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At least 1,783 records · Page 99

Particle simulation in a multiprocessor environment

A parallel implementation of a particle simulation method that is portable between a wide class of multiprocessor computers is presented. A fine grain spatial decomposition is utilized where several subdomains having a regular structure are computed at each processing node. This leads directly to an efficient and straightforward load balancing scheme if the number of subdomains at each processor is permitted to vary in an appropriate manner. Three dimensional simulations incorporating full thermochemical nonequilibrium are possible using the resulting code. Vectorizable algorithms are retained from earlier work allowing efficient use of deeply pipelined node processors where available. Performance results are presented from three different machine architectures demonstrating the portability of the code. On a 128-node Intel iPSC/860, performance is twice that of a single Cray-Y/MP CPU running a highly vectorized simulation code. Speedup is linear over the full range of number of processors on all target machines, indicating scalability of the method to higher degrees of parallelism.

Mcdonald, Jeffrey D.↗

Addressing Load Imbalance in Bioinformatics and Biomedical Applications: Efficient Scheduling across Multiple GPUs

Computational bioinformatics and biomedical applications frequently contain heterogeneously sized units of work or tasks, for instance due to variability in the sizes of biological sequences and molecules. Variable-sized workloads lead to load imbalances in parallel implementations which detract from efficiency and performance. Many modern computing resources now have multiple graphics processing units(GPUs) per computer for acceleration. These multiple GPU resources need to be used efficiently through balancing of workloads across the GPUs. OpenMP is a portable directive-based parallel programming API used ubiquitously in bioscience applications to program CPUs; recently, the use of OpenMP directives for GPU acceleration has become possible. Here, motivated by experiences with imbalanced loads in GPU-accelerated bioinformatics applications, we address the load balancing problem using OpenMP task-to-GPU scheduling combined with OpenMP GPU offloading for multiply heterogeneous workloads – loads with both variable input sizes, and simultaneously, variable convergence rates for algorithms with a stochastic component – scheduled across multiple GPUs. We aim to develop strategies which are both easy to use and have lower overheads, and may be incorporated incrementally in existing programs which already make use of OpenMP for CPU-based threading in order to make use of multi-GPU computers. We test different combinations of input size variability and convergence rate variability, and characterize the effects of these different scenarios on the performance of scheduling strategies across multiple GPUs with OpenMP. We present several dynamic scheduling solutions for different parallel patterns, explore optimizations, and provide publicly available example computational kernels to make these strategies easy to use in programs. This work will enable application developers to efficiently and easily use multiple GPUs for imbalanced workloads found in bioinformatics and biomedical applications.

Thavappiragasam, Mathialakan↗

Systematic generation of multibody equations of motion suitable for recursive and parallel manipulation

The formulation of a method known as the joint coordinate method for automatic generation of the equations of motion for multibody systems is summarized. For systems containing open or closed kinematic loops, the equations of motion can be reduced systematically to a minimum number of second order differential equations. The application of recursive and nonrecursive algorithms to this formulation, computational considerations and the feasibility of implementing this formulation on multiprocessor computers are discussed.

Nikravesh, Parviz E.↗

Did the GPU obfuscate the load imbalance in my MPI simulation?

The current proliferation of GPU-based HPC systems necessitates a method for assessing the performance of simulations on heterogeneous machines. The addition of GPUs to a system adds multiple hierarchical levels of parallelism to the node architecture. In this paper, we demonstrate that the traditional load imbalance metric is insufficient for capturing the load imbalance on GPU-based machines, since it treats the GPU as a monolithic entity and ignores the internal parallelism. We propose a new hierarchical metric that improves the correlation of measured performance and application workload by up to 20.61%. Using our metric for determining application load instead of the traditional metric as the input for the load balancing algorithm reduces the residual load imbalance by up to 4× in our application.

Eberius, David↗

Global Pathway Selection with Zero-RK

Global Pathway Selection (GPS) is an algorithm to effectively generates reduced (skeletal) chemistry mechanisms, which speeds up simulations and can be used as a systematic analytics tool to extract insights from complex reacting system. This release is an extension of the original code to run in parallel and to use LLNL's Zero-RK solver for fast solution of chemical problems.

Whitesides, RussellA↗

Global Pathway Selection with Zero-RK v0.5

Global Pathway Selection (GPS) is an algorithm to effectively generates reduced (skeletal) chemistry mechanisms, which speeds up simulations and can be used as a systematic analytics tool to extract insights from complex reacting system. This release is an extension of the original code to run in parallel and to use LLNL's Zero-RK solver for fast solution of chemical problems.

Whitesides, RussellA [Lawrence Livermore National ↗

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗

CSRI Summer Proceedings 2021

The Computer Science Research Institute (CSRI) brings university faculty and students to Sandia National Laboratories for focused collaborative research on Department of Energy (DOE) computer and computational science problems. The institute provides an opportunity for university researches to learn about problems in computer and computational science at DOE laboratories, and help transfer results of their research to programs at the labs. Some specific CSRI research interest areas are: scalable solvers, optimization, algebraic preconditioners, graph-based, discrete, and combinatorial algorithms, uncertainty estimation, validation and verification methods, mesh generation, dynamic load-balancing, virus and other malicious-code defense, visualization, scalable cluster computers, beyond Moore’s Law computing, exascale computing tools and application design, reduced order and multiscale modeling, parallel input/output, and theoretical computer science. The CSRI Summer Program is organized by CSRI and includes a weekly seminar series and the publication of a summer proceedings.

97 MATHEMATICS AND COMPUTING↗

Structural synthesis: Precursor and catalyst

More than twenty five years have elapsed since it was recognized that a rather general class of structural design optimization tasks could be properly posed as an inequality constrained minimization problem. It is suggested that, independent of primary discipline area, it will be useful to think about: (1) posing design problems in terms of an objective function and inequality constraints; (2) generating design oriented approximate analysis methods (giving special attention to behavior sensitivity analysis); (3) distinguishing between decisions that lead to an analysis model and those that lead to a design model; (4) finding ways to generate a sequence of approximate design optimization problems that capture the essential characteristics of the primary problem, while still having an explicit algebraic form that is matched to one or more of the established optimization algorithms; (5) examining the potential of optimum design sensitivity analysis to facilitate quantitative trade-off studies as well as participation in multilevel design activities. It should be kept in mind that multilevel methods are inherently well suited to a parallel mode of operation in computer terms or to a division of labor between task groups in organizational terms. Based on structural experience with multilevel methods general guidelines are suggested.

Schmit, L. A.↗

Route planning in a four-dimensional environment

Robots must be able to function in the real world. The real world involves processes and agents that move independently of the actions of the robot, sometimes in an unpredictable manner. A real-time integrated route planning and spatial representation system for planning routes through dynamic domains is presented. The system will find the safest most efficient route through space-time as described by a set of user defined evaluation functions. Because the route planning algorthims is highly parallel and can run on an SIMD machine in O(p) time (p is the length of a path), the system will find real-time paths through unpredictable domains when used in an incremental mode. Spatial representation, an SIMD algorithm for route planning in a dynamic domain, and results from an implementation on a traditional computer architecture are discussed.

Slack, M. G.↗

Fluid/chemistry modeling for hypersonic flight analysis

Design studies are underway for a variety of hypersonic flight vehicles. The National Aero-Space Plane will provide a reusable, single-stage-to-orbit capability for routine access to low earth orbit. Flight-capable satellites will dip into the atmosphere to maneuver to new orbits, while planetary probes will decelerate at their destination by atmospheric aerobraking. To supplement limited experimental capabilities in the hypersonic regime, computational fluid dynamics is being used to analyze the flow about these configurations. The governing equations include fluid dynamic as well as chemical species equations, which are being solved with new, robust numerical algorithms. Examples of CFD applications to hypersonic vehicles suggest an important role this technology will play in the development of future aerospace systems. The computational resources needed to obtain solutions are large, but solution-adaptive grids, convergence acceleration, and parallel processing may make run times manageable.

Edwards, Thomas A.↗

Newton-Krylov-Schwarz: An implicit solver for CFD

Newton-Krylov methods and Krylov-Schwarz (domain decomposition) methods have begun to become established in computational fluid dynamics (CFD) over the past decade. The former employ a Krylov method inside of Newton's method in a Jacobian-free manner, through directional differencing. The latter employ an overlapping Schwarz domain decomposition to derive a preconditioner for the Krylov accelerator that relies primarily on local information, for data-parallel concurrency. They may be composed as Newton-Krylov-Schwarz (NKS) methods, which seem particularly well suited for solving nonlinear elliptic systems in high-latency, distributed-memory environments. We give a brief description of this family of algorithms, with an emphasis on domain decomposition iterative aspects. We then describe numerical simulations with Newton-Krylov-Schwarz methods on aerodynamics applications emphasizing comparisons with a standard defect-correction approach, subdomain preconditioner consistency, subdomain preconditioner quality, and the effect of a coarse grid.

Cai, Xiao-Chuan↗

Task 7: ADPAC User's Manual

The overall objective of this study was to develop a 3-D numerical analysis for compressor casing treatment flowfields. The current version of the computer code resulting from this study is referred to as ADPAC (Advanced Ducted Propfan Analysis Codes-Version 7). This report is intended to serve as a computer program user's manual for the ADPAC code developed under Tasks 6 and 7 of the NASA Contract. The ADPAC program is based on a flexible multiple- block grid discretization scheme permitting coupled 2-D/3-D mesh block solutions with application to a wide variety of geometries. Aerodynamic calculations are based on a four-stage Runge-Kutta time-marching finite volume solution technique with added numerical dissipation. Steady flow predictions are accelerated by a multigrid procedure. An iterative implicit algorithm is available for rapid time-dependent flow calculations, and an advanced two equation turbulence model is incorporated to predict complex turbulent flows. The consolidated code generated during this study is capable of executing in either a serial or parallel computing mode from a single source code. Numerous examples are given in the form of test cases to demonstrate the utility of this approach for predicting the aerodynamics of modem turbomachinery configurations.

Hall, E. J.↗

System and method for embedding emotion in logic systems

A system, method, and computer readable-media for creating a stable synthetic neural system. The method includes training an intellectual choice-driven synthetic neural system (SNS), training an emotional rule-driven SNS by generating emotions from rules, incorporating the rule-driven SNS into the choice-driven SNS through an evolvable interface, and balancing the emotional SNS and the intellectual SNS to achieve stability in a nontrivial autonomous environment with a Stability Algorithm for Neural Entities (SANE). Generating emotions from rules can include coding the rules into the rule-driven SNS in a self-consistent way. Training the emotional rule-driven SNS can occur during a training stage in parallel with training the choice-driven SNS. The training stage can include a self assessment loop which measures performance characteristics of the rule-driven SNS against core genetic code. The method uses a stability threshold to measure stability of the incorporated rule-driven SNS and choice-driven SNS using SANE.

Curtis, Steven A.↗

Radiative Characteristics of Clouds Embedded in Smoke Derived from Airborne Multiangular Measurements

Clouds in the presence of absorbing aerosols result in their apparent darkening, observed at the top of atmosphere (TOA), which is associated with the radiative effects of aerosol absorption. Owing to the large radiative effect and potential impacts on regional climate, above-cloud aerosols have recently been characterized in multiple satellite-based studies. While satellite data are particularly useful in showing the radiative impact of above-cloud aerosols at the TOA, recent literature indicates large uncertainties in satellite retrievals of above-cloud aerosol optical depth (AOD) and single scattering albedo (SSA), which are among the most important parameters in the assessment of associated radiative effects. In this study, we analyze radiative characteristics of clouds in the presence of wildfire smoke using airborne data primarily from NASA's Cloud Absorption Radiometer, collected during the Arctic Research of the Composition of the Troposphere from Aircraft and Satellites campaign in Canada during the 2008 summer season. We found a strong positive reflectance (R) gradient in the UV-visible (VIS)-near infrared (NIR) spectrum for clouds embedded in dense smoke, as opposed to an (expected) negative gradient for cloud-free smoke and a flat spectrum for smoke-free cloud cover. Several cases of clouds embedded in thick smoke were found, when the aircraft made circular/spiral measurements, which not only allowed the complete characterization of angular distribution of smoke scattering but also provided the vertical distribution of smoke and clouds (within 0.5-5 km). Specifically, the largest darkening by smoke was found in the UV/VIS, with R(sub 0.34 microns) reducing to 0.2 (or 20%), in contrast to 0.8 at NIR wavelengths (e.g., 1.27 microns). The observed darkening is associated with large AODs (0.5-3.0) and moderately low SSA (0.85-0.93 at 0.53 microns), resulting in a significantly large instantaneous aerosol forcing efficiency of 254 +/- 47 W/sq m/τ. Our observations of smoke-cloud radiative interactions were found to be physically consistent with theoretical plane-parallel 1-D and Monte Carlo 3-D radiative transfer calculations, capturing the observed gradient across UV-VIS-NIR. Results from this study offer insights into aerosol-cloud radiative interactions and may help in better constraining satellite retrieval algorithms.

absorbing aerosols↗

Testing Fortran Software with pFunit

Over the past two decades, the emergence of highly effective software testing frameworks has greatly simplified the development and use of unit tests and has led to new software development paradigms such as test driven development (TDD). However, technical computing introduces a number of unique testing challenges, including distributed parallelism and numerical accuracy. This webinar will begin with a basic introduction to the use of pFUnit (parallel Fortran Unit testing framework) to develop tests for Message Passing Interface (MPI) plus Fortran (MPI+Fortran) software and then present some of the new capabilities in the latest release. We will also discuss some specialized methodologies for testing numerical algorithms and speculate about future framework capabilities that may improve our ability to test at exascale.

Clune, Tom↗

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↗

Video Mosaicking for Inspection of Gas Pipelines

A vision system that includes a specially designed video camera and an image-data-processing computer is under development as a prototype of robotic systems for visual inspection of the interior surfaces of pipes and especially of gas pipelines. The system is capable of providing both forward views and mosaicked radial views that can be displayed in real time or after inspection. To avoid the complexities associated with moving parts and to provide simultaneous forward and radial views, the video camera is equipped with a wide-angle (>165 ) fish-eye lens aimed along the axis of a pipe to be inspected. Nine white-light-emitting diodes (LEDs) placed just outside the field of view of the lens (see Figure 1) provide ample diffuse illumination for a high-contrast image of the interior pipe wall. The video camera contains a 2/3-in. (1.7-cm) charge-coupled-device (CCD) photodetector array and functions according to the National Television Standards Committee (NTSC) standard. The video output of the camera is sent to an off-the-shelf video capture board (frame grabber) by use of a peripheral component interconnect (PCI) interface in the computer, which is of the 400-MHz, Pentium II (or equivalent) class. Prior video-mosaicking techniques are applicable to narrow-field-of-view (low-distortion) images of evenly illuminated, relatively flat surfaces viewed along approximately perpendicular lines by cameras that do not rotate and that move approximately parallel to the viewed surfaces. One such technique for real-time creation of mosaic images of the ocean floor involves the use of visual correspondences based on area correlation, during both the acquisition of separate images of adjacent areas and the consolidation (equivalently, integration) of the separate images into a mosaic image, in order to insure that there are no gaps in the mosaic image. The data-processing technique used for mosaicking in the present system also involves area correlation, but with several notable differences: Because the wide-angle lens introduces considerable distortion, the image data must be processed to effectively unwarp the images (see Figure 2). The computer executes special software that includes an unwarping algorithm that takes explicit account of the cylindrical pipe geometry. To reduce the processing time needed for unwarping, parameters of the geometric mapping between the circular view of a fisheye lens and pipe wall are determined in advance from calibration images and compiled into an electronic lookup table. The software incorporates the assumption that the optical axis of the camera is parallel (rather than perpendicular) to the direction of motion of the camera. The software also compensates for the decrease in illumination with distance from the ring of LEDs.

Magruder, Darby↗