Improving resilience of scientific software through a domain-specific approach
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Reguly, I. Z. (ORCID:0000000243854204)↗
SEARCH · Engineering Papers
Results for “Mesh optimization”
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Texture analysis improves level set segmentation of the anterior abdominal wall
Purpose: The treatment of ventral hernias (VH) has been a challenging problem for medical care. Repair of these hernias is fraught with failure; recurrence rates ranging from 24% to 43% have been reported, even with the use of biocompatible mesh. Currently, computed tomography (CT) is used to guide intervention through expert, but qualitative, clinical judgments, notably, quantitative metrics based on image-processing are not used. The authors propose that image segmentation methods to capture the three-dimensional structure of the abdominal wall and its abnormalities will provide a foundation on which to measure geometric properties of hernias and surrounding tissues and, therefore, to optimize intervention.Methods: In this study with 20 clinically acquired CT scans on postoperative patients, the authors demonstrated a novel approach to geometric classification of the abdominal. The authors’ approach uses a texture analysis based on Gabor filters to extract feature vectors and follows a fuzzy c-means clustering method to estimate voxelwise probability memberships for eight clusters. The memberships estimated from the texture analysis are helpful to identify anatomical structures with inhomogeneous intensities. The membership was used to guide the level set evolution, as well as to derive an initial start close to the abdominal wall.Results: Segmentation results on abdominal walls were both quantitatively and qualitatively validated with surface errors based on manually labeled ground truth. Using texture, mean surface errors for the outer surface of the abdominal wall were less than 2 mm, with 91% of the outer surface less than 5 mm away from the manual tracings; errors were significantly greater (2–5 mm) for methods that did not use the texture.Conclusions: The authors’ approach establishes a baseline for characterizing the abdominal wall for improving VH care. Inherent texture patterns in CT scans are helpful to the tissue classification, and texture analysis can improve the level set segmentation around the abdominal region.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Geometric Mapping of Tasks to Processors on Parallel Computers with Mesh or Torus Networks
We present a new method for reducing parallel applications' communication time by mapping their MPI tasks to processors in a way that lowers the distance messages travel and the amount of congestion in the network. Assuming geometric proximity among the tasks is a good approximation of their communication interdependence, we use a geometric partitioning algorithm to order both the tasks and the processors, assigning task parts to the corresponding processor parts. In this way, interdependent tasks are assigned to “nearby” cores in the network. We also present a number of algorithmic optimizations that exploit specific features of the network or application to further improve the quality of the mapping. We specifically address the case of sparse node allocation, where the nodes assigned to a job are not necessarily located in a contiguous block nor within close proximity to each other in the network. Furthermore, our methods generalize to contiguous allocations as well, and results are shown for both contiguous and non-contiguous allocations. We show that, for the structured finite difference mini-application MiniGhost, our mapping methods reduced communication time up to 75% relative to MiniGhost's default mapping on 128K cores of a Cray XK7 with sparse allocation. For the atmospheric modeling code E3SM/HOMME, our methods reduced communication time up to 31% on 16K cores of an IBM BlueGene/Q with contiguous allocation.
97 MATHEMATICS AND COMPUTING↗
Dissipation and Bathymetric Sensitivities in an Unstructured Mesh Global Tidal Model
Abstract The mechanisms and geographic distribution of global tidal dissipation in barotropic tidal models are examined using a high resolution unstructured mesh finite element model. Mesh resolution varies between 2 and 25 km and is especially focused on inner shelves and steep bathymetric gradients. Tidal response sensitivities to bathymetric changes are examined to put into context response sensitivities to frictional processes. We confirm that the Ronne Ice Shelf dramatically affects Atlantic tides but also find that bathymetry in the Hudson Bay system is a critical control. We follow a sequential frictional parameter optimization process and use TPXO9 data‐assimilated tidal elevations as a reference solution. From simulated velocities and depths, dissipation within the global model is estimated and allows us to pinpoint dissipation at high resolution. Boundary layer dissipation is extremely focused with 1.4% of the ocean accounting for 90% of the total. Internal tide friction is much more distributed with 16.7% of the ocean accounting for 90% of the total. Often highly regional dissipation can impact basin‐scale and even ocean wide tides. Optimized boundary layer friction parameters correlate very well with the physical characteristics of the locality with high friction factors associated with energetic tidal regions, deep ocean island chains, and ice covered areas. Global complex M 2 tide errors are 1.94 cm in deep waters. Total global boundary layer and internal tide dissipation are estimated, respectively, at 1.83 and 1.49 TW. This continues the trend in the literature toward attributing more dissipation to internal tides.
54 ENVIRONMENTAL SCIENCES↗
Network Uncertainty Quantification for Analysis of Multi-Component Systems
To impact physical mechanical system design decisions and realize the full promise of high-fidelity computational tools, simulation results must be integrated at the earliest stages of the design process. This is particularly challenging when dealing with uncertainty and optimizing for system-level performance metrics, as full-system models (often notoriously expensive and time-consuming to develop) are generally required to propagate uncertainties to system-level quantities of interest. Methods for propagating parameter and boundary condition uncertainty in networks of interconnected components hold promise for enabling design under uncertainty in real-world applications. These methods avoid the need for time consuming mesh generation of full-system geometries when changes are made to components or subassemblies. Additionally, they explicitly tie full-system model predictions to component/subassembly validation data which is valuable for qualification. These methods work by leveraging the fact that many engineered systems are inherently modular, being comprised of a hierarchy of components and subassemblies that are individually modified or replaced to define new system designs. By doing so, these methods enable rapid model development and the incorporation of uncertainty quantification earlier in the design process. The resulting formulation of the uncertainty propagation problem is iterative. We express the system model as a network of interconnected component models, which exchange solution information at component boundaries. We present a pair of approaches for propagating uncertainty in this type of decomposed system and provide implementations in the form of an open-source software library. We demonstrate these tools on a variety of applications and demonstrate the impact of problem-specific details on the performance and accuracy of the resulting UQ analysis. This work represents the most comprehensive investigation of these network uncertainty propagation methods to date.
42 ENGINEERING↗
Ume: Unstructured Mesh Explorations
Ume is an open-source collection of data structures for unstructured computational meshes and some simple algorithms that operate on them. These algorithms mimic the memory access patterns of a common class of operations found in several of the computational physics simulation codes developed at Los Alamos National Laboratory. The intent is that Ume can be used by hardware vendors to understand the memory traffic created by complex codes in a simplified environment, and to explore new means of optimization for that traffic. Ume is provided as a source-code C++ library and includes several applications that demonstrate the use of that library.
Henning, Paul↗
The L sub 1 finite element method for pure convection problems
The least squares (L sub 2) finite element method is introduced for 2-D steady state pure convection problems with smooth solutions. It is proven that the L sub 2 method has the same stability estimate as the original equation, i.e., the L sub 2 method has better control of the streamline derivative. Numerical convergence rates are given to show that the L sub 2 method is almost optimal. This L sub 2 method was then used as a framework to develop an iteratively reweighted L sub 2 finite element method to obtain a least absolute residual (L sub 1) solution for problems with discontinuous solutions. This L sub 1 finite element method produces a nonoscillatory, nondiffusive and highly accurate numerical solution that has a sharp discontinuity in one element on both coarse and fine meshes. A robust reweighting strategy was also devised to obtain the L sub 1 solution in a few iterations. A number of examples solved by using triangle and bilinear elements are presented.
Jiang, Bo-Nan↗
The L sub 1 finite element method for pure convection problems
The least squares (L sub 2) finite element method is introduced for 2-D steady state pure convection problems with smooth solutions. It is proven that the L sub 2 method has the same stability estimate as the original equation, i.e., the L sub 2 method has better control of the streamline derivative. Numerical convergence rates are given to show that the L sub 2 method is almost optimal. This L sub 2 method was then used as a framework to develop an iteratively reweighted L sub 2 finite element method to obtain a least absolute residual (L sub 1) solution for problems with discontinuous solutions. This L sub 1 finite element method produces a nonoscillatory, nondiffusive and highly accurate numerical solution that has a sharp discontinuity in one element on both coarse and fine meshes. A robust reweighting strategy was also devised to obtain the L sub 1 solution in a few iterations. A number of examples solved by using triangle and bilinear elements are presented.
Jiang, Bo-Nan↗
Acceleration of Thermochemistry Solves in MOOSE and Pronghorn
This work focuses on the development and implementation of strategies to accelerate thermochemical calculations within MOOSE-based multiphysics simulations, particularly for applications in MSRs. We highlight the inherent complexity of nuclear materials, which require a multiscale approach to accurately model their behavior across various physical domains, including mechanical, chemical, and thermal phenomena. Thermochemical equilibrium calculations are crucial for predicting material properties and enhancing the fidelity of these simulations. The integration of Thermochimica, a Gibbs energy minimizer, into MOOSE allows for the direct minimization of Gibbs energy at every point on the mesh. However, the computational cost of such integration is significant. To address this, we explored acceleration strategies such as multi-threading support and the use of a thermodynamic ValueCache to reduce redundant calculations. Additionally, we investigated modifications to Thermochimica to enable phase constraints and improve its coupling with phase-field models, which are essential for simulating microstructural evolution and corrosion in MSR. These efforts aim to optimize the computational efficiency and accuracy of multiphysics simulations, thereby supporting the development of reliable and efficient nuclear materials for next-generation reactor technologies.
36 - MATERIALS SCIENCE↗
Evaluating an Exterior Insulation and Finish System for Deep Energy Retrofits
This report provides a case study of a deep energy retrofit using a site-applied exterior insulation and finish system (EIFS). Prefabricated EIFS panels are also discussed as a potential wall insulation retrofit solution. EIFSs are common in new and retrofit commercial construction. Such products typically consist of five layers installed over the top of a water resistive barrier as follows: (1) Adhesive (2) Foam insulation (3) Base coat (4) Reinforcing mesh embedded in the base coat (5) Top or finish coat. They can be applied to new or existing buildings that employ wood or masonry construction, and can utilize an insulation thickness of up to 16 in. However, such systems are rarely used in lowrise residential retrofits. Reasons for this might include a lack of demand for or knowledge of the systems in residential retrofit industry, high cost, and/or lack of suitable distribution channels serving the residential market. While the final appearance of an EIFS installation resembles stucco, it is a distinctly different system. Stucco is a generic cementitious-based material, whereas EIFSs are proprietary synthetic formulations distributed by manufacturers to a network of authorized applicators. An EIFS is composed of polymeric (organic) bonded aggregate and cement reinforced with a glass mesh. Stucco is made of inorganic cement, sand, and lime. In this project, a home was retrofitted using a site-applied 4-in.-thick EIFS. Site-specific details were developed as required for the residential retrofit application. Site work and the costs of the EIFS were documented. The case study home was modeled using version 2 of the National Renewable Energy Laboratory-developed Building Energy Optimization (BEopt) energy and cost analysis software. While a package utilizing the 4-in. EIFS is the optimal retrofit of the options analyzed in terms of annualized energy-related costs, it is higher cost than replacing the siding with midrange vinyl alone. However, compared to high-end vinyl, the EIFS package has a lower annualized energy cost. This held true for both the Islip, New York (climate zone 4) and Boston (climate zone 5) case studies. The report discusses the risks, selection criteria, interactions with other building systems, cost, performance, and other aspects of using an EIFS in a deep energy retrofit. EIFSs do not require special site safety precautions beyond general construction site precautions. Moisture design is important. Trapping moisture between two vapor/air barriers is a risk of all wall systems, including EIFS cladding applications if an interior vapor barrier exists and if there is not adequate ventilation through the drainage plane behind the insulation layer. Face-sealed approaches that rely on exposed sealants do not provide acceptable rain control or durability and are very risky. Generally, fire codes permit EIFSs for most building types and conditions.
airtightness↗
An evaluation of soundings, analyses and model forecasts derived from TIROS-N and NOAA-6 satellite data
TIROS-N and NOAA-6 temperature soundings over North America during three days in January 1980, and synoptic analyses and numerical-model forecasts derived from them, are compared with conventional data and analyses from NMC's limited-area fine-mesh model (LFM). The collocated sounding comparison revealed significant errors, especially near the surface and the tropopause. Satellite-derived thermal gradients were found to be weak, and thickness-analysis difference fields to propagate eastward, suggesting that sounding errors are correlated with synoptic patterns. The same pattern of anomalies is seen in the model forecasts. More detailed determinations of the correlation detected here could be used to optimize the assimilation of satellite soundings to conventional data.
Koehler, T. L.↗
Reverse-Mode Algorithmic Differentiation of an OpenMP-Parallel Compressible Flow Solver
y Reverse-mode algorithmic differentiation (AD) is an established method for obtaining adjoint derivatives of computer simulation applications. In computational fluid dynamics (CFD), adjoint derivatives of a cost function output such as drag or lift with respect to design parameters such as surface coordinates or geometry control points are a key ingredient for shape optimization, uncertainty quantification and flow control. The computational cost of CFD applications and their derivatives makes it essential to use high-performance computing hardware efficiently, including multi- and many-core architectures. Nevertheless, OpenMP is not supported in most AD tools, and previously shown methods achieve poor scalability of the derivative code. We present the AD of an OpenMP-parallelized finite volume compressible flow solver for unstructured meshes. Our approach enables us to reuse the parallelization of the original code in the computation of adjoint derivatives. The method works by identifying code segments that can be differentiated in reverse-mode without changing their memory access pattern. The OpenMP parallelization is integrated into the derivative code during the build process in a way that is robust to modifications of the original code and independent of the OpenMP support of the differentiation tool. We show the scalability of our adjoint CFD solver on test cases ranging from thousands to millions of finite volume mesh cells on CPUs with up to 16 threads as well as on an Intel XeonPhi card with 236 threads. We demonstrate that our approach is more practical to implement for production-sized CFD codes and produces more efficient adjoint derivative code than previously shown AD methods.
Huckelheim, Jan↗
The practical impact of elastohydrodynamic lubrication
Elastohydrodynamic lubrication has had its most significant impact on, among all the types of concentrated contact mechanisms, rolling element bearings. EHL technology, through its inclusion in computer codes, now provides us with more effective methods for optimizing bearing design and for predicting bearing life, power loss, temperature and dynamic behavior. Bearing life prediction has advanced to a much more sophisticated level as compared to the calculation of fatigue life based on Lundberg-Palmgren theory. Application of elastohydrodynamics to gearing has, more or less, been limited to the calculation of pitch point film thicknesses. Techniques for calculating film thicknesses over the entire range of tooth meshes for arbitrarily shaped gear teeth (noninvolute, spur, helical, etc.) need to be developed. Elastomer seals with both unidirectional and reciprocating motion offer a fruitful application for the elastohydrodynamics of low modulus materials.
Anderson, W. J.↗
Generation of gear tooth surfaces by application of CNC machines
This study will demonstrate the importance of application of computer numerically controlled (CNC) machines in generation of gear tooth surfaces with new topology. This topology decreases gear vibration and will extend the gear capacity and service life. A preliminary investigation by a tooth contact analysis (TCA) program has shown that gear tooth surfaces in line contact (for instance, involute helical gears with parallel axes, worm gear drives with cylindrical worms, etc.) are very sensitive to angular errors of misalignment that cause edge contact and an unfavorable shape of transmission errors and vibration. The new topology of gear tooth surfaces is based on the localization of bearing contact, and the synthesis of a predesigned parabolic function of transmission errors that is able to absorb a piecewise linear function of transmission errors caused by gear misalignment. The report will describe the following topics: description of kinematics of CNC machines with six degrees of freedom that can be applied for generation of gear tooth surfaces with new topology. A new method for grinding of gear tooth surfaces by a cone surface or surface of revolution based on application of CNC machines is described. This method provides an optimal approximation of the ground surface to the given one. This method is especially beneficial when undeveloped ruled surfaces are to be ground. Execution of motions of the CNC machine is also described. The solution to this problem can be applied as well for the transfer of machine tool settings from a conventional generator to the CNC machine. The developed theory required the derivation of a modified equation of meshing based on application of the concept of space curves, space curves represented on surfaces, geodesic curvature, surface torsion, etc. Condensed information on these topics of differential geometry is provided as well.
Litvin, F. L.↗
Quasi-Optimal Schwarz Methods for the Conforming Spectral Element Discretization
Fast methods are proposed for solving the system K(sub N)x = b resulting from the discretization of self-adjoint elliptic equations in three dimensional domains by the spectral element method. The domain is decomposed into hexahedral elements, and in each of these elements the discretization space is formed by polynomials of degree N in each variable. Gauss-Lobatto-Legendre (GLL) quadrature rules replace the integrals in the Galerkin formulation. This system is solved by the preconditioned conjugate gradients method. The conforming finite element space on the GLL mesh consisting of piecewise Q(sub 1) elements produces a stiffness matrix K(sub h) that is spectrally equivalent to the spectral element stiffness matrix K(sub N). The action of the inverse of K(sub h) is expensive for large problems, and is therefore replaced by a Schwarz preconditioner B(sub h) of this finite element stiffness matrix. The preconditioned operator then becomes B(sub h)(exp -l)K(sub N). The technical difficulties stem from the nonregularity of the mesh. Tools to estimate the convergence of a large class of new iterative substructuring and overlapping Schwarz preconditioners are developed. This technique also provides a new analysis for an iterative substructuring method proposed by Pavarino and Widlund for the spectral element discretization.
Casarin, Mario↗
Higher-order adaptive finite-element methods for orbital-free density functional theory
In the present work, we study various numerical aspects of higher-order finite-element discretizations of the non-linear saddle-point formulation of orbital-free density-functional theory. We first investigate the robustness of viable solution schemes by analyzing the solvability conditions of the discrete problem. We find that a staggered solution procedure where the potential fields are computed consistently for every trial electron-density is a robust solution procedure for higher-order finite-element discretizations. We next study the convergence properties of higher-order finite-element discretizations of orbital-free density functional theory by considering benchmark problems that include calculations involving both pseudopotential as well as Coulomb singular potential fields. Our numerical studies suggest close to optimal rates of convergence on all benchmark problems for various orders of finite-element approximations considered in the present study. We finally investigate the computational efficiency afforded by various higher-order finite-element discretizations, which constitutes the main aspect of the present work, by measuring the CPU time for the solution of discrete equations on benchmark problems that include large Aluminum clusters. In these studies, we use mesh coarse-graining rates that are derived from error estimates and an a priori knowledge of the asymptotic solution of the far-field electronic fields. Our studies reveal a significant 100-1000 fold computational savings afforded by the use of higher-order finite-element discretization, alongside providing the desired chemical accuracy. We consider this study as a step towards developing a robust and computationally efficient discretization of electronic structure calculations using the finite-element basis.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Strong and Weak Scaling of the Sierra/SD Eigenvector Problem to a Billion Degrees of Freedom
Sierra/SD is a structural dynamics finite element software package that is known for its scalability and performance on DOE supercomputers. While there are historical documents demonstrating weak and strong scaling on DOE systems such as Redsky, no such formal studies have been done on modern architectures. This report demonstrates that Sierra/SD still scales on modern architectures. Non structured meshes in the shape of an I-Beam are solved in sizes ranging from fifty thousand degrees of freedom in serial up to one and a half billion degrees of freedom on over eighteen thousand processors using only default solver options. The report serves as a baseline for users to estimate computation cost of finite element analyses in Sierra/SD, understand how solver options relate to computational costs, and pick optimal processor counts to solve a given problem size, as well as a baseline for evaluating computational cost and scalability on next generation architectures.
42 ENGINEERING↗
A geometric nonlinear degenerated shell element using a mixed formulation with independently assumed strain fields
A mixed formulation is chosen to overcome deficiencies of the standard displacement-based shell model. Element development is traced from the incremental variational principle on through to the final set of equilibrium equations. Particular attention is paid to developing specific guidelines for selecting the optimal set of strain parameters. A discussion of constraint index concepts and their predictive capability related to locking is included. Performance characteristics of the elements are assessed in a wide variety of linear and nonlinear plate/shell problems. Despite limiting the study to geometric nonlinear analysis, a substantial amount of additional insight concerning the finite element modeling of thin plate/shell structures is provided. For example, in nonlinear analysis, given the same mesh and load step size, mixed elements converge in fewer iterations than equivalent displacement-based models. It is also demonstrated that, in mixed formulations, lower order elements are preferred. Additionally, meshes used to obtain accurate linear solutions do not necessarily converge to the correct nonlinear solution. Finally, a new form of locking was identified associated with employing elements designed for biaxial bending in uniaxial bending applications.
Graf, Wiley E.↗