazuhiro
2000-01-01
We have developed a concurrent visualization system RVSLIB (Real-time Visual Simulation Library). This paper shows the effectiveness of the system when it is applied to large-scale unsteady simulations, for which the conventional post-processing approach may no longer work, on high-performance parallel vector supercomputers. The system performs almost all of the visualization tasks on a computation server and uses compressed visualized image data for efficient communication between the server and the user terminal. We have introduced several techniques, including vectorization and parallelization, into the system to minimize the computational costs of the visualization tools. The performance of RVSLIB was evaluated by using an actual CFD code on an NEC SX-4. The computational time increase due to the concurrent visualization was at most 3% for a smaller (1.6 million) grid and less than 1% for a larger (6.2 million) one. (author)
High performance shallow water kernels for parallel overland flow simulations based on FullSWOF2D
Wittmann, Roland
2017-01-25
We describe code optimization and parallelization procedures applied to the sequential overland flow solver FullSWOF2D. Major difficulties when simulating overland flows comprise dealing with high resolution datasets of large scale areas which either cannot be computed on a single node either due to limited amount of memory or due to too many (time step) iterations resulting from the CFL condition. We address these issues in terms of two major contributions. First, we demonstrate a generic step-by-step transformation of the second order finite volume scheme in FullSWOF2D towards MPI parallelization. Second, the computational kernels are optimized by the use of templates and a portable vectorization approach. We discuss the load imbalance of the flux computation due to dry and wet cells and propose a solution using an efficient cell counting approach. Finally, scalability results are shown for different test scenarios along with a flood simulation benchmark using the Shaheen II supercomputer.
Pronk, Sander; Pouya, Iman; Lundborg, Magnus; Rotskoff, Grant; Wesén, Björn; Kasson, Peter M; Lindahl, Erik
2015-06-09
Computational chemistry and other simulation fields are critically dependent on computing resources, but few problems scale efficiently to the hundreds of thousands of processors available in current supercomputers-particularly for molecular dynamics. This has turned into a bottleneck as new hardware generations primarily provide more processing units rather than making individual units much faster, which simulation applications are addressing by increasingly focusing on sampling with algorithms such as free-energy perturbation, Markov state modeling, metadynamics, or milestoning. All these rely on combining results from multiple simulations into a single observation. They are potentially powerful approaches that aim to predict experimental observables directly, but this comes at the expense of added complexity in selecting sampling strategies and keeping track of dozens to thousands of simulations and their dependencies. Here, we describe how the distributed execution framework Copernicus allows the expression of such algorithms in generic workflows: dataflow programs. Because dataflow algorithms explicitly state dependencies of each constituent part, algorithms only need to be described on conceptual level, after which the execution is maximally parallel. The fully automated execution facilitates the optimization of these algorithms with adaptive sampling, where undersampled regions are automatically detected and targeted without user intervention. We show how several such algorithms can be formulated for computational chemistry problems, and how they are executed efficiently with many loosely coupled simulations using either distributed or parallel resources with Copernicus.
Multiphysics modelling and experimental validation of high concentration photovoltaic modules
International Nuclear Information System (INIS)
Theristis, Marios; Fernández, Eduardo F.; Sumner, Mike; O'Donovan, Tadhg S.
2017-01-01
Highlights: • A multiphysics modelling approach for concentrating photovoltaics was developed. • An experimental campaign was conducted to validate the models. • The experimental results were in good agreement with the models. • The multiphysics modelling allows the concentrator’s optimisation. - Abstract: High concentration photovoltaics, equipped with high efficiency multijunction solar cells, have great potential in achieving cost-effective and clean electricity generation at utility scale. Such systems are more complex compared to conventional photovoltaics because of the multiphysics effect that is present. Modelling the power output of such systems is therefore crucial for their further market penetration. Following this line, a multiphysics modelling procedure for high concentration photovoltaics is presented in this work. It combines an open source spectral model, a single diode electrical model and a three-dimensional finite element thermal model. In order to validate the models and the multiphysics modelling procedure against actual data, an outdoor experimental campaign was conducted in Albuquerque, New Mexico using a high concentration photovoltaic monomodule that is thoroughly described in terms of its geometry and materials. The experimental results were in good agreement (within 2.7%) with the predicted maximum power point. This multiphysics approach is relatively more complex when compared to empirical models, but besides the overall performance prediction it can also provide better understanding of the physics involved in the conversion of solar irradiance into electricity. It can therefore be used for the design and optimisation of high concentration photovoltaic modules.
Directory of Open Access Journals (Sweden)
Julián A García-Grajales
Full Text Available With the growing body of research on traumatic brain injury and spinal cord injury, computational neuroscience has recently focused its modeling efforts on neuronal functional deficits following mechanical loading. However, in most of these efforts, cell damage is generally only characterized by purely mechanistic criteria, functions of quantities such as stress, strain or their corresponding rates. The modeling of functional deficits in neurites as a consequence of macroscopic mechanical insults has been rarely explored. In particular, a quantitative mechanically based model of electrophysiological impairment in neuronal cells, Neurite, has only very recently been proposed. In this paper, we present the implementation details of this model: a finite difference parallel program for simulating electrical signal propagation along neurites under mechanical loading. Following the application of a macroscopic strain at a given strain rate produced by a mechanical insult, Neurite is able to simulate the resulting neuronal electrical signal propagation, and thus the corresponding functional deficits. The simulation of the coupled mechanical and electrophysiological behaviors requires computational expensive calculations that increase in complexity as the network of the simulated cells grows. The solvers implemented in Neurite--explicit and implicit--were therefore parallelized using graphics processing units in order to reduce the burden of the simulation costs of large scale scenarios. Cable Theory and Hodgkin-Huxley models were implemented to account for the electrophysiological passive and active regions of a neurite, respectively, whereas a coupled mechanical model accounting for the neurite mechanical behavior within its surrounding medium was adopted as a link between electrophysiology and mechanics. This paper provides the details of the parallel implementation of Neurite, along with three different application examples: a long myelinated axon
International Nuclear Information System (INIS)
Marzouk, Youssef M.; Ghoniem, Ahmed F.
2005-01-01
A number of complex physical problems can be approached through N-body simulation, from fluid flow at high Reynolds number to gravitational astrophysics and molecular dynamics. In all these applications, direct summation is prohibitively expensive for large N and thus hierarchical methods are employed for fast summation. This work introduces new algorithms, based on k-means clustering, for partitioning parallel hierarchical N-body interactions. We demonstrate that the number of particle-cluster interactions and the order at which they are performed are directly affected by partition geometry. Weighted k-means partitions minimize the sum of clusters' second moments and create well-localized domains, and thus reduce the computational cost of N-body approximations by enabling the use of lower-order approximations and fewer cells. We also introduce compatible techniques for dynamic load balancing, including adaptive scaling of cluster volumes and adaptive redistribution of cluster centroids. We demonstrate the performance of these algorithms by constructing a parallel treecode for vortex particle simulations, based on the serial variable-order Cartesian code developed by Lindsay and Krasny [Journal of Computational Physics 172 (2) (2001) 879-907]. The method is applied to vortex simulations of a transverse jet. Results show outstanding parallel efficiencies even at high concurrencies, with velocity evaluation errors maintained at or below their serial values; on a realistic distribution of 1.2 million vortex particles, we observe a parallel efficiency of 98% on 1024 processors. Excellent load balance is achieved even in the face of several obstacles, such as an irregular, time-evolving particle distribution containing a range of length scales and the continual introduction of new vortex particles throughout the domain. Moreover, results suggest that k-means yields a more efficient partition of the domain than a global oct-tree
Multiscale multiphysics and multidomain models—Flexibility and rigidity
International Nuclear Information System (INIS)
Xia, Kelin; Opron, Kristopher; Wei, Guo-Wei
2013-01-01
The emerging complexity of large macromolecules has led to challenges in their full scale theoretical description and computer simulation. Multiscale multiphysics and multidomain models have been introduced to reduce the number of degrees of freedom while maintaining modeling accuracy and achieving computational efficiency. A total energy functional is constructed to put energies for polar and nonpolar solvation, chemical potential, fluid flow, molecular mechanics, and elastic dynamics on an equal footing. The variational principle is utilized to derive coupled governing equations for the above mentioned multiphysical descriptions. Among these governing equations is the Poisson-Boltzmann equation which describes continuum electrostatics with atomic charges. The present work introduces the theory of continuum elasticity with atomic rigidity (CEWAR). The essence of CEWAR is to formulate the shear modulus as a continuous function of atomic rigidity. As a result, the dynamics complexity of a macromolecular system is separated from its static complexity so that the more time-consuming dynamics is handled with continuum elasticity theory, while the less time-consuming static analysis is pursued with atomic approaches. We propose a simple method, flexibility-rigidity index (FRI), to analyze macromolecular flexibility and rigidity in atomic detail. The construction of FRI relies on the fundamental assumption that protein functions, such as flexibility, rigidity, and energy, are entirely determined by the structure of the protein and its environment, although the structure is in turn determined by all the interactions. As such, the FRI measures the topological connectivity of protein atoms or residues and characterizes the geometric compactness of the protein structure. As a consequence, the FRI does not resort to the interaction Hamiltonian and bypasses matrix diagonalization, which underpins most other flexibility analysis methods. FRI's computational complexity is of O
International Nuclear Information System (INIS)
Lichters, R.; Pfund, R.E.W.; Meyer-ter-Vehn, J.
1997-08-01
The code LPIC++ presented here, is based on a one-dimensional, electromagnetic, relativistic PIC code that has originally been developed by one of the authors during a PhD thesis at the Max-Planck-Institut fuer Quantenoptik for kinetic simulations of high harmonic generation from overdense plasma surfaces. The code uses essentially the algorithm of Birdsall and Langdon and Villasenor and Bunemann. It is written in C++ in order to be easily extendable and has been parallelized to be able to grow in power linearly with the size of accessable hardware, e.g. massively parallel machines like Cray T3E. The parallel LPIC++ version uses PVM for communication between processors. PVM is public domain software, can be downloaded from the world wide web. A particular strength of LPIC++ lies in its clear program and data structure, which uses chained lists for the organization of grid cells and enables dynamic adjustment of spatial domain sizes in a very convenient way, and therefore easy balancing of processor loads. Also particles belonging to one cell are linked in a chained list and are immediately accessable from this cell. In addition to this convenient type of data organization in a PIC code, the code shows excellent performance in both its single processor and parallel version. (orig.)
International Nuclear Information System (INIS)
Jejcic, A.; Maillard, J.; Maurel, G.; Silva, J.; Wolff-Bacha, F.
1997-01-01
The work in the field of parallel processing has developed as research activities using several numerical Monte Carlo simulations related to basic or applied current problems of nuclear and particle physics. For the applications utilizing the GEANT code development or improvement works were done on parts simulating low energy physical phenomena like radiation, transport and interaction. The problem of actinide burning by means of accelerators was approached using a simulation with the GEANT code. A program of neutron tracking in the range of low energies up to the thermal region has been developed. It is coupled to the GEANT code and permits in a single pass the simulation of a hybrid reactor core receiving a proton burst. Other works in this field refers to simulations for nuclear medicine applications like, for instance, development of biological probes, evaluation and characterization of the gamma cameras (collimators, crystal thickness) as well as the method for dosimetric calculations. Particularly, these calculations are suited for a geometrical parallelization approach especially adapted to parallel machines of the TN310 type. Other works mentioned in the same field refer to simulation of the electron channelling in crystals and simulation of the beam-beam interaction effect in colliders. The GEANT code was also used to simulate the operation of germanium detectors designed for natural and artificial radioactivity monitoring of environment
Using cellular automata for parallel simulation of laser dynamics with dynamic load balancing
Guisado, J.L.; Fernández de Vega, F.; Jiménez Morales, F.; Iskra, K.A.; Sloot, P.M.A.
2008-01-01
We present an analysis of the feasibility of executing a parallel bioinspired model of laser dynamics, based on cellular automata (CA), on the usual target platform of this kind of applications: a heterogeneous non-dedicated cluster. As this model employs a synchronous CA, using the single program,
Convergence order vs. parallelism in the numerical simulation of the bidomain equations
International Nuclear Information System (INIS)
Sharomi, Oluwaseun; Spiteri, Raymond J
2012-01-01
The propagation of electrical activity in the human heart can be modelled mathematically by the bidomain equations. The bidomain equations represent a multi-scale reaction-diffusion model that consists of a set of ordinary differential equations governing the dynamics at the cellular level coupled with a set of partial differential equations governing the dynamics at the tissue level. Significant computation is generally required to generate clinically useful data from the bidomain equations. Contemporary developments in computer architecture, in particular multi- and many-core computers and graphics processing units, have made such computations feasible. However, the zeal to take advantage to parallel architectures has typically caused another important aspect of numerical methods for the solution of differential equations to be overlooked, namely the convergence order. It is well known that higher-order methods are generally more efficient than lower-order ones when solutions are smooth and relatively high accuracy is desired. In these situations, serial implementations of high-order methods may remain surprisingly competitive with parallel implementations of low-order methods. In this paper, we examine the effect of order on the numerical solution of the bidomain equations in parallel. We find that high-order methods, in particular high-order time-integration methods with relatively better stability properties, tend to outperform their low-order counterparts, even when the latter are run in parallel. In other words, increasing integration order often trumps increasing available computational resources, especially when relatively high accuracy is desired.
Efficient Heuristics for the Simulation of Buffer Overflow in Series and Parallel Queueing Networks
Nicola, V.F.; Zaburnenko, T.S.
2006-01-01
In this paper we propose state-dependent importance sampling heuristics to estimate the probability of population overï¬‚ow in Markovian networks of series and parallel queues. These heuristics capture state-dependence along the boundaries (when one or more queues are empty) which is critical for
Modelling and simulation of multiple single - phase induction motor in parallel connection
Directory of Open Access Journals (Sweden)
Sujitjorn, S.
2006-11-01
Full Text Available A mathematical model for parallel connected n-multiple single-phase induction motors in generalized state-space form is proposed in this paper. The motor group draws electric power from one inverter. The model is developed by the dq-frame theory and was tested against four loading scenarios in which satisfactory results were obtained.
International Nuclear Information System (INIS)
Azadeh, A.; Asadzadeh, S.M.; Salehi, N.; Firoozi, M.
2015-01-01
Condition-based maintenance (CBM) is an increasingly applicable policy in the competitive marketplace as a means of improving equipment reliability and efficiency. Not only has maintenance a close relationship with safety but its costs also make it even more attractive issue for researchers. This study proposes a model to evaluate the effectiveness of CBM policy compared to two other maintenance policies: Corrective Maintenance (CM) and Preventive Maintenance (PM). Maintenance policies are compared through two system performance indicators: reliability and cost. To estimate the reliability and costs of the system, the proposed Markovian discrete-event simulation model is developed under each of these policies. The applicability and usefulness of the proposed Markovian simulation model is illustrated for a series–parallel power generation system. The simulated characteristics of CBM system include its prognostics efficiency to estimate remaining useful life of the equipment. Results show that with an efficient prognostics, CBM policy is an effective strategy compared to other maintenance strategies. - Highlights: • A model is developed to evaluate the effectiveness of CBM policy. • Maintenance policies are compared through reliability and cost. • A Markovian simulation model is developed. • A series–parallel power generation system is considered. • CBM is an effective strategy compared to others
Directory of Open Access Journals (Sweden)
Xueli Chen
2010-01-01
Full Text Available During the past decade, Monte Carlo method has obtained wide applications in optical imaging to simulate photon transport process inside tissues. However, this method has not been effectively extended to the simulation of free-space photon transport at present. In this paper, a uniform framework for noncontact optical imaging is proposed based on Monte Carlo method, which consists of the simulation of photon transport both in tissues and in free space. Specifically, the simplification theory of lens system is utilized to model the camera lens equipped in the optical imaging system, and Monte Carlo method is employed to describe the energy transformation from the tissue surface to the CCD camera. Also, the focusing effect of camera lens is considered to establish the relationship of corresponding points between tissue surface and CCD camera. Furthermore, a parallel version of the framework is realized, making the simulation much more convenient and effective. The feasibility of the uniform framework and the effectiveness of the parallel version are demonstrated with a cylindrical phantom based on real experimental results.
O'Keeffe, C J; Ren