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At least 1,009 records · Page 56

Parallel volume ray-casting for unstructured-grid data on distributed-memory architectures

As computing technology continues to advance, computational modeling of scientific and engineering problems produces data of increasing complexity: large in size and unstructured in shape. Volume visualization of such data is a challenging problem. This paper proposes a distributed parallel solution that makes ray-casting volume rendering of unstructured-grid data practical. Both the data and the rendering process are distributed among processors. At each processor, ray-casting of local data is performed independent of the other processors. The global image composing processes, which require inter-processor communication, are overlapped with the local ray-casting processes to achieve maximum parallel efficiency. This algorithm differs from previous ones in four ways: it is completely distributed, less view-dependent, reasonably scalable, and flexible. Without using dynamic load balancing, test results on the Intel Paragon using from two to 128 processors show, on average, about 60% parallel efficiency.

Ma, Kwan-Liu↗

Dynamic remapping of parallel computations with varying resource demands

A large class of computational problems is characterized by frequent synchronization, and computational requirements which change as a function of time. When such a problem must be solved on a message passing multiprocessor machine, the combination of these characteristics lead to system performance which decreases in time. Performance can be improved with periodic redistribution of computational load; however, redistribution can exact a sometimes large delay cost. We study the issue of deciding when to invoke a global load remapping mechanism. Such a decision policy must effectively weigh the costs of remapping against the performance benefits. We treat this problem by constructing two analytic models which exhibit stochastically decreasing performance. One model is quite tractable; we are able to describe the optimal remapping algorithm, and the optimal decision policy governing when to invoke that algorithm. However, computational complexity prohibits the use of the optimal remapping decision policy. We then study the performance of a general remapping policy on both analytic models. This policy attempts to minimize a statistic W(n) which measures the system degradation (including the cost of remapping) per computation step over a period of n steps. We show that as a function of time, the expected value of W(n) has at most one minimum, and that when this minimum exists it defines the optimal fixed-interval remapping policy. Our decision policy appeals to this result by remapping when it estimates that W(n) is minimized. Our performance data suggests that this policy effectively finds the natural frequency of remapping. We also use the analytic models to express the relationship between performance and remapping cost, number of processors, and the computation's stochastic activity.

Nicol, D. M.↗

Fragme∩t: An Open‐Source Framework for Multiscale Quantum Chemistry Based on Fragmentation

Fragment-based quantum chemistry offers a means to circumvent the nonlinear computational scaling of conventional electronic structure calculations, by partitioning a large calculation into smaller subsystems then considering the many-body interactions between them. Variants of this approach have been used to parameterize classical force fields and machine learning potentials, applications that benefit from interoperability between quantum chemistry codes. However, there is a dearth of software that provides interoperability yet is purpose-built to handle the combinatorial complexity of fragment-based calculations. To fill this void we introduce “Fragme∩t”, an open-source software application that provides a tool for community validation of fragment-based methods, a platform for developing new approximations, and a framework for analyzing many-body interactions. Fragme∩t includes algorithms for automatic fragment generation and structure modification, and for distance- and energy-based screening of the requisite subsystems. Checkpointing, database management, and parallelization are handled internally and results are archived in a portable database. Interfaces to various quantum chemistry engines are easy to write and exist already for Q-Chem, PySCF, xTB, Orca, CP2K, MRCC, Psi4, NWChem, GAMESS, and MOPAC. Applications reported here demonstrate parallel efficiencies around 96% on more than 1000 processors but also showcase that the code can handle large-scale protein fragmentation using only workstation hardware, all with a codebase that is designed to be usable by non-experts. Fragme∩t conforms to modern software engineering best practices and is built upon well established technologies including Python, SQLite, and Ray. The source code is available under the Apache 2.0 license.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An implicit-explicit time splitting strategy for the far SOL plasma fluid model with DG-FEM discretization

We consider a far scrape-off layer (SOL) plasma fluid model of ions that is governed by a Braginskiitype model: a one-dimensional, nonlinear system of advection-diffusion equations coupled with a diffusion equation for neutral particles. Our motivation for studying this system arises from the coupling between the edge plasma and radio-frequency (RF) heating, where solving a far SOL plasma fluid model provides critical insights into edge plasma dynamics. Numerical simulations of plasma fluid models require advanced computational techniques to achieve both efficiency and accuracy, especially when resolving the boundary layer in magnetically confined plasmas. In this work, we propose an implicit-explicit time operator splitting strategy that allows for an efficient solution algorithm, where the diffusive terms are treated semi-implicitly requiring only a linear solve, while the advection part is handled explicitly using a strong-stability-preserving Runge-Kutta (SSP-RK3) scheme. This leads to a fully decoupled system in which the diffusion and advection sub-problems can be solved separately, simplifying the overall solution procedure and allowing for efficient parallelization, which is particularly relevant for exploring the impact of RF heating on the SOL plasma. The main challenge of the discretization is due to the strong coupling between diffusion and advection, particularly through the boundary conditions. This makes implementation of such a scheme in an accurate and stable manner nontrivial. We discuss in detail how to split the equations and manage boundary conditions to maintain stability and well-posedness for each subsystem. We also describe a spatial discretization approach, based on the discontinuous Galerkin finite element method (DG-FEM) and present numerical results for a one-dimensional system.

Burkovska, Olena [ORNL] (ORCID:0000000163101130)↗

Algorithmic considerations of integrated design for CSI on a hypercube architecture

An approach is presented to the integrated design problem for actively controlled large, flexible mechanical systems for which Control Structure Interaction (CSI) problems are of concern. The two coupled design problems were identified as the optimal Structural Design problem the optimal Controller Design problem. These two problems can be addressed within a decision making loop that would consider each separately, and then sequentially analyze the effects of one on the other. Embedded in such a loop would be the simulation and coordination tasks as part of the decision tools required in a total (software) package. All of the above are compute-intensive tasks. In any such task, possible decompositions and gains due to the inherent parallelism have to be exploited. The problems under consideration, as applied to large flexible mechanical structures, are particularly suited to be mapped onto multicomputer systems in a hypercube topology.

Oezguener, UE.↗

A robot conditioned reflex system modeled after the cerebellum.

Reduction of a theory of cerebellar function to computer software for the control of a mechanical manipulator. This reduction is achieved by considering the cerebellum, along with the higher-level brain centers which control it, as a type of finite-state machine with input entering the cerebellum via mossy fibers from the periphery and output from the cerebellum occurring via Purkinje cells. It is hypothesized that the cerebellum learns by an error-correction system similar to Perceptron training algorithms. An electromechanical model of the cerebellum is then developed for the control of a mechanical arm. The problem of modeling the granular layer which selects the set of parallel fibers which are active at any instant of time is considered, and a relevance matrix is constructed to model the relative degree of influence which mossy fibers from the various joints have on the sets of granule cells unique to each joint.

Albus, J. S.↗

Sparse Gaussian elimination with controlled fill-in on a shared memory multiprocessor

It is shown that in sparse matrices arising from electronic circuits, it is possible to do computations on many diagonal elements simultaneously. A technique for obtaining an ordered compatible set directly from the ordered incompatible table is given. The ordering is based on the Markowitz number of the pivot candidates. This technique generates a set of compatible pivots with the property of generating few fills. A novel heuristic algorithm is presented that combines the idea of an order-compatible set with a limited binary tree search to generate several sets of compatible pivots in linear time. An elimination set for reducing the matrix is generated and selected on the basis of a minimum Markowitz sum number. The parallel pivoting technique presented is a stepwise algorithm and can be applied to any submatrix of the original matrix. Thus, it is not a preordering of the sparse matrix and is applied dynamically as the decomposition proceeds. Parameters are suggested to obtain a balance between parallelism and fill-ins. Results of applying the proposed algorithms on several large application matrices using the HEP multiprocessor (Kowalik, 1985) are presented and analyzed.

Alaghband, Gita↗

Fast Multipole Methods for Three-Dimensional N-body Problems

We are developing computational tools for the simulations of three-dimensional flows past bodies undergoing arbitrary motions. High resolution viscous vortex methods have been developed that allow for extended simulations of two-dimensional configurations such as vortex generators. Our objective is to extend this methodology to three dimensions and develop a robust computational scheme for the simulation of such flows. A fundamental issue in the use of vortex methods is the ability of employing efficiently large numbers of computational elements to resolve the large range of scales that exist in complex flows. The traditional cost of the method scales as Omicron (N(sup 2)) as the N computational elements/particles induce velocities at each other, making the method unacceptable for simulations involving more than a few tens of thousands of particles. In the last decade fast methods have been developed that have operation counts of Omicron (N log N) or Omicron (N) (referred to as BH and GR respectively) depending on the details of the algorithm. These methods are based on the observation that the effect of a cluster of particles at a certain distance may be approximated by a finite series expansion. In order to exploit this observation we need to decompose the element population spatially into clusters of particles and build a hierarchy of clusters (a tree data structure) - smaller neighboring clusters combine to form a cluster of the next size up in the hierarchy and so on. This hierarchy of clusters allows one to determine efficiently when the approximation is valid. This algorithm is an N-body solver that appears in many fields of engineering and science. Some examples of its diverse use are in astrophysics, molecular dynamics, micro-magnetics, boundary element simulations of electromagnetic problems, and computer animation. More recently these N-body solvers have been implemented and applied in simulations involving vortex methods. Koumoutsakos and Leonard (1995) implemented the GR scheme in two dimensions for vector computer architectures allowing for simulations of bluff body flows using millions of particles. Winckelmans presented three-dimensional, viscous simulations of interacting vortex rings, using vortons and an implementation of a BH scheme for parallel computer architectures. Bhatt presented a vortex filament method to perform inviscid vortex ring interactions, with an alternative implementation of a BH scheme for a Connection Machine parallel computer architecture.

Koumoutsakos, P.↗

Numerical eigen-spectrum slicing, accurate orthogonal eigen-basis, and mixed-precision eigenvalue refinement using OpenMP data-dependent tasks and accelerator offload

Performing a variety of numerical computations efficiently and, at the same time, in a portable fashion requires both an overarching design followed by a number of implementation strategies. All of these are exemplified below as we present transitioning the PLASMA numerical library from relying on dependence-driven large tasks to achieving utilization of fine grain tasking and offload to hardware accelerators while keeping its core dependence sets: OpenMP source code pragmas and runtime for most system-level functionality and basic low-level numerical kernels provided directly by hardware vendors or open source projects with vendor contributions. We also present new algorithmic methods and their efficient parallel implementations including fine grained tasking for eigen-spectrum slicing and offload for mixed-precision eigenvalue refinement. We provide performance, scaling, and numerical results showing sizable gains over the available solutions from either the open source and vendor-provided packages.

Luszczek, Piotr↗

Unconditionally stable concurrent procedures for transient finite-element analysis

A family of algorithms was outlined which would appear to be particularly well-suited for implementation in a parallel environment. This is due to the fact that for any partition of the mesh each subdomain in the partition can be processed over a time step simultaneously and independently of the rest. The method eliminates the need for assembling and factorizing large global arrays while retaining the unconditional stability properties of the algorithms used at the local level. To critically appraise the proposed methodology, two limiting cases were considered: element-by-element mesh partitions, and coarse mesh partitions. It was concluded that while the proposed methodology can be useful in sequential machines, it would appear to be promising as it bears on computation. It should also be emphasized that extensions of the method to nonlinear problems are possible.

Ortiz, Michael↗

A Large-Grain Mapping Approach for Multiprocessor Systems Through Data Flow Model Ph.D. Thesis

A large-grain level mapping method is presented of numerical oriented applications onto multiprocessor systems. The method is based on the large-grain data flow representation of the input application and it assumes a general interconnection topology of the multiprocessor system. The large-grain data flow model was used because such representation best exhibits inherited parallelism in many important applications, e.g., CFD models based on partial differential equations can be presented in large-grain data flow format, very effectively. A generalized interconnection topology of the multiprocessor architecture is considered, including such architectural issues as interprocessor communication cost, with the aim to identify the 'best matching' between the application and the multiprocessor structure. The objective is to minimize the total execution time of the input algorithm running on the target system. The mapping strategy consists of the following: (1) large-grain data flow graph generation from the input application using compilation techniques; (2) data flow graph partitioning into basic computation blocks; and (3) physical mapping onto the target multiprocessor using a priority allocation scheme for the computation blocks.

Kim, Hwa-Soo↗

Parallel VLSI architecture emulation and the organization of APSA/MPP

The Applicative Programming System Architecture (APSA) combines an applicative language interpreter with a novel parallel computer architecture that is well suited for Very Large Scale Integration (VLSI) implementation. The Massively Parallel Processor (MPP) can simulate VLSI circuits by allocating one processing element in its square array to an area on a square VLSI chip. As long as there are not too many long data paths, the MPP can simulate a VLSI clock cycle very rapidly. The APSA circuit contains a binary tree with a few long paths and many short ones. A skewed H-tree layout allows every processing element to simulate a leaf cell and up to four tree nodes, with no loss in parallelism. Emulation of a key APSA algorithm on the MPP resulted in performance 16,000 times faster than a Vax. This speed will make it possible for the APSA language interpreter to run fast enough to support research in parallel list processing algorithms.

Odonnell, John T.↗

Constrained Multipoint Aerodynamic Shape Optimization Using an Adjoint Formulation and Parallel Computers

An aerodynamic shape optimization method that treats the design of complex aircraft configurations subject to high fidelity computational fluid dynamics (CFD), geometric constraints and multiple design points is described. The design process will be greatly accelerated through the use of both control theory and distributed memory computer architectures. Control theory is employed to derive the adjoint differential equations whose solution allows for the evaluation of design gradient information at a fraction of the computational cost required by previous design methods. The resulting problem is implemented on parallel distributed memory architectures using a domain decomposition approach, an optimized communication schedule, and the MPI (Message Passing Interface) standard for portability and efficiency. The final result achieves very rapid aerodynamic design based on a higher order CFD method. In order to facilitate the integration of these high fidelity CFD approaches into future multi-disciplinary optimization (NW) applications, new methods must be developed which are capable of simultaneously addressing complex geometries, multiple objective functions, and geometric design constraints. In our earlier studies, we coupled the adjoint based design formulations with unconstrained optimization algorithms and showed that the approach was effective for the aerodynamic design of airfoils, wings, wing-bodies, and complex aircraft configurations. In many of the results presented in these earlier works, geometric constraints were satisfied either by a projection into feasible space or by posing the design space parameterization such that it automatically satisfied constraints. Furthermore, with the exception of reference 9 where the second author initially explored the use of multipoint design in conjunction with adjoint formulations, our earlier works have focused on single point design efforts. Here we demonstrate that the same methodology may be extended to treat complete configuration designs subject to multiple design points and geometric constraints. Examples are presented for both transonic and supersonic configurations ranging from wing alone designs to complex configuration designs involving wing, fuselage, nacelles and pylons.

Reuther, James↗

Verification and Validation of Elastodynamic Simulation Software for Aerospace Research

Physics-based simulation of nondestructive evaluation (NDE) inspection can help to advance the inspectability and reliability of mechanical systems. However, NDE simulations applicable to non-idealized mechanical components often require large compute domains and long run times. This has prompted development of custom NDE simulation software tailored to high performance computing (HPC) hardware. Verification and validation (V&V) is an integral part of developing this software to ensure implementations are robust and applicable to inspection problems, producing tools and simulations suitable for computational NDE research. This presentation addresses factors common to V&V of several elastodynamic simulation codes applicable to ultrasonic NDE. Examples are drawn from in-house simulation software at NASA Langley Research Center, ranging from ensuring reliability in a 1D heterogeneous media wave equation solver to the V&V needs of 3D cluster-parallel elastodynamic software. Factors specific to a research environment are addressed, where individual simulation results can be as relevant as the software product itself. Distinct facets of V&V are discussed including testing to establish software reliability, employing systematic approaches for consistency with fundamental conservation laws, establishing the numerical stability of algorithms, and demonstrating concurrence with empirical data. This talk also addresses V&V practices for small groups of researchers. This includes establishing resources (e.g. time and personnel) for V&V during project planning to mitigate and control the risk of setbacks. Similarly, we identify ways for individual researchers to use V&V during simulation software development itself to both speed up the development process and reduce incurred technical debt.

NDE↗

Electrical Impedance Tomography Technology: 2013 Center Innovation Fund Final Report

Electrical impedance tomography is a medical noninvasive imaging technology which has advantages over other medical imaging technologies for medically safe long term real time internal imaging monitoring applications in human patients. The technology is much more compact, portable, low power and potentially more low cost compared to other medical image technologies, making it very well suited for medical aerospace and spaceflight applications. EIT technology’s main drawback has been low image resolution, and consequently improving EIT resolution is the primary research goal, as well as increasing imaging speed for real time animation imaging. In a relatively short time the BERL group has brought together design plans, technical resources and has built and tested hardware with the purpose of improving EIT imaging technology. EIT prototype system development plans and system designs have been made to target needed EIT technical improvement in electronic and computer hardware as well as EIT software technology. New hardware design and fabrication resources and technologies have been brought together through resourceful use of existing equipment and software at BERL, and a significant advance has been made in custom electronic hardware prototyping capabilities in collaboration with EFAL, for mutual benefit for both NASA KSC laboratories. BERL has gained significant EIT software capability and tested EIT imaging algorithm code through collaboration with an internationally recognized EIT software development and research forum. A new custom workstation has been developed, built and tested using internal resources, equipment and expertise, that includes a new state-of-the-art massively parallel technology that is commercially available. Custom prototype hardware has been designed and tested, a high priority electronic design, key to improving electronic performance and image quality, has been researched and tested in four designs, with a summary of test results of the selected design illustrated here. The selected design performance exceeds the developed EIT design hardware specifications.

Michael R Lapointe↗

The Plane-parallel Albedo Bias of Liquid Clouds from MODIS Observations

In our most advanced modeling tools for climate change prediction, namely General Circulation Models (GCMs), the schemes used to calculate the budget of solar and thermal radiation commonly assume that clouds are horizontally homogeneous at scales as large as a few hundred kilometers. However, this assumption, used for convenience, computational speed, and lack of knowledge on cloud small scale variability, leads to erroneous estimates of the radiation budget. This paper provides a global picture of the solar radiation errors at scales of approximately 100 km due to warm (liquid phase) clouds only. To achieve this, we use cloud retrievals from the instrument MODIS on the Terra and Aqua satellites, along with atmospheric and surface information, as input into a GCM-style radiative transfer algorithm. Since the MODIS product contains information on cloud variability below 100 km we can run the radiation algorithm both for the variable and the (assumed) homogeneous clouds. The difference between these calculations for reflected or transmitted solar radiation constitutes the bias that GCMs would commit if they were able to perfectly predict the properties of warm clouds, but then assumed they were homogeneous for radiation calculations. We find that the global average of this bias is approx.2-3 times larger in terms of energy than the additional amount of thermal energy that would be trapped if we were to double carbon dioxide from current concentrations. We should therefore make a greater effort to predict horizontal cloud variability in GCMs and account for its effects in radiation calculations.

Oreopoulos, Lazaros↗

Monte-Carlo methods make Dempster-Shafer formalism feasible

One of the main obstacles to the applications of Dempster-Shafer formalism is its computational complexity. If we combine m different pieces of knowledge, then in general case we have to perform up to 2(sup m) computational steps, which for large m is infeasible. For several important cases algorithms with smaller running time were proposed. We prove, however, that if we want to compute the belief bel(Q) in any given query Q, then exponential time is inevitable. It is still inevitable, if we want to compute bel(Q) with given precision epsilon. This restriction corresponds to the natural idea that since initial masses are known only approximately, there is no sense in trying to compute bel(Q) precisely. A further idea is that there is always some doubt in the whole knowledge, so there is always a probability p(sub o) that the expert's knowledge is wrong. In view of that it is sufficient to have an algorithm that gives a correct answer a probability greater than 1-p(sub o). If we use the original Dempster's combination rule, this possibility diminishes the running time, but still leaves the problem infeasible in the general case. We show that for the alternative combination rules proposed by Smets and Yager feasible methods exist. We also show how these methods can be parallelized, and what parallelization model fits this problem best.

Kreinovich, Vladik YA.↗

A Universal Formula for Extracting the Euler Angles

Recently, the authors completed a study of the Davenport angles, which are a generalization of the Euler angles for which the initial and final Euler axes need not be either mutually parallel or mutually perpendicular or even along the coordinate axes. During the conduct of that study, those authors discovered a relationship which can be used to compute straightforwardly the Euler angles characterizing a proper-orthogonal direction-cosine matrix for an arbitrary Euler-axis set satisfying n(sub 1) x n(sub 2) = 0 and n(sub 3) x n(sub 1) = 0, which is also satisfied by the more usual Euler angles we encounter commonly in the practice of Astronautics. Rather than leave that relationship hidden in an article with very different focus from the present Engineering note, we present it and the universal algorithm derived from it for extracting the Euler angles from the direction-cosine matrix here. We also offer literal "code" for performing the operations, numerical examples, and general considerations about the extraction of Euler angles which are not universally known, particularly, the treatment of statistical error.

Shuster, Malcolm D.↗