Wasatch: An architecture-proof multiphysics development environment using a Domain Specific Language and graph theory

DOE PAGES

Saad, Tony; Sutherland, James C.

2016-05-04

To address the coding and software challenges of modern hybrid architectures, we propose an approach to multiphysics code development for high-performance computing. This approach is based on using a Domain Specific Language (DSL) in tandem with a directed acyclic graph (DAG) representation of the problem to be solved that allows runtime algorithm generation. When coupled with a large-scale parallel framework, the result is a portable development framework capable of executing on hybrid platforms and handling the challenges of multiphysics applications. In addition, we share our experience developing a code in such an environment – an effort that spans an interdisciplinarymore » team of engineers and computer scientists.« less

A Generic Mesh Data Structure with Parallel Applications

ERIC Educational Resources Information Center

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…

Jali - Unstructured Mesh Infrastructure for Multi-Physics Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garimella, Rao V; Berndt, Markus; Coon, Ethan

2017-04-13

Jali is a parallel unstructured mesh infrastructure library designed for use by multi-physics simulations. It supports 2D and 3D arbitrary polyhedral meshes distributed over hundreds to thousands of nodes. Jali can read write Exodus II meshes along with fields and sets on the mesh and support for other formats is partially implemented or is (https://github.com/MeshToolkit/MSTK), an open source general purpose unstructured mesh infrastructure library from Los Alamos National Laboratory. While it has been made to work with other mesh frameworks such as MOAB and STKmesh in the past, support for maintaining the interface to these frameworks has been suspended formore » now. Jali supports distributed as well as on-node parallelism. Support of on-node parallelism is through direct use of the the mesh in multi-threaded constructs or through the use of "tiles" which are submeshes or sub-partitions of a partition destined for a compute node.« less

NREL Multiphysics Modeling Tools and ISC Device for Designing Safer Li-Ion Batteries

DOE Office of Scientific and Technical Information (OSTI.GOV)

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.

Multi-physics CFD simulations in engineering

NASA Astrophysics Data System (ADS)

Yamamoto, Makoto

2013-08-01

Nowadays Computational Fluid Dynamics (CFD) software is adopted as a design and analysis tool in a great number of engineering fields. We can say that single-physics CFD has been sufficiently matured in the practical point of view. The main target of existing CFD software is single-phase flows such as water and air. However, many multi-physics problems exist in engineering. Most of them consist of flow and other physics, and the interactions between different physics are very important. Obviously, multi-physics phenomena are critical in developing machines and processes. A multi-physics phenomenon seems to be very complex, and it is so difficult to be predicted by adding other physics to flow phenomenon. Therefore, multi-physics CFD techniques are still under research and development. This would be caused from the facts that processing speed of current computers is not fast enough for conducting a multi-physics simulation, and furthermore physical models except for flow physics have not been suitably established. Therefore, in near future, we have to develop various physical models and efficient CFD techniques, in order to success multi-physics simulations in engineering. In the present paper, I will describe the present states of multi-physics CFD simulations, and then show some numerical results such as ice accretion and electro-chemical machining process of a three-dimensional compressor blade which were obtained in my laboratory. Multi-physics CFD simulations would be a key technology in near future.

FleCSPH - a parallel and distributed SPH implementation based on the FleCSI framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Junghans, Christoph; Loiseau, Julien

2017-06-20

FleCSPH is a multi-physics compact application that exercises FleCSI parallel data structures for tree-based particle methods. In particular, FleCSPH implements a smoothed-particle hydrodynamics (SPH) solver for the solution of Lagrangian problems in astrophysics and cosmology. FleCSPH includes support for gravitational forces using the fast multipole method (FMM).

Multiscale and Multiphysics Modeling of Additive Manufacturing of Advanced Materials

NASA Technical Reports Server (NTRS)

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, after investigating various methods, a Smoothed Particle Hydrodynamics Model (SPH Model) was developed to model wire feeding process. Its computational efficiency and simple architecture makes it more robust and flexible than other models. More research on material properties may be needed to realistically model the AAM processes. A microscale model was developed to investigate heterogeneous nucleation, dendritic grain growth, epitaxial growth of columnar grains, columnar-to-equiaxed transition, grain transport in melt, and other properties. The orientations of the columnar grains were almost perpendicular to the laser motion's direction. Compared to the similar studies in the literature, the multiple grain morphology modeling result is in the same order of magnitude as optical morphologies in the experiment. Experimental work was conducted to validate different models. An infrared camera was incorporated as a process monitoring and validating tool to identify the solidus and mushy zones during deposition. The images were successfully processed to identify these regions. This research project has investigated multiscale and multiphysics of the complex AAM processes thus leading to advanced understanding of these processes. The project has also developed several modeling tools and experimental validation tools that will be very critical in the future of AAM process qualification and certification.

OECD-NEA Expert Group on Multi-Physics Experimental Data, Benchmarks and Validation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Valentine, Timothy; Rohatgi, Upendra S.

High-fidelity, multi-physics modeling and simulation (M&S) tools are being developed and utilized for a variety of applications in nuclear science and technology and show great promise in their abilities to reproduce observed phenomena for many applications. Even with the increasing fidelity and sophistication of coupled multi-physics M&S tools, the underpinning models and data still need to be validated against experiments that may require a more complex array of validation data because of the great breadth of the time, energy and spatial domains of the physical phenomena that are being simulated. The Expert Group on Multi-Physics Experimental Data, Benchmarks and Validationmore » (MPEBV) of the Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) was formed to address the challenges with the validation of such tools. The work of the MPEBV expert group is shared among three task forces to fulfill its mandate and specific exercises are being developed to demonstrate validation principles for common industrial challenges. This paper describes the overall mission of the group, the specific objectives of the task forces, the linkages among the task forces, and the development of a validation exercise that focuses on a specific reactor challenge problem.« less

Pika: A snow science simulation tool built using the open-source framework MOOSE

NASA Astrophysics Data System (ADS)

Slaughter, A.; Johnson, M.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase-field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture and crack propagation (via the extended finite-element method), flow in porous media, and others. The heat conduction, tensor mechanics, and phase-field modules, in particular, are well-suited for snow science problems. Pika--an open-source MOOSE-based application--is capable of simulating both 3D, coupled nonlinear continuum heat transfer and large-deformation mechanics applications (such as settlement) and phase-field based micro-structure applications. Additionally, these types of problems may be coupled tightly in a single solve or across length and time scales using a loosely coupled Picard iteration approach. In addition to the wide range of physics capabilities, MOOSE-based applications also inherit an extensible testing framework, graphical user interface, and documentation system; tools that allow MOOSE and other applications to adhere to nuclear software quality standards. The snow science community can learn from the nuclear industry and harness the existing effort to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other applications. The snow science community should build on existing tools to enable collaboration between researchers and practitioners throughout the world, and advance the state-of-the-art in line with other scientific research efforts.

Multiphysics Application Coupling Toolkit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, Michael T.

2013-12-02

This particular consortium implementation of the software integration infrastructure will, in large part, refactor portions of the Rocstar multiphysics infrastructure. Development of this infrastructure originated at the University of Illinois DOE ASCI Center for Simulation of Advanced Rockets (CSAR) to support the center's massively parallel multiphysics simulation application, Rocstar, and has continued at IllinoisRocstar, a small company formed near the end of the University-based program. IllinoisRocstar is now licensing these new developments as free, open source, in hopes to help improve their own and others' access to infrastructure which can be readily utilized in developing coupled or composite software systems;more » with particular attention to more rapid production and utilization of multiphysics applications in the HPC environment. There are two major pieces to the consortium implementation, the Application Component Toolkit (ACT), and the Multiphysics Application Coupling Toolkit (MPACT). The current development focus is the ACT, which is (will be) the substrate for MPACT. The ACT itself is built up from the components described in the technical approach. In particular, the ACT has the following major components: 1.The Component Object Manager (COM): The COM package provides encapsulation of user applications, and their data. COM also provides the inter-component function call mechanism. 2.The System Integration Manager (SIM): The SIM package provides constructs and mechanisms for orchestrating composite systems of multiply integrated pieces.« less

PRELIMINARY COUPLING OF THE MONTE CARLO CODE OPENMC AND THE MULTIPHYSICS OBJECT-ORIENTED SIMULATION ENVIRONMENT (MOOSE) FOR ANALYZING DOPPLER FEEDBACK IN MONTE CARLO SIMULATIONS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Matthew Ellis; Derek Gaston; Benoit Forget

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.more » 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.« less

Integration of Advanced Probabilistic Analysis Techniques with Multi-Physics Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cetiner, Mustafa Sacit; none,; Flanagan, George F.

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 typesmore » 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.« less

Coarse-grained component concurrency in Earth system modeling: parallelizing atmospheric radiative transfer in the GFDL AM3 model using the Flexible Modeling System coupling framework

NASA Astrophysics Data System (ADS)

Balaji, V.; Benson, Rusty; Wyman, Bruce; Held, Isaac

2016-10-01

Climate models represent a large variety of processes on a variety of timescales and space scales, a canonical example of multi-physics multi-scale modeling. Current hardware trends, such as Graphical Processing Units (GPUs) and Many Integrated Core (MIC) chips, are based on, at best, marginal increases in clock speed, coupled with vast increases in concurrency, particularly at the fine grain. Multi-physics codes face particular challenges in achieving fine-grained concurrency, as different physics and dynamics components have different computational profiles, and universal solutions are hard to come by. We propose here one approach for multi-physics codes. These codes are typically structured as components interacting via software frameworks. The component structure of a typical Earth system model consists of a hierarchical and recursive tree of components, each representing a different climate process or dynamical system. This recursive structure generally encompasses a modest level of concurrency at the highest level (e.g., atmosphere and ocean on different processor sets) with serial organization underneath. We propose to extend concurrency much further by running more and more lower- and higher-level components in parallel with each other. Each component can further be parallelized on the fine grain, potentially offering a major increase in the scalability of Earth system models. We present here first results from this approach, called coarse-grained component concurrency, or CCC. Within the Geophysical Fluid Dynamics Laboratory (GFDL) Flexible Modeling System (FMS), the atmospheric radiative transfer component has been configured to run in parallel with a composite component consisting of every other atmospheric component, including the atmospheric dynamics and all other atmospheric physics components. We will explore the algorithmic challenges involved in such an approach, and present results from such simulations. Plans to achieve even greater levels of coarse-grained concurrency by extending this approach within other components, such as the ocean, will be discussed.

Multi-Physics Modelling of Fault Mechanics Using REDBACK: A Parallel Open-Source Simulator for Tightly Coupled Problems

NASA Astrophysics Data System (ADS)

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.

MASTODON: A geosciences simulation tool built using the open-source framework MOOSE

NASA Astrophysics Data System (ADS)

Slaughter, A.

2017-12-01

The Department of Energy (DOE) is currently investing millions of dollars annually into various modeling and simulation tools for all aspects of nuclear energy. An important part of this effort includes developing applications based on the open-source Multiphysics Object Oriented Simulation Environment (MOOSE; mooseframework.org) from Idaho National Laboratory (INL).Thanks to the efforts of the DOE and outside collaborators, MOOSE currently contains a large set of physics modules, including phase field, level set, heat conduction, tensor mechanics, Navier-Stokes, fracture (extended finite-element method), and porous media, among others. The tensor mechanics and contact modules, in particular, are well suited for nonlinear geosciences problems. Multi-hazard Analysis for STOchastic time-DOmaiN phenomena (MASTODON; https://seismic-research.inl.gov/SitePages/Mastodon.aspx)--a MOOSE-based application--is capable of analyzing the response of 3D soil-structure systems to external hazards with current development focused on earthquakes. It is capable of simulating seismic events and can perform extensive "source-to-site" simulations including earthquake fault rupture, nonlinear wave propagation, and nonlinear soil-structure interaction analysis. MASTODON also includes a dynamic probabilistic risk assessment capability that enables analysts to not only perform deterministic analyses, but also easily perform probabilistic or stochastic simulations for the purpose of risk assessment. Although MASTODON has been developed for the nuclear industry, it can be used to assess the risk for any structure subjected to earthquakes.The geosciences community can learn from the nuclear industry and harness the enormous effort underway to build simulation tools that are open, modular, and share a common framework. In particular, MOOSE-based multiphysics solvers are inherently parallel, dimension agnostic, adaptive in time and space, fully coupled, and capable of interacting with other applications. The geosciences community could benefit from existing tools by enabling collaboration between researchers and practitioners throughout the world and advance the state-of-the-art in line with other scientific research efforts.

Wide-Field Imaging System and Rapid Direction of Optical Zoom (WOZ)

DTIC Science & Technology

2011-03-25

COMSOL Multiphysics, and ZEMAX optical design. The multiphysics design tool is nearing completion. We have demonstrated the ability to create a model in...and mechanical modeling to calculate the deformation resulting from the applied voltages. Finally, the deformed surface can be exported to ZEMAX via...MatLab. From ZEMAX , various analyses can be conducted to determine important parameters such as focal point, aberrations, and wavefront distortion

A Computational Framework for Efficient Low Temperature Plasma Simulations

NASA Astrophysics Data System (ADS)

Verma, Abhishek Kumar; Venkattraman, Ayyaswamy

2016-10-01

Over the past years, scientific computing has emerged as an essential tool for the investigation and prediction of low temperature plasmas (LTP) applications which includes electronics, nanomaterial synthesis, metamaterials etc. To further explore the LTP behavior with greater fidelity, we present a computational toolbox developed to perform LTP simulations. This framework will allow us to enhance our understanding of multiscale plasma phenomenon using high performance computing tools mainly based on OpenFOAM FVM distribution. Although aimed at microplasma simulations, the modular framework is able to perform multiscale, multiphysics simulations of physical systems comprises of LTP. Some salient introductory features are capability to perform parallel, 3D simulations of LTP applications on unstructured meshes. Performance of the solver is tested based on numerical results assessing accuracy and efficiency of benchmarks for problems in microdischarge devices. Numerical simulation of microplasma reactor at atmospheric pressure with hemispherical dielectric coated electrodes will be discussed and hence, provide an overview of applicability and future scope of this framework.

ParaView visualization of Abaqus output on the mechanical deformation of complex microstructures

NASA Astrophysics Data System (ADS)

Liu, Qingbin; Li, Jiang; Liu, Jie

2017-02-01

Abaqus® is a popular software suite for finite element analysis. It delivers linear and nonlinear analyses of mechanical and fluid dynamics, includes multi-body system and multi-physics coupling. However, the visualization capability of Abaqus using its CAE module is limited. Models from microtomography have extremely complicated structures, and datasets of Abaqus output are huge, requiring a visualization tool more powerful than Abaqus/CAE. We convert Abaqus output into the XML-based VTK format by developing a Python script and then using ParaView to visualize the results. Such capabilities as volume rendering, tensor glyphs, superior animation and other filters allow ParaView to offer excellent visualizing manifestations. ParaView's parallel visualization makes it possible to visualize very big data. To support full parallel visualization, the Python script achieves data partitioning by reorganizing all nodes, elements and the corresponding results on those nodes and elements. The data partition scheme minimizes data redundancy and works efficiently. Given its good readability and extendibility, the script can be extended to the processing of more different problems in Abaqus. We share the script with Abaqus users on GitHub.

The Data Transfer Kit: A geometric rendezvous-based tool for multiphysics data transfer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slattery, S. R.; Wilson, P. P. H.; Pawlowski, R. P.

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 multiphysicsmore » 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)« less

Mixed-Dimensionality VLSI-Type Configurable Tools for Virtual Prototyping of Biomicrofluidic Devices and Integrated Systems

NASA Astrophysics Data System (ADS)

Makhijani, Vinod B.; Przekwas, Andrzej J.

2002-10-01

This report presents results of a DARPA/MTO Composite CAD Project aimed to develop a comprehensive microsystem CAD environment, CFD-ACE+ Multiphysics, for bio and microfluidic devices and complete microsystems. The project began in July 1998, and was a three-year team effort between CFD Research Corporation, California Institute of Technology (CalTech), University of California, Berkeley (UCB), and Tanner Research, with Mr. Don Verlee from Abbott Labs participating as a consultant on the project. The overall objective of this project was to develop, validate and demonstrate several applications of a user-configurable VLSI-type mixed-dimensionality software tool for design of biomicrofluidics devices and integrated systems. The developed tool would provide high fidelity 3-D multiphysics modeling capability, l-D fluidic circuits modeling, and SPICE interface for system level simulations, and mixed-dimensionality design. It would combine tools for layouts and process fabrication, geometric modeling, and automated grid generation, and interfaces to EDA tools (e.g. Cadence) and MCAD tools (e.g. ProE).

The Integrated Plasma Simulator: A Flexible Python Framework for Coupled Multiphysics Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foley, Samantha S; Elwasif, Wael R; Bernholdt, David E

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 ofmore » 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.« less

AC losses in horizontally parallel HTS tapes for possible wireless power transfer applications

NASA Astrophysics Data System (ADS)

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.

ALE3D: An Arbitrary Lagrangian-Eulerian Multi-Physics Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Noble, Charles R.; Anderson, Andrew T.; Barton, Nathan R.

ALE3D is a multi-physics numerical simulation software tool utilizing arbitrary-Lagrangian- Eulerian (ALE) techniques. The code is written to address both two-dimensional (2D plane and axisymmetric) and three-dimensional (3D) physics and engineering problems using a hybrid finite element and finite volume formulation to model fluid and elastic-plastic response of materials on an unstructured grid. As shown in Figure 1, ALE3D is a single code that integrates many physical phenomena.

SHARP User Manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Y. Q.; Shemon, E. R.; Thomas, J. W.

SHARP is an advanced modeling and simulation toolkit for the analysis of nuclear reactors. It is comprised of several components including physical modeling tools, tools to integrate the physics codes for multi-physics analyses, and a set of tools to couple the codes within the MOAB framework. Physics modules currently include the neutronics code PROTEUS, the thermal-hydraulics code Nek5000, and the structural mechanics code Diablo. This manual focuses on performing multi-physics calculations with the SHARP ToolKit. Manuals for the three individual physics modules are available with the SHARP distribution to help the user to either carry out the primary multi-physics calculationmore » with basic knowledge or perform further advanced development with in-depth knowledge of these codes. This manual provides step-by-step instructions on employing SHARP, including how to download and install the code, how to build the drivers for a test case, how to perform a calculation and how to visualize the results. Since SHARP has some specific library and environment dependencies, it is highly recommended that the user read this manual prior to installing SHARP. Verification tests cases are included to check proper installation of each module. It is suggested that the new user should first follow the step-by-step instructions provided for a test problem in this manual to understand the basic procedure of using SHARP before using SHARP for his/her own analysis. Both reference output and scripts are provided along with the test cases in order to verify correct installation and execution of the SHARP package. At the end of this manual, detailed instructions are provided on how to create a new test case so that user can perform novel multi-physics calculations with SHARP. Frequently asked questions are listed at the end of this manual to help the user to troubleshoot issues.« less

Supercomputing with TOUGH2 family codes for coupled multi-physics simulations of geologic carbon sequestration

NASA Astrophysics Data System (ADS)

Yamamoto, H.; Nakajima, K.; Zhang, K.; Nanai, S.

2015-12-01

Powerful numerical codes that are capable of modeling complex coupled processes of physics and chemistry have been developed for predicting the fate of CO2 in reservoirs as well as its potential impacts on groundwater and subsurface environments. However, they are often computationally demanding for solving highly non-linear models in sufficient spatial and temporal resolutions. Geological heterogeneity and uncertainties further increase the challenges in modeling works. Two-phase flow simulations in heterogeneous media usually require much longer computational time than that in homogeneous media. Uncertainties in reservoir properties may necessitate stochastic simulations with multiple realizations. Recently, massively parallel supercomputers with more than thousands of processors become available in scientific and engineering communities. Such supercomputers may attract attentions from geoscientist and reservoir engineers for solving the large and non-linear models in higher resolutions within a reasonable time. However, for making it a useful tool, it is essential to tackle several practical obstacles to utilize large number of processors effectively for general-purpose reservoir simulators. We have implemented massively-parallel versions of two TOUGH2 family codes (a multi-phase flow simulator TOUGH2 and a chemically reactive transport simulator TOUGHREACT) on two different types (vector- and scalar-type) of supercomputers with a thousand to tens of thousands of processors. After completing implementation and extensive tune-up on the supercomputers, the computational performance was measured for three simulations with multi-million grid models, including a simulation of the dissolution-diffusion-convection process that requires high spatial and temporal resolutions to simulate the growth of small convective fingers of CO2-dissolved water to larger ones in a reservoir scale. The performance measurement confirmed that the both simulators exhibit excellent scalabilities showing almost linear speedup against number of processors up to over ten thousand cores. Generally this allows us to perform coupled multi-physics (THC) simulations on high resolution geologic models with multi-million grid in a practical time (e.g., less than a second per time step).

CFD Multiphysics Tool

NASA Technical Reports Server (NTRS)

Perrell, Eric R.

2005-01-01

The recent bold initiatives to expand the human presence in space require innovative approaches to the design of propulsion systems whose underlying technology is not yet mature. The space propulsion community has identified a number of candidate concepts. A short list includes solar sails, high-energy-density chemical propellants, electric and electromagnetic accelerators, solar-thermal and nuclear-thermal expanders. For each of these, the underlying physics are relatively well understood. One could easily cite authoritative texts, addressing both the governing equations, and practical solution methods for, e.g. electromagnetic fields, heat transfer, radiation, thermophysics, structural dynamics, particulate kinematics, nuclear energy, power conversion, and fluid dynamics. One could also easily cite scholarly works in which complete equation sets for any one of these physical processes have been accurately solved relative to complex engineered systems. The Advanced Concepts and Analysis Office (ACAO), Space Transportation Directorate, NASA Marshall Space Flight Center, has recently released the first alpha version of a set of computer utilities for performing the applicable physical analyses relative to candidate deep-space propulsion systems such as those listed above. PARSEC, Preliminary Analysis of Revolutionary in-Space Engineering Concepts, enables rapid iterative calculations using several physics tools developed in-house. A complete cycle of the entire tool set takes about twenty minutes. PARSEC is a level-zero/level-one design tool. For PARSEC s proof-of-concept, and preliminary design decision-making, assumptions that significantly simplify the governing equation sets are necessary. To proceed to level-two, one wishes to retain modeling of the underlying physics as close as practical to known applicable first principles. This report describes results of collaboration between ACAO, and Embry-Riddle Aeronautical University (ERAU), to begin building a set of level-two design tools for PARSEC. The "CFD Multiphysics Tool" will be the propulsive element of the tool set. The name acknowledges that space propulsion performance assessment is primarily a fluid mechanics problem. At the core of the CFD Multiphysics Tool is an open-source CFD code, HYP, under development at ERAU. ERAU is renowned for its undergraduate degree program in Aerospace Engineering the largest in the nation. The strength of the program is its applications-oriented curriculum, which culminates in one of three two-course Engineering Design sequences: Aerospace Propulsion, Spacecraft, or Aircraft. This same philosophy applies to the HYP Project, albeit with fluid physics modeling commensurate with graduate research. HYP s purpose, like the Multiphysics Tool s, is to enable calculations of real (three-dimensional; geometrically complex; intended for hardware development) applications of high speed and propulsive fluid flows.

Lattice Boltzmann modeling of transport phenomena in fuel cells and flow batteries

NASA Astrophysics Data System (ADS)

Xu, Ao; Shyy, Wei; Zhao, Tianshou

2017-06-01

Fuel cells and flow batteries are promising technologies to address climate change and air pollution problems. An understanding of the complex multiscale and multiphysics transport phenomena occurring in these electrochemical systems requires powerful numerical tools. Over the past decades, the lattice Boltzmann (LB) method has attracted broad interest in the computational fluid dynamics and the numerical heat transfer communities, primarily due to its kinetic nature making it appropriate for modeling complex multiphase transport phenomena. More importantly, the LB method fits well with parallel computing due to its locality feature, which is required for large-scale engineering applications. In this article, we review the LB method for gas-liquid two-phase flows, coupled fluid flow and mass transport in porous media, and particulate flows. Examples of applications are provided in fuel cells and flow batteries. Further developments of the LB method are also outlined.

Particle Laden Turbulence in a Radiation Environment Using a Portable High Preformace Solver Based on the Legion Runtime System

NASA Astrophysics Data System (ADS)

Torres, Hilario; Iaccarino, Gianluca

2017-11-01

Soleil-X is a multi-physics solver being developed at Stanford University as a part of the Predictive Science Academic Alliance Program II. Our goal is to conduct high fidelity simulations of particle laden turbulent flows in a radiation environment for solar energy receiver applications as well as to demonstrate our readiness to effectively utilize next generation Exascale machines. The novel aspect of Soleil-X is that it is built upon the Legion runtime system to enable easy portability to different parallel distributed heterogeneous architectures while also being written entirely in high-level/high-productivity languages (Ebb and Regent). An overview of the Soleil-X software architecture will be given. Results from coupled fluid flow, Lagrangian point particle tracking, and thermal radiation simulations will be presented. Performance diagnostic tools and metrics corresponding the the same cases will also be discussed. US Department of Energy, National Nuclear Security Administration.

Making it Easy to Construct Accurate Hydrological Models that Exploit High Performance Computers (Invited)

NASA Astrophysics Data System (ADS)

Kees, C. E.; Farthing, M. W.; Terrel, A.; Certik, O.; Seljebotn, D.

2013-12-01

This presentation will focus on two barriers to progress in the hydrological modeling community, and research and development conducted to lessen or eliminate them. The first is a barrier to sharing hydrological models among specialized scientists that is caused by intertwining the implementation of numerical methods with the implementation of abstract numerical modeling information. In the Proteus toolkit for computational methods and simulation, we have decoupled these two important parts of computational model through separate "physics" and "numerics" interfaces. More recently we have begun developing the Strong Form Language for easy and direct representation of the mathematical model formulation in a domain specific language embedded in Python. The second major barrier is sharing ANY scientific software tools that have complex library or module dependencies, as most parallel, multi-physics hydrological models must have. In this setting, users and developer are dependent on an entire distribution, possibly depending on multiple compilers and special instructions depending on the environment of the target machine. To solve these problem we have developed, hashdist, a stateless package management tool and a resulting portable, open source scientific software distribution.

High-order Spatio-temporal Schemes for Coupled, Multi-physics Reactor Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mr. Vijay S. Mahadevan; Dr. Jean C. Ragusa

2008-09-01

This report summarizes the work done in the summer of 08 by the Ph.D. student Vijay Mahadevan. The main focus of the work was to coupled 3-D neutron difusion to 3-D heat conduction in parallel with accuracy greater than or equal to 2nd order in space and time. Results show that the goal was attained.

Interface COMSOL-PHREEQC (iCP), an efficient numerical framework for the solution of coupled multiphysics and geochemistry

NASA Astrophysics Data System (ADS)

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.

Coupling between a multi-physics workflow engine and an optimization framework

NASA Astrophysics Data System (ADS)

Di Gallo, L.; Reux, C.; Imbeaux, F.; Artaud, J.-F.; Owsiak, M.; Saoutic, B.; Aiello, G.; Bernardi, P.; Ciraolo, G.; Bucalossi, J.; Duchateau, J.-L.; Fausser, C.; Galassi, D.; Hertout, P.; Jaboulay, J.-C.; Li-Puma, A.; Zani, L.

2016-03-01

A generic coupling method between a multi-physics workflow engine and an optimization framework is presented in this paper. The coupling architecture has been developed in order to preserve the integrity of the two frameworks. The objective is to provide the possibility to replace a framework, a workflow or an optimizer by another one without changing the whole coupling procedure or modifying the main content in each framework. The coupling is achieved by using a socket-based communication library for exchanging data between the two frameworks. Among a number of algorithms provided by optimization frameworks, Genetic Algorithms (GAs) have demonstrated their efficiency on single and multiple criteria optimization. Additionally to their robustness, GAs can handle non-valid data which may appear during the optimization. Consequently GAs work on most general cases. A parallelized framework has been developed to reduce the time spent for optimizations and evaluation of large samples. A test has shown a good scaling efficiency of this parallelized framework. This coupling method has been applied to the case of SYCOMORE (SYstem COde for MOdeling tokamak REactor) which is a system code developed in form of a modular workflow for designing magnetic fusion reactors. The coupling of SYCOMORE with the optimization platform URANIE enables design optimization along various figures of merit and constraints.

Parallelization of the preconditioned IDR solver for modern multicore computer systems

NASA Astrophysics Data System (ADS)

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).

IShTAR ICRF antenna field characterization in vacuum and plasma by using probe diagnostic

NASA Astrophysics Data System (ADS)

Usoltceva, Mariia; Ochoukov, Roman; D'Inca, Rodolphe; Jacquot, Jonathan; Crombé, Kristel; Kostic, Ana; Heuraux, Stéphane; Faudot, Eric; Noterdaeme, Jean-Marie

2017-10-01

RF sheath physics is one of the key topics relevant for improvements of ICRF heating systems, which are present on nearly all modern magnetic fusion machines. This paper introduces developement and validation of a new approach to understanding general RF sheath physics. The presumed reason of enhanced plasma-antenna interactions, parallel electric field, is not measured directly, but proposed to be obtained from simulations in COMSOL Multiphysics® Modeling Software. Measurements of RF magnetic field components with B-dot probes are done on a linear device IShTAR (Ion cyclotron Sheath Test ARrangement) and then compared to simulations. Good resulting accordance is suggested to be the criterion for trustworthiness of parallel electric field estimation as a component of electromagnetic field in modeling. A comparison between simulation and experiment for one magnetic field component in vacuum has demonstrated a close match. An additional complication to this ICRF antenna field characterization study is imposed by the helicon antenna which is used as a plasma ignition tool in the test arrangement. The plasma case, in contrast to the vacuum case, must be approached carefully, since the overlapping of ICRF antenna and helicon antenna fields occurs. Distinguishing of the two fields is done by an analysis of correlation between measurements with both antennas together and with each one separately.

Mesh-free data transfer algorithms for partitioned multiphysics problems: Conservation, accuracy, and parallelism

DOE PAGES

Slattery, Stuart R.

2015-12-02

In this study we analyze and extend mesh-free algorithms for three-dimensional data transfer problems in partitioned multiphysics simulations. We first provide a direct comparison between a mesh-based weighted residual method using the common-refinement scheme and two mesh-free algorithms leveraging compactly supported radial basis functions: one using a spline interpolation and one using a moving least square reconstruction. Through the comparison we assess both the conservation and accuracy of the data transfer obtained from each of the methods. We do so for a varying set of geometries with and without curvature and sharp features and for functions with and without smoothnessmore » and with varying gradients. Our results show that the mesh-based and mesh-free algorithms are complementary with cases where each was demonstrated to perform better than the other. We then focus on the mesh-free methods by developing a set of algorithms to parallelize them based on sparse linear algebra techniques. This includes a discussion of fast parallel radius searching in point clouds and restructuring the interpolation algorithms to leverage data structures and linear algebra services designed for large distributed computing environments. The scalability of our new algorithms is demonstrated on a leadership class computing facility using a set of basic scaling studies. Finally, these scaling studies show that for problems with reasonable load balance, our new algorithms for both spline interpolation and moving least square reconstruction demonstrate both strong and weak scalability using more than 100,000 MPI processes with billions of degrees of freedom in the data transfer operation.« less

Advances in High-Fidelity Multi-Physics Simulation Techniques

DTIC Science & Technology

2008-01-01

predictor - corrector method is used to advance the solution in time. 33 x (m) y (m ) 0 1 2 3.00001 0 1 2 3 4 5 40 x 50 Grid 3 Figure 17: Typical...Unclassified c . THIS PAGE Unclassified 17. LIMITATION OF ABSTRACT: SAR 18. NUMBER OF PAGES 60 Datta Gaitonde 19b. TELEPHONE...advanced parallel computing platforms. The motivation to develop high-fidelity algorithms derives from considerations in various areas of current

Investigating Darcy-scale assumptions by means of a multiphysics algorithm

NASA Astrophysics Data System (ADS)

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 permeability) should account for the fact that they depend not only on the saturation but also on the actual characteristics of the fluid distribution.

A multiphysics and multiscale software environment for modeling astrophysical systems

NASA Astrophysics Data System (ADS)

Portegies Zwart, Simon; McMillan, Steve; Harfst, Stefan; Groen, Derek; Fujii, Michiko; Nualláin, Breanndán Ó.; Glebbeek, Evert; Heggie, Douglas; Lombardi, James; Hut, Piet; Angelou, Vangelis; Banerjee, Sambaran; Belkus, Houria; Fragos, Tassos; Fregeau, John; Gaburov, Evghenii; Izzard, Rob; Jurić, Mario; Justham, Stephen; Sottoriva, Andrea; Teuben, Peter; van Bever, Joris; Yaron, Ofer; Zemp, Marcel

2009-05-01

We present MUSE, a software framework for combining existing computational tools for different astrophysical domains into a single multiphysics, multiscale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a "Noah's Ark" milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multiscale and multiphysics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe three examples calculated using MUSE: the merger of two galaxies, the merger of two evolving stars, and a hybrid N-body simulation. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.

ADHydro: A Parallel Implementation of a Large-scale High-Resolution Multi-Physics Distributed Water Resources Model Using the Charm++ Run Time System

NASA Astrophysics Data System (ADS)

Steinke, R. C.; Ogden, F. L.; Lai, W.; Moreno, H. A.; Pureza, L. G.

2014-12-01

Physics-based watershed models are useful tools for hydrologic studies, water resources management and economic analyses in the contexts of climate, land-use, and water-use changes. This poster presents a parallel implementation of a quasi 3-dimensional, physics-based, high-resolution, distributed water resources model suitable for simulating large watersheds in a massively parallel computing environment. Developing this model is one of the objectives of the NSF EPSCoR RII Track II CI-WATER project, which is joint between Wyoming and Utah EPSCoR jurisdictions. The model, which we call ADHydro, is aimed at simulating important processes in the Rocky Mountain west, including: rainfall and infiltration, snowfall and snowmelt in complex terrain, vegetation and evapotranspiration, soil heat flux and freezing, overland flow, channel flow, groundwater flow, water management and irrigation. Model forcing is provided by the Weather Research and Forecasting (WRF) model, and ADHydro is coupled with the NOAH-MP land-surface scheme for calculating fluxes between the land and atmosphere. The ADHydro implementation uses the Charm++ parallel run time system. Charm++ is based on location transparent message passing between migrateable C++ objects. Each object represents an entity in the model such as a mesh element. These objects can be migrated between processors or serialized to disk allowing the Charm++ system to automatically provide capabilities such as load balancing and checkpointing. Objects interact with each other by passing messages that the Charm++ system routes to the correct destination object regardless of its current location. This poster discusses the algorithms, communication patterns, and caching strategies used to implement ADHydro with Charm++. The ADHydro model code will be released to the hydrologic community in late 2014.

Developing Discontinuous Galerkin Methods for Solving Multiphysics Problems in General Relativity

NASA Astrophysics Data System (ADS)

Kidder, Lawrence; Field, Scott; Teukolsky, Saul; Foucart, Francois; SXS Collaboration

2016-03-01

Multi-messenger observations of the merger of black hole-neutron star and neutron star-neutron star binaries, and of supernova explosions will probe fundamental physics inaccessible to terrestrial experiments. Modeling these systems requires a relativistic treatment of hydrodynamics, including magnetic fields, as well as neutrino transport and nuclear reactions. The accuracy, efficiency, and robustness of current codes that treat all of these problems is not sufficient to keep up with the observational needs. We are building a new numerical code that uses the Discontinuous Galerkin method with a task-based parallelization strategy, a promising combination that will allow multiphysics applications to be treated both accurately and efficiently on petascale and exascale machines. The code will scale to more than 100,000 cores for efficient exploration of the parameter space of potential sources and allowed physics, and the high-fidelity predictions needed to realize the promise of multi-messenger astronomy. I will discuss the current status of the development of this new code.

ATDM LANL FleCSI: Topology and Execution Framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bergen, Benjamin Karl

FleCSI is a compile-time configurable C++ framework designed to support multi-physics application development. As such, FleCSI attempts to provide a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. This means that FleCSI is potentially useful to many different ECP projects. Current support includes multidimensional mesh topology, mesh geometry, and mesh adjacency information, n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures (to identify data dependencies between distributed-memory address spaces). FleCSI introduces a functional programming model with control, execution, and data abstractionsmore » that are consistent with state-of-the-art task-based runtimes such as Legion and Charm++. The model also provides support for fine-grained, data-parallel execution with backend support for runtimes such as OpenMP and C++17. The FleCSI abstraction layer provides the developer with insulation from the underlying runtimes, while allowing support for multiple runtime systems, including conventional models like asynchronous MPI. The intent is to give developers a concrete set of user-friendly programming tools that can be used now, while allowing flexibility in choosing runtime implementations and optimizations that can be applied to architectures and runtimes that arise in the future. This project is essential to the ECP Ristra Next-Generation Code project, part of ASC ATDM, because it provides a hierarchically parallel programming model that is consistent with the design of modern system architectures, but which allows for the straightforward expression of algorithmic parallelism in a portably performant manner.« less

Parallel satellite orbital situational problems solver for space missions design and control

NASA Astrophysics Data System (ADS)

Atanassov, Atanas Marinov

2016-11-01

Solving different scientific problems for space applications demands implementation of observations, measurements or realization of active experiments during time intervals in which specific geometric and physical conditions are fulfilled. The solving of situational problems for determination of these time intervals when the satellite instruments work optimally is a very important part of all activities on every stage of preparation and realization of space missions. The elaboration of universal, flexible and robust approach for situation analysis, which is easily portable toward new satellite missions, is significant for reduction of missions' preparation times and costs. Every situation problem could be based on one or more situation conditions. Simultaneously solving different kinds of situation problems based on different number and types of situational conditions, each one of them satisfied on different segments of satellite orbit requires irregular calculations. Three formal approaches are presented. First one is related to situation problems description that allows achieving flexibility in situation problem assembling and presentation in computer memory. The second formal approach is connected with developing of situation problem solver organized as processor that executes specific code for every particular situational condition. The third formal approach is related to solver parallelization utilizing threads and dynamic scheduling based on "pool of threads" abstraction and ensures a good load balance. The developed situation problems solver is intended for incorporation in the frames of multi-physics multi-satellite space mission's design and simulation tools.

Commnity Petascale Project for Accelerator Science And Simulation: Advancing Computational Science for Future Accelerators And Accelerator Technologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spentzouris, Panagiotis; /Fermilab; Cary, John

The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessarymore » accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors.« less

Spatial Modeling Tools for Cell Biology

DTIC Science & Technology

2006-10-01

multiphysics modeling expertise. A graphical user interface (GUI) for CoBi, JCoBi, was written in Java and interactive 3D graphics. CoBi has been...tools (C++ and Java ) to simulate complex cell and organ biology problems. CoBi has been designed to interact with the other Bio-SPICE software...fall of 2002. VisIt supports C++, Python and Java interfaces. The C++ and Java interfaces make it possible to provide alternate user interfaces for

Flexible parallel implicit modelling of coupled thermal-hydraulic-mechanical processes in fractured rocks

NASA Astrophysics Data System (ADS)

Cacace, Mauro; Jacquey, Antoine B.

2017-09-01

Theory and numerical implementation describing groundwater flow and the transport of heat and solute mass in fully saturated fractured rocks with elasto-plastic mechanical feedbacks are developed. In our formulation, fractures are considered as being of lower dimension than the hosting deformable porous rock and we consider their hydraulic and mechanical apertures as scaling parameters to ensure continuous exchange of fluid mass and energy within the fracture-solid matrix system. The coupled system of equations is implemented in a new simulator code that makes use of a Galerkin finite-element technique. The code builds on a flexible, object-oriented numerical framework (MOOSE, Multiphysics Object Oriented Simulation Environment) which provides an extensive scalable parallel and implicit coupling to solve for the multiphysics problem. The governing equations of groundwater flow, heat and mass transport, and rock deformation are solved in a weak sense (either by classical Newton-Raphson or by free Jacobian inexact Newton-Krylow schemes) on an underlying unstructured mesh. Nonlinear feedbacks among the active processes are enforced by considering evolving fluid and rock properties depending on the thermo-hydro-mechanical state of the system and the local structure, i.e. degree of connectivity, of the fracture system. A suite of applications is presented to illustrate the flexibility and capability of the new simulator to address problems of increasing complexity and occurring at different spatial (from centimetres to tens of kilometres) and temporal scales (from minutes to hundreds of years).

Case studies on optimization problems in MATLAB and COMSOL multiphysics by means of the livelink

NASA Astrophysics Data System (ADS)

Ozana, Stepan; Pies, Martin; Docekal, Tomas

2016-06-01

LiveLink for COMSOL is a tool that integrates COMSOL Multiphysics with MATLAB to extend one's modeling with scripting programming in the MATLAB environment. It allows user to utilize the full power of MATLAB and its toolboxes in preprocessing, model manipulation, and post processing. At first, the head script launches COMSOL with MATLAB and defines initial value of all parameters, refers to the objective function J described in the objective function and creates and runs the defined optimization task. Once the task is launches, the COMSOL model is being called in the iteration loop (from MATLAB environment by use of API interface), changing defined optimization parameters so that the objective function is minimized, using fmincon function to find a local or global minimum of constrained linear or nonlinear multivariable function. Once the minimum is found, it returns exit flag, terminates optimization and returns the optimized values of the parameters. The cooperation with MATLAB via LiveLink enhances a powerful computational environment with complex multiphysics simulations. The paper will introduce using of the LiveLink for COMSOL for chosen case studies in the field of technical cybernetics and bioengineering.

Three-dimensional fuel pin model validation by prediction of hydrogen distribution in cladding and comparison with experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aly, A.; Avramova, Maria; Ivanov, Kostadin

To correctly describe and predict this hydrogen distribution there is a need for multi-physics coupling to provide accurate three-dimensional azimuthal, radial, and axial temperature distributions in the cladding. Coupled high-fidelity reactor-physics codes with a sub-channel code as well as with a computational fluid dynamics (CFD) tool have been used to calculate detailed temperature distributions. These high-fidelity coupled neutronics/thermal-hydraulics code systems are coupled further with the fuel-performance BISON code with a kernel (module) for hydrogen. Both hydrogen migration and precipitation/dissolution are included in the model. Results from this multi-physics analysis is validated utilizing calculations of hydrogen distribution using models informed bymore » data from hydrogen experiments and PIE data.« less

Physics-based multiscale coupling for full core nuclear reactor simulation

DOE PAGES

Gaston, Derek R.; Permann, Cody J.; Peterson, John W.; ...

2015-10-01

Numerical simulation of nuclear reactors is a key technology in the quest for improvements in efficiency, safety, and reliability of both existing and future reactor designs. Historically, simulation of an entire reactor was accomplished by linking together multiple existing codes that each simulated a subset of the relevant multiphysics phenomena. Recent advances in the MOOSE (Multiphysics Object Oriented Simulation Environment) framework have enabled a new approach: multiple domain-specific applications, all built on the same software framework, are efficiently linked to create a cohesive application. This is accomplished with a flexible coupling capability that allows for a variety of different datamore » exchanges to occur simultaneously on high performance parallel computational hardware. Examples based on the KAIST-3A benchmark core, as well as a simplified Westinghouse AP-1000 configuration, demonstrate the power of this new framework for tackling—in a coupled, multiscale manner—crucial reactor phenomena such as CRUD-induced power shift and fuel shuffle. 2014 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY-NC-SA license« less

Development of FAST.Farm: A New Multiphysics Engineering Tool for Wind Farm Design and Analysis: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jonkman, Jason; Annoni, Jennifer; Hayman, Greg

2017-01-01

This paper presents the development of FAST.Farm, a new multiphysics tool applicable to engineering problems in research and industry involving wind farm performance and cost optimization that is needed to address the current underperformance, failures, and expenses plaguing the wind industry. Achieving wind cost-of-energy targets - which requires improvements in wind farm performance and reliability, together with reduced uncertainty and expenditures - has been eluded by the complicated nature of the wind farm design problem, especially the sophisticated interaction between atmospheric phenomena and wake dynamics and array effects. FAST.Farm aims to balance the need for accurate modeling of the relevantmore » physics for predicting power performance and loads while maintaining low computational cost to support a highly iterative and probabilistic design process and system-wide optimization. FAST.Farm makes use of FAST to model the aero-hydro-servo-elastics of distinct turbines in the wind farm, and it is based on some of the principles of the Dynamic Wake Meandering (DWM) model, but avoids many of the limitations of existing DWM implementations.« less

A Multiphysics and Multiscale Software Environment for Modeling Astrophysical Systems

NASA Astrophysics Data System (ADS)

Portegies Zwart, Simon; McMillan, Steve; O'Nualláin, Breanndán; Heggie, Douglas; Lombardi, James; Hut, Piet; Banerjee, Sambaran; Belkus, Houria; Fragos, Tassos; Fregeau, John; Fuji, Michiko; Gaburov, Evghenii; Glebbeek, Evert; Groen, Derek; Harfst, Stefan; Izzard, Rob; Jurić, Mario; Justham, Stephen; Teuben, Peter; van Bever, Joris; Yaron, Ofer; Zemp, Marcel

We present MUSE, a software framework for tying together existing computational tools for different astrophysical domains into a single multiphysics, multiscale workload. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly-coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for a generalized stellar systems workload. MUSE has now reached a "Noah's Ark" milestone, with two available numerical solvers for each domain. MUSE can treat small stellar associations, galaxies and everything in between, including planetary systems, dense stellar clusters and galactic nuclei. Here we demonstrate an examples calculated with MUSE: the merger of two galaxies. In addition we demonstrate the working of MUSE on a distributed computer. The current MUSE code base is publicly available as open source at http://muse.li.

Multiphysics Object Oriented Simulation Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

The Multiphysics Object Oriented Simulation Environment (MOOSE) software library developed at Idaho National Laboratory is a tool. MOOSE, like other tools, doesn't actually complete a task. Instead, MOOSE seeks to reduce the effort required to create engineering simulation applications. MOOSE itself is a software library: a blank canvas upon which you write equations and then MOOSE can help you solve them. MOOSE is comparable to a spreadsheet application. A spreadsheet, by itself, doesn't do anything. Only once equations are entered into it will a spreadsheet application compute anything. Such is the same for MOOSE. An engineer or scientist can utilizemore » the equation solvers within MOOSE to solve equations related to their area of study. For instance, a geomechanical scientist can input equations related to water flow in underground reservoirs and MOOSE can solve those equations to give the scientist an idea of how water could move over time. An engineer might input equations related to the forces in steel beams in order to understand the load bearing capacity of a bridge. Because MOOSE is a blank canvas it can be useful in many scientific and engineering pursuits.« less

Integral Full Core Multi-Physics PWR Benchmark with Measured Data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Forget, Benoit; Smith, Kord; Kumar, Shikhar

In recent years, the importance of modeling and simulation has been highlighted extensively in the DOE research portfolio with concrete examples in nuclear engineering with the CASL and NEAMS programs. These research efforts and similar efforts worldwide aim at the development of high-fidelity multi-physics analysis tools for the simulation of current and next-generation nuclear power reactors. Like all analysis tools, verification and validation is essential to guarantee proper functioning of the software and methods employed. The current approach relies mainly on the validation of single physic phenomena (e.g. critical experiment, flow loops, etc.) and there is a lack of relevantmore » multiphysics benchmark measurements that are necessary to validate high-fidelity methods being developed today. This work introduces a new multi-cycle full-core Pressurized Water Reactor (PWR) depletion benchmark based on two operational cycles of a commercial nuclear power plant that provides a detailed description of fuel assemblies, burnable absorbers, in-core fission detectors, core loading and re-loading patterns. This benchmark enables analysts to develop extremely detailed reactor core models that can be used for testing and validation of coupled neutron transport, thermal-hydraulics, and fuel isotopic depletion. The benchmark also provides measured reactor data for Hot Zero Power (HZP) physics tests, boron letdown curves, and three-dimensional in-core flux maps from 58 instrumented assemblies. The benchmark description is now available online and has been used by many groups. However, much work remains to be done on the quantification of uncertainties and modeling sensitivities. This work aims to address these deficiencies and make this benchmark a true non-proprietary international benchmark for the validation of high-fidelity tools. This report details the BEAVRS uncertainty quantification for the first two cycle of operations and serves as the final report of the project.« less

Pedagogical Approach to the Modeling and Simulation of Oscillating Chemical Systems with Modern Software: The Brusselator Model

ERIC Educational Resources Information Center

Lozano-Parada, Jaime H.; Burnham, Helen; Martinez, Fiderman Machuca

2018-01-01

A classical nonlinear system, the "Brusselator", was used to illustrate the modeling and simulation of oscillating chemical systems using stability analysis techniques with modern software tools such as Comsol Multiphysics, Matlab, and Excel. A systematic approach is proposed in order to establish a regime of parametric conditions that…

Modelling fully-coupled Thermo-Hydro-Mechanical (THM) processes in fractured reservoirs using GOLEM: a massively parallel open-source simulator

NASA Astrophysics Data System (ADS)

Jacquey, Antoine; Cacace, Mauro

2017-04-01

Utilization of the underground for energy-related purposes have received increasing attention in the last decades as a source for carbon-free energy and for safe storage solutions. Understanding the key processes controlling fluid and heat flow around geological discontinuities such as faults and fractures as well as their mechanical behaviours is therefore of interest in order to design safe and sustainable reservoir operations. These processes occur in a naturally complex geological setting, comprising natural or engineered discrete heterogeneities as faults and fractures, span a relatively large spectrum of temporal and spatial scales and they interact in a highly non-linear fashion. In this regard, numerical simulators have become necessary in geological studies to model coupled processes and complex geological geometries. In this study, we present a new simulator GOLEM, using multiphysics coupling to characterize geological reservoirs. In particular, special attention is given to discrete geological features such as faults and fractures. GOLEM is based on the Multiphysics Object-Oriented Simulation Environment (MOOSE). The MOOSE framework provides a powerful and flexible platform to solve multiphysics problems implicitly and in a tightly coupled manner on unstructured meshes which is of interest for the considered non-linear context. Governing equations in 3D for fluid flow, heat transfer (conductive and advective), saline transport as well as deformation (elastic and plastic) have been implemented into the GOLEM application. Coupling between rock deformation and fluid and heat flow is considered using theories of poroelasticity and thermoelasticity. Furthermore, considering material properties such as density and viscosity and transport properties such as porosity as dependent on the state variables (based on the International Association for the Properties of Water and Steam models) increase the coupling complexity of the problem. The GOLEM application aims therefore at integrating more physical processes observed in the field or in the laboratory to simulate more realistic scenarios. The use of high-level nonlinear solver technology allow us to tackle these complex multiphysics problems in three dimensions. Basic concepts behing the GOLEM simulator will be presented in this study as well as a few application examples to illustrate its main features.

Droplet flow along the wall of rectangular channel with gradient of wettability

NASA Astrophysics Data System (ADS)

Kupershtokh, A. L.

2018-03-01

The lattice Boltzmann equations (LBE) method (LBM) is applicable for simulating the multiphysics problems of fluid flows with free boundaries, taking into account the viscosity, surface tension, evaporation and wetting degree of a solid surface. Modeling of the nonstationary motion of a drop of liquid along a solid surface with a variable level of wettability is carried out. For the computer simulation of such a problem, the three-dimensional lattice Boltzmann equations method D3Q19 is used. The LBE method allows us to parallelize the calculations on multiprocessor graphics accelerators using the CUDA programming technology.

Community Petascale Project for Accelerator Science and Simulation: Advancing Computational Science for Future Accelerators and Accelerator Technologies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spentzouris, P.; /Fermilab; Cary, J.

The design and performance optimization of particle accelerators are essential for the success of the DOE scientific program in the next decade. Particle accelerators are very complex systems whose accurate description involves a large number of degrees of freedom and requires the inclusion of many physics processes. Building on the success of the SciDAC-1 Accelerator Science and Technology project, the SciDAC-2 Community Petascale Project for Accelerator Science and Simulation (ComPASS) is developing a comprehensive set of interoperable components for beam dynamics, electromagnetics, electron cooling, and laser/plasma acceleration modelling. ComPASS is providing accelerator scientists the tools required to enable the necessarymore » accelerator simulation paradigm shift from high-fidelity single physics process modeling (covered under SciDAC1) to high-fidelity multiphysics modeling. Our computational frameworks have been used to model the behavior of a large number of accelerators and accelerator R&D experiments, assisting both their design and performance optimization. As parallel computational applications, the ComPASS codes have been shown to make effective use of thousands of processors. ComPASS is in the first year of executing its plan to develop the next-generation HPC accelerator modeling tools. ComPASS aims to develop an integrated simulation environment that will utilize existing and new accelerator physics modules with petascale capabilities, by employing modern computing and solver technologies. The ComPASS vision is to deliver to accelerator scientists a virtual accelerator and virtual prototyping modeling environment, with the necessary multiphysics, multiscale capabilities. The plan for this development includes delivering accelerator modeling applications appropriate for each stage of the ComPASS software evolution. Such applications are already being used to address challenging problems in accelerator design and optimization. The ComPASS organization for software development and applications accounts for the natural domain areas (beam dynamics, electromagnetics, and advanced acceleration), and all areas depend on the enabling technologies activities, such as solvers and component technology, to deliver the desired performance and integrated simulation environment. The ComPASS applications focus on computationally challenging problems important for design or performance optimization to all major HEP, NP, and BES accelerator facilities. With the cost and complexity of particle accelerators rising, the use of computation to optimize their designs and find improved operating regimes becomes essential, potentially leading to significant cost savings with modest investment.« less

Pervasive Restart In MOOSE-based Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Derek Gaston; Cody Permann; David Andrs

Multiphysics applications are inherently complicated. Solving for multiple, interacting physical phenomena involves the solution of multiple equations, and each equation has its own data dependencies. Feeding the correct data to these equations at exactly the right time requires extensive effort in software design. In an ideal world, multiphysics applications always run to completion and produce correct answers. Unfortunately, in reality, there can be many reasons why a simulation might fail: power outage, system failure, exceeding a runtime allotment on a supercomputer, failure of the solver to converge, etc. A failure after many hours spent computing can be a significant setbackmore » for a project. Therefore, the ability to “continue” a solve from the point of failure, rather than starting again from scratch, is an essential component of any high-quality simulation tool. This process of “continuation” is commonly termed “restart” in the computational community. While the concept of restarting an application sounds ideal, the aforementioned complexities and data dependencies present in multiphysics applications make its implementation decidedly non-trivial. A running multiphysics calculation accumulates an enormous amount of “state”: current time, solution history, material properties, status of mechanical contact, etc. This “state” data comes in many different forms, including scalar, tensor, vector, and arbitrary, application-specific data types. To be able to restart an application, you must be able to both store and retrieve this data, effectively recreating the state of the application before the failure. When utilizing the Multiphysics Object Oriented Simulation Environment (MOOSE) framework developed at Idaho National Laboratory, this state data is stored both internally within the framework itself (such as solution vectors and the current time) and within the applications that use the framework. In order to implement restart in MOOSE-based applications, the total state of the system (both within the framework and without) must be stored and retrieved. To this end, the MOOSE team has implemented a “pervasive” restart capability which allows any object within MOOSE (or within a MOOSE-based application) to be declared as “state” data, and handles the storage and retrieval of said data.« less

A parallel multi-domain solution methodology applied to nonlinear thermal transport problems in nuclear fuel pins

DOE PAGES

Philip, Bobby; Berrill, Mark A.; Allu, Srikanth; ...

2015-01-26

We describe an efficient and nonlinearly consistent parallel solution methodology for solving coupled nonlinear thermal transport problems that occur in nuclear reactor applications over hundreds of individual 3D physical subdomains. Efficiency is obtained by leveraging knowledge of the physical domains, the physics on individual domains, and the couplings between them for preconditioning within a Jacobian Free Newton Krylov method. Details of the computational infrastructure that enabled this work, namely the open source Advanced Multi-Physics (AMP) package developed by the authors are described. The details of verification and validation experiments, and parallel performance analysis in weak and strong scaling studies demonstratingmore » the achieved efficiency of the algorithm are presented. Moreover, numerical experiments demonstrate that the preconditioner developed is independent of the number of fuel subdomains in a fuel rod, which is particularly important when simulating different types of fuel rods. Finally, we demonstrate the power of the coupling methodology by considering problems with couplings between surface and volume physics and coupling of nonlinear thermal transport in fuel rods to an external radiation transport code.« less

PROTO-PLASM: parallel language for adaptive and scalable modelling of biosystems.

PubMed

Bajaj, Chandrajit; DiCarlo, Antonio; Paoluzzi, Alberto

2008-09-13

This paper discusses the design goals and the first developments of PROTO-PLASM, a novel computational environment to produce libraries of executable, combinable and customizable computer models of natural and synthetic biosystems, aiming to provide a supporting framework for predictive understanding of structure and behaviour through multiscale geometric modelling and multiphysics simulations. Admittedly, the PROTO-PLASM platform is still in its infancy. Its computational framework--language, model library, integrated development environment and parallel engine--intends to provide patient-specific computational modelling and simulation of organs and biosystem, exploiting novel functionalities resulting from the symbolic combination of parametrized models of parts at various scales. PROTO-PLASM may define the model equations, but it is currently focused on the symbolic description of model geometry and on the parallel support of simulations. Conversely, CellML and SBML could be viewed as defining the behavioural functions (the model equations) to be used within a PROTO-PLASM program. Here we exemplify the basic functionalities of PROTO-PLASM, by constructing a schematic heart model. We also discuss multiscale issues with reference to the geometric and physical modelling of neuromuscular junctions.

Proto-Plasm: parallel language for adaptive and scalable modelling of biosystems

PubMed Central

Bajaj, Chandrajit; DiCarlo, Antonio; Paoluzzi, Alberto

2008-01-01

This paper discusses the design goals and the first developments of Proto-Plasm, a novel computational environment to produce libraries of executable, combinable and customizable computer models of natural and synthetic biosystems, aiming to provide a supporting framework for predictive understanding of structure and behaviour through multiscale geometric modelling and multiphysics simulations. Admittedly, the Proto-Plasm platform is still in its infancy. Its computational framework—language, model library, integrated development environment and parallel engine—intends to provide patient-specific computational modelling and simulation of organs and biosystem, exploiting novel functionalities resulting from the symbolic combination of parametrized models of parts at various scales. Proto-Plasm may define the model equations, but it is currently focused on the symbolic description of model geometry and on the parallel support of simulations. Conversely, CellML and SBML could be viewed as defining the behavioural functions (the model equations) to be used within a Proto-Plasm program. Here we exemplify the basic functionalities of Proto-Plasm, by constructing a schematic heart model. We also discuss multiscale issues with reference to the geometric and physical modelling of neuromuscular junctions. PMID:18559320

Computational simulation of biomolecules transport with multi-physics near microchannel surface for development of biomolecules-detection devices.

PubMed

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.

Multiphysics Simulations: Challenges and Opportunities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keyes, David; McInnes, Lois C.; Woodward, Carol

2013-02-12

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 somemore » commonalities among them, and attempt to extrapolate best practices to future systems. From our study, we summarize challenges and forecast opportunities.« less

Advances in simulation of wave interactions with extended MHD phenomena

NASA Astrophysics Data System (ADS)

Batchelor, D.; Abla, G.; D'Azevedo, E.; Bateman, G.; Bernholdt, D. E.; Berry, L.; Bonoli, P.; Bramley, R.; Breslau, J.; Chance, M.; Chen, J.; Choi, M.; Elwasif, W.; Foley, S.; Fu, G.; Harvey, R.; Jaeger, E.; Jardin, S.; Jenkins, T.; Keyes, D.; Klasky, S.; Kruger, S.; Ku, L.; Lynch, V.; McCune, D.; Ramos, J.; Schissel, D.; Schnack, D.; Wright, J.

2009-07-01

The Integrated Plasma Simulator (IPS) provides a framework within which some of the most advanced, massively-parallel fusion modeling codes can be interoperated to provide a detailed picture of the multi-physics processes involved in fusion experiments. The presentation will cover four topics: 1) recent improvements to the IPS, 2) application of the IPS for very high resolution simulations of ITER scenarios, 3) studies of resistive and ideal MHD stability in tokamk discharges using IPS facilities, and 4) the application of RF power in the electron cyclotron range of frequencies to control slowly growing MHD modes in tokamaks and initial evaluations of optimized location for RF power deposition.

Wide-field Imaging System and Rapid Direction of Optical Zoom (WOZ)

DTIC Science & Technology

2010-12-24

The modeling tools are based on interaction between three commercial software packages: SolidWorks, COMSOL Multiphysics, and ZEMAX optical design...deformation resulting from the applied voltages. Finally, the deformed surface can be exported to ZEMAX via MatLab. From ZEMAX , various analyses can...results to extract from ZEMAX to support the optimization remains to be determined. Figure 1 shows the deformation calculated using a model of an

FAST Modularization Framework for Wind Turbine Simulation: Full-System Linearization

DOE PAGES

Jonkman, Jason M.; Jonkman, Bonnie J.

2016-10-03

The wind engineering community relies on multiphysics engineering software to run nonlinear time-domain simulations e.g. for design-standards-based loads analysis. Although most physics involved in wind energy are nonlinear, linearization of the underlying nonlinear system equations is often advantageous to understand the system response and exploit well-established methods and tools for analyzing linear systems. Here, this paper presents the development and verification of the new linearization functionality of the open-source engineering tool FAST v8 for land-based wind turbines, as well as the concepts and mathematical background needed to understand and apply it correctly.

AeroDyn V15.04: Design tool for wind and MHK turbines

DOE Data Explorer

Murray, Robynne; Hayman, Greg; Jonkman, Jason

2017-04-28

AeroDyn is a time-domain wind and MHK turbine aerodynamics module that can be coupled into the FAST version 8 multi-physics engineering tool to enable aero-elastic simulation of horizontal-axis wind turbines. AeroDyn V15.04 has been updated to include a cavitation check for MHK turbines, and can be driven as a standalone code to compute wind turbine aerodynamic response uncoupled from FAST. Note that while AeroDyn has been updated to v15.04, FAST v8.16 has not yet been updated and still uses AeroDyn v15.03.

FAST modularization framework for wind turbine simulation: full-system linearization

NASA Astrophysics Data System (ADS)

Jonkman, J. M.; Jonkman, B. J.

2016-09-01

The wind engineering community relies on multiphysics engineering software to run nonlinear time-domain simulations e.g. for design-standards-based loads analysis. Although most physics involved in wind energy are nonlinear, linearization of the underlying nonlinear system equations is often advantageous to understand the system response and exploit well- established methods and tools for analyzing linear systems. This paper presents the development and verification of the new linearization functionality of the open-source engineering tool FAST v8 for land-based wind turbines, as well as the concepts and mathematical background needed to understand and apply it correctly.

Experimental Evaluation of Acoustic Engine Liner Models Developed with COMSOL Multiphysics

NASA Technical Reports Server (NTRS)

Schiller, Noah H.; Jones, Michael G.; Bertolucci, Brandon

2017-01-01

Accurate modeling tools are needed to design new engine liners capable of reducing aircraft noise. The purpose of this study is to determine if a commercially-available finite element package, COMSOL Multiphysics, can be used to accurately model a range of different acoustic engine liner designs, and in the process, collect and document a benchmark dataset that can be used in both current and future code evaluation activities. To achieve these goals, a variety of liner samples, ranging from conventional perforate-over-honeycomb to extended-reaction designs, were installed in one wall of the grazing flow impedance tube at the NASA Langley Research Center. The liners were exposed to high sound pressure levels and grazing flow, and the effect of the liner on the sound field in the flow duct was measured. These measurements were then compared with predictions. While this report only includes comparisons for a subset of the configurations, the full database of all measurements and predictions is available in electronic format upon request. The results demonstrate that both conventional perforate-over-honeycomb and extended-reaction liners can be accurately modeled using COMSOL. Therefore, this modeling tool can be used with confidence to supplement the current suite of acoustic propagation codes, and ultimately develop new acoustic engine liners designed to reduce aircraft noise.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keyes, D.; McInnes, L. C.; Woodward, C.

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 alwaysmore » 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.« less

Exploring a Multiphysics Resolution Approach for Additive Manufacturing

NASA Astrophysics Data System (ADS)

Estupinan Donoso, Alvaro Antonio; Peters, Bernhard

2018-06-01

Metal additive manufacturing (AM) is a fast-evolving technology aiming to efficiently produce complex parts while saving resources. Worldwide, active research is being performed to solve the existing challenges of this growing technique. Constant computational advances have enabled multiscale and multiphysics numerical tools that complement the traditional physical experimentation. In this contribution, an advanced discrete-continuous concept is proposed to address the physical phenomena involved during laser powder bed fusion. The concept treats powder as discrete by the extended discrete element method, which predicts the thermodynamic state and phase change for each particle. The fluid surrounding is solved with multiphase computational fluid dynamics techniques to determine momentum, heat, gas and liquid transfer. Thus, results track the positions and thermochemical history of individual particles in conjunction with the prevailing fluid phases' temperature and composition. It is believed that this methodology can be employed to complement experimental research by analysis of the comprehensive results, which can be extracted from it to enable AM processes optimization for parts qualification.

An Object-Oriented Finite Element Framework for Multiphysics Phase Field Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Michael R Tonks; Derek R Gaston; Paul C Millett

2012-01-01

The phase field approach is a powerful and popular method for modeling microstructure evolution. In this work, advanced numerical tools are used to create a phase field framework that facilitates rapid model development. This framework, called MARMOT, is based on Idaho National Laboratory's finite element Multiphysics Object-Oriented Simulation Environment. In MARMOT, the system of phase field partial differential equations (PDEs) are solved simultaneously with PDEs describing additional physics, such as solid mechanics and heat conduction, using the Jacobian-Free Newton Krylov Method. An object-oriented architecture is created by taking advantage of commonalities in phase fields models to facilitate development of newmore » models with very little written code. In addition, MARMOT provides access to mesh and time step adaptivity, reducing the cost for performing simulations with large disparities in both spatial and temporal scales. In this work, phase separation simulations are used to show the numerical performance of MARMOT. Deformation-induced grain growth and void growth simulations are included to demonstrate the muliphysics capability.« less

RF Wave Simulation Using the MFEM Open Source FEM Package

NASA Astrophysics Data System (ADS)

Stillerman, J.; Shiraiwa, S.; Bonoli, P. T.; Wright, J. C.; Green, D. L.; Kolev, T.

2016-10-01

A new plasma wave simulation environment based on the finite element method is presented. MFEM, a scalable open-source FEM library, is used as the basis for this capability. MFEM allows for assembling an FEM matrix of arbitrarily high order in a parallel computing environment. A 3D frequency domain RF physics layer was implemented using a python wrapper for MFEM and a cold collisional plasma model was ported. This physics layer allows for defining the plasma RF wave simulation model without user knowledge of the FEM weak-form formulation. A graphical user interface is built on πScope, a python-based scientific workbench, such that a user can build a model definition file interactively. Benchmark cases have been ported to this new environment, with results being consistent with those obtained using COMSOL multiphysics, GENRAY, and TORIC/TORLH spectral solvers. This work is a first step in bringing to bear the sophisticated computational tool suite that MFEM provides (e.g., adaptive mesh refinement, solver suite, element types) to the linear plasma-wave interaction problem, and within more complicated integrated workflows, such as coupling with core spectral solver, or incorporating additional physics such as an RF sheath potential model or kinetic effects. USDoE Awards DE-FC02-99ER54512, DE-FC02-01ER54648.

Multiphysics Code Demonstrated for Propulsion Applications

NASA Technical Reports Server (NTRS)

Lawrence, Charles; Melis, Matthew E.

1998-01-01

The utility of multidisciplinary analysis tools for aeropropulsion applications is being investigated at the NASA Lewis Research Center. The goal of this project is to apply Spectrum, a multiphysics code developed by Centric Engineering Systems, Inc., to simulate multidisciplinary effects in turbomachinery components. Many engineering problems today involve detailed computer analyses to predict the thermal, aerodynamic, and structural response of a mechanical system as it undergoes service loading. Analysis of aerospace structures generally requires attention in all three disciplinary areas to adequately predict component service behavior, and in many cases, the results from one discipline substantially affect the outcome of the other two. There are numerous computer codes currently available in the engineering community to perform such analyses in each of these disciplines. Many of these codes are developed and used in-house by a given organization, and many are commercially available. However, few, if any, of these codes are designed specifically for multidisciplinary analyses. The Spectrum code has been developed for performing fully coupled fluid, thermal, and structural analyses on a mechanical system with a single simulation that accounts for all simultaneous interactions, thus eliminating the requirement for running a large number of sequential, separate, disciplinary analyses. The Spectrum code has a true multiphysics analysis capability, which improves analysis efficiency as well as accuracy. Centric Engineering, Inc., working with a team of Lewis and AlliedSignal Engines engineers, has been evaluating Spectrum for a variety of propulsion applications including disk quenching, drum cavity flow, aeromechanical simulations, and a centrifugal compressor flow simulation.

VERAView

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Ronald W.; Collins, Benjamin S.; Godfrey, Andrew T.

2016-12-09

In order to support engineering analysis of Virtual Environment for Reactor Analysis (VERA) model results, the Consortium for Advanced Simulation of Light Water Reactors (CASL) needs a tool that provides visualizations of HDF5 files that adhere to the VERAOUT specification. VERAView provides an interactive graphical interface for the visualization and engineering analyses of output data from VERA. The Python-based software provides instantaneous 2D and 3D images, 1D plots, and alphanumeric data from VERA multi-physics simulations.

Multiphysics Modeling and Simulations of Mil A46100 Armor-Grade Martensitic Steel Gas Metal Arc Welding Process

DTIC Science & Technology

2013-05-23

simulation of the conventional Gas Metal Arc Welding (GMAW) process, and the application of the developed methods and tools for prediction of the...technology in many industries such as chemical, oil , aerospace, and shipbuilding construction. In fact, within the metal fabrication industry as a...Mechanical Properties of Low Alloy Steel Products. Hardenability Concepts with Applications to Steel, The Metallurgical Society of AIME, Chicago, 1978, p

RELAP-7 Level 2 Milestone Report: Demonstration of a Steady State Single Phase PWR Simulation with RELAP-7

DOE Office of Scientific and Technical Information (OSTI.GOV)

David Andrs; Ray Berry; Derek Gaston

The document contains the simulation results of a steady state model PWR problem with the RELAP-7 code. The RELAP-7 code is the next generation nuclear reactor system safety analysis code being developed at Idaho National Laboratory (INL). The code is based on INL's modern scientific software development framework - MOOSE (Multi-Physics Object-Oriented Simulation Environment). This report summarizes the initial results of simulating a model steady-state single phase PWR problem using the current version of the RELAP-7 code. The major purpose of this demonstration simulation is to show that RELAP-7 code can be rapidly developed to simulate single-phase reactor problems. RELAP-7more » is a new project started on October 1st, 2011. It will become the main reactor systems simulation toolkit for RISMC (Risk Informed Safety Margin Characterization) and the next generation tool in the RELAP reactor safety/systems analysis application series (the replacement for RELAP5). The key to the success of RELAP-7 is the simultaneous advancement of physical models, numerical methods, and software design while maintaining a solid user perspective. Physical models include both PDEs (Partial Differential Equations) and ODEs (Ordinary Differential Equations) and experimental based closure models. RELAP-7 will eventually utilize well posed governing equations for multiphase flow, which can be strictly verified. Closure models used in RELAP5 and newly developed models will be reviewed and selected to reflect the progress made during the past three decades. RELAP-7 uses modern numerical methods, which allow implicit time integration, higher order schemes in both time and space, and strongly coupled multi-physics simulations. RELAP-7 is written with object oriented programming language C++. Its development follows modern software design paradigms. The code is easy to read, develop, maintain, and couple with other codes. Most importantly, the modern software design allows the RELAP-7 code to evolve with time. RELAP-7 is a MOOSE-based application. MOOSE (Multiphysics Object-Oriented Simulation Environment) is a framework for solving computational engineering problems in a well-planned, managed, and coordinated way. By leveraging millions of lines of open source software packages, such as PETSC (a nonlinear solver developed at Argonne National Laboratory) and LibMesh (a Finite Element Analysis package developed at University of Texas), MOOSE significantly reduces the expense and time required to develop new applications. Numerical integration methods and mesh management for parallel computation are provided by MOOSE. Therefore RELAP-7 code developers only need to focus on physics and user experiences. By using the MOOSE development environment, RELAP-7 code is developed by following the same modern software design paradigms used for other MOOSE development efforts. There are currently over 20 different MOOSE based applications ranging from 3-D transient neutron transport, detailed 3-D transient fuel performance analysis, to long-term material aging. Multi-physics and multiple dimensional analyses capabilities can be obtained by coupling RELAP-7 and other MOOSE based applications and by leveraging with capabilities developed by other DOE programs. This allows restricting the focus of RELAP-7 to systems analysis-type simulations and gives priority to retain and significantly extend RELAP5's capabilities.« less

Coupling molecular dynamics with lattice Boltzmann method based on the immersed boundary method

NASA Astrophysics Data System (ADS)

Tan, Jifu; Sinno, Talid; Diamond, Scott

2017-11-01

The study of viscous fluid flow coupled with rigid or deformable solids has many applications in biological and engineering problems, e.g., blood cell transport, drug delivery, and particulate flow. We developed a partitioned approach to solve this coupled Multiphysics problem. The fluid motion was solved by Palabos (Parallel Lattice Boltzmann Solver), while the solid displacement and deformation was simulated by LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator). The coupling was achieved through the immersed boundary method (IBM). The code modeled both rigid and deformable solids exposed to flow. The code was validated with the classic problem of rigid ellipsoid particle orbit in shear flow, blood cell stretching test and effective blood viscosity, and demonstrated essentially linear scaling over 16 cores. An example of the fluid-solid coupling was given for flexible filaments (drug carriers) transport in a flowing blood cell suspensions, highlighting the advantages and capabilities of the developed code. NIH 1U01HL131053-01A1.

GEOS. User Tutorials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fu, Pengchen; Settgast, Randolph R.; Johnson, Scott M.

2014-12-17

GEOS is a massively parallel, multi-physics simulation application utilizing high performance computing (HPC) to address subsurface reservoir stimulation activities with the goal of optimizing current operations and evaluating innovative stimulation methods. GEOS enables coupling of di erent solvers associated with the various physical processes occurring during reservoir stimulation in unique and sophisticated ways, adapted to various geologic settings, materials and stimulation methods. Developed at the Lawrence Livermore National Laboratory (LLNL) as a part of a Laboratory-Directed Research and Development (LDRD) Strategic Initiative (SI) project, GEOS represents the culmination of a multi-year ongoing code development and improvement e ort that hasmore » leveraged existing code capabilities and sta expertise to design new computational geosciences software.« less

Status and future of MUSE

NASA Astrophysics Data System (ADS)

Harfst, S.; Portegies Zwart, S.; McMillan, S.

2008-12-01

We present MUSE, a software framework for combining existing computational tools from different astrophysical domains into a single multi-physics, multi-scale application. MUSE facilitates the coupling of existing codes written in different languages by providing inter-language tools and by specifying an interface between each module and the framework that represents a balance between generality and computational efficiency. This approach allows scientists to use combinations of codes to solve highly-coupled problems without the need to write new codes for other domains or significantly alter their existing codes. MUSE currently incorporates the domains of stellar dynamics, stellar evolution and stellar hydrodynamics for studying generalized stellar systems. We have now reached a ``Noah's Ark'' milestone, with (at least) two available numerical solvers for each domain. MUSE can treat multi-scale and multi-physics systems in which the time- and size-scales are well separated, like simulating the evolution of planetary systems, small stellar associations, dense stellar clusters, galaxies and galactic nuclei. In this paper we describe two examples calculated using MUSE: the merger of two galaxies and an N-body simulation with live stellar evolution. In addition, we demonstrate an implementation of MUSE on a distributed computer which may also include special-purpose hardware, such as GRAPEs or GPUs, to accelerate computations. The current MUSE code base is publicly available as open source at http://muse.li.

Optimization of coupled multiphysics methodology for safety analysis of pebble bed modular reactor

NASA Astrophysics Data System (ADS)

Mkhabela, Peter Tshepo

The research conducted within the framework of this PhD thesis is devoted to the high-fidelity multi-physics (based on neutronics/thermal-hydraulics coupling) analysis of Pebble Bed Modular Reactor (PBMR), which is a High Temperature Reactor (HTR). The Next Generation Nuclear Plant (NGNP) will be a HTR design. The core design and safety analysis methods are considerably less developed and mature for HTR analysis than those currently used for Light Water Reactors (LWRs). Compared to LWRs, the HTR transient analysis is more demanding since it requires proper treatment of both slower and much longer transients (of time scale in hours and days) and fast and short transients (of time scale in minutes and seconds). There is limited operation and experimental data available for HTRs for validation of coupled multi-physics methodologies. This PhD work developed and verified reliable high fidelity coupled multi-physics models subsequently implemented in robust, efficient, and accurate computational tools to analyse the neutronics and thermal-hydraulic behaviour for design optimization and safety evaluation of PBMR concept The study provided a contribution to a greater accuracy of neutronics calculations by including the feedback from thermal hydraulics driven temperature calculation and various multi-physics effects that can influence it. Consideration of the feedback due to the influence of leakage was taken into account by development and implementation of improved buckling feedback models. Modifications were made in the calculation procedure to ensure that the xenon depletion models were accurate for proper interpolation from cross section tables. To achieve this, the NEM/THERMIX coupled code system was developed to create the system that is efficient and stable over the duration of transient calculations that last over several tens of hours. Another achievement of the PhD thesis was development and demonstration of full-physics, three-dimensional safety analysis methodology for the PBMR to provide reference solutions. Investigation of different aspects of the coupled methodology and development of efficient kinetics treatment for the PBMR were carried out, which accounts for all feedback phenomena in an efficient manner. The OECD/NEA PBMR-400 coupled code benchmark was used as a test matrix for the proposed investigations. The integrated thermal-hydraulics and neutronics (multi-physics) methods were extended to enable modeling of a wider range of transients pertinent to the PBMR. First, the effect of the spatial mapping schemes (spatial coupling) was studied and quantified for different types of transients, which resulted in implementation of improved mapping methodology based on user defined criteria. The second aspect that was studied and optimized is the temporal coupling and meshing schemes between the neutronics and thermal-hydraulics time step selection algorithms. The coupled code convergence was achieved supplemented by application of methods to accelerate it. Finally, the modeling of all feedback phenomena in PBMRs was investigated and a novel treatment of cross-section dependencies was introduced for improving the representation of cross-section variations. The added benefit was that in the process of studying and improving the coupled multi-physics methodology more insight was gained into the physics and dynamics of PBMR, which will help also to optimize the PBMR design and improve its safety. One unique contribution of the PhD research is the investigation of the importance of the correct representation of the three-dimensional (3-D) effects in the PBMR analysis. The performed studies demonstrated that explicit 3-D modeling of control rod movement is superior and removes the errors associated with the grey curtain (2-D homogenized) approximation.

Scalable Methods for Uncertainty Quantification, Data Assimilation and Target Accuracy Assessment for Multi-Physics Advanced Simulation of Light Water Reactors

NASA Astrophysics Data System (ADS)

Khuwaileh, Bassam

High fidelity simulation of nuclear reactors entails large scale applications characterized with high dimensionality and tremendous complexity where various physics models are integrated in the form of coupled models (e.g. neutronic with thermal-hydraulic feedback). Each of the coupled modules represents a high fidelity formulation of the first principles governing the physics of interest. Therefore, new developments in high fidelity multi-physics simulation and the corresponding sensitivity/uncertainty quantification analysis are paramount to the development and competitiveness of reactors achieved through enhanced understanding of the design and safety margins. Accordingly, this dissertation introduces efficient and scalable algorithms for performing efficient Uncertainty Quantification (UQ), Data Assimilation (DA) and Target Accuracy Assessment (TAA) for large scale, multi-physics reactor design and safety problems. This dissertation builds upon previous efforts for adaptive core simulation and reduced order modeling algorithms and extends these efforts towards coupled multi-physics models with feedback. The core idea is to recast the reactor physics analysis in terms of reduced order models. This can be achieved via identifying the important/influential degrees of freedom (DoF) via the subspace analysis, such that the required analysis can be recast by considering the important DoF only. In this dissertation, efficient algorithms for lower dimensional subspace construction have been developed for single physics and multi-physics applications with feedback. Then the reduced subspace is used to solve realistic, large scale forward (UQ) and inverse problems (DA and TAA). Once the elite set of DoF is determined, the uncertainty/sensitivity/target accuracy assessment and data assimilation analysis can be performed accurately and efficiently for large scale, high dimensional multi-physics nuclear engineering applications. Hence, in this work a Karhunen-Loeve (KL) based algorithm previously developed to quantify the uncertainty for single physics models is extended for large scale multi-physics coupled problems with feedback effect. Moreover, a non-linear surrogate based UQ approach is developed, used and compared to performance of the KL approach and brute force Monte Carlo (MC) approach. On the other hand, an efficient Data Assimilation (DA) algorithm is developed to assess information about model's parameters: nuclear data cross-sections and thermal-hydraulics parameters. Two improvements are introduced in order to perform DA on the high dimensional problems. First, a goal-oriented surrogate model can be used to replace the original models in the depletion sequence (MPACT -- COBRA-TF - ORIGEN). Second, approximating the complex and high dimensional solution space with a lower dimensional subspace makes the sampling process necessary for DA possible for high dimensional problems. Moreover, safety analysis and design optimization depend on the accurate prediction of various reactor attributes. Predictions can be enhanced by reducing the uncertainty associated with the attributes of interest. Accordingly, an inverse problem can be defined and solved to assess the contributions from sources of uncertainty; and experimental effort can be subsequently directed to further improve the uncertainty associated with these sources. In this dissertation a subspace-based gradient-free and nonlinear algorithm for inverse uncertainty quantification namely the Target Accuracy Assessment (TAA) has been developed and tested. The ideas proposed in this dissertation were first validated using lattice physics applications simulated using SCALE6.1 package (Pressurized Water Reactor (PWR) and Boiling Water Reactor (BWR) lattice models). Ultimately, the algorithms proposed her were applied to perform UQ and DA for assembly level (CASL progression problem number 6) and core wide problems representing Watts Bar Nuclear 1 (WBN1) for cycle 1 of depletion (CASL Progression Problem Number 9) modeled via simulated using VERA-CS which consists of several multi-physics coupled models. The analysis and algorithms developed in this dissertation were encoded and implemented in a newly developed tool kit algorithms for Reduced Order Modeling based Uncertainty/Sensitivity Estimator (ROMUSE).

Multi-Physics Modeling of Molten Salt Transport in Solid Oxide Membrane (SOM) Electrolysis and Recycling of Magnesium

DOE Office of Scientific and Technical Information (OSTI.GOV)

Powell, Adam; Pati, Soobhankar

2012-03-11

Solid Oxide Membrane (SOM) Electrolysis is a new energy-efficient zero-emissions process for producing high-purity magnesium and high-purity oxygen directly from industrial-grade MgO. SOM Recycling combines SOM electrolysis with electrorefining, continuously and efficiently producing high-purity magnesium from low-purity partially oxidized scrap. In both processes, electrolysis and/or electrorefining take place in the crucible, where raw material is continuously fed into the molten salt electrolyte, producing magnesium vapor at the cathode and oxygen at the inert anode inside the SOM. This paper describes a three-dimensional multi-physics finite-element model of ionic current, fluid flow driven by argon bubbling and thermal buoyancy, and heat andmore » mass transport in the crucible. The model predicts the effects of stirring on the anode boundary layer and its time scale of formation, and the effect of natural convection at the outer wall. MOxST has developed this model as a tool for scale-up design of these closely-related processes.« less

Advanced Multi-Physics (AMP)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Philip, Bobby

2012-06-01

The Advanced Multi-Physics (AMP) code, in its present form, will allow a user to build a multi-physics application code for existing mechanics and diffusion operators and extend them with user-defined material models and new physics operators. There are examples that demonstrate mechanics, thermo-mechanics, coupled diffusion, and mechanical contact. The AMP code is designed to leverage a variety of mathematical solvers (PETSc, Trilinos, SUNDIALS, and AMP solvers) and mesh databases (LibMesh and AMP) in a consistent interchangeable approach.

General linear methods and friends: Toward efficient solutions of multiphysics problems

NASA Astrophysics Data System (ADS)

Sandu, Adrian

2017-07-01

Time dependent multiphysics partial differential equations are of great practical importance as they model diverse phenomena that appear in mechanical and chemical engineering, aeronautics, astrophysics, meteorology and oceanography, financial modeling, environmental sciences, etc. There is no single best time discretization for the complex multiphysics systems of practical interest. We discuss "multimethod" approaches that combine different time steps and discretizations using the rigourous frameworks provided by Partitioned General Linear Methods and Generalize-structure Additive Runge Kutta Methods..

Design and multi-physics optimization of rotary MRF brakes

NASA Astrophysics Data System (ADS)

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.

MODELING MICROBUBBLE DYNAMICS IN BIOMEDICAL APPLICATIONS*

PubMed Central

CHAHINE, Georges L.; HSIAO, Chao-Tsung

2012-01-01

Controlling microbubble dynamics to produce desirable biomedical outcomes when and where necessary and avoid deleterious effects requires advanced knowledge, which can be achieved only through a combination of experimental and numerical/analytical techniques. The present communication presents a multi-physics approach to study the dynamics combining viscous- in-viscid effects, liquid and structure dynamics, and multi bubble interaction. While complex numerical tools are developed and used, the study aims at identifying the key parameters influencing the dynamics, which need to be included in simpler models. PMID:22833696

FY17 Status Report on NEAMS Neutronics Activities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, C. H.; Jung, Y. S.; Smith, M. A.

2017-09-30

Under the U.S. DOE NEAMS program, the high-fidelity neutronics code system has been developed to support the multiphysics modeling and simulation capability named SHARP. The neutronics code system includes the high-fidelity neutronics code PROTEUS, the cross section library and preprocessing tools, the multigroup cross section generation code MC2-3, the in-house meshing generation tool, the perturbation and sensitivity analysis code PERSENT, and post-processing tools. The main objectives of the NEAMS neutronics activities in FY17 are to continue development of an advanced nodal solver in PROTEUS for use in nuclear reactor design and analysis projects, implement a simplified sub-channel based thermal-hydraulic (T/H)more » capability into PROTEUS to efficiently compute the thermal feedback, improve the performance of PROTEUS-MOCEX using numerical acceleration and code optimization, improve the cross section generation tools including MC2-3, and continue to perform verification and validation tests for PROTEUS.« less

Improvements to Nuclear Data and Its Uncertainties by Theoretical Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Danon, Yaron; Nazarewicz, Witold; Talou, Patrick

2013-02-18

This project addresses three important gaps in existing evaluated nuclear data libraries that represent a significant hindrance against highly advanced modeling and simulation capabilities for the Advanced Fuel Cycle Initiative (AFCI). This project will: Develop advanced theoretical tools to compute prompt fission neutrons and gamma-ray characteristics well beyond average spectra and multiplicity, and produce new evaluated files of U and Pu isotopes, along with some minor actinides; Perform state-of-the-art fission cross-section modeling and calculations using global and microscopic model input parameters, leading to truly predictive fission cross-sections capabilities. Consistent calculations for a suite of Pu isotopes will be performed; Implementmore » innovative data assimilation tools, which will reflect the nuclear data evaluation process much more accurately, and lead to a new generation of uncertainty quantification files. New covariance matrices will be obtained for Pu isotopes and compared to existing ones. The deployment of a fleet of safe and efficient advanced reactors that minimize radiotoxic waste and are proliferation-resistant is a clear and ambitious goal of AFCI. While in the past the design, construction and operation of a reactor were supported through empirical trials, this new phase in nuclear energy production is expected to rely heavily on advanced modeling and simulation capabilities. To be truly successful, a program for advanced simulations of innovative reactors will have to develop advanced multi-physics capabilities, to be run on massively parallel super- computers, and to incorporate adequate and precise underlying physics. And all these areas have to be developed simultaneously to achieve those ambitious goals. Of particular interest are reliable fission cross-section uncertainty estimates (including important correlations) and evaluations of prompt fission neutrons and gamma-ray spectra and uncertainties.« less

Quinoa - Adaptive Computational Fluid Dynamics, 0.2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bakosi, Jozsef; Gonzalez, Francisco; Rogers, Brandon

Quinoa is a set of computational tools that enables research and numerical analysis in fluid dynamics. At this time it remains a test-bed to experiment with various algorithms using fully asynchronous runtime systems. Currently, Quinoa consists of the following tools: (1) Walker, a numerical integrator for systems of stochastic differential equations in time. It is a mathematical tool to analyze and design the behavior of stochastic differential equations. It allows the estimation of arbitrary coupled statistics and probability density functions and is currently used for the design of statistical moment approximations for multiple mixing materials in variable-density turbulence. (2) Inciter,more » an overdecomposition-aware finite element field solver for partial differential equations using 3D unstructured grids. Inciter is used to research asynchronous mesh-based algorithms and to experiment with coupling asynchronous to bulk-synchronous parallel code. Two planned new features of Inciter, compared to the previous release (LA-CC-16-015), to be implemented in 2017, are (a) a simple Navier-Stokes solver for ideal single-material compressible gases, and (b) solution-adaptive mesh refinement (AMR), which enables dynamically concentrating compute resources to regions with interesting physics. Using the NS-AMR problem we plan to explore how to scale such high-load-imbalance simulations, representative of large production multiphysics codes, to very large problems on very large computers using an asynchronous runtime system. (3) RNGTest, a test harness to subject random number generators to stringent statistical tests enabling quantitative ranking with respect to their quality and computational cost. (4) UnitTest, a unit test harness, running hundreds of tests per second, capable of testing serial, synchronous, and asynchronous functions. (5) MeshConv, a mesh file converter that can be used to convert 3D tetrahedron meshes from and to either of the following formats: Gmsh, (http://www.geuz.org/gmsh), Netgen, (http://sourceforge.net/apps/mediawiki/netgen-mesher), ExodusII, (http://sourceforge.net/projects/exodusii), HyperMesh, (http://www.altairhyperworks.com/product/HyperMesh).« less

FEM and Multiphysics Applications at NASA/GSFC

NASA Technical Reports Server (NTRS)

Loughlin, James

2004-01-01

FEM software available to the Mechanical Systems Analysis and Simulation Branch at Goddard Space Flight Center (GSFC) include: 1) MSC/Nastran; 2) Abaqus; 3) Ansys/Multiphysics; 4) COSMOS/M; 5) 'Home-grown' programs; 6) Pre/post processors such as Patran and FEMAP. This viewgraph presentation provides additional information on MSC/Nastran and Ansys/Multiphysics, and includes screen shots of analyzed equipment, including the Wilkinson Microwave Anistropy Probe, a micro-mirror, a MEMS tunable filter, and a micro-shutter array. The presentation also includes information on the verification of results.

Efficient parallelization for AMR MHD multiphysics calculations; implementation in AstroBEAR

NASA Astrophysics Data System (ADS)

Carroll-Nellenback, Jonathan J.; Shroyer, Brandon; Frank, Adam; Ding, Chen

2013-03-01

Current adaptive mesh refinement (AMR) simulations require algorithms that are highly parallelized and manage memory efficiently. As compute engines grow larger, AMR simulations will require algorithms that achieve new levels of efficient parallelization and memory management. We have attempted to employ new techniques to achieve both of these goals. Patch or grid based AMR often employs ghost cells to decouple the hyperbolic advances of each grid on a given refinement level. This decoupling allows each grid to be advanced independently. In AstroBEAR we utilize this independence by threading the grid advances on each level with preference going to the finer level grids. This allows for global load balancing instead of level by level load balancing and allows for greater parallelization across both physical space and AMR level. Threading of level advances can also improve performance by interleaving communication with computation, especially in deep simulations with many levels of refinement. While we see improvements of up to 30% on deep simulations run on a few cores, the speedup is typically more modest (5-20%) for larger scale simulations. To improve memory management we have employed a distributed tree algorithm that requires processors to only store and communicate local sections of the AMR tree structure with neighboring processors. Using this distributed approach we are able to get reasonable scaling efficiency (>80%) out to 12288 cores and up to 8 levels of AMR - independent of the use of threading.

A mathematical model for predicting photo-induced voltage and photostriction of PLZT with coupled multi-physics fields and its application

NASA Astrophysics Data System (ADS)

Huang, J. H.; Wang, X. J.; Wang, J.

2016-02-01

The primary purpose of this paper is to propose a mathematical model of PLZT ceramic with coupled multi-physics fields, e.g. thermal, electric, mechanical and light field. To this end, the coupling relationships of multi-physics fields and the mechanism of some effects resulting in the photostrictive effect are analyzed theoretically, based on which a mathematical model considering coupled multi-physics fields is established. According to the analysis and experimental results, the mathematical model can explain the hysteresis phenomenon and the variation trend of the photo-induced voltage very well and is in agreement with the experimental curves. In addition, the PLZT bimorph is applied as an energy transducer for a photovoltaic-electrostatic hybrid actuated micromirror, and the relation of the rotation angle and the photo-induced voltage is discussed based on the novel photostrictive mathematical model.

Advances in Geologic Disposal System Modeling and Application to Crystalline Rock

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mariner, Paul E.; Stein, Emily R.; Frederick, Jennifer M.

The Used Fuel Disposition Campaign (UFDC) of the U.S. Department of Energy (DOE) Office of Nuclear Energy (NE), Office of Fuel Cycle Technology (OFCT) is conducting research and development (R&D) on geologic disposal of used nuclear fuel (UNF) and high-level nuclear waste (HLW). Two of the high priorities for UFDC disposal R&D are design concept development and disposal system modeling (DOE 2011). These priorities are directly addressed in the UFDC Generic Disposal Systems Analysis (GDSA) work package, which is charged with developing a disposal system modeling and analysis capability for evaluating disposal system performance for nuclear waste in geologic mediamore » (e.g., salt, granite, clay, and deep borehole disposal). This report describes specific GDSA activities in fiscal year 2016 (FY 2016) toward the development of the enhanced disposal system modeling and analysis capability for geologic disposal of nuclear waste. The GDSA framework employs the PFLOTRAN thermal-hydrologic-chemical multi-physics code and the Dakota uncertainty sampling and propagation code. Each code is designed for massively-parallel processing in a high-performance computing (HPC) environment. Multi-physics representations in PFLOTRAN are used to simulate various coupled processes including heat flow, fluid flow, waste dissolution, radionuclide release, radionuclide decay and ingrowth, precipitation and dissolution of secondary phases, and radionuclide transport through engineered barriers and natural geologic barriers to the biosphere. Dakota is used to generate sets of representative realizations and to analyze parameter sensitivity.« less

Absorption and emission properties of photonic crystals and metamaterials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Lili

We study the emission and absorption properties of photonic crystals and metamaterials using Comsol Multiphysics and Ansoft HFSS as simulation tools. We calculate the emission properties of metallic designs using drude model and the results illustrate that an appropriate termination of the surface of the metallic structure can significantly increase the absorption and therefore the thermal emissivity. We investigate the spontaneous emission rate modifications that occur for emitters inside two-dimensional photonic crystals and find the isotropic and directional emissions with respect to different frequencies as we have expected.

Multi-physics modelling approach for oscillatory microengines: application for a microStirling generator design

NASA Astrophysics Data System (ADS)

Formosa, F.; Fréchette, L. G.

2015-12-01

An electrical circuit equivalent (ECE) approach has been set up allowing elementary oscillatory microengine components to be modelled. They cover gas channel/chamber thermodynamics, viscosity and thermal effects, mechanical structure and electromechanical transducers. The proposed tool has been validated on a centimeter scale Free Piston membrane Stirling engine [1]. We propose here new developments taking into account scaling effects to establish models suitable for any microengines. They are based on simplifications derived from the comparison of the hydraulic radius with respect to the viscous and thermal penetration depths respectively).

Explicit integration with GPU acceleration for large kinetic networks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brock, Benjamin; Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830; Belt, Andrew

2015-12-01

We demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. This orders-of-magnitude decrease in computation time for solving systems of realistic kinetic networks implies that important coupled, multiphysics problems inmore » various scientific and technical fields that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.« less

LAURA Users Manual: 5.3-48528

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Chirstopher O.; Kleb, Bil

2010-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multi-physics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the FUN3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

LAURA Users Manual: 5.5-64987

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, William L.

2013-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintain ability by eliminating the requirement for problem dependent recompilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multi-physics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the Fun3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

LAURA Users Manual: 5.4-54166

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2011-01-01

This users manual provides in-depth information concerning installation and execution of Laura, version 5. Laura is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 Laura code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multi-physics coupling. As a result, Laura now shares gas-physics modules, MPI modules, and other low-level modules with the Fun3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

LAURA Users Manual: 5.2-43231

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2009-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multiphysics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the FUN3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

Laura Users Manual: 5.1-41601

NASA Technical Reports Server (NTRS)

Mazaheri, Alireza; Gnoffo, Peter A.; Johnston, Christopher O.; Kleb, Bil

2009-01-01

This users manual provides in-depth information concerning installation and execution of LAURA, version 5. LAURA is a structured, multi-block, computational aerothermodynamic simulation code. Version 5 represents a major refactoring of the original Fortran 77 LAURA code toward a modular structure afforded by Fortran 95. The refactoring improved usability and maintainability by eliminating the requirement for problem-dependent re-compilations, providing more intuitive distribution of functionality, and simplifying interfaces required for multiphysics coupling. As a result, LAURA now shares gas-physics modules, MPI modules, and other low-level modules with the FUN3D unstructured-grid code. In addition to internal refactoring, several new features and capabilities have been added, e.g., a GNU-standard installation process, parallel load balancing, automatic trajectory point sequencing, free-energy minimization, and coupled ablation and flowfield radiation.

Prediction of the Lorentz Force Detuning and pressure sensitivity for a Pillbox cavity

DOE PAGES

Parise, M.

2018-05-18

The Lorentz Force Detuning (LFD) and the pressure sensitivity are two critical concerns during the design of a Superconducting Radio Frequency (SRF) cavity resonator. The mechanical deformation of the bare Niobium cavity walls, due to the electromagnetic fields and fluctuation of the external pressure in the Helium bath, can dynamically and statically detune the frequency of the cavity and can cause beam phase errors. The frequency shift can be compensated by additional RF power, that is required to maintain the accelerating gradient, or by sophisticated tuning mechanisms and control-compensation algorithms. Passive stiffening is one of the simplest and most effectivemore » tools that can be used during the early design phase, capable of satisfying the Radio Frequency (RF) requisites. This approach requires several multiphysics simulations as well as a deep mechanical and RF knowledge of the phenomena involved. In this paper, is presented a new numerical model for a pillbox cavity that can predict the frequency shifts caused by the LFD and external pressure. This method allows to greatly reduce the computational effort, which is necessary to meet the RF requirements and to keep track of the frequency shifts without using the time consuming multiphysics simulations.« less

Prediction of the Lorentz Force Detuning and pressure sensitivity for a Pillbox cavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parise, M.

The Lorentz Force Detuning (LFD) and the pressure sensitivity are two critical concerns during the design of a Superconducting Radio Frequency (SRF) cavity resonator. The mechanical deformation of the bare Niobium cavity walls, due to the electromagnetic fields and fluctuation of the external pressure in the Helium bath, can dynamically and statically detune the frequency of the cavity and can cause beam phase errors. The frequency shift can be compensated by additional RF power, that is required to maintain the accelerating gradient, or by sophisticated tuning mechanisms and control-compensation algorithms. Passive stiffening is one of the simplest and most effectivemore » tools that can be used during the early design phase, capable of satisfying the Radio Frequency (RF) requisites. This approach requires several multiphysics simulations as well as a deep mechanical and RF knowledge of the phenomena involved. In this paper, is presented a new numerical model for a pillbox cavity that can predict the frequency shifts caused by the LFD and external pressure. This method allows to greatly reduce the computational effort, which is necessary to meet the RF requirements and to keep track of the frequency shifts without using the time consuming multiphysics simulations.« less

Prediction of the Lorentz Force Detuning and pressure sensitivity for a Pillbox cavity

NASA Astrophysics Data System (ADS)

Parise, M.

2018-05-01

The Lorentz Force Detuning (LFD) and the pressure sensitivity are two critical concerns during the design of a Superconducting Radio Frequency (SRF) cavity resonator. The mechanical deformation of the bare Niobium cavity walls, due to the electromagnetic fields and fluctuation of the external pressure in the Helium bath, can dynamically and statically detune the frequency of the cavity and can cause beam phase errors. The frequency shift can be compensated by additional RF power, that is required to maintain the accelerating gradient, or by sophisticated tuning mechanisms and control-compensation algorithms. Passive stiffening is one of the simplest and most effective tools that can be used during the early design phase, capable of satisfying the Radio Frequency (RF) requisites. This approach requires several multiphysics simulations as well as a deep mechanical and RF knowledge of the phenomena involved. In this paper, is presented a new numerical model for a pillbox cavity that can predict the frequency shifts caused by the LFD and external pressure. This method allows to greatly reduce the computational effort, which is necessary to meet the RF requirements and to keep track of the frequency shifts without using the time consuming multiphysics simulations.

Unstructured LES of Reacting Multiphase Flows in Realistic Gas Turbine Combustors

NASA Technical Reports Server (NTRS)

Ham, Frank; Apte, Sourabh; Iaccarino, Gianluca; Wu, Xiao-Hua; Herrmann, Marcus; Constantinescu, George; Mahesh, Krishnan; Moin, Parviz

2003-01-01

As part of the Accelerated Strategic Computing Initiative (ASCI) program, an accurate and robust simulation tool is being developed to perform high-fidelity LES studies of multiphase, multiscale turbulent reacting flows in aircraft gas turbine combustor configurations using hybrid unstructured grids. In the combustor, pressurized gas from the upstream compressor is reacted with atomized liquid fuel to produce the combustion products that drive the downstream turbine. The Large Eddy Simulation (LES) approach is used to simulate the combustor because of its demonstrated superiority over RANS in predicting turbulent mixing, which is central to combustion. This paper summarizes the accomplishments of the combustor group over the past year, concentrating mainly on the two major milestones achieved this year: 1) Large scale simulation: A major rewrite and redesign of the flagship unstructured LES code has allowed the group to perform large eddy simulations of the complete combustor geometry (all 18 injectors) with over 100 million control volumes; 2) Multi-physics simulation in complex geometry: The first multi-physics simulations including fuel spray breakup, coalescence, evaporation, and combustion are now being performed in a single periodic sector (1/18th) of an actual Pratt & Whitney combustor geometry.

Prediction of the Lorentz Force Detuning and Pressure Sensitivity for a Pillbox Cavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Parise, M.

2018-04-23

The Lorentz Force Detuning (LFD) and the pressure sensitivity are two critical concerns during the design of a Superconducting Radio Frequency (SRF) cavity resonator. The mechanical deformation of the bare Niobium cavity walls, due to the electromagnetic fields and fluctuation of the external pressure in the Helium bath, can dynamically and statically detune the frequency of the cavity and can cause beam phase errors. The frequency shift can be compensated by additional RF power, that is required to maintain the accelerating gradient, or by sophisticated tuning mechanisms and control-compensation algorithms. Passive stiffening is one of the simplest and most effectivemore » tools that can be used during the early design phase, capable of satisfying the Radio Frequency (RF) requisites. This approach requires several multiphysics simulations as well as a deep mechanical and RF knowledge of the phenomena involved. In this paper, is presented a new numerical model for a pillbox cavity that can predict the frequency shifts caused by the LFD and external pressure. This method allows to greatly reduce the computational effort, which is necessary to meet the RF requirements and to keep track of the frequency shifts without using the time consuming multiphysics simulations.« less

A survey of parallel programming tools

NASA Technical Reports Server (NTRS)

Cheng, Doreen Y.

1991-01-01

This survey examines 39 parallel programming tools. Focus is placed on those tool capabilites needed for parallel scientific programming rather than for general computer science. The tools are classified with current and future needs of Numerical Aerodynamic Simulator (NAS) in mind: existing and anticipated NAS supercomputers and workstations; operating systems; programming languages; and applications. They are divided into four categories: suggested acquisitions, tools already brought in; tools worth tracking; and tools eliminated from further consideration at this time.

A Comparison of Automatic Parallelization Tools/Compilers on the SGI Origin 2000 Using the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Saini, Subhash; Frumkin, Michael; Hribar, Michelle; Jin, Hao-Qiang; Waheed, Abdul; Yan, Jerry

1998-01-01

Porting applications to new high performance parallel and distributed computing platforms is a challenging task. Since writing parallel code by hand is extremely time consuming and costly, porting codes would ideally be automated by using some parallelization tools and compilers. In this paper, we compare the performance of the hand written NAB Parallel Benchmarks against three parallel versions generated with the help of tools and compilers: 1) CAPTools: an interactive computer aided parallelization too] that generates message passing code, 2) the Portland Group's HPF compiler and 3) using compiler directives with the native FORTAN77 compiler on the SGI Origin2000.

Parallel workflow tools to facilitate human brain MRI post-processing

PubMed Central

Cui, Zaixu; Zhao, Chenxi; Gong, Gaolang

2015-01-01

Multi-modal magnetic resonance imaging (MRI) techniques are widely applied in human brain studies. To obtain specific brain measures of interest from MRI datasets, a number of complex image post-processing steps are typically required. Parallel workflow tools have recently been developed, concatenating individual processing steps and enabling fully automated processing of raw MRI data to obtain the final results. These workflow tools are also designed to make optimal use of available computational resources and to support the parallel processing of different subjects or of independent processing steps for a single subject. Automated, parallel MRI post-processing tools can greatly facilitate relevant brain investigations and are being increasingly applied. In this review, we briefly summarize these parallel workflow tools and discuss relevant issues. PMID:26029043

Automatic Generation of OpenMP Directives and Its Application to Computational Fluid Dynamics Codes

NASA Technical Reports Server (NTRS)

Yan, Jerry; Jin, Haoqiang; Frumkin, Michael; Yan, Jerry (Technical Monitor)

2000-01-01

The shared-memory programming model is a very effective way to achieve parallelism on shared memory parallel computers. As great progress was made in hardware and software technologies, performance of parallel programs with compiler directives has demonstrated large improvement. The introduction of OpenMP directives, the industrial standard for shared-memory programming, has minimized the issue of portability. In this study, we have extended CAPTools, a computer-aided parallelization toolkit, to automatically generate OpenMP-based parallel programs with nominal user assistance. We outline techniques used in the implementation of the tool and discuss the application of this tool on the NAS Parallel Benchmarks and several computational fluid dynamics codes. This work demonstrates the great potential of using the tool to quickly port parallel programs and also achieve good performance that exceeds some of the commercial tools.

ADHydro: A Large-scale High Resolution Multi-Physics Distributed Water Resources Model for Water Resource Simulations in a Parallel Computing Environment

NASA Astrophysics Data System (ADS)

lai, W.; Steinke, R. C.; Ogden, F. L.

2013-12-01

Physics-based watershed models are useful tools for hydrologic studies, water resources management and economic analyses in the contexts of climate, land-use, and water-use changes. This poster presents development of a physics-based, high-resolution, distributed water resources model suitable for simulating large watersheds in a massively parallel computing environment. Developing this model is one of the objectives of the NSF EPSCoR RII Track II CI-WATER project, which is joint between Wyoming and Utah. The model, which we call ADHydro, is aimed at simulating important processes in the Rocky Mountain west, includes: rainfall and infiltration, snowfall and snowmelt in complex terrain, vegetation and evapotranspiration, soil heat flux and freezing, overland flow, channel flow, groundwater flow and water management. The ADHydro model uses the explicit finite volume method to solve PDEs for 2D overland flow, 2D saturated groundwater flow coupled to 1D channel flow. The model has a quasi-3D formulation that couples 2D overland flow and 2D saturated groundwater flow using the 1D Talbot-Ogden finite water-content infiltration and redistribution model. This eliminates difficulties in solving the highly nonlinear 3D Richards equation, while the finite volume Talbot-Ogden infiltration solution is computationally efficient, guaranteed to conserve mass, and allows simulation of the effect of near-surface groundwater tables on runoff generation. The process-level components of the model are being individually tested and validated. The model as a whole will be tested on the Green River basin in Wyoming and ultimately applied to the entire Upper Colorado River basin. ADHydro development has necessitated development of tools for large-scale watershed modeling, including open-source workflow steps to extract hydromorphological information from GIS data, integrate hydrometeorological and water management forcing input, and post-processing and visualization of large output data sets. The ADHydro model will be coupled with relevant components of the NOAH-MP land surface scheme and the WRF mesoscale meteorological model. Model objectives include well documented Application Programming Interfaces (APIs) to facilitate modifications and additions by others. We will release the model as open-source in 2014 and begin establishing a users' community.

Evaluation of mechanical deformation and distributive magnetic loads with different mechanical constraints in two parallel conducting bars

NASA Astrophysics Data System (ADS)

Lee, Ho-Young; Lee, Se-Hee

2017-08-01

Mechanical deformation, bending deformation, and distributive magnetic loads were evaluated numerically and experimentally for conducting materials excited with high current. Until now, many research works have extensively studied the area of magnetic force and mechanical deformation by using coupled approaches such as multiphysics solvers. In coupled analysis for magnetoelastic problems, some articles and commercial software have presented the resultant mechanical deformation and stress on the body. To evaluate the mechanical deformation, the Lorentz force density method (LZ) and the Maxwell stress tensor method (MX) have been widely used for conducting materials. However, it is difficult to find any experimental verification regarding mechanical deformation or bending deformation due to magnetic force density. Therefore, we compared our numerical results to those from experiments with two parallel conducting bars to verify our numerical setup for bending deformation. Before showing this, the basic and interesting coupled simulation was conducted to test the mechanical deformations by the LZ (body force density) and the MX (surface force density) methods. This resulted in MX gave the same total force as LZ, but the local force distribution in MX introduced an incorrect mechanical deformation in the simulation of a solid conductor.

Explicit integration with GPU acceleration for large kinetic networks

DOE PAGES

Brock, Benjamin; Belt, Andrew; Billings, Jay Jay; ...

2015-09-15

In this study, we demonstrate the first implementation of recently-developed fast explicit kinetic integration algorithms on modern graphics processing unit (GPU) accelerators. Taking as a generic test case a Type Ia supernova explosion with an extremely stiff thermonuclear network having 150 isotopic species and 1604 reactions coupled to hydrodynamics using operator splitting, we demonstrate the capability to solve of order 100 realistic kinetic networks in parallel in the same time that standard implicit methods can solve a single such network on a CPU. In addition, this orders-of-magnitude decrease in computation time for solving systems of realistic kinetic networks implies thatmore » important coupled, multiphysics problems in various scientific and technical fields that were intractable, or could be simulated only with highly schematic kinetic networks, are now computationally feasible.« less

Coupling LAMMPS with Lattice Boltzmann fluid solver: theory, implementation, and applications

NASA Astrophysics Data System (ADS)

Tan, Jifu; Sinno, Talid; Diamond, Scott

2016-11-01

Studying of fluid flow coupled with solid has many applications in biological and engineering problems, e.g., blood cell transport, particulate flow, drug delivery. We present a partitioned approach to solve the coupled Multiphysics problem. The fluid motion is solved by the Lattice Boltzmann method, while the solid displacement and deformation is simulated by Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The coupling is achieved through the immersed boundary method so that the expensive remeshing step is eliminated. The code can model both rigid and deformable solids. The code also shows very good scaling results. It was validated with classic problems such as migration of rigid particles, ellipsoid particle's orbit in shear flow. Examples of the applications in blood flow, drug delivery, platelet adhesion and rupture are also given in the paper. NIH.

Performance Analysis and Scaling Behavior of the Terrestrial Systems Modeling Platform TerrSysMP in Large-Scale Supercomputing Environments

NASA Astrophysics Data System (ADS)

Kollet, S. J.; Goergen, K.; Gasper, F.; Shresta, P.; Sulis, M.; Rihani, J.; Simmer, C.; Vereecken, H.

2013-12-01

In studies of the terrestrial hydrologic, energy and biogeochemical cycles, integrated multi-physics simulation platforms take a central role in characterizing non-linear interactions, variances and uncertainties of system states and fluxes in reciprocity with observations. Recently developed integrated simulation platforms attempt to honor the complexity of the terrestrial system across multiple time and space scales from the deeper subsurface including groundwater dynamics into the atmosphere. Technically, this requires the coupling of atmospheric, land surface, and subsurface-surface flow models in supercomputing environments, while ensuring a high-degree of efficiency in the utilization of e.g., standard Linux clusters and massively parallel resources. A systematic performance analysis including profiling and tracing in such an application is crucial in the understanding of the runtime behavior, to identify optimum model settings, and is an efficient way to distinguish potential parallel deficiencies. On sophisticated leadership-class supercomputers, such as the 28-rack 5.9 petaFLOP IBM Blue Gene/Q 'JUQUEEN' of the Jülich Supercomputing Centre (JSC), this is a challenging task, but even more so important, when complex coupled component models are to be analysed. Here we want to present our experience from coupling, application tuning (e.g. 5-times speedup through compiler optimizations), parallel scaling and performance monitoring of the parallel Terrestrial Systems Modeling Platform TerrSysMP. The modeling platform consists of the weather prediction system COSMO of the German Weather Service; the Community Land Model, CLM of NCAR; and the variably saturated surface-subsurface flow code ParFlow. The model system relies on the Multiple Program Multiple Data (MPMD) execution model where the external Ocean-Atmosphere-Sea-Ice-Soil coupler (OASIS3) links the component models. TerrSysMP has been instrumented with the performance analysis tool Scalasca and analyzed on JUQUEEN with processor counts on the order of 10,000. The instrumentation is used in weak and strong scaling studies with real data cases and hypothetical idealized numerical experiments for detailed profiling and tracing analysis. The profiling is not only useful in identifying wait states that are due to the MPMD execution model, but also in fine-tuning resource allocation to the component models in search of the most suitable load balancing. This is especially necessary, as with numerical experiments that cover multiple (high resolution) spatial scales, the time stepping, coupling frequencies, and communication overheads are constantly shifting, which makes it necessary to re-determine the model setup with each new experimental design.

Enabling Predictive Simulation and UQ of Complex Multiphysics PDE Systems by the Development of Goal-Oriented Variational Sensitivity Analysis and a-Posteriori Error Estimation Methods

DOE Office of Scientific and Technical Information (OSTI.GOV)

Estep, Donald

2015-11-30

This project addressed the challenge of predictive computational analysis of strongly coupled, highly nonlinear multiphysics systems characterized by multiple physical phenomena that span a large range of length- and time-scales. Specifically, the project was focused on computational estimation of numerical error and sensitivity analysis of computational solutions with respect to variations in parameters and data. In addition, the project investigated the use of accurate computational estimates to guide efficient adaptive discretization. The project developed, analyzed and evaluated new variational adjoint-based techniques for integration, model, and data error estimation/control and sensitivity analysis, in evolutionary multiphysics multiscale simulations.

CPMIP: measurements of real computational performance of Earth system models in CMIP6

NASA Astrophysics Data System (ADS)

Balaji, Venkatramani; Maisonnave, Eric; Zadeh, Niki; Lawrence, Bryan N.; Biercamp, Joachim; Fladrich, Uwe; Aloisio, Giovanni; Benson, Rusty; Caubel, Arnaud; Durachta, Jeffrey; Foujols, Marie-Alice; Lister, Grenville; Mocavero, Silvia; Underwood, Seth; Wright, Garrett

2017-01-01

A climate model represents a multitude of processes on a variety of timescales and space scales: a canonical example of multi-physics multi-scale modeling. The underlying climate system is physically characterized by sensitive dependence on initial conditions, and natural stochastic variability, so very long integrations are needed to extract signals of climate change. Algorithms generally possess weak scaling and can be I/O and/or memory-bound. Such weak-scaling, I/O, and memory-bound multi-physics codes present particular challenges to computational performance. Traditional metrics of computational efficiency such as performance counters and scaling curves do not tell us enough about real sustained performance from climate models on different machines. They also do not provide a satisfactory basis for comparative information across models. codes present particular challenges to computational performance. We introduce a set of metrics that can be used for the study of computational performance of climate (and Earth system) models. These measures do not require specialized software or specific hardware counters, and should be accessible to anyone. They are independent of platform and underlying parallel programming models. We show how these metrics can be used to measure actually attained performance of Earth system models on different machines, and identify the most fruitful areas of research and development for performance engineering. codes present particular challenges to computational performance. We present results for these measures for a diverse suite of models from several modeling centers, and propose to use these measures as a basis for a CPMIP, a computational performance model intercomparison project (MIP).

Effect of volcanic dykes on coastal groundwater flow and saltwater intrusion: A field-scale multiphysics approach and parameter evaluation

NASA Astrophysics Data System (ADS)

Comte, J.-C.; Wilson, C.; Ofterdinger, U.; González-Quirós, A.

2017-03-01

Volcanic dykes are common discrete heterogeneities in aquifers; however, there is a lack of field examples of, and methodologies for, comprehensive in situ characterization of their properties with respect to groundwater flow and solute transport. We have applied an integrated multiphysics approach to quantify the effect of dolerite dykes on saltwater intrusion in a coastal sandstone aquifer. The approach involved ground geophysical imaging (passive magnetics and electrical resistivity tomography), well hydraulic testing, and tidal propagation analysis, which provided constraints on the geometry of the dyke network, the subsurface saltwater distribution, and the sandstone hydrodynamic properties and connectivity. A three-dimensional variable-density groundwater model coupled with a resistivity model was further calibrated using groundwater and geophysical observations. A good agreement of model simulations with tide-induced head fluctuations, geophysically derived pore water salinities, and measured apparent resistivities was obtained when dykes' hydraulic conductivity, storativity, and effective porosity are respectively about 3, 1, and 1 orders of magnitude lower than the host aquifer. The presence of the dykes results in barrier-like alterations of groundwater flow and saltwater intrusion. Preferential flow paths occur parallel to observed dyke orientations. Freshwater inflows from upland recharge areas concentrate on the land-facing side of the dykes and saltwater penetration is higher on their sea-facing side. This has major implications for managing groundwater resources in dyke-intruded aquifers, including in coastal and island regions and provides wider insights on preferential pathways of groundwater flow and transport in highly heterogeneous aquifer systems.

Dependency graph for code analysis on emerging architectures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shashkov, Mikhail Jurievich; Lipnikov, Konstantin

Direct acyclic dependency (DAG) graph is becoming the standard for modern multi-physics codes.The ideal DAG is the true block-scheme of a multi-physics code. Therefore, it is the convenient object for insitu analysis of the cost of computations and algorithmic bottlenecks related to statistical frequent data motion and dymanical machine state.

Integration of topological modification within the modeling of multi-physics systems: Application to a Pogo-stick

NASA Astrophysics Data System (ADS)

Abdeljabbar Kharrat, Nourhene; Plateaux, Régis; Miladi Chaabane, Mariem; Choley, Jean-Yves; Karra, Chafik; Haddar, Mohamed

2018-05-01

The present work tackles the modeling of multi-physics systems applying a topological approach while proceeding with a new methodology using a topological modification to the structure of systems. Then the comparison with the Magos' methodology is made. Their common ground is the use of connectivity within systems. The comparison and analysis of the different types of modeling show the importance of the topological methodology through the integration of the topological modification to the topological structure of a multi-physics system. In order to validate this methodology, the case of Pogo-stick is studied. The first step consists in generating a topological graph of the system. Then the connectivity step takes into account the contact with the ground. During the last step of this research; the MGS language (Modeling of General System) is used to model the system through equations. Finally, the results are compared to those obtained by MODELICA. Therefore, this proposed methodology may be generalized to model multi-physics systems that can be considered as a set of local elements.

A multiphysical ensemble system of numerical snow modelling

NASA Astrophysics Data System (ADS)

Lafaysse, Matthieu; Cluzet, Bertrand; Dumont, Marie; Lejeune, Yves; Vionnet, Vincent; Morin, Samuel

2017-05-01

Physically based multilayer snowpack models suffer from various modelling errors. To represent these errors, we built the new multiphysical ensemble system ESCROC (Ensemble System Crocus) by implementing new representations of different physical processes in the deterministic coupled multilayer ground/snowpack model SURFEX/ISBA/Crocus. This ensemble was driven and evaluated at Col de Porte (1325 m a.s.l., French alps) over 18 years with a high-quality meteorological and snow data set. A total number of 7776 simulations were evaluated separately, accounting for the uncertainties of evaluation data. The ability of the ensemble to capture the uncertainty associated to modelling errors is assessed for snow depth, snow water equivalent, bulk density, albedo and surface temperature. Different sub-ensembles of the ESCROC system were studied with probabilistic tools to compare their performance. Results show that optimal members of the ESCROC system are able to explain more than half of the total simulation errors. Integrating members with biases exceeding the range corresponding to observational uncertainty is necessary to obtain an optimal dispersion, but this issue can also be a consequence of the fact that meteorological forcing uncertainties were not accounted for. The ESCROC system promises the integration of numerical snow-modelling errors in ensemble forecasting and ensemble assimilation systems in support of avalanche hazard forecasting and other snowpack-modelling applications.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Simunovic, Srdjan; Piro, Markus H.A.

Thermochimica is a software library that determines a unique combination of phases and their compositions at thermochemical equilibrium. Thermochimica can be used for stand-alone calculations or it can be directly coupled to other codes. This release of the software does not have a graphical user interface (GUI) and it can be executed from the command line or from an Application Programming Interface (API). Also, it is not intended for thermodynamic model development or for constructing phase diagrams. The main purpose of the software is to be directly coupled with a multi-physics code to provide material properties and boundary conditions formore » various physical phenomena. Significant research efforts have been dedicated to enhance computational performance through advanced algorithm development, such as improved estimation techniques and non-linear solvers. Various useful parameters can be provided as output from Thermochimica, such as: determination of which phases are stable at equilibrium, the mass of solution species and phases at equilibrium, mole fractions of solution phase constituents, thermochemical activities (which are related to partial pressures for gaseous species), chemical potentials of solution species and phases, and integral Gibbs energy (referenced relative to standard state). The overall goal is to provide an open source computational tool to enhance the predictive capability of multi-physics codes without significantly impeding computational performance.« less

A Multi-physics Approach to Understanding Low Porosity Soils and Reservoir Rocks

NASA Astrophysics Data System (ADS)

Prasad, M.; Mapeli, C.; Livo, K.; Hasanov, A.; Schindler, M.; Ou, L.

2017-12-01

We present recent results on our multiphysics approach to rock physics. Thus, we evaluate geophysical measurements by simultaneously measuring petrophysical properties or imaging strains. In this paper, we present simultaneously measured acoustic and electrical anisotropy data as functions of pressure. Similarly, we present strains and strain localization images simultaneously acquired with acoustic measurements as well as NMR T2 relaxations on pressurized fluids as well as rocks saturated with these pressurized fluids. Such multiphysics experiments allow us to constrain and assign appropriate causative mechanisms to development rock physics models. They also allow us to decouple various effects, for example, fluid versus pressure, on geophysical measurements. We show applications towards reservoir characterization as well as CO2 sequestration applications.

Fully Parallel MHD Stability Analysis Tool

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2014-10-01

Progress on full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. It is a powerful tool for studying MHD and MHD-kinetic instabilities and it is widely used by fusion community. Parallel version of MARS is intended for simulations on local parallel clusters. It will be an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, already implemented in MARS. Parallelization of the code includes parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the present MARS algorithm using parallel libraries and procedures. Initial results of the code parallelization will be reported. Work is supported by the U.S. DOE SBIR program.

Parallelization of NAS Benchmarks for Shared Memory Multiprocessors

NASA Technical Reports Server (NTRS)

Waheed, Abdul; Yan, Jerry C.; Saini, Subhash (Technical Monitor)

1998-01-01

This paper presents our experiences of parallelizing the sequential implementation of NAS benchmarks using compiler directives on SGI Origin2000 distributed shared memory (DSM) system. Porting existing applications to new high performance parallel and distributed computing platforms is a challenging task. Ideally, a user develops a sequential version of the application, leaving the task of porting to new generations of high performance computing systems to parallelization tools and compilers. Due to the simplicity of programming shared-memory multiprocessors, compiler developers have provided various facilities to allow the users to exploit parallelism. Native compilers on SGI Origin2000 support multiprocessing directives to allow users to exploit loop-level parallelism in their programs. Additionally, supporting tools can accomplish this process automatically and present the results of parallelization to the users. We experimented with these compiler directives and supporting tools by parallelizing sequential implementation of NAS benchmarks. Results reported in this paper indicate that with minimal effort, the performance gain is comparable with the hand-parallelized, carefully optimized, message-passing implementations of the same benchmarks.

Multi-Modalities Sensor Science

DTIC Science & Technology

2015-02-28

enhanced multi-mode sensor science. bio -sensing, cross-discipling, multi-physics, nano-technology sailing He +46-8790 8465 1 Final Report for SOARD Project...spectroscopy, nano-technology, biophotonics and multi-physics modeling to produce adaptable bio -nanostructure enhanced multi-mode sensor science. 1...adaptable bio -nanostructure enhanced multi-mode sensor science. The accomplishments includes 1) A General Method for Designing a Radome to Enhance

Edge Vortex Flow Due to Inhomogeneous Ion Concentration

NASA Astrophysics Data System (ADS)

Sugioka, Hideyuki

2017-04-01

The ion distribution of an open parallel electrode system is not known even though it is often used to measure the electrical characteristics of an electrolyte. Thus, for an open electrode system, we perform a non-steady direct multiphysics simulation based on the coupled Poisson-Nernst-Planck and Stokes equations and find that inhomogeneous ion concentrations at edges cause vortex flows and suppress the anomalous increase in the ion concentration near the electrodes. A surprising aspect of our findings is that the large vortex flows at the edges approximately maintain the ion-conserving condition, and thus the ion distribution of an open electrode system can be approximated by the solution of a closed electrode system that considers the ion-conserving condition rather than the Gouy-Chapman solution, which neglects the ion-conserving condition. We believe that our findings make a significant contribution to the understanding of surface science.

Implementation and Assessment of a Virtual Laboratory of Parallel Robots Developed for Engineering Students

ERIC Educational Resources Information Center

Gil, Arturo; Peidró, Adrián; Reinoso, Óscar; Marín, José María

2017-01-01

This paper presents a tool, LABEL, oriented to the teaching of parallel robotics. The application, organized as a set of tools developed using Easy Java Simulations, enables the study of the kinematics of parallel robotics. A set of classical parallel structures was implemented such that LABEL can solve the inverse and direct kinematic problem of…

Multiphysics Analysis of Frequency Detuning in Superconducting RF Cavities for Proton Particle Accelerators

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awida, M. H.; Gonin, I.; Passarelli, D.

2016-01-22

Multiphysics analyses for superconducting cavities are essential in the course of cavity design to meet stringent requirements on cavity frequency detuning. Superconducting RF cavities are the core accelerating elements in modern particle accelerators whether it is proton or electron machine, as they offer extremely high quality factors thus reducing the RF losses per cavity. However, the superior quality factor comes with the challenge of controlling the resonance frequency of the cavity within few tens of hertz bandwidth. In this paper, we investigate how the multiphysics analysis plays a major role in proactively minimizing sources of frequency detuning, specifically; microphonics andmore » Lorentz Force Detuning (LFD) in the stage of RF design of the cavity and mechanical design of the niobium shell and the helium vessel.« less

Unsteady Cascade Aerodynamic Response Using a Multiphysics Simulation Code

NASA Technical Reports Server (NTRS)

Lawrence, C.; Reddy, T. S. R.; Spyropoulos, E.

2000-01-01

The multiphysics code Spectrum(TM) is applied to calculate the unsteady aerodynamic pressures of oscillating cascade of airfoils representing a blade row of a turbomachinery component. Multiphysics simulation is based on a single computational framework for the modeling of multiple interacting physical phenomena, in the present case being between fluids and structures. Interaction constraints are enforced in a fully coupled manner using the augmented-Lagrangian method. The arbitrary Lagrangian-Eulerian method is utilized to account for deformable fluid domains resulting from blade motions. Unsteady pressures are calculated for a cascade designated as the tenth standard, and undergoing plunging and pitching oscillations. The predicted unsteady pressures are compared with those obtained from an unsteady Euler co-de refer-red in the literature. The Spectrum(TM) code predictions showed good correlation for the cases considered.

A Debugger for Computational Grid Applications

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele; Biegel, Bryan (Technical Monitor)

2001-01-01

This viewgraph presentation gives an overview of a debugger for computational grid applications. Details are given on NAS parallel tools groups (including parallelization support tools, evaluation of various parallelization strategies, and distributed and aggregated computing), debugger dependencies, scalability, initial implementation, the process grid, and information on Globus.

Image Processing Using a Parallel Architecture.

DTIC Science & Technology

1987-12-01

ENG/87D-25 Abstract This study developed a set o± low level image processing tools on a parallel computer that allows concurrent processing of images...environment, the set of tools offers a significant reduction in the time required to perform some commonly used image processing operations. vI IMAGE...step toward developing these systems, a structured set of image processing tools was implemented using a parallel computer. More important than

Parallelization of ARC3D with Computer-Aided Tools

NASA Technical Reports Server (NTRS)

Jin, Haoqiang; Hribar, Michelle; Yan, Jerry; Saini, Subhash (Technical Monitor)

1998-01-01

A series of efforts have been devoted to investigating methods of porting and parallelizing applications quickly and efficiently for new architectures, such as the SCSI Origin 2000 and Cray T3E. This report presents the parallelization of a CFD application, ARC3D, using the computer-aided tools, Cesspools. Steps of parallelizing this code and requirements of achieving better performance are discussed. The generated parallel version has achieved reasonably well performance, for example, having a speedup of 30 for 36 Cray T3E processors. However, this performance could not be obtained without modification of the original serial code. It is suggested that in many cases improving serial code and performing necessary code transformations are important parts for the automated parallelization process although user intervention in many of these parts are still necessary. Nevertheless, development and improvement of useful software tools, such as Cesspools, can help trim down many tedious parallelization details and improve the processing efficiency.

Multiphysics modeling of the steel continuous casting process

NASA Astrophysics Data System (ADS)

Hibbeler, Lance C.

This work develops a macroscale, multiphysics model of the continuous casting of steel. The complete model accounts for the turbulent flow and nonuniform distribution of superheat in the molten steel, the elastic-viscoplastic thermal shrinkage of the solidifying shell, the heat transfer through the shell-mold interface with variable gap size, and the thermal distortion of the mold. These models are coupled together with carefully constructed boundary conditions with the aid of reduced-order models into a single tool to investigate behavior in the mold region, for practical applications such as predicting ideal tapers for a beam-blank mold. The thermal and mechanical behaviors of the mold are explored as part of the overall modeling effort, for funnel molds and for beam-blank molds. These models include high geometric detail and reveal temperature variations on the mold-shell interface that may be responsible for cracks in the shell. Specifically, the funnel mold has a column of mold bolts in the middle of the inside-curve region of the funnel that disturbs the uniformity of the hot face temperatures, which combined with the bending effect of the mold on the shell, can lead to longitudinal facial cracks. The shoulder region of the beam-blank mold shows a local hot spot that can be reduced with additional cooling in this region. The distorted shape of the funnel mold narrow face is validated with recent inclinometer measurements from an operating caster. The calculated hot face temperatures and distorted shapes of the mold are transferred into the multiphysics model of the solidifying shell. The boundary conditions for the first iteration of the multiphysics model come from reduced-order models of the process; one such model is derived in this work for mold heat transfer. The reduced-order model relies on the physics of the solution to the one-dimensional heat-conduction equation to maintain the relationships between inputs and outputs of the model. The geometric parameters in the model are calibrated such that the reduced-order model temperatures match a small, periodic subdomain of the mold. These parameters are demonstrated to be insensitive to the calibration conditions. The thermal behavior of the detailed, three-dimensional mold models used in this work can be approximated closely with a few arithmetic calculations after calibrating the reduced-order model of mold heat transfer. The example application of the model includes the effects of the molten steel jet on the solidification front and the ferrostatic pressure. The model is demonstrated to match measurements of mold heat removal and the thickness of a breakout shell all the way around the perimeter of the mold, and gives insight to the cause of breakouts in a beam-blank caster. This multiphysics modeling approach redefines the state of the art of process modeling for continuous casting, and can be~used in future work to explore the formation and prevention of defects and other practical issues. This work also explores the eigen-problem for an arbitrary 3x3 matrix. An explicit, algebraic formula for the eigenvectors is presented.

The Oceanographic Multipurpose Software Environment (OMUSE v1.0)

NASA Astrophysics Data System (ADS)

Pelupessy, Inti; van Werkhoven, Ben; van Elteren, Arjen; Viebahn, Jan; Candy, Adam; Portegies Zwart, Simon; Dijkstra, Henk

2017-08-01

In this paper we present the Oceanographic Multipurpose Software Environment (OMUSE). OMUSE aims to provide a homogeneous environment for existing or newly developed numerical ocean simulation codes, simplifying their use and deployment. In this way, numerical experiments that combine ocean models representing different physics or spanning different ranges of physical scales can be easily designed. Rapid development of simulation models is made possible through the creation of simple high-level scripts. The low-level core of the abstraction in OMUSE is designed to deploy these simulations efficiently on heterogeneous high-performance computing resources. Cross-verification of simulation models with different codes and numerical methods is facilitated by the unified interface that OMUSE provides. Reproducibility in numerical experiments is fostered by allowing complex numerical experiments to be expressed in portable scripts that conform to a common OMUSE interface. Here, we present the design of OMUSE as well as the modules and model components currently included, which range from a simple conceptual quasi-geostrophic solver to the global circulation model POP (Parallel Ocean Program). The uniform access to the codes' simulation state and the extensive automation of data transfer and conversion operations aids the implementation of model couplings. We discuss the types of couplings that can be implemented using OMUSE. We also present example applications that demonstrate the straightforward model initialization and the concurrent use of data analysis tools on a running model. We give examples of multiscale and multiphysics simulations by embedding a regional ocean model into a global ocean model and by coupling a surface wave propagation model with a coastal circulation model.

Reactor Pressure Vessel Integrity Assessments with the Grizzly Aging Simulation Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spencer, Benjamin; Backman, Marie; Hoffman, William

Grizzly is a simulation tool being developed at Idaho National Laboratory (INL) as part of the US Department of Energy’s Light Water Reactor Sustainability program to provide improved safety assessments of systems, components, and structures in nuclear power plants subjected to age-related degradation. Its goal is to provide an improved scientific basis for decisions surrounding license renewal, which would permit operation of commercial nuclear power plants beyond 60 years. Grizzly is based on INL’s MOOSE framework, which enables multiphysics simulations in a parallel computing environment. It will address a wide variety of aging issues in nuclear power plant systems, components,more » and structures, modelling both the aging processes and the ability of age-degraded components to perform safely. The reactor pressure vessel (RPV) was chosen as the initial application for Grizzly. Grizzly solves tightly coupled equations of heat conduction and solid mechanics to simulate the global response of the RPV to accident conditions, and uses submodels to represent regions with pre-existing flaws. Domain integrals are used to calculate stress intensity factors on those flaws. A physically based empirical model is used to evaluate material embrittlement, and is used to evaluate whether crack growth would occur. Grizzly can represent the RPV in 2D or 3D, allowing it to evaluate effects that require higher dimensionality models to capture. Work is underway to use lower length scale models of material evolution to inform engineering models of embrittlement. This paper demonstrates an application of Grizzly to RPV failure assessment, and summarizes on-going work.« less

Multi-Dimensional Simulation of LWR Fuel Behavior in the BISON Fuel Performance Code

NASA Astrophysics Data System (ADS)

Williamson, R. L.; Capps, N. A.; Liu, W.; Rashid, Y. R.; Wirth, B. D.

2016-11-01

Nuclear fuel operates in an extreme environment that induces complex multiphysics phenomena occurring over distances ranging from inter-atomic spacing to meters, and times scales ranging from microseconds to years. To simulate this behavior requires a wide variety of material models that are often complex and nonlinear. The recently developed BISON code represents a powerful fuel performance simulation tool based on its material and physical behavior capabilities, finite-element versatility of spatial representation, and use of parallel computing. The code can operate in full three dimensional (3D) mode, as well as in reduced two dimensional (2D) modes, e.g., axisymmetric radial-axial ( R- Z) or plane radial-circumferential ( R- θ), to suit the application and to allow treatment of global and local effects. A BISON case study was used to illustrate analysis of Pellet Clad Mechanical Interaction failures from manufacturing defects using combined 2D and 3D analyses. The analysis involved commercial fuel rods and demonstrated successful computation of metrics of interest to fuel failures, including cladding peak hoop stress and strain energy density. In comparison with a failure threshold derived from power ramp tests, results corroborate industry analyses of the root cause of the pellet-clad interaction failures and illustrate the importance of modeling 3D local effects around fuel pellet defects, which can produce complex effects including cold spots in the cladding, stress concentrations, and hot spots in the fuel that can lead to enhanced cladding degradation such as hydriding, oxidation, CRUD formation, and stress corrosion cracking.

Multi-Dimensional Simulation of LWR Fuel Behavior in the BISON Fuel Performance Code

DOE PAGES

Williamson, R. L.; Capps, N. A.; Liu, W.; ...

2016-09-27

Nuclear fuel operates in an extreme environment that induces complex multiphysics phenomena occurring over distances ranging from inter-atomic spacing to meters, and times scales ranging from microseconds to years. To simulate this behavior requires a wide variety of material models that are often complex and nonlinear. The recently developed BISON code represents a powerful fuel performance simulation tool based on its material and physical behavior capabilities, finite-element versatility of spatial representation, and use of parallel computing. The code can operate in full three dimensional (3D) mode, as well as in reduced two dimensional (2D) modes, e.g., axisymmetric radial-axial (R-Z) ormore » plane radial-circumferential (R-θ), to suit the application and to allow treatment of global and local effects. A BISON case study was used in this paper to illustrate analysis of Pellet Clad Mechanical Interaction failures from manufacturing defects using combined 2D and 3D analyses. The analysis involved commercial fuel rods and demonstrated successful computation of metrics of interest to fuel failures, including cladding peak hoop stress and strain energy density. Finally, in comparison with a failure threshold derived from power ramp tests, results corroborate industry analyses of the root cause of the pellet-clad interaction failures and illustrate the importance of modeling 3D local effects around fuel pellet defects, which can produce complex effects including cold spots in the cladding, stress concentrations, and hot spots in the fuel that can lead to enhanced cladding degradation such as hydriding, oxidation, CRUD formation, and stress corrosion cracking.« less

A Posteriori Error Analysis and Uncertainty Quantification for Adaptive Multiscale Operator Decomposition Methods for Multiphysics Problems

DTIC Science & Technology

2014-04-01

Barrier methods for critical exponent problems in geometric analysis and mathematical physics, J. Erway and M. Holst, Submitted for publication ...TR-14-33 A Posteriori Error Analysis and Uncertainty Quantification for Adaptive Multiscale Operator Decomposition Methods for Multiphysics...Problems Approved for public release, distribution is unlimited. April 2014 HDTRA1-09-1-0036 Donald Estep and Michael

Fully Parallel MHD Stability Analysis Tool

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2015-11-01

Progress on full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. It is a powerful tool for studying MHD and MHD-kinetic instabilities and it is widely used by fusion community. Parallel version of MARS is intended for simulations on local parallel clusters. It will be an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, already implemented in MARS. Parallelization of the code includes parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the present MARS algorithm using parallel libraries and procedures. Results of MARS parallelization and of the development of a new fix boundary equilibrium code adapted for MARS input will be reported. Work is supported by the U.S. DOE SBIR program.

Data-driven multi-scale multi-physics models to derive process-structure-property relationships for additive manufacturing

NASA Astrophysics Data System (ADS)

Yan, Wentao; Lin, Stephen; Kafka, Orion L.; Lian, Yanping; Yu, Cheng; Liu, Zeliang; Yan, Jinhui; Wolff, Sarah; Wu, Hao; Ndip-Agbor, Ebot; Mozaffar, Mojtaba; Ehmann, Kornel; Cao, Jian; Wagner, Gregory J.; Liu, Wing Kam

2018-05-01

Additive manufacturing (AM) possesses appealing potential for manipulating material compositions, structures and properties in end-use products with arbitrary shapes without the need for specialized tooling. Since the physical process is difficult to experimentally measure, numerical modeling is a powerful tool to understand the underlying physical mechanisms. This paper presents our latest work in this regard based on comprehensive material modeling of process-structure-property relationships for AM materials. The numerous influencing factors that emerge from the AM process motivate the need for novel rapid design and optimization approaches. For this, we propose data-mining as an effective solution. Such methods—used in the process-structure, structure-properties and the design phase that connects them—would allow for a design loop for AM processing and materials. We hope this article will provide a road map to enable AM fundamental understanding for the monitoring and advanced diagnostics of AM processing.

Data-driven multi-scale multi-physics models to derive process-structure-property relationships for additive manufacturing

NASA Astrophysics Data System (ADS)

Yan, Wentao; Lin, Stephen; Kafka, Orion L.; Lian, Yanping; Yu, Cheng; Liu, Zeliang; Yan, Jinhui; Wolff, Sarah; Wu, Hao; Ndip-Agbor, Ebot; Mozaffar, Mojtaba; Ehmann, Kornel; Cao, Jian; Wagner, Gregory J.; Liu, Wing Kam

2018-01-01

Additive manufacturing (AM) possesses appealing potential for manipulating material compositions, structures and properties in end-use products with arbitrary shapes without the need for specialized tooling. Since the physical process is difficult to experimentally measure, numerical modeling is a powerful tool to understand the underlying physical mechanisms. This paper presents our latest work in this regard based on comprehensive material modeling of process-structure-property relationships for AM materials. The numerous influencing factors that emerge from the AM process motivate the need for novel rapid design and optimization approaches. For this, we propose data-mining as an effective solution. Such methods—used in the process-structure, structure-properties and the design phase that connects them—would allow for a design loop for AM processing and materials. We hope this article will provide a road map to enable AM fundamental understanding for the monitoring and advanced diagnostics of AM processing.

An alternative low-loss stack topology for vanadium redox flow battery: Comparative assessment

NASA Astrophysics Data System (ADS)

Moro, Federico; Trovò, Andrea; Bortolin, Stefano; Del, Davide, , Col; Guarnieri, Massimo

2017-02-01

Two vanadium redox flow battery topologies have been compared. In the conventional series stack, bipolar plates connect cells electrically in series and hydraulically in parallel. The alternative topology consists of cells connected in parallel inside stacks by means of monopolar plates in order to reduce shunt currents along channels and manifolds. Channelled and flat current collectors interposed between cells were considered in both topologies. In order to compute the stack losses, an equivalent circuit model of a VRFB cell was built from a 2D FEM multiphysics numerical model based on Comsol®, accounting for coupled electrical, electrochemical, and charge and mass transport phenomena. Shunt currents were computed inside the cells with 3D FEM models and in the piping and manifolds by means of equivalent circuits solved with Matlab®. Hydraulic losses were computed with analytical models in piping and manifolds and with 3D numerical analyses based on ANSYS Fluent® in the cell porous electrodes. Total losses in the alternative topology resulted one order of magnitude lower than in an equivalent conventional battery. The alternative topology with channelled current collectors exhibits the lowest shunt currents and hydraulic losses, with round-trip efficiency higher by about 10%, as compared to the conventional topology.

Two-Step Multi-Physics Analysis of an Annular Linear Induction Pump for Fission Power Systems

NASA Technical Reports Server (NTRS)

Geng, Steven M.; Reid, Terry V.

2016-01-01

One of the key technologies associated with fission power systems (FPS) is the annular linear induction pump (ALIP). ALIPs are used to circulate liquid-metal fluid for transporting thermal energy from the nuclear reactor to the power conversion device. ALIPs designed and built to date for FPS project applications have not performed up to expectations. A unique, two-step approach was taken toward the multi-physics examination of an ALIP using ANSYS Maxwell 3D and Fluent. This multi-physics approach was developed so that engineers could investigate design variations that might improve pump performance. Of interest was to determine if simple geometric modifications could be made to the ALIP components with the goal of increasing the Lorentz forces acting on the liquid-metal fluid, which in turn would increase pumping capacity. The multi-physics model first calculates the Lorentz forces acting on the liquid metal fluid in the ALIP annulus. These forces are then used in a computational fluid dynamics simulation as (a) internal boundary conditions and (b) source functions in the momentum equations within the Navier-Stokes equations. The end result of the two-step analysis is a predicted pump pressure rise that can be compared with experimental data.

Parallel software tools at Langley Research Center

NASA Technical Reports Server (NTRS)

Moitra, Stuti; Tennille, Geoffrey M.; Lakeotes, Christopher D.; Randall, Donald P.; Arthur, Jarvis J.; Hammond, Dana P.; Mall, Gerald H.

1993-01-01

This document gives a brief overview of parallel software tools available on the Intel iPSC/860 parallel computer at Langley Research Center. It is intended to provide a source of information that is somewhat more concise than vendor-supplied material on the purpose and use of various tools. Each of the chapters on tools is organized in a similar manner covering an overview of the functionality, access information, how to effectively use the tool, observations about the tool and how it compares to similar software, known problems or shortfalls with the software, and reference documentation. It is primarily intended for users of the iPSC/860 at Langley Research Center and is appropriate for both the experienced and novice user.

Synthesizing parallel imaging applications using the CAP (computer-aided parallelization) tool

NASA Astrophysics Data System (ADS)

Gennart, Benoit A.; Mazzariol, Marc; Messerli, Vincent; Hersch, Roger D.

1997-12-01

Imaging applications such as filtering, image transforms and compression/decompression require vast amounts of computing power when applied to large data sets. These applications would potentially benefit from the use of parallel processing. However, dedicated parallel computers are expensive and their processing power per node lags behind that of the most recent commodity components. Furthermore, developing parallel applications remains a difficult task: writing and debugging the application is difficult (deadlocks), programs may not be portable from one parallel architecture to the other, and performance often comes short of expectations. In order to facilitate the development of parallel applications, we propose the CAP computer-aided parallelization tool which enables application programmers to specify at a high-level of abstraction the flow of data between pipelined-parallel operations. In addition, the CAP tool supports the programmer in developing parallel imaging and storage operations. CAP enables combining efficiently parallel storage access routines and image processing sequential operations. This paper shows how processing and I/O intensive imaging applications must be implemented to take advantage of parallelism and pipelining between data access and processing. This paper's contribution is (1) to show how such implementations can be compactly specified in CAP, and (2) to demonstrate that CAP specified applications achieve the performance of custom parallel code. The paper analyzes theoretically the performance of CAP specified applications and demonstrates the accuracy of the theoretical analysis through experimental measurements.

Applications of Parallel Process HiMAP for Large Scale Multidisciplinary Problems

NASA Technical Reports Server (NTRS)

Guruswamy, Guru P.; Potsdam, Mark; Rodriguez, David; Kwak, Dochay (Technical Monitor)

2000-01-01

HiMAP is a three level parallel middleware that can be interfaced to a large scale global design environment for code independent, multidisciplinary analysis using high fidelity equations. Aerospace technology needs are rapidly changing. Computational tools compatible with the requirements of national programs such as space transportation are needed. Conventional computation tools are inadequate for modern aerospace design needs. Advanced, modular computational tools are needed, such as those that incorporate the technology of massively parallel processors (MPP).

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface flow and reactive transport simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processesmore » receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of subsurface electrical conductivity changes, in both the saturated and unsaturated zones, arising from river stage fluctuations and associated river water intrusion into the aquifer. Furthermore, the results also demonstrate the sensitivity of surface based ERT measurements to those changes over time.« less

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

DOE PAGES

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

2016-09-22

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface flow and reactive transport simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processesmore » receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of subsurface electrical conductivity changes, in both the saturated and unsaturated zones, arising from river stage fluctuations and associated river water intrusion into the aquifer. Furthermore, the results also demonstrate the sensitivity of surface based ERT measurements to those changes over time.« less

Performance Characterization and Optimization of Microgrid-Based Energy Generation and Storage Technologies

DTIC Science & Technology

2012-01-01

A. Rufer, “Multiphysics and energetic modeling of a vanadium redox flow battery ,” in Proc. 2008 IEEE International Conference on Sustainable...p. 81. [11] K.W. Knehr and E.C. Kumbur, "Open circuit voltage of vanadium redox flow batteries : Discrepancy between models and experiments...Blanc and A. Rufer, “Multiphysics and energetic modeling of a vanadium redox flow battery ,” in Proc. 2008 IEEE International Conference on Sustainable

Applications of ANSYS/Multiphysics at NASA/Goddard Space Flight Center

NASA Technical Reports Server (NTRS)

Loughlin, Jim

2007-01-01

This viewgraph presentation reviews some of the uses that the ANSYS/Multiphysics system is used for at the NASA Goddard Space Flight Center. Some of the uses of the ANSYS system is used for is MEMS Structural Analysis of Micro-mirror Array for the James Web Space Telescope (JWST), Micro-shutter Array for JWST, MEMS FP Tunable Filter, AstroE2 Micro-calorimeter. Various views of these projects are shown in this presentation.

COMPUTATIONAL CHALLENGES IN BUILDING MULTI-SCALE AND MULTI-PHYSICS MODELS OF CARDIAC ELECTRO-MECHANICS

PubMed Central

Plank, G; Prassl, AJ; Augustin, C

2014-01-01

Despite the evident multiphysics nature of the heart – it is an electrically controlled mechanical pump – most modeling studies considered electrophysiology and mechanics in isolation. In no small part, this is due to the formidable modeling challenges involved in building strongly coupled anatomically accurate and biophyically detailed multi-scale multi-physics models of cardiac electro-mechanics. Among the main challenges are the selection of model components and their adjustments to achieve integration into a consistent organ-scale model, dealing with technical difficulties such as the exchange of data between electro-physiological and mechanical model, particularly when using different spatio-temporal grids for discretization, and, finally, the implementation of advanced numerical techniques to deal with the substantial computational. In this study we report on progress made in developing a novel modeling framework suited to tackle these challenges. PMID:24043050

Analysis of image formation in optical coherence elastography using a multiphysics approach

PubMed Central

Chin, Lixin; Curatolo, Andrea; Kennedy, Brendan F.; Doyle, Barry J.; Munro, Peter R. T.; McLaughlin, Robert A.; Sampson, David D.

2014-01-01

Image formation in optical coherence elastography (OCE) results from a combination of two processes: the mechanical deformation imparted to the sample and the detection of the resulting displacement using optical coherence tomography (OCT). We present a multiphysics model of these processes, validated by simulating strain elastograms acquired using phase-sensitive compression OCE, and demonstrating close correspondence with experimental results. Using the model, we present evidence that the approximation commonly used to infer sample displacement in phase-sensitive OCE is invalidated for smaller deformations than has been previously considered, significantly affecting the measurement precision, as quantified by the displacement sensitivity and the elastogram signal-to-noise ratio. We show how the precision of OCE is affected not only by OCT shot-noise, as is usually considered, but additionally by phase decorrelation due to the sample deformation. This multiphysics model provides a general framework that could be used to compare and contrast different OCE techniques. PMID:25401007

Charon Toolkit for Parallel, Implicit Structured-Grid Computations: Functional Design

NASA Technical Reports Server (NTRS)

VanderWijngaart, Rob F.; Kutler, Paul (Technical Monitor)

1997-01-01

In a previous report the design concepts of Charon were presented. Charon is a toolkit that aids engineers in developing scientific programs for structured-grid applications to be run on MIMD parallel computers. It constitutes an augmentation of the general-purpose MPI-based message-passing layer, and provides the user with a hierarchy of tools for rapid prototyping and validation of parallel programs, and subsequent piecemeal performance tuning. Here we describe the implementation of the domain decomposition tools used for creating data distributions across sets of processors. We also present the hierarchy of parallelization tools that allows smooth translation of legacy code (or a serial design) into a parallel program. Along with the actual tool descriptions, we will present the considerations that led to the particular design choices. Many of these are motivated by the requirement that Charon must be useful within the traditional computational environments of Fortran 77 and C. Only the Fortran 77 syntax will be presented in this report.

Otto Laporte Award Talk - In light of Fluid Mechanics

NASA Astrophysics Data System (ADS)

Gharib, Morteza

2015-11-01

Fluid mechanics, in its inherent non-linear beauty, has been its own laboratory, testing our perseverance and dedication to a branch of science that, despite its perceived maturity, still has many surprises to offer. For many of us, the study of fluid flow has been our path to understanding the complexity of nature. My journey has taken me through many interesting projects including the development of new visualization tools, scrutinizing the rhythms of the human heart, observing flow vortices and studying the dynamics of soap films. But this lecture is mainly devoted to a new example of my research activities where light and flow physics interweave to display another intriguing multi-physics beauty of nature.

Dynamics of the Vacuum and Casimir Analogs to the Hydrogen Atom

NASA Technical Reports Server (NTRS)

White, Harold; Vera, Jerry; Bailey, Paul; March, Paul; Lawrence, Tim; Sylvester, Andre; Brady, David

2015-01-01

This paper will discuss the current viewpoint of the vacuum state and explore the idea of a "natural" vacuum as opposed to immutable, non-degradable vacuum. This concept will be explored for all primary quantum numbers to show consistency with observation at the level of Bohr theory. A comparison with the Casimir force per unit area will be made, and an explicit function for the spatial variation of the vacuum density around the atomic nucleus will be derived. This explicit function will be numerically modeled using the industry multi-physics tool, COMSOL(trademark), and the eigenfrequencies for the n = 1 to n = 7 states will be found and compared to expectation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Nalu is a Sierra ToolKit (STK) based application module, and it has provided a set of "lessons learned" for the STK transition effort through its early adoption of STK. It makes use of the open-sourced Trilinos/ Tpetra library. Through the investment of LORD and ASCR projects, the Nalu code module has been extended beyond prototype status. Physics capability includes low Mach, variable density turbulent flow. The ongoing objective for Nalu is to facilitate partnerships with external organizations in order to extend code capability and knowledge; however, it is not intended to support routine CFD analysis. The targeted usage of thismore » module is for non-NW applications that support work-for-others in the multiphysics energy sector.« less

Toward a VPH/Physiome ToolKit.

PubMed

Garny, Alan; Cooper, Jonathan; Hunter, Peter J

2010-01-01

The Physiome Project was officially launched in 1997 and has since brought together teams from around the world to work on the development of a computational framework for the modeling of the human body. At the European level, this effort is focused around patient-specific solutions and is known as the Virtual Physiological Human (VPH) Initiative.Such modeling is both multiscale (in space and time) and multiphysics. This, therefore, requires careful interaction and collaboration between the teams involved in the VPH/Physiome effort, if we are to produce computer models that are not only quantitative, but also integrative and predictive.In that context, several technologies and solutions are already available, developed both by groups involved in the VPH/Physiome effort, and by others. They address areas such as data handling/fusion, markup languages, model repositories, ontologies, tools (for simulation, imaging, data fitting, etc.), as well as grid, middleware, and workflow.Here, we provide an overview of resources that should be considered for inclusion in the VPH/Physiome ToolKit (i.e., the set of tools that addresses the needs and requirements of the Physiome Project and VPH Initiative) and discuss some of the challenges that we are still facing.

Determination of Specific Forces and Tool Deflections in Micro-milling of Ti-6Al-4V alloy using Finite Element Simulations and Analysis

NASA Astrophysics Data System (ADS)

Farina, Simone; Thepsonti, Thanongsak; Ceretti, Elisabetta; Özel, Tugrul

2011-05-01

Titanium alloys offer superb properties in strength, corrosion resistance and biocompatibility and are commonly utilized in medical devices and implants. Micro-end milling process is a direct and rapid fabrication method for manufacturing medical devices and implants in titanium alloys. Process performance and quality depend upon an understanding of the relationship between cutting parameters and forces and resultant tool deflections to avoid tool breakage. For this purpose, FE simulations of chip formation during micro-end milling of Ti-6Al-4V alloy with an ultra-fine grain solid carbide two-flute micro-end mill are investigated using DEFORM software. At first, specific forces in tangential and radial directions of cutting during micro-end milling for varying feed advance and rotational speeds have been determined using designed FE simulations for chip formation process. Later, these forces are applied to the micro-end mill geometry along the axial depth of cut in 3D analysis of ABAQUS. Consequently, 3D distributions for tool deflections & von Misses stress are determined. These analyses will yield in establishing integrated multi-physics process models for high performance micro-end milling and a leap-forward to process improvements.

Multiphysics superensemble forecast applied to Mediterranean heavy precipitation situations

NASA Astrophysics Data System (ADS)

Vich, M.; Romero, R.

2010-11-01

The high-impact precipitation events that regularly affect the western Mediterranean coastal regions are still difficult to predict with the current prediction systems. Bearing this in mind, this paper focuses on the superensemble technique applied to the precipitation field. Encouraged by the skill shown by a previous multiphysics ensemble prediction system applied to western Mediterranean precipitation events, the superensemble is fed with this ensemble. The training phase of the superensemble contributes to the actual forecast with weights obtained by comparing the past performance of the ensemble members and the corresponding observed states. The non-hydrostatic MM5 mesoscale model is used to run the multiphysics ensemble. Simulations are performed with a 22.5 km resolution domain (Domain 1 in http://mm5forecasts.uib.es) nested in the ECMWF forecast fields. The period between September and December 2001 is used to train the superensemble and a collection of 19~MEDEX cyclones is used to test it. The verification procedure involves testing the superensemble performance and comparing it with that of the poor-man and bias-corrected ensemble mean and the multiphysic EPS control member. The results emphasize the need of a well-behaved training phase to obtain good results with the superensemble technique. A strategy to obtain this improved training phase is already outlined.

Computer-aided programming for message-passing system; Problems and a solution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, M.Y.; Gajski, D.D.

1989-12-01

As the number of processors and the complexity of problems to be solved increase, programming multiprocessing systems becomes more difficult and error-prone. Program development tools are necessary since programmers are not able to develop complex parallel programs efficiently. Parallel models of computation, parallelization problems, and tools for computer-aided programming (CAP) are discussed. As an example, a CAP tool that performs scheduling and inserts communication primitives automatically is described. It also generates the performance estimates and other program quality measures to help programmers in improving their algorithms and programs.

Automatic Generation of Directive-Based Parallel Programs for Shared Memory Parallel Systems

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Yan, Jerry; Frumkin, Michael

2000-01-01

The shared-memory programming model is a very effective way to achieve parallelism on shared memory parallel computers. As great progress was made in hardware and software technologies, performance of parallel programs with compiler directives has demonstrated large improvement. The introduction of OpenMP directives, the industrial standard for shared-memory programming, has minimized the issue of portability. Due to its ease of programming and its good performance, the technique has become very popular. In this study, we have extended CAPTools, a computer-aided parallelization toolkit, to automatically generate directive-based, OpenMP, parallel programs. We outline techniques used in the implementation of the tool and present test results on the NAS parallel benchmarks and ARC3D, a CFD application. This work demonstrates the great potential of using computer-aided tools to quickly port parallel programs and also achieve good performance.

Petascale Simulation Initiative Tech Base: FY2007 Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

May, J; Chen, R; Jefferson, D

The Petascale Simulation Initiative began as an LDRD project in the middle of Fiscal Year 2004. The goal of the project was to develop techniques to allow large-scale scientific simulation applications to better exploit the massive parallelism that will come with computers running at petaflops per second. One of the major products of this work was the design and prototype implementation of a programming model and a runtime system that lets applications extend data-parallel applications to use task parallelism. By adopting task parallelism, applications can use processing resources more flexibly, exploit multiple forms of parallelism, and support more sophisticated multiscalemore » and multiphysics models. Our programming model was originally called the Symponents Architecture but is now known as Cooperative Parallelism, and the runtime software that supports it is called Coop. (However, we sometimes refer to the programming model as Coop for brevity.) We have documented the programming model and runtime system in a submitted conference paper [1]. This report focuses on the specific accomplishments of the Cooperative Parallelism project (as we now call it) under Tech Base funding in FY2007. Development and implementation of the model under LDRD funding alone proceeded to the point of demonstrating a large-scale materials modeling application using Coop on more than 1300 processors by the end of FY2006. Beginning in FY2007, the project received funding from both LDRD and the Computation Directorate Tech Base program. Later in the year, after the three-year term of the LDRD funding ended, the ASC program supported the project with additional funds. The goal of the Tech Base effort was to bring Coop from a prototype to a production-ready system that a variety of LLNL users could work with. Specifically, the major tasks that we planned for the project were: (1) Port SARS [former name of the Coop runtime system] to another LLNL platform, probably Thunder or Peloton (depending on when Peloton becomes available); (2) Improve SARS's robustness and ease-of-use, and develop user documentation; and (3) Work with LLNL code teams to help them determine how Symponents could benefit their applications. The original funding request was $296,000 for the year, and we eventually received $252,000. The remainder of this report describes our efforts and accomplishments for each of the goals listed above.« less

The Application of COMSOL Multiphysics Package on the Modelling of Complex 3-D Lithospheric Electrical Resistivity Structures - A Case Study from the Proterozoic Orogenic belt within the North China Craton

NASA Astrophysics Data System (ADS)

Guo, L.; Yin, Y.; Deng, M.; Guo, L.; Yan, J.

2017-12-01

At present, most magnetotelluric (MT) forward modelling and inversion codes are based on finite difference method. But its structured mesh gridding cannot be well adapted for the conditions with arbitrary topography or complex tectonic structures. By contrast, the finite element method is more accurate in calculating complex and irregular 3-D region and has lower requirement of function smoothness. However, the complexity of mesh gridding and limitation of computer capacity has been affecting its application. COMSOL Multiphysics is a cross-platform finite element analysis, solver and multiphysics full-coupling simulation software. It achieves highly accurate numerical simulations with high computational performance and outstanding multi-field bi-directional coupling analysis capability. In addition, its AC/DC and RF module can be used to easily calculate the electromagnetic responses of complex geological structures. Using the adaptive unstructured grid, the calculation is much faster. In order to improve the discretization technique of computing area, we use the combination of Matlab and COMSOL Multiphysics to establish a general procedure for calculating the MT responses for arbitrary resistivity models. The calculated responses include the surface electric and magnetic field components, impedance components, magnetic transfer functions and phase tensors. Then, the reliability of this procedure is certificated by 1-D, 2-D and 3-D and anisotropic forward modeling tests. Finally, we establish the 3-D lithospheric resistivity model for the Proterozoic Wutai-Hengshan Mts. within the North China Craton by fitting the real MT data collected there. The reliability of the model is also verified by induced vectors and phase tensors. Our model shows more details and better resolution, compared with the previously published 3-D model based on the finite difference method. In conclusion, COMSOL Multiphysics package is suitable for modeling the 3-D lithospheric resistivity structures under complex tectonic deformation backgrounds, which could be a good complement to the existing finite-difference inversion algorithms.

IMPETUS - Interactive MultiPhysics Environment for Unified Simulations.

PubMed

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.

Mingus Discontinuous Multiphysics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pat Notz, Dan Turner

Mingus provides hybrid coupled local/non-local mechanics analysis capabilities that extend several traditional methods to applications with inherent discontinuities. Its primary features include adaptations of solid mechanics, fluid dynamics and digital image correlation that naturally accommodate dijointed data or irregular solution fields by assimilating a variety of discretizations (such as control volume finite elements, peridynamics and meshless control point clouds). The goal of this software is to provide an analysis framework form multiphysics engineering problems with an integrated image correlation capability that can be used for experimental validation and model

Integration of OpenMC methods into MAMMOTH and Serpent

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kerby, Leslie; DeHart, Mark; Tumulak, Aaron

OpenMC, a Monte Carlo particle transport simulation code focused on neutron criticality calculations, contains several methods we wish to emulate in MAMMOTH and Serpent. First, research coupling OpenMC and the Multiphysics Object-Oriented Simulation Environment (MOOSE) has shown promising results. Second, the utilization of Functional Expansion Tallies (FETs) allows for a more efficient passing of multiphysics data between OpenMC and MOOSE. Both of these capabilities have been preliminarily implemented into Serpent. Results are discussed and future work recommended.

A fast ultrasonic simulation tool based on massively parallel implementations

NASA Astrophysics Data System (ADS)

Lambert, Jason; Rougeron, Gilles; Lacassagne, Lionel; Chatillon, Sylvain

2014-02-01

This paper presents a CIVA optimized ultrasonic inspection simulation tool, which takes benefit of the power of massively parallel architectures: graphical processing units (GPU) and multi-core general purpose processors (GPP). This tool is based on the classical approach used in CIVA: the interaction model is based on Kirchoff, and the ultrasonic field around the defect is computed by the pencil method. The model has been adapted and parallelized for both architectures. At this stage, the configurations addressed by the tool are : multi and mono-element probes, planar specimens made of simple isotropic materials, planar rectangular defects or side drilled holes of small diameter. Validations on the model accuracy and performances measurements are presented.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merzari, E.; Yuan, Haomin; Kraus, A.

The NEAMS program aims to develop an integrated multi-physics simulation capability “pellet-to-plant” for the design and analysis of future generations of nuclear power plants. In particular, the Reactor Product Line code suite's multi-resolution hierarchy is being designed to ultimately span the full range of length and time scales present in relevant reactor design and safety analyses, as well as scale from desktop to petaflop computing platforms. Flow-induced vibration (FIV) is widespread problem in energy systems because they rely on fluid movement for energy conversion. Vibrating structures may be damaged as fatigue or wear occurs. Given the importance of reliable componentsmore » in the nuclear industry, flow-induced vibration has long been a major concern in safety and operation of nuclear reactors. In particular, nuclear fuel rods and steam generators have been known to suffer from flow-induced vibration and related failures. Advanced reactors, such as integral Pressurized Water Reactors (PWRs) considered for Small Modular Reactors (SMR), often rely on innovative component designs to meet cost and safety targets. One component that is the subject of advanced designs is the steam generator, some designs of which forego the usual shell-and-tube architecture in order to fit within the primary vessel. In addition to being more cost- and space-efficient, such steam generators need to be more reliable, since failure of the primary vessel represents a potential loss of coolant and a safety concern. A significant amount of data exists on flow-induced vibration in shell-and-tube heat exchangers, and heuristic methods are available to predict their occurrence based on a set of given assumptions. In contrast, advanced designs have far less data available. Advanced modeling and simulation based on coupled structural and fluid simulations have the potential to predict flow-induced vibration in a variety of designs, reducing the need for expensive experimental programs, especially at the design stage. Over the past five years, the Reactor Product Line has developed the integrated multi-physics code suite SHARP. The goal of developing such a tool is to perform multi-physics neutronics, thermal/fluid, and structural mechanics modeling of the components inside the full reactor core or portions of it with a user-specified fidelity. In particular SHARP contains high-fidelity single-physics codes Diablo for structural mechanics and Nek5000 for fluid mechanics calculations. Both codes are state-of-the-art, highly scalable tools that have been extensively validated. These tools form a strong basis on which to build a flow-induced vibration modeling capability. In this report we discuss one-way coupled calculations performed with Nek5000 and Diablo aimed at simulating available FIV experiments in helical steam generators in the turbulent buffeting regime. In this regime one-way coupling is judged sufficient because the pressure loads do not cause substantial displacements. It is also the most common source of vibration in helical steam generators at the low flows expected in integral PWRs. The legacy data is obtained from two datasets developed at Argonne and B&W.« less

Tailoring microfluidic systems for organ-like cell culture applications using multiphysics simulations

NASA Astrophysics Data System (ADS)

Hagmeyer, Britta; Schütte, Julia; Böttger, Jan; Gebhardt, Rolf; Stelzle, Martin

2013-03-01

Replacing animal testing with in vitro cocultures of human cells is a long-term goal in pre-clinical drug tests used to gain reliable insight into drug-induced cell toxicity. However, current state-of-the-art 2D or 3D cell cultures aiming at mimicking human organs in vitro still lack organ-like morphology and perfusion and thus organ-like functions. To this end, microfluidic systems enable construction of cell culture devices which can be designed to more closely resemble the smallest functional unit of organs. Multiphysics simulations represent a powerful tool to study the various relevant physical phenomena and their impact on functionality inside microfluidic structures. This is particularly useful as it allows for assessment of system functions already during the design stage prior to actual chip fabrication. In the HepaChip®, dielectrophoretic forces are used to assemble human hepatocytes and human endothelial cells in liver sinusoid-like structures. Numerical simulations of flow distribution, shear stress, electrical fields and heat dissipation inside the cell assembly chambers as well as surface wetting and surface tension effects during filling of the microchannel network supported the design of this human-liver-on-chip microfluidic system for cell culture applications. Based on the device design resulting thereof, a prototype chip was injection-moulded in COP (cyclic olefin polymer). Functional hepatocyte and endothelial cell cocultures were established inside the HepaChip® showing excellent metabolic and secretory performance.

Snow Micro-Structure Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Micah Johnson, Andrew Slaughter

PIKA is a MOOSE-based application for modeling micro-structure evolution of seasonal snow. The model will be useful for environmental, atmospheric, and climate scientists. Possible applications include application to energy balance models, ice sheet modeling, and avalanche forecasting. The model implements physics from published, peer-reviewed articles. The main purpose is to foster university and laboratory collaboration to build a larger multi-scale snow model using MOOSE. The main feature of the code is that it is implemented using the MOOSE framework, thus making features such as multiphysics coupling, adaptive mesh refinement, and parallel scalability native to the application. PIKA implements three equations:more » the phase-field equation for tracking the evolution of the ice-air interface within seasonal snow at the grain-scale; the heat equation for computing the temperature of both the ice and air within the snow; and the mass transport equation for monitoring the diffusion of water vapor in the pore space of the snow.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christon, Mark A.; Baksoi, Jozsef; Barnett, Nathan

This report describes the work carried out for completion of the Thermal Hydraulics Methods (THM) Level 2 Milestone THM.CFD.P5.01 for the Consortium for Advanced Simulation of Light Water Reactors (CASL). This milestone focused primarily on the initial integration of Hydra-TH in VERA. The primary objective for this milestone was the integration of Hydra-TH as a standalone executable in VERA. A series of code extensions/modifications have been made to Hydra-TH to facilitate integration of Hydra-TH in VERA and to permit future tighter integration and physics coupling. A total of 61 serial and 64 parallel regression tests have been supplied with Hydra-TH.more » These tests are are being executed in the TriBITS environment. Once the VERA team enables the full suite of tests, the results can be posted to the VERA CDash site. Future work will consider the use of the LIME 2.0 interface for tighter integration in VERA with additional efforts focused on multiphysics coupling with radiation transport, fuel performance, and solid/structural mechanics.« less

pcircle - A Suite of Scalable Parallel File System Tools

DOE Office of Scientific and Technical Information (OSTI.GOV)

WANG, FEIYI

2015-10-01

Most of the software related to file system are written for conventional local file system, they are serialized and can't take advantage of the benefit of a large scale parallel file system. "pcircle" software builds on top of ubiquitous MPI in cluster computing environment and "work-stealing" pattern to provide a scalable, high-performance suite of file system tools. In particular - it implemented parallel data copy and parallel data checksumming, with advanced features such as async progress report, checkpoint and restart, as well as integrity checking.

A capacitive CMOS-MEMS sensor designed by multi-physics simulation for integrated CMOS-MEMS technology

NASA Astrophysics Data System (ADS)

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.

Multiphysics Thermal-Fluid Design Analysis of a Non-Nuclear Tester for Hot-Hydrogen Materials and Component Development

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Foote, John; Litchford, Ron

2006-01-01

The objective of this effort is to perform design analyses for a non-nuclear hot-hydrogen materials tester, as a first step towards developing efficient and accurate multiphysics, thermo-fluid computational methodology to predict environments for hypothetical solid-core, nuclear thermal engine thrust chamber design and analysis. The computational methodology is based on a multidimensional, finite-volume, turbulent, chemically reacting, thermally radiating, unstructured-grid, and pressure-based formulation. The multiphysics invoked in this study include hydrogen dissociation kinetics and thermodynamics, turbulent flow, convective, and thermal radiative heat transfers. The goals of the design analyses are to maintain maximum hot-hydrogen jet impingement energy and to minimize chamber wall heating. The results of analyses on three test fixture configurations and the rationale for final selection are presented. The interrogation of physics revealed that reactions of hydrogen dissociation and recombination are highly correlated with local temperature and are necessary for accurate prediction of the hot-hydrogen jet temperature.

A novel phenomenological multi-physics model of Li-ion battery cells

NASA Astrophysics Data System (ADS)

Oh, Ki-Yong; Samad, Nassim A.; Kim, Youngki; Siegel, Jason B.; Stefanopoulou, Anna G.; Epureanu, Bogdan I.

2016-09-01

A novel phenomenological multi-physics model of Lithium-ion battery cells is developed for control and state estimation purposes. The model can capture electrical, thermal, and mechanical behaviors of battery cells under constrained conditions, e.g., battery pack conditions. Specifically, the proposed model predicts the core and surface temperatures and reaction force induced from the volume change of battery cells because of electrochemically- and thermally-induced swelling. Moreover, the model incorporates the influences of changes in preload and ambient temperature on the force considering severe environmental conditions electrified vehicles face. Intensive experimental validation demonstrates that the proposed multi-physics model accurately predicts the surface temperature and reaction force for a wide operational range of preload and ambient temperature. This high fidelity model can be useful for more accurate and robust state of charge estimation considering the complex dynamic behaviors of the battery cell. Furthermore, the inherent simplicity of the mechanical measurements offers distinct advantages to improve the existing power and thermal management strategies for battery management.

Multiphysics elastodynamic finite element analysis of space debris deorbit stability and efficiency by electrodynamic tethers

NASA Astrophysics Data System (ADS)

Li, Gangqiang; Zhu, Zheng H.; Ruel, Stephane; Meguid, S. A.

2017-08-01

This paper developed a new multiphysics finite element method for the elastodynamic analysis of space debris deorbit by a bare flexible electrodynamic tether. Orbital motion limited theory and dynamics of flexible electrodynamic tethers are discretized by the finite element method, where the motional electric field is variant along the tether and coupled with tether deflection and motion. Accordingly, the electrical current and potential bias profiles of tether are solved together with the tether dynamics by the nodal position finite element method. The newly proposed multiphysics finite element method is applied to analyze the deorbit dynamics of space debris by electrodynamic tethers with a two-stage energy control strategy to ensure an efficient and stable deorbit process. Numerical simulations are conducted to study the coupled effect between the motional electric field and the tether dynamics. The results reveal that the coupling effect has a significant influence on the tether stability and the deorbit performance. It cannot be ignored when the libration and deflection of the tether are significant.

Transient multi-physics analysis of a magnetorheological shock absorber with the inverse Jiles-Atherton hysteresis model

NASA Astrophysics Data System (ADS)

Zheng, Jiajia; Li, Yancheng; Li, Zhaochun; Wang, Jiong

2015-10-01

This paper presents multi-physics modeling of an MR absorber considering the magnetic hysteresis to capture the nonlinear relationship between the applied current and the generated force under impact loading. The magnetic field, temperature field, and fluid dynamics are represented by the Maxwell equations, conjugate heat transfer equations, and Navier-Stokes equations. These fields are coupled through the apparent viscosity and the magnetic force, both of which in turn depend on the magnetic flux density and the temperature. Based on a parametric study, an inverse Jiles-Atherton hysteresis model is used and implemented for the magnetic field simulation. The temperature rise of the MR fluid in the annular gap caused by core loss (i.e. eddy current loss and hysteresis loss) and fluid motion is computed to investigate the current-force behavior. A group of impulsive tests was performed for the manufactured MR absorber with step exciting currents. The numerical and experimental results showed good agreement, which validates the effectiveness of the proposed multi-physics FEA model.

A Parallel Algorithm for Contact in a Finite Element Hydrocode

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pierce, Timothy G.

A parallel algorithm is developed for contact/impact of multiple three dimensional bodies undergoing large deformation. As time progresses the relative positions of contact between the multiple bodies changes as collision and sliding occurs. The parallel algorithm is capable of tracking these changes and enforcing an impenetrability constraint and momentum transfer across the surfaces in contact. Portions of the various surfaces of the bodies are assigned to the processors of a distributed-memory parallel machine in an arbitrary fashion, known as the primary decomposition. A secondary, dynamic decomposition is utilized to bring opposing sections of the contacting surfaces together on the samemore » processors, so that opposing forces may be balanced and the resultant deformation of the bodies calculated. The secondary decomposition is accomplished and updated using only local communication with a limited subset of neighbor processors. Each processor represents both a domain of the primary decomposition and a domain of the secondary, or contact, decomposition. Thus each processor has four sets of neighbor processors: (a) those processors which represent regions adjacent to it in the primary decomposition, (b) those processors which represent regions adjacent to it in the contact decomposition, (c) those processors which send it the data from which it constructs its contact domain, and (d) those processors to which it sends its primary domain data, from which they construct their contact domains. The latter three of these neighbor sets change dynamically as the simulation progresses. By constraining all communication to these sets of neighbors, all global communication, with its attendant nonscalable performance, is avoided. A set of tests are provided to measure the degree of scalability achieved by this algorithm on up to 1024 processors. Issues related to the operating system of the test platform which lead to some degradation of the results are analyzed. This algorithm has been implemented as the contact capability of the ALE3D multiphysics code, and is currently in production use.« less

Interfacing Computer Aided Parallelization and Performance Analysis

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Jin, Haoqiang; Labarta, Jesus; Gimenez, Judit; Biegel, Bryan A. (Technical Monitor)

2003-01-01

When porting sequential applications to parallel computer architectures, the program developer will typically go through several cycles of source code optimization and performance analysis. We have started a project to develop an environment where the user can jointly navigate through program structure and performance data information in order to make efficient optimization decisions. In a prototype implementation we have interfaced the CAPO computer aided parallelization tool with the Paraver performance analysis tool. We describe both tools and their interface and give an example for how the interface helps within the program development cycle of a benchmark code.

The Shale Hills Critical Zone Observatory for Embedded Sensing and Simulation

NASA Astrophysics Data System (ADS)

Duffy, C.; Davis, K.; Kane, T.; Boyer, E.

2009-04-01

The future of environmental observing systems will utilize embedded sensor networks with continuous real-time measurement of hydrologic, atmospheric, biogeochemical, and ecological variables across diverse terrestrial environments. Embedded environmental sensors, benefitting from advances in information sciences, networking technology, materials science, computing capacity, and data synthesis methods, are undergoing revolutionary change. It is now possible to field spatially-distributed, multi-node sensor networks that provide density and spatial coverage previously accessible only via numerical simulation. At the same time, computational tools are advancing rapidly to the point where it is now possible to simulate the physical processes controlling individual parcels of water and solutes through the complete terrestrial water cycle. Our goal for the Penn State Critical Zone Observatory is to apply environmental sensor arrays, integrated hydrologic models deployed and coordinated at a testbed within the Penn State Experimental Forest. The NSF-funded CZO is designed to observe the detailed space and time complexities of the water and energy cycle for a watershed and ultimately the river basin for all physical states and fluxes (groundwater, soil moisture, temperature, streamflow, latent heat, snowmelt, chemistry, isotopes etc.). Presently fully-coupled physical models are being developed that link the atmosphere-land-vegetation-subsurface system into a fully-coupled distributed system. During the last 5 years the Penn State Integrated Hydrologic Modeling System has been under development as an open-source community modeling project funded by NSF EAR/GEO and NSF CBET/ENG. PIHM represents a strategy for the formulation and solution of fully-coupled process equations at the watershed and river basin scales, and includes a tightly coupled GIS tool for data handling, domain decomposition, optimal unstructured grid generation, and model parameterization. (PIHM; http://sourceforge.net/projects/pihmmodel/; http://sourceforge.net/projects/pihmgis/ ) The CZO sensor and simulation system is being developed to have the following elements: 1) extensive, spatially-distributed smart sensor networks to gather intensive soil, geologic, hydrologic, geochemical and isotopic data; 2) spatially-explicit multiphysics models/solutions of the land-subsurface-vegetation-atmosphere system; and 3) parallel/distributed, adaptive algorithms for rapidly simulating the states of the watershed at high resolution, and 4) signal processing tools for data mining and parameter estimation. The prototype proposed sensor array and simulation system proposed is demonstrated with preliminary results from our first year.

Algorithms and programming tools for image processing on the MPP

NASA Technical Reports Server (NTRS)

Reeves, A. P.

1985-01-01

Topics addressed include: data mapping and rotational algorithms for the Massively Parallel Processor (MPP); Parallel Pascal language; documentation for the Parallel Pascal Development system; and a description of the Parallel Pascal language used on the MPP.

High Precision Thermal, Structural and Optical Analysis of an External Occulter Using a Common Model and the General Purpose Multi-Physics Analysis Tool Cielo

NASA Technical Reports Server (NTRS)

Hoff, Claus; Cady, Eric; Chainyk, Mike; Kissil, Andrew; Levine, Marie; Moore, Greg

2011-01-01

The efficient simulation of multidisciplinary thermo-opto-mechanical effects in precision deployable systems has for years been limited by numerical toolsets that do not necessarily share the same finite element basis, level of mesh discretization, data formats, or compute platforms. Cielo, a general purpose integrated modeling tool funded by the Jet Propulsion Laboratory and the Exoplanet Exploration Program, addresses shortcomings in the current state of the art via features that enable the use of a single, common model for thermal, structural and optical aberration analysis, producing results of greater accuracy, without the need for results interpolation or mapping. This paper will highlight some of these advances, and will demonstrate them within the context of detailed external occulter analyses, focusing on in-plane deformations of the petal edges for both steady-state and transient conditions, with subsequent optical performance metrics including intensity distributions at the pupil and image plane.

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processes receives subsurface states frommore » PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of changes subsurface electrical conductivity, in both the saturated and unsaturated zones, arising from water table changes and from river water intrusion into the aquifer. The results also demonstrate the sensitivity of surface based ERT measurements to those changes over time. PFLOTRAN-E4D is available with the PFLOTRAN development version with an open-source license at https://bitbucket.org/pflotran/pflotran-dev .« less

PFLOTRAN-E4D: A parallel open source PFLOTRAN module for simulating time-lapse electrical resistivity data

NASA Astrophysics Data System (ADS)

Johnson, Timothy C.; Hammond, Glenn E.; Chen, Xingyuan

2017-02-01

Time-lapse electrical resistivity tomography (ERT) is finding increased application for remotely monitoring processes occurring in the near subsurface in three-dimensions (i.e. 4D monitoring). However, there are few codes capable of simulating the evolution of subsurface resistivity and corresponding tomographic measurements arising from a particular process, particularly in parallel and with an open source license. Herein we describe and demonstrate an electrical resistivity tomography module for the PFLOTRAN subsurface flow and reactive transport simulation code, named PFLOTRAN-E4D. The PFLOTRAN-E4D module operates in parallel using a dedicated set of compute cores in a master-slave configuration. At each time step, the master processes receives subsurface states from PFLOTRAN, converts those states to bulk electrical conductivity, and instructs the slave processes to simulate a tomographic data set. The resulting multi-physics simulation capability enables accurate feasibility studies for ERT imaging, the identification of the ERT signatures that are unique to a given process, and facilitates the joint inversion of ERT data with hydrogeological data for subsurface characterization. PFLOTRAN-E4D is demonstrated herein using a field study of stage-driven groundwater/river water interaction ERT monitoring along the Columbia River, Washington, USA. Results demonstrate the complex nature of subsurface electrical conductivity changes, in both the saturated and unsaturated zones, arising from river stage fluctuations and associated river water intrusion into the aquifer. The results also demonstrate the sensitivity of surface based ERT measurements to those changes over time. PFLOTRAN-E4D is available with the PFLOTRAN development version with an open-source license at https://bitbucket.org/pflotran/pflotran-dev.

Modeling borehole microseismic and strain signals measured by a distributed fiber optic sensor

NASA Astrophysics Data System (ADS)

Mellors, R. J.; Sherman, C. S.; Ryerson, F. J.; Morris, J.; Allen, G. S.; Messerly, M. J.; Carr, T.; Kavousi, P.

2017-12-01

The advent of distributed fiber optic sensors installed in boreholes provides a new and data-rich perspective on the subsurface environment. This includes the long-term capability for vertical seismic profiles, monitoring of active borehole processes such as well stimulation, and measuring of microseismic signals. The distributed fiber sensor, which measures strain (or strain-rate), is an active sensor with highest sensitivity parallel to the fiber and subject to varying types of noise, both external and internal. We take a systems approach and include the response of the electronics, fiber/cable, and subsurface to improve interpretation of the signals. This aids in understanding noise sources, assessing error bounds on amplitudes, and developing appropriate algorithms for improving the image. Ultimately, a robust understanding will allow identification of areas for future improvement and possible optimization in fiber and cable design. The subsurface signals are simulated in two ways: 1) a massively parallel multi-physics code that is capable of modeling hydraulic stimulation of heterogeneous reservoir with a pre-existing discrete fracture network, and 2) a parallelized 3D finite difference code for high-frequency seismic signals. Geometry and parameters for the simulations are derived from fiber deployments, including the Marcellus Shale Energy and Environment Laboratory (MSEEL) project in West Virginia. The combination mimics both the low-frequency strain signals generated during the fracture process and high-frequency signals from microseismic and perforation shots. Results are compared with available fiber data and demonstrate that quantitative interpretation of the fiber data provides valuable constraints on the fracture geometry and microseismic activity. These constraints appear difficult, if not impossible, to obtain otherwise.

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Hood, Robert; Biegel, Bryan (Technical Monitor)

2001-01-01

We describe a system that simplifies the process of debugging programs produced by computer-aided parallelization tools. The system uses relative debugging techniques to compare serial and parallel executions in order to show where the computations begin to differ. If the original serial code is correct, errors due to parallelization will be isolated by the comparison. One of the primary goals of the system is to minimize the effort required of the user. To that end, the debugging system uses information produced by the parallelization tool to drive the comparison process. In particular the debugging system relies on the parallelization tool to provide information about where variables may have been modified and how arrays are distributed across multiple processes. User effort is also reduced through the use of dynamic instrumentation. This allows us to modify the program execution without changing the way the user builds the executable. The use of dynamic instrumentation also permits us to compare the executions in a fine-grained fashion and only involve the debugger when a difference has been detected. This reduces the overhead of executing instrumentation.

Relative Debugging of Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Hood, Robert; Biegel, Bryan (Technical Monitor)

2002-01-01

We describe a system that simplifies the process of debugging programs produced by computer-aided parallelization tools. The system uses relative debugging techniques to compare serial and parallel executions in order to show where the computations begin to differ. If the original serial code is correct, errors due to parallelization will be isolated by the comparison. One of the primary goals of the system is to minimize the effort required of the user. To that end, the debugging system uses information produced by the parallelization tool to drive the comparison process. In particular, the debugging system relies on the parallelization tool to provide information about where variables may have been modified and how arrays are distributed across multiple processes. User effort is also reduced through the use of dynamic instrumentation. This allows us to modify, the program execution with out changing the way the user builds the executable. The use of dynamic instrumentation also permits us to compare the executions in a fine-grained fashion and only involve the debugger when a difference has been detected. This reduces the overhead of executing instrumentation.

FY17Q4 Ristra project: Release Version 1.0 of a production toolkit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hungerford, Aimee L.; Daniel, David John

2017-09-21

The Next Generation Code project will release Version 1.0 of a production toolkit for multi-physics application development on advanced architectures. Features of this toolkit will include remap and link utilities, control and state manager, setup, visualization and I/O, as well as support for a variety of mesh and particle data representations. Numerical physics packages that operate atop this foundational toolkit will be employed in a multi-physics demonstration problem and released to the community along with results from the demonstration.

Advanced graphical user interface for multi-physics simulations using AMST

NASA Astrophysics Data System (ADS)

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.

B-MIC: An Ultrafast Three-Level Parallel Sequence Aligner Using MIC.

PubMed

Cui, Yingbo; Liao, Xiangke; Zhu, Xiaoqian; Wang, Bingqiang; Peng, Shaoliang

2016-03-01

Sequence alignment is the central process for sequence analysis, where mapping raw sequencing data to reference genome. The large amount of data generated by NGS is far beyond the process capabilities of existing alignment tools. Consequently, sequence alignment becomes the bottleneck of sequence analysis. Intensive computing power is required to address this challenge. Intel recently announced the MIC coprocessor, which can provide massive computing power. The Tianhe-2 is the world's fastest supercomputer now equipped with three MIC coprocessors each compute node. A key feature of sequence alignment is that different reads are independent. Considering this property, we proposed a MIC-oriented three-level parallelization strategy to speed up BWA, a widely used sequence alignment tool, and developed our ultrafast parallel sequence aligner: B-MIC. B-MIC contains three levels of parallelization: firstly, parallelization of data IO and reads alignment by a three-stage parallel pipeline; secondly, parallelization enabled by MIC coprocessor technology; thirdly, inter-node parallelization implemented by MPI. In this paper, we demonstrate that B-MIC outperforms BWA by a combination of those techniques using Inspur NF5280M server and the Tianhe-2 supercomputer. To the best of our knowledge, B-MIC is the first sequence alignment tool to run on Intel MIC and it can achieve more than fivefold speedup over the original BWA while maintaining the alignment precision.

Advanced multiphysics coupling for LWR fuel performance analysis

DOE PAGES

Hales, J. D.; Tonks, M. R.; Gleicher, F. N.; ...

2015-10-01

Even the most basic nuclear fuel analysis is a multiphysics undertaking, as a credible simulation must consider at a minimum coupled heat conduction and mechanical deformation. The need for more realistic fuel modeling under a variety of conditions invariably leads to a desire to include coupling between a more complete set of the physical phenomena influencing fuel behavior, including neutronics, thermal hydraulics, and mechanisms occurring at lower length scales. This paper covers current efforts toward coupled multiphysics LWR fuel modeling in three main areas. The first area covered in this paper concerns thermomechanical coupling. The interaction of these two physics,more » particularly related to the feedback effect associated with heat transfer and mechanical contact at the fuel/clad gap, provides numerous computational challenges. An outline is provided of an effective approach used to manage the nonlinearities associated with an evolving gap in BISON, a nuclear fuel performance application. A second type of multiphysics coupling described here is that of coupling neutronics with thermomechanical LWR fuel performance. DeCART, a high-fidelity core analysis program based on the method of characteristics, has been coupled to BISON. DeCART provides sub-pin level resolution of the multigroup neutron flux, with resonance treatment, during a depletion or a fast transient simulation. Two-way coupling between these codes was achieved by mapping fission rate density and fast neutron flux fields from DeCART to BISON and the temperature field from BISON to DeCART while employing a Picard iterative algorithm. Finally, the need for multiscale coupling is considered. Fission gas production and evolution significantly impact fuel performance by causing swelling, a reduction in the thermal conductivity, and fission gas release. The mechanisms involved occur at the atomistic and grain scale and are therefore not the domain of a fuel performance code. However, it is possible to use lower length scale models such as those used in the mesoscale MARMOT code to compute average properties, e.g. swelling or thermal conductivity. These may then be used by an engineering-scale model. Examples of this type of multiscale, multiphysics modeling are shown.« less

Design and multiphysics analysis of a 176Â MHz continuous-wave radio-frequency quadrupole

NASA Astrophysics Data System (ADS)

Kutsaev, S. V.; Mustapha, B.; Ostroumov, P. N.; Barcikowski, A.; Schrage, D.; Rodnizki, J.; Berkovits, D.

2014-07-01

We have developed a new design for a 176 MHz cw radio-frequency quadrupole (RFQ) for the SARAF upgrade project. At this frequency, the proposed design is a conventional four-vane structure. The main design goals are to provide the highest possible shunt impedance while limiting the required rf power to about 120 kW for reliable cw operation, and the length to about 4 meters. If built as designed, the proposed RFQ will be the first four-vane cw RFQ built as a single cavity (no resonant coupling required) that does not require π-mode stabilizing loops or dipole rods. For this, we rely on very detailed 3D simulations of all aspects of the structure and the level of machining precision achieved on the recently developed ATLAS upgrade RFQ. A full 3D model of the structure including vane modulation was developed. The design was optimized using electromagnetic and multiphysics simulations. Following the choice of the vane type and geometry, the vane undercuts were optimized to produce a flat field along the structure. The final design has good mode separation and should not need dipole rods if built as designed, but their effect was studied in the case of manufacturing errors. The tuners were also designed and optimized to tune the main mode without affecting the field flatness. Following the electromagnetic (EM) design optimization, a multiphysics engineering analysis of the structure was performed. The multiphysics analysis is a coupled electromagnetic, thermal and mechanical analysis. The cooling channels, including their paths and sizes, were optimized based on the limiting temperature and deformation requirements. The frequency sensitivity to the RFQ body and vane cooling water temperatures was carefully studied in order to use it for frequency fine-tuning. Finally, an inductive rf power coupler design based on the ATLAS RFQ coupler was developed and simulated. The EM design optimization was performed using cst Microwave Studio and the results were verified using both hfss and ansys. The engineering analysis was performed using hfss and ansys and most of the results were verified using the newly developed cst Multiphysics package.

Solution of task related to control of swiss-type automatic lathe to get planes parallel to part axis

NASA Astrophysics Data System (ADS)

Tabekina, N. A.; Chepchurov, M. S.; Evtushenko, E. I.; Dmitrievsky, B. S.

2018-05-01

The work solves the problem of automation of machining process namely turning to produce parts having the planes parallel to an axis of rotation of part without using special tools. According to the results, the availability of the equipment of a high speed electromechanical drive to control the operative movements of lathe machine will enable one to get the planes parallel to the part axis. The method of getting planes parallel to the part axis is based on the mathematical model, which is presented as functional dependency between the conveying velocity of the driven element and the time. It describes the operative movements of lathe machine all over the tool path. Using the model of movement of the tool, it has been found that the conveying velocity varies from the maximum to zero value. It will allow one to carry out the reverse of the drive. The scheme of tool placement regarding the workpiece has been proposed for unidirectional movement of the driven element at high conveying velocity. The control method of CNC machines can be used for getting geometrically complex parts on the lathe without using special milling tools.

Coordinated Fault-Tolerance for High-Performance Computing Final Project Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panda, Dhabaleswar Kumar; Beckman, Pete

2011-07-28

With the Coordinated Infrastructure for Fault Tolerance Systems (CIFTS, as the original project came to be called) project, our aim has been to understand and tackle the following broad research questions, the answers to which will help the HEC community analyze and shape the direction of research in the field of fault tolerance and resiliency on future high-end leadership systems. Will availability of global fault information, obtained by fault information exchange between the different HEC software on a system, allow individual system software to better detect, diagnose, and adaptively respond to faults? If fault-awareness is raised throughout the system throughmore » fault information exchange, is it possible to get all system software working together to provide a more comprehensive end-to-end fault management on the system? What are the missing fault-tolerance features that widely used HEC system software lacks today that would inhibit such software from taking advantage of systemwide global fault information? What are the practical limitations of a systemwide approach for end-to-end fault management based on fault awareness and coordination? What mechanisms, tools, and technologies are needed to bring about fault awareness and coordination of responses on a leadership-class system? What standards, outreach, and community interaction are needed for adoption of the concept of fault awareness and coordination for fault management on future systems? Keeping our overall objectives in mind, the CIFTS team has taken a parallel fourfold approach. Our central goal was to design and implement a light-weight, scalable infrastructure with a simple, standardized interface to allow communication of fault-related information through the system and facilitate coordinated responses. This work led to the development of the Fault Tolerance Backplane (FTB) publish-subscribe API specification, together with a reference implementation and several experimental implementations on top of existing publish-subscribe tools. We enhanced the intrinsic fault tolerance capabilities representative implementations of a variety of key HPC software subsystems and integrated them with the FTB. Targeting software subsystems included: MPI communication libraries, checkpoint/restart libraries, resource managers and job schedulers, and system monitoring tools. Leveraging the aforementioned infrastructure, as well as developing and utilizing additional tools, we have examined issues associated with expanded, end-to-end fault response from both system and application viewpoints. From the standpoint of system operations, we have investigated log and root cause analysis, anomaly detection and fault prediction, and generalized notification mechanisms. Our applications work has included libraries for fault-tolerance linear algebra, application frameworks for coupled multiphysics applications, and external frameworks to support the monitoring and response for general applications. Our final goal was to engage the high-end computing community to increase awareness of tools and issues around coordinated end-to-end fault management.« less

Open | SpeedShop: An Open Source Infrastructure for Parallel Performance Analysis

DOE PAGES

Schulz, Martin; Galarowicz, Jim; Maghrak, Don; ...

2008-01-01

Over the last decades a large number of performance tools has been developed to analyze and optimize high performance applications. Their acceptance by end users, however, has been slow: each tool alone is often limited in scope and comes with widely varying interfaces and workflow constraints, requiring different changes in the often complex build and execution infrastructure of the target application. We started the Open | SpeedShop project about 3 years ago to overcome these limitations and provide efficient, easy to apply, and integrated performance analysis for parallel systems. Open | SpeedShop has two different faces: it provides an interoperable tool set covering themore » most common analysis steps as well as a comprehensive plugin infrastructure for building new tools. In both cases, the tools can be deployed to large scale parallel applications using DPCL/Dyninst for distributed binary instrumentation. Further, all tools developed within or on top of Open | SpeedShop are accessible through multiple fully equivalent interfaces including an easy-to-use GUI as well as an interactive command line interface reducing the usage threshold for those tools.« less

Multiscale Concrete Modeling of Aging Degradation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hammi, Yousseff; Gullett, Philipp; Horstemeyer, Mark F.

In this work a numerical finite element framework is implemented to enable the integration of coupled multiscale and multiphysics transport processes. A User Element subroutine (UEL) in Abaqus is used to simultaneously solve stress equilibrium, heat conduction, and multiple diffusion equations for 2D and 3D linear and quadratic elements. Transport processes in concrete structures and their degradation mechanisms are presented along with the discretization of the governing equations. The multiphysics modeling framework is theoretically extended to the linear elastic fracture mechanics (LEFM) by introducing the eXtended Finite Element Method (XFEM) and based on the XFEM user element implementation of Ginermore » et al. [2009]. A damage model that takes into account the damage contribution from the different degradation mechanisms is theoretically developed. The total contribution of damage is forwarded to a Multi-Stage Fatigue (MSF) model to enable the assessment of the fatigue life and the deterioration of reinforced concrete structures in a nuclear power plant. Finally, two examples are presented to illustrate the developed multiphysics user element implementation and the XFEM implementation of Giner et al. [2009].« less

Multiphysics modelling and experimental validation of an air-coupled array of PMUTs with residual stresses

NASA Astrophysics Data System (ADS)

Massimino, G.; Colombo, A.; D'Alessandro, L.; Procopio, F.; Ardito, R.; Ferrera, M.; Corigliano, A.

2018-05-01

In this paper a complete multiphysics modelling via the finite element method (FEM) of an air-coupled array of piezoelectric micromachined ultrasonic transducers (PMUT) and its experimental validation are presented. Two numerical models are described for the single transducer, axisymmetric and 3D, with the following features: the presence of fabrication induced residual stresses, which determine a non-linear initial deformed configuration of the diaphragm and a substantial fundamental mode frequency shift; the multiple coupling between different physics, namely electro-mechanical coupling for the piezo-electric model, thermo-acoustic-structural interaction and thermo-acoustic-pressure interaction for the waves propagation in the surrounding fluid. The model for the single transducer is enhanced considering the full set of PMUTs belonging to the silicon dye in a 4 × 4 array configuration. The results of the numerical multiphysics models are compared with experimental ones in terms of the initial static pre-deflection, of the diaphragm central point spectrum and of the sound intensity at 3.5 cm on the vertical direction along the axis of the diaphragm.

AZTEC. Parallel Iterative method Software for Solving Linear Systems

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, S.; Shadid, J.; Tuminaro, R.

1995-07-01

AZTEC is an interactive library that greatly simplifies the parrallelization process when solving the linear systems of equations Ax=b where A is a user supplied n X n sparse matrix, b is a user supplied vector of length n and x is a vector of length n to be computed. AZTEC is intended as a software tool for users who want to avoid cumbersome parallel programming details but who have large sparse linear systems which require an efficiently utilized parallel processing system. A collection of data transformation tools are provided that allow for easy creation of distributed sparse unstructured matricesmore » for parallel solutions.« less

Computation of Thermodynamic Equilibria Pertinent to Nuclear Materials in Multi-Physics Codes

NASA Astrophysics Data System (ADS)

Piro, Markus Hans Alexander

Nuclear energy plays a vital role in supporting electrical needs and fulfilling commitments to reduce greenhouse gas emissions. Research is a continuing necessity to improve the predictive capabilities of fuel behaviour in order to reduce costs and to meet increasingly stringent safety requirements by the regulator. Moreover, a renewed interest in nuclear energy has given rise to a "nuclear renaissance" and the necessity to design the next generation of reactors. In support of this goal, significant research efforts have been dedicated to the advancement of numerical modelling and computational tools in simulating various physical and chemical phenomena associated with nuclear fuel behaviour. This undertaking in effect is collecting the experience and observations of a past generation of nuclear engineers and scientists in a meaningful way for future design purposes. There is an increasing desire to integrate thermodynamic computations directly into multi-physics nuclear fuel performance and safety codes. A new equilibrium thermodynamic solver is being developed with this matter as a primary objective. This solver is intended to provide thermodynamic material properties and boundary conditions for continuum transport calculations. There are several concerns with the use of existing commercial thermodynamic codes: computational performance; limited capabilities in handling large multi-component systems of interest to the nuclear industry; convenient incorporation into other codes with quality assurance considerations; and, licensing entanglements associated with code distribution. The development of this software in this research is aimed at addressing all of these concerns. The approach taken in this work exploits fundamental principles of equilibrium thermodynamics to simplify the numerical optimization equations. In brief, the chemical potentials of all species and phases in the system are constrained by estimates of the chemical potentials of the system components at each iterative step, and the objective is to minimize the residuals of the mass balance equations. Several numerical advantages are achieved through this simplification. In particular, computational expense is reduced and the rate of convergence is enhanced. Furthermore, the software has demonstrated the ability to solve systems involving as many as 118 component elements. An early version of the code has already been integrated into the Advanced Multi-Physics (AMP) code under development by the Oak Ridge National Laboratory, Los Alamos National Laboratory, Idaho National Laboratory and Argonne National Laboratory. Keywords: Engineering, Nuclear -- 0552, Engineering, Material Science -- 0794, Chemistry, Mathematics -- 0405, Computer Science -- 0984

An Expert Assistant for Computer Aided Parallelization

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Chun, Robert; Jin, Haoqiang; Labarta, Jesus; Gimenez, Judit

2004-01-01

The prototype implementation of an expert system was developed to assist the user in the computer aided parallelization process. The system interfaces to tools for automatic parallelization and performance analysis. By fusing static program structure information and dynamic performance analysis data the expert system can help the user to filter, correlate, and interpret the data gathered by the existing tools. Sections of the code that show poor performance and require further attention are rapidly identified and suggestions for improvements are presented to the user. In this paper we describe the components of the expert system and discuss its interface to the existing tools. We present a case study to demonstrate the successful use in full scale scientific applications.

Musculoskeletal Modeling of the Lumbar Spine to Explore Functional Interactions between Back Muscle Loads and Intervertebral Disk Multiphysics

PubMed Central

Toumanidou, Themis; Noailly, Jérôme

2015-01-01

During daily activities, complex biomechanical interactions influence the biophysical regulation of intervertebral disks (IVDs), and transfers of mechanical loads are largely controlled by the stabilizing action of spine muscles. Muscle and other internal forces cannot be easily measured directly in the lumbar spine. Hence, biomechanical models are important tools for the evaluation of the loads in those tissues involved in low-back disorders. Muscle force estimations in most musculoskeletal models mainly rely, however, on inverse calculations and static optimizations that limit the predictive power of the numerical calculations. In order to contribute to the development of predictive systems, we coupled a predictive muscle model with the passive resistance of the spine tissues, in a L3–S1 musculoskeletal finite element model with osmo-poromechanical IVD descriptions. The model included 46 fascicles of the major back muscles that act on the lower spine. The muscle model interacted with activity-related loads imposed to the osteoligamentous structure, as standing position and night rest were simulated through distributed upper body mass and free IVD swelling, respectively. Calculations led to intradiscal pressure values within ranges of values measured in vivo. Disk swelling led to muscle activation and muscle force distributions that seemed particularly appropriate to counterbalance the anterior body mass effect in standing. Our simulations pointed out a likely existence of a functional balance between stretch-induced muscle activation and IVD multiphysics toward improved mechanical stability of the lumbar spine understanding. This balance suggests that proper night rest contributes to mechanically strengthen the spine during day activity. PMID:26301218

Deep geothermal systems interpreted by coupled thermo-hydraulic-mechanical-chemical numerical modeling

NASA Astrophysics Data System (ADS)

Peters, Max; Lesueur, Martin; Held, Sebastian; Poulet, Thomas; Veveakis, Manolis; Regenauer-Lieb, Klaus; Kohl, Thomas

2017-04-01

The dynamic response of the geothermal reservoirs of Soultz-sous-Forêts (NE France) and a new site in Iceland are theoretically studied upon fluid injection and production. Since the Soultz case can be considered the most comprehensive project in the area of enhanced geothermal systems (EGS), it is tailored for the testing of forward modeling techniques that aim at the characterization of fluid dynamics and mechanical properties in any deeply-seated fractured cystalline reservoir [e.g. Held et al., 2014]. We present multi-physics finite element models using the recently developed framework MOOSE (mooseframework.org) that implicitly consider fully-coupled feedback mechanisms of fluid-rock interaction at depth where EGS are located (depth > 5 km), i.e. the effects of dissipative strain softening on chemical reactions and reactive transport [Poulet et al., 2016]. In a first suite of numerical experiments, we show that an accurate simulation of propagation fronts allows studying coupled fluid and heat transport, following preferred pathways, and the transport time of the geothermal fluid between injection and production wells, which is in good agreement with tracer experiments performed inside the natural reservoir. Based on induced seismicity experiments and related damage along boreholes, we concern with borehole instabilities resulting from pore pressure variations and (a)seismic creep in a second series of simulations. To this end, we account for volumetric and deviatoric components, following the approach of Veveakis et al. (2016), and discuss the mechanisms triggering slow earthquakes in the stimulated reservoirs. Our study will allow applying concepts of unconventional geomechanics, which were previously reviewed on a theoretical basis [Regenauer-Lieb et al., 2015], to substantial engineering problems of deep geothermal reservoirs in the future. REFERENCES Held, S., Genter, A., Kohl, T., Kölbel, T., Sausse, J. and Schoenball, M. (2014). Economic evaluation of geothermal reservoir performance through modeling the complexity of the operating EGS in Soultz-sous-Forêts. Geothermics, 51, 270-280, doi:10.1016/j.geothermics.2014.01.016 Poulet, T., Paesold, M. and Veveakis, M. (2016). Multi-Physics Modelling of Fault Mechanics Using REDBACK: A Parallel Open-Source Simulator for Tightly Coupled Problems. Rock Mechanics and Rock Engineering, doi:10.1007/s00603-016-0927-y Regenauer-Lieb, K., Bunger, A., Chua, H. T., et al., 2015. Deep Geothermal: The 'Moon Landing' Mission in the Unconventional Energy and Minerals Space. Journal of Earth Science, 26(1): 2-10, doi:10.1007/s12583-015-0515-1 Veveakis, M., Alevizos, S., Poulet, T. (2016). Episodic Tremor and Slip (ETS) as a chaotic Multiphysics spring. Physics of the Earth and Planetary Interiors, in press, doi:10.1016/j.pepi.2016.10.002

Keeping it Together: Advanced algorithms and software for magma dynamics (and other coupled multi-physics problems)

NASA Astrophysics Data System (ADS)

Spiegelman, M.; Wilson, C. R.

2011-12-01

A quantitative theory of magma production and transport is essential for understanding the dynamics of magmatic plate boundaries, intra-plate volcanism and the geochemical evolution of the planet. It also provides one of the most challenging computational problems in solid Earth science, as it requires consistent coupling of fluid and solid mechanics together with the thermodynamics of melting and reactive flows. Considerable work on these problems over the past two decades shows that small changes in assumptions of coupling (e.g. the relationship between melt fraction and solid rheology), can have profound changes on the behavior of these systems which in turn affects critical computational choices such as discretizations, solvers and preconditioners. To make progress in exploring and understanding this physically rich system requires a computational framework that allows more flexible, high-level description of multi-physics problems as well as increased flexibility in composing efficient algorithms for solution of the full non-linear coupled system. Fortunately, recent advances in available computational libraries and algorithms provide a platform for implementing such a framework. We present results from a new model building system that leverages functionality from both the FEniCS project (www.fenicsproject.org) and PETSc libraries (www.mcs.anl.gov/petsc) along with a model independent options system and gui, Spud (amcg.ese.ic.ac.uk/Spud). Key features from FEniCS include fully unstructured FEM with a wide range of elements; a high-level language (ufl) and code generation compiler (FFC) for describing the weak forms of residuals and automatic differentiation for calculation of exact and approximate jacobians. The overall strategy is to monitor/calculate residuals and jacobians for the entire non-linear system of equations within a global non-linear solve based on PETSc's SNES routines. PETSc already provides a wide range of solvers and preconditioners, from parallel sparse direct to algebraic multigrid, that can be chosen at runtime. In particular, we make extensive use of PETSc's FieldSplit block preconditioners that allow us to use optimal solvers for subproblems (such as Stokes, or advection/diffusion of temperature) as preconditioners for the full problem. Thus these routines let us reuse effective solving recipes/splittings from previous experience while monitoring the convergence of the global problem. These techniques often yield quadratic (Newton like) convergence for the work of standard Picard schemes. We will illustrate this new framework with examples from the Magma Dynamic Demonstration suite (MADDs) of well understood magma dynamics benchmark problems including stokes flow in ridge geometries, magmatic solitary waves and shear-driven melt bands. While development of this system has been driven by magma dynamics, this framework is much more general and can be used for a wide range of PDE based multi-physics models.

Instrumentation, performance visualization, and debugging tools for multiprocessors

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Fineman, Charles E.; Hontalas, Philip J.

1991-01-01

The need for computing power has forced a migration from serial computation on a single processor to parallel processing on multiprocessor architectures. However, without effective means to monitor (and visualize) program execution, debugging, and tuning parallel programs becomes intractably difficult as program complexity increases with the number of processors. Research on performance evaluation tools for multiprocessors is being carried out at ARC. Besides investigating new techniques for instrumenting, monitoring, and presenting the state of parallel program execution in a coherent and user-friendly manner, prototypes of software tools are being incorporated into the run-time environments of various hardware testbeds to evaluate their impact on user productivity. Our current tool set, the Ames Instrumentation Systems (AIMS), incorporates features from various software systems developed in academia and industry. The execution of FORTRAN programs on the Intel iPSC/860 can be automatically instrumented and monitored. Performance data collected in this manner can be displayed graphically on workstations supporting X-Windows. We have successfully compared various parallel algorithms for computational fluid dynamics (CFD) applications in collaboration with scientists from the Numerical Aerodynamic Simulation Systems Division. By performing these comparisons, we show that performance monitors and debuggers such as AIMS are practical and can illuminate the complex dynamics that occur within parallel programs.

Full speed ahead for software

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wolfe, A.

1986-03-10

Supercomputing software is moving into high gear, spurred by the rapid spread of supercomputers into new applications. The critical challenge is how to develop tools that will make it easier for programmers to write applications that take advantage of vectorizing in the classical supercomputer and the parallelism that is emerging in supercomputers and minisupercomputers. Writing parallel software is a challenge that every programmer must face because parallel architectures are springing up across the range of computing. Cray is developing a host of tools for programmers. Tools to support multitasking (in supercomputer parlance, multitasking means dividing up a single program tomore » run on multiple processors) are high on Cray's agenda. On tap for multitasking is Premult, dubbed a microtasking tool. As a preprocessor for Cray's CFT77 FORTRAN compiler, Premult will provide fine-grain multitasking.« less

Multi-Physics Analysis of the Fermilab Booster RF Cavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awida, M.; Reid, J.; Yakovlev, V.

After about 40 years of operation the RF accelerating cavities in Fermilab Booster need an upgrade to improve their reliability and to increase the repetition rate in order to support a future experimental program. An increase in the repetitio n rate from 7 to 15 Hz entails increasing the power dissipation in the RF cavities, their ferrite loaded tuners, and HOM dampers. The increased duty factor requires careful modelling for the RF heating effects in the cavity. A multi-physic analysis invest igating both the RF and thermal properties of Booster cavity under various operating conditions is presented in this paper.

Multi-Physics Analysis of the Fermilab Booster RF Cavity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Awida, M.; Reid, J.; Yakovlev, V.

After about 40 years of operation the RF accelerating cavities in Fermilab Booster need an upgrade to improve their reliability and to increase the repetition rate in order to support a future experimental program. An increase in the repetition rate from 7 to 15 Hz entails increasing the power dissipation in the RF cavities, their ferrite loaded tuners, and HOM dampers. The increased duty factor requires careful modelling for the RF heating effects in the cavity. A multi-physic analysis investigating both the RF and thermal properties of Booster cavity under various operating conditions is presented in this paper.

Modeling of the thermal comfort in vehicles using COMSOL multiphysics

NASA Astrophysics Data System (ADS)

Gavrila, Camelia; Vartires, Andreea

2016-12-01

The environmental quality in vehicles is a very important aspect of building design and evaluation of the influence of the thermal comfort inside the car for ensuring a safe trip. The aim of this paper is to modeling and simulating the thermal comfort inside the vehicles, using COMSOL Multiphysics program, for different ventilation grilles. The objective will be the implementing innovative air diffusion grilles in a prototype vehicle. The idea behind this goal is to introduce air diffusers with a special geometry allowing improving mixing between the hot or the cold conditioned air introduced in the cockpit and the ambient.

An Anisotropic Multiphysics Model for Intervertebral Disk

PubMed Central

Gao, Xin; Zhu, Qiaoqiao; Gu, Weiyong

2016-01-01

Intervertebral disk (IVD) is the largest avascular structure in human body, consisting of three types of charged hydrated soft tissues. Its mechanical behavior is nonlinear and anisotropic, due mainly to nonlinear interactions among different constituents within tissues. In this study, a more realistic anisotropic multiphysics model was developed based on the continuum mixture theory and employed to characterize the couplings of multiple physical fields in the IVD. Numerical simulations demonstrate that this model is capable of systematically predicting the mechanical and electrochemical signals within the disk under various loading conditions, which is essential in understanding the mechanobiology of IVD. PMID:27099402

Multiphysics processes in partially saturated fractured rock: Experiments and models from Yucca Mountain

NASA Astrophysics Data System (ADS)

Rutqvist, Jonny; Tsang, Chin-Fu

2012-09-01

The site investigations at Yucca Mountain, Nevada, have provided us with an outstanding data set, one that has significantly advanced our knowledge of multiphysics processes in partially saturated fractured geological media. Such advancement was made possible, foremost, by substantial investments in multiyear field experiments that enabled the study of thermally driven multiphysics and testing of numerical models at a large spatial scale. The development of coupled-process models within the project have resulted in a number of new, advanced multiphysics numerical models that are today applied over a wide range of geoscientific research and geoengineering applications. Using such models, the potential impact of thermal-hydrological-mechanical (THM) multiphysics processes over the long-term (e.g., 10,000 years) could be predicted and bounded with some degree of confidence. The fact that the rock mass at Yucca Mountain is intensively fractured enabled continuum models to be used, although discontinuum models were also applied and are better suited for analyzing some issues, especially those related to predictions of rockfall within open excavations. The work showed that in situ tests (rather than small-scale laboratory experiments alone) are essential for determining appropriate input parameters for multiphysics models of fractured rocks, especially related to parameters defining how permeability might evolve under changing stress and temperature. A significant laboratory test program at Yucca Mountain also made important contributions to the field of rock mechanics, showing a unique relation between porosity and mechanical properties, a time dependency of strength that is significant for long-term excavation stability, a decreasing rock strength with sample size using very large core experiments, and a strong temperature dependency of the thermal expansion coefficient for temperatures up to 200°C. The analysis of in situ heater experiments showed that fracture closure/opening caused by changes in normal stress across fractures was the dominant mechanism for thermally induced changes in intrinsic fracture permeability during rock mass heating/cooling and that fracture shear dilation appears to be less significant. Significant effort was devoted to predicting the long-term stability of underground excavations under (mechanical) strength degradation and seismic loading, perhaps one of the most challenging tasks within the project. We note that such long-term strength degradation is actually an example of a chemically mediated process governed by underlying (microscopic) stress corrosion and chemical diffusion processes. In the Yucca Mountain Project, such chemically mediated mechanical changes were considered implicitly through model calibrations against laboratory and in situ heater experiments at temperatures anticipated to be experienced by the rock. A possible future research direction would be to simulate such processes mechanistically in a complete coupled THMC framework where C denotes chemical processes.

TerraFERMA: Harnessing Advanced Computational Libraries in Earth Science

NASA Astrophysics Data System (ADS)

Wilson, C. R.; Spiegelman, M.; van Keken, P.

2012-12-01

Many important problems in Earth sciences can be described by non-linear coupled systems of partial differential equations. These "multi-physics" problems include thermo-chemical convection in Earth and planetary interiors, interactions of fluids and magmas with the Earth's mantle and crust and coupled flow of water and ice. These problems are of interest to a large community of researchers but are complicated to model and understand. Much of this complexity stems from the nature of multi-physics where small changes in the coupling between variables or constitutive relations can lead to radical changes in behavior, which in turn affect critical computational choices such as discretizations, solvers and preconditioners. To make progress in understanding such coupled systems requires a computational framework where multi-physics problems can be described at a high-level while maintaining the flexibility to easily modify the solution algorithm. Fortunately, recent advances in computational science provide a basis for implementing such a framework. Here we present the Transparent Finite Element Rapid Model Assembler (TerraFERMA), which leverages several advanced open-source libraries for core functionality. FEniCS (fenicsproject.org) provides a high level language for describing the weak forms of coupled systems of equations, and an automatic code generator that produces finite element assembly code. PETSc (www.mcs.anl.gov/petsc) provides a wide range of scalable linear and non-linear solvers that can be composed into effective multi-physics preconditioners. SPuD (amcg.ese.ic.ac.uk/Spud) is an application neutral options system that provides both human and machine-readable interfaces based on a single xml schema. Our software integrates these libraries and provides the user with a framework for exploring multi-physics problems. A single options file fully describes the problem, including all equations, coefficients and solver options. Custom compiled applications are generated from this file but share an infrastructure for services common to all models, e.g. diagnostics, checkpointing and global non-linear convergence monitoring. This maximizes code reusability, reliability and longevity ensuring that scientific results and the methods used to acquire them are transparent and reproducible. TerraFERMA has been tested against many published geodynamic benchmarks including 2D/3D thermal convection problems, the subduction zone benchmarks and benchmarks for magmatic solitary waves. It is currently being used in the investigation of reactive cracking phenomena with applications to carbon sequestration, but we will principally discuss its use in modeling the migration of fluids in subduction zones. Subduction zones require an understanding of the highly nonlinear interactions of fluids with solids and thus provide an excellent scientific driver for the development of multi-physics software.

Integrating Cache Performance Modeling and Tuning Support in Parallelization Tools

NASA Technical Reports Server (NTRS)

Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1998-01-01

With the resurgence of distributed shared memory (DSM) systems based on cache-coherent Non Uniform Memory Access (ccNUMA) architectures and increasing disparity between memory and processors speeds, data locality overheads are becoming the greatest bottlenecks in the way of realizing potential high performance of these systems. While parallelization tools and compilers facilitate the users in porting their sequential applications to a DSM system, a lot of time and effort is needed to tune the memory performance of these applications to achieve reasonable speedup. In this paper, we show that integrating cache performance modeling and tuning support within a parallelization environment can alleviate this problem. The Cache Performance Modeling and Prediction Tool (CPMP), employs trace-driven simulation techniques without the overhead of generating and managing detailed address traces. CPMP predicts the cache performance impact of source code level "what-if" modifications in a program to assist a user in the tuning process. CPMP is built on top of a customized version of the Computer Aided Parallelization Tools (CAPTools) environment. Finally, we demonstrate how CPMP can be applied to tune a real Computational Fluid Dynamics (CFD) application.

Design and analysis of a magneto-rheological damper for an all terrain vehicle

NASA Astrophysics Data System (ADS)

Krishnan Unni, R.; Tamilarasan, N.

2018-02-01

A shock absorber design intended to replace the existing conventional shock absorber with a controllable system using a Magneto-rheological damper is introduced for an All Terrain Vehicle (ATV) that was designed for Baja SAE competitions. Suspensions are a vital part of an All Terrain Vehicles as it endures various surfaces and requires utmost attention while designing. COMSOL multi-physics software is used for applications that have coupled physics problems and is a unique tool that is used for the designing and analysis phase of the Magneto-rheological damper for the considered application and the model is optimized based on Taguchi using DOE software. The magneto-rheological damper is designed to maximize the damping force with the measured geometric constraints for the All Terrain Vehicle.

MPI, HPF or OpenMP: A Study with the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Hribar, Michelle; Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1999-01-01

Porting applications to new high performance parallel and distributed platforms is a challenging task. Writing parallel code by hand is time consuming and costly, but the task can be simplified by high level languages and would even better be automated by parallelizing tools and compilers. The definition of HPF (High Performance Fortran, based on data parallel model) and OpenMP (based on shared memory parallel model) standards has offered great opportunity in this respect. Both provide simple and clear interfaces to language like FORTRAN and simplify many tedious tasks encountered in writing message passing programs. In our study we implemented the parallel versions of the NAS Benchmarks with HPF and OpenMP directives. Comparison of their performance with the MPI implementation and pros and cons of different approaches will be discussed along with experience of using computer-aided tools to help parallelize these benchmarks. Based on the study,potentials of applying some of the techniques to realistic aerospace applications will be presented

MPI, HPF or OpenMP: A Study with the NAS Benchmarks

NASA Technical Reports Server (NTRS)

Jin, H.; Frumkin, M.; Hribar, M.; Waheed, A.; Yan, J.; Saini, Subhash (Technical Monitor)

1999-01-01

Porting applications to new high performance parallel and distributed platforms is a challenging task. Writing parallel code by hand is time consuming and costly, but this task can be simplified by high level languages and would even better be automated by parallelizing tools and compilers. The definition of HPF (High Performance Fortran, based on data parallel model) and OpenMP (based on shared memory parallel model) standards has offered great opportunity in this respect. Both provide simple and clear interfaces to language like FORTRAN and simplify many tedious tasks encountered in writing message passing programs. In our study, we implemented the parallel versions of the NAS Benchmarks with HPF and OpenMP directives. Comparison of their performance with the MPI implementation and pros and cons of different approaches will be discussed along with experience of using computer-aided tools to help parallelize these benchmarks. Based on the study, potentials of applying some of the techniques to realistic aerospace applications will be presented.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Slattery, Stuart R.

In this study we analyze and extend mesh-free algorithms for three-dimensional data transfer problems in partitioned multiphysics simulations. We first provide a direct comparison between a mesh-based weighted residual method using the common-refinement scheme and two mesh-free algorithms leveraging compactly supported radial basis functions: one using a spline interpolation and one using a moving least square reconstruction. Through the comparison we assess both the conservation and accuracy of the data transfer obtained from each of the methods. We do so for a varying set of geometries with and without curvature and sharp features and for functions with and without smoothnessmore » and with varying gradients. Our results show that the mesh-based and mesh-free algorithms are complementary with cases where each was demonstrated to perform better than the other. We then focus on the mesh-free methods by developing a set of algorithms to parallelize them based on sparse linear algebra techniques. This includes a discussion of fast parallel radius searching in point clouds and restructuring the interpolation algorithms to leverage data structures and linear algebra services designed for large distributed computing environments. The scalability of our new algorithms is demonstrated on a leadership class computing facility using a set of basic scaling studies. Finally, these scaling studies show that for problems with reasonable load balance, our new algorithms for both spline interpolation and moving least square reconstruction demonstrate both strong and weak scalability using more than 100,000 MPI processes with billions of degrees of freedom in the data transfer operation.« less

Learning in Parallel: Using Parallel Corpora to Enhance Written Language Acquisition at the Beginning Level

ERIC Educational Resources Information Center

Bluemel, Brody

2014-01-01

This article illustrates the pedagogical value of incorporating parallel corpora in foreign language education. It explores the development of a Chinese/English parallel corpus designed specifically for pedagogical application. The corpus tool was created to aid language learners in reading comprehension and writing development by making foreign…

SBML-PET-MPI: a parallel parameter estimation tool for Systems Biology Markup Language based models.

PubMed

Zi, Zhike

2011-04-01

Parameter estimation is crucial for the modeling and dynamic analysis of biological systems. However, implementing parameter estimation is time consuming and computationally demanding. Here, we introduced a parallel parameter estimation tool for Systems Biology Markup Language (SBML)-based models (SBML-PET-MPI). SBML-PET-MPI allows the user to perform parameter estimation and parameter uncertainty analysis by collectively fitting multiple experimental datasets. The tool is developed and parallelized using the message passing interface (MPI) protocol, which provides good scalability with the number of processors. SBML-PET-MPI is freely available for non-commercial use at http://www.bioss.uni-freiburg.de/cms/sbml-pet-mpi.html or http://sites.google.com/site/sbmlpetmpi/.

Scalable Visual Analytics of Massive Textual Datasets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Krishnan, Manoj Kumar; Bohn, Shawn J.; Cowley, Wendy E.

2007-04-01

This paper describes the first scalable implementation of text processing engine used in Visual Analytics tools. These tools aid information analysts in interacting with and understanding large textual information content through visual interfaces. By developing parallel implementation of the text processing engine, we enabled visual analytics tools to exploit cluster architectures and handle massive dataset. The paper describes key elements of our parallelization approach and demonstrates virtually linear scaling when processing multi-gigabyte data sets such as Pubmed. This approach enables interactive analysis of large datasets beyond capabilities of existing state-of-the art visual analytics tools.

The Spherical Tokamak MEDUSA for Mexico

NASA Astrophysics Data System (ADS)

Ribeiro, C.; Salvador, M.; Gonzalez, J.; Munoz, O.; Tapia, A.; Arredondo, V.; Chavez, R.; Nieto, A.; Gonzalez, J.; Garza, A.; Estrada, I.; Jasso, E.; Acosta, C.; Briones, C.; Cavazos, G.; Martinez, J.; Morones, J.; Almaguer, J.; Fonck, R.

2011-10-01

The former spherical tokamak MEDUSA (Madison EDUcation Small Aspect.ratio tokamak, R < 0.14m, a < 0.10m, BT < 0.5T, Ip < 40kA, 3ms pulse) is currently being recomissioned at the Universidad Autónoma de Nuevo León, Mexico, as part of an agreement between the Faculties of Mech.-Elect. Eng. and Phy. Sci.-Maths. The main objective for having MEDUSA is to train students in plasma physics & technical related issues, aiming a full design of a medium size device (e.g. Tokamak-T). Details of technical modifications and a preliminary scientific programme will be presented. MEDUSA-MX will also benefit any developments in the existing Mexican Fusion Network. Strong liaison within national and international plasma physics communities is expected. New activities on plasma & engineering modeling are expected to be developed in parallel by using the existing facilities such as a multi-platform computer (Silicon Graphics Altix XE250, 128G RAM, 3.7TB HD, 2.7GHz, quad-core processor), ancillary graph system (NVIDIA Quadro FE 2000/1GB GDDR-5 PCI X16 128, 3.2GHz), and COMSOL Multiphysics-Solid Works programs.

Co-Simulation for Advanced Process Design and Optimization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stephen E. Zitney

2009-01-01

Meeting the increasing demand for clean, affordable, and secure energy is arguably the most important challenge facing the world today. Fossil fuels can play a central role in a portfolio of carbon-neutral energy options provided CO{sub 2} emissions can be dramatically reduced by capturing CO{sub 2} and storing it safely and effectively. Fossil energy industry faces the challenge of meeting aggressive design goals for next-generation power plants with CCS. Process designs will involve large, highly-integrated, and multipurpose systems with advanced equipment items with complex geometries and multiphysics. APECS is enabling software to facilitate effective integration, solution, and analysis of high-fidelitymore » process/equipment (CFD) co-simulations. APECS helps to optimize fluid flow and related phenomena that impact overall power plant performance. APECS offers many advanced capabilities including ROMs, design optimization, parallel execution, stochastic analysis, and virtual plant co-simulations. NETL and its collaborative R&D partners are using APECS to reduce the time, cost, and technical risk of developing high-efficiency, zero-emission power plants with CCS.« less

Capabilities and performance of the new generation ice-sheet model Elmer/Ice

NASA Astrophysics Data System (ADS)

Gagliardini, O.; Zwinger, T.; Durand, G.; Favier, L.; de Fleurian, B.; Gillet-chaulet, F.; Seddik, H.; Greve, R.; Mallinen, M.; Martin, C.; Raback, P.; Ruokolainen, J.; Schäfer, M.; Thies, J.

2012-12-01

Since the Fourth IPCC Assessment Report, and its conclusion about the inability of ice-sheet flow models to forecast the current increase of polar ice sheet discharge and associated contribution to sea-level rise, a huge development effort has been undertaken by the glaciological community. All around the world, models have been improved and, interestingly, a significant number of new ice-sheet models have emerged. Among them, the parallel finite-element model Elmer/Ice (based on the open-source multi-physics code Elmer) was one of the first full-Stokes models used to make projections of the future of the whole Greenland ice sheet for the coming two centuries. Originally developed to solve dedicated local ice flow problems of high mechanical and physical complexity, Elmer/Ice has today reached the maturity to solve larger scale problems, earning the status of an ice-sheet model. In this presentation, we summarise the almost 10 years of development performed by different groups. We present the components already included in Elmer/Ice, its numerical performance, selected applications, as well as developments planed for the future.

Capabilities and performance of Elmer/Ice, a new generation ice-sheet model

NASA Astrophysics Data System (ADS)

Gagliardini, O.; Zwinger, T.; Gillet-Chaulet, F.; Durand, G.; Favier, L.; de Fleurian, B.; Greve, R.; Malinen, M.; Martín, C.; Råback, P.; Ruokolainen, J.; Sacchettini, M.; Schäfer, M.; Seddik, H.; Thies, J.

2013-03-01

The Fourth IPCC Assessment Report concluded that ice-sheet flow models are unable to forecast the current increase of polar ice sheet discharge and the associated contribution to sea-level rise. Since then, the glaciological community has undertaken a huge effort to develop and improve a new generation of ice-flow models, and as a result, a significant number of new ice-sheet models have emerged. Among them is the parallel finite-element model Elmer/Ice, based on the open-source multi-physics code Elmer. It was one of the first full-Stokes models used to make projections for the evolution of the whole Greenland ice sheet for the coming two centuries. Originally developed to solve local ice flow problems of high mechanical and physical complexity, Elmer/Ice has today reached the maturity to solve larger scale problems, earning the status of an ice-sheet model. Here, we summarise almost 10 yr of development performed by different groups. We present the components already included in Elmer/Ice, its numerical performance, selected applications, as well as developments planned for the future.

Development of the US3D Code for Advanced Compressible and Reacting Flow Simulations

NASA Technical Reports Server (NTRS)

Candler, Graham V.; Johnson, Heath B.; Nompelis, Ioannis; Subbareddy, Pramod K.; Drayna, Travis W.; Gidzak, Vladimyr; Barnhardt, Michael D.

2015-01-01

Aerothermodynamics and hypersonic flows involve complex multi-disciplinary physics, including finite-rate gas-phase kinetics, finite-rate internal energy relaxation, gas-surface interactions with finite-rate oxidation and sublimation, transition to turbulence, large-scale unsteadiness, shock-boundary layer interactions, fluid-structure interactions, and thermal protection system ablation and thermal response. Many of the flows have a large range of length and time scales, requiring large computational grids, implicit time integration, and large solution run times. The University of Minnesota NASA US3D code was designed for the simulation of these complex, highly-coupled flows. It has many of the features of the well-established DPLR code, but uses unstructured grids and has many advanced numerical capabilities and physical models for multi-physics problems. The main capabilities of the code are described, the physical modeling approaches are discussed, the different types of numerical flux functions and time integration approaches are outlined, and the parallelization strategy is overviewed. Comparisons between US3D and the NASA DPLR code are presented, and several advanced simulations are presented to illustrate some of novel features of the code.

Interaction between the lower hybrid wave and density fluctuations in the scrape-off layer

NASA Astrophysics Data System (ADS)

Peysson, Y.; Madi, M.; Decker, J.; Kabalan, K.

2015-12-01

In the present paper, the perturbation of the launched power spectrum of the Lower Hybrid wave at the separatrix by electron density fluctuations in the scrape-off layer is investigated. Considering a slab geometry with magnetic field lines parallel to the toroidal direction, the full wave equation is solved using Comsol Multiphysics® for a fully active multi-junction like LH antenna made of two modules. When electron density fluctuations are incorporated in the dielectric tensor over a thin perturbed layer in front of the grill, it is shown that the power spectrum may be strongly modified from the antenna mouth to the plasma separatrix as the wave propagates. The diffraction effect leads to the appearance of multiple satellite lobes with randomly varying positions, a feature consistent with the recently developed model that has been applied successfully to high density discharges on the Tokamak Tore Supra corresponding to the large spectral gap regime [Decker J. et al. Phys. Plasma 21 (2014) 092504]. The perturbation is found to be maximum for the Fourier components of the fluctuating spectrum in the vicinity of the launched LH wavelength.

Automatic Multilevel Parallelization Using OpenMP

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Jost, Gabriele; Yan, Jerry; Ayguade, Eduard; Gonzalez, Marc; Martorell, Xavier; Biegel, Bryan (Technical Monitor)

2002-01-01

In this paper we describe the extension of the CAPO (CAPtools (Computer Aided Parallelization Toolkit) OpenMP) parallelization support tool to support multilevel parallelism based on OpenMP directives. CAPO generates OpenMP directives with extensions supported by the NanosCompiler to allow for directive nesting and definition of thread groups. We report some results for several benchmark codes and one full application that have been parallelized using our system.

High-performance computing — an overview

NASA Astrophysics Data System (ADS)

Marksteiner, Peter

1996-08-01

An overview of high-performance computing (HPC) is given. Different types of computer architectures used in HPC are discussed: vector supercomputers, high-performance RISC processors, various parallel computers like symmetric multiprocessors, workstation clusters, massively parallel processors. Software tools and programming techniques used in HPC are reviewed: vectorizing compilers, optimization and vector tuning, optimization for RISC processors; parallel programming techniques like shared-memory parallelism, message passing and data parallelism; and numerical libraries.

Development of Modeling Capabilities for Launch Pad Acoustics and Ignition Transient Environment Prediction

NASA Technical Reports Server (NTRS)

West, Jeff; Strutzenberg, Louise L.; Putnam, Gabriel C.; Liever, Peter A.; Williams, Brandon R.

2012-01-01

This paper presents development efforts to establish modeling capabilities for launch vehicle liftoff acoustics and ignition transient environment predictions. Peak acoustic loads experienced by the launch vehicle occur during liftoff with strong interaction between the vehicle and the launch facility. Acoustic prediction engineering tools based on empirical models are of limited value in efforts to proactively design and optimize launch vehicles and launch facility configurations for liftoff acoustics. Modeling approaches are needed that capture the important details of the plume flow environment including the ignition transient, identify the noise generation sources, and allow assessment of the effects of launch pad geometric details and acoustic mitigation measures such as water injection. This paper presents a status of the CFD tools developed by the MSFC Fluid Dynamics Branch featuring advanced multi-physics modeling capabilities developed towards this goal. Validation and application examples are presented along with an overview of application in the prediction of liftoff environments and the design of targeted mitigation measures such as launch pad configuration and sound suppression water placement.

AEROELASTIC SIMULATION TOOL FOR INFLATABLE BALLUTE AEROCAPTURE

NASA Technical Reports Server (NTRS)

Liever, P. A.; Sheta, E. F.; Habchi, S. D.

2006-01-01

A multidisciplinary analysis tool is under development for predicting the impact of aeroelastic effects on the functionality of inflatable ballute aeroassist vehicles in both the continuum and rarefied flow regimes. High-fidelity modules for continuum and rarefied aerodynamics, structural dynamics, heat transfer, and computational grid deformation are coupled in an integrated multi-physics, multi-disciplinary computing environment. This flexible and extensible approach allows the integration of state-of-the-art, stand-alone NASA and industry leading continuum and rarefied flow solvers and structural analysis codes into a computing environment in which the modules can run concurrently with synchronized data transfer. Coupled fluid-structure continuum flow demonstrations were conducted on a clamped ballute configuration. The feasibility of implementing a DSMC flow solver in the simulation framework was demonstrated, and loosely coupled rarefied flow aeroelastic demonstrations were performed. A NASA and industry technology survey identified CFD, DSMC and structural analysis codes capable of modeling non-linear shape and material response of thin-film inflated aeroshells. The simulation technology will find direct and immediate applications with NASA and industry in ongoing aerocapture technology development programs.

On-Line Monitoring the Growth of E. coli or HeLa Cells Using an Annular Microelectrode Piezoelectric Biosensor.

PubMed

Tong, Feifei; Lian, Yan; Han, Junliang

2016-12-18

Biological information is obtained from the interaction between the series detection electrode and the organism or the physical field of biological cultures in the non-mass responsive piezoelectric biosensor. Therefore, electric parameter of the electrode will affect the biosensor signal. The electric field distribution of the microelectrode used in this study was simulated using the COMSOL Multiphysics analytical tool. This process showed that the electric field spatial distribution is affected by the width of the electrode finger or the space between the electrodes. In addition, the characteristic response of the piezoelectric sensor constructed serially with an annular microelectrode was tested and applied for the continuous detection of Escherichia coli culture or HeLa cell culture. Results indicated that the piezoelectric biosensor with an annular microelectrode meets the requirements for the real-time detection of E. coli or HeLa cells in culture. Moreover, this kind of piezoelectric biosensor is more sensitive than the sensor with an interdigital microelectrode. Thus, the piezoelectric biosensor acts as an effective analysis tool for acquiring online cell or microbial culture information.

Advanced laser modeling with BLAZE multiphysics

NASA Astrophysics Data System (ADS)

Palla, Andrew D.; Carroll, David L.; Gray, Michael I.; Suzuki, Lui

2017-01-01

The BLAZE Multiphysics™ software simulation suite was specifically developed to model highly complex multiphysical systems in a computationally efficient and highly scalable manner. These capabilities are of particular use when applied to the complexities associated with high energy laser systems that combine subsonic/transonic/supersonic fluid dynamics, chemically reacting flows, laser electronics, heat transfer, optical physics, and in some cases plasma discharges. In this paper we present detailed cw and pulsed gas laser calculations using the BLAZE model with comparisons to data. Simulations of DPAL, XPAL, ElectricOIL (EOIL), and the optically pumped rare gas laser were found to be in good agreement with experimental data.

Achieving bifunctional cloak via combination of passive and active schemes

NASA Astrophysics Data System (ADS)

Lan, Chuwen; Bi, Ke; Gao, Zehua; Li, Bo; Zhou, Ji

2016-11-01

In this study, a simple and delicate approach to realizing manipulation of multi-physics field simultaneously through combination of passive and active schemes is proposed. In the design, one physical field is manipulated with passive scheme while the other with active scheme. As a proof of this concept, a bifunctional device is designed and fabricated to behave as electric and thermal invisibility cloak simultaneously. It is found that the experimental results are consistent with the simulated ones well, confirming the feasibility of our method. Furthermore, the proposed method could also be extended to other multi-physics fields, which might lead to potential applications in thermal, electric, and acoustic areas.

Studying the Effect of Deposition Conditions on the Performance and Reliability of MEMS Gas Sensors

PubMed Central

Sadek, Khaled; Moussa, Walied

2007-01-01

In this paper, the reliability of a micro-electro-mechanical system (MEMS)-based gas sensor has been investigated using Three Dimensional (3D) coupled multiphysics Finite Element (FE) analysis. The coupled field analysis involved a two-way sequential electrothermal fields coupling and a one-way sequential thermal-structural fields coupling. An automated substructuring code was developed to reduce the computational cost involved in simulating this complicated coupled multiphysics FE analysis by up to 76 percent. The substructured multiphysics model was then used to conduct a parametric study of the MEMS-based gas sensor performance in response to the variations expected in the thermal and mechanical characteristics of thin films layers composing the sensing MEMS device generated at various stages of the microfabrication process. Whenever possible, the appropriate deposition variables were correlated in the current work to the design parameters, with good accuracy, for optimum operation conditions of the gas sensor. This is used to establish a set of design rules, using linear and nonlinear empirical relations, which can be utilized in real-time at the design and development decision-making stages of similar gas sensors to enable the microfabrication of these sensors with reliable operation.

Highly scalable parallel processing of extracellular recordings of Multielectrode Arrays.

PubMed

Gehring, Tiago V; Vasilaki, Eleni; Giugliano, Michele

2015-01-01

Technological advances of Multielectrode Arrays (MEAs) used for multisite, parallel electrophysiological recordings, lead to an ever increasing amount of raw data being generated. Arrays with hundreds up to a few thousands of electrodes are slowly seeing widespread use and the expectation is that more sophisticated arrays will become available in the near future. In order to process the large data volumes resulting from MEA recordings there is a pressing need for new software tools able to process many data channels in parallel. Here we present a new tool for processing MEA data recordings that makes use of new programming paradigms and recent technology developments to unleash the power of modern highly parallel hardware, such as multi-core CPUs with vector instruction sets or GPGPUs. Our tool builds on and complements existing MEA data analysis packages. It shows high scalability and can be used to speed up some performance critical pre-processing steps such as data filtering and spike detection, helping to make the analysis of larger data sets tractable.

The Parallel System for Integrating Impact Models and Sectors (pSIMS)

NASA Technical Reports Server (NTRS)

Elliott, Joshua; Kelly, David; Chryssanthacopoulos, James; Glotter, Michael; Jhunjhnuwala, Kanika; Best, Neil; Wilde, Michael; Foster, Ian

2014-01-01

We present a framework for massively parallel climate impact simulations: the parallel System for Integrating Impact Models and Sectors (pSIMS). This framework comprises a) tools for ingesting and converting large amounts of data to a versatile datatype based on a common geospatial grid; b) tools for translating this datatype into custom formats for site-based models; c) a scalable parallel framework for performing large ensemble simulations, using any one of a number of different impacts models, on clusters, supercomputers, distributed grids, or clouds; d) tools and data standards for reformatting outputs to common datatypes for analysis and visualization; and e) methodologies for aggregating these datatypes to arbitrary spatial scales such as administrative and environmental demarcations. By automating many time-consuming and error-prone aspects of large-scale climate impacts studies, pSIMS accelerates computational research, encourages model intercomparison, and enhances reproducibility of simulation results. We present the pSIMS design and use example assessments to demonstrate its multi-model, multi-scale, and multi-sector versatility.

Composing Data Parallel Code for a SPARQL Graph Engine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castellana, Vito G.; Tumeo, Antonino; Villa, Oreste

Big data analytics process large amount of data to extract knowledge from them. Semantic databases are big data applications that adopt the Resource Description Framework (RDF) to structure metadata through a graph-based representation. The graph based representation provides several benefits, such as the possibility to perform in memory processing with large amounts of parallelism. SPARQL is a language used to perform queries on RDF-structured data through graph matching. In this paper we present a tool that automatically translates SPARQL queries to parallel graph crawling and graph matching operations. The tool also supports complex SPARQL constructs, which requires more than basicmore » graph matching for their implementation. The tool generates parallel code annotated with OpenMP pragmas for x86 Shared-memory Multiprocessors (SMPs). With respect to commercial database systems such as Virtuoso, our approach reduces memory occupation due to join operations and provides higher performance. We show the scaling of the automatically generated graph-matching code on a 48-core SMP.« less

Dynamic Load-Balancing for Distributed Heterogeneous Computing of Parallel CFD Problems

NASA Technical Reports Server (NTRS)

Ecer, A.; Chien, Y. P.; Boenisch, T.; Akay, H. U.

2000-01-01

The developed methodology is aimed at improving the efficiency of executing block-structured algorithms on parallel, distributed, heterogeneous computers. The basic approach of these algorithms is to divide the flow domain into many sub- domains called blocks, and solve the governing equations over these blocks. Dynamic load balancing problem is defined as the efficient distribution of the blocks among the available processors over a period of several hours of computations. In environments with computers of different architecture, operating systems, CPU speed, memory size, load, and network speed, balancing the loads and managing the communication between processors becomes crucial. Load balancing software tools for mutually dependent parallel processes have been created to efficiently utilize an advanced computation environment and algorithms. These tools are dynamic in nature because of the chances in the computer environment during execution time. More recently, these tools were extended to a second operating system: NT. In this paper, the problems associated with this application will be discussed. Also, the developed algorithms were combined with the load sharing capability of LSF to efficiently utilize workstation clusters for parallel computing. Finally, results will be presented on running a NASA based code ADPAC to demonstrate the developed tools for dynamic load balancing.

A parallel algorithm for multi-level logic synthesis using the transduction method. M.S. Thesis

NASA Technical Reports Server (NTRS)

Lim, Chieng-Fai

1991-01-01

The Transduction Method has been shown to be a powerful tool in the optimization of multilevel networks. Many tools such as the SYLON synthesis system (X90), (CM89), (LM90) have been developed based on this method. A parallel implementation is presented of SYLON-XTRANS (XM89) on an eight processor Encore Multimax shared memory multiprocessor. It minimizes multilevel networks consisting of simple gates through parallel pruning, gate substitution, gate merging, generalized gate substitution, and gate input reduction. This implementation, called Parallel TRANSduction (PTRANS), also uses partitioning to break large circuits up and performs inter- and intra-partition dynamic load balancing. With this, good speedups and high processor efficiencies are achievable without sacrificing the resulting circuit quality.

Architecture-Adaptive Computing Environment: A Tool for Teaching Parallel Programming

NASA Technical Reports Server (NTRS)

Dorband, John E.; Aburdene, Maurice F.

2002-01-01

Recently, networked and cluster computation have become very popular. This paper is an introduction to a new C based parallel language for architecture-adaptive programming, aCe C. The primary purpose of aCe (Architecture-adaptive Computing Environment) is to encourage programmers to implement applications on parallel architectures by providing them the assurance that future architectures will be able to run their applications with a minimum of modification. A secondary purpose is to encourage computer architects to develop new types of architectures by providing an easily implemented software development environment and a library of test applications. This new language should be an ideal tool to teach parallel programming. In this paper, we will focus on some fundamental features of aCe C.

Light-weight Parallel Python Tools for Earth System Modeling Workflows

NASA Astrophysics Data System (ADS)

Mickelson, S. A.; Paul, K.; Xu, H.; Dennis, J.; Brown, D. I.

2015-12-01

With the growth in computing power over the last 30 years, earth system modeling codes have become increasingly data-intensive. As an example, it is expected that the data required for the next Intergovernmental Panel on Climate Change (IPCC) Assessment Report (AR6) will increase by more than 10x to an expected 25PB per climate model. Faced with this daunting challenge, developers of the Community Earth System Model (CESM) have chosen to change the format of their data for long-term storage from time-slice to time-series, in order to reduce the required download bandwidth needed for later analysis and post-processing by climate scientists. Hence, efficient tools are required to (1) perform the transformation of the data from time-slice to time-series format and to (2) compute climatology statistics, needed for many diagnostic computations, on the resulting time-series data. To address the first of these two challenges, we have developed a parallel Python tool for converting time-slice model output to time-series format. To address the second of these challenges, we have developed a parallel Python tool to perform fast time-averaging of time-series data. These tools are designed to be light-weight, be easy to install, have very few dependencies, and can be easily inserted into the Earth system modeling workflow with negligible disruption. In this work, we present the motivation, approach, and testing results of these two light-weight parallel Python tools, as well as our plans for future research and development.

Automatic Multilevel Parallelization Using OpenMP

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Jost, Gabriele; Yan, Jerry; Ayguade, Eduard; Gonzalez, Marc; Martorell, Xavier; Biegel, Bryan (Technical Monitor)

2002-01-01

In this paper we describe the extension of the CAPO parallelization support tool to support multilevel parallelism based on OpenMP directives. CAPO generates OpenMP directives with extensions supported by the NanosCompiler to allow for directive nesting and definition of thread groups. We report first results for several benchmark codes and one full application that have been parallelized using our system.

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele; Biegel, Bryan (Technical Monitor)

2001-01-01

This viewgraph presentation provides information on the technical aspects of debugging computer code that has been automatically converted for use in a parallel computing system. Shared memory parallelization and distributed memory parallelization entail separate and distinct challenges for a debugging program. A prototype system has been developed which integrates various tools for the debugging of automatically parallelized programs including the CAPTools Database which provides variable definition information across subroutines as well as array distribution information.

Code Parallelization with CAPO: A User Manual

NASA Technical Reports Server (NTRS)

Jin, Hao-Qiang; Frumkin, Michael; Yan, Jerry; Biegel, Bryan (Technical Monitor)

2001-01-01

A software tool has been developed to assist the parallelization of scientific codes. This tool, CAPO, extends an existing parallelization toolkit, CAPTools developed at the University of Greenwich, to generate OpenMP parallel codes for shared memory architectures. This is an interactive toolkit to transform a serial Fortran application code to an equivalent parallel version of the software - in a small fraction of the time normally required for a manual parallelization. We first discuss the way in which loop types are categorized and how efficient OpenMP directives can be defined and inserted into the existing code using the in-depth interprocedural analysis. The use of the toolkit on a number of application codes ranging from benchmark to real-world application codes is presented. This will demonstrate the great potential of using the toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of toolkit to quickly parallelize serial programs as well as the good performance achievable on a large number of processors. The second part of the document gives references to the parameters and the graphic user interface implemented in the toolkit. Finally a set of tutorials is included for hands-on experiences with this toolkit.

Parallel evolution of image processing tools for multispectral imagery

NASA Astrophysics Data System (ADS)

Harvey, Neal R.; Brumby, Steven P.; Perkins, Simon J.; Porter, Reid B.; Theiler, James P.; Young, Aaron C.; Szymanski, John J.; Bloch, Jeffrey J.

2000-11-01

We describe the implementation and performance of a parallel, hybrid evolutionary-algorithm-based system, which optimizes image processing tools for feature-finding tasks in multi-spectral imagery (MSI) data sets. Our system uses an integrated spatio-spectral approach and is capable of combining suitably-registered data from different sensors. We investigate the speed-up obtained by parallelization of the evolutionary process via multiple processors (a workstation cluster) and develop a model for prediction of run-times for different numbers of processors. We demonstrate our system on Landsat Thematic Mapper MSI , covering the recent Cerro Grande fire at Los Alamos, NM, USA.

Multiphysics and multiscale modelling, data-model fusion and integration of organ physiology in the clinic: ventricular cardiac mechanics.

PubMed

Chabiniok, Radomir; Wang, Vicky Y; Hadjicharalambous, Myrianthi; Asner, Liya; Lee, Jack; Sermesant, Maxime; Kuhl, Ellen; Young, Alistair A; Moireau, Philippe; Nash, Martyn P; Chapelle, Dominique; Nordsletten, David A

2016-04-06

With heart and cardiovascular diseases continually challenging healthcare systems worldwide, translating basic research on cardiac (patho)physiology into clinical care is essential. Exacerbating this already extensive challenge is the complexity of the heart, relying on its hierarchical structure and function to maintain cardiovascular flow. Computational modelling has been proposed and actively pursued as a tool for accelerating research and translation. Allowing exploration of the relationships between physics, multiscale mechanisms and function, computational modelling provides a platform for improving our understanding of the heart. Further integration of experimental and clinical data through data assimilation and parameter estimation techniques is bringing computational models closer to use in routine clinical practice. This article reviews developments in computational cardiac modelling and how their integration with medical imaging data is providing new pathways for translational cardiac modelling.

Towards a supported common NEAMS software stack

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cormac Garvey

2012-04-01

The NEAMS IPSC's are developing multidimensional, multiphysics, multiscale simulation codes based on first principles that will be capable of predicting all aspects of current and future nuclear reactor systems. These new breeds of simulation codes will include rigorous verification, validation and uncertainty quantification checks to quantify the accuracy and quality of the simulation results. The resulting NEAMS IPSC simulation codes will be an invaluable tool in designing the next generation of Nuclear Reactors and also contribute to a more speedy process in the acquisition of licenses from the NRC for new Reactor designs. Due to the high resolution of themore » models, the complexity of the physics and the added computational resources to quantify the accuracy/quality of the results, the NEAMS IPSC codes will require large HPC resources to carry out the production simulation runs.« less

Deformation measurements by ESPI of the surface of a heated mirror and comparison with numerical model

NASA Astrophysics Data System (ADS)

Languy, Fabian; Vandenrijt, Jean-François; Saint-Georges, Philippe; Georges, Marc P.

2017-06-01

The manufacture of mirrors for space application is expensive and the requirements on the optical performance increase over years. To achieve higher performance, larger mirrors are manufactured but the larger the mirror the higher the sensitivity to temperature variation and therefore the higher the degradation of optical performances. To avoid the use of an expensive thermal regulation, we need to develop tools able to predict how optics behaves with thermal constraints. This paper presents the comparison between experimental surface mirror deformation and theoretical results from a multiphysics model. The local displacements of the mirror surface have been measured with the use of electronic speckle pattern interferometry (ESPI) and the deformation itself has been calculated by subtracting the rigid body motion. After validation of the mechanical model, experimental and numerical wave front errors are compared.

Methodologies and Tools for Tuning Parallel Programs: 80% Art, 20% Science, and 10% Luck

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Bailey, David (Technical Monitor)

1996-01-01

The need for computing power has forced a migration from serial computation on a single processor to parallel processing on multiprocessors. However, without effective means to monitor (and analyze) program execution, tuning the performance of parallel programs becomes exponentially difficult as program complexity and machine size increase. In the past few years, the ubiquitous introduction of performance tuning tools from various supercomputer vendors (Intel's ParAide, TMC's PRISM, CRI's Apprentice, and Convex's CXtrace) seems to indicate the maturity of performance instrumentation/monitor/tuning technologies and vendors'/customers' recognition of their importance. However, a few important questions remain: What kind of performance bottlenecks can these tools detect (or correct)? How time consuming is the performance tuning process? What are some important technical issues that remain to be tackled in this area? This workshop reviews the fundamental concepts involved in analyzing and improving the performance of parallel and heterogeneous message-passing programs. Several alternative strategies will be contrasted, and for each we will describe how currently available tuning tools (e.g. AIMS, ParAide, PRISM, Apprentice, CXtrace, ATExpert, Pablo, IPS-2) can be used to facilitate the process. We will characterize the effectiveness of the tools and methodologies based on actual user experiences at NASA Ames Research Center. Finally, we will discuss their limitations and outline recent approaches taken by vendors and the research community to address them.

Multi-Physics Simulation of TREAT Kinetics using MAMMOTH

DOE Office of Scientific and Technical Information (OSTI.GOV)

DeHart, Mark; Gleicher, Frederick; Ortensi, Javier

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 amore » 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.« less

Tackling some of the most intricate geophysical challenges via high-performance computing

NASA Astrophysics Data System (ADS)

Khosronejad, A.

2016-12-01

Recently, world has been witnessing significant enhancements in computing power of supercomputers. Computer clusters in conjunction with the advanced mathematical algorithms has set the stage for developing and applying powerful numerical tools to tackle some of the most intricate geophysical challenges that today`s engineers face. One such challenge is to understand how turbulent flows, in real-world settings, interact with (a) rigid and/or mobile complex bed bathymetry of waterways and sea-beds in the coastal areas; (b) objects with complex geometry that are fully or partially immersed; and (c) free-surface of waterways and water surface waves in the coastal area. This understanding is especially important because the turbulent flows in real-world environments are often bounded by geometrically complex boundaries, which dynamically deform and give rise to multi-scale and multi-physics transport phenomena, and characterized by multi-lateral interactions among various phases (e.g. air/water/sediment phases). Herein, I present some of the multi-scale and multi-physics geophysical fluid mechanics processes that I have attempted to study using an in-house high-performance computational model, the so-called VFS-Geophysics. More specifically, I will present the simulation results of turbulence/sediment/solute/turbine interactions in real-world settings. Parts of the simulations I present are performed to gain scientific insights into the processes such as sand wave formation (A. Khosronejad, and F. Sotiropoulos, (2014), Numerical simulation of sand waves in a turbulent open channel flow, Journal of Fluid Mechanics, 753:150-216), while others are carried out to predict the effects of climate change and large flood events on societal infrastructures ( A. Khosronejad, et al., (2016), Large eddy simulation of turbulence and solute transport in a forested headwater stream, Journal of Geophysical Research:, doi: 10.1002/2014JF003423).

GPURFSCREEN: a GPU based virtual screening tool using random forest classifier.

PubMed

Jayaraj, P B; Ajay, Mathias K; Nufail, M; Gopakumar, G; Jaleel, U C A

2016-01-01

In-silico methods are an integral part of modern drug discovery paradigm. Virtual screening, an in-silico method, is used to refine data models and reduce the chemical space on which wet lab experiments need to be performed. Virtual screening of a ligand data model requires large scale computations, making it a highly time consuming task. This process can be speeded up by implementing parallelized algorithms on a Graphical Processing Unit (GPU). Random Forest is a robust classification algorithm that can be employed in the virtual screening. A ligand based virtual screening tool (GPURFSCREEN) that uses random forests on GPU systems has been proposed and evaluated in this paper. This tool produces optimized results at a lower execution time for large bioassay data sets. The quality of results produced by our tool on GPU is same as that on a regular serial environment. Considering the magnitude of data to be screened, the parallelized virtual screening has a significantly lower running time at high throughput. The proposed parallel tool outperforms its serial counterpart by successfully screening billions of molecules in training and prediction phases.

Parallelizing Timed Petri Net simulations

NASA Technical Reports Server (NTRS)

Nicol, David M.

1993-01-01

The possibility of using parallel processing to accelerate the simulation of Timed Petri Nets (TPN's) was studied. It was recognized that complex system development tools often transform system descriptions into TPN's or TPN-like models, which are then simulated to obtain information about system behavior. Viewed this way, it was important that the parallelization of TPN's be as automatic as possible, to admit the possibility of the parallelization being embedded in the system design tool. Later years of the grant were devoted to examining the problem of joint performance and reliability analysis, to explore whether both types of analysis could be accomplished within a single framework. In this final report, the results of our studies are summarized. We believe that the problem of parallelizing TPN's automatically for MIMD architectures has been almost completely solved for a large and important class of problems. Our initial investigations into joint performance/reliability analysis are two-fold; it was shown that Monte Carlo simulation, with importance sampling, offers promise of joint analysis in the context of a single tool, and methods for the parallel simulation of general Continuous Time Markov Chains, a model framework within which joint performance/reliability models can be cast, were developed. However, very much more work is needed to determine the scope and generality of these approaches. The results obtained in our two studies, future directions for this type of work, and a list of publications are included.

Techniques and Tools for Performance Tuning of Parallel and Distributed Scientific Applications

NASA Technical Reports Server (NTRS)

Sarukkai, Sekhar R.; VanderWijngaart, Rob F.; Castagnera, Karen (Technical Monitor)

1994-01-01

Performance degradation in scientific computing on parallel and distributed computer systems can be caused by numerous factors. In this half-day tutorial we explain what are the important methodological issues involved in obtaining codes that have good performance potential. Then we discuss what are the possible obstacles in realizing that potential on contemporary hardware platforms, and give an overview of the software tools currently available for identifying the performance bottlenecks. Finally, some realistic examples are used to illustrate the actual use and utility of such tools.

Parallel Logic Programming and Parallel Systems Software and Hardware

DTIC Science & Technology

1989-07-29

Conference, Dallas TX. January 1985. (55) [Rous75] Roussel, P., "PROLOG: Manuel de Reference et d’Uilisation", Group d’ Intelligence Artificielle , Universite d...completed. Tools were provided for software development using artificial intelligence techniques. Al software for massively parallel architectures was...using artificial intelligence tech- niques. Al software for massively parallel architectures was started. 1. Introduction We describe research conducted

Parallelization and automatic data distribution for nuclear reactor simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liebrock, L.M.

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 directlymore » 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.« less

The development of a scalable parallel 3-D CFD algorithm for turbomachinery. M.S. Thesis Final Report

NASA Technical Reports Server (NTRS)

Luke, Edward Allen

1993-01-01

Two algorithms capable of computing a transonic 3-D inviscid flow field about rotating machines are considered for parallel implementation. During the study of these algorithms, a significant new method of measuring the performance of parallel algorithms is developed. The theory that supports this new method creates an empirical definition of scalable parallel algorithms that is used to produce quantifiable evidence that a scalable parallel application was developed. The implementation of the parallel application and an automated domain decomposition tool are also discussed.

Validation Data and Model Development for Fuel Assembly Response to Seismic Loads

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bardet, Philippe; Ricciardi, Guillaume

2016-01-31

Vibrations are inherently present in nuclear reactors, especially in cores and steam generators of pressurized water reactors (PWR). They can have significant effects on local heat transfer and wear and tear in the reactor and often set safety margins. The simulation of these multiphysics phenomena from first principles requires the coupling of several codes, which is one the most challenging tasks in modern computer simulation. Here an ambitious multiphysics multidisciplinary validation campaign is conducted. It relied on an integrated team of experimentalists and code developers to acquire benchmark and validation data for fluid-structure interaction codes. Data are focused on PWRmore » fuel bundle behavior during seismic transients.« less

Consistent multiphysics simulation of a central tower CSP plant as applied to ISTORE

NASA Astrophysics Data System (ADS)

Votyakov, Evgeny V.; Papanicolas, Costas N.

2017-06-01

We present a unified consistent multiphysics approach to model a central tower CSP plant. The framework for the model includes Monte Carlo ray tracing (RT) and computational fluid dynamics (CFD) components utilizing the OpenFOAM C++ software library. The RT part works effectively with complex surfaces of engineering design given in CAD formats. The CFD simulation, which is based on 3D Navier-Stokes equations, takes into account all possible heat transfer mechanisms: radiation, conduction, and convection. Utilizing this package, the solar field of the experimental Platform for Research, Observation, and TEchnological Applications in Solar Energy (PROTEAS) and the Integrated STOrage and Receiver (ISTORE), developed at the Cyprus Institute, are being examined.

Modeling of Lithium Niobate (LiNbO3) and Aluminum Nitride (AlN) Nanowires Using Comsol Multiphysics Software: The Case of Pressure Sensor

NASA Astrophysics Data System (ADS)

Ahmad, A. A.; Alsaad, A.; Al-Bataineh, Q. M.; Al-Naafa, M. A.

2018-02-01

In this study, Lithium niobate (LiNbO3) and Aluminum nitride (AlN) nanostructures were designed and investigated using the COMSOL Multiphysics software for pressure sensing applications. The Finite Element Method (FEM) was used for solving the differential equations with various parameters such as size, length, force, etc. The variation of the total maximum displacement as a function of applied force for various NWs lengths and the variation of the voltage as a function of applied force were plotted and discussed. AlN nanowires exhibit a better piezoelectric response than LiNbO3 nanowires do.

Parallel machine architecture and compiler design facilities

NASA Technical Reports Server (NTRS)

Kuck, David J.; Yew, Pen-Chung; Padua, David; Sameh, Ahmed; Veidenbaum, Alex

1990-01-01

The objective is to provide an integrated simulation environment for studying and evaluating various issues in designing parallel systems, including machine architectures, parallelizing compiler techniques, and parallel algorithms. The status of Delta project (which objective is to provide a facility to allow rapid prototyping of parallelized compilers that can target toward different machine architectures) is summarized. Included are the surveys of the program manipulation tools developed, the environmental software supporting Delta, and the compiler research projects in which Delta has played a role.

Efficient development of memory bounded geo-applications to scale on modern supercomputers

NASA Astrophysics Data System (ADS)

Räss, Ludovic; Omlin, Samuel; Licul, Aleksandar; Podladchikov, Yuri; Herman, Frédéric

2016-04-01

Numerical modeling is an actual key tool in the area of geosciences. The current challenge is to solve problems that are multi-physics and for which the length scale and the place of occurrence might not be known in advance. Also, the spatial extend of the investigated domain might strongly vary in size, ranging from millimeters for reactive transport to kilometers for glacier erosion dynamics. An efficient way to proceed is to develop simple but robust algorithms that perform well and scale on modern supercomputers and permit therefore very high-resolution simulations. We propose an efficient approach to solve memory bounded real-world applications on modern supercomputers architectures. We optimize the software to run on our newly acquired state-of-the-art GPU cluster "octopus". Our approach shows promising preliminary results on important geodynamical and geomechanical problematics: we have developed a Stokes solver for glacier flow and a poromechanical solver including complex rheologies for nonlinear waves in stressed rocks porous rocks. We solve the system of partial differential equations on a regular Cartesian grid and use an iterative finite difference scheme with preconditioning of the residuals. The MPI communication happens only locally (point-to-point); this method is known to scale linearly by construction. The "octopus" GPU cluster, which we use for the computations, has been designed to achieve maximal data transfer throughput at minimal hardware cost. It is composed of twenty compute nodes, each hosting four Nvidia Titan X GPU accelerators. These high-density nodes are interconnected with a parallel (dual-rail) FDR InfiniBand network. Our efforts show promising preliminary results for the different physics investigated. The glacier flow solver achieves good accuracy in the relevant benchmarks and the coupled poromechanical solver permits to explain previously unresolvable focused fluid flow as a natural outcome of the porosity setup. In both cases, near peak memory bandwidth transfer is achieved. Our approach allows us to get the best out of the current hardware.

Using CellML with OpenCMISS to Simulate Multi-Scale Physiology

PubMed Central

Nickerson, David P.; Ladd, David; Hussan, Jagir R.; Safaei, Soroush; Suresh, Vinod; Hunter, Peter J.; Bradley, Christopher P.

2014-01-01

OpenCMISS is an open-source modeling environment aimed, in particular, at the solution of bioengineering problems. OpenCMISS consists of two main parts: a computational library (OpenCMISS-Iron) and a field manipulation and visualization library (OpenCMISS-Zinc). OpenCMISS is designed for the solution of coupled multi-scale, multi-physics problems in a general-purpose parallel environment. CellML is an XML format designed to encode biophysically based systems of ordinary differential equations and both linear and non-linear algebraic equations. A primary design goal of CellML is to allow mathematical models to be encoded in a modular and reusable format to aid reproducibility and interoperability of modeling studies. In OpenCMISS, we make use of CellML models to enable users to configure various aspects of their multi-scale physiological models. This avoids the need for users to be familiar with the OpenCMISS internal code in order to perform customized computational experiments. Examples of this are: cellular electrophysiology models embedded in tissue electrical propagation models; material constitutive relationships for mechanical growth and deformation simulations; time-varying boundary conditions for various problem domains; and fluid constitutive relationships and lumped-parameter models. In this paper, we provide implementation details describing how CellML models are integrated into multi-scale physiological models in OpenCMISS. The external interface OpenCMISS presents to users is also described, including specific examples exemplifying the extensibility and usability these tools provide the physiological modeling and simulation community. We conclude with some thoughts on future extension of OpenCMISS to make use of other community developed information standards, such as FieldML, SED-ML, and BioSignalML. Plans for the integration of accelerator code (graphical processing unit and field programmable gate array) generated from CellML models is also discussed. PMID:25601911

A fluid–structure interaction model to characterize bone cell stimulation in parallel-plate flow chamber systems

PubMed Central

Vaughan, T. J.; Haugh, M. G.; McNamara, L. M.

2013-01-01

Bone continuously adapts its internal structure to accommodate the functional demands of its mechanical environment and strain-induced flow of interstitial fluid is believed to be the primary mediator of mechanical stimuli to bone cells in vivo. In vitro investigations have shown that bone cells produce important biochemical signals in response to fluid flow applied using parallel-plate flow chamber (PPFC) systems. However, the exact mechanical stimulus experienced by the cells within these systems remains unclear. To fully understand this behaviour represents a most challenging multi-physics problem involving the interaction between deformable cellular structures and adjacent fluid flows. In this study, we use a fluid–structure interaction computational approach to investigate the nature of the mechanical stimulus being applied to a single osteoblast cell under fluid flow within a PPFC system. The analysis decouples the contribution of pressure and shear stress on cellular deformation and for the first time highlights that cell strain under flow is dominated by the pressure in the PPFC system rather than the applied shear stress. Furthermore, it was found that strains imparted on the cell membrane were relatively low whereas significant strain amplification occurred at the cell–substrate interface. These results suggest that strain transfer through focal attachments at the base of the cell are the primary mediators of mechanical signals to the cell under flow in a PPFC system. Such information is vital in order to correctly interpret biological responses of bone cells under in vitro stimulation and elucidate the mechanisms associated with mechanotransduction in vivo. PMID:23365189

The Shale Hills Sensorium for Embedded Sensors, Simulation, & Visualization: A Prototype for Land-Vegetation-Atmosphere Interactions

NASA Astrophysics Data System (ADS)

Duffy, C.

2008-12-01

The future of environmental observing systems will utilize embedded sensor networks with continuous real- time measurement of hydrologic, atmospheric, biogeochemical, and ecological variables across diverse terrestrial environments. Embedded environmental sensors, benefitting from advances in information sciences, networking technology, materials science, computing capacity, and data synthesis methods, are undergoing revolutionary change. It is now possible to field spatially-distributed, multi-node sensor networks that provide density and spatial coverage previously accessible only via numerical simulation. At the same time, computational tools are advancing rapidly to the point where it is now possible to simulate the physical processes controlling individual parcels of water and solutes through the complete terrestrial water cycle. Our goal for the Penn State Critical Zone Observatory is to apply environmental sensor arrays, integrated hydrologic models, and state-of-the-art visualization deployed and coordinated at a testbed within the Penn State Experimental Forest. The Shale Hills Hydro_Sensorium prototype proposed here is designed to observe land-atmosphere interactions in four-dimensional (space and time). The term Hydro_Sensorium implies the totality of physical sensors, models and visualization tools that allow us to perceive the detailed space and time complexities of the water and energy cycle for a watershed or river basin for all physical states and fluxes (groundwater, soil moisture, temperature, streamflow, latent heat, snowmelt, chemistry, isotopes etc.). This research will ultimately catalyze the study of complex interactions between the land surface, subsurface, biological and atmospheric systems over a broad range of scales. The sensor array would be real-time and fully controllable by remote users for "computational steering" and data fusion. Presently fully-coupled physical models are being developed that link the atmosphere-land-vegetation-subsurface system into a fully-coupled distributed system. During the last 5 years the Penn State Integrated Hydrologic Modeling System has been under development as an open-source community modeling project funded by NSF EAR/GEO and NSF CBET/ENG. PIHM represents a strategy for the formulation and solution of fully-coupled process equations at the watershed and river basin scales, and includes a tightly coupled GIS tool for data handling, domain decomposition, optimal unstructured grid generation, and model parameterization. The sensor and simulation system has the following elements: 1) extensive, spatially-distributed, non- invasive, smart sensor networks to gather massive geologic, hydrologic, and geochemical data; 2) stochastic information fusion methods; 3) spatially-explicit multiphysics models/solutions of the land-vegetation- atmosphere system; and 4) asynchronous, parallel/distributed, adaptive algorithms for rapidly simulating the states of a basin at high resolution, 5) signal processing tools for data mining and parameter estimation, and 6) visualization tools. The prototype proposed sensor array and simulation system proposed here will offer a coherent new approach to environmental predictions with a fully integrated observing system design. We expect that the Shale Hills Hydro_Sensorium may provide the needed synthesis of information and conceptualization necessary to advance predictive understanding in complex hydrologic systems.

Finite Element Analysis in the Estimation of Air-Gap Torque and Surface Temperature of Induction Machine

NASA Astrophysics Data System (ADS)

Mr., J. Ravi Kumar; Banakara, Basavaraja, Dr.

2017-08-01

This paper presents electromagnetic and thermal behavior of Induction Motor (IM) through the modeling and analysis by applying multiphysics coupled Finite Element Analysis (FEA). Therefore prediction of the magnetic flux, electromagnetic torque, stator and rotor losses and temperature distribution inside an operating electric motor are the most important issues during its design. Prediction and estimation of these parameters allows design engineers to decide capability of the machine for the proposed load, temperature rating and its application for which it is being designed ensuring normal motor operation at rated conditions. In this work, multiphysics coupled electromagnetic - thermal modeling and analysis of induction motor at rated and high frequency has carried out applying Arkkio’s torque method. COMSOL Multiphysics software is used for modeling and finite element analysis of IM. Transient electromagnetic torque, magnetic field distribution, speed-torque characteristics of IM were plotted and studied at different frequencies. This proposed work helps in the design and prediction of accurate performance of induction motor specific to various industrial drive applications. Results obtained are also validated with experimental analysis. The main purpose of this model is to use it as an integral part of the design aiming to system optimization of Variable Speed Drive (VSD) and its components using coupled simulations.

High frequency electromagnetism, heat transfer and fluid flow coupling in ANSYS multiphysics.

PubMed

Sabliov, Cristina M; Salvi, Deepti A; Boldor, Dorin

2007-01-01

The goal of this study was to numerically predict the temperature of a liquid product heated in a continuous-flow focused microwave system by coupling high frequency electromagnetism, heat transfer, and fluid flow in ANSYS Multiphysics. The developed model was used to determine the temperature change in water processed in a 915 MHz microwave unit, under steady-state conditions. The influence of the flow rates on the temperature distribution in the liquid was assessed. Results showed that the average temperature of water increased from 25 degrees C to 34 degrees C at 2 l/min, and to 42 degrees C at 1 l/min. The highest temperature regions were found in the liquid near the center of the tube, followed by progressively lower temperature regions as the radial distance from the center increased, and finally followed by a slightly higher temperature region near the tube's wall corresponding to the energy distribution given by the Mathieu function. The energy distribution resulted in a similar temperature pattern, with the highest temperatures close to the center of the tube and lower at the walls. The presented ANSYS Multiphysics model can be easily improved to account for complex boundary conditions, phase change, temperature dependent properties, and non-Newtonian flows, which makes for an objective of future studies.

Heat Source Characterization In A TREAT Fuel Particle Using Coupled Neutronics Binary Collision Monte-Carlo Calculations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schunert, Sebastian; Schwen, Daniel; Ghassemi, Pedram

This work presents a multi-physics, multi-scale approach to modeling the Transient Test Reactor (TREAT) currently prepared for restart at the Idaho National Laboratory. TREAT fuel is made up of microscopic fuel grains (r ˜ 20µm) dispersed in a graphite matrix. The novelty of this work is in coupling a binary collision Monte-Carlo (BCMC) model to the Finite Element based code Moose for solving a microsopic heat-conduction problem whose driving source is provided by the BCMC model tracking fission fragment energy deposition. This microscopic model is driven by a transient, engineering scale neutronics model coupled to an adiabatic heating model. Themore » macroscopic model provides local power densities and neutron energy spectra to the microscpic model. Currently, no feedback from the microscopic to the macroscopic model is considered. TREAT transient 15 is used to exemplify the capabilities of the multi-physics, multi-scale model, and it is found that the average fuel grain temperature differs from the average graphite temperature by 80 K despite the low-power transient. The large temperature difference has strong implications on the Doppler feedback a potential LEU TREAT core would see, and it underpins the need for multi-physics, multi-scale modeling of a TREAT LEU core.« less

Multiphysics Nuclear Thermal Rocket Thrust Chamber Analysis

NASA Technical Reports Server (NTRS)

Wang, Ten-See

2005-01-01

The objective of this effort is t o develop an efficient and accurate thermo-fluid computational methodology to predict environments for hypothetical thrust chamber design and analysis. The current task scope is to perform multidimensional, multiphysics analysis of thrust performance and heat transfer analysis for a hypothetical solid-core, nuclear thermal engine including thrust chamber and nozzle. The multiphysics aspects of the model include: real fluid dynamics, chemical reactivity, turbulent flow, and conjugate heat transfer. The model will be designed to identify thermal, fluid, and hydrogen environments in all flow paths and materials. This model would then be used to perform non- nuclear reproduction of the flow element failures demonstrated in the Rover/NERVA testing, investigate performance of specific configurations and assess potential issues and enhancements. A two-pronged approach will be employed in this effort: a detailed analysis of a multi-channel, flow-element, and global modeling of the entire thrust chamber assembly with a porosity modeling technique. It is expected that the detailed analysis of a single flow element would provide detailed fluid, thermal, and hydrogen environments for stress analysis, while the global thrust chamber assembly analysis would promote understanding of the effects of hydrogen dissociation and heat transfer on thrust performance. These modeling activities will be validated as much as possible by testing performed by other related efforts.

Support for Debugging Automatically Parallelized Programs

NASA Technical Reports Server (NTRS)

Hood, Robert; Jost, Gabriele

2001-01-01

This viewgraph presentation provides information on support sources available for the automatic parallelization of computer program. CAPTools, a support tool developed at the University of Greenwich, transforms, with user guidance, existing sequential Fortran code into parallel message passing code. Comparison routines are then run for debugging purposes, in essence, ensuring that the code transformation was accurate.

DooSo6: Easy Collaboration over Shared Projects

NASA Astrophysics Data System (ADS)

Ignat, Claudia-Lavinia; Oster, Gérald; Molli, Pascal

Existing tools for supporting parallel work feature some disadvantages that prevent them to be widely used. Very often they require a complex installation and creation of accounts for all group members. Users need to learn and deal with complex commands for efficiently using these collaborative tools. Some tools require users to abandon their favourite editors and impose them to use a certain co-authorship application. In this paper, we propose the DooSo6 collaboration tool that offers support for parallel work, requires no installation, no creation of accounts and that is easy to use, users being able to continue working with their favourite editors. User authentication is achieved by means of a capability-based mechanism.

PROTEUS-SN User Manual

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shemon, Emily R.; Smith, Micheal A.; Lee, Changho

2016-02-16

PROTEUS-SN is a three-dimensional, highly scalable, high-fidelity neutron transport code developed at Argonne National Laboratory. The code is applicable to all spectrum reactor transport calculations, particularly those in which a high degree of fidelity is needed either to represent spatial detail or to resolve solution gradients. PROTEUS-SN solves the second order formulation of the transport equation using the continuous Galerkin finite element method in space, the discrete ordinates approximation in angle, and the multigroup approximation in energy. PROTEUS-SN’s parallel methodology permits the efficient decomposition of the problem by both space and angle, permitting large problems to run efficiently on hundredsmore » of thousands of cores. PROTEUS-SN can also be used in serial or on smaller compute clusters (10’s to 100’s of cores) for smaller homogenized problems, although it is generally more computationally expensive than traditional homogenized methodology codes. PROTEUS-SN has been used to model partially homogenized systems, where regions of interest are represented explicitly and other regions are homogenized to reduce the problem size and required computational resources. PROTEUS-SN solves forward and adjoint eigenvalue problems and permits both neutron upscattering and downscattering. An adiabatic kinetics option has recently been included for performing simple time-dependent calculations in addition to standard steady state calculations. PROTEUS-SN handles void and reflective boundary conditions. Multigroup cross sections can be generated externally using the MC2-3 fast reactor multigroup cross section generation code or internally using the cross section application programming interface (API) which can treat the subgroup or resonance table libraries. PROTEUS-SN is written in Fortran 90 and also includes C preprocessor definitions. The code links against the PETSc, METIS, HDF5, and MPICH libraries. It optionally links against the MOAB library and is a part of the SHARP multi-physics suite for coupled multi-physics analysis of nuclear reactors. This user manual describes how to set up a neutron transport simulation with the PROTEUS-SN code. A companion methodology manual describes the theory and algorithms within PROTEUS-SN.« less

Development of Multi-physics (Multiphase CFD + MCNP) simulation for generic solution vessel power calculation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Seung Jun; Buechler, Cynthia Eileen

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 operatingmore » 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 methodology and preliminary results from various coupled calculations (power prediction and heat transfer coefficient) can be further utilized for the system code validation and generic solution vessel design improvement.« less

Communication library for run-time visualization of distributed, asynchronous data

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rowlan, J.; Wightman, B.T.

1994-04-01

In this paper we present a method for collecting and visualizing data generated by a parallel computational simulation during run time. Data distributed across multiple processes is sent across parallel communication lines to a remote workstation, which sorts and queues the data for visualization. We have implemented our method in a set of tools called PORTAL (for Parallel aRchitecture data-TrAnsfer Library). The tools comprise generic routines for sending data from a parallel program (callable from either C or FORTRAN), a semi-parallel communication scheme currently built upon Unix Sockets, and a real-time connection to the scientific visualization program AVS. Our methodmore » is most valuable when used to examine large datasets that can be efficiently generated and do not need to be stored on disk. The PORTAL source libraries, detailed documentation, and a working example can be obtained by anonymous ftp from info.mcs.anl.gov from the file portal.tar.Z from the directory pub/portal.« less

ParCAT: A Parallel Climate Analysis Toolkit

NASA Astrophysics Data System (ADS)

Haugen, B.; Smith, B.; Steed, C.; Ricciuto, D. M.; Thornton, P. E.; Shipman, G.

2012-12-01

Climate science has employed increasingly complex models and simulations to analyze the past and predict the future of our climate. The size and dimensionality of climate simulation data has been growing with the complexity of the models. This growth in data is creating a widening gap between the data being produced and the tools necessary to analyze large, high dimensional data sets. With single run data sets increasing into 10's, 100's and even 1000's of gigabytes, parallel computing tools are becoming a necessity in order to analyze and compare climate simulation data. The Parallel Climate Analysis Toolkit (ParCAT) provides basic tools that efficiently use parallel computing techniques to narrow the gap between data set size and analysis tools. ParCAT was created as a collaborative effort between climate scientists and computer scientists in order to provide efficient parallel implementations of the computing tools that are of use to climate scientists. Some of the basic functionalities included in the toolkit are the ability to compute spatio-temporal means and variances, differences between two runs and histograms of the values in a data set. ParCAT is designed to facilitate the "heavy lifting" that is required for large, multidimensional data sets. The toolkit does not focus on performing the final visualizations and presentation of results but rather, reducing large data sets to smaller, more manageable summaries. The output from ParCAT is provided in commonly used file formats (NetCDF, CSV, ASCII) to allow for simple integration with other tools. The toolkit is currently implemented as a command line utility, but will likely also provide a C library for developers interested in tighter software integration. Elements of the toolkit are already being incorporated into projects such as UV-CDAT and CMDX. There is also an effort underway to implement portions of the CCSM Land Model Diagnostics package using ParCAT in conjunction with Python and gnuplot. ParCAT is implemented in C to provide efficient file IO. The file IO operations in the toolkit use the parallel-netcdf library; this enables the code to use the parallel IO capabilities of modern HPC systems. Analysis that currently requires an estimated 12+ hours with the traditional CCSM Land Model Diagnostics Package can now be performed in as little as 30 minutes on a single desktop workstation and a few minutes for relatively small jobs completed on modern HPC systems such as ORNL's Jaguar.

Parallel tools GUI framework-DOE SBIR phase I final technical report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galarowicz, James

2013-12-05

Many parallel performance, profiling, and debugging tools require a graphical way of displaying the very large datasets typically gathered from high performance computing (HPC) applications. Most tool projects create their graphical user interfaces (GUI) from scratch, many times spending their project resources on simply redeveloping commonly used infrastructure. Our goal was to create a multiplatform GUI framework, based on Nokia/Digia’s popular Qt libraries, which will specifically address the needs of these parallel tools. The Parallel Tools GUI Framework (PTGF) uses a plugin architecture facilitating rapid GUI development and reduced development costs for new and existing tool projects by allowing themore » reuse of many common GUI elements, called “widgets.” Widgets created include, 2D data visualizations, a source code viewer with syntax highlighting, and integrated help and welcome screens. Application programming interface (API) design was focused on minimizing the time to getting a functional tool working. Having a standard, unified, and userfriendly interface which operates on multiple platforms will benefit HPC application developers by reducing training time and allowing users to move between tools rapidly during a single session. However, Argo Navis Technologies LLC will not be submitting a DOE SBIR Phase II proposal and commercialization plan for the PTGF project. Our preliminary estimates for gross income over the next several years was based upon initial customer interest and income generated by similar projects. Unfortunately, as we further assessed the market during Phase I, we grew to realize that there was not enough demand to warrant such a large investment. While we do find that the project is worth our continued investment of time and money, we do not think it worthy of the DOE's investment at this time. We are grateful that the DOE has afforded us the opportunity to make this assessment, and come to this conclusion.« less

"METHOD": A tool for mechanical, electrical, thermal, and optical characterization of single lens module design

NASA Astrophysics Data System (ADS)

Besson, Pierre; Dominguez, Cesar; Voarino, Philippe; Garcia-Linares, Pablo; Weick, Clement; Lemiti, Mustapha; Baudrit, Mathieu

2015-09-01

The optical characterization and electrical performance evaluation are essential in the design and optimization of a concentrator photovoltaic system. The geometry, materials, and size of concentrator optics are diverse and different environmental conditions impact their performance. CEA has developed a new concentrator photovoltaic system characterization bench, METHOD, which enables multi-physics optimization studies. The lens and cell temperatures are controlled independently with the METHOD to study their isolated effects on the electrical and optical performance of the system. These influences can be studied in terms of their effect on optical efficiency, focal distance, spectral sensitivity, electrical efficiency, or cell current matching. Furthermore, the irradiance map of a concentrator optic can be mapped to study its variations versus the focal length or the lens temperature. The present work shows this application to analyze the performance of a Fresnel lens linking temperature to optical and electrical performance.

Guided self-assembly of magnetic beads for biomedical applications

NASA Astrophysics Data System (ADS)

Gusenbauer, Markus; Nguyen, Ha; Reichel, Franz; Exl, Lukas; Bance, Simon; Fischbacher, Johann; Özelt, Harald; Kovacs, Alexander; Brandl, Martin; Schrefl, Thomas

2014-02-01

Micromagnetic beads are widely used in biomedical applications for cell separation, drug delivery, and hyperthermia cancer treatment. Here we propose to use self-organized magnetic bead structures which accumulate on fixed magnetic seeding points to isolate circulating tumor cells. The analysis of circulating tumor cells is an emerging tool for cancer biology research and clinical cancer management including the detection, diagnosis and monitoring of cancer. Microfluidic chips for isolating circulating tumor cells use either affinity, size or density capturing methods. We combine multiphysics simulation techniques to understand the microscopic behavior of magnetic beads interacting with soft magnetic accumulation points used in lab-on-chip technologies. Our proposed chip technology offers the possibility to combine affinity and size capturing with special antibody-coated bead arrangements using a magnetic gradient field created by Neodymium Iron Boron permanent magnets. The multiscale simulation environment combines magnetic field computation, fluid dynamics and discrete particle dynamics.

Extracting Damping Ratio from Dynamic Data and Numerical Solutions

NASA Technical Reports Server (NTRS)

Casiano, M. J.

2016-01-01

There are many ways to extract damping parameters from data or models. This Technical Memorandum provides a quick reference for some of the more common approaches used in dynamics analysis. Described are six methods of extracting damping from data: the half-power method, logarithmic decrement (decay rate) method, an autocorrelation/power spectral density fitting method, a frequency response fitting method, a random decrement fitting method, and a newly developed half-quadratic gain method. Additionally, state-space models and finite element method modeling tools, such as COMSOL Multiphysics (COMSOL), provide a theoretical damping via complex frequency. Each method has its advantages which are briefly noted. There are also likely many other advanced techniques in extracting damping within the operational modal analysis discipline, where an input excitation is unknown; however, these approaches discussed here are objective, direct, and can be implemented in a consistent manner.

High-resolution coupled physics solvers for analysing fine-scale nuclear reactor design problems.

PubMed

Mahadevan, Vijay S; Merzari, Elia; Tautges, Timothy; Jain, Rajeev; Obabko, Aleksandr; Smith, Michael; Fischer, Paul

2014-08-06

An integrated multi-physics simulation capability for the design and analysis of current and future nuclear reactor models is being investigated, to tightly couple neutron transport and thermal-hydraulics physics under the SHARP framework. Over several years, high-fidelity, validated mono-physics solvers with proven scalability on petascale architectures have been developed independently. Based on a unified component-based architecture, these existing codes can be coupled with a mesh-data backplane and a flexible coupling-strategy-based driver suite to produce a viable tool for analysts. The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The coupling methodology and software interfaces of the framework are presented, along with verification studies on two representative fast sodium-cooled reactor demonstration problems to prove the usability of the SHARP framework.

High-fidelity plasma codes for burn physics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cooley, James; Graziani, Frank; Marinak, Marty

Accurate predictions of equation of state (EOS), ionic and electronic transport properties are of critical importance for high-energy-density plasma science. Transport coefficients inform radiation-hydrodynamic codes and impact diagnostic interpretation, which in turn impacts our understanding of the development of instabilities, the overall energy balance of burning plasmas, and the efficacy of self-heating from charged-particle stopping. Important processes include thermal and electrical conduction, electron-ion coupling, inter-diffusion, ion viscosity, and charged particle stopping. However, uncertainties in these coefficients are not well established. Fundamental plasma science codes, also called high-fidelity plasma codes, are a relatively recent computational tool that augments both experimental datamore » and theoretical foundations of transport coefficients. This paper addresses the current status of HFPC codes and their future development, and the potential impact they play in improving the predictive capability of the multi-physics hydrodynamic codes used in HED design.« less

Magnetic biosensors: Modelling and simulation.

PubMed

Nabaei, Vahid; Chandrawati, Rona; Heidari, Hadi

2018-04-30

In the past few years, magnetoelectronics has emerged as a promising new platform technology in various biosensors for detection, identification, localisation and manipulation of a wide spectrum of biological, physical and chemical agents. The methods are based on the exposure of the magnetic field of a magnetically labelled biomolecule interacting with a complementary biomolecule bound to a magnetic field sensor. This Review presents various schemes of magnetic biosensor techniques from both simulation and modelling as well as analytical and numerical analysis points of view, and the performance variations under magnetic fields at steady and nonstationary states. This is followed by magnetic sensors modelling and simulations using advanced Multiphysics modelling software (e.g. Finite Element Method (FEM) etc.) and home-made developed tools. Furthermore, outlook and future directions of modelling and simulations of magnetic biosensors in different technologies and materials are critically discussed. Crown Copyright © 2017. Published by Elsevier B.V. All rights reserved.

Joule-Heated Molten Regolith Electrolysis Reactor Concepts for Oxygen and Metals Production on the Moon and Mars

NASA Technical Reports Server (NTRS)

Sibille, Laurent; Dominques, Jesus A.

2012-01-01

The maturation of Molten Regolith Electrolysis (MRE) as a viable technology for oxygen and metals production on explored planets relies on the realization of the self-heating mode for the reactor. Joule heat generated during regolith electrolysis creates thermal energy that should be able to maintain the molten phase (similar to electrolytic Hall-Heroult process for aluminum production). Self-heating via Joule heating offers many advantages: (1) The regolith itself is the crucible material, it protects the vessel walls (2) Simplifies the engineering of the reactor (3) Reduces power consumption (no external heating) (4) Extends the longevity of the reactor. Predictive modeling is a tool chosen to perform dimensional analysis of a self-heating reactor: (1) Multiphysics modeling (COMSOL) was selected for Joule heat generation and heat transfer (2) Objective is to identify critical dimensions for first reactor prototype.

High-resolution coupled physics solvers for analysing fine-scale nuclear reactor design problems

PubMed Central

Mahadevan, Vijay S.; Merzari, Elia; Tautges, Timothy; Jain, Rajeev; Obabko, Aleksandr; Smith, Michael; Fischer, Paul

2014-01-01

An integrated multi-physics simulation capability for the design and analysis of current and future nuclear reactor models is being investigated, to tightly couple neutron transport and thermal-hydraulics physics under the SHARP framework. Over several years, high-fidelity, validated mono-physics solvers with proven scalability on petascale architectures have been developed independently. Based on a unified component-based architecture, these existing codes can be coupled with a mesh-data backplane and a flexible coupling-strategy-based driver suite to produce a viable tool for analysts. The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The coupling methodology and software interfaces of the framework are presented, along with verification studies on two representative fast sodium-cooled reactor demonstration problems to prove the usability of the SHARP framework. PMID:24982250

A Multi-Scale, Multi-Physics Optimization Framework for Additively Manufactured Structural Components

NASA Astrophysics Data System (ADS)

El-Wardany, Tahany; Lynch, Mathew; Gu, Wenjiong; Hsu, Arthur; Klecka, Michael; Nardi, Aaron; Viens, Daniel

This paper proposes an optimization framework enabling the integration of multi-scale / multi-physics simulation codes to perform structural optimization design for additively manufactured components. Cold spray was selected as the additive manufacturing (AM) process and its constraints were identified and included in the optimization scheme. The developed framework first utilizes topology optimization to maximize stiffness for conceptual design. The subsequent step applies shape optimization to refine the design for stress-life fatigue. The component weight was reduced by 20% while stresses were reduced by 75% and the rigidity was improved by 37%. The framework and analysis codes were implemented using Altair software as well as an in-house loading code. The optimized design was subsequently produced by the cold spray process.

Numerical modeling of continuous flow microwave heating: a critical comparison of COMSOL and ANSYS.

PubMed

Salvi, D; Boldor, Dorin; Ortego, J; Aita, G M; Sabliov, C M

2010-01-01

Numerical models were developed to simulate temperature profiles in Newtonian fluids during continuous flow microwave heating by one way coupling electromagnetism, fluid flow, and heat transport in ANSYS 8.0 and COMSOL Multiphysics v3.4. Comparison of the results from the COMSOL model with the results from a pre-developed and validated ANSYS model ensured accuracy of the COMSOL model. Prediction of power Loss by both models was in close agreement (5-13% variation) and the predicted temperature profiles were similar. COMSOL provided a flexible model setup whereas ANSYS required coupling incompatible elements to transfer load between electromagnetic, fluid flow, and heat transport modules. Overall, both software packages provided the ability to solve multiphysics phenomena accurately.

Multi-Physics MRI-Based Two-Layer Fluid-Structure Interaction Anisotropic Models of Human Right and Left Ventricles with Different Patch Materials: Cardiac Function Assessment and Mechanical Stress Analysis

PubMed Central

Tang, Dalin; Yang, Chun; Geva, Tal; Gaudette, Glenn; del Nido, Pedro J.

2011-01-01

Multi-physics right and left ventricle (RV/LV) fluid-structure interaction (FSI) models were introduced to perform mechanical stress analysis and evaluate the effect of patch materials on RV function. The FSI models included three different patch materials (Dacron scaffold, treated pericardium, and contracting myocardium), two-layer construction, fiber orientation, and active anisotropic material properties. The models were constructed based on cardiac magnetic resonance (CMR) images acquired from a patient with severe RV dilatation and solved by ADINA. Our results indicate that the patch model with contracting myocardium leads to decreased stress level in the patch area, improved RV function and patch area contractility. PMID:21765559

Multi-physics optimization of three-dimensional microvascular polymeric components

NASA Astrophysics Data System (ADS)

Aragón, Alejandro M.; Saksena, Rajat; Kozola, Brian D.; Geubelle, Philippe H.; Christensen, Kenneth T.; White, Scott R.

2013-01-01

This work discusses the computational design of microvascular polymeric materials, which aim at mimicking the behavior found in some living organisms that contain a vascular system. The optimization of the topology of the embedded three-dimensional microvascular network is carried out by coupling a multi-objective constrained genetic algorithm with a finite-element based physics solver, the latter validated through experiments. The optimization is carried out on multiple conflicting objective functions, namely the void volume fraction left by the network, the energy required to drive the fluid through the network and the maximum temperature when the material is subjected to thermal loads. The methodology presented in this work results in a viable alternative for the multi-physics optimization of these materials for active-cooling applications.

P-Hint-Hunt: a deep parallelized whole genome DNA methylation detection tool.

PubMed

Peng, Shaoliang; Yang, Shunyun; Gao, Ming; Liao, Xiangke; Liu, Jie; Yang, Canqun; Wu, Chengkun; Yu, Wenqiang

2017-03-14

The increasing studies have been conducted using whole genome DNA methylation detection as one of the most important part of epigenetics research to find the significant relationships among DNA methylation and several typical diseases, such as cancers and diabetes. In many of those studies, mapping the bisulfite treated sequence to the whole genome has been the main method to study DNA cytosine methylation. However, today's relative tools almost suffer from inaccuracies and time-consuming problems. In our study, we designed a new DNA methylation prediction tool ("Hint-Hunt") to solve the problem. By having an optimal complex alignment computation and Smith-Waterman matrix dynamic programming, Hint-Hunt could analyze and predict the DNA methylation status. But when Hint-Hunt tried to predict DNA methylation status with large-scale dataset, there are still slow speed and low temporal-spatial efficiency problems. In order to solve the problems of Smith-Waterman dynamic programming and low temporal-spatial efficiency, we further design a deep parallelized whole genome DNA methylation detection tool ("P-Hint-Hunt") on Tianhe-2 (TH-2) supercomputer. To the best of our knowledge, P-Hint-Hunt is the first parallel DNA methylation detection tool with a high speed-up to process large-scale dataset, and could run both on CPU and Intel Xeon Phi coprocessors. Moreover, we deploy and evaluate Hint-Hunt and P-Hint-Hunt on TH-2 supercomputer in different scales. The experimental results illuminate our tools eliminate the deviation caused by bisulfite treatment in mapping procedure and the multi-level parallel program yields a 48 times speed-up with 64 threads. P-Hint-Hunt gain a deep acceleration on CPU and Intel Xeon Phi heterogeneous platform, which gives full play of the advantages of multi-cores (CPU) and many-cores (Phi).

Automated and Assistive Tools for Accelerated Code migration of Scientific Computing on to Heterogeneous MultiCore Systems

DTIC Science & Technology

2017-04-13

modelling code, a parallel benchmark , and a communication avoiding version of the QR algorithm. Further, several improvements to the OmpSs model were...movement; and a port of the dynamic load balancing library to OmpSs. Finally, several updates to the tools infrastructure were accomplished, including: an...OmpSs: a basic algorithm on image processing applications, a mini application representative of an ocean modelling code, a parallel benchmark , and a

Paramedir: A Tool for Programmable Performance Analysis

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Labarta, Jesus; Gimenez, Judit

2004-01-01

Performance analysis of parallel scientific applications is time consuming and requires great expertise in areas such as programming paradigms, system software, and computer hardware architectures. In this paper we describe a tool that facilitates the programmability of performance metric calculations thereby allowing the automation of the analysis and reducing the application development time. We demonstrate how the system can be used to capture knowledge and intuition acquired by advanced parallel programmers in order to be transferred to novice users.

Parallel-Processing Test Bed For Simulation Software

NASA Technical Reports Server (NTRS)

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).

A tool for simulating parallel branch-and-bound methods

NASA Astrophysics Data System (ADS)

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.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Janjusic, Tommy; Kartsaklis, Christos

Memory scalability is an enduring problem and bottleneck that plagues many parallel codes. Parallel codes designed for High Performance Systems are typically designed over the span of several, and in some instances 10+, years. As a result, optimization practices which were appropriate for earlier systems may no longer be valid and thus require careful optimization consideration. Specifically, parallel codes whose memory footprint is a function of their scalability must be carefully considered for future exa-scale systems. In this paper we present a methodology and tool to study the memory scalability of parallel codes. Using our methodology we evaluate an applicationmore » s memory footprint as a function of scalability, which we coined memory efficiency, and describe our results. In particular, using our in-house tools we can pinpoint the specific application components which contribute to the application s overall memory foot-print (application data- structures, libraries, etc.).« less

Simulation of finite-strain inelastic phenomena governed by creep and plasticity

NASA Astrophysics Data System (ADS)

Li, Zhen; Bloomfield, Max O.; Oberai, Assad A.

2017-11-01

Inelastic mechanical behavior plays an important role in many applications in science and engineering. Phenomenologically, this behavior is often modeled as plasticity or creep. Plasticity is used to represent the rate-independent component of inelastic deformation and creep is used to represent the rate-dependent component. In several applications, especially those at elevated temperatures and stresses, these processes occur simultaneously. In order to model these process, we develop a rate-objective, finite-deformation constitutive model for plasticity and creep. The plastic component of this model is based on rate-independent J_2 plasticity, and the creep component is based on a thermally activated Norton model. We describe the implementation of this model within a finite element formulation, and present a radial return mapping algorithm for it. This approach reduces the additional complexity of modeling plasticity and creep, over thermoelasticity, to just solving one nonlinear scalar equation at each quadrature point. We implement this algorithm within a multiphysics finite element code and evaluate the consistent tangent through automatic differentiation. We verify and validate the implementation, apply it to modeling the evolution of stresses in the flip chip manufacturing process, and test its parallel strong-scaling performance.

Physics-Based Preconditioning of a Compressible Flow Solver for Large-Scale Simulations of Additive Manufacturing Processes

NASA Astrophysics Data System (ADS)

Weston, Brian; Nourgaliev, Robert; Delplanque, Jean-Pierre

2017-11-01

We present a new block-based Schur complement preconditioner for simulating all-speed compressible flow with phase change. The conservation equations are discretized with a reconstructed Discontinuous Galerkin method and integrated in time with fully implicit time discretization schemes. The resulting set of non-linear equations is converged using a robust Newton-Krylov framework. Due to the stiffness of the underlying physics associated with stiff acoustic waves and viscous material strength effects, we solve for the primitive-variables (pressure, velocity, and temperature). To enable convergence of the highly ill-conditioned linearized systems, we develop a physics-based preconditioner, utilizing approximate block factorization techniques to reduce the fully-coupled 3×3 system to a pair of reduced 2×2 systems. We demonstrate that our preconditioned Newton-Krylov framework converges on very stiff multi-physics problems, corresponding to large CFL and Fourier numbers, with excellent algorithmic and parallel scalability. Results are shown for the classic lid-driven cavity flow problem as well as for 3D laser-induced phase change. This work was performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

Earth Science Computational Architecture for Multi-disciplinary Investigations

NASA Astrophysics Data System (ADS)

Parker, J. W.; Blom, R.; Gurrola, E.; Katz, D.; Lyzenga, G.; Norton, C.

2005-12-01

Understanding the processes underlying Earth's deformation and mass transport requires a non-traditional, integrated, interdisciplinary, approach dependent on multiple space and ground based data sets, modeling, and computational tools. Currently, details of geophysical data acquisition, analysis, and modeling largely limit research to discipline domain experts. Interdisciplinary research requires a new computational architecture that is optimized to perform complex data processing of multiple solid Earth science data types in a user-friendly environment. A web-based computational framework is being developed and integrated with applications for automatic interferometric radar processing, and models for high-resolution deformation & gravity, forward models of viscoelastic mass loading over short wavelengths & complex time histories, forward-inverse codes for characterizing surface loading-response over time scales of days to tens of thousands of years, and inversion of combined space magnetic & gravity fields to constrain deep crustal and mantle properties. This framework combines an adaptation of the QuakeSim distributed services methodology with the Pyre framework for multiphysics development. The system uses a three-tier architecture, with a middle tier server that manages user projects, available resources, and security. This ensures scalability to very large networks of collaborators. Users log into a web page and have a personal project area, persistently maintained between connections, for each application. Upon selection of an application and host from a list of available entities, inputs may be uploaded or constructed from web forms and available data archives, including gravity, GPS and imaging radar data. The user is notified of job completion and directed to results posted via URLs. Interdisciplinary work is supported through easy availability of all applications via common browsers, application tutorials and reference guides, and worked examples with visual response. At the platform level, multi-physics application development and workflow are available in the enriched environment of the Pyre framework. Advantages for combining separate expert domains include: multiple application components efficiently interact through Python shared libraries, investigators may nimbly swap models and try new parameter values, and a rich array of common tools are inherent in the Pyre system. The first four specific investigations to use this framework are: Gulf Coast subsidence: understanding of partitioning between compaction, subsidence and growth faulting; Gravity & deformation of a layered spherical earth model due to large earthquakes; Rift setting of Lake Vostok, Antarctica; and global ice mass changes.

Impact of Representing Model Error in a Hybrid Ensemble-Variational Data Assimilation System for Track Forecast of Tropical Cyclones over the Bay of Bengal

NASA Astrophysics Data System (ADS)

Kutty, Govindan; Muraleedharan, Rohit; Kesarkar, Amit P.

2018-03-01

Uncertainties in the numerical weather prediction models are generally not well-represented in ensemble-based data assimilation (DA) systems. The performance of an ensemble-based DA system becomes suboptimal, if the sources of error are undersampled in the forecast system. The present study examines the effect of accounting for model error treatments in the hybrid ensemble transform Kalman filter—three-dimensional variational (3DVAR) DA system (hybrid) in the track forecast of two tropical cyclones viz. Hudhud and Thane, formed over the Bay of Bengal, using Advanced Research Weather Research and Forecasting (ARW-WRF) model. We investigated the effect of two types of model error treatment schemes and their combination on the hybrid DA system; (i) multiphysics approach, which uses different combination of cumulus, microphysics and planetary boundary layer schemes, (ii) stochastic kinetic energy backscatter (SKEB) scheme, which perturbs the horizontal wind and potential temperature tendencies, (iii) a combination of both multiphysics and SKEB scheme. Substantial improvements are noticed in the track positions of both the cyclones, when flow-dependent ensemble covariance is used in 3DVAR framework. Explicit model error representation is found to be beneficial in treating the underdispersive ensembles. Among the model error schemes used in this study, a combination of multiphysics and SKEB schemes has outperformed the other two schemes with improved track forecast for both the tropical cyclones.

Multiphysics Simulation of Low-Amplitude Acoustic Wave Detection by Piezoelectric Wafer Active Sensors Validated by In-Situ AE-Fatigue Experiment

PubMed Central

Giurgiutiu, Victor

2017-01-01

Piezoelectric wafer active sensors (PWAS) are commonly used for detecting Lamb waves for structural health monitoring application. However, in most applications of active sensing, the signals are of high-amplitude and easy to detect. In this article, we have shown a new avenue of using the PWAS transducer for detecting the low-amplitude fatigue-crack related acoustic emission (AE) signals. Multiphysics finite element (FE) simulations were performed with two PWAS transducers bonded to the structure. Various configurations of the sensors were studied by using the simulations. One PWAS was placed near to the fatigue-crack and the other one was placed at a certain distance from the crack. The simulated AE event was generated at the crack tip. The simulation results showed that both PWAS transducers were capable of sensing the AE signals. To validate the multiphysics simulation results, an in-situ AE-fatigue experiment was performed. Two PWAS transducers were bonded to the thin aerospace test coupon. The fatigue crack was generated in the test coupon which had produced low-amplitude acoustic waves. The low-amplitude fatigue-crack related AE signals were successfully captured by the PWAS transducers. The distance effect on the captured AE signals was also studied. It has been shown that some high-frequency contents of the AE signal have developed as they travel away from the crack. PMID:28817081

Dry calibration of electromagnetic flowmeters based on numerical models combining multiple physical phenomena (multiphysics)

NASA Astrophysics Data System (ADS)

Fu, X.; Hu, L.; Lee, K. M.; Zou, J.; Ruan, X. D.; Yang, H. Y.

2010-10-01

This paper presents a method for dry calibration of an electromagnetic flowmeter (EMF). This method, which determines the voltage induced in the EMF as conductive liquid flows through a magnetic field, numerically solves a coupled set of multiphysical equations with measured boundary conditions for the magnetic, electric, and flow fields in the measuring pipe of the flowmeter. Specifically, this paper details the formulation of dry calibration and an efficient algorithm (that adaptively minimizes the number of measurements and requires only the normal component of the magnetic flux density as boundary conditions on the pipe surface to reconstruct the magnetic field involved) for computing the sensitivity of EMF. Along with an in-depth discussion on factors that could significantly affect the final precision of a dry calibrated EMF, the effects of flow disturbance on measuring errors have been experimentally studied by installing a baffle at the inflow port of the EMF. Results of the dry calibration on an actual EMF were compared against flow-rig calibration; excellent agreements (within 0.3%) between dry calibration and flow-rig tests verify the multiphysical computation of the fields and the robustness of the method. As requiring no actual flow, the dry calibration is particularly useful for calibrating large-diameter EMFs where conventional flow-rig methods are often costly and difficult to implement.

War and peace: morphemes and full forms in a noninteractive activation parallel dual-route model.

PubMed

Baayen, H; Schreuder, R

This article introduces a computational tool for modeling the process of morphological segmentation in visual and auditory word recognition in the framework of a parallel dual-route model. Copyright 1999 Academic Press.

On extending parallelism to serial simulators

NASA Technical Reports Server (NTRS)

Nicol, David; Heidelberger, Philip

1994-01-01

This paper describes an approach to discrete event simulation modeling that appears to be effective for developing portable and efficient parallel execution of models of large distributed systems and communication networks. In this approach, the modeler develops submodels using an existing sequential simulation modeling tool, using the full expressive power of the tool. A set of modeling language extensions permit automatically synchronized communication between submodels; however, the automation requires that any such communication must take a nonzero amount off simulation time. Within this modeling paradigm, a variety of conservative synchronization protocols can transparently support conservative execution of submodels on potentially different processors. A specific implementation of this approach, U.P.S. (Utilitarian Parallel Simulator), is described, along with performance results on the Intel Paragon.

Final Report: Correctness Tools for Petascale Computing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mellor-Crummey, John

2014-10-27

In the course of developing parallel programs for leadership computing systems, subtle programming errors often arise that are extremely difficult to diagnose without tools. To meet this challenge, University of Maryland, the University of Wisconsin—Madison, and Rice University worked to develop lightweight tools to help code developers pinpoint a variety of program correctness errors that plague parallel scientific codes. The aim of this project was to develop software tools that help diagnose program errors including memory leaks, memory access errors, round-off errors, and data races. Research at Rice University focused on developing algorithms and data structures to support efficient monitoringmore » of multithreaded programs for memory access errors and data races. This is a final report about research and development work at Rice University as part of this project.« less

A Virtual Laboratory for the 4 Bed Molecular Sieve of the Carbon Dioxide Removal Assembly

NASA Technical Reports Server (NTRS)

Coker, Robert; Knox, James; O'Connor, Brian

2016-01-01

Ongoing work to improve water and carbon dioxide separation systems to be used on crewed space vehicles combines sub-scale systems testing and multi-physics simulations. Thus, as part of NASA's Advanced Exploration Systems (AES) program and the Life Support Systems Project (LSSP), fully predictive COMSOL Multiphysics models of the Four Bed Molecular Sieve (4BMS) of the Carbon Dioxide Removal Assembly (CDRA) on the International Space Station (ISS) have been developed. This Virtual Laboratory is being used to help reduce mass, power, and volume requirements for exploration missions. In this paper we describe current and planned modeling developments in the area of carbon dioxide removal to support future missions as well as the resolution of anomalies observed in the ISS CDRA.

Modelling in conventional electroporation for model cell with organelles using COMSOL Multiphysics

NASA Astrophysics Data System (ADS)

Sulaeman, M. Y.; Widita, R.

2016-03-01

Conventional electroporation is a formation of pores in the membrane cell due to the external electric field applied to the cell. The purpose of creating pores in the cell using conventional electroporation are to increase the effectiveness of chemotherapy (electrochemotherapy) and to kill cancer tissue using irreversible electroporation. Modeling of electroporation phenomenon on a model cell had been done by using software COMSOL Multiphysics 4.3b with the applied external electric field with intensity at 1.1 kV/cm to find transmembrane voltage and pore density. It can be concluded from the results of potential distribution and transmembrane voltage, it show that pores formation only occurs in the membrane cells and it could not penetrate into inside the model cell so there is not pores formation in its organells.

Evaluation of a transient, simultaneous, arbitrary Lagrange-Euler based multi-physics method for simulating the mitral heart valve.

PubMed

Espino, Daniel M; Shepherd, Duncan E T; Hukins, David W L

2014-01-01

A transient multi-physics model of the mitral heart valve has been developed, which allows simultaneous calculation of fluid flow and structural deformation. A recently developed contact method has been applied to enable simulation of systole (the stage when blood pressure is elevated within the heart to pump blood to the body). The geometry was simplified to represent the mitral valve within the heart walls in two dimensions. Only the mitral valve undergoes deformation. A moving arbitrary Lagrange-Euler mesh is used to allow true fluid-structure interaction (FSI). The FSI model requires blood flow to induce valve closure by inducing strains in the region of 10-20%. Model predictions were found to be consistent with existing literature and will undergo further development.

Real time software tools and methodologies

NASA Technical Reports Server (NTRS)

Christofferson, M. J.

1981-01-01

Real time systems are characterized by high speed processing and throughput as well as asynchronous event processing requirements. These requirements give rise to particular implementations of parallel or pipeline multitasking structures, of intertask or interprocess communications mechanisms, and finally of message (buffer) routing or switching mechanisms. These mechanisms or structures, along with the data structue, describe the essential character of the system. These common structural elements and mechanisms are identified, their implementation in the form of routines, tasks or macros - in other words, tools are formalized. The tools developed support or make available the following: reentrant task creation, generalized message routing techniques, generalized task structures/task families, standardized intertask communications mechanisms, and pipeline and parallel processing architectures in a multitasking environment. Tools development raise some interesting prospects in the areas of software instrumentation and software portability. These issues are discussed following the description of the tools themselves.

A high performance data parallel tensor contraction framework: Application to coupled electro-mechanics

NASA Astrophysics Data System (ADS)

Poya, Roman; Gil, Antonio J.; Ortigosa, Rogelio

2017-07-01

The paper presents aspects of implementation of a new high performance tensor contraction framework for the numerical analysis of coupled and multi-physics problems on streaming architectures. In addition to explicit SIMD instructions and smart expression templates, the framework introduces domain specific constructs for the tensor cross product and its associated algebra recently rediscovered by Bonet et al. (2015, 2016) in the context of solid mechanics. The two key ingredients of the presented expression template engine are as follows. First, the capability to mathematically transform complex chains of operations to simpler equivalent expressions, while potentially avoiding routes with higher levels of computational complexity and, second, to perform a compile time depth-first or breadth-first search to find the optimal contraction indices of a large tensor network in order to minimise the number of floating point operations. For optimisations of tensor contraction such as loop transformation, loop fusion and data locality optimisations, the framework relies heavily on compile time technologies rather than source-to-source translation or JIT techniques. Every aspect of the framework is examined through relevant performance benchmarks, including the impact of data parallelism on the performance of isomorphic and nonisomorphic tensor products, the FLOP and memory I/O optimality in the evaluation of tensor networks, the compilation cost and memory footprint of the framework and the performance of tensor cross product kernels. The framework is then applied to finite element analysis of coupled electro-mechanical problems to assess the speed-ups achieved in kernel-based numerical integration of complex electroelastic energy functionals. In this context, domain-aware expression templates combined with SIMD instructions are shown to provide a significant speed-up over the classical low-level style programming techniques.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Haugen, Carl C.; Forget, Benoit; Smith, Kord S.

Most high performance computing systems being deployed currently and envisioned for the future are based on making use of heavy parallelism across many computational nodes and many concurrent cores. These types of heavily parallel systems often have relatively little memory per core but large amounts of computing capability. This places a significant constraint on how data storage is handled in many Monte Carlo codes. This is made even more significant in fully coupled multiphysics simulations, which requires simulations of many physical phenomena be carried out concurrently on individual processing nodes, which further reduces the amount of memory available for storagemore » of Monte Carlo data. As such, there has been a move towards on-the-fly nuclear data generation to reduce memory requirements associated with interpolation between pre-generated large nuclear data tables for a selection of system temperatures. Methods have been previously developed and implemented in MIT’s OpenMC Monte Carlo code for both the resolved resonance regime and the unresolved resonance regime, but are currently absent for the thermal energy regime. While there are many components involved in generating a thermal neutron scattering cross section on-the-fly, this work will focus on a proposed method for determining the energy and direction of a neutron after a thermal incoherent inelastic scattering event. This work proposes a rejection sampling based method using the thermal scattering kernel to determine the correct outgoing energy and angle. The goal of this project is to be able to treat the full S (a, ß) kernel for graphite, to assist in high fidelity simulations of the TREAT reactor at Idaho National Laboratory. The method is, however, sufficiently general to be applicable in other thermal scattering materials, and can be initially validated with the continuous analytic free gas model.« less

An Assessment of Some Design Constraints on Heat Production of a 3D Conceptual EGS Model Using an Open-Source Geothermal Reservoir Simulation Code

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yidong Xia; Mitch Plummer; Robert Podgorney

2016-02-01

Performance of heat production process over a 30-year period is assessed in a conceptual EGS model with a geothermal gradient of 65K per km depth in the reservoir. Water is circulated through a pair of parallel wells connected by a set of single large wing fractures. The results indicate that the desirable output electric power rate and lifespan could be obtained under suitable material properties and system parameters. A sensitivity analysis on some design constraints and operation parameters indicates that 1) the fracture horizontal spacing has profound effect on the long-term performance of heat production, 2) the downward deviation anglemore » for the parallel doublet wells may help overcome the difficulty of vertical drilling to reach a favorable production temperature, and 3) the thermal energy production rate and lifespan has close dependence on water mass flow rate. The results also indicate that the heat production can be improved when the horizontal fracture spacing, well deviation angle, and production flow rate are under reasonable conditions. To conduct the reservoir modeling and simulations, an open-source, finite element based, fully implicit, fully coupled hydrothermal code, namely FALCON, has been developed and used in this work. Compared with most other existing codes that are either closed-source or commercially available in this area, this new open-source code has demonstrated a code development strategy that aims to provide an unparalleled easiness for user-customization and multi-physics coupling. Test results have shown that the FALCON code is able to complete the long-term tests efficiently and accurately, thanks to the state-of-the-art nonlinear and linear solver algorithms implemented in the code.« less

Large scale cardiac modeling on the Blue Gene supercomputer.

PubMed

Reumann, Matthias; Fitch, Blake G; Rayshubskiy, Aleksandr; Keller, David U; Weiss, Daniel L; Seemann, Gunnar; Dössel, Olaf; Pitman, Michael C; Rice, John J

2008-01-01

Multi-scale, multi-physical heart models have not yet been able to include a high degree of accuracy and resolution with respect to model detail and spatial resolution due to computational limitations of current systems. We propose a framework to compute large scale cardiac models. Decomposition of anatomical data in segments to be distributed on a parallel computer is carried out by optimal recursive bisection (ORB). The algorithm takes into account a computational load parameter which has to be adjusted according to the cell models used. The diffusion term is realized by the monodomain equations. The anatomical data-set was given by both ventricles of the Visible Female data-set in a 0.2 mm resolution. Heterogeneous anisotropy was included in the computation. Model weights as input for the decomposition and load balancing were set to (a) 1 for tissue and 0 for non-tissue elements; (b) 10 for tissue and 1 for non-tissue elements. Scaling results for 512, 1024, 2048, 4096 and 8192 computational nodes were obtained for 10 ms simulation time. The simulations were carried out on an IBM Blue Gene/L parallel computer. A 1 s simulation was then carried out on 2048 nodes for the optimal model load. Load balances did not differ significantly across computational nodes even if the number of data elements distributed to each node differed greatly. Since the ORB algorithm did not take into account computational load due to communication cycles, the speedup is close to optimal for the computation time but not optimal overall due to the communication overhead. However, the simulation times were reduced form 87 minutes on 512 to 11 minutes on 8192 nodes. This work demonstrates that it is possible to run simulations of the presented detailed cardiac model within hours for the simulation of a heart beat.

A new package in MODFLOW to simulate unconfined groundwater flow in sloping aquifers.

PubMed

Wang, Quanrong; Zhan, Hongbin; Tang, Zhonghua

2014-01-01

The nonhorizontal-model-layer (NHML) grid system is more accurate than the horizontal-model-layer grid system to describe groundwater flow in an unconfined sloping aquifer on the basis of MODFLOW-2000. However, the finite-difference scheme of NHML was based on the Dupuit-Forchheimer assumption that the streamlines were horizontal, which was acceptable for slope less than 0.10. In this study, we presented a new finite-difference scheme of NHML based on the Boussinesq assumption and developed a new package SLOPE which was incorporated into MODFLOW-2000 to become the MODFLOW-SP model. The accuracy of MODFLOW-SP was tested against solution of Mac Cormack (1969). The differences between the solutions of MODFLOW-2000 and MODFLOW-SP were nearly negligible when the slope was less than 0.27, and they were noticeable during the transient flow stage and vanished in steady state when the slope increased above 0.27. We established a model considering the vertical flow using COMSOL Multiphysics to test the robustness of constrains used in MODFLOW-SP. The results showed that streamlines quickly became parallel with the aquifer base except in the narrow regions near the boundaries when the initial flow was not parallel to the aquifer base. MODFLOW-SP can be used to predict the hydraulic head of an unconfined aquifer along the profile perpendicular to the aquifer base when the slope was smaller than 0.50. The errors associated with constrains used in MODFLOW-SP were small but noticeable when the slope increased to 0.75, and became significant for the slope of 1.0. © 2013, National Ground Water Association.

Computational modeling of magnetic particle margination within blood flow through LAMMPS

NASA Astrophysics Data System (ADS)

Ye, Huilin; Shen, Zhiqiang; Li, Ying

2017-11-01

We develop a multiscale and multiphysics computational method to investigate the transport of magnetic particles as drug carriers in blood flow under influence of hydrodynamic interaction and external magnetic field. A hybrid coupling method is proposed to handle red blood cell (RBC)-fluid interface (CFI) and magnetic particle-fluid interface (PFI), respectively. Immersed boundary method (IBM)-based velocity coupling is used to account for CFI, which is validated by tank-treading and tumbling behaviors of a single RBC in simple shear flow. While PFI is captured by IBM-based force coupling, which is verified through movement of a single magnetic particle under non-uniform external magnetic field and breakup of a magnetic chain in rotating magnetic field. These two components are seamlessly integrated within the LAMMPS framework, which is a highly parallelized molecular dynamics solver. In addition, we also implement a parallelized lattice Boltzmann simulator within LAMMPS to handle the fluid flow simulation. Based on the proposed method, we explore the margination behaviors of magnetic particles and magnetic chains within blood flow. We find that the external magnetic field can be used to guide the motion of these magnetic materials and promote their margination to the vascular wall region. Moreover, the scaling performance and speedup test further confirm the high efficiency and robustness of proposed computational method. Therefore, it provides an efficient way to simulate the transport of nanoparticle-based drug carriers within blood flow in a large scale. The simulation results can be applied in the design of efficient drug delivery vehicles that optimally accumulate within diseased tissue, thus providing better imaging sensitivity, therapeutic efficacy and lower toxicity.

Implicit SPH v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kim, Kyungjoo; Parks, Michael L.; Perego, Mauro

2016-11-09

ISPH code is developed to solve multi-physics meso-scale flow problems using implicit SPH method. In particular, the code can provides solutions for incompressible, multi phase flow and electro-kinetic flows.

The development of a thermal hydraulic feedback mechanism with a quasi-fixed point iteration scheme for control rod position modeling for the TRIGSIMS-TH application

NASA Astrophysics Data System (ADS)

Karriem, Veronica V.

Nuclear reactor design incorporates the study and application of nuclear physics, nuclear thermal hydraulic and nuclear safety. Theoretical models and numerical methods implemented in computer programs are utilized to analyze and design nuclear reactors. The focus of this PhD study's is the development of an advanced high-fidelity multi-physics code system to perform reactor core analysis for design and safety evaluations of research TRIGA-type reactors. The fuel management and design code system TRIGSIMS was further developed to fulfill the function of a reactor design and analysis code system for the Pennsylvania State Breazeale Reactor (PSBR). TRIGSIMS, which is currently in use at the PSBR, is a fuel management tool, which incorporates the depletion code ORIGEN-S (part of SCALE system) and the Monte Carlo neutronics solver MCNP. The diffusion theory code ADMARC-H is used within TRIGSIMS to accelerate the MCNP calculations. It manages the data and fuel isotopic content and stores it for future burnup calculations. The contribution of this work is the development of an improved version of TRIGSIMS, named TRIGSIMS-TH. TRIGSIMS-TH incorporates a thermal hydraulic module based on the advanced sub-channel code COBRA-TF (CTF). CTF provides the temperature feedback needed in the multi-physics calculations as well as the thermal hydraulics modeling capability of the reactor core. The temperature feedback model is using the CTF-provided local moderator and fuel temperatures for the cross-section modeling for ADMARC-H and MCNP calculations. To perform efficient critical control rod calculations, a methodology for applying a control rod position was implemented in TRIGSIMS-TH, making this code system a modeling and design tool for future core loadings. The new TRIGSIMS-TH is a computer program that interlinks various other functional reactor analysis tools. It consists of the MCNP5, ADMARC-H, ORIGEN-S, and CTF. CTF was coupled with both MCNP and ADMARC-H to provide the heterogeneous temperature distribution throughout the core. Each of these codes is written in its own computer language performing its function and outputs a set of data. TRIGSIMS-TH provides an effective use and data manipulation and transfer between different codes. With the implementation of feedback and control- rod-position modeling methodologies, the TRIGSIMS-TH calculations are more accurate and in a better agreement with measured data. The PSBR is unique in many ways and there are no "off-the-shelf" codes, which can model this design in its entirety. In particular, PSBR has an open core design, which is cooled by natural convection. Combining several codes into a unique system brings many challenges. It also requires substantial knowledge of both operation and core design of the PSBR. This reactor is in operation decades and there is a fair amount of studies and developments in both PSBR thermal hydraulics and neutronics. Measured data is also available for various core loadings and can be used for validation activities. The previous studies and developments in PSBR modeling also aids as a guide to assess the findings of the work herein. In order to incorporate new methods and codes into exiting TRIGSIMS, a re-evaluation of various components of the code was performed to assure the accuracy and efficiency of the existing CTF/MCNP5/ADMARC-H multi-physics coupling. A new set of ADMARC-H diffusion coefficients and cross sections was generated using the SERPENT code. This was needed as the previous data was not generated with thermal hydraulic feedback and the ARO position was used as the critical rod position. The B4C was re-evaluated for this update. The data exchange between ADMARC-H and MCNP5 was modified. The basic core model is given a flexibility to allow for various changes within the core model, and this feature was implemented in TRIGSIMS-TH. The PSBR core in the new code model can be expanded and changed. This allows the new code to be used as a modeling tool for design and analyses of future code loadings.

Information criteria for quantifying loss of reversibility in parallelized KMC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gourgoulias, Konstantinos, E-mail: gourgoul@math.umass.edu; Katsoulakis, Markos A., E-mail: markos@math.umass.edu; Rey-Bellet, Luc, E-mail: luc@math.umass.edu

Parallel Kinetic Monte Carlo (KMC) is a potent tool to simulate stochastic particle systems efficiently. However, despite literature on quantifying domain decomposition errors of the particle system for this class of algorithms in the short and in the long time regime, no study yet explores and quantifies the loss of time-reversibility in Parallel KMC. Inspired by concepts from non-equilibrium statistical mechanics, we propose the entropy production per unit time, or entropy production rate, given in terms of an observable and a corresponding estimator, as a metric that quantifies the loss of reversibility. Typically, this is a quantity that cannot bemore » computed explicitly for Parallel KMC, which is why we develop a posteriori estimators that have good scaling properties with respect to the size of the system. Through these estimators, we can connect the different parameters of the scheme, such as the communication time step of the parallelization, the choice of the domain decomposition, and the computational schedule, with its performance in controlling the loss of reversibility. From this point of view, the entropy production rate can be seen both as an information criterion to compare the reversibility of different parallel schemes and as a tool to diagnose reversibility issues with a particular scheme. As a demonstration, we use Sandia Lab's SPPARKS software to compare different parallelization schemes and different domain (lattice) decompositions.« less

Information criteria for quantifying loss of reversibility in parallelized KMC

NASA Astrophysics Data System (ADS)

Gourgoulias, Konstantinos; Katsoulakis, Markos A.; Rey-Bellet, Luc

2017-01-01

Parallel Kinetic Monte Carlo (KMC) is a potent tool to simulate stochastic particle systems efficiently. However, despite literature on quantifying domain decomposition errors of the particle system for this class of algorithms in the short and in the long time regime, no study yet explores and quantifies the loss of time-reversibility in Parallel KMC. Inspired by concepts from non-equilibrium statistical mechanics, we propose the entropy production per unit time, or entropy production rate, given in terms of an observable and a corresponding estimator, as a metric that quantifies the loss of reversibility. Typically, this is a quantity that cannot be computed explicitly for Parallel KMC, which is why we develop a posteriori estimators that have good scaling properties with respect to the size of the system. Through these estimators, we can connect the different parameters of the scheme, such as the communication time step of the parallelization, the choice of the domain decomposition, and the computational schedule, with its performance in controlling the loss of reversibility. From this point of view, the entropy production rate can be seen both as an information criterion to compare the reversibility of different parallel schemes and as a tool to diagnose reversibility issues with a particular scheme. As a demonstration, we use Sandia Lab's SPPARKS software to compare different parallelization schemes and different domain (lattice) decompositions.

Tools for Collaboration: Using and Designing Tools in Interorganizational Economic-Crime Investigation

ERIC Educational Resources Information Center

Puonti, Anne

2004-01-01

Economic-crime investigation in Finland is in transition from hierarchically organized, sequential collaboration between authorities toward parallel, interorganizational collaboration. This article describes the tools used and developed for managing the new collaborative economic-crime-investigation process. The challenge is to find…

Accessing and Visualizing scientific spatiotemporal data

NASA Technical Reports Server (NTRS)

Katz, Daniel S.; Bergou, Attila; Berriman, Bruce G.; Block, Gary L.; Collier, Jim; Curkendall, David W.; Good, John; Husman, Laura; Jacob, Joseph C.; Laity, Anastasia;

Modeling Coupled Physical and Chemical Erosional Processes Using Structure from Motion Reconstruction and Multiphysics Simulation: Applications to Knickpoints in Bedrock Streams in Limestone Caves and on Earth's Surface

NASA Astrophysics Data System (ADS)

Bosch, R.; Ward, D.

2017-12-01

Investigation of erosion rates and processes at knickpoints in surface bedrock streams is an active area of research, involving complex feedbacks in the coupled relationships between dissolution, abrasion, and plucking that have not been sufficiently addressed. Even less research has addressed how these processes operate to propagate knickpoints through cave passages in layered sedimentary rocks, despite these features being common along subsurface streams. In both settings, there is evidence for mechanical and chemical erosion, but in cave passages the different hydrologic and hydraulic regimes, combined with an important role for the dissolution process, affect the relative roles and coupled interactions between these processes, and distinguish them from surface stream knickpoints. Using a novel approach of imaging cave passages using Structure from Motion (SFM), we create 3D geometry meshes to explore these systems using multiphysics simulation, and compare the processes as they occur in caves with those in surface streams. Here we focus on four field sites with actively eroding streambeds that include knickpoints: Upper River Acheron and Devil's Cooling Tub in Mammoth Cave, Kentucky; and two surface streams in Clermont County, Ohio, Avey's Run and Fox Run. SFM 3D reconstructions are built using images exported from 4K video shot at each field location. We demonstrate that SFM is a viable imaging approach for reconstructing cave passages with complex morphologies. We then use these reconstructions to create meshes upon which to run multiphysics simulations using STAR-CCM+. Our approach incorporates multiphase free-surface computational fluid dynamics simulations with sediment transport modeled using discrete element method grains. Physical and chemical properties of the water, bedrock, and sediment enable computation of shear stress, sediment impact forces, and chemical kinetic conditions at the bed surface. Preliminary results prove the efficacy of commercially available multiphysics simulation software for modeling various flow conditions, erosional processes, and their complex coupled interactions in cave passages and in surface stream channels to expand knowledge and understanding of overall cave system development and river profile erosion.

SIAM Conference on Parallel Processing for Scientific Computing, 4th, Chicago, IL, Dec. 11-13, 1989, Proceedings

NASA Technical Reports Server (NTRS)

Dongarra, Jack (Editor); Messina, Paul (Editor); Sorensen, Danny C. (Editor); Voigt, Robert G. (Editor)

1990-01-01

Attention is given to such topics as an evaluation of block algorithm variants in LAPACK and presents a large-grain parallel sparse system solver, a multiprocessor method for the solution of the generalized Eigenvalue problem on an interval, and a parallel QR algorithm for iterative subspace methods on the CM2. A discussion of numerical methods includes the topics of asynchronous numerical solutions of PDEs on parallel computers, parallel homotopy curve tracking on a hypercube, and solving Navier-Stokes equations on the Cedar Multi-Cluster system. A section on differential equations includes a discussion of a six-color procedure for the parallel solution of elliptic systems using the finite quadtree structure, data parallel algorithms for the finite element method, and domain decomposition methods in aerodynamics. Topics dealing with massively parallel computing include hypercube vs. 2-dimensional meshes and massively parallel computation of conservation laws. Performance and tools are also discussed.

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, Olaf O.; Nguyen, Duc T.; Baddourah, Majdi; Qin, Jiangning

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigensolution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization search analysis and domain decomposition. The source code for many of these algorithms is available.

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

Population structure inference using the software STRUCTURE has become an integral part of population genetic studies covering a broad spectrum of taxa including humans. The ever-expanding size of genetic data sets poses computational challenges for this analysis. Although at least one tool currently implements parallel computing to reduce computational overload of this analysis, it does not fully automate the use of replicate STRUCTURE analysis runs required for downstream inference of optimal K. There is pressing need for a tool that can deploy population structure analysis on high performance computing clusters. We present an updated version of the popular Python program StrAuto, to streamline population structure analysis using parallel computing. StrAuto implements a pipeline that combines STRUCTURE analysis with the Evanno Δ K analysis and visualization of results using STRUCTURE HARVESTER. Using benchmarking tests, we demonstrate that StrAuto significantly reduces the computational time needed to perform iterative STRUCTURE analysis by distributing runs over two or more processors. StrAuto is the first tool to integrate STRUCTURE analysis with post-processing using a pipeline approach in addition to implementing parallel computation - a set up ideal for deployment on computing clusters. StrAuto is distributed under the GNU GPL (General Public License) and available to download from http://strauto.popgen.org .

Backtracking and Re-execution in the Automatic Debugging of Parallelized Programs

NASA Technical Reports Server (NTRS)

Matthews, Gregory; Hood, Robert; Johnson, Stephen; Leggett, Peter; Biegel, Bryan (Technical Monitor)

2002-01-01

In this work we describe a new approach using relative debugging to find differences in computation between a serial program and a parallel version of th it program. We use a combination of re-execution and backtracking in order to find the first difference in computation that may ultimately lead to an incorrect value that the user has indicated. In our prototype implementation we use static analysis information from a parallelization tool in order to perform the backtracking as well as the mapping required between serial and parallel computations.

Next Generation Parallelization Systems for Processing and Control of PDS Image Node Assets

NASA Astrophysics Data System (ADS)

Verma, R.

2017-06-01

We present next-generation parallelization tools to help Planetary Data System (PDS) Imaging Node (IMG) better monitor, process, and control changes to nearly 650 million file assets and over a dozen machines on which they are referenced or stored.

Program Correctness, Verification and Testing for Exascale (Corvette)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sen, Koushik; Iancu, Costin; Demmel, James W

The goal of this project is to provide tools to assess the correctness of parallel programs written using hybrid parallelism. There is a dire lack of both theoretical and engineering know-how in the area of finding bugs in hybrid or large scale parallel programs, which our research aims to change. In the project we have demonstrated novel approaches in several areas: 1. Low overhead automated and precise detection of concurrency bugs at scale. 2. Using low overhead bug detection tools to guide speculative program transformations for performance. 3. Techniques to reduce the concurrency required to reproduce a bug using partialmore » program restart/replay. 4. Techniques to provide reproducible execution of floating point programs. 5. Techniques for tuning the floating point precision used in codes.« less

Scalable Unix tools on parallel processors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gropp, W.; Lusk, E.

1994-12-31

The introduction of parallel processors that run a separate copy of Unix on each process has introduced new problems in managing the user`s environment. This paper discusses some generalizations of common Unix commands for managing files (e.g. 1s) and processes (e.g. ps) that are convenient and scalable. These basic tools, just like their Unix counterparts, are text-based. We also discuss a way to use these with a graphical user interface (GUI). Some notes on the implementation are provided. Prototypes of these commands are publicly available.

A Queue Simulation Tool for a High Performance Scientific Computing Center

NASA Technical Reports Server (NTRS)

Spear, Carrie; McGalliard, James

2007-01-01

The NASA Center for Computational Sciences (NCCS) at the Goddard Space Flight Center provides high performance highly parallel processors, mass storage, and supporting infrastructure to a community of computational Earth and space scientists. Long running (days) and highly parallel (hundreds of CPUs) jobs are common in the workload. NCCS management structures batch queues and allocates resources to optimize system use and prioritize workloads. NCCS technical staff use a locally developed discrete event simulation tool to model the impacts of evolving workloads, potential system upgrades, alternative queue structures and resource allocation policies.

An evaluation of the performance of a WRF multi-physics ensemble for heatwave events over the city of Melbourne in southeast Australia

NASA Astrophysics Data System (ADS)

Imran, H. M.; Kala, J.; Ng, A. W. M.; Muthukumaran, S.

2018-04-01

Appropriate choice of physics options among many physics parameterizations is important when using the Weather Research and Forecasting (WRF) model. The responses of different physics parameterizations of the WRF model may vary due to geographical locations, the application of interest, and the temporal and spatial scales being investigated. Several studies have evaluated the performance of the WRF model in simulating the mean climate and extreme rainfall events for various regions in Australia. However, no study has explicitly evaluated the sensitivity of the WRF model in simulating heatwaves. Therefore, this study evaluates the performance of a WRF multi-physics ensemble that comprises 27 model configurations for a series of heatwave events in Melbourne, Australia. Unlike most previous studies, we not only evaluate temperature, but also wind speed and relative humidity, which are key factors influencing heatwave dynamics. No specific ensemble member for all events explicitly showed the best performance, for all the variables, considering all evaluation metrics. This study also found that the choice of planetary boundary layer (PBL) scheme had largest influence, the radiation scheme had moderate influence, and the microphysics scheme had the least influence on temperature simulations. The PBL and microphysics schemes were found to be more sensitive than the radiation scheme for wind speed and relative humidity. Additionally, the study tested the role of Urban Canopy Model (UCM) and three Land Surface Models (LSMs). Although the UCM did not play significant role, the Noah-LSM showed better performance than the CLM4 and NOAH-MP LSMs in simulating the heatwave events. The study finally identifies an optimal configuration of WRF that will be a useful modelling tool for further investigations of heatwaves in Melbourne. Although our results are invariably region-specific, our results will be useful to WRF users investigating heatwave dynamics elsewhere.

Multiphysics Modeling of an Annular Linear Induction Pump With Applications to Space Nuclear Power Systems

NASA Technical Reports Server (NTRS)

Kilbane, J.; Polzin, K. A.

2014-01-01

An annular linear induction pump (ALIP) that could be used for circulating liquid-metal coolant in a fission surface power reactor system is modeled in the present work using the computational COMSOL Multiphysics package. The pump is modeled using a two-dimensional, axisymmetric geometry and solved under conditions similar to those used during experimental pump testing. Real, nonlinear, temperature-dependent material properties can be incorporated into the model for both the electrically-conducting working fluid in the pump (NaK-78) and structural components of the pump. The intricate three-phase coil configuration of the pump is implemented in the model to produce an axially-traveling magnetic wave that is qualitatively similar to the measured magnetic wave. The model qualitatively captures the expected feature of a peak in efficiency as a function of flow rate.

Multiscale Multiphysics Developments for Accident Tolerant Fuel Concepts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gamble, K. A.; Hales, J. D.; Yu, J.

2015-09-01

U 3Si 2 and iron-chromium-aluminum (Fe-Cr-Al) alloys are two of many proposed accident-tolerant fuel concepts for the fuel and cladding, respectively. The behavior of these materials under normal operating and accident reactor conditions is not well known. As part of the Department of Energy’s Accident Tolerant Fuel High Impact Problem program significant work has been conducted to investigate the U 3Si 2 and FeCrAl behavior under reactor conditions. This report presents the multiscale and multiphysics effort completed in fiscal year 2015. The report is split into four major categories including Density Functional Theory Developments, Molecular Dynamics Developments, Mesoscale Developments, andmore » Engineering Scale Developments. The work shown here is a compilation of a collaborative effort between Idaho National Laboratory, Los Alamos National Laboratory, Argonne National Laboratory and Anatech Corp.« less

iTOUGH2: A multiphysics simulation-optimization framework for analyzing subsurface systems

NASA Astrophysics Data System (ADS)

Finsterle, S.; Commer, M.; Edmiston, J. K.; Jung, Y.; Kowalsky, M. B.; Pau, G. S. H.; Wainwright, H. M.; Zhang, Y.

2017-11-01

iTOUGH2 is a simulation-optimization framework for the TOUGH suite of nonisothermal multiphase flow models and related simulators of geophysical, geochemical, and geomechanical processes. After appropriate parameterization of subsurface structures and their properties, iTOUGH2 runs simulations for multiple parameter sets and analyzes the resulting output for parameter estimation through automatic model calibration, local and global sensitivity analyses, data-worth analyses, and uncertainty propagation analyses. Development of iTOUGH2 is driven by scientific challenges and user needs, with new capabilities continually added to both the forward simulator and the optimization framework. This review article provides a summary description of methods and features implemented in iTOUGH2, and discusses the usefulness and limitations of an integrated simulation-optimization workflow in support of the characterization and analysis of complex multiphysics subsurface systems.

Using Appropriate Tools Strategically for Instruction

ERIC Educational Resources Information Center

Sherman, Milan; Cayton, Charity

2015-01-01

Students' ability to use appropriate tools strategically is an important skill of mathematically proficient students (SMP 5, CCSSI 2010, p. 7). A parallel practice for teachers is using appropriate tools strategically for mathematics instruction. An important element of this practice is that the use of technology depends on the goals of…

Thermoplastic welding apparatus and method

DOEpatents

Matsen, Marc R.; Negley, Mark A.; Geren, William Preston; Miller, Robert James

2017-03-07

A thermoplastic welding apparatus includes a thermoplastic welding tool, at least one tooling surface in the thermoplastic welding tool, a magnetic induction coil in the thermoplastic welding tool and generally encircling the at least one tooling surface and at least one smart susceptor in the thermoplastic welding tool at the at least one tooling surface. The magnetic induction coil is adapted to generate a magnetic flux field oriented generally parallel to a plane of the at least one smart susceptor.

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Möckel, M.; Wiedemann, C.; Flegel, S.; Gelhaus, J.; Vörsmann, P.; Klinkrad, H.; Krag, H.

2011-07-01

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction to OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Using parallel computing for the display and simulation of the space debris environment

NASA Astrophysics Data System (ADS)

Moeckel, Marek; Wiedemann, Carsten; Flegel, Sven Kevin; Gelhaus, Johannes; Klinkrad, Heiner; Krag, Holger; Voersmann, Peter

Parallelism is becoming the leading paradigm in today's computer architectures. In order to take full advantage of this development, new algorithms have to be specifically designed for parallel execution while many old ones have to be upgraded accordingly. One field in which parallel computing has been firmly established for many years is computer graphics. Calculating and displaying three-dimensional computer generated imagery in real time requires complex numerical operations to be performed at high speed on a large number of objects. Since most of these objects can be processed independently, parallel computing is applicable in this field. Modern graphics processing units (GPUs) have become capable of performing millions of matrix and vector operations per second on multiple objects simultaneously. As a side project, a software tool is currently being developed at the Institute of Aerospace Systems that provides an animated, three-dimensional visualization of both actual and simulated space debris objects. Due to the nature of these objects it is possible to process them individually and independently from each other. Therefore, an analytical orbit propagation algorithm has been implemented to run on a GPU. By taking advantage of all its processing power a huge performance increase, compared to its CPU-based counterpart, could be achieved. For several years efforts have been made to harness this computing power for applications other than computer graphics. Software tools for the simulation of space debris are among those that could profit from embracing parallelism. With recently emerged software development tools such as OpenCL it is possible to transfer the new algorithms used in the visualization outside the field of computer graphics and implement them, for example, into the space debris simulation environment. This way they can make use of parallel hardware such as GPUs and Multi-Core-CPUs for faster computation. In this paper the visualization software will be introduced, including a comparison between the serial and the parallel method of orbit propagation. Ways of how to use the benefits of the latter method for space debris simulation will be discussed. An introduction of OpenCL will be given as well as an exemplary algorithm from the field of space debris simulation.

Interactive Parallel Data Analysis within Data-Centric Cluster Facilities using the IPython Notebook

NASA Astrophysics Data System (ADS)

Pascoe, S.; Lansdowne, J.; Iwi, A.; Stephens, A.; Kershaw, P.

2012-12-01

The data deluge is making traditional analysis workflows for many researchers obsolete. Support for parallelism within popular tools such as matlab, IDL and NCO is not well developed and rarely used. However parallelism is necessary for processing modern data volumes on a timescale conducive to curiosity-driven analysis. Furthermore, for peta-scale datasets such as the CMIP5 archive, it is no longer practical to bring an entire dataset to a researcher's workstation for analysis, or even to their institutional cluster. Therefore, there is an increasing need to develop new analysis platforms which both enable processing at the point of data storage and which provides parallelism. Such an environment should, where possible, maintain the convenience and familiarity of our current analysis environments to encourage curiosity-driven research. We describe how we are combining the interactive python shell (IPython) with our JASMIN data-cluster infrastructure. IPython has been specifically designed to bridge the gap between the HPC-style parallel workflows and the opportunistic curiosity-driven analysis usually carried out using domain specific languages and scriptable tools. IPython offers a web-based interactive environment, the IPython notebook, and a cluster engine for parallelism all underpinned by the well-respected Python/Scipy scientific programming stack. JASMIN is designed to support the data analysis requirements of the UK and European climate and earth system modeling community. JASMIN, with its sister facility CEMS focusing the earth observation community, has 4.5 PB of fast parallel disk storage alongside over 370 computing cores provide local computation. Through the IPython interface to JASMIN, users can make efficient use of JASMIN's multi-core virtual machines to perform interactive analysis on all cores simultaneously or can configure IPython clusters across multiple VMs. Larger-scale clusters can be provisioned through JASMIN's batch scheduling system. Outputs can be summarised and visualised using the full power of Python's many scientific tools, including Scipy, Matplotlib, Pandas and CDAT. This rich user experience is delivered through the user's web browser; maintaining the interactive feel of a workstation-based environment with the parallel power of a remote data-centric processing facility.

cljam: a library for handling DNA sequence alignment/map (SAM) with parallel processing.

PubMed

Takeuchi, Toshiki; Yamada, Atsuo; Aoki, Takashi; Nishimura, Kunihiro

2016-01-01

Next-generation sequencing can determine DNA bases and the results of sequence alignments are generally stored in files in the Sequence Alignment/Map (SAM) format and the compressed binary version (BAM) of it. SAMtools is a typical tool for dealing with files in the SAM/BAM format. SAMtools has various functions, including detection of variants, visualization of alignments, indexing, extraction of parts of the data and loci, and conversion of file formats. It is written in C and can execute fast. However, SAMtools requires an additional implementation to be used in parallel with, for example, OpenMP (Open Multi-Processing) libraries. For the accumulation of next-generation sequencing data, a simple parallelization program, which can support cloud and PC cluster environments, is required. We have developed cljam using the Clojure programming language, which simplifies parallel programming, to handle SAM/BAM data. Cljam can run in a Java runtime environment (e.g., Windows, Linux, Mac OS X) with Clojure. Cljam can process and analyze SAM/BAM files in parallel and at high speed. The execution time with cljam is almost the same as with SAMtools. The cljam code is written in Clojure and has fewer lines than other similar tools.

Visual analysis of inter-process communication for large-scale parallel computing.

PubMed

Muelder, Chris; Gygi, Francois; Ma, Kwan-Liu

2009-01-01

In serial computation, program profiling is often helpful for optimization of key sections of code. When moving to parallel computation, not only does the code execution need to be considered but also communication between the different processes which can induce delays that are detrimental to performance. As the number of processes increases, so does the impact of the communication delays on performance. For large-scale parallel applications, it is critical to understand how the communication impacts performance in order to make the code more efficient. There are several tools available for visualizing program execution and communications on parallel systems. These tools generally provide either views which statistically summarize the entire program execution or process-centric views. However, process-centric visualizations do not scale well as the number of processes gets very large. In particular, the most common representation of parallel processes is a Gantt char t with a row for each process. As the number of processes increases, these charts can become difficult to work with and can even exceed screen resolution. We propose a new visualization approach that affords more scalability and then demonstrate it on systems running with up to 16,384 processes.

Computational mechanics analysis tools for parallel-vector supercomputers

NASA Technical Reports Server (NTRS)

Storaasli, O. O.; Nguyen, D. T.; Baddourah, M. A.; Qin, J.

1993-01-01

Computational algorithms for structural analysis on parallel-vector supercomputers are reviewed. These parallel algorithms, developed by the authors, are for the assembly of structural equations, 'out-of-core' strategies for linear equation solution, massively distributed-memory equation solution, unsymmetric equation solution, general eigen-solution, geometrically nonlinear finite element analysis, design sensitivity analysis for structural dynamics, optimization algorithm and domain decomposition. The source code for many of these algorithms is available from NASA Langley.

Chaste: A test-driven approach to software development for biological modelling

NASA Astrophysics Data System (ADS)

Pitt-Francis, Joe; Pathmanathan, Pras; Bernabeu, Miguel O.; Bordas, Rafel; Cooper, Jonathan; Fletcher, Alexander G.; Mirams, Gary R.; Murray, Philip; Osborne, James M.; Walter, Alex; Chapman, S. Jon; Garny, Alan; van Leeuwen, Ingeborg M. M.; Maini, Philip K.; Rodríguez, Blanca; Waters, Sarah L.; Whiteley, Jonathan P.; Byrne, Helen M.; Gavaghan, David J.

2009-12-01

Chaste ('Cancer, heart and soft-tissue environment') is a software library and a set of test suites for computational simulations in the domain of biology. Current functionality has arisen from modelling in the fields of cancer, cardiac physiology and soft-tissue mechanics. It is released under the LGPL 2.1 licence. Chaste has been developed using agile programming methods. The project began in 2005 when it was reasoned that the modelling of a variety of physiological phenomena required both a generic mathematical modelling framework, and a generic computational/simulation framework. The Chaste project evolved from the Integrative Biology (IB) e-Science Project, an inter-institutional project aimed at developing a suitable IT infrastructure to support physiome-level computational modelling, with a primary focus on cardiac and cancer modelling. Program summaryProgram title: Chaste Catalogue identifier: AEFD_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEFD_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: LGPL 2.1 No. of lines in distributed program, including test data, etc.: 5 407 321 No. of bytes in distributed program, including test data, etc.: 42 004 554 Distribution format: tar.gz Programming language: C++ Operating system: Unix Has the code been vectorised or parallelized?: Yes. Parallelized using MPI. RAM:<90 Megabytes for two of the scenarios described in Section 6 of the manuscript (Monodomain re-entry on a slab or Cylindrical crypt simulation). Up to 16 Gigabytes (distributed across processors) for full resolution bidomain cardiac simulation. Classification: 3. External routines: Boost, CodeSynthesis XSD, CxxTest, HDF5, METIS, MPI, PETSc, Triangle, Xerces Nature of problem: Chaste may be used for solving coupled ODE and PDE systems arising from modelling biological systems. Use of Chaste in two application areas are described in this paper: cardiac electrophysiology and intestinal crypt dynamics. Solution method: Coupled multi-physics with PDE, ODE and discrete mechanics simulation. Running time: The largest cardiac simulation described in the manuscript takes about 6 hours to run on a single 3 GHz core. See results section (Section 6) of the manuscript for discussion on parallel scaling.

Distributed File System Utilities to Manage Large DatasetsVersion 0.5

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-05-21

FileUtils provides a suite of tools to manage large datasets typically created by large parallel MPI applications. They are written in C and use standard POSIX I/Ocalls. The current suite consists of tools to copy, compare, remove, and list. The tools provide dramatic speedup over existing Linux tools, which often run as a single process.

National Centers for Environmental Prediction

Science.gov Websites

Reference List Table of Contents NCEP OPERATIONAL MODEL FORECAST GRAPHICS PARALLEL/EXPERIMENTAL MODEL Developmental Air Quality Forecasts and Verification Back to Table of Contents 2. PARALLEL/EXPERIMENTAL GRAPHICS VERIFICATION (GRID VS.OBS) WEB PAGE (NCEP EXPERIMENTAL PAGE, INTERNAL USE ONLY) Interactive web page tool for

CellML and associated tools and techniques.

PubMed

Garny, Alan; Nickerson, David P; Cooper, Jonathan; Weber dos Santos, Rodrigo; Miller, Andrew K; McKeever, Steve; Nielsen, Poul M F; Hunter, Peter J

2008-09-13

We have, in the last few years, witnessed the development and availability of an ever increasing number of computer models that describe complex biological structures and processes. The multi-scale and multi-physics nature of these models makes their development particularly challenging, not only from a biological or biophysical viewpoint but also from a mathematical and computational perspective. In addition, the issue of sharing and reusing such models has proved to be particularly problematic, with the published models often lacking information that is required to accurately reproduce the published results. The International Union of Physiological Sciences Physiome Project was launched in 1997 with the aim of tackling the aforementioned issues by providing a framework for the modelling of the human body. As part of this initiative, the specifications of the CellML mark-up language were released in 2001. Now, more than 7 years later, the time has come to assess the situation, in particular with regard to the tools and techniques that are now available to the modelling community. Thus, after introducing CellML, we review and discuss existing editors, validators, online repository, code generators and simulation environments, as well as the CellML Application Program Interface. We also address possible future directions including the need for additional mark-up languages.

Advanced semi-active engine and transmission mounts: tools for modelling, analysis, design, and tuning

NASA Astrophysics Data System (ADS)

Farjoud, Alireza; Taylor, Russell; Schumann, Eric; Schlangen, Timothy

2014-02-01

This paper is focused on modelling, design, and testing of semi-active magneto-rheological (MR) engine and transmission mounts used in the automotive industry. The purpose is to develop a complete analysis, synthesis, design, and tuning tool that reduces the need for expensive and time-consuming laboratory and field tests. A detailed mathematical model of such devices is developed using multi-physics modelling techniques for physical systems with various energy domains. The model includes all major features of an MR mount including fluid dynamics, fluid track, elastic components, decoupler, rate-dip, gas-charged chamber, MR fluid rheology, magnetic circuit, electronic driver, and control algorithm. Conventional passive hydraulic mounts can also be studied using the same mathematical model. The model is validated using standard experimental procedures. It is used for design and parametric study of mounts; effects of various geometric and material parameters on dynamic response of mounts can be studied. Additionally, this model can be used to test various control strategies to obtain best vibration isolation performance by tuning control parameters. Another benefit of this work is that nonlinear interactions between sub-components of the mount can be observed and investigated. This is not possible by using simplified linear models currently available.

Applications of colored petri net and genetic algorithms to cluster tool scheduling

NASA Astrophysics Data System (ADS)

Liu, Tung-Kuan; Kuo, Chih-Jen; Hsiao, Yung-Chin; Tsai, Jinn-Tsong; Chou, Jyh-Horng

2005-12-01

In this paper, we propose a method, which uses Coloured Petri Net (CPN) and genetic algorithm (GA) to obtain an optimal deadlock-free schedule and to solve re-entrant problem for the flexible process of the cluster tool. The process of the cluster tool for producing a wafer usually can be classified into three types: 1) sequential process, 2) parallel process, and 3) sequential parallel process. But these processes are not economical enough to produce a variety of wafers in small volume. Therefore, this paper will propose the flexible process where the operations of fabricating wafers are randomly arranged to achieve the best utilization of the cluster tool. However, the flexible process may have deadlock and re-entrant problems which can be detected by CPN. On the other hand, GAs have been applied to find the optimal schedule for many types of manufacturing processes. Therefore, we successfully integrate CPN and GAs to obtain an optimal schedule with the deadlock and re-entrant problems for the flexible process of the cluster tool.

Transputer parallel processing at NASA Lewis Research Center

NASA Technical Reports Server (NTRS)

Ellis, Graham K.

1989-01-01

The transputer parallel processing lab at NASA Lewis Research Center (LeRC) consists of 69 processors (transputers) that can be connected into various networks for use in general purpose concurrent processing applications. The main goal of the lab is to develop concurrent scientific and engineering application programs that will take advantage of the computational speed increases available on a parallel processor over the traditional sequential processor. Current research involves the development of basic programming tools. These tools will help standardize program interfaces to specific hardware by providing a set of common libraries for applications programmers. The thrust of the current effort is in developing a set of tools for graphics rendering/animation. The applications programmer currently has two options for on-screen plotting. One option can be used for static graphics displays and the other can be used for animated motion. The option for static display involves the use of 2-D graphics primitives that can be called from within an application program. These routines perform the standard 2-D geometric graphics operations in real-coordinate space as well as allowing multiple windows on a single screen.

CFD research, parallel computation and aerodynamic optimization

NASA Technical Reports Server (NTRS)

Ryan, James S.

1995-01-01

Over five years of research in Computational Fluid Dynamics and its applications are covered in this report. Using CFD as an established tool, aerodynamic optimization on parallel architectures is explored. The objective of this work is to provide better tools to vehicle designers. Submarine design requires accurate force and moment calculations in flow with thick boundary layers and large separated vortices. Low noise production is critical, so flow into the propulsor region must be predicted accurately. The High Speed Civil Transport (HSCT) has been the subject of recent work. This vehicle is to be a passenger vehicle with the capability of cutting overseas flight times by more than half. A successful design must surpass the performance of comparable planes. Fuel economy, other operational costs, environmental impact, and range must all be improved substantially. For all these reasons, improved design tools are required, and these tools must eventually integrate optimization, external aerodynamics, propulsion, structures, heat transfer and other disciplines.

A parallel approach of COFFEE objective function to multiple sequence alignment

NASA Astrophysics Data System (ADS)

Zafalon, G. F. D.; Visotaky, J. M. V.; Amorim, A. R.; Valêncio, C. R.; Neves, L. A.; de Souza, R. C. G.; Machado, J. M.

2015-09-01

The computational tools to assist genomic analyzes show even more necessary due to fast increasing of data amount available. With high computational costs of deterministic algorithms for sequence alignments, many works concentrate their efforts in the development of heuristic approaches to multiple sequence alignments. However, the selection of an approach, which offers solutions with good biological significance and feasible execution time, is a great challenge. Thus, this work aims to show the parallelization of the processing steps of MSA-GA tool using multithread paradigm in the execution of COFFEE objective function. The standard objective function implemented in the tool is the Weighted Sum of Pairs (WSP), which produces some distortions in the final alignments when sequences sets with low similarity are aligned. Then, in studies previously performed we implemented the COFFEE objective function in the tool to smooth these distortions. Although the nature of COFFEE objective function implies in the increasing of execution time, this approach presents points, which can be executed in parallel. With the improvements implemented in this work, we can verify the execution time of new approach is 24% faster than the sequential approach with COFFEE. Moreover, the COFFEE multithreaded approach is more efficient than WSP, because besides it is slightly fast, its biological results are better.

An Expert System for the Development of Efficient Parallel Code

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Chun, Robert; Jin, Hao-Qiang; Labarta, Jesus; Gimenez, Judit

2004-01-01

We have built the prototype of an expert system to assist the user in the development of efficient parallel code. The system was integrated into the parallel programming environment that is currently being developed at NASA Ames. The expert system interfaces to tools for automatic parallelization and performance analysis. It uses static program structure information and performance data in order to automatically determine causes of poor performance and to make suggestions for improvements. In this paper we give an overview of our programming environment, describe the prototype implementation of our expert system, and demonstrate its usefulness with several case studies.

Methodology Development for Passive Component Reliability Modeling in a Multi-Physics Simulation Environment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aldemir, Tunc; Denning, Richard; Catalyurek, Umit

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, suchmore » 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.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jonkman, Jason; Annoni, Jennifer; Hayman, Greg

This paper presents the development of FAST.Farm, a new multiphysics tool applicable to engineering problems in research and industry involving wind farm performance and cost optimization that is needed to address the current underperformance, failures, and expenses plaguing the wind industry. Achieving wind cost-of-energy targets - which requires improvements in wind farm performance and reliability, together with reduced uncertainty and expenditures - has been eluded by the complicated nature of the wind farm design problem, especially the sophisticated interaction between atmospheric phenomena and wake dynamics and array effects. FAST.Farm aims to balance the need for accurate modeling of the relevantmore » physics for predicting power performance and loads while maintaining low computational cost to support a highly iterative and probabilistic design process and system-wide optimization. FAST.Farm makes use of FAST to model the aero-hydro-servo-elastics of distinct turbines in the wind farm, and it is based on some of the principles of the Dynamic Wake Meandering (DWM) model, but avoids many of the limitations of existing DWM implementations.« less

Simulations of Interdigitated Electrode Interactions with Gold Nanoparticles for Impedance-Based Biosensing Applications

PubMed Central

MacKay, Scott; Hermansen, Peter; Wishart, David; Chen, Jie

2015-01-01

In this paper, we describe a point-of-care biosensor design. The uniqueness of our design is in its capability for detecting a wide variety of target biomolecules and the simplicity of nanoparticle enhanced electrical detection. The electrical properties of interdigitated electrodes (IDEs) and the mechanism for gold nanoparticle-enhanced impedance-based biosensor systems based on these electrodes are simulated using COMSOL Multiphysics software. Understanding these properties and how they can be affected is vital in designing effective biosensor devices. Simulations were used to show electrical screening develop over time for IDEs in a salt solution, as well as the electric field between individual digits of electrodes. Using these simulations, it was observed that gold nanoparticles bound closely to IDEs can lower the electric field magnitude between the digits of the electrode. The simulations are also shown to be a useful design tool in optimizing sensor function. Various different conditions, such as electrode dimensions and background ion concentrations, are shown to have a significant impact on the simulations. PMID:26364638

Measurement of the transient shielding effectiveness of shielding cabinets

NASA Astrophysics Data System (ADS)

Herlemann, H.; Koch, M.

2008-05-01

Recently, new definitions of shielding effectiveness (SE) for high-frequency and transient electromagnetic fields were introduced by Klinkenbusch (2005). Analytical results were shown for closed as well as for non closed cylindrical shields. In the present work, the shielding performance of different shielding cabinets is investigated by means of numerical simulations and measurements inside a fully anechoic chamber and a GTEM-cell. For the GTEM-cell-measurements, a downscaled model of the shielding cabinet is used. For the simulations, the numerical tools CONCEPT II and COMSOL MULTIPHYSICS were available. The numerical results agree well with the measurements. They can be used to interpret the behaviour of the shielding effectiveness of enclosures as function of frequency. From the measurement of the electric and magnetic fields with and without the enclosure in place, the electric and magnetic shielding effectiveness as well as the transient shielding effectiveness of the enclosure are calculated. The transient SE of four different shielding cabinets is determined and discussed.

The Space Weather Modeling Framework (SWMF): Models and Validation

NASA Astrophysics Data System (ADS)

Gombosi, Tamas; Toth, Gabor; Sokolov, Igor; de Zeeuw, Darren; van der Holst, Bart; Ridley, Aaron; Manchester, Ward, IV

In the last decade our group at the Center for Space Environment Modeling (CSEM) has developed the Space Weather Modeling Framework (SWMF) that efficiently couples together different models describing the interacting regions of the space environment. Many of these domain models (such as the global solar corona, the inner heliosphere or the global magneto-sphere) are based on MHD and are represented by our multiphysics code, BATS-R-US. SWMF is a powerful tool for coupling regional models describing the space environment from the solar photosphere to the bottom of the ionosphere. Presently, SWMF contains over a dozen components: the solar corona (SC), eruptive event generator (EE), inner heliosphere (IE), outer heliosphere (OH), solar energetic particles (SE), global magnetosphere (GM), inner magnetosphere (IM), radiation belts (RB), plasmasphere (PS), ionospheric electrodynamics (IE), polar wind (PW), upper atmosphere (UA) and lower atmosphere (LA). This talk will present an overview of SWMF, new results obtained with improved physics as well as some validation studies.

Industry Application ECCS / LOCA Integrated Cladding/Emergency Core Cooling System Performance: Demonstration of LOTUS-Baseline Coupled Analysis of the South Texas Plant Model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Hongbin; Szilard, Ronaldo; Epiney, Aaron

Under the auspices of the DOE LWRS Program RISMC Industry Application ECCS/LOCA, INL has engaged staff from both South Texas Project (STP) and the Texas A&M University (TAMU) to produce a generic pressurized water reactor (PWR) model including reactor core, clad/fuel design and systems thermal hydraulics based on the South Texas Project (STP) nuclear power plant, a 4-Loop Westinghouse PWR. A RISMC toolkit, named LOCA Toolkit for the U.S. (LOTUS), has been developed for use in this generic PWR plant model to assess safety margins for the proposed NRC 10 CFR 50.46c rule, Emergency Core Cooling System (ECCS) performance duringmore » LOCA. This demonstration includes coupled analysis of core design, fuel design, thermalhydraulics and systems analysis, using advanced risk analysis tools and methods to investigate a wide range of results. Within this context, a multi-physics best estimate plus uncertainty (MPBEPU) methodology framework is proposed.« less

High-resolution coupled physics solvers for analysing fine-scale nuclear reactor design problems

DOE PAGES

Mahadevan, Vijay S.; Merzari, Elia; Tautges, Timothy; ...

2014-06-30

An integrated multi-physics simulation capability for the design and analysis of current and future nuclear reactor models is being investigated, to tightly couple neutron transport and thermal-hydraulics physics under the SHARP framework. Over several years, high-fidelity, validated mono-physics solvers with proven scalability on petascale architectures have been developed independently. Based on a unified component-based architecture, these existing codes can be coupled with a mesh-data backplane and a flexible coupling-strategy-based driver suite to produce a viable tool for analysts. The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in ordermore » to reduce the overall numerical uncertainty while leveraging available computational resources. Finally, the coupling methodology and software interfaces of the framework are presented, along with verification studies on two representative fast sodium-cooled reactor demonstration problems to prove the usability of the SHARP framework.« less

Numerical modelling of needle-grid electrodes for negative surface corona charging system

NASA Astrophysics Data System (ADS)

Zhuang, Y.; Chen, G.; Rotaru, M.

2011-08-01

Surface potential decay measurement is a simple and low cost tool to examine electrical properties of insulation materials. During the corona charging stage, a needle-grid electrodes system is often used to achieve uniform charge distribution on the surface of the sample. In this paper, a model using COMSOL Multiphysics has been developed to simulate the gas discharge. A well-known hydrodynamic drift-diffusion model was used. The model consists of a set of continuity equations accounting for the movement, generation and loss of charge carriers (electrons, positive and negative ions) coupled with Poisson's equation to take into account the effect of space and surface charges on the electric field. Four models with the grid electrode in different positions and several mesh sizes are compared with a model that only has the needle electrode. The results for impulse current and surface charge density on the sample clearly show the effect of the extra grid electrode with various positions.

The Exercise: An Exercise Generator Tool for the SOURCe Project

ERIC Educational Resources Information Center

Kakoyianni-Doa, Fryni; Tziafa, Eleni; Naskos, Athanasios

2016-01-01

The Exercise, an Exercise generator in the SOURCe project, is a tool that complements the properties and functionalities of the SOURCe project, which includes the search engine for the Searchable Online French-Greek parallel corpus for the UniveRsity of Cyprus (SOURCe) (Kakoyianni-Doa & Tziafa, 2013), the PENCIL (an alignment tool)…

Software Tools for Design and Performance Evaluation of Intelligent Systems

DTIC Science & Technology

2004-08-01

Self-calibration of Three-Legged Modular Reconfigurable Parallel Robots Based on Leg-End Distance Errors,” Robotica , Vol. 19, pp. 187-198. [4...9] Lintott, A. B., and Dunlop, G. R., “Parallel Topology Robot Calibration,” Robotica . [10] Vischer, P., and Clavel, R., “Kinematic Calibration...of the Parallel Delta Robot,” Robotica , Vol. 16, pp.207- 218, 1998. [11] Joshi, S.A., and Surianarayan, A., “Calibration of a 6-DOF Cable Robot Using

Applying Parallel Processing Techniques to Tether Dynamics Simulation

NASA Technical Reports Server (NTRS)

Wells, B. Earl

1996-01-01

The focus of this research has been to determine the effectiveness of applying parallel processing techniques to a sizable real-world problem, the simulation of the dynamics associated with a tether which connects two objects in low earth orbit, and to explore the degree to which the parallelization process can be automated through the creation of new software tools. The goal has been to utilize this specific application problem as a base to develop more generally applicable techniques.

Arcmancer: Geodesics and polarized radiative transfer library

NASA Astrophysics Data System (ADS)

Pihajoki, Pauli; Mannerkoski, Matias; Nättilä, Joonas; Johansson, Peter H.

2018-05-01

Arcmancer computes geodesics and performs polarized radiative transfer in user-specified spacetimes. The library supports Riemannian and semi-Riemannian spaces of any dimension and metric; it also supports multiple simultaneous coordinate charts, embedded geometric shapes, local coordinate systems, and automatic parallel propagation. Arcmancer can be used to solve various problems in numerical geometry, such as solving the curve equation of motion using adaptive integration with configurable tolerances and differential equations along precomputed curves. It also provides support for curves with an arbitrary acceleration term and generic tools for generating ray initial conditions and performing parallel computation over the image, among other tools.

A Comparison of Curing Process-Induced Residual Stresses and Cure Shrinkage in Micro-Scale Composite Structures with Different Constitutive Laws

NASA Astrophysics Data System (ADS)

Li, Dongna; Li, Xudong; Dai, Jianfeng; Xi, Shangbin

2018-02-01

In this paper, three kinds of constitutive laws, elastic, "cure hardening instantaneously linear elastic (CHILE)" and viscoelastic law, are used to predict curing process-induced residual stress for the thermoset polymer composites. A multi-physics coupling finite element analysis (FEA) model implementing the proposed three approaches is established in COMSOL Multiphysics-Version 4.3b. The evolution of thermo-physical properties with temperature and degree of cure (DOC), which improved the accuracy of numerical simulations, and cure shrinkage are taken into account for the three models. Subsequently, these three proposed constitutive models are implemented respectively in a 3D micro-scale composite laminate structure. Compared the differences between these three numerical results, it indicates that big error in residual stress and cure shrinkage generates by elastic model, but the results calculated by the modified CHILE model are in excellent agreement with those estimated by the viscoelastic model.

Comprehensive preclinical evaluation of a multi-physics model of liver tumor radiofrequency ablation.

PubMed

Audigier, Chloé; Mansi, Tommaso; Delingette, Hervé; Rapaka, Saikiran; Passerini, Tiziano; Mihalef, Viorel; Jolly, Marie-Pierre; Pop, Raoul; Diana, Michele; Soler, Luc; Kamen, Ali; Comaniciu, Dorin; Ayache, Nicholas

2017-09-01

We aim at developing a framework for the validation of a subject-specific multi-physics model of liver tumor radiofrequency ablation (RFA). The RFA computation becomes subject specific after several levels of personalization: geometrical and biophysical (hemodynamics, heat transfer and an extended cellular necrosis model). We present a comprehensive experimental setup combining multimodal, pre- and postoperative anatomical and functional images, as well as the interventional monitoring of intra-operative signals: the temperature and delivered power. To exploit this dataset, an efficient processing pipeline is introduced, which copes with image noise, variable resolution and anisotropy. The validation study includes twelve ablations from five healthy pig livers: a mean point-to-mesh error between predicted and actual ablation extent of 5.3 ± 3.6 mm is achieved. This enables an end-to-end preclinical validation framework that considers the available dataset.

Multiphysics Simulations of Hot-Spot Initiation in Shocked Insensitive High-Explosive

NASA Astrophysics Data System (ADS)

Najjar, Fady; Howard, W. M.; Fried, L. E.

2010-11-01

Solid plastic-bonded high-explosive materials consist of crystals with micron-sized pores embedded. Under mechanical or thermal insults, these voids increase the ease of shock initiation by generating high-temperature regions during their collapse that might lead to ignition. Understanding the mechanisms of hot-spot initiation has significant research interest due to safety, reliability and development of new insensitive munitions. Multi-dimensional high-resolution meso-scale simulations are performed using the multiphysics software, ALE3D, to understand the hot-spot initiation. The Cheetah code is coupled to ALE3D, creating multi-dimensional sparse tables for the HE properties. The reaction rates were obtained from MD Quantum computations. Our current predictions showcase several interesting features regarding hot spot dynamics including the formation of a "secondary" jet. We will discuss the results obtained with hydro-thermo-chemical processes leading to ignition growth for various pore sizes and different shock pressures.

Hot-spot contributions in shocked high explosives from mesoscale ignition models

NASA Astrophysics Data System (ADS)

Levesque, G.; Vitello, P.; Howard, W. M.

2013-06-01

High explosive performance and sensitivity is strongly related to the mesoscale defect densities. Bracketing the population of mesoscale hot spots that are active in the shocked ignition of explosives is important for the development of predictive reactive flow models. By coupling a multiphysics-capable hydrodynamics code (ale3d) with a chemical kinetics solver (cheetah), we can parametrically analyze different pore sizes undergoing collapse in high pressure shock conditions with evolving physical parameter fields. Implementing first-principles based decomposition kinetics, burning hot spots are monitored, and the regimes of pore sizes that contribute significantly to burnt mass faction and those that survive thermal conduction on the time scales of ignition are elucidated. Comparisons are drawn between the thermal explosion theory and the multiphysics models for the determination of nominal pore sizes that burn significantly during ignition for the explosive 1,3,5-triamino-2,4,6-trinitrobenzene.

Analysis of Material Sample Heated by Impinging Hot Hydrogen Jet in a Non-Nuclear Tester

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Foote, John; Litchford, Ron

2006-01-01

A computational conjugate heat transfer methodology was developed and anchored with data obtained from a hot-hydrogen jet heated, non-nuclear materials tester, as a first step towards developing an efficient and accurate multiphysics, thermo-fluid computational methodology to predict environments for hypothetical solid-core, nuclear thermal engine thrust chamber. The computational methodology is based on a multidimensional, finite-volume, turbulent, chemically reacting, thermally radiating, unstructured-grid, and pressure-based formulation. The multiphysics invoked in this study include hydrogen dissociation kinetics and thermodynamics, turbulent flow, convective and thermal radiative, and conjugate heat transfers. Predicted hot hydrogen jet and material surface temperatures were compared with those of measurement. Predicted solid temperatures were compared with those obtained with a standard heat transfer code. The interrogation of physics revealed that reactions of hydrogen dissociation and recombination are highly correlated with local temperature and are necessary for accurate prediction of the hot-hydrogen jet temperature.

Comprehensive pulsed electric field (PEF) system analysis for microalgae processing.

PubMed

Buchmann, Leandro; Bloch, Robin; Mathys, Alexander

2018-06-07

Pulsed electric field (PEF) is an emerging nonthermal technique with promising applications in microalgae biorefinery concepts. In this work, the flow field in continuous PEF processing and its influencing factors were analyzed and energy input distributions in PEF treatment chambers were investigated. The results were obtained using an interdisciplinary approach that combined multiphysics simulations with ultrasonic Doppler velocity profiling (UVP) and rheological measurements of Arthrospira platensis suspensions as a case study for applications in the biobased industry. UVP enabled non-invasive validation of multiphysics simulations. A. platensis suspensions follow a non-Newtonian, shear-thinning behavior, and measurement data could be fitted with rheological functions, which were used as an input for fluid dynamics simulations. Within the present work, a comprehensive system characterization was achieved that will facilitate research in the field of PEF processing. Copyright © 2018 The Author(s). Published by Elsevier Ltd.. All rights reserved.

Multiphysics Simulation of Welding-Arc and Nozzle-Arc System: Mathematical-Model, Solution-Methodology and Validation

NASA Astrophysics Data System (ADS)

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.

Mechanical behavior simulation of MEMS-based cantilever beam using COMSOL multiphysics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Acheli, A., E-mail: aacheli@cdta.dz; Serhane, R.

This paper presents the studies of mechanical behavior of MEMS cantilever beam made of poly-silicon material, using the coupling of three application modes (plane strain, electrostatics and the moving mesh) of COMSOL Multi-physics software. The cantilevers playing a key role in Micro Electro-Mechanical Systems (MEMS) devices (switches, resonators, etc) working under potential shock. This is why they require actuation under predetermined conditions, such as electrostatic force or inertial force. In this paper, we present mechanical behavior of a cantilever actuated by an electrostatic force. In addition to the simplification of calculations, the weight of the cantilever was not taken intomore » account. Different parameters like beam displacement, electrostatics force and stress over the beam have been calculated by finite element method after having defining the geometry, the material of the cantilever model (fixed at one of ends but is free to move otherwise) and his operational space.« less

Multiphysics Model of Palladium Hydride Isotope Exchange Accounting for Higher Dimensionality

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gharagozloo, Patricia E.; Eliassi, Mehdi; Bon, Bradley Luis

2015-03-01

This report summarizes computational model developm ent and simulations results for a series of isotope exchange dynamics experiments i ncluding long and thin isothermal beds similar to the Foltz and Melius beds and a lar ger non-isothermal experiment on the NENG7 test bed. The multiphysics 2D axi-symmetr ic model simulates the temperature and pressure dependent exchange reactio n kinetics, pressure and isotope dependent stoichiometry, heat generation from the r eaction, reacting gas flow through porous media, and non-uniformities in the bed perme ability. The new model is now able to replicate the curved reaction front and asy mmetry of themore » exit gas mass fractions over time. The improved understanding of the exchange process and its dependence on the non-uniform bed properties and te mperatures in these larger systems is critical to the future design of such sy stems.« less

Progress in development of HEDP capabilities in FLASH's Unsplit Staggered Mesh MHD solver

NASA Astrophysics Data System (ADS)

Lee, D.; Xia, G.; Daley, C.; Dubey, A.; Gopal, S.; Graziani, C.; Lamb, D.; Weide, K.

2011-11-01

FLASH is a publicly available astrophysical community code designed to solve highly compressible multi-physics reactive flows. We are adding capabilities to FLASH that will make it an open science code for the academic HEDP community. Among many important numerical requirements, we consider the following features to be important components necessary to meet our goals for FLASH as an HEDP open toolset. First, we are developing computationally efficient time-stepping integration methods that overcome the stiffness that arises in the equations describing a physical problem when there are disparate time scales. To this end, we are adding two different time-stepping schemes to FLASH that relax the time step limit when diffusive effects are present: an explicit super-time-stepping algorithm (Alexiades et al. in Com. Num. Mech. Eng. 12:31-42, 1996) and a Jacobian-Free Newton-Krylov implicit formulation. These two methods will be integrated into a robust, efficient, and high-order accurate Unsplit Staggered Mesh MHD (USM) solver (Lee and Deane in J. Comput. Phys. 227, 2009). Second, we have implemented an anisotropic Spitzer-Braginskii conductivity model to treat thermal heat conduction along magnetic field lines. Finally, we are implementing the Biermann Battery term to account for spontaneous generation of magnetic fields in the presence of non-parallel temperature and density gradients.

Computational Meso-Scale Study of Representative Unit Cubes for Inert Spheres Subject to Intense Shocks

NASA Astrophysics Data System (ADS)

Stewart, Cameron; Najjar, Fady; Stewart, D. Scott; Bdzil, John

2012-11-01

Modern-engineered high explosive (HE) materials can consist of a matrix of solid, inert particles embedded into an HE charge. When this charge is detonated, intense shock waves are generated. As these intense shocks interact with the inert particles, large deformations occur in the particles while the incident shock diffracts around the particle interface. We will present results from a series of 3-D DNS of an intense shock interacting with unit-cube configurations of inert particles embedded into nitromethane. The LLNL multi-physics massively parallel hydrodynamics code ALE3D is used to carry out high-resolution (4 million nodes) simulations. Three representative unit-cube configurations are considered: primitive cubic, face-centered and body-centered cubic for two particle material types of varying impedance ratios. Previous work has only looked at in-line particles configurations. We investigate the time evolution of the unit cell configurations, vorticity being generated by the shock interaction, as well as the velocity and acceleration of the particles until they reach the quasi-steady regime. LLNL-ABS-567694. CSS was supported by a summer internship through the HEDP program at LLNL. FMN's work performed under the auspices of the U.S. Department of Energy by Lawrence Livermore National Laboratory under Contract DE-AC52-07NA27344.

A square wave is the most efficient and reliable waveform for resonant actuation of micro switches

NASA Astrophysics Data System (ADS)

Ben Sassi, S.; Khater, M. E.; Najar, F.; Abdel-Rahman, E. M.

2018-05-01

This paper investigates efficient actuation methods of shunt MEMS switches and other parallel-plate actuators. We start by formulating a multi-physics model of the micro switch, coupling the nonlinear Euler-Bernoulli beam theory with the nonlinear Reynolds equation to describe the structural and fluidic domains, respectively. The model takes into account fringing field effects as well as mid-plane stretching and squeeze film damping nonlinearities. Static analysis is undertaken using the differential quadrature method (DQM) to obtain the pull-in voltage, which is verified by means of the finite element model and validated experimentally. We develop a reduced order model employing the Galerkin method for the structural domain and DQM for the fluidic domain. The proposed waveforms are intended to be more suitable for integrated circuit standards. The dynamic response of the micro switch to harmonic, square and triangular waveforms are evaluated and compared experimentally and analytically. Low voltage actuation is obtained using dynamic pull-in with the proposed waveforms. In addition, global stability analysis carried out for the three signals shows advantages of employing the square signal as the actuation method in enhancing the performance of the micro switch in terms of actuation voltage, switching time, and sensitivity to initial conditions.

An Update on Improvements to NiCE Support for RELAP-7

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCaskey, Alex; Wojtowicz, Anna; Deyton, Jordan H.

The Multiphysics Object-Oriented Simulation Environment (MOOSE) is a framework that facilitates the development of applications that rely on finite-element analysis to solve a coupled, nonlinear system of partial differential equations. RELAP-7 represents an update to the venerable RELAP-5 simulator that is built upon this framework and attempts to model the balance-of-plant concerns in a full nuclear plant. This report details the continued support and integration of RELAP-7 and the NEAMS Integrated Computational Environment (NiCE). RELAP-7 is fully supported by the NiCE due to on-going work to tightly integrate NiCE with the MOOSE framework, and subsequently the applications built upon it.more » NiCE development throughout the first quarter of FY15 has focused on improvements, bug fixes, and feature additions to existing MOOSE-based application support. Specifically, this report will focus on improvements to the NiCE MOOSE Model Builder, the MOOSE application job launcher, and the 3D Nuclear Plant Viewer. This report also includes a comprehensive tutorial that guides RELAP-7 users through the basic NiCE workflow: from input generation and 3D Plant modeling, to massively parallel job launch and post-simulation data visualization.« less

A reliability design method for a lithium-ion battery pack considering the thermal disequilibrium in electric vehicles

NASA Astrophysics Data System (ADS)

Xia, Quan; Wang, Zili; Ren, Yi; Sun, Bo; Yang, Dezhen; Feng, Qiang

2018-05-01

With the rapid development of lithium-ion battery technology in the electric vehicle (EV) industry, the lifetime of the battery cell increases substantially; however, the reliability of the battery pack is still inadequate. Because of the complexity of the battery pack, a reliability design method for a lithium-ion battery pack considering the thermal disequilibrium is proposed in this paper based on cell redundancy. Based on this method, a three-dimensional electric-thermal-flow-coupled model, a stochastic degradation model of cells under field dynamic conditions and a multi-state system reliability model of a battery pack are established. The relationships between the multi-physics coupling model, the degradation model and the system reliability model are first constructed to analyze the reliability of the battery pack and followed by analysis examples with different redundancy strategies. By comparing the reliability of battery packs of different redundant cell numbers and configurations, several conclusions for the redundancy strategy are obtained. More notably, the reliability does not monotonically increase with the number of redundant cells for the thermal disequilibrium effects. In this work, the reliability of a 6 × 5 parallel-series configuration is the optimal system structure. In addition, the effect of the cell arrangement and cooling conditions are investigated.

Supporting 64-bit global indices in Epetra and other Trilinos packages :

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jhurani, Chetan; Austin, Travis M.; Heroux, Michael Allen

The Trilinos Project is an effort to facilitate the design, development, integration and ongoing support of mathematical software libraries within an object-oriented framework. It is intended for large-scale, complex multiphysics engineering and scientific applications [2, 4, 3]. Epetra is one of its basic packages. It provides serial and parallel linear algebra capabilities. Before Trilinos version 11.0, released in 2012, Epetra used the C++ int data-type for storing global and local indices for degrees of freedom (DOFs). Since int is typically 32-bit, this limited the largest problem size to be smaller than approximately two billion DOFs. This was true even ifmore » a distributed memory machine could handle larger problems. We have added optional support for C++ long long data-type, which is at least 64-bit wide, for global indices. To save memory, maintain the speed of memory-bound operations, and reduce further changes to the code, the local indices are still 32-bit. We document the changes required to achieve this feature and how the new functionality can be used. We also report on the lessons learned in modifying a mature and popular package from various perspectives design goals, backward compatibility, engineering decisions, C++ language features, effects on existing users and other packages, and build integration.« less

LIGHT WATER REACTOR ACCIDENT TOLERANT FUELS IRRADIATION TESTING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carmack, William Jonathan; Barrett, Kristine Eloise; Chichester, Heather Jean MacLean

2015-09-01

The purpose of Accident Tolerant Fuels (ATF) experiments is to test novel fuel and cladding concepts designed to replace the current zirconium alloy uranium dioxide (UO2) fuel system. The objective of this Research and Development (R&D) is to develop novel ATF concepts that will be able to withstand loss of active cooling in the reactor core for a considerably longer time period than the current fuel system while maintaining or improving the fuel performance during normal operations, operational transients, design basis, and beyond design basis events. It was necessary to design, analyze, and fabricate drop-in capsules to meet the requirementsmore » for testing under prototypic LWR temperatures in Idaho National Laboratory's Advanced Test Reactor (ATR). Three industry led teams and one DOE team from Oak Ridge National Laboratory provided fuel rodlet samples for their new concepts for ATR insertion in 2015. As-built projected temperature calculations were performed on the ATF capsules using the BISON fuel performance code. BISON is an application of INL’s Multi-physics Object Oriented Simulation Environment (MOOSE), which is a massively parallel finite element based framework used to solve systems of fully coupled nonlinear partial differential equations. Both 2D and 3D models were set up to examine cladding and fuel performance.« less

Unified Lambert Tool for Massively Parallel Applications in Space Situational Awareness

NASA Astrophysics Data System (ADS)

Woollands, Robyn M.; Read, Julie; Hernandez, Kevin; Probe, Austin; Junkins, John L.

2018-03-01

This paper introduces a parallel-compiled tool that combines several of our recently developed methods for solving the perturbed Lambert problem using modified Chebyshev-Picard iteration. This tool (unified Lambert tool) consists of four individual algorithms, each of which is unique and better suited for solving a particular type of orbit transfer. The first is a Keplerian Lambert solver, which is used to provide a good initial guess (warm start) for solving the perturbed problem. It is also used to determine the appropriate algorithm to call for solving the perturbed problem. The arc length or true anomaly angle spanned by the transfer trajectory is the parameter that governs the automated selection of the appropriate perturbed algorithm, and is based on the respective algorithm convergence characteristics. The second algorithm solves the perturbed Lambert problem using the modified Chebyshev-Picard iteration two-point boundary value solver. This algorithm does not require a Newton-like shooting method and is the most efficient of the perturbed solvers presented herein, however the domain of convergence is limited to about a third of an orbit and is dependent on eccentricity. The third algorithm extends the domain of convergence of the modified Chebyshev-Picard iteration two-point boundary value solver to about 90% of an orbit, through regularization with the Kustaanheimo-Stiefel transformation. This is the second most efficient of the perturbed set of algorithms. The fourth algorithm uses the method of particular solutions and the modified Chebyshev-Picard iteration initial value solver for solving multiple revolution perturbed transfers. This method does require "shooting" but differs from Newton-like shooting methods in that it does not require propagation of a state transition matrix. The unified Lambert tool makes use of the General Mission Analysis Tool and we use it to compute thousands of perturbed Lambert trajectories in parallel on the Space Situational Awareness computer cluster at the LASR Lab, Texas A&M University. We demonstrate the power of our tool by solving a highly parallel example problem, that is the generation of extremal field maps for optimal spacecraft rendezvous (and eventual orbit debris removal). In addition we demonstrate the need for including perturbative effects in simulations for satellite tracking or data association. The unified Lambert tool is ideal for but not limited to space situational awareness applications.

Sub-Second Parallel State Estimation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Yousu; Rice, Mark J.; Glaesemann, Kurt R.

This report describes the performance of Pacific Northwest National Laboratory (PNNL) sub-second parallel state estimation (PSE) tool using the utility data from the Bonneville Power Administrative (BPA) and discusses the benefits of the fast computational speed for power system applications. The test data were provided by BPA. They are two-days’ worth of hourly snapshots that include power system data and measurement sets in a commercial tool format. These data are extracted out from the commercial tool box and fed into the PSE tool. With the help of advanced solvers, the PSE tool is able to solve each BPA hourly statemore » estimation problem within one second, which is more than 10 times faster than today’s commercial tool. This improved computational performance can help increase the reliability value of state estimation in many aspects: (1) the shorter the time required for execution of state estimation, the more time remains for operators to take appropriate actions, and/or to apply automatic or manual corrective control actions. This increases the chances of arresting or mitigating the impact of cascading failures; (2) the SE can be executed multiple times within time allowance. Therefore, the robustness of SE can be enhanced by repeating the execution of the SE with adaptive adjustments, including removing bad data and/or adjusting different initial conditions to compute a better estimate within the same time as a traditional state estimator’s single estimate. There are other benefits with the sub-second SE, such as that the PSE results can potentially be used in local and/or wide-area automatic corrective control actions that are currently dependent on raw measurements to minimize the impact of bad measurements, and provides opportunities to enhance the power grid reliability and efficiency. PSE also can enable other advanced tools that rely on SE outputs and could be used to further improve operators’ actions and automated controls to mitigate effects of severe events on the grid. The power grid continues to grow and the number of measurements is increasing at an accelerated rate due to the variety of smart grid devices being introduced. A parallel state estimation implementation will have better performance than traditional, sequential state estimation by utilizing the power of high performance computing (HPC). This increased performance positions parallel state estimators as valuable tools for operating the increasingly more complex power grid.« less

Parallel digital forensics infrastructure.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liebrock, Lorie M.; Duggan, David Patrick

2009-10-01

This report documents the architecture and implementation of a Parallel Digital Forensics infrastructure. This infrastructure is necessary for supporting the design, implementation, and testing of new classes of parallel digital forensics tools. Digital Forensics has become extremely difficult with data sets of one terabyte and larger. The only way to overcome the processing time of these large sets is to identify and develop new parallel algorithms for performing the analysis. To support algorithm research, a flexible base infrastructure is required. A candidate architecture for this base infrastructure was designed, instantiated, and tested by this project, in collaboration with New Mexicomore » Tech. Previous infrastructures were not designed and built specifically for the development and testing of parallel algorithms. With the size of forensics data sets only expected to increase significantly, this type of infrastructure support is necessary for continued research in parallel digital forensics. This report documents the implementation of the parallel digital forensics (PDF) infrastructure architecture and implementation.« less

DVS-SOFTWARE: An Effective Tool for Applying Highly Parallelized Hardware To Computational Geophysics

NASA Astrophysics Data System (ADS)

Herrera, I.; Herrera, G. S.

2015-12-01

Most geophysical systems are macroscopic physical systems. The behavior prediction of such systems is carried out by means of computational models whose basic models are partial differential equations (PDEs) [1]. Due to the enormous size of the discretized version of such PDEs it is necessary to apply highly parallelized super-computers. For them, at present, the most efficient software is based on non-overlapping domain decomposition methods (DDM). However, a limiting feature of the present state-of-the-art techniques is due to the kind of discretizations used in them. Recently, I. Herrera and co-workers using 'non-overlapping discretizations' have produced the DVS-Software which overcomes this limitation [2]. The DVS-software can be applied to a great variety of geophysical problems and achieves very high parallel efficiencies (90%, or so [3]). It is therefore very suitable for effectively applying the most advanced parallel supercomputers available at present. In a parallel talk, in this AGU Fall Meeting, Graciela Herrera Z. will present how this software is being applied to advance MOD-FLOW. Key Words: Parallel Software for Geophysics, High Performance Computing, HPC, Parallel Computing, Domain Decomposition Methods (DDM)REFERENCES [1]. Herrera Ismael and George F. Pinder, Mathematical Modelling in Science and Engineering: An axiomatic approach", John Wiley, 243p., 2012. [2]. Herrera, I., de la Cruz L.M. and Rosas-Medina A. "Non Overlapping Discretization Methods for Partial, Differential Equations". NUMER METH PART D E, 30: 1427-1454, 2014, DOI 10.1002/num 21852. (Open source) [3]. Herrera, I., & Contreras Iván "An Innovative Tool for Effectively Applying Highly Parallelized Software To Problems of Elasticity". Geofísica Internacional, 2015 (In press)

Multiphysics analysis of liquid metal annular linear induction pumps: A project overview

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maidana, Carlos Omar; Nieminen, Juha E.

Liquid metal-cooled fission reactors are both moderated and cooled by a liquid metal solution. These reactors are typically very compact and they can be used in regular electric power production, for naval and space propulsion systems or in fission surface power systems for planetary exploration. The coupling between the electromagnetics and thermo-fluid mechanical phenomena observed in liquid metal thermo-magnetic systems for nuclear and space applications gives rise to complex engineering magnetohydrodynamics and numerical problems. It is known that electromagnetic pumps have a number of advantages over rotating mechanisms: absence of moving parts, low noise and vibration level, simplicity of flowmore » rate regulation, easy maintenance and so on. However, while developing annular linear induction pumps, we are faced with a significant problem of magnetohydrodynamic instability arising in the device. The complex flow behavior in this type of devices includes a time-varying Lorentz force and pressure pulsation due to the time-varying electromagnetic fields and the induced convective currents that originates from the liquid metal flow, leading to instability problems along the device geometry. The determinations of the geometry and electrical configuration of liquid metal thermo-magnetic devices give rise to a complex inverse magnetohydrodynamic field problem were techniques for global optimization should be used, magnetohydrodynamics instabilities understood –or quantified- and multiphysics models developed and analyzed. Lastly, we present a project overview as well as a few computational models developed to study liquid metal annular linear induction pumps using first principles and the a few results of our multi-physics analysis.« less

Multiphysics analysis of liquid metal annular linear induction pumps: A project overview

DOE PAGES

Maidana, Carlos Omar; Nieminen, Juha E.

2016-03-14

Liquid metal-cooled fission reactors are both moderated and cooled by a liquid metal solution. These reactors are typically very compact and they can be used in regular electric power production, for naval and space propulsion systems or in fission surface power systems for planetary exploration. The coupling between the electromagnetics and thermo-fluid mechanical phenomena observed in liquid metal thermo-magnetic systems for nuclear and space applications gives rise to complex engineering magnetohydrodynamics and numerical problems. It is known that electromagnetic pumps have a number of advantages over rotating mechanisms: absence of moving parts, low noise and vibration level, simplicity of flowmore » rate regulation, easy maintenance and so on. However, while developing annular linear induction pumps, we are faced with a significant problem of magnetohydrodynamic instability arising in the device. The complex flow behavior in this type of devices includes a time-varying Lorentz force and pressure pulsation due to the time-varying electromagnetic fields and the induced convective currents that originates from the liquid metal flow, leading to instability problems along the device geometry. The determinations of the geometry and electrical configuration of liquid metal thermo-magnetic devices give rise to a complex inverse magnetohydrodynamic field problem were techniques for global optimization should be used, magnetohydrodynamics instabilities understood –or quantified- and multiphysics models developed and analyzed. Lastly, we present a project overview as well as a few computational models developed to study liquid metal annular linear induction pumps using first principles and the a few results of our multi-physics analysis.« less

TerraFERMA: The Transparent Finite Element Rapid Model Assembler for multiphysics problems in Earth sciences

NASA Astrophysics Data System (ADS)

Wilson, Cian R.; Spiegelman, Marc; van Keken, Peter E.

2017-02-01

We introduce and describe a new software infrastructure TerraFERMA, the Transparent Finite Element Rapid Model Assembler, for the rapid and reproducible description and solution of coupled multiphysics problems. The design of TerraFERMA is driven by two computational needs in Earth sciences. The first is the need for increased flexibility in both problem description and solution strategies for coupled problems where small changes in model assumptions can lead to dramatic changes in physical behavior. The second is the need for software and models that are more transparent so that results can be verified, reproduced, and modified in a manner such that the best ideas in computation and Earth science can be more easily shared and reused. TerraFERMA leverages three advanced open-source libraries for scientific computation that provide high-level problem description (FEniCS), composable solvers for coupled multiphysics problems (PETSc), and an options handling system (SPuD) that allows the hierarchical management of all model options. TerraFERMA integrates these libraries into an interface that organizes the scientific and computational choices required in a model into a single options file from which a custom compiled application is generated and run. Because all models share the same infrastructure, models become more reusable and reproducible, while still permitting the individual researcher considerable latitude in model construction. TerraFERMA solves partial differential equations using the finite element method. It is particularly well suited for nonlinear problems with complex coupling between components. TerraFERMA is open-source and available at http://terraferma.github.io, which includes links to documentation and example input files.

FleCSPH notes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lim, Hyun; Loiseau, Julien

FleCSI is a compile-time con gurable framework designed to support multi-physics application development. As such, FleCSI provides a very general set of infrastructure design patterns that can be specialized and extended to suit the needs of a broad variety of solver and data requirements. FleCSI currently supports multi-dimensional mesh topology, geometry, and adjacency information, as well as n-dimensional hashed-tree data structures, graph partitioning interfaces, and dependency closures. FleCSI introduces a functional programming model with control, execution, and data abstractions that are consistent both with MPI and with state-of-the-art, task-based runtimes such as Legion and Charm++. The abstraction layer insulates developersmore » from the underlying runtime, while allowing support for multiple runtime systems including conventional models like asynchronous MPI. The intent is to provide developers with a concrete set of user-friendly programming tools that can be used now, while allowing exibility in choosing runtime implementations and optimization that can be applied to future architectures and runtimes. FleCSI's control and execution models provide formal nomenclature for describing poorly understood concepts such as kernels and tasks. FleCSI's data model provides a low-buy-in approach that makes it an attractive option for many application projects, as developers are not locked into particular layouts or data structure representations. FleCSI currently provides a parallel but not distributed implementation of Binary, Quad and Oct-tree topology. This implementation is base on space lling curves domain decomposition, the Morton order. The current FleCSI version requires the implementation of a driver and a specialization driver. The role of the specialization driver is to provide the data distribution. This feature is not complete in FleCSI code and we provide it. The next step will be to incorporate it directly from FleCSPH to FleCSI as we reach a good level of performance. Then the driver represent the general execution of the resolution without worrying of the data locality and communications. As FleCSI is an On-Development code the structure may change in the future and we keep track of these changes in FleCSPH.« less

Concurrency-based approaches to parallel programming

NASA Technical Reports Server (NTRS)

Kale, L.V.; Chrisochoides, N.; Kohl, J.; Yelick, K.

1995-01-01

The inevitable transition to parallel programming can be facilitated by appropriate tools, including languages and libraries. After describing the needs of applications developers, this paper presents three specific approaches aimed at development of efficient and reusable parallel software for irregular and dynamic-structured problems. A salient feature of all three approaches in their exploitation of concurrency within a processor. Benefits of individual approaches such as these can be leveraged by an interoperability environment which permits modules written using different approaches to co-exist in single applications.

A Parallel Trade Study Architecture for Design Optimization of Complex Systems

NASA Technical Reports Server (NTRS)

Kim, Hongman; Mullins, James; Ragon, Scott; Soremekun, Grant; Sobieszczanski-Sobieski, Jaroslaw

2005-01-01

Design of a successful product requires evaluating many design alternatives in a limited design cycle time. This can be achieved through leveraging design space exploration tools and available computing resources on the network. This paper presents a parallel trade study architecture to integrate trade study clients and computing resources on a network using Web services. The parallel trade study solution is demonstrated to accelerate design of experiments, genetic algorithm optimization, and a cost as an independent variable (CAIV) study for a space system application.

Terrace Layout Using a Computer Assisted System

USDA-ARS?s Scientific Manuscript database

Development of a web-based terrace design tool based on the MOTERR program is presented, along with representative layouts for conventional and parallel terrace systems. Using digital elevation maps and geographic information systems (GIS), this tool utilizes personal computers to rapidly construct ...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Harrison, Cyrus; Larsen, Matt; Brugger, Eric

Strawman is a system designed to explore the in situ visualization and analysis needs of simulation code teams running multi-physics calculations on many-core HPC architectures. It porvides rendering pipelines that can leverage both many-core CPUs and GPUs to render images of simulation meshes.

OpenMP parallelization of a gridded SWAT (SWATG)

NASA Astrophysics Data System (ADS)

Zhang, Ying; Hou, Jinliang; Cao, Yongpan; Gu, Juan; Huang, Chunlin

2017-12-01

Large-scale, long-term and high spatial resolution simulation is a common issue in environmental modeling. A Gridded Hydrologic Response Unit (HRU)-based Soil and Water Assessment Tool (SWATG) that integrates grid modeling scheme with different spatial representations also presents such problems. The time-consuming problem affects applications of very high resolution large-scale watershed modeling. The OpenMP (Open Multi-Processing) parallel application interface is integrated with SWATG (called SWATGP) to accelerate grid modeling based on the HRU level. Such parallel implementation takes better advantage of the computational power of a shared memory computer system. We conducted two experiments at multiple temporal and spatial scales of hydrological modeling using SWATG and SWATGP on a high-end server. At 500-m resolution, SWATGP was found to be up to nine times faster than SWATG in modeling over a roughly 2000 km2 watershed with 1 CPU and a 15 thread configuration. The study results demonstrate that parallel models save considerable time relative to traditional sequential simulation runs. Parallel computations of environmental models are beneficial for model applications, especially at large spatial and temporal scales and at high resolutions. The proposed SWATGP model is thus a promising tool for large-scale and high-resolution water resources research and management in addition to offering data fusion and model coupling ability.

Accelerating large-scale protein structure alignments with graphics processing units

PubMed Central

2012-01-01

Background Large-scale protein structure alignment, an indispensable tool to structural bioinformatics, poses a tremendous challenge on computational resources. To ensure structure alignment accuracy and efficiency, efforts have been made to parallelize traditional alignment algorithms in grid environments. However, these solutions are costly and of limited accessibility. Others trade alignment quality for speedup by using high-level characteristics of structure fragments for structure comparisons. Findings We present ppsAlign, a parallel protein structure Alignment framework designed and optimized to exploit the parallelism of Graphics Processing Units (GPUs). As a general-purpose GPU platform, ppsAlign could take many concurrent methods, such as TM-align and Fr-TM-align, into the parallelized algorithm design. We evaluated ppsAlign on an NVIDIA Tesla C2050 GPU card, and compared it with existing software solutions running on an AMD dual-core CPU. We observed a 36-fold speedup over TM-align, a 65-fold speedup over Fr-TM-align, and a 40-fold speedup over MAMMOTH. Conclusions ppsAlign is a high-performance protein structure alignment tool designed to tackle the computational complexity issues from protein structural data. The solution presented in this paper allows large-scale structure comparisons to be performed using massive parallel computing power of GPU. PMID:22357132

Tolerant (parallel) Programming

NASA Technical Reports Server (NTRS)

DiNucci, David C.; Bailey, David H. (Technical Monitor)

1997-01-01

In order to be truly portable, a program must be tolerant of a wide range of development and execution environments, and a parallel program is just one which must be tolerant of a very wide range. This paper first defines the term "tolerant programming", then describes many layers of tools to accomplish it. The primary focus is on F-Nets, a formal model for expressing computation as a folded partial-ordering of operations, thereby providing an architecture-independent expression of tolerant parallel algorithms. For implementing F-Nets, Cooperative Data Sharing (CDS) is a subroutine package for implementing communication efficiently in a large number of environments (e.g. shared memory and message passing). Software Cabling (SC), a very-high-level graphical programming language for building large F-Nets, possesses many of the features normally expected from today's computer languages (e.g. data abstraction, array operations). Finally, L2(sup 3) is a CASE tool which facilitates the construction, compilation, execution, and debugging of SC programs.

A parallel finite element simulator for ion transport through three-dimensional ion channel systems.

PubMed

Tu, Bin; Chen, Minxin; Xie, Yan; Zhang, Linbo; Eisenberg, Bob; Lu, Benzhuo

2013-09-15

A parallel finite element simulator, ichannel, is developed for ion transport through three-dimensional ion channel systems that consist of protein and membrane. The coordinates of heavy atoms of the protein are taken from the Protein Data Bank and the membrane is represented as a slab. The simulator contains two components: a parallel adaptive finite element solver for a set of Poisson-Nernst-Planck (PNP) equations that describe the electrodiffusion process of ion transport, and a mesh generation tool chain for ion channel systems, which is an essential component for the finite element computations. The finite element method has advantages in modeling irregular geometries and complex boundary conditions. We have built a tool chain to get the surface and volume mesh for ion channel systems, which consists of a set of mesh generation tools. The adaptive finite element solver in our simulator is implemented using the parallel adaptive finite element package Parallel Hierarchical Grid (PHG) developed by one of the authors, which provides the capability of doing large scale parallel computations with high parallel efficiency and the flexibility of choosing high order elements to achieve high order accuracy. The simulator is applied to a real transmembrane protein, the gramicidin A (gA) channel protein, to calculate the electrostatic potential, ion concentrations and I - V curve, with which both primitive and transformed PNP equations are studied and their numerical performances are compared. To further validate the method, we also apply the simulator to two other ion channel systems, the voltage dependent anion channel (VDAC) and α-Hemolysin (α-HL). The simulation results agree well with Brownian dynamics (BD) simulation results and experimental results. Moreover, because ionic finite size effects can be included in PNP model now, we also perform simulations using a size-modified PNP (SMPNP) model on VDAC and α-HL. It is shown that the size effects in SMPNP can effectively lead to reduced current in the channel, and the results are closer to BD simulation results. Copyright © 2013 Wiley Periodicals, Inc.

A Parallel Framework with Block Matrices of a Discrete Fourier Transform for Vector-Valued Discrete-Time Signals.

PubMed

Soto-Quiros, Pablo

2015-01-01

This paper presents a parallel implementation of a kind of discrete Fourier transform (DFT): the vector-valued DFT. The vector-valued DFT is a novel tool to analyze the spectra of vector-valued discrete-time signals. This parallel implementation is developed in terms of a mathematical framework with a set of block matrix operations. These block matrix operations contribute to analysis, design, and implementation of parallel algorithms in multicore processors. In this work, an implementation and experimental investigation of the mathematical framework are performed using MATLAB with the Parallel Computing Toolbox. We found that there is advantage to use multicore processors and a parallel computing environment to minimize the high execution time. Additionally, speedup increases when the number of logical processors and length of the signal increase.

Engineering on-chip nanoporous gold material libraries via precision photothermal treatment

NASA Astrophysics Data System (ADS)

Chapman, Christopher A. R.; Wang, Ling; Biener, Juergen; Seker, Erkin; Biener, Monika M.; Matthews, Manyalibo J.

2015-12-01

Libraries of nanostructured materials on a single chip are a promising platform for high throughput and combinatorial studies of structure-property relationships in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material specifically suited for such studies because of its self-similar thermally induced coarsening behavior. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Here, laser micro-processing offers an attractive solution to this problem by providing a means to apply energy with high spatial and temporal resolution. In the present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and thermal conductivity of the supporting substrate on the local np-Au film temperatures during photothermal annealing. Based on these results we discuss the mechanisms by which the np-Au network is coarsened. Thermal transport simulations predict that continuous-wave mode laser irradiation of np-Au thin films on a silicon substrate supports the widest range of morphologies that can be created through photothermal annealing of np-Au. Using the guidance provided by simulations, we successfully fabricate an on-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in the parallel study of structure-property relationships.Libraries of nanostructured materials on a single chip are a promising platform for high throughput and combinatorial studies of structure-property relationships in the fields of physics and biology. Nanoporous gold (np-Au), produced by an alloy corrosion process, is a nanostructured material specifically suited for such studies because of its self-similar thermally induced coarsening behavior. However, traditional heat application techniques for the modification of np-Au are bulk processes that cannot be used to generate a library of different pore sizes on a single chip. Here, laser micro-processing offers an attractive solution to this problem by providing a means to apply energy with high spatial and temporal resolution. In the present study we use finite element multiphysics simulations to predict the effects of laser mode (continuous-wave vs. pulsed) and thermal conductivity of the supporting substrate on the local np-Au film temperatures during photothermal annealing. Based on these results we discuss the mechanisms by which the np-Au network is coarsened. Thermal transport simulations predict that continuous-wave mode laser irradiation of np-Au thin films on a silicon substrate supports the widest range of morphologies that can be created through photothermal annealing of np-Au. Using the guidance provided by simulations, we successfully fabricate an on-chip material library consisting of 81 np-Au samples of 9 different morphologies for use in the parallel study of structure-property relationships. Electronic supplementary information (ESI) available: Details of sample preparation, fabrication of material libraries, as well as further analysis and supporting scanning electron micrographs can be found in ESI. See DOI: 10.1039/c5nr04580k

Access and visualization using clusters and other parallel computers

NASA Technical Reports Server (NTRS)

Katz, Daniel S.; Bergou, Attila; Berriman, Bruce; Block, Gary; Collier, Jim; Curkendall, Dave; Good, John; Husman, Laura; Jacob, Joe; Laity, Anastasia;

Experiences with hypercube operating system instrumentation

NASA Technical Reports Server (NTRS)

Reed, Daniel A.; Rudolph, David C.

1989-01-01

The difficulties in conceptualizing the interactions among a large number of processors make it difficult both to identify the sources of inefficiencies and to determine how a parallel program could be made more efficient. This paper describes an instrumentation system that can trace the execution of distributed memory parallel programs by recording the occurrence of parallel program events. The resulting event traces can be used to compile summary statistics that provide a global view of program performance. In addition, visualization tools permit the graphic display of event traces. Visual presentation of performance data is particularly useful, indeed, necessary for large-scale parallel computers; the enormous volume of performance data mandates visual display.

Checkpoint-Restart in User Space

DOE Office of Scientific and Technical Information (OSTI.GOV)

CRUISE implements a user-space file system that stores data in main memory and transparently spills over to other storage, like local flash memory or the parallel file system, as needed. CRUISE also exposes file contents fo remote direct memory access, allowing external tools to copy files to the parallel file system in the background with reduced CPU interruption.

CMOS VLSI Layout and Verification of a SIMD Computer

NASA Technical Reports Server (NTRS)

Zheng, Jianqing

1996-01-01

A CMOS VLSI layout and verification of a 3 x 3 processor parallel computer has been completed. The layout was done using the MAGIC tool and the verification using HSPICE. Suggestions for expanding the computer into a million processor network are presented. Many problems that might be encountered when implementing a massively parallel computer are discussed.

Implementation of a parallel unstructured Euler solver on shared and distributed memory architectures

NASA Technical Reports Server (NTRS)

Mavriplis, D. J.; Das, Raja; Saltz, Joel; Vermeland, R. E.

1992-01-01

An efficient three dimensional unstructured Euler solver is parallelized on a Cray Y-MP C90 shared memory computer and on an Intel Touchstone Delta distributed memory computer. This paper relates the experiences gained and describes the software tools and hardware used in this study. Performance comparisons between two differing architectures are made.

Capabilities of Fully Parallelized MHD Stability Code MARS

NASA Astrophysics Data System (ADS)

Svidzinski, Vladimir; Galkin, Sergei; Kim, Jin-Soo; Liu, Yueqiang

2016-10-01

Results of full parallelization of the plasma stability code MARS will be reported. MARS calculates eigenmodes in 2D axisymmetric toroidal equilibria in MHD-kinetic plasma models. Parallel version of MARS, named PMARS, has been recently developed at FAR-TECH. Parallelized MARS is an efficient tool for simulation of MHD instabilities with low, intermediate and high toroidal mode numbers within both fluid and kinetic plasma models, implemented in MARS. Parallelization of the code included parallelization of the construction of the matrix for the eigenvalue problem and parallelization of the inverse vector iterations algorithm, implemented in MARS for the solution of the formulated eigenvalue problem. Construction of the matrix is parallelized by distributing the load among processors assigned to different magnetic surfaces. Parallelization of the solution of the eigenvalue problem is made by repeating steps of the MARS algorithm using parallel libraries and procedures. Parallelized MARS is capable of calculating eigenmodes with significantly increased spatial resolution: up to 5,000 adapted radial grid points with up to 500 poloidal harmonics. Such resolution is sufficient for simulation of kink, tearing and peeling-ballooning instabilities with physically relevant parameters. Work is supported by the U.S. DOE SBIR program.

Computer-Aided Parallelizer and Optimizer

NASA Technical Reports Server (NTRS)

Jin, Haoqiang

2011-01-01

The Computer-Aided Parallelizer and Optimizer (CAPO) automates the insertion of compiler directives (see figure) to facilitate parallel processing on Shared Memory Parallel (SMP) machines. While CAPO currently is integrated seamlessly into CAPTools (developed at the University of Greenwich, now marketed as ParaWise), CAPO was independently developed at Ames Research Center as one of the components for the Legacy Code Modernization (LCM) project. The current version takes serial FORTRAN programs, performs interprocedural data dependence analysis, and generates OpenMP directives. Due to the widely supported OpenMP standard, the generated OpenMP codes have the potential to run on a wide range of SMP machines. CAPO relies on accurate interprocedural data dependence information currently provided by CAPTools. Compiler directives are generated through identification of parallel loops in the outermost level, construction of parallel regions around parallel loops and optimization of parallel regions, and insertion of directives with automatic identification of private, reduction, induction, and shared variables. Attempts also have been made to identify potential pipeline parallelism (implemented with point-to-point synchronization). Although directives are generated automatically, user interaction with the tool is still important for producing good parallel codes. A comprehensive graphical user interface is included for users to interact with the parallelization process.

Reactive Transport Modeling of Induced Calcite Precipitation Reaction Fronts in Porous Media Using A Parallel, Fully Coupled, Fully Implicit Approach

NASA Astrophysics Data System (ADS)

Guo, L.; Huang, H.; Gaston, D.; Redden, G. D.; Fox, D. T.; Fujita, Y.

2010-12-01

Inducing mineral precipitation in the subsurface is one potential strategy for immobilizing trace metal and radionuclide contaminants. Generating mineral precipitates in situ can be achieved by manipulating chemical conditions, typically through injection or in situ generation of reactants. How these reactants transport, mix and react within the medium controls the spatial distribution and composition of the resulting mineral phases. Multiple processes, including fluid flow, dispersive/diffusive transport of reactants, biogeochemical reactions and changes in porosity-permeability, are tightly coupled over a number of scales. Numerical modeling can be used to investigate the nonlinear coupling effects of these processes which are quite challenging to explore experimentally. Many subsurface reactive transport simulators employ a de-coupled or operator-splitting approach where transport equations and batch chemistry reactions are solved sequentially. However, such an approach has limited applicability for biogeochemical systems with fast kinetics and strong coupling between chemical reactions and medium properties. A massively parallel, fully coupled, fully implicit Reactive Transport simulator (referred to as “RAT”) based on a parallel multi-physics object-oriented simulation framework (MOOSE) has been developed at the Idaho National Laboratory. Within this simulator, systems of transport and reaction equations can be solved simultaneously in a fully coupled, fully implicit manner using the Jacobian Free Newton-Krylov (JFNK) method with additional advanced computing capabilities such as (1) physics-based preconditioning for solution convergence acceleration, (2) massively parallel computing and scalability, and (3) adaptive mesh refinements for 2D and 3D structured and unstructured mesh. The simulator was first tested against analytical solutions, then applied to simulating induced calcium carbonate mineral precipitation in 1D columns and 2D flow cells as analogs to homogeneous and heterogeneous porous media, respectively. In 1D columns, calcium carbonate mineral precipitation was driven by urea hydrolysis catalyzed by urease enzyme, and in 2D flow cells, calcium carbonate mineral forming reactants were injected sequentially, forming migrating reaction fronts that are typically highly nonuniform. The RAT simulation results for the spatial and temporal distributions of precipitates, reaction rates and major species in the system, and also for changes in porosity and permeability, were compared to both laboratory experimental data and computational results obtained using other reactive transport simulators. The comparisons demonstrate the ability of RAT to simulate complex nonlinear systems and the advantages of fully coupled approaches, over de-coupled methods, for accurate simulation of complex, dynamic processes such as engineered mineral precipitation in subsurface environments.

Multiphysics Object-Oriented Simulation Environment (MOOSE)

ScienceCinema

None

2017-12-09

Nuclear reactor operators can expand safety margins with more precise information about how materials behave inside operating reactors. INL's new simulation platform makes such studies easier & more informative by letting researchers "plug-n-play" their mathematical models, skipping years of computer code development.

LLNL contributions to ANL Report ANL/NE-16/6 "Sharp User Manual"

DOE Office of Scientific and Technical Information (OSTI.GOV)

Solberg, J. M.

Diablo is a Multiphysics implicit finite element code with an emphasis on coupled structural/thermal analysis. In the SHARP framework, it is used as the structural solver, and may also be used as the mesh smoother.

Clock Agreement Among Parallel Supercomputer Nodes

DOE Data Explorer

Jones, Terry R.; Koenig, Gregory A.

2014-04-30

This dataset presents measurements that quantify the clock synchronization time-agreement characteristics among several high performance computers including the current world's most powerful machine for open science, the U.S. Department of Energy's Titan machine sited at Oak Ridge National Laboratory. These ultra-fast machines derive much of their computational capability from extreme node counts (over 18000 nodes in the case of the Titan machine). Time-agreement is commonly utilized by parallel programming applications and tools, distributed programming application and tools, and system software. Our time-agreement measurements detail the degree of time variance between nodes and how that variance changes over time. The dataset includes empirical measurements and the accompanying spreadsheets.

On Designing Multicore-Aware Simulators for Systems Biology Endowed with OnLine Statistics

PubMed Central

Calcagno, Cristina; Coppo, Mario

2014-01-01

The paper arguments are on enabling methodologies for the design of a fully parallel, online, interactive tool aiming to support the bioinformatics scientists .In particular, the features of these methodologies, supported by the FastFlow parallel programming framework, are shown on a simulation tool to perform the modeling, the tuning, and the sensitivity analysis of stochastic biological models. A stochastic simulation needs thousands of independent simulation trajectories turning into big data that should be analysed by statistic and data mining tools. In the considered approach the two stages are pipelined in such a way that the simulation stage streams out the partial results of all simulation trajectories to the analysis stage that immediately produces a partial result. The simulation-analysis workflow is validated for performance and effectiveness of the online analysis in capturing biological systems behavior on a multicore platform and representative proof-of-concept biological systems. The exploited methodologies include pattern-based parallel programming and data streaming that provide key features to the software designers such as performance portability and efficient in-memory (big) data management and movement. Two paradigmatic classes of biological systems exhibiting multistable and oscillatory behavior are used as a testbed. PMID:25050327

On designing multicore-aware simulators for systems biology endowed with OnLine statistics.

PubMed

Aldinucci, Marco; Calcagno, Cristina; Coppo, Mario; Damiani, Ferruccio; Drocco, Maurizio; Sciacca, Eva; Spinella, Salvatore; Torquati, Massimo; Troina, Angelo

2014-01-01

The paper arguments are on enabling methodologies for the design of a fully parallel, online, interactive tool aiming to support the bioinformatics scientists .In particular, the features of these methodologies, supported by the FastFlow parallel programming framework, are shown on a simulation tool to perform the modeling, the tuning, and the sensitivity analysis of stochastic biological models. A stochastic simulation needs thousands of independent simulation trajectories turning into big data that should be analysed by statistic and data mining tools. In the considered approach the two stages are pipelined in such a way that the simulation stage streams out the partial results of all simulation trajectories to the analysis stage that immediately produces a partial result. The simulation-analysis workflow is validated for performance and effectiveness of the online analysis in capturing biological systems behavior on a multicore platform and representative proof-of-concept biological systems. The exploited methodologies include pattern-based parallel programming and data streaming that provide key features to the software designers such as performance portability and efficient in-memory (big) data management and movement. Two paradigmatic classes of biological systems exhibiting multistable and oscillatory behavior are used as a testbed.

Integration of tools for the Design and Assessment of High-Performance, Highly Reliable Computing Systems (DAHPHRS), phase 1

NASA Technical Reports Server (NTRS)

Scheper, C.; Baker, R.; Frank, G.; Yalamanchili, S.; Gray, G.

1992-01-01

Systems for Space Defense Initiative (SDI) space applications typically require both high performance and very high reliability. These requirements present the systems engineer evaluating such systems with the extremely difficult problem of conducting performance and reliability trade-offs over large design spaces. A controlled development process supported by appropriate automated tools must be used to assure that the system will meet design objectives. This report describes an investigation of methods, tools, and techniques necessary to support performance and reliability modeling for SDI systems development. Models of the JPL Hypercubes, the Encore Multimax, and the C.S. Draper Lab Fault-Tolerant Parallel Processor (FTPP) parallel-computing architectures using candidate SDI weapons-to-target assignment algorithms as workloads were built and analyzed as a means of identifying the necessary system models, how the models interact, and what experiments and analyses should be performed. As a result of this effort, weaknesses in the existing methods and tools were revealed and capabilities that will be required for both individual tools and an integrated toolset were identified.

Parallel and serial computing tools for testing single-locus and epistatic SNP effects of quantitative traits in genome-wide association studies

PubMed Central

Ma, Li; Runesha, H Birali; Dvorkin, Daniel; Garbe, John R; Da, Yang

2008-01-01

Background Genome-wide association studies (GWAS) using single nucleotide polymorphism (SNP) markers provide opportunities to detect epistatic SNPs associated with quantitative traits and to detect the exact mode of an epistasis effect. Computational difficulty is the main bottleneck for epistasis testing in large scale GWAS. Results The EPISNPmpi and EPISNP computer programs were developed for testing single-locus and epistatic SNP effects on quantitative traits in GWAS, including tests of three single-locus effects for each SNP (SNP genotypic effect, additive and dominance effects) and five epistasis effects for each pair of SNPs (two-locus interaction, additive × additive, additive × dominance, dominance × additive, and dominance × dominance) based on the extended Kempthorne model. EPISNPmpi is the parallel computing program for epistasis testing in large scale GWAS and achieved excellent scalability for large scale analysis and portability for various parallel computing platforms. EPISNP is the serial computing program based on the EPISNPmpi code for epistasis testing in small scale GWAS using commonly available operating systems and computer hardware. Three serial computing utility programs were developed for graphical viewing of test results and epistasis networks, and for estimating CPU time and disk space requirements. Conclusion The EPISNPmpi parallel computing program provides an effective computing tool for epistasis testing in large scale GWAS, and the epiSNP serial computing programs are convenient tools for epistasis analysis in small scale GWAS using commonly available computer hardware. PMID:18644146

Vipie: web pipeline for parallel characterization of viral populations from multiple NGS samples.

PubMed

Lin, Jake; Kramna, Lenka; Autio, Reija; Hyöty, Heikki; Nykter, Matti; Cinek, Ondrej

2017-05-15

Next generation sequencing (NGS) technology allows laboratories to investigate virome composition in clinical and environmental samples in a culture-independent way. There is a need for bioinformatic tools capable of parallel processing of virome sequencing data by exactly identical methods: this is especially important in studies of multifactorial diseases, or in parallel comparison of laboratory protocols. We have developed a web-based application allowing direct upload of sequences from multiple virome samples using custom parameters. The samples are then processed in parallel using an identical protocol, and can be easily reanalyzed. The pipeline performs de-novo assembly, taxonomic classification of viruses as well as sample analyses based on user-defined grouping categories. Tables of virus abundance are produced from cross-validation by remapping the sequencing reads to a union of all observed reference viruses. In addition, read sets and reports are created after processing unmapped reads against known human and bacterial ribosome references. Secured interactive results are dynamically plotted with population and diversity charts, clustered heatmaps and a sortable and searchable abundance table. The Vipie web application is a unique tool for multi-sample metagenomic analysis of viral data, producing searchable hits tables, interactive population maps, alpha diversity measures and clustered heatmaps that are grouped in applicable custom sample categories. Known references such as human genome and bacterial ribosomal genes are optionally removed from unmapped ('dark matter') reads. Secured results are accessible and shareable on modern browsers. Vipie is a freely available web-based tool whose code is open source.

A Parallel Saturation Algorithm on Shared Memory Architectures

NASA Technical Reports Server (NTRS)

Ezekiel, Jonathan; Siminiceanu

2007-01-01

Symbolic state-space generators are notoriously hard to parallelize. However, the Saturation algorithm implemented in the SMART verification tool differs from other sequential symbolic state-space generators in that it exploits the locality of ring events in asynchronous system models. This paper explores whether event locality can be utilized to efficiently parallelize Saturation on shared-memory architectures. Conceptually, we propose to parallelize the ring of events within a decision diagram node, which is technically realized via a thread pool. We discuss the challenges involved in our parallel design and conduct experimental studies on its prototypical implementation. On a dual-processor dual core PC, our studies show speed-ups for several example models, e.g., of up to 50% for a Kanban model, when compared to running our algorithm only on a single core.

Distributed and parallel Ada and the Ada 9X recommendations

NASA Technical Reports Server (NTRS)

Volz, Richard A.; Goldsack, Stephen J.; Theriault, R.; Waldrop, Raymond S.; Holzbacher-Valero, A. A.

1992-01-01

Recently, the DoD has sponsored work towards a new version of Ada, intended to support the construction of distributed systems. The revised version, often called Ada 9X, will become the new standard sometimes in the 1990s. It is intended that Ada 9X should provide language features giving limited support for distributed system construction. The requirements for such features are given. Many of the most advanced computer applications involve embedded systems that are comprised of parallel processors or networks of distributed computers. If Ada is to become the widely adopted language envisioned by many, it is essential that suitable compilers and tools be available to facilitate the creation of distributed and parallel Ada programs for these applications. The major languages issues impacting distributed and parallel programming are reviewed, and some principles upon which distributed/parallel language systems should be built are suggested. Based upon these, alternative language concepts for distributed/parallel programming are analyzed.

Parallel programming with Easy Java Simulations

NASA Astrophysics Data System (ADS)

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.

Use Computer-Aided Tools to Parallelize Large CFD Applications

NASA Technical Reports Server (NTRS)

Jin, H.; Frumkin, M.; Yan, J.

2000-01-01

Porting applications to high performance parallel computers is always a challenging task. It is time consuming and costly. With rapid progressing in hardware architectures and increasing complexity of real applications in recent years, the problem becomes even more sever. Today, scalability and high performance are mostly involving handwritten parallel programs using message-passing libraries (e.g. MPI). However, this process is very difficult and often error-prone. The recent reemergence of shared memory parallel (SMP) architectures, such as the cache coherent Non-Uniform Memory Access (ccNUMA) architecture used in the SGI Origin 2000, show good prospects for scaling beyond hundreds of processors. Programming on an SMP is simplified by working in a globally accessible address space. The user can supply compiler directives, such as OpenMP, to parallelize the code. As an industry standard for portable implementation of parallel programs for SMPs, OpenMP is a set of compiler directives and callable runtime library routines that extend Fortran, C and C++ to express shared memory parallelism. It promises an incremental path for parallel conversion of existing software, as well as scalability and performance for a complete rewrite or an entirely new development. Perhaps the main disadvantage of programming with directives is that inserted directives may not necessarily enhance performance. In the worst cases, it can create erroneous results. While vendors have provided tools to perform error-checking and profiling, automation in directive insertion is very limited and often failed on large programs, primarily due to the lack of a thorough enough data dependence analysis. To overcome the deficiency, we have developed a toolkit, CAPO, to automatically insert OpenMP directives in Fortran programs and apply certain degrees of optimization. CAPO is aimed at taking advantage of detailed inter-procedural dependence analysis provided by CAPTools, developed by the University of Greenwich, to reduce potential errors made by users. Earlier tests on NAS Benchmarks and ARC3D have demonstrated good success of this tool. In this study, we have applied CAPO to parallelize three large applications in the area of computational fluid dynamics (CFD): OVERFLOW, TLNS3D and INS3D. These codes are widely used for solving Navier-Stokes equations with complicated boundary conditions and turbulence model in multiple zones. Each one comprises of from 50K to 1,00k lines of FORTRAN77. As an example, CAPO took 77 hours to complete the data dependence analysis of OVERFLOW on a workstation (SGI, 175MHz, R10K processor). A fair amount of effort was spent on correcting false dependencies due to lack of necessary knowledge during the analysis. Even so, CAPO provides an easy way for user to interact with the parallelization process. The OpenMP version was generated within a day after the analysis was completed. Due to sequential algorithms involved, code sections in TLNS3D and INS3D need to be restructured by hand to produce more efficient parallel codes. An included figure shows preliminary test results of the generated OVERFLOW with several test cases in single zone. The MPI data points for the small test case were taken from a handcoded MPI version. As we can see, CAPO's version has achieved 18 fold speed up on 32 nodes of the SGI O2K. For the small test case, it outperformed the MPI version. These results are very encouraging, but further work is needed. For example, although CAPO attempts to place directives on the outer- most parallel loops in an interprocedural framework, it does not insert directives based on the best manual strategy. In particular, it lacks the support of parallelization at the multi-zone level. Future work will emphasize on the development of methodology to work in a multi-zone level and with a hybrid approach. Development of tools to perform more complicated code transformation is also needed.

PRAIS: Distributed, real-time knowledge-based systems made easy

NASA Technical Reports Server (NTRS)

Goldstein, David G.

1990-01-01

This paper discusses an architecture for real-time, distributed (parallel) knowledge-based systems called the Parallel Real-time Artificial Intelligence System (PRAIS). PRAIS strives for transparently parallelizing production (rule-based) systems, even when under real-time constraints. PRAIS accomplishes these goals by incorporating a dynamic task scheduler, operating system extensions for fact handling, and message-passing among multiple copies of CLIPS executing on a virtual blackboard. This distributed knowledge-based system tool uses the portability of CLIPS and common message-passing protocols to operate over a heterogeneous network of processors.

Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications

NASA Technical Reports Server (NTRS)

OKeefe, Matthew (Editor); Kerr, Christopher L. (Editor)

1998-01-01

This report contains the abstracts and technical papers from the Second International Workshop on Software Engineering and Code Design in Parallel Meteorological and Oceanographic Applications, held June 15-18, 1998, in Scottsdale, Arizona. The purpose of the workshop is to bring together software developers in meteorology and oceanography to discuss software engineering and code design issues for parallel architectures, including Massively Parallel Processors (MPP's), Parallel Vector Processors (PVP's), Symmetric Multi-Processors (SMP's), Distributed Shared Memory (DSM) multi-processors, and clusters. Issues to be discussed include: (1) code architectures for current parallel models, including basic data structures, storage allocation, variable naming conventions, coding rules and styles, i/o and pre/post-processing of data; (2) designing modular code; (3) load balancing and domain decomposition; (4) techniques that exploit parallelism efficiently yet hide the machine-related details from the programmer; (5) tools for making the programmer more productive; and (6) the proliferation of programming models (F--, OpenMP, MPI, and HPF).

Oscillation-Mark Formation and Liquid-Slag Consumption in Continuous Casting Mold

NASA Astrophysics Data System (ADS)

Yang, Jie; Meng, Xiangning; Wang, Ning; Zhu, Miaoyong

2017-04-01

Traditional understanding on the complex multiphysics phenomenon of the meniscus in the oscillating mold for continuously cast steel, including oscillation-mark formation and liquid-slag consumption, has never considered the shape influence of the flux channel between the mold wall and the solidifying shell surface. Based on the reciprocating oscillation of mold, this study was carried out to calculate theoretically the periodic pressure and the liquid-slag layer thickness in the flux channel for the upper and the lower meniscus that possess different shapes in combination with a transient equilibrium profile of the flux channel as well as the sinusoidal and the nonsinusoidal oscillation modes of mold. The effect of flux channel shape on the multiphysics phenomenon in the meniscus was determined by the physical oscillation simulation by using an experimental cold model mold. The results show that the shape difference between the upper and the lower meniscus leads to the opposite direction of pressure in the flux channel. The pressure in the opposite direction plays a respective role in oscillation-mark formation and liquid-slag consumption in an oscillation cycle of mold, and thus, it makes a new mechanism for explaining the multiphysics phenomenon in the meniscus. The oscillation mark is initially formed by the rapid increase of positive channel pressure in the upper meniscus, and most of the liquid slag is infiltrated into the flux channel by the negative channel pressure in the lower meniscus from the end of a positive strip time to the beginning of the next positive strip time, including the negative strip time in between. Furthermore, the physical characteristics of the lubrication behavior in the meniscus are summarized, including liquid-slag infiltration, solidifying shell deformation, and the thickness change of the liquid-slag layer.

Multiphysics phase field modeling of hydrogen diffusion and delta-hydride precipitation in alpha-zirconium

NASA Astrophysics Data System (ADS)

Jokisaari, Andrea M.

Hydride precipitation in zirconium is a significant factor limiting the lifetime of nuclear fuel cladding, because hydride microstructures play a key role in the degradation of fuel cladding. However, the behavior of hydrogen in zirconium has typically been modeled using mean field approaches, which do not consider microstructural evolution. This thesis describes a quantitative microstructural evolution model for the alpha-zirconium/delta-hydride system and the associated numerical methods and algorithms that were developed. The multiphysics, phase field-based model incorporates CALPHAD free energy descriptions, linear elastic solid mechanics, and classical nucleation theory. A flexible simulation software implementing the model, Hyrax, is built on the Multiphysics Object Oriented Simulation Environment (MOOSE) finite element framework. Hyrax is open-source and freely available; moreover, the numerical methods and algorithms that have been developed are generalizable to other systems. The algorithms are described in detail, and verification studies for each are discussed. In addition, analyses of the sensitivity of the simulation results to the choice of numerical parameters are presented. For example, threshold values for the CALPHAD free energy algorithm and the use of mesh and time adaptivity when employing the nucleation algorithm are studied. Furthermore, preliminary insights into the nucleation behavior of delta-hydrides are described. These include a) the sensitivities of the nucleation rate to temperature, interfacial energy, composition and elastic energy, b) the spatial variation of the nucleation rate around a single precipitate, and c) the effect of interfacial energy and nucleation rate on the precipitate microstructure. Finally, several avenues for future work are discussed. Topics encompass the terminal solid solubility hysteresis of hydrogen in zirconium and the effects of the alpha/delta interfacial energy, as well as thermodiffusion, plasticity, and irradiation, which are not yet accounted for in the model.

Integrated Network Decompositions and Dynamic Programming for Graph Optimization (INDDGO)

DOE Office of Scientific and Technical Information (OSTI.GOV)

The INDDGO software package offers a set of tools for finding exact solutions to graph optimization problems via tree decompositions and dynamic programming algorithms. Currently the framework offers serial and parallel (distributed memory) algorithms for finding tree decompositions and solving the maximum weighted independent set problem. The parallel dynamic programming algorithm is implemented on top of the MADNESS task-based runtime.

A Knowledge-Based Approach for Item Exposure Control in Computerized Adaptive Testing

ERIC Educational Resources Information Center

Doong, Shing H.

2009-01-01

The purpose of this study is to investigate a functional relation between item exposure parameters (IEPs) and item parameters (IPs) over parallel pools. This functional relation is approximated by a well-known tool in machine learning. Let P and Q be parallel item pools and suppose IEPs for P have been obtained via a Sympson and Hetter-type…

Software Issues at the User Interface

DTIC Science & Technology

1991-05-01

successful integration of parallel computers into mainstream scientific computing. Clearly a compiler is the most important software tool available to a...Computer Science University of Colorado Boulder, CO 80309 ABSTRACT We review software issues that are critical to the successful integration of parallel...The development of an optimizing compiler of this quality, addressing communicaton instructions as well as computational instructions is a major

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koniges, A.E.

The author describes the new T3D parallel computer at NERSC. The adaptive mesh ICF3D code is one of the current applications being ported and developed for use on the T3D. It has been stressed in other papers in this proceedings that the development environment and tools available on the parallel computer is similar to any planned for the future including networks of workstations.

Accuracy of Revised and Traditional Parallel Analyses for Assessing Dimensionality with Binary Data

ERIC Educational Resources Information Center

Green, Samuel B.; Redell, Nickalus; Thompson, Marilyn S.; Levy, Roy

2016-01-01

Parallel analysis (PA) is a useful empirical tool for assessing the number of factors in exploratory factor analysis. On conceptual and empirical grounds, we argue for a revision to PA that makes it more consistent with hypothesis testing. Using Monte Carlo methods, we evaluated the relative accuracy of the revised PA (R-PA) and traditional PA…

Parallel processing implementation for the coupled transport of photons and electrons using OpenMP

NASA Astrophysics Data System (ADS)

Doerner, Edgardo

2016-05-01

In this work the use of OpenMP to implement the parallel processing of the Monte Carlo (MC) simulation of the coupled transport for photons and electrons is presented. This implementation was carried out using a modified EGSnrc platform which enables the use of the Microsoft Visual Studio 2013 (VS2013) environment, together with the developing tools available in the Intel Parallel Studio XE 2015 (XE2015). The performance study of this new implementation was carried out in a desktop PC with a multi-core CPU, taking as a reference the performance of the original platform. The results were satisfactory, both in terms of scalability as parallelization efficiency.

Shared Memory Parallelism for 3D Cartesian Discrete Ordinates Solver

NASA Astrophysics Data System (ADS)

Moustafa, Salli; Dutka-Malen, Ivan; Plagne, Laurent; Ponçot, Angélique; Ramet, Pierre

2014-06-01

This paper describes the design and the performance of DOMINO, a 3D Cartesian SN solver that implements two nested levels of parallelism (multicore+SIMD) on shared memory computation nodes. DOMINO is written in C++, a multi-paradigm programming language that enables the use of powerful and generic parallel programming tools such as Intel TBB and Eigen. These two libraries allow us to combine multi-thread parallelism with vector operations in an efficient and yet portable way. As a result, DOMINO can exploit the full power of modern multi-core processors and is able to tackle very large simulations, that usually require large HPC clusters, using a single computing node. For example, DOMINO solves a 3D full core PWR eigenvalue problem involving 26 energy groups, 288 angular directions (S16), 46 × 106 spatial cells and 1 × 1012 DoFs within 11 hours on a single 32-core SMP node. This represents a sustained performance of 235 GFlops and 40:74% of the SMP node peak performance for the DOMINO sweep implementation. The very high Flops/Watt ratio of DOMINO makes it a very interesting building block for a future many-nodes nuclear simulation tool.

Aztec user`s guide. Version 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hutchinson, S.A.; Shadid, J.N.; Tuminaro, R.S.

1995-10-01

Aztec is an iterative library that greatly simplifies the parallelization process when solving the linear systems of equations Ax = b where A is a user supplied n x n sparse matrix, b is a user supplied vector of length n and x is a vector of length n to be computed. Aztec is intended as a software tool for users who want to avoid cumbersome parallel programming details but who have large sparse linear systems which require an efficiently utilized parallel processing system. A collection of data transformation tools are provided that allow for easy creation of distributed sparsemore » unstructured matrices for parallel solution. Once the distributed matrix is created, computation can be performed on any of the parallel machines running Aztec: nCUBE 2, IBM SP2 and Intel Paragon, MPI platforms as well as standard serial and vector platforms. Aztec includes a number of Krylov iterative methods such as conjugate gradient (CG), generalized minimum residual (GMRES) and stabilized biconjugate gradient (BICGSTAB) to solve systems of equations. These Krylov methods are used in conjunction with various preconditioners such as polynomial or domain decomposition methods using LU or incomplete LU factorizations within subdomains. Although the matrix A can be general, the package has been designed for matrices arising from the approximation of partial differential equations (PDEs). In particular, the Aztec package is oriented toward systems arising from PDE applications.« less

Legacy Code Modernization

NASA Technical Reports Server (NTRS)

Hribar, Michelle R.; Frumkin, Michael; Jin, Haoqiang; Waheed, Abdul; Yan, Jerry; Saini, Subhash (Technical Monitor)

1998-01-01

Over the past decade, high performance computing has evolved rapidly; systems based on commodity microprocessors have been introduced in quick succession from at least seven vendors/families. Porting codes to every new architecture is a difficult problem; in particular, here at NASA, there are many large CFD applications that are very costly to port to new machines by hand. The LCM ("Legacy Code Modernization") Project is the development of an integrated parallelization environment (IPE) which performs the automated mapping of legacy CFD (Fortran) applications to state-of-the-art high performance computers. While most projects to port codes focus on the parallelization of the code, we consider porting to be an iterative process consisting of several steps: 1) code cleanup, 2) serial optimization,3) parallelization, 4) performance monitoring and visualization, 5) intelligent tools for automated tuning using performance prediction and 6) machine specific optimization. The approach for building this parallelization environment is to build the components for each of the steps simultaneously and then integrate them together. The demonstration will exhibit our latest research in building this environment: 1. Parallelizing tools and compiler evaluation. 2. Code cleanup and serial optimization using automated scripts 3. Development of a code generator for performance prediction 4. Automated partitioning 5. Automated insertion of directives. These demonstrations will exhibit the effectiveness of an automated approach for all the steps involved with porting and tuning a legacy code application for a new architecture.

Using CLIPS in the domain of knowledge-based massively parallel programming

NASA Technical Reports Server (NTRS)

Dvorak, Jiri J.

1994-01-01

The Program Development Environment (PDE) is a tool for massively parallel programming of distributed-memory architectures. Adopting a knowledge-based approach, the PDE eliminates the complexity introduced by parallel hardware with distributed memory and offers complete transparency in respect of parallelism exploitation. The knowledge-based part of the PDE is realized in CLIPS. Its principal task is to find an efficient parallel realization of the application specified by the user in a comfortable, abstract, domain-oriented formalism. A large collection of fine-grain parallel algorithmic skeletons, represented as COOL objects in a tree hierarchy, contains the algorithmic knowledge. A hybrid knowledge base with rule modules and procedural parts, encoding expertise about application domain, parallel programming, software engineering, and parallel hardware, enables a high degree of automation in the software development process. In this paper, important aspects of the implementation of the PDE using CLIPS and COOL are shown, including the embedding of CLIPS with C++-based parts of the PDE. The appropriateness of the chosen approach and of the CLIPS language for knowledge-based software engineering are discussed.

Cross-Discipline Bio-Nanostructured Enhanced Photonic Multimode-Sensor Science

DTIC Science & Technology

2017-05-23

experimental study aimed to combine soft material science with nanotechnology and multi-physics modeling to produce adaptable bio-nanostructure based on...degradation through optical analysis and tracking programs Protein and DNA engineering . - The properties of proteins to be used in sensors were studies

Using COMSOL Multiphysics Software to Model Anisotropic Dielectric and Metamaterial Effects in Folded-Waveguide Traveling-Wave Tube Slow-Wave Circuits

NASA Technical Reports Server (NTRS)

Starinshak, David P.; Smith, Nathan D.; Wilson, Jeffrey D.

2008-01-01

The electromagnetic effects of conventional dielectrics, anisotropic dielectrics, and metamaterials were modeled in a terahertz-frequency folded-waveguide slow-wave circuit. Results of attempts to utilize these materials to increase efficiency are presented.

Multiphysics modeling of microwave heating of whole tomato

USDA-ARS?s Scientific Manuscript database

A mathematical model of a food is useful for prediction of temperature profiles during microwave heating. However, due to their complex geometry and interaction with electromagnetic fields, whole tomatoes resist an analytical approach to modeling the fruit as it is subjected to microwave energy. T...

Prediction of SOFC Performance with or without Experiments: A Study on Minimum Requirements for Experimental Data

DOE PAGES

Yang, Tao; Sezer, Hayri; Celik, Ismail B.; ...

2015-06-02

In the present paper, a physics-based procedure combining experiments and multi-physics numerical simulations is developed for overall analysis of SOFCs operational diagnostics and performance predictions. In this procedure, essential information for the fuel cell is extracted first by utilizing empirical polarization analysis in conjunction with experiments and refined by multi-physics numerical simulations via simultaneous analysis and calibration of polarization curve and impedance behavior. The performance at different utilization cases and operating currents is also predicted to confirm the accuracy of the proposed model. It is demonstrated that, with the present electrochemical model, three air/fuel flow conditions are needed to producemore » a set of complete data for better understanding of the processes occurring within SOFCs. After calibration against button cell experiments, the methodology can be used to assess performance of planar cell without further calibration. The proposed methodology would accelerate the calibration process and improve the efficiency of design and diagnostics.« less

Dynamic implicit 3D adaptive mesh refinement for non-equilibrium radiation diffusion

NASA Astrophysics Data System (ADS)

Philip, B.; Wang, Z.; Berrill, M. A.; Birke, M.; Pernice, M.

2014-04-01

The time dependent non-equilibrium radiation diffusion equations are important for solving the transport of energy through radiation in optically thick regimes and find applications in several fields including astrophysics and inertial confinement fusion. The associated initial boundary value problems that are encountered often exhibit a wide range of scales in space and time and are extremely challenging to solve. To efficiently and accurately simulate these systems we describe our research on combining techniques that will also find use more broadly for long term time integration of nonlinear multi-physics systems: implicit time integration for efficient long term time integration of stiff multi-physics systems, local control theory based step size control to minimize the required global number of time steps while controlling accuracy, dynamic 3D adaptive mesh refinement (AMR) to minimize memory and computational costs, Jacobian Free Newton-Krylov methods on AMR grids for efficient nonlinear solution, and optimal multilevel preconditioner components that provide level independent solver convergence.

SMITHERS: An object-oriented modular mapping methodology for MCNP-based neutronic–thermal hydraulic multiphysics

DOE PAGES

Richard, Joshua; Galloway, Jack; Fensin, Michael; ...

2015-04-04

A novel object-oriented modular mapping methodology for externally coupled neutronics–thermal hydraulics multiphysics simulations was developed. The Simulator using MCNP with Integrated Thermal-Hydraulics for Exploratory Reactor Studies (SMITHERS) code performs on-the-fly mapping of material-wise power distribution tallies implemented by MCNP-based neutron transport/depletion solvers for use in estimating coolant temperature and density distributions with a separate thermal-hydraulic solver. The key development of SMITHERS is that it reconstructs the hierarchical geometry structure of the material-wise power generation tallies from the depletion solver automatically, with only a modicum of additional information required from the user. In addition, it performs the basis mapping from themore » combinatorial geometry of the depletion solver to the required geometry of the thermal-hydraulic solver in a generalizable manner, such that it can transparently accommodate varying levels of thermal-hydraulic solver geometric fidelity, from the nodal geometry of multi-channel analysis solvers to the pin-cell level of discretization for sub-channel analysis solvers.« less

Electromagnetic pulsed thermography for natural cracks inspection

NASA Astrophysics Data System (ADS)

Gao, Yunlai; Tian, Gui Yun; Wang, Ping; Wang, Haitao; Gao, Bin; Woo, Wai Lok; Li, Kongjing

2017-02-01

Emerging integrated sensing and monitoring of material degradation and cracks are increasingly required for characterizing the structural integrity and safety of infrastructure. However, most conventional nondestructive evaluation (NDE) methods are based on single modality sensing which is not adequate to evaluate structural integrity and natural cracks. This paper proposed electromagnetic pulsed thermography for fast and comprehensive defect characterization. It hybrids multiple physical phenomena i.e. magnetic flux leakage, induced eddy current and induction heating linking to physics as well as signal processing algorithms to provide abundant information of material properties and defects. New features are proposed using 1st derivation that reflects multiphysics spatial and temporal behaviors to enhance the detection of cracks with different orientations. Promising results that robust to lift-off changes and invariant features for artificial and natural cracks detection have been demonstrated that the proposed method significantly improves defect detectability. It opens up multiphysics sensing and integrated NDE with potential impact for natural understanding and better quantitative evaluation of natural cracks including stress corrosion crack (SCC) and rolling contact fatigue (RCF).

Interfacial mixing in high energy-density matter with a multiphysics kinetic model

NASA Astrophysics Data System (ADS)

Haack, Jeff; Hauck, Cory; Murillo, Michael

2017-10-01

We have extended a recently-developed multispecies, multitemperature BGK model to include multiphysics capability that allows modeling of a wider range of plasma conditions. In particular, we have extended the model to describe one spatial dimension, and included a multispecies atomic ionization model, accurate collision physics across coupling regimes, self-consistent electric fields, and degeneracy in the electronic screening. We apply the new model to a warm dense matter scenario in which the ablator-fuel interface of an inertial confinement fusion target is heated, similar to a recent molecular dynamics study, but for larger length and time scales and for much higher temperatures. From our numerical results we are able to explore a variety of phenomena, including hydrogen jetting, kinetic effects (non-Maxwellian and anisotropic distributions), plasma physics (size, persistence and role of electric fields) and transport (relative sizes of Fickean diffision, electrodiffusion and barodiffusion). As compared with the recent molecular dynamics work the kinetic model greatly extends the accessible physical domains we are able to model.

Multi-Physics Demonstration Problem with the SHARP Reactor Simulation Toolkit

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merzari, E.; Shemon, E. R.; Yu, Y. Q.

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 ofmore » 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.« less

Current Developments in DETER Cybersecurity Testbed Technology

DTIC Science & Technology

2015-12-08

management on PlanetLab [12], such as Plush and Nebula [4], PlMan [19], Stork [20], pShell [21], Planetlab Application Manager [22], parallel open...SSH tools [23], plDist [24], Nixes [25], PLDeploy [26] and vxargs [27]. With the exception of Plush and Nebula , these tools are all low-level

Sight Application Analysis Tool

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bronevetsky, G.

2014-09-17

The scale and complexity of scientific applications makes it very difficult to optimize, debug and extend them to support new capabilities. We have developed a tool that supports developers’ efforts to understand the logical flow of their applications and interactions between application components and hardware in a way that scales with application complexity and parallelism.

The Automated Instrumentation and Monitoring System (AIMS): Design and Architecture. 3.2

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Schmidt, Melisa; Schulbach, Cathy; Bailey, David (Technical Monitor)

1997-01-01

Whether a researcher is designing the 'next parallel programming paradigm', another 'scalable multiprocessor' or investigating resource allocation algorithms for multiprocessors, a facility that enables parallel program execution to be captured and displayed is invaluable. Careful analysis of such information can help computer and software architects to capture, and therefore, exploit behavioral variations among/within various parallel programs to take advantage of specific hardware characteristics. A software tool-set that facilitates performance evaluation of parallel applications on multiprocessors has been put together at NASA Ames Research Center under the sponsorship of NASA's High Performance Computing and Communications Program over the past five years. The Automated Instrumentation and Monitoring Systematic has three major software components: a source code instrumentor which automatically inserts active event recorders into program source code before compilation; a run-time performance monitoring library which collects performance data; and a visualization tool-set which reconstructs program execution based on the data collected. Besides being used as a prototype for developing new techniques for instrumenting, monitoring and presenting parallel program execution, AIMS is also being incorporated into the run-time environments of various hardware testbeds to evaluate their impact on user productivity. Currently, the execution of FORTRAN and C programs on the Intel Paragon and PALM workstations can be automatically instrumented and monitored. Performance data thus collected can be displayed graphically on various workstations. The process of performance tuning with AIMS will be illustrated using various NAB Parallel Benchmarks. This report includes a description of the internal architecture of AIMS and a listing of the source code.

Characterizing Task-Based OpenMP Programs

PubMed Central

Muddukrishna, Ananya; Jonsson, Peter A.; Brorsson, Mats

2015-01-01

Programmers struggle to understand performance of task-based OpenMP programs since profiling tools only report thread-based performance. Performance tuning also requires task-based performance in order to balance per-task memory hierarchy utilization against exposed task parallelism. We provide a cost-effective method to extract detailed task-based performance information from OpenMP programs. We demonstrate the utility of our method by quickly diagnosing performance problems and characterizing exposed task parallelism and per-task instruction profiles of benchmarks in the widely-used Barcelona OpenMP Tasks Suite. Programmers can tune performance faster and understand performance tradeoffs more effectively than existing tools by using our method to characterize task-based performance. PMID:25860023

A Fusion Nuclear Science Facility for a fast-track path to DEMO

DOE PAGES

Garofalo, Andrea M.; Abdou, M.; Canik, John M.; ...

2014-10-01

An accelerated fusion energy development program, a “fast-track” approach, requires developing an understanding of fusion nuclear science (FNS) in parallel with research on ITER to study burning plasmas. A Fusion Nuclear Science Facility (FNSF) in parallel with ITER provides the capability to resolve FNS feasibility issues related to power extraction, tritium fuel sustainability, and reliability, and to begin construction of DEMO upon the achievement of Q~10 in ITER. Fusion nuclear components, including the first wall (FW)/blanket, divertor, heating/fueling systems, etc. are complex systems with many inter-related functions and different materials, fluids, and physical interfaces. These in-vessel nuclear components must operatemore » continuously and reliably with: (a) Plasma exposure, surface particle & radiation loads, (b) High energy 2 neutron fluxes and their interactions in materials (e.g. peaked volumetric heating with steep gradients, tritium production, activation, atomic displacements, gas production, etc.), (c) Strong magnetic fields with temporal and spatial variations (electromagnetic coupling to the plasma including off-normal events like disruptions), and (d) a High temperature, high vacuum, chemically active environment. While many of these conditions and effects are being studied with separate and multiple effect experimental test stands and modeling, fusion nuclear conditions cannot be completely simulated outside the fusion environment. This means there are many new multi-physics, multi-scale phenomena and synergistic effects yet to be discovered and accounted for in the understanding, design and operation of fusion as a self-sustaining, energy producing system, and significant experimentation and operational experience in a true fusion environment is an essential requirement. In the following sections we discuss the FNSF objectives, describe the facility requirements and a facility concept and operation approach that can accomplish those objectives, and assess the readiness to construct with respect to several key FNSF issues: materials, steady-state operation, disruptions, power exhaust, and breeding blanket. Finally we present our conclusions.« less

The Fortran-P Translator: Towards Automatic Translation of Fortran 77 Programs for Massively Parallel Processors

DOE PAGES

O'keefe, Matthew; Parr, Terence; Edgar, B. Kevin; ...

1995-01-01

Massively parallel processors (MPPs) hold the promise of extremely high performance that, if realized, could be used to study problems of unprecedented size and complexity. One of the primary stumbling blocks to this promise has been the lack of tools to translate application codes to MPP form. In this article we show how applications codes written in a subset of Fortran 77, called Fortran-P, can be translated to achieve good performance on several massively parallel machines. This subset can express codes that are self-similar, where the algorithm applied to the global data domain is also applied to each subdomain. Wemore » have found many codes that match the Fortran-P programming style and have converted them using our tools. We believe a self-similar coding style will accomplish what a vectorizable style has accomplished for vector machines by allowing the construction of robust, user-friendly, automatic translation systems that increase programmer productivity and generate fast, efficient code for MPPs.« less

Parallel programming of industrial applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heroux, M; Koniges, A; Simon, H

1998-07-21

In the introductory material, we overview the typical MPP environment for real application computing and the special tools available such as parallel debuggers and performance analyzers. Next, we draw from a series of real applications codes and discuss the specific challenges and problems that are encountered in parallelizing these individual applications. The application areas drawn from include biomedical sciences, materials processing and design, plasma and fluid dynamics, and others. We show how it was possible to get a particular application to run efficiently and what steps were necessary. Finally we end with a summary of the lessons learned from thesemore » applications and predictions for the future of industrial parallel computing. This tutorial is based on material from a forthcoming book entitled: "Industrial Strength Parallel Computing" to be published by Morgan Kaufmann Publishers (ISBN l-55860-54).« less

PARAMESH: A Parallel Adaptive Mesh Refinement Community Toolkit

NASA Technical Reports Server (NTRS)

MacNeice, Peter; Olson, Kevin M.; Mobarry, Clark; deFainchtein, Rosalinda; Packer, Charles

1999-01-01

In this paper, we describe a community toolkit which is designed to provide parallel support with adaptive mesh capability for a large and important class of computational models, those using structured, logically cartesian meshes. The package of Fortran 90 subroutines, called PARAMESH, is designed to provide an application developer with an easy route to extend an existing serial code which uses a logically cartesian structured mesh into a parallel code with adaptive mesh refinement. Alternatively, in its simplest use, and with minimal effort, it can operate as a domain decomposition tool for users who want to parallelize their serial codes, but who do not wish to use adaptivity. The package can provide them with an incremental evolutionary path for their code, converting it first to uniformly refined parallel code, and then later if they so desire, adding adaptivity.

Massively Parallel Processing for Fast and Accurate Stamping Simulations

NASA Astrophysics Data System (ADS)

Gress, Jeffrey J.; Xu, Siguang; Joshi, Ramesh; Wang, Chuan-tao; Paul, Sabu

2005-08-01

The competitive automotive market drives automotive manufacturers to speed up the vehicle development cycles and reduce the lead-time. Fast tooling development is one of the key areas to support fast and short vehicle development programs (VDP). In the past ten years, the stamping simulation has become the most effective validation tool in predicting and resolving all potential formability and quality problems before the dies are physically made. The stamping simulation and formability analysis has become an critical business segment in GM math-based die engineering process. As the simulation becomes as one of the major production tools in engineering factory, the simulation speed and accuracy are the two of the most important measures for stamping simulation technology. The speed and time-in-system of forming analysis becomes an even more critical to support the fast VDP and tooling readiness. Since 1997, General Motors Die Center has been working jointly with our software vendor to develop and implement a parallel version of simulation software for mass production analysis applications. By 2001, this technology was matured in the form of distributed memory processing (DMP) of draw die simulations in a networked distributed memory computing environment. In 2004, this technology was refined to massively parallel processing (MPP) and extended to line die forming analysis (draw, trim, flange, and associated spring-back) running on a dedicated computing environment. The evolution of this technology and the insight gained through the implementation of DM0P/MPP technology as well as performance benchmarks are discussed in this publication.

Parallel pumping for magnon spintronics: Amplification and manipulation of magnon spin currents on the micron-scale

NASA Astrophysics Data System (ADS)

Brächer, T.; Pirro, P.; Hillebrands, B.

2017-06-01

Magnonics and magnon spintronics aim at the utilization of spin waves and magnons, their quanta, for the construction of wave-based logic networks via the generation of pure all-magnon spin currents and their interfacing with electric charge transport. The promise of efficient parallel data processing and low power consumption renders this field one of the most promising research areas in spintronics. In this context, the process of parallel parametric amplification, i.e., the conversion of microwave photons into magnons at one half of the microwave frequency, has proven to be a versatile tool to excite and to manipulate spin waves. Its beneficial and unique properties such as frequency and mode-selectivity, the possibility to excite spin waves in a wide wavevector range and the creation of phase-correlated wave pairs, have enabled the achievement of important milestones like the magnon Bose-Einstein condensation and the cloning and trapping of spin-wave packets. Parallel parametric amplification, which allows for the selective amplification of magnons while conserving their phase is, thus, one of the key methods of spin-wave generation and amplification. The application of parallel parametric amplification to CMOS-compatible micro- and nano-structures is an important step towards the realization of magnonic networks. This is motivated not only by the fact that amplifiers are an important tool for the construction of any extended logic network but also by the unique properties of parallel parametric amplification. In particular, the creation of phase-correlated wave pairs allows for rewarding alternative logic operations such as a phase-dependent amplification of the incident waves. Recently, the successful application of parallel parametric amplification to metallic microstructures has been reported which constitutes an important milestone for the application of magnonics in practical devices. It has been demonstrated that parametric amplification provides an excellent tool to generate and to amplify spin waves in these systems in a wide wavevector range. In particular, the amplification greatly benefits from the discreteness of the spin-wave spectra since the size of the microstructures is comparable to the spin-wave wavelength. This opens up new, interesting routes of spin-wave amplification and manipulation. In this review, we will give an overview over the recent developments and achievements in this field.

Development and characterization of hollow microprobe array as a potential tool for versatile and massively parallel manipulation of single cells.

PubMed

Nagai, Moeto; Oohara, Kiyotaka; Kato, Keita; Kawashima, Takahiro; Shibata, Takayuki

2015-04-01

Parallel manipulation of single cells is important for reconstructing in vivo cellular microenvironments and studying cell functions. To manipulate single cells and reconstruct their environments, development of a versatile manipulation tool is necessary. In this study, we developed an array of hollow probes using microelectromechanical systems fabrication technology and demonstrated the manipulation of single cells. We conducted a cell aspiration experiment with a glass pipette and modeled a cell using a standard linear solid model, which provided information for designing hollow stepped probes for minimally invasive single-cell manipulation. We etched a silicon wafer on both sides and formed through holes with stepped structures. The inner diameters of the holes were reduced by SiO2 deposition of plasma-enhanced chemical vapor deposition to trap cells on the tips. This fabrication process makes it possible to control the wall thickness, inner diameter, and outer diameter of the probes. With the fabricated probes, single cells were manipulated and placed in microwells at a single-cell level in a parallel manner. We studied the capture, release, and survival rates of cells at different suction and release pressures and found that the cell trapping rate was directly proportional to the suction pressure, whereas the release rate and viability decreased with increasing the suction pressure. The proposed manipulation system makes it possible to place cells in a well array and observe the adherence, spreading, culture, and death of the cells. This system has potential as a tool for massively parallel manipulation and for three-dimensional hetero cellular assays.

RELAP-7 Development Updates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Hongbin; Zhao, Haihua; Gleicher, Frederick Nathan

RELAP-7 is a nuclear systems safety analysis code being developed at the Idaho National Laboratory, and is the next generation tool in the RELAP reactor safety/systems analysis application series. RELAP-7 development began in 2011 to support the Risk Informed Safety Margins Characterization (RISMC) Pathway of the Light Water Reactor Sustainability (LWRS) program. The overall design goal of RELAP-7 is to take advantage of the previous thirty years of advancements in computer architecture, software design, numerical methods, and physical models in order to provide capabilities needed for the RISMC methodology and to support nuclear power safety analysis. The code is beingmore » developed based on Idaho National Laboratory’s modern scientific software development framework – MOOSE (the Multi-Physics Object-Oriented Simulation Environment). The initial development goal of the RELAP-7 approach focused primarily on the development of an implicit algorithm capable of strong (nonlinear) coupling of the dependent hydrodynamic variables contained in the 1-D/2-D flow models with the various 0-D system reactor components that compose various boiling water reactor (BWR) and pressurized water reactor nuclear power plants (NPPs). During Fiscal Year (FY) 2015, the RELAP-7 code has been further improved with expanded capability to support boiling water reactor (BWR) and pressurized water reactor NPPs analysis. The accumulator model has been developed. The code has also been coupled with other MOOSE-based applications such as neutronics code RattleSnake and fuel performance code BISON to perform multiphysics analysis. A major design requirement for the implicit algorithm in RELAP-7 is that it is capable of second-order discretization accuracy in both space and time, which eliminates the traditional first-order approximation errors. The second-order temporal is achieved by a second-order backward temporal difference, and the one-dimensional second-order accurate spatial discretization is achieved with the Galerkin approximation of Lagrange finite elements. During FY-2015, we have done numerical verification work to verify that the RELAP-7 code indeed achieves 2nd-order accuracy in both time and space for single phase models at the system level.« less

Scaling Support Vector Machines On Modern HPC Platforms

DOE Office of Scientific and Technical Information (OSTI.GOV)

You, Yang; Fu, Haohuan; Song, Shuaiwen

2015-02-01

We designed and implemented MIC-SVM, a highly efficient parallel SVM for x86 based multicore and many-core architectures, such as the Intel Ivy Bridge CPUs and Intel Xeon Phi co-processor (MIC). We propose various novel analysis methods and optimization techniques to fully utilize the multilevel parallelism provided by these architectures and serve as general optimization methods for other machine learning tools.

The JASMIN Analysis Platform - bridging the gap between traditional climate data practicies and data-centric analysis paradigms

NASA Astrophysics Data System (ADS)

Pascoe, Stephen; Iwi, Alan; kershaw, philip; Stephens, Ag; Lawrence, Bryan

2014-05-01

The advent of large-scale data and the consequential analysis problems have led to two new challenges for the research community: how to share such data to get the maximum value and how to carry out efficient analysis. Solving both challenges require a form of parallelisation: the first is social parallelisation (involving trust and information sharing), the second data parallelisation (involving new algorithms and tools). The JASMIN infrastructure supports both kinds of parallelism by providing a multi-tennent environment with petabyte-scale storage, VM provisioning and batch cluster facilities. The JASMIN Analysis Platform (JAP) is an analysis software layer for JASMIN which emphasises ease of transition from a researcher's local environment to JASMIN. JAP brings together tools traditionally used by multiple communities and configures them to work together, enabling users to move analysis from their local environment to JASMIN without rewriting code. JAP also provides facilities to exploit JASMIN's parallel capabilities whilst maintaining their familiar analysis environment where ever possible. Modern opensource analysis tools typically have multiple dependent packages, increasing the installation burden on system administrators. When you consider a suite of tools, often with both common and conflicting dependencies, analysis pipelines can become locked to a particular installation simply because of the effort required to reconstruct the dependency tree. JAP addresses this problem by providing a consistent suite of RPMs compatible with RedHat Enterprise Linux and CentOS 6.4. Researchers can install JAP locally, either as RPMs or through a pre-built VM image, giving them the confidence to know moving analysis to JASMIN will not disrupt their environment. Analysis parallelisation is in it's infancy in climate sciences, with few tools capable of exploiting any parallel environment beyond manual scripting of the use of multiple processors. JAP begins to bridge this gap through a veriety of higher-level tools for parallelisation and job scheduling such as IPython-parallel and MPI support for interactive analysis languages. We find that enabling even simple parallelisation of workflows, together with the state of the art I/O performance of JASMIN storage, provides many users with the large increases in efficiency they need to scale their analyses to conteporary data volumes and tackly new, previously inaccessible, problems.

Parallels in Computer-Aided Design Framework and Software Development Environment Efforts.

DTIC Science & Technology

1992-05-01

de - sign kits, and tool and design management frameworks. Also, books about software engineer- ing environments [Long 91] and electronic design...tool integration [Zarrella 90], and agreement upon a universal de - sign automation framework, such as the CAD Framework Initiative (CFI) [Malasky 91...ments: identification, control, status accounting, and audit and review. The paper by Dart ex- tracts 15 CM concepts from existing SDEs and tools

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

DOE PAGES

Yim, Won Cheol; Cushman, John C.

2017-07-22

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

Divide and Conquer (DC) BLAST: fast and easy BLAST execution within HPC environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yim, Won Cheol; Cushman, John C.

Bioinformatics is currently faced with very large-scale data sets that lead to computational jobs, especially sequence similarity searches, that can take absurdly long times to run. For example, the National Center for Biotechnology Information (NCBI) Basic Local Alignment Search Tool (BLAST and BLAST+) suite, which is by far the most widely used tool for rapid similarity searching among nucleic acid or amino acid sequences, is highly central processing unit (CPU) intensive. While the BLAST suite of programs perform searches very rapidly, they have the potential to be accelerated. In recent years, distributed computing environments have become more widely accessible andmore » used due to the increasing availability of high-performance computing (HPC) systems. Therefore, simple solutions for data parallelization are needed to expedite BLAST and other sequence analysis tools. However, existing software for parallel sequence similarity searches often requires extensive computational experience and skill on the part of the user. In order to accelerate BLAST and other sequence analysis tools, Divide and Conquer BLAST (DCBLAST) was developed to perform NCBI BLAST searches within a cluster, grid, or HPC environment by using a query sequence distribution approach. Scaling from one (1) to 256 CPU cores resulted in significant improvements in processing speed. Thus, DCBLAST dramatically accelerates the execution of BLAST searches using a simple, accessible, robust, and parallel approach. DCBLAST works across multiple nodes automatically and it overcomes the speed limitation of single-node BLAST programs. DCBLAST can be used on any HPC system, can take advantage of hundreds of nodes, and has no output limitations. Thus, this freely available tool simplifies distributed computation pipelines to facilitate the rapid discovery of sequence similarities between very large data sets.« less

On the effects of assembly compression on the performance of liquid-feed DMFCs under methanol-limiting conditions: A 2D numerical study

NASA Astrophysics Data System (ADS)

García-Salaberri, P. A.; Vera, M.

2015-07-01

The influence of assembly compression on the performance of liquid-feed DMFCs under methanol-limiting conditions is explored by means of a 2D/1D multiphysics across-the-channel model. The numerical formulation incorporates a comprehensive 2D description of the anode GDL, including two-phase phenomena, non-uniform anisotropic transport properties, and electrical contact resistances at the GDL/BPP interface. GDL effective properties are evaluated using empirical data corresponding to Toray® carbon paper. A simplified but physically sound 1D description, locally coupled to the 2D anode GDL model, is adopted to describe transport processes in the MPLs, membrane and cathode GDL, whereas the catalyst layers are treated as infinitely thin surfaces. Good agreement is found between the numerical results and previous experimental data. The interplay between assembly compression, bipolar plate material, and channel configuration is also investigated. The results show that there is an optimum GDL compression ratio in terms of overall power density, the optimal compression level being strongly dependent on bipolar plate material. Beyond the optimum, the detrimental effect of compression is larger in non-parallel flow fields due to the additional reduction of methanol transported by under-rib convection. The results suggest that, under certain conditions, this transport mechanism could be more important than diffusion in the anode of liquid-feed DMFCs.

Simulation and Fabrication of Wagon-Wheel-Shaped Piezoelectric Transducer for Raindrop Energy Harvesting Application

NASA Astrophysics Data System (ADS)

Wong, Chin Hong; Dahari, Zuraini; Jumali, Mohammad Hafizuddin; Mohamed, Khairudin; Mohamed, Julie Juliewatty

2017-03-01

Harvesting vibrational energy from impacting raindrops using piezoelectric material has been proven to be a promising approach for future outdoor applications, providing a good alternative resource that can be applied in outdoor rainy environments. We present herein an optimum novel polyvinylidene fluoride (PVDF) piezoelectric transducer specifically developed to harvest raindrop energy. The finite-element method was applied for simulation and optimization of the piezoelectric raindrop energy harvester (PREH) using COMSOL Multiphysics software, investigating the electrical potential, surface charge density, and total displacement for different transducer dimensions. According to the simulation results, the structure that generated the highest electrical potential and surface charge density was a wagon-wheel-shaped structure consisting of six spokes with wheel diameter of 30 mm, spoke width of 2 mm, center pad diameter of 6 mm, and thickness of 25 μm. This optimum wagon-wheel-shaped device was then fabricated by spin coating of PVDF, sputtering of aluminum, a poling process, and computer numerical control machining of a polytetrafluoroethylene stand. The fabricated PREH was characterized by x-ray diffraction analysis and Fourier-transform infrared spectroscopy. Finally, the fabricated PREH was tested under actual rain conditions with an alternating current to direct current converter connected in parallel, revealing that a single cell could generate average peak voltage of 22.5 mV and produce electrical energy of 3.4 nJ from ten impacts in 20 s.

Gas transfer model to design a ventilator for neonatal total liquid ventilation.

PubMed

Bonfanti, Mirko; Cammi, Antonio; Bagnoli, Paola

2015-12-01

The study was aimed to optimize the gas transfer in an innovative ventilator for neonatal Total Liquid Ventilation (TLV) that integrates the pumping and oxygenation functions in a non-volumetric pulsatile device made of parallel flat silicone membranes. A computational approach was adopted to evaluate oxygen (O2) and carbon dioxide (CO2) exchanges between the liquid perfluorocarbon (PFC) and the oxygenating gas, as a function of the geometrical parameter of the device. A 2D semi-empirical model was implemented to this purpose using Comsol Multiphysics to study both the fluid dynamics and the gas exchange in the ventilator. Experimental gas exchanges measured with a preliminary prototype were compared to the simulation outcomes to prove the model reliability. Different device configurations were modeled to identify the optimal design able to guarantee the desired gas transfer. Good agreement between experimental and simulation outcomes was obtained, validating the model. The optimal configuration, able to achieve the desired gas exchange (ΔpCO2 = 16.5 mmHg and ΔpO2 = 69 mmHg), is a device comprising 40 modules, 300 mm in length (total exchange area = 2.28 m(2)). With this configuration gas transfer performance is satisfactory for all the simulated settings, proving good adaptability of the device. Copyright © 2015 IPEM. Published by Elsevier Ltd. All rights reserved.

Portable parallel portfolio optimization in the Aurora Financial Management System

NASA Astrophysics Data System (ADS)

Laure, Erwin; Moritsch, Hans

2001-07-01

Financial planning problems are formulated as large scale, stochastic, multiperiod, tree structured optimization problems. An efficient technique for solving this kind of problems is the nested Benders decomposition method. In this paper we present a parallel, portable, asynchronous implementation of this technique. To achieve our portability goals we elected the programming language Java for our implementation and used a high level Java based framework, called OpusJava, for expressing the parallelism potential as well as synchronization constraints. Our implementation is embedded within a modular decision support tool for portfolio and asset liability management, the Aurora Financial Management System.

Simulation of the spatial frequency-dependent sensitivities of Acoustic Emission sensors

NASA Astrophysics Data System (ADS)

Boulay, N.; Lhémery, A.; Zhang, F.

2018-05-01

Typical configurations of nondestructive testing by Acoustic Emission (NDT/AE) make use of multiple sensors positioned on the tested structure for detecting evolving flaws and possibly locating them by triangulation. Sensors positions must be optimized for ensuring global coverage sensitivity to AE events and minimizing their number. A simulator of NDT/AE is under development to provide help with designing testing configurations and with interpreting measurements. A global model performs sub-models simulating the various phenomena taking place at different spatial and temporal scales (crack growth, AE source and radiation, wave propagation in the structure, reception by sensors). In this context, accurate modelling of sensors behaviour must be developed. These sensors generally consist of a cylindrical piezoelectric element of radius approximately equal to its thickness, without damping and bonded to its case. Sensors themselves are bonded to the structure being tested. Here, a multiphysics finite element simulation tool is used to study the complex behaviour of AE sensor. The simulated behaviour is shown to accurately reproduce the high-amplitude measured contributions used in the AE practice.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Heroux, Michael; Lethin, Richard

Programming models and environments play the essential roles in high performance computing of enabling the conception, design, implementation and execution of science and engineering application codes. Programmer productivity is strongly influenced by the effectiveness of our programming models and environments, as is software sustainability since our codes have lifespans measured in decades, so the advent of new computing architectures, increased concurrency, concerns for resilience, and the increasing demands for high-fidelity, multi-physics, multi-scale and data-intensive computations mean that we have new challenges to address as part of our fundamental R&D requirements. Fortunately, we also have new tools and environments that makemore » design, prototyping and delivery of new programming models easier than ever. The combination of new and challenging requirements and new, powerful toolsets enables significant synergies for the next generation of programming models and environments R&D. This report presents the topics discussed and results from the 2014 DOE Office of Science Advanced Scientific Computing Research (ASCR) Programming Models & Environments Summit, and subsequent discussions among the summit participants and contributors to topics in this report.« less

3D optimization of a polymer MOEMS for active focusing of VCSEL beam

NASA Astrophysics Data System (ADS)

Abada, S.; Camps, T.; Reig, B.; Doucet, JB; Daran, E.; Bardinal, V.

2014-05-01

We report on the optimized design of a polymer-based actuator that can be directly integrated on a VCSEL for vertical beam scanning. Its operation principle is based on the vertical displacement of a SU-8 membrane including a polymer microlens. Under an applied thermal gradient, the membrane is shifted vertically due to thermal expansion in the actuation arms induced by Joule effect. This leads to a modification of microlens position and thus to a vertical scan of the laser beam. Membrane vertical displacements as high as 8μm for only 3V applied were recently experimentally obtained. To explain these performances, we developed a comprehensive tri-dimensional thermo-mechanical model that takes into account SU-8 material properties and precise MOEMS geometry. Out-of-plane mechanical coefficients and thermal conductivity were thus integrated in our 3D model (COMSOL Multiphysics). Vertical displacements extracted from these data for different actuation powers were successfully compared to experimental values, validating this modelling tool. Thereby, it was exploited to increase MOEMS electrothermal performance by a factor higher than 5.

A new design approach based on differential evolution algorithm for geometric optimization of magnetorheological brakes

NASA Astrophysics Data System (ADS)

Le-Duc, Thang; Ho-Huu, Vinh; Nguyen-Thoi, Trung; Nguyen-Quoc, Hung

2016-12-01

In recent years, various types of magnetorheological brakes (MRBs) have been proposed and optimized by different optimization algorithms that are integrated in commercial software such as ANSYS and Comsol Multiphysics. However, many of these optimization algorithms often possess some noteworthy shortcomings such as the trap of solutions at local extremes, or the limited number of design variables or the difficulty of dealing with discrete design variables. Thus, to overcome these limitations and develop an efficient computation tool for optimal design of the MRBs, an optimization procedure that combines differential evolution (DE), a gradient-free global optimization method with finite element analysis (FEA) is proposed in this paper. The proposed approach is then applied to the optimal design of MRBs with different configurations including conventional MRBs and MRBs with coils placed on the side housings. Moreover, to approach a real-life design, some necessary design variables of MRBs are considered as discrete variables in the optimization process. The obtained optimal design results are compared with those of available optimal designs in the literature. The results reveal that the proposed method outperforms some traditional approaches.

Stabilized FE simulation of prototype thermal-hydraulics problems with integrated adjoint-based capabilities

NASA Astrophysics Data System (ADS)

Shadid, J. N.; Smith, T. M.; Cyr, E. C.; Wildey, T. M.; Pawlowski, R. P.

2016-09-01

A critical aspect of applying modern computational solution methods to complex multiphysics systems of relevance to nuclear reactor modeling, is the assessment of the predictive capability of specific proposed mathematical models. In this respect the understanding of numerical error, the sensitivity of the solution to parameters associated with input data, boundary condition uncertainty, and mathematical models is critical. Additionally, the ability to evaluate and or approximate the model efficiently, to allow development of a reasonable level of statistical diagnostics of the mathematical model and the physical system, is of central importance. In this study we report on initial efforts to apply integrated adjoint-based computational analysis and automatic differentiation tools to begin to address these issues. The study is carried out in the context of a Reynolds averaged Navier-Stokes approximation to turbulent fluid flow and heat transfer using a particular spatial discretization based on implicit fully-coupled stabilized FE methods. Initial results are presented that show the promise of these computational techniques in the context of nuclear reactor relevant prototype thermal-hydraulics problems.

A Generalized Perturbation Theory Solver In Rattlesnake Based On PETSc With Application To TREAT Steady State Uncertainty Quantification

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schunert, Sebastian; Wang, Congjian; Wang, Yaqi

Rattlesnake and MAMMOTH are the designated TREAT analysis tools currently being developed at the Idaho National Laboratory. Concurrent with development of the multi-physics, multi-scale capabilities, sensitivity analysis and uncertainty quantification (SA/UQ) capabilities are required for predicitive modeling of the TREAT reactor. For steady-state SA/UQ, that is essential for setting initial conditions for the transients, generalized perturbation theory (GPT) will be used. This work describes the implementation of a PETSc based solver for the generalized adjoint equations that constitute a inhomogeneous, rank deficient problem. The standard approach is to use an outer iteration strategy with repeated removal of the fundamental modemore » contamination. The described GPT algorithm directly solves the GPT equations without the need of an outer iteration procedure by using Krylov subspaces that are orthogonal to the operator’s nullspace. Three test problems are solved and provide sufficient verification for the Rattlesnake’s GPT capability. We conclude with a preliminary example evaluating the impact of the Boron distribution in the TREAT reactor using perturbation theory.« less

An Efficient Modelling Approach for Prediction of Porosity Severity in Composite Structures

NASA Technical Reports Server (NTRS)

Bedayat, Houman; Forghani, Alireza; Hickmott, Curtis; Roy, Martin; Palmieri, Frank; Grimsley, Brian; Coxon, Brian; Fernlund, Goran

2017-01-01

Porosity, as a manufacturing process-induced defect, highly affects the mechanical properties of cured composites. Multiple phenomena affect the formation of porosity during the cure process. Porosity sources include entrapped air, volatiles and off-gassing as well as bag and tool leaks. Porosity sinks are the mechanisms that contribute to reducing porosity, including gas transport, void shrinkage and collapse as well as resin flow into void space. Despite the significant progress in porosity research, the fundamentals of porosity in composites are not yet fully understood. The highly coupled multi-physics and multi-scale nature of porosity make it a complicated problem to predict. Experimental evidence shows that resin pressure history throughout the cure cycle plays an important role in the porosity of the cured part. Maintaining high resin pressure results in void shrinkage and collapse keeps volatiles in solution thus preventing off-gassing and bubble formation. This study summarizes the latest development of an efficient FE modeling framework to simulate the gas and resin transport mechanisms that are among the major phenomena contributing to porosity.

Stabilized FE simulation of prototype thermal-hydraulics problems with integrated adjoint-based capabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shadid, J.N., E-mail: jnshadi@sandia.gov; Department of Mathematics and Statistics, University of New Mexico; Smith, T.M.

A critical aspect of applying modern computational solution methods to complex multiphysics systems of relevance to nuclear reactor modeling, is the assessment of the predictive capability of specific proposed mathematical models. In this respect the understanding of numerical error, the sensitivity of the solution to parameters associated with input data, boundary condition uncertainty, and mathematical models is critical. Additionally, the ability to evaluate and or approximate the model efficiently, to allow development of a reasonable level of statistical diagnostics of the mathematical model and the physical system, is of central importance. In this study we report on initial efforts tomore » apply integrated adjoint-based computational analysis and automatic differentiation tools to begin to address these issues. The study is carried out in the context of a Reynolds averaged Navier–Stokes approximation to turbulent fluid flow and heat transfer using a particular spatial discretization based on implicit fully-coupled stabilized FE methods. Initial results are presented that show the promise of these computational techniques in the context of nuclear reactor relevant prototype thermal-hydraulics problems.« less

Stabilized FE simulation of prototype thermal-hydraulics problems with integrated adjoint-based capabilities

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shadid, J. N.; Smith, T. M.; Cyr, E. C.

A critical aspect of applying modern computational solution methods to complex multiphysics systems of relevance to nuclear reactor modeling, is the assessment of the predictive capability of specific proposed mathematical models. The understanding of numerical error, the sensitivity of the solution to parameters associated with input data, boundary condition uncertainty, and mathematical models is critical. Additionally, the ability to evaluate and or approximate the model efficiently, to allow development of a reasonable level of statistical diagnostics of the mathematical model and the physical system, is of central importance. In our study we report on initial efforts to apply integrated adjoint-basedmore » computational analysis and automatic differentiation tools to begin to address these issues. The study is carried out in the context of a Reynolds averaged Navier–Stokes approximation to turbulent fluid flow and heat transfer using a particular spatial discretization based on implicit fully-coupled stabilized FE methods. We present the initial results that show the promise of these computational techniques in the context of nuclear reactor relevant prototype thermal-hydraulics problems.« less

Stabilized FE simulation of prototype thermal-hydraulics problems with integrated adjoint-based capabilities

DOE PAGES

Shadid, J. N.; Smith, T. M.; Cyr, E. C.; ...

2016-05-20

A critical aspect of applying modern computational solution methods to complex multiphysics systems of relevance to nuclear reactor modeling, is the assessment of the predictive capability of specific proposed mathematical models. The understanding of numerical error, the sensitivity of the solution to parameters associated with input data, boundary condition uncertainty, and mathematical models is critical. Additionally, the ability to evaluate and or approximate the model efficiently, to allow development of a reasonable level of statistical diagnostics of the mathematical model and the physical system, is of central importance. In our study we report on initial efforts to apply integrated adjoint-basedmore » computational analysis and automatic differentiation tools to begin to address these issues. The study is carried out in the context of a Reynolds averaged Navier–Stokes approximation to turbulent fluid flow and heat transfer using a particular spatial discretization based on implicit fully-coupled stabilized FE methods. We present the initial results that show the promise of these computational techniques in the context of nuclear reactor relevant prototype thermal-hydraulics problems.« less

Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Williams, Dean N.

2011-07-20

This report summarizes work carried out by the Ultra-scale Visualization Climate Data Analysis Tools (UV-CDAT) Team for the period of January 1, 2011 through June 30, 2011. It discusses highlights, overall progress, period goals, and collaborations and lists papers and presentations. To learn more about our project, please visit our UV-CDAT website (URL: http://uv-cdat.org). This report will be forwarded to the program manager for the Department of Energy (DOE) Office of Biological and Environmental Research (BER), national and international collaborators and stakeholders, and to researchers working on a wide range of other climate model, reanalysis, and observation evaluation activities. Themore » UV-CDAT executive committee consists of Dean N. Williams of Lawrence Livermore National Laboratory (LLNL); Dave Bader and Galen Shipman of Oak Ridge National Laboratory (ORNL); Phil Jones and James Ahrens of Los Alamos National Laboratory (LANL), Claudio Silva of Polytechnic Institute of New York University (NYU-Poly); and Berk Geveci of Kitware, Inc. The UV-CDAT team consists of researchers and scientists with diverse domain knowledge whose home institutions also include the National Aeronautics and Space Administration (NASA) and the University of Utah. All work is accomplished under DOE open-source guidelines and in close collaboration with the project's stakeholders, domain researchers, and scientists. Working directly with BER climate science analysis projects, this consortium will develop and deploy data and computational resources useful to a wide variety of stakeholders, including scientists, policymakers, and the general public. Members of this consortium already collaborate with other institutions and universities in researching data discovery, management, visualization, workflow analysis, and provenance. The UV-CDAT team will address the following high-level visualization requirements: (1) Alternative parallel streaming statistics and analysis pipelines - Data parallelism, Task parallelism, Visualization parallelism; (2) Optimized parallel input/output (I/O); (3) Remote interactive execution; (4) Advanced intercomparison visualization; (5) Data provenance processing and capture; and (6) Interfaces for scientists - Workflow data analysis and visualization construction tools, and Visualization interfaces.« less

By Hand or Not By-Hand: A Case Study of Alternative Approaches to Parallelize CFD Applications

NASA Technical Reports Server (NTRS)

Yan, Jerry C.; Bailey, David (Technical Monitor)

1997-01-01

While parallel processing promises to speed up applications by several orders of magnitude, the performance achieved still depends upon several factors, including the multiprocessor architecture, system software, data distribution and alignment, as well as the methods used for partitioning the application and mapping its components onto the architecture. The existence of the Gorden Bell Prize given out at Supercomputing every year suggests that while good performance can be attained for real applications on general purpose multiprocessors, the large investment in man-power and time still has to be repeated for each application-machine combination. As applications and machine architectures become more complex, the cost and time-delays for obtaining performance by hand will become prohibitive. Computer users today can turn to three possible avenues for help: parallel libraries, parallel languages and compilers, interactive parallelization tools. The success of these methodologies, in turn, depends on proper application of data dependency analysis, program structure recognition and transformation, performance prediction as well as exploitation of user supplied knowledge. NASA has been developing multidisciplinary applications on highly parallel architectures under the High Performance Computing and Communications Program. Over the past six years, the transition of underlying hardware and system software have forced the scientists to spend a large effort to migrate and recede their applications. Various attempts to exploit software tools to automate the parallelization process have not produced favorable results. In this paper, we report our most recent experience with CAPTOOL, a package developed at Greenwich University. We have chosen CAPTOOL for three reasons: 1. CAPTOOL accepts a FORTRAN 77 program as input. This suggests its potential applicability to a large collection of legacy codes currently in use. 2. CAPTOOL employs domain decomposition to obtain parallelism. Although the fact that not all kinds of parallelism are handled may seem unappealing, many NASA applications in computational aerosciences as well as earth and space sciences are amenable to domain decomposition. 3. CAPTOOL generates code for a large variety of environments employed across NASA centers: MPI/PVM on network of workstations to the IBS/SP2 and CRAY/T3D.

Electro-Thermal-Mechanical Simulation Capability Final Report

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, D

This is the Final Report for LDRD 04-ERD-086, 'Electro-Thermal-Mechanical Simulation Capability'. The accomplishments are well documented in five peer-reviewed publications and six conference presentations and hence will not be detailed here. The purpose of this LDRD was to research and develop numerical algorithms for three-dimensional (3D) Electro-Thermal-Mechanical simulations. LLNL has long been a world leader in the area of computational mechanics, and recently several mechanics codes have become 'multiphysics' codes with the addition of fluid dynamics, heat transfer, and chemistry. However, these multiphysics codes do not incorporate the electromagnetics that is required for a coupled Electro-Thermal-Mechanical (ETM) simulation. There aremore » numerous applications for an ETM simulation capability, such as explosively-driven magnetic flux compressors, electromagnetic launchers, inductive heating and mixing of metals, and MEMS. A robust ETM simulation capability will enable LLNL physicists and engineers to better support current DOE programs, and will prepare LLNL for some very exciting long-term DoD opportunities. We define a coupled Electro-Thermal-Mechanical (ETM) simulation as a simulation that solves, in a self-consistent manner, the equations of electromagnetics (primarily statics and diffusion), heat transfer (primarily conduction), and non-linear mechanics (elastic-plastic deformation, and contact with friction). There is no existing parallel 3D code for simulating ETM systems at LLNL or elsewhere. While there are numerous magnetohydrodynamic codes, these codes are designed for astrophysics, magnetic fusion energy, laser-plasma interaction, etc. and do not attempt to accurately model electromagnetically driven solid mechanics. This project responds to the Engineering R&D Focus Areas of Simulation and Energy Manipulation, and addresses the specific problem of Electro-Thermal-Mechanical simulation for design and analysis of energy manipulation systems such as magnetic flux compression generators and railguns. This project compliments ongoing DNT projects that have an experimental emphasis. Our research efforts have been encapsulated in the Diablo and ALE3D simulation codes. This new ETM capability already has both internal and external users, and has spawned additional research in plasma railgun technology. By developing this capability Engineering has become a world-leader in ETM design, analysis, and simulation. This research has positioned LLNL to be able to compete for new business opportunities with the DoD in the area of railgun design. We currently have a three-year $1.5M project with the Office of Naval Research to apply our ETM simulation capability to railgun bore life issues and we expect to be a key player in the railgun community.« less

Gage Measures Recessed Gaps

NASA Technical Reports Server (NTRS)

Zepeda, J. L.

1983-01-01

New tool measures separation between recessed parallel surfaces. Tiles have overhanging edges, tool designed to slip into gap from end so it extends through 0.040-inch crack. Measure gaps between 0.200 and 0.400 inch so gap fillers of proper thickness can be selected. Useful in numerous industrial situation involving gap measurements in inaccessable places.

Education Faculty Students' Views about Use of E-Books

ERIC Educational Resources Information Center

Yalman, Murat

2015-01-01

Parallel to technological developments, numerous new tools are now available for people's use. Societies adapt these tools to their professional lives by learning how to use them. In this way, they try to establish more comfortable working environments. Universities giving vocational education are supposed to teach these new technologies to their…

Laptop Paintings

ERIC Educational Resources Information Center

Gilman, Lisa

2005-01-01

All of the seventh-grade students in Lisa Gilman's school have laptop computers. She wanted them to use the computers not just as a research tool, but also as a tool for artistic expression. Since Impressionism is part of the seventh-grade curriculum, she had them identify parallels between the Impressionists' use of technology and artists' use of…

Combining Phase Identification and Statistic Modeling for Automated Parallel Benchmark Generation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jin, Ye; Ma, Xiaosong; Liu, Qing Gary

2015-01-01

Parallel application benchmarks are indispensable for evaluating/optimizing HPC software and hardware. However, it is very challenging and costly to obtain high-fidelity benchmarks reflecting the scale and complexity of state-of-the-art parallel applications. Hand-extracted synthetic benchmarks are time-and labor-intensive to create. Real applications themselves, while offering most accurate performance evaluation, are expensive to compile, port, reconfigure, and often plainly inaccessible due to security or ownership concerns. This work contributes APPRIME, a novel tool for trace-based automatic parallel benchmark generation. Taking as input standard communication-I/O traces of an application's execution, it couples accurate automatic phase identification with statistical regeneration of event parameters tomore » create compact, portable, and to some degree reconfigurable parallel application benchmarks. Experiments with four NAS Parallel Benchmarks (NPB) and three real scientific simulation codes confirm the fidelity of APPRIME benchmarks. They retain the original applications' performance characteristics, in particular the relative performance across platforms.« less

Preconditioned implicit solvers for the Navier-Stokes equations on distributed-memory machines

NASA Technical Reports Server (NTRS)

Ajmani, Kumud; Liou, Meng-Sing; Dyson, Rodger W.

1994-01-01

The GMRES method is parallelized, and combined with local preconditioning to construct an implicit parallel solver to obtain steady-state solutions for the Navier-Stokes equations of fluid flow on distributed-memory machines. The new implicit parallel solver is designed to preserve the convergence rate of the equivalent 'serial' solver. A static domain-decomposition is used to partition the computational domain amongst the available processing nodes of the parallel machine. The SPMD (Single-Program Multiple-Data) programming model is combined with message-passing tools to develop the parallel code on a 32-node Intel Hypercube and a 512-node Intel Delta machine. The implicit parallel solver is validated for internal and external flow problems, and is found to compare identically with flow solutions obtained on a Cray Y-MP/8. A peak computational speed of 2300 MFlops/sec has been achieved on 512 nodes of the Intel Delta machine,k for a problem size of 1024 K equations (256 K grid points).

An Undergraduate Course in Modeling and Simulation of Multiphysics Systems

ERIC Educational Resources Information Center

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…

Real-time implementations of image segmentation algorithms on shared memory multicore architecture: a survey (Conference Presentation)

NASA Astrophysics Data System (ADS)

Akil, Mohamed

2017-05-01

The real-time processing is getting more and more important in many image processing applications. Image segmentation is one of the most fundamental tasks image analysis. As a consequence, many different approaches for image segmentation have been proposed. The watershed transform is a well-known image segmentation tool. The watershed transform is a very data intensive task. To achieve acceleration and obtain real-time processing of watershed algorithms, parallel architectures and programming models for multicore computing have been developed. This paper focuses on the survey of the approaches for parallel implementation of sequential watershed algorithms on multicore general purpose CPUs: homogeneous multicore processor with shared memory. To achieve an efficient parallel implementation, it's necessary to explore different strategies (parallelization/distribution/distributed scheduling) combined with different acceleration and optimization techniques to enhance parallelism. In this paper, we give a comparison of various parallelization of sequential watershed algorithms on shared memory multicore architecture. We analyze the performance measurements of each parallel implementation and the impact of the different sources of overhead on the performance of the parallel implementations. In this comparison study, we also discuss the advantages and disadvantages of the parallel programming models. Thus, we compare the OpenMP (an application programming interface for multi-Processing) with Ptheads (POSIX Threads) to illustrate the impact of each parallel programming model on the performance of the parallel implementations.