ICASE/LaRC Workshop on Benchmark Problems in Computational Aeroacoustics (CAA)

NASA Technical Reports Server (NTRS)

Hardin, Jay C. (Editor); Ristorcelli, J. Ray (Editor); Tam, Christopher K. W. (Editor)

1995-01-01

The proceedings of the Benchmark Problems in Computational Aeroacoustics Workshop held at NASA Langley Research Center are the subject of this report. The purpose of the Workshop was to assess the utility of a number of numerical schemes in the context of the unusual requirements of aeroacoustical calculations. The schemes were assessed from the viewpoint of dispersion and dissipation -- issues important to long time integration and long distance propagation in aeroacoustics. Also investigated were the effect of implementation of different boundary conditions. The Workshop included a forum in which practical engineering problems related to computational aeroacoustics were discussed. This discussion took the form of a dialogue between an industrial panel and the workshop participants and was an effort to suggest the direction of evolution of this field in the context of current engineering needs.

Radiation Detection Computational Benchmark Scenarios

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

Shaver, Mark W.; Casella, Andrew M.; Wittman, Richard S.

2013-09-24

Modeling forms an important component of radiation detection development, allowing for testing of new detector designs, evaluation of existing equipment against a wide variety of potential threat sources, and assessing operation performance of radiation detection systems. This can, however, result in large and complex scenarios which are time consuming to model. A variety of approaches to radiation transport modeling exist with complementary strengths and weaknesses for different problems. This variety of approaches, and the development of promising new tools (such as ORNL’s ADVANTG) which combine benefits of multiple approaches, illustrates the need for a means of evaluating or comparing differentmore » techniques for radiation detection problems. This report presents a set of 9 benchmark problems for comparing different types of radiation transport calculations, identifying appropriate tools for classes of problems, and testing and guiding the development of new methods. The benchmarks were drawn primarily from existing or previous calculations with a preference for scenarios which include experimental data, or otherwise have results with a high level of confidence, are non-sensitive, and represent problem sets of interest to NA-22. From a technical perspective, the benchmarks were chosen to span a range of difficulty and to include gamma transport, neutron transport, or both and represent different important physical processes and a range of sensitivity to angular or energy fidelity. Following benchmark identification, existing information about geometry, measurements, and previous calculations were assembled. Monte Carlo results (MCNP decks) were reviewed or created and re-run in order to attain accurate computational times and to verify agreement with experimental data, when present. Benchmark information was then conveyed to ORNL in order to guide testing and development of hybrid calculations. The results of those ADVANTG calculations were then sent to PNNL for compilation. This is a report describing the details of the selected Benchmarks and results from various transport codes.« less

Benchmark Problems Used to Assess Computational Aeroacoustics Codes

NASA Technical Reports Server (NTRS)

Dahl, Milo D.; Envia, Edmane

2005-01-01

The field of computational aeroacoustics (CAA) encompasses numerical techniques for calculating all aspects of sound generation and propagation in air directly from fundamental governing equations. Aeroacoustic problems typically involve flow-generated noise, with and without the presence of a solid surface, and the propagation of the sound to a receiver far away from the noise source. It is a challenge to obtain accurate numerical solutions to these problems. The NASA Glenn Research Center has been at the forefront in developing and promoting the development of CAA techniques and methodologies for computing the noise generated by aircraft propulsion systems. To assess the technological advancement of CAA, Glenn, in cooperation with the Ohio Aerospace Institute and the AeroAcoustics Research Consortium, organized and hosted the Fourth CAA Workshop on Benchmark Problems. Participants from industry and academia from both the United States and abroad joined to present and discuss solutions to benchmark problems. These demonstrated technical progress ranging from the basic challenges to accurate CAA calculations to the solution of CAA problems of increasing complexity and difficulty. The results are documented in the proceedings of the workshop. Problems were solved in five categories. In three of the five categories, exact solutions were available for comparison with CAA results. A fourth category of problems representing sound generation from either a single airfoil or a blade row interacting with a gust (i.e., problems relevant to fan noise) had approximate analytical or completely numerical solutions. The fifth category of problems involved sound generation in a viscous flow. In this case, the CAA results were compared with experimental data.

Evolutionary Optimization of a Geometrically Refined Truss

NASA Technical Reports Server (NTRS)

Hull, P. V.; Tinker, M. L.; Dozier, G. V.

2007-01-01

Structural optimization is a field of research that has experienced noteworthy growth for many years. Researchers in this area have developed optimization tools to successfully design and model structures, typically minimizing mass while maintaining certain deflection and stress constraints. Numerous optimization studies have been performed to minimize mass, deflection, and stress on a benchmark cantilever truss problem. Predominantly traditional optimization theory is applied to this problem. The cross-sectional area of each member is optimized to minimize the aforementioned objectives. This Technical Publication (TP) presents a structural optimization technique that has been previously applied to compliant mechanism design. This technique demonstrates a method that combines topology optimization, geometric refinement, finite element analysis, and two forms of evolutionary computation: genetic algorithms and differential evolution to successfully optimize a benchmark structural optimization problem. A nontraditional solution to the benchmark problem is presented in this TP, specifically a geometrically refined topological solution. The design process begins with an alternate control mesh formulation, multilevel geometric smoothing operation, and an elastostatic structural analysis. The design process is wrapped in an evolutionary computing optimization toolset.

Integrating CFD, CAA, and Experiments Towards Benchmark Datasets for Airframe Noise Problems

NASA Technical Reports Server (NTRS)

Choudhari, Meelan M.; Yamamoto, Kazuomi

2012-01-01

Airframe noise corresponds to the acoustic radiation due to turbulent flow in the vicinity of airframe components such as high-lift devices and landing gears. The combination of geometric complexity, high Reynolds number turbulence, multiple regions of separation, and a strong coupling with adjacent physical components makes the problem of airframe noise highly challenging. Since 2010, the American Institute of Aeronautics and Astronautics has organized an ongoing series of workshops devoted to Benchmark Problems for Airframe Noise Computations (BANC). The BANC workshops are aimed at enabling a systematic progress in the understanding and high-fidelity predictions of airframe noise via collaborative investigations that integrate state of the art computational fluid dynamics, computational aeroacoustics, and in depth, holistic, and multifacility measurements targeting a selected set of canonical yet realistic configurations. This paper provides a brief summary of the BANC effort, including its technical objectives, strategy, and selective outcomes thus far.

Summary of comparison and analysis of results from exercises 1 and 2 of the OECD PBMR coupled neutronics/thermal hydraulics transient benchmark

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

Mkhabela, P.; Han, J.; Tyobeka, B.

2006-07-01

The Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) has accepted, through the Nuclear Science Committee (NSC), the inclusion of the Pebble-Bed Modular Reactor 400 MW design (PBMR-400) coupled neutronics/thermal hydraulics transient benchmark problem as part of their official activities. The scope of the benchmark is to establish a well-defined problem, based on a common given library of cross sections, to compare methods and tools in core simulation and thermal hydraulics analysis with a specific focus on transient events through a set of multi-dimensional computational test problems. The benchmark includes three steady state exercises andmore » six transient exercises. This paper describes the first two steady state exercises, their objectives and the international participation in terms of organization, country and computer code utilized. This description is followed by a comparison and analysis of the participants' results submitted for these two exercises. The comparison of results from different codes allows for an assessment of the sensitivity of a result to the method employed and can thus help to focus the development efforts on the most critical areas. The two first exercises also allow for removing of user-related modeling errors and prepare core neutronics and thermal-hydraulics models of the different codes for the rest of the exercises in the benchmark. (authors)« less

Piping benchmark problems. Volume 1. Dynamic analysis uniform support motion response spectrum method

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

Bezler, P.; Hartzman, M.; Reich, M.

1980-08-01

A set of benchmark problems and solutions have been developed for verifying the adequacy of computer programs used for dynamic analysis and design of nuclear piping systems by the Response Spectrum Method. The problems range from simple to complex configurations which are assumed to experience linear elastic behavior. The dynamic loading is represented by uniform support motion, assumed to be induced by seismic excitation in three spatial directions. The solutions consist of frequencies, participation factors, nodal displacement components and internal force and moment components. Solutions to associated anchor point motion static problems are not included.

Augmented neural networks and problem structure-based heuristics for the bin-packing problem

NASA Astrophysics Data System (ADS)

Kasap, Nihat; Agarwal, Anurag

2012-08-01

In this article, we report on a research project where we applied augmented-neural-networks (AugNNs) approach for solving the classical bin-packing problem (BPP). AugNN is a metaheuristic that combines a priority rule heuristic with the iterative search approach of neural networks to generate good solutions fast. This is the first time this approach has been applied to the BPP. We also propose a decomposition approach for solving harder BPP, in which subproblems are solved using a combination of AugNN approach and heuristics that exploit the problem structure. We discuss the characteristics of problems on which such problem structure-based heuristics could be applied. We empirically show the effectiveness of the AugNN and the decomposition approach on many benchmark problems in the literature. For the 1210 benchmark problems tested, 917 problems were solved to optimality and the average gap between the obtained solution and the upper bound for all the problems was reduced to under 0.66% and computation time averaged below 33 s per problem. We also discuss the computational complexity of our approach.

An Integrated Development Environment for Adiabatic Quantum Programming

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

Humble, Travis S; McCaskey, Alex; Bennink, Ryan S

2014-01-01

Adiabatic quantum computing is a promising route to the computational power afforded by quantum information processing. The recent availability of adiabatic hardware raises the question of how well quantum programs perform. Benchmarking behavior is challenging since the multiple steps to synthesize an adiabatic quantum program are highly tunable. We present an adiabatic quantum programming environment called JADE that provides control over all the steps taken during program development. JADE captures the workflow needed to rigorously benchmark performance while also allowing a variety of problem types, programming techniques, and processor configurations. We have also integrated JADE with a quantum simulation enginemore » that enables program profiling using numerical calculation. The computational engine supports plug-ins for simulation methodologies tailored to various metrics and computing resources. We present the design, integration, and deployment of JADE and discuss its use for benchmarking adiabatic quantum programs.« less

Accurate ω-ψ Spectral Solution of the Singular Driven Cavity Problem

NASA Astrophysics Data System (ADS)

Auteri, F.; Quartapelle, L.; Vigevano, L.

2002-08-01

This article provides accurate spectral solutions of the driven cavity problem, calculated in the vorticity-stream function representation without smoothing the corner singularities—a prima facie impossible task. As in a recent benchmark spectral calculation by primitive variables of Botella and Peyret, closed-form contributions of the singular solution for both zero and finite Reynolds numbers are subtracted from the unknown of the problem tackled here numerically in biharmonic form. The method employed is based on a split approach to the vorticity and stream function equations, a Galerkin-Legendre approximation of the problem for the perturbation, and an evaluation of the nonlinear terms by Gauss-Legendre numerical integration. Results computed for Re=0, 100, and 1000 compare well with the benchmark steady solutions provided by the aforementioned collocation-Chebyshev projection method. The validity of the proposed singularity subtraction scheme for computing time-dependent solutions is also established.

PFLOTRAN Verification: Development of a Testing Suite to Ensure Software Quality

NASA Astrophysics Data System (ADS)

Hammond, G. E.; Frederick, J. M.

2016-12-01

In scientific computing, code verification ensures the reliability and numerical accuracy of a model simulation by comparing the simulation results to experimental data or known analytical solutions. The model is typically defined by a set of partial differential equations with initial and boundary conditions, and verification ensures whether the mathematical model is solved correctly by the software. Code verification is especially important if the software is used to model high-consequence systems which cannot be physically tested in a fully representative environment [Oberkampf and Trucano (2007)]. Justified confidence in a particular computational tool requires clarity in the exercised physics and transparency in its verification process with proper documentation. We present a quality assurance (QA) testing suite developed by Sandia National Laboratories that performs code verification for PFLOTRAN, an open source, massively-parallel subsurface simulator. PFLOTRAN solves systems of generally nonlinear partial differential equations describing multiphase, multicomponent and multiscale reactive flow and transport processes in porous media. PFLOTRAN's QA test suite compares the numerical solutions of benchmark problems in heat and mass transport against known, closed-form, analytical solutions, including documentation of the exercised physical process models implemented in each PFLOTRAN benchmark simulation. The QA test suite development strives to follow the recommendations given by Oberkampf and Trucano (2007), which describes four essential elements in high-quality verification benchmark construction: (1) conceptual description, (2) mathematical description, (3) accuracy assessment, and (4) additional documentation and user information. Several QA tests within the suite will be presented, including details of the benchmark problems and their closed-form analytical solutions, implementation of benchmark problems in PFLOTRAN simulations, and the criteria used to assess PFLOTRAN's performance in the code verification procedure. References Oberkampf, W. L., and T. G. Trucano (2007), Verification and Validation Benchmarks, SAND2007-0853, 67 pgs., Sandia National Laboratories, Albuquerque, NM.

SeSBench - An initiative to benchmark reactive transport models for environmental subsurface processes

NASA Astrophysics Data System (ADS)

Jacques, Diederik

2017-04-01

As soil functions are governed by a multitude of interacting hydrological, geochemical and biological processes, simulation tools coupling mathematical models for interacting processes are needed. Coupled reactive transport models are a typical example of such coupled tools mainly focusing on hydrological and geochemical coupling (see e.g. Steefel et al., 2015). Mathematical and numerical complexity for both the tool itself or of the specific conceptual model can increase rapidly. Therefore, numerical verification of such type of models is a prerequisite for guaranteeing reliability and confidence and qualifying simulation tools and approaches for any further model application. In 2011, a first SeSBench -Subsurface Environmental Simulation Benchmarking- workshop was held in Berkeley (USA) followed by four other ones. The objective is to benchmark subsurface environmental simulation models and methods with a current focus on reactive transport processes. The final outcome was a special issue in Computational Geosciences (2015, issue 3 - Reactive transport benchmarks for subsurface environmental simulation) with a collection of 11 benchmarks. Benchmarks, proposed by the participants of the workshops, should be relevant for environmental or geo-engineering applications; the latter were mostly related to radioactive waste disposal issues - excluding benchmarks defined for pure mathematical reasons. Another important feature is the tiered approach within a benchmark with the definition of a single principle problem and different sub problems. The latter typically benchmarked individual or simplified processes (e.g. inert solute transport, simplified geochemical conceptual model) or geometries (e.g. batch or one-dimensional, homogeneous). Finally, three codes should be involved into a benchmark. The SeSBench initiative contributes to confidence building for applying reactive transport codes. Furthermore, it illustrates the use of those type of models for different environmental and geo-engineering applications. SeSBench will organize new workshops to add new benchmarks in a new special issue. Steefel, C. I., et al. (2015). "Reactive transport codes for subsurface environmental simulation." Computational Geosciences 19: 445-478.

New NAS Parallel Benchmarks Results

NASA Technical Reports Server (NTRS)

Yarrow, Maurice; Saphir, William; VanderWijngaart, Rob; Woo, Alex; Kutler, Paul (Technical Monitor)

1997-01-01

NPB2 (NAS (NASA Advanced Supercomputing) Parallel Benchmarks 2) is an implementation, based on Fortran and the MPI (message passing interface) message passing standard, of the original NAS Parallel Benchmark specifications. NPB2 programs are run with little or no tuning, in contrast to NPB vendor implementations, which are highly optimized for specific architectures. NPB2 results complement, rather than replace, NPB results. Because they have not been optimized by vendors, NPB2 implementations approximate the performance a typical user can expect for a portable parallel program on distributed memory parallel computers. Together these results provide an insightful comparison of the real-world performance of high-performance computers. New NPB2 features: New implementation (CG), new workstation class problem sizes, new serial sample versions, more performance statistics.

NAS Grid Benchmarks: A Tool for Grid Space Exploration

NASA Technical Reports Server (NTRS)

Frumkin, Michael; VanderWijngaart, Rob F.; Biegel, Bryan (Technical Monitor)

2001-01-01

We present an approach for benchmarking services provided by computational Grids. It is based on the NAS Parallel Benchmarks (NPB) and is called NAS Grid Benchmark (NGB) in this paper. We present NGB as a data flow graph encapsulating an instance of an NPB code in each graph node, which communicates with other nodes by sending/receiving initialization data. These nodes may be mapped to the same or different Grid machines. Like NPB, NGB will specify several different classes (problem sizes). NGB also specifies the generic Grid services sufficient for running the bench-mark. The implementor has the freedom to choose any specific Grid environment. However, we describe a reference implementation in Java, and present some scenarios for using NGB.

Nonlinear model updating applied to the IMAC XXXII Round Robin benchmark system

NASA Astrophysics Data System (ADS)

Kurt, Mehmet; Moore, Keegan J.; Eriten, Melih; McFarland, D. Michael; Bergman, Lawrence A.; Vakakis, Alexander F.

2017-05-01

We consider the application of a new nonlinear model updating strategy to a computational benchmark system. The approach relies on analyzing system response time series in the frequency-energy domain by constructing both Hamiltonian and forced and damped frequency-energy plots (FEPs). The system parameters are then characterized and updated by matching the backbone branches of the FEPs with the frequency-energy wavelet transforms of experimental and/or computational time series. The main advantage of this method is that no nonlinearity model is assumed a priori, and the system model is updated solely based on simulation and/or experimental measured time series. By matching the frequency-energy plots of the benchmark system and its reduced-order model, we show that we are able to retrieve the global strongly nonlinear dynamics in the frequency and energy ranges of interest, identify bifurcations, characterize local nonlinearities, and accurately reconstruct time series. We apply the proposed methodology to a benchmark problem, which was posed to the system identification community prior to the IMAC XXXII (2014) and XXXIII (2015) Conferences as a "Round Robin Exercise on Nonlinear System Identification". We show that we are able to identify the parameters of the non-linear element in the problem with a priori knowledge about its position.

Least-squares Legendre spectral element solutions to sound propagation problems.

PubMed

Lin, W H

2001-02-01

This paper presents a novel algorithm and numerical results of sound wave propagation. The method is based on a least-squares Legendre spectral element approach for spatial discretization and the Crank-Nicolson [Proc. Cambridge Philos. Soc. 43, 50-67 (1947)] and Adams-Bashforth [D. Gottlieb and S. A. Orszag, Numerical Analysis of Spectral Methods: Theory and Applications (CBMS-NSF Monograph, Siam 1977)] schemes for temporal discretization to solve the linearized acoustic field equations for sound propagation. Two types of NASA Computational Aeroacoustics (CAA) Workshop benchmark problems [ICASE/LaRC Workshop on Benchmark Problems in Computational Aeroacoustics, edited by J. C. Hardin, J. R. Ristorcelli, and C. K. W. Tam, NASA Conference Publication 3300, 1995a] are considered: a narrow Gaussian sound wave propagating in a one-dimensional space without flows, and the reflection of a two-dimensional acoustic pulse off a rigid wall in the presence of a uniform flow of Mach 0.5 in a semi-infinite space. The first problem was used to examine the numerical dispersion and dissipation characteristics of the proposed algorithm. The second problem was to demonstrate the capability of the algorithm in treating sound propagation in a flow. Comparisons were made of the computed results with analytical results and results obtained by other methods. It is shown that all results computed by the present method are in good agreement with the analytical solutions and results of the first problem agree very well with those predicted by other schemes.

Generalizable open source urban water portfolio simulation framework demonstrated using a multi-objective risk-based planning benchmark problem.

NASA Astrophysics Data System (ADS)

Trindade, B. C.; Reed, P. M.

2017-12-01

The growing access and reduced cost for computing power in recent years has promoted rapid development and application of multi-objective water supply portfolio planning. As this trend continues there is a pressing need for flexible risk-based simulation frameworks and improved algorithm benchmarking for emerging classes of water supply planning and management problems. This work contributes the Water Utilities Management and Planning (WUMP) model: a generalizable and open source simulation framework designed to capture how water utilities can minimize operational and financial risks by regionally coordinating planning and management choices, i.e. making more efficient and coordinated use of restrictions, water transfers and financial hedging combined with possible construction of new infrastructure. We introduce the WUMP simulation framework as part of a new multi-objective benchmark problem for planning and management of regionally integrated water utility companies. In this problem, a group of fictitious water utilities seek to balance the use of the mentioned reliability driven actions (e.g., restrictions, water transfers and infrastructure pathways) and their inherent financial risks. Several traits of this problem make it ideal for a benchmark problem, namely the presence of (1) strong non-linearities and discontinuities in the Pareto front caused by the step-wise nature of the decision making formulation and by the abrupt addition of storage through infrastructure construction, (2) noise due to the stochastic nature of the streamflows and water demands, and (3) non-separability resulting from the cooperative formulation of the problem, in which decisions made by stakeholder may substantially impact others. Both the open source WUMP simulation framework and its demonstration in a challenging benchmarking example hold value for promoting broader advances in urban water supply portfolio planning for regions confronting change.

Sustainable aggregate production planning in the chemical process industry - A benchmark problem and dataset.

PubMed

Brandenburg, Marcus; Hahn, Gerd J

2018-06-01

Process industries typically involve complex manufacturing operations and thus require adequate decision support for aggregate production planning (APP). The need for powerful and efficient approaches to solve complex APP problems persists. Problem-specific solution approaches are advantageous compared to standardized approaches that are designed to provide basic decision support for a broad range of planning problems but inadequate to optimize under consideration of specific settings. This in turn calls for methods to compare different approaches regarding their computational performance and solution quality. In this paper, we present a benchmarking problem for APP in the chemical process industry. The presented problem focuses on (i) sustainable operations planning involving multiple alternative production modes/routings with specific production-related carbon emission and the social dimension of varying operating rates and (ii) integrated campaign planning with production mix/volume on the operational level. The mutual trade-offs between economic, environmental and social factors can be considered as externalized factors (production-related carbon emission and overtime working hours) as well as internalized ones (resulting costs). We provide data for all problem parameters in addition to a detailed verbal problem statement. We refer to Hahn and Brandenburg [1] for a first numerical analysis based on and for future research perspectives arising from this benchmarking problem.

A suite of exercises for verifying dynamic earthquake rupture codes

USGS Publications Warehouse

Harris, Ruth A.; Barall, Michael; Aagaard, Brad T.; Ma, Shuo; Roten, Daniel; Olsen, Kim B.; Duan, Benchun; Liu, Dunyu; Luo, Bin; Bai, Kangchen; Ampuero, Jean-Paul; Kaneko, Yoshihiro; Gabriel, Alice-Agnes; Duru, Kenneth; Ulrich, Thomas; Wollherr, Stephanie; Shi, Zheqiang; Dunham, Eric; Bydlon, Sam; Zhang, Zhenguo; Chen, Xiaofei; Somala, Surendra N.; Pelties, Christian; Tago, Josue; Cruz-Atienza, Victor Manuel; Kozdon, Jeremy; Daub, Eric; Aslam, Khurram; Kase, Yuko; Withers, Kyle; Dalguer, Luis

2018-01-01

We describe a set of benchmark exercises that are designed to test if computer codes that simulate dynamic earthquake rupture are working as intended. These types of computer codes are often used to understand how earthquakes operate, and they produce simulation results that include earthquake size, amounts of fault slip, and the patterns of ground shaking and crustal deformation. The benchmark exercises examine a range of features that scientists incorporate in their dynamic earthquake rupture simulations. These include implementations of simple or complex fault geometry, off‐fault rock response to an earthquake, stress conditions, and a variety of formulations for fault friction. Many of the benchmarks were designed to investigate scientific problems at the forefronts of earthquake physics and strong ground motions research. The exercises are freely available on our website for use by the scientific community.

Benchmarking comparison and validation of MCNP photon interaction data

NASA Astrophysics Data System (ADS)

Colling, Bethany; Kodeli, I.; Lilley, S.; Packer, L. W.

2017-09-01

The objective of the research was to test available photoatomic data libraries for fusion relevant applications, comparing against experimental and computational neutronics benchmarks. Photon flux and heating was compared using the photon interaction data libraries (mcplib 04p, 05t, 84p and 12p). Suitable benchmark experiments (iron and water) were selected from the SINBAD database and analysed to compare experimental values with MCNP calculations using mcplib 04p, 84p and 12p. In both the computational and experimental comparisons, the majority of results with the 04p, 84p and 12p photon data libraries were within 1σ of the mean MCNP statistical uncertainty. Larger differences were observed when comparing computational results with the 05t test photon library. The Doppler broadening sampling bug in MCNP-5 is shown to be corrected for fusion relevant problems through use of the 84p photon data library. The recommended libraries for fusion neutronics are 84p (or 04p) with MCNP6 and 84p if using MCNP-5.

Validation and Comparison of 2D and 3D Codes for Nearshore Motion of Long Waves Using Benchmark Problems

NASA Astrophysics Data System (ADS)

Velioǧlu, Deniz; Cevdet Yalçıner, Ahmet; Zaytsev, Andrey

2016-04-01

Tsunamis are huge waves with long wave periods and wave lengths that can cause great devastation and loss of life when they strike a coast. The interest in experimental and numerical modeling of tsunami propagation and inundation increased considerably after the 2011 Great East Japan earthquake. In this study, two numerical codes, FLOW 3D and NAMI DANCE, that analyze tsunami propagation and inundation patterns are considered. Flow 3D simulates linear and nonlinear propagating surface waves as well as long waves by solving three-dimensional Navier-Stokes (3D-NS) equations. NAMI DANCE uses finite difference computational method to solve 2D depth-averaged linear and nonlinear forms of shallow water equations (NSWE) in long wave problems, specifically tsunamis. In order to validate these two codes and analyze the differences between 3D-NS and 2D depth-averaged NSWE equations, two benchmark problems are applied. One benchmark problem investigates the runup of long waves over a complex 3D beach. The experimental setup is a 1:400 scale model of Monai Valley located on the west coast of Okushiri Island, Japan. Other benchmark problem is discussed in 2015 National Tsunami Hazard Mitigation Program (NTHMP) Annual meeting in Portland, USA. It is a field dataset, recording the Japan 2011 tsunami in Hilo Harbor, Hawaii. The computed water surface elevation and velocity data are compared with the measured data. The comparisons showed that both codes are in fairly good agreement with each other and benchmark data. The differences between 3D-NS and 2D depth-averaged NSWE equations are highlighted. All results are presented with discussions and comparisons. Acknowledgements: Partial support by Japan-Turkey Joint Research Project by JICA on earthquakes and tsunamis in Marmara Region (JICA SATREPS - MarDiM Project), 603839 ASTARTE Project of EU, UDAP-C-12-14 project of AFAD Turkey, 108Y227, 113M556 and 213M534 projects of TUBITAK Turkey, RAPSODI (CONCERT_Dis-021) of CONCERT-Japan Joint Call and Istanbul Metropolitan Municipality are all acknowledged.

Validation and Performance Comparison of Numerical Codes for Tsunami Inundation

NASA Astrophysics Data System (ADS)

Velioglu, D.; Kian, R.; Yalciner, A. C.; Zaytsev, A.

2015-12-01

In inundation zones, tsunami motion turns from wave motion to flow of water. Modelling of this phenomenon is a complex problem since there are many parameters affecting the tsunami flow. In this respect, the performance of numerical codes that analyze tsunami inundation patterns becomes important. The computation of water surface elevation is not sufficient for proper analysis of tsunami behaviour in shallow water zones and on land and hence for the development of mitigation strategies. Velocity and velocity patterns are also crucial parameters and have to be computed at the highest accuracy. There are numerous numerical codes to be used for simulating tsunami inundation. In this study, FLOW 3D and NAMI DANCE codes are selected for validation and performance comparison. Flow 3D simulates linear and nonlinear propagating surface waves as well as long waves by solving three-dimensional Navier-Stokes (3D-NS) equations. FLOW 3D is used specificaly for flood problems. NAMI DANCE uses finite difference computational method to solve linear and nonlinear forms of shallow water equations (NSWE) in long wave problems, specifically tsunamis. In this study, these codes are validated and their performances are compared using two benchmark problems which are discussed in 2015 National Tsunami Hazard Mitigation Program (NTHMP) Annual meeting in Portland, USA. One of the problems is an experiment of a single long-period wave propagating up a piecewise linear slope and onto a small-scale model of the town of Seaside, Oregon. Other benchmark problem is an experiment of a single solitary wave propagating up a triangular shaped shelf with an island feature located at the offshore point of the shelf. The computed water surface elevation and velocity data are compared with the measured data. The comparisons showed that both codes are in fairly good agreement with each other and benchmark data. All results are presented with discussions and comparisons. The research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement No 603839 (Project ASTARTE - Assessment, Strategy and Risk Reduction for Tsunamis in Europe)

Solving satisfiability problems using a novel microarray-based DNA computer.

PubMed

Lin, Che-Hsin; Cheng, Hsiao-Ping; Yang, Chang-Biau; Yang, Chia-Ning

2007-01-01

An algorithm based on a modified sticker model accompanied with an advanced MEMS-based microarray technology is demonstrated to solve SAT problem, which has long served as a benchmark in DNA computing. Unlike conventional DNA computing algorithms needing an initial data pool to cover correct and incorrect answers and further executing a series of separation procedures to destroy the unwanted ones, we built solutions in parts to satisfy one clause in one step, and eventually solve the entire Boolean formula through steps. No time-consuming sample preparation procedures and delicate sample applying equipment were required for the computing process. Moreover, experimental results show the bound DNA sequences can sustain the chemical solutions during computing processes such that the proposed method shall be useful in dealing with large-scale problems.

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

Cohen, J; Dossa, D; Gokhale, M

Critical data science applications requiring frequent access to storage perform poorly on today's computing architectures. This project addresses efficient computation of data-intensive problems in national security and basic science by exploring, advancing, and applying a new form of computing called storage-intensive supercomputing (SISC). Our goal is to enable applications that simply cannot run on current systems, and, for a broad range of data-intensive problems, to deliver an order of magnitude improvement in price/performance over today's data-intensive architectures. This technical report documents much of the work done under LDRD 07-ERD-063 Storage Intensive Supercomputing during the period 05/07-09/07. The following chapters describe:more » (1) a new file I/O monitoring tool iotrace developed to capture the dynamic I/O profiles of Linux processes; (2) an out-of-core graph benchmark for level-set expansion of scale-free graphs; (3) an entity extraction benchmark consisting of a pipeline of eight components; and (4) an image resampling benchmark drawn from the SWarp program in the LSST data processing pipeline. The performance of the graph and entity extraction benchmarks was measured in three different scenarios: data sets residing on the NFS file server and accessed over the network; data sets stored on local disk; and data sets stored on the Fusion I/O parallel NAND Flash array. The image resampling benchmark compared performance of software-only to GPU-accelerated. In addition to the work reported here, an additional text processing application was developed that used an FPGA to accelerate n-gram profiling for language classification. The n-gram application will be presented at SC07 at the High Performance Reconfigurable Computing Technologies and Applications Workshop. The graph and entity extraction benchmarks were run on a Supermicro server housing the NAND Flash 40GB parallel disk array, the Fusion-io. The Fusion system specs are as follows: SuperMicro X7DBE Xeon Dual Socket Blackford Server Motherboard; 2 Intel Xeon Dual-Core 2.66 GHz processors; 1 GB DDR2 PC2-5300 RAM (2 x 512); 80GB Hard Drive (Seagate SATA II Barracuda). The Fusion board is presently capable of 4X in a PCIe slot. The image resampling benchmark was run on a dual Xeon workstation with NVIDIA graphics card (see Chapter 5 for full specification). An XtremeData Opteron+FPGA was used for the language classification application. We observed that these benchmarks are not uniformly I/O intensive. The only benchmark that showed greater that 50% of the time in I/O was the graph algorithm when it accessed data files over NFS. When local disk was used, the graph benchmark spent at most 40% of its time in I/O. The other benchmarks were CPU dominated. The image resampling benchmark and language classification showed order of magnitude speedup over software by using co-processor technology to offload the CPU-intensive kernels. Our experiments to date suggest that emerging hardware technologies offer significant benefit to boosting the performance of data-intensive algorithms. Using GPU and FPGA co-processors, we were able to improve performance by more than an order of magnitude on the benchmark algorithms, eliminating the processor bottleneck of CPU-bound tasks. Experiments with a prototype solid state nonvolative memory available today show 10X better throughput on random reads than disk, with a 2X speedup on a graph processing benchmark when compared to the use of local SATA disk.« less

High-Order Methods for Computational Physics

DTIC Science & Technology

1999-03-01

computation is running in 278 Ronald D. Henderson parallel. Instead we use the concept of a voxel database (VDB) of geometric positions in the mesh [85...processor 0 Fig. 4.19. Connectivity and communications axe established by building a voxel database (VDB) of positions. A VDB maps each position to a...studies such as the highly accurate stability computations considered help expand the database for this benchmark problem. The two-dimensional linear

Viscous flow computations using a second-order upwind differencing scheme

NASA Technical Reports Server (NTRS)

Chen, Y. S.

1988-01-01

In the present computations of a wide range of fluid flow problems by means of the primitive variables-incorporating Navier-Stokes equations, a mixed second-order upwinding scheme approximates the convective terms of the transport equations and the scheme's accuracy is verified for convection-dominated high Re number flow problems. An adaptive dissipation scheme is used as a monotonic supersonic shock flow capture mechanism. Many benchmark fluid flow problems, including the compressible and incompressible, laminar and turbulent, over a wide range of M and Re numbers, are presently studied to verify the accuracy and robustness of this numerical method.

Parallel computation with molecular-motor-propelled agents in nanofabricated networks.

PubMed

Nicolau, Dan V; Lard, Mercy; Korten, Till; van Delft, Falco C M J M; Persson, Malin; Bengtsson, Elina; Månsson, Alf; Diez, Stefan; Linke, Heiner; Nicolau, Dan V

2016-03-08

The combinatorial nature of many important mathematical problems, including nondeterministic-polynomial-time (NP)-complete problems, places a severe limitation on the problem size that can be solved with conventional, sequentially operating electronic computers. There have been significant efforts in conceiving parallel-computation approaches in the past, for example: DNA computation, quantum computation, and microfluidics-based computation. However, these approaches have not proven, so far, to be scalable and practical from a fabrication and operational perspective. Here, we report the foundations of an alternative parallel-computation system in which a given combinatorial problem is encoded into a graphical, modular network that is embedded in a nanofabricated planar device. Exploring the network in a parallel fashion using a large number of independent, molecular-motor-propelled agents then solves the mathematical problem. This approach uses orders of magnitude less energy than conventional computers, thus addressing issues related to power consumption and heat dissipation. We provide a proof-of-concept demonstration of such a device by solving, in a parallel fashion, the small instance {2, 5, 9} of the subset sum problem, which is a benchmark NP-complete problem. Finally, we discuss the technical advances necessary to make our system scalable with presently available technology.

Benchmarking NNWSI flow and transport codes: COVE 1 results

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

Hayden, N.K.

1985-06-01

The code verification (COVE) activity of the Nevada Nuclear Waste Storage Investigations (NNWSI) Project is the first step in certification of flow and transport codes used for NNWSI performance assessments of a geologic repository for disposing of high-level radioactive wastes. The goals of the COVE activity are (1) to demonstrate and compare the numerical accuracy and sensitivity of certain codes, (2) to identify and resolve problems in running typical NNWSI performance assessment calculations, and (3) to evaluate computer requirements for running the codes. This report describes the work done for COVE 1, the first step in benchmarking some of themore » codes. Isothermal calculations for the COVE 1 benchmarking have been completed using the hydrologic flow codes SAGUARO, TRUST, and GWVIP; the radionuclide transport codes FEMTRAN and TRUMP; and the coupled flow and transport code TRACR3D. This report presents the results of three cases of the benchmarking problem solved for COVE 1, a comparison of the results, questions raised regarding sensitivities to modeling techniques, and conclusions drawn regarding the status and numerical sensitivities of the codes. 30 refs.« less

A Benchmark Problem for Development of Autonomous Structural Modal Identification

NASA Technical Reports Server (NTRS)

Pappa, Richard S.; Woodard, Stanley E.; Juang, Jer-Nan

1996-01-01

This paper summarizes modal identification results obtained using an autonomous version of the Eigensystem Realization Algorithm on a dynamically complex, laboratory structure. The benchmark problem uses 48 of 768 free-decay responses measured in a complete modal survey test. The true modal parameters of the structure are well known from two previous, independent investigations. Without user involvement, the autonomous data analysis identified 24 to 33 structural modes with good to excellent accuracy in 62 seconds of CPU time (on a DEC Alpha 4000 computer). The modal identification technique described in the paper is the baseline algorithm for NASA's Autonomous Dynamics Determination (ADD) experiment scheduled to fly on International Space Station assembly flights in 1997-1999.

Statistical benchmark for BosonSampling

NASA Astrophysics Data System (ADS)

Walschaers, Mattia; Kuipers, Jack; Urbina, Juan-Diego; Mayer, Klaus; Tichy, Malte Christopher; Richter, Klaus; Buchleitner, Andreas

2016-03-01

Boson samplers—set-ups that generate complex many-particle output states through the transmission of elementary many-particle input states across a multitude of mutually coupled modes—promise the efficient quantum simulation of a classically intractable computational task, and challenge the extended Church-Turing thesis, one of the fundamental dogmas of computer science. However, as in all experimental quantum simulations of truly complex systems, one crucial problem remains: how to certify that a given experimental measurement record unambiguously results from enforcing the claimed dynamics, on bosons, fermions or distinguishable particles? Here we offer a statistical solution to the certification problem, identifying an unambiguous statistical signature of many-body quantum interference upon transmission across a multimode, random scattering device. We show that statistical analysis of only partial information on the output state allows to characterise the imparted dynamics through particle type-specific features of the emerging interference patterns. The relevant statistical quantifiers are classically computable, define a falsifiable benchmark for BosonSampling, and reveal distinctive features of many-particle quantum dynamics, which go much beyond mere bunching or anti-bunching effects.

Comparing the OpenMP, MPI, and Hybrid Programming Paradigm on an SMP Cluster

NASA Technical Reports Server (NTRS)

Jost, Gabriele; Jin, Haoqiang; anMey, Dieter; Hatay, Ferhat F.

2003-01-01

With the advent of parallel hardware and software technologies users are faced with the challenge to choose a programming paradigm best suited for the underlying computer architecture. With the current trend in parallel computer architectures towards clusters of shared memory symmetric multi-processors (SMP), parallel programming techniques have evolved to support parallelism beyond a single level. Which programming paradigm is the best will depend on the nature of the given problem, the hardware architecture, and the available software. In this study we will compare different programming paradigms for the parallelization of a selected benchmark application on a cluster of SMP nodes. We compare the timings of different implementations of the same CFD benchmark application employing the same numerical algorithm on a cluster of Sun Fire SMP nodes. The rest of the paper is structured as follows: In section 2 we briefly discuss the programming models under consideration. We describe our compute platform in section 3. The different implementations of our benchmark code are described in section 4 and the performance results are presented in section 5. We conclude our study in section 6.

Exact solutions for the collaborative pickup and delivery problem.

PubMed

Gansterer, Margaretha; Hartl, Richard F; Salzmann, Philipp E H

2018-01-01

In this study we investigate the decision problem of a central authority in pickup and delivery carrier collaborations. Customer requests are to be redistributed among participants, such that the total cost is minimized. We formulate the problem as multi-depot traveling salesman problem with pickups and deliveries. We apply three well-established exact solution approaches and compare their performance in terms of computational time. To avoid unrealistic solutions with unevenly distributed workload, we extend the problem by introducing minimum workload constraints. Our computational results show that, while for the original problem Benders decomposition is the method of choice, for the newly formulated problem this method is clearly dominated by the proposed column generation approach. The obtained results can be used as benchmarks for decentralized mechanisms in collaborative pickup and delivery problems.

A Benders based rolling horizon algorithm for a dynamic facility location problem

DOE PAGES

Marufuzzaman,, Mohammad; Gedik, Ridvan; Roni, Mohammad S.

2016-06-28

This study presents a well-known capacitated dynamic facility location problem (DFLP) that satisfies the customer demand at a minimum cost by determining the time period for opening, closing, or retaining an existing facility in a given location. To solve this challenging NP-hard problem, this paper develops a unique hybrid solution algorithm that combines a rolling horizon algorithm with an accelerated Benders decomposition algorithm. Extensive computational experiments are performed on benchmark test instances to evaluate the hybrid algorithm’s efficiency and robustness in solving the DFLP problem. Computational results indicate that the hybrid Benders based rolling horizon algorithm consistently offers high qualitymore » feasible solutions in a much shorter computational time period than the standalone rolling horizon and accelerated Benders decomposition algorithms in the experimental range.« less

Present Status and Extensions of the Monte Carlo Performance Benchmark

NASA Astrophysics Data System (ADS)

Hoogenboom, J. Eduard; Petrovic, Bojan; Martin, William R.

2014-06-01

The NEA Monte Carlo Performance benchmark started in 2011 aiming to monitor over the years the abilities to perform a full-size Monte Carlo reactor core calculation with a detailed power production for each fuel pin with axial distribution. This paper gives an overview of the contributed results thus far. It shows that reaching a statistical accuracy of 1 % for most of the small fuel zones requires about 100 billion neutron histories. The efficiency of parallel execution of Monte Carlo codes on a large number of processor cores shows clear limitations for computer clusters with common type computer nodes. However, using true supercomputers the speedup of parallel calculations is increasing up to large numbers of processor cores. More experience is needed from calculations on true supercomputers using large numbers of processors in order to predict if the requested calculations can be done in a short time. As the specifications of the reactor geometry for this benchmark test are well suited for further investigations of full-core Monte Carlo calculations and a need is felt for testing other issues than its computational performance, proposals are presented for extending the benchmark to a suite of benchmark problems for evaluating fission source convergence for a system with a high dominance ratio, for coupling with thermal-hydraulics calculations to evaluate the use of different temperatures and coolant densities and to study the correctness and effectiveness of burnup calculations. Moreover, other contemporary proposals for a full-core calculation with realistic geometry and material composition will be discussed.

Classical and modern control strategies for the deployment, reconfiguration, and station-keeping of the National Aeronautics and Space Administration (NASA) Benchmark Tetrahedron Constellation

NASA Astrophysics Data System (ADS)

Capo-Lugo, Pedro A.

Formation flying consists of multiple spacecraft orbiting in a required configuration about a planet or through Space. The National Aeronautics and Space Administration (NASA) Benchmark Tetrahedron Constellation is one of the proposed constellations to be launched in the year 2009 and provides the motivation for this investigation. The problem that will be researched here consists of three stages. The first stage contains the deployment of the satellites; the second stage is the reconfiguration process to transfer the satellites through different specific sizes of the NASA benchmark problem; and, the third stage is the station-keeping procedure for the tetrahedron constellation. Every stage contains different control schemes and transfer procedures to obtain/maintain the proposed tetrahedron constellation. In the first stage, the deployment procedure will depend on a combination of two techniques in which impulsive maneuvers and a digital controller are used to deploy the satellites and to maintain the tetrahedron constellation at the following apogee point. The second stage that corresponds to the reconfiguration procedure shows a different control scheme in which the intelligent control systems are implemented to perform this procedure. In this research work, intelligent systems will eliminate the use of complex mathematical models and will reduce the computational time to perform different maneuvers. Finally, the station-keeping process, which is the third stage of this research problem, will be implemented with a two-level hierarchical control scheme to maintain the separation distance constraints of the NASA Benchmark Tetrahedron Constellation. For this station-keeping procedure, the system of equations defining the dynamics of a pair of satellites is transformed to take in account the perturbation due to the oblateness of the Earth and the disturbances due to solar pressure. The control procedures used in this research will be transformed from a continuous control system to a digital control system which will simplify the implementation into the computer onboard the satellite. In addition, this research will show an introductory chapter on attitude dynamics that can be used to maintain the orientation of the satellites, and an adaptive intelligent control scheme will be proposed to maintain the desired orientation of the spacecraft. In conclusion, a solution for the dynamics of the NASA Benchmark Tetrahedron Constellation will be presented in this research work. The main contribution of this work is the use of discrete control schemes, impulsive maneuvers, and intelligent control schemes that can be used to reduce the computational time in which these control schemes can be easily implemented in the computer onboard the satellite. These contributions are explained through the deployment, reconfiguration, and station-keeping process of the proposed NASA Benchmark Tetrahedron Constellation.

High-resolution Self-Organizing Maps for advanced visualization and dimension reduction.

PubMed

Saraswati, Ayu; Nguyen, Van Tuc; Hagenbuchner, Markus; Tsoi, Ah Chung

2018-05-04

Kohonen's Self Organizing feature Map (SOM) provides an effective way to project high dimensional input features onto a low dimensional display space while preserving the topological relationships among the input features. Recent advances in algorithms that take advantages of modern computing hardware introduced the concept of high resolution SOMs (HRSOMs). This paper investigates the capabilities and applicability of the HRSOM as a visualization tool for cluster analysis and its suitabilities to serve as a pre-processor in ensemble learning models. The evaluation is conducted on a number of established benchmarks and real-world learning problems, namely, the policeman benchmark, two web spam detection problems, a network intrusion detection problem, and a malware detection problem. It is found that the visualization resulted from an HRSOM provides new insights concerning these learning problems. It is furthermore shown empirically that broad benefits from the use of HRSOMs in both clustering and classification problems can be expected. Copyright © 2018 Elsevier Ltd. All rights reserved.

Benchmark problems in computational aeroacoustics

NASA Technical Reports Server (NTRS)

Porter-Locklear, Freda

1994-01-01

A recent directive at NASA Langley is aimed at numerically predicting principal noise sources. During my summer stay, I worked with high-order ENO code, developed by Dr. Harold Atkins, for solving the unsteady compressible Navier-Stokes equations, as it applies to computational aeroacoustics (CAA). A CAA workshop, composed of six categories of benchmark problems, has been organized to test various numerical properties of code. My task was to determine the robustness of Atkins' code for these test problems. In one category, we tested the nonlinear wave propagation of the code for the one-dimensional Euler equations, with initial pressure, density, and velocity conditions. Using freestream boundary conditions, our results were plausible. In another category, we solved the linearized two-dimensional Euler equations to test the effectiveness of radiation boundary conditions. Here we utilized MAPLE to compute eigenvalues and eigenvectors of the Jacobian given variable and flux vectors. We experienced a minor problem with inflow and outflow boundary conditions. Next, we solved the quasi one dimensional unsteady flow equations with an incoming acoustic wave of amplitude 10(exp -6). The small amplitude sound wave was incident on a convergent-divergent nozzle. After finding a steady-state solution and then marching forward, our solution indicated that after 30 periods the acoustic wave had dissipated (a period is time required for sound wave to traverse one end of nozzle to other end).

Computational Efficiency of the Simplex Embedding Method in Convex Nondifferentiable Optimization

NASA Astrophysics Data System (ADS)

Kolosnitsyn, A. V.

2018-02-01

The simplex embedding method for solving convex nondifferentiable optimization problems is considered. A description of modifications of this method based on a shift of the cutting plane intended for cutting off the maximum number of simplex vertices is given. These modification speed up the problem solution. A numerical comparison of the efficiency of the proposed modifications based on the numerical solution of benchmark convex nondifferentiable optimization problems is presented.

Computer simulation of multigrid body dynamics and control

NASA Technical Reports Server (NTRS)

Swaminadham, M.; Moon, Young I.; Venkayya, V. B.

1990-01-01

The objective is to set up and analyze benchmark problems on multibody dynamics and to verify the predictions of two multibody computer simulation codes. TREETOPS and DISCOS have been used to run three example problems - one degree-of-freedom spring mass dashpot system, an inverted pendulum system, and a triple pendulum. To study the dynamics and control interaction, an inverted planar pendulum with an external body force and a torsional control spring was modeled as a hinge connected two-rigid body system. TREETOPS and DISCOS affected the time history simulation of this problem. System state space variables and their time derivatives from two simulation codes were compared.

Computational Chemistry Comparison and Benchmark Database

National Institute of Standards and Technology Data Gateway

SRD 101 NIST Computational Chemistry Comparison and Benchmark Database (Web, free access)   The NIST Computational Chemistry Comparison and Benchmark Database is a collection of experimental and ab initio thermochemical properties for a selected set of molecules. The goals are to provide a benchmark set of molecules for the evaluation of ab initio computational methods and allow the comparison between different ab initio computational methods for the prediction of thermochemical properties.

Benchmark results in the 2D lattice Thirring model with a chemical potential

NASA Astrophysics Data System (ADS)

Ayyar, Venkitesh; Chandrasekharan, Shailesh; Rantaharju, Jarno

2018-03-01

We study the two-dimensional lattice Thirring model in the presence of a fermion chemical potential. Our model is asymptotically free and contains massive fermions that mimic a baryon and light bosons that mimic pions. Hence, it is a useful toy model for QCD, especially since it, too, suffers from a sign problem in the auxiliary field formulation in the presence of a fermion chemical potential. In this work, we formulate the model in both the world line and fermion-bag representations and show that the sign problem can be completely eliminated with open boundary conditions when the fermions are massless. Hence, we are able accurately compute a variety of interesting quantities in the model, and these results could provide benchmarks for other methods that are being developed to solve the sign problem in QCD.

Information Based Numerical Practice.

DTIC Science & Technology

1987-02-01

characterization by comparative computational studies of various benchmark problems. See e.g. [MacNeal, Harder (1985)], [Robinson, Blackham (1981)] any...FOR NONADAPTIVE METHODS 2.1. THE QUADRATURE FORMULA The simplest example studied in detail in the literature is the problem of the optimal quadrature...formulae and the functional analytic prerequisites for the study of optimal formulae, we refer to the large monography (808 p) of [Sobolev (1974)]. Let us

Design of Unstructured Adaptive (UA) NAS Parallel Benchmark Featuring Irregular, Dynamic Memory Accesses

NASA Technical Reports Server (NTRS)

Feng, Hui-Yu; VanderWijngaart, Rob; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2001-01-01

We describe the design of a new method for the measurement of the performance of modern computer systems when solving scientific problems featuring irregular, dynamic memory accesses. The method involves the solution of a stylized heat transfer problem on an unstructured, adaptive grid. A Spectral Element Method (SEM) with an adaptive, nonconforming mesh is selected to discretize the transport equation. The relatively high order of the SEM lowers the fraction of wall clock time spent on inter-processor communication, which eases the load balancing task and allows us to concentrate on the memory accesses. The benchmark is designed to be three-dimensional. Parallelization and load balance issues of a reference implementation will be described in detail in future reports.

BIGHORN Computational Fluid Dynamics Theory, Methodology, and Code Verification & Validation Benchmark Problems

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

Xia, Yidong; Andrs, David; Martineau, Richard Charles

This document presents the theoretical background for a hybrid finite-element / finite-volume fluid flow solver, namely BIGHORN, based on the Multiphysics Object Oriented Simulation Environment (MOOSE) computational framework developed at the Idaho National Laboratory (INL). An overview of the numerical methods used in BIGHORN are discussed and followed by a presentation of the formulation details. The document begins with the governing equations for the compressible fluid flow, with an outline of the requisite constitutive relations. A second-order finite volume method used for solving the compressible fluid flow problems is presented next. A Pressure-Corrected Implicit Continuous-fluid Eulerian (PCICE) formulation for timemore » integration is also presented. The multi-fluid formulation is being developed. Although multi-fluid is not fully-developed, BIGHORN has been designed to handle multi-fluid problems. Due to the flexibility in the underlying MOOSE framework, BIGHORN is quite extensible, and can accommodate both multi-species and multi-phase formulations. This document also presents a suite of verification & validation benchmark test problems for BIGHORN. The intent for this suite of problems is to provide baseline comparison data that demonstrates the performance of the BIGHORN solution methods on problems that vary in complexity from laminar to turbulent flows. Wherever possible, some form of solution verification has been attempted to identify sensitivities in the solution methods, and suggest best practices when using BIGHORN.« less

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.

PubMed

Villaverde, Alejandro F; Henriques, David; Smallbone, Kieran; Bongard, Sophia; Schmid, Joachim; Cicin-Sain, Damjan; Crombach, Anton; Saez-Rodriguez, Julio; Mauch, Klaus; Balsa-Canto, Eva; Mendes, Pedro; Jaeger, Johannes; Banga, Julio R

2015-02-20

Dynamic modelling is one of the cornerstones of systems biology. Many research efforts are currently being invested in the development and exploitation of large-scale kinetic models. The associated problems of parameter estimation (model calibration) and optimal experimental design are particularly challenging. The community has already developed many methods and software packages which aim to facilitate these tasks. However, there is a lack of suitable benchmark problems which allow a fair and systematic evaluation and comparison of these contributions. Here we present BioPreDyn-bench, a set of challenging parameter estimation problems which aspire to serve as reference test cases in this area. This set comprises six problems including medium and large-scale kinetic models of the bacterium E. coli, baker's yeast S. cerevisiae, the vinegar fly D. melanogaster, Chinese Hamster Ovary cells, and a generic signal transduction network. The level of description includes metabolism, transcription, signal transduction, and development. For each problem we provide (i) a basic description and formulation, (ii) implementations ready-to-run in several formats, (iii) computational results obtained with specific solvers, (iv) a basic analysis and interpretation. This suite of benchmark problems can be readily used to evaluate and compare parameter estimation methods. Further, it can also be used to build test problems for sensitivity and identifiability analysis, model reduction and optimal experimental design methods. The suite, including codes and documentation, can be freely downloaded from the BioPreDyn-bench website, https://sites.google.com/site/biopredynbenchmarks/ .

Algorithm and Architecture Independent Benchmarking with SEAK

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

Tallent, Nathan R.; Manzano Franco, Joseph B.; Gawande, Nitin A.

2016-05-23

Many applications of high performance embedded computing are limited by performance or power bottlenecks. We have designed the Suite for Embedded Applications & Kernels (SEAK), a new benchmark suite, (a) to capture these bottlenecks in a way that encourages creative solutions; and (b) to facilitate rigorous, objective, end-user evaluation for their solutions. To avoid biasing solutions toward existing algorithms, SEAK benchmarks use a mission-centric (abstracted from a particular algorithm) and goal-oriented (functional) specification. To encourage solutions that are any combination of software or hardware, we use an end-user black-box evaluation that can capture tradeoffs between performance, power, accuracy, size, andmore » weight. The tradeoffs are especially informative for procurement decisions. We call our benchmarks future proof because each mission-centric interface and evaluation remains useful despite shifting algorithmic preferences. It is challenging to create both concise and precise goal-oriented specifications for mission-centric problems. This paper describes the SEAK benchmark suite and presents an evaluation of sample solutions that highlights power and performance tradeoffs.« less

Advances and trends in the development of computational models for tires

NASA Technical Reports Server (NTRS)

Noor, A. K.; Tanner, J. A.

1985-01-01

Status and some recent developments of computational models for tires are summarized. Discussion focuses on a number of aspects of tire modeling and analysis including: tire materials and their characterization; evolution of tire models; characteristics of effective finite element models for analyzing tires; analysis needs for tires; and impact of the advances made in finite element technology, computational algorithms, and new computing systems on tire modeling and analysis. An initial set of benchmark problems has been proposed in concert with the U.S. tire industry. Extensive sets of experimental data will be collected for these problems and used for evaluating and validating different tire models. Also, the new Aircraft Landing Dynamics Facility (ALDF) at NASA Langley Research Center is described.

Implementation, capabilities, and benchmarking of Shift, a massively parallel Monte Carlo radiation transport code

DOE PAGES

Pandya, Tara M.; Johnson, Seth R.; Evans, Thomas M.; ...

2015-12-21

This paper discusses the implementation, capabilities, and validation of Shift, a massively parallel Monte Carlo radiation transport package developed and maintained at Oak Ridge National Laboratory. It has been developed to scale well from laptop to small computing clusters to advanced supercomputers. Special features of Shift include hybrid capabilities for variance reduction such as CADIS and FW-CADIS, and advanced parallel decomposition and tally methods optimized for scalability on supercomputing architectures. Shift has been validated and verified against various reactor physics benchmarks and compares well to other state-of-the-art Monte Carlo radiation transport codes such as MCNP5, CE KENO-VI, and OpenMC. Somemore » specific benchmarks used for verification and validation include the CASL VERA criticality test suite and several Westinghouse AP1000 ® problems. These benchmark and scaling studies show promising results.« less

Lattice gas methods for computational aeroacoustics

NASA Technical Reports Server (NTRS)

Sparrow, Victor W.

1995-01-01

This paper presents the lattice gas solution to the category 1 problems of the ICASE/LaRC Workshop on Benchmark Problems in Computational Aeroacoustics. The first and second problems were solved for Delta t = Delta x = 1, and additionally the second problem was solved for Delta t = 1/4 and Delta x = 1/2. The results are striking: even for these large time and space grids the lattice gas numerical solutions are almost indistinguishable from the analytical solutions. A simple bug in the Mathematica code was found in the solutions submitted for comparison, and the comparison plots shown at the end of this volume show the bug. An Appendix to the present paper shows an example lattice gas solution with and without the bug.

Optimally Stopped Optimization

NASA Astrophysics Data System (ADS)

Vinci, Walter; Lidar, Daniel A.

2016-11-01

We combine the fields of heuristic optimization and optimal stopping. We propose a strategy for benchmarking randomized optimization algorithms that minimizes the expected total cost for obtaining a good solution with an optimal number of calls to the solver. To do so, rather than letting the objective function alone define a cost to be minimized, we introduce a further cost-per-call of the algorithm. We show that this problem can be formulated using optimal stopping theory. The expected cost is a flexible figure of merit for benchmarking probabilistic solvers that can be computed when the optimal solution is not known and that avoids the biases and arbitrariness that affect other measures. The optimal stopping formulation of benchmarking directly leads to a real-time optimal-utilization strategy for probabilistic optimizers with practical impact. We apply our formulation to benchmark simulated annealing on a class of maximum-2-satisfiability (MAX2SAT) problems. We also compare the performance of a D-Wave 2X quantum annealer to the Hamze-Freitas-Selby (HFS) solver, a specialized classical heuristic algorithm designed for low-tree-width graphs. On a set of frustrated-loop instances with planted solutions defined on up to N =1098 variables, the D-Wave device is 2 orders of magnitude faster than the HFS solver, and, modulo known caveats related to suboptimal annealing times, exhibits identical scaling with problem size.

Benchmarking optimization software with COPS.

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

Dolan, E.D.; More, J.J.

2001-01-08

The COPS test set provides a modest selection of difficult nonlinearly constrained optimization problems from applications in optimal design, fluid dynamics, parameter estimation, and optimal control. In this report we describe version 2.0 of the COPS problems. The formulation and discretization of the original problems have been streamlined and improved. We have also added new problems. The presentation of COPS follows the original report, but the description of the problems has been streamlined. For each problem we discuss the formulation of the problem and the structural data in Table 0.1 on the formulation. The aim of presenting this data ismore » to provide an approximate idea of the size and sparsity of the problem. We also include the results of computational experiments with the LANCELOT, LOQO, MINOS, and SNOPT solvers. These computational experiments differ from the original results in that we have deleted problems that were considered to be too easy. Moreover, in the current version of the computational experiments, each problem is tested with four variations. An important difference between this report and the original report is that the tables that present the computational experiments are generated automatically from the testing script. This is explained in more detail in the report.« less

Parameters that affect parallel processing for computational electromagnetic simulation codes on high performance computing clusters

NASA Astrophysics Data System (ADS)

Moon, Hongsik

What is the impact of multicore and associated advanced technologies on computational software for science? Most researchers and students have multicore laptops or desktops for their research and they need computing power to run computational software packages. Computing power was initially derived from Central Processing Unit (CPU) clock speed. That changed when increases in clock speed became constrained by power requirements. Chip manufacturers turned to multicore CPU architectures and associated technological advancements to create the CPUs for the future. Most software applications benefited by the increased computing power the same way that increases in clock speed helped applications run faster. However, for Computational ElectroMagnetics (CEM) software developers, this change was not an obvious benefit - it appeared to be a detriment. Developers were challenged to find a way to correctly utilize the advancements in hardware so that their codes could benefit. The solution was parallelization and this dissertation details the investigation to address these challenges. Prior to multicore CPUs, advanced computer technologies were compared with the performance using benchmark software and the metric was FLoting-point Operations Per Seconds (FLOPS) which indicates system performance for scientific applications that make heavy use of floating-point calculations. Is FLOPS an effective metric for parallelized CEM simulation tools on new multicore system? Parallel CEM software needs to be benchmarked not only by FLOPS but also by the performance of other parameters related to type and utilization of the hardware, such as CPU, Random Access Memory (RAM), hard disk, network, etc. The codes need to be optimized for more than just FLOPs and new parameters must be included in benchmarking. In this dissertation, the parallel CEM software named High Order Basis Based Integral Equation Solver (HOBBIES) is introduced. This code was developed to address the needs of the changing computer hardware platforms in order to provide fast, accurate and efficient solutions to large, complex electromagnetic problems. The research in this dissertation proves that the performance of parallel code is intimately related to the configuration of the computer hardware and can be maximized for different hardware platforms. To benchmark and optimize the performance of parallel CEM software, a variety of large, complex projects are created and executed on a variety of computer platforms. The computer platforms used in this research are detailed in this dissertation. The projects run as benchmarks are also described in detail and results are presented. The parameters that affect parallel CEM software on High Performance Computing Clusters (HPCC) are investigated. This research demonstrates methods to maximize the performance of parallel CEM software code.

Monte Carlo Perturbation Theory Estimates of Sensitivities to System Dimensions

DOE PAGES

Burke, Timothy P.; Kiedrowski, Brian C.

2017-12-11

Here, Monte Carlo methods are developed using adjoint-based perturbation theory and the differential operator method to compute the sensitivities of the k-eigenvalue, linear functions of the flux (reaction rates), and bilinear functions of the forward and adjoint flux (kinetics parameters) to system dimensions for uniform expansions or contractions. The calculation of sensitivities to system dimensions requires computing scattering and fission sources at material interfaces using collisions occurring at the interface—which is a set of events with infinitesimal probability. Kernel density estimators are used to estimate the source at interfaces using collisions occurring near the interface. The methods for computing sensitivitiesmore » of linear and bilinear ratios are derived using the differential operator method and adjoint-based perturbation theory and are shown to be equivalent to methods previously developed using a collision history–based approach. The methods for determining sensitivities to system dimensions are tested on a series of fast, intermediate, and thermal critical benchmarks as well as a pressurized water reactor benchmark problem with iterated fission probability used for adjoint-weighting. The estimators are shown to agree within 5% and 3σ of reference solutions obtained using direct perturbations with central differences for the majority of test problems.« less

Simulated annealing with probabilistic analysis for solving traveling salesman problems

NASA Astrophysics Data System (ADS)

Hong, Pei-Yee; Lim, Yai-Fung; Ramli, Razamin; Khalid, Ruzelan

2013-09-01

Simulated Annealing (SA) is a widely used meta-heuristic that was inspired from the annealing process of recrystallization of metals. Therefore, the efficiency of SA is highly affected by the annealing schedule. As a result, in this paper, we presented an empirical work to provide a comparable annealing schedule to solve symmetric traveling salesman problems (TSP). Randomized complete block design is also used in this study. The results show that different parameters do affect the efficiency of SA and thus, we propose the best found annealing schedule based on the Post Hoc test. SA was tested on seven selected benchmarked problems of symmetric TSP with the proposed annealing schedule. The performance of SA was evaluated empirically alongside with benchmark solutions and simple analysis to validate the quality of solutions. Computational results show that the proposed annealing schedule provides a good quality of solution.

Modified reactive tabu search for the symmetric traveling salesman problems

NASA Astrophysics Data System (ADS)

Lim, Yai-Fung; Hong, Pei-Yee; Ramli, Razamin; Khalid, Ruzelan

2013-09-01

Reactive tabu search (RTS) is an improved method of tabu search (TS) and it dynamically adjusts tabu list size based on how the search is performed. RTS can avoid disadvantage of TS which is in the parameter tuning in tabu list size. In this paper, we proposed a modified RTS approach for solving symmetric traveling salesman problems (TSP). The tabu list size of the proposed algorithm depends on the number of iterations when the solutions do not override the aspiration level to achieve a good balance between diversification and intensification. The proposed algorithm was tested on seven chosen benchmarked problems of symmetric TSP. The performance of the proposed algorithm is compared with that of the TS by using empirical testing, benchmark solution and simple probabilistic analysis in order to validate the quality of solution. The computational results and comparisons show that the proposed algorithm provides a better quality solution than that of the TS.

Automatically Generated Algorithms for the Vertex Coloring Problem

PubMed Central

Contreras Bolton, Carlos; Gatica, Gustavo; Parada, Víctor

2013-01-01

The vertex coloring problem is a classical problem in combinatorial optimization that consists of assigning a color to each vertex of a graph such that no adjacent vertices share the same color, minimizing the number of colors used. Despite the various practical applications that exist for this problem, its NP-hardness still represents a computational challenge. Some of the best computational results obtained for this problem are consequences of hybridizing the various known heuristics. Automatically revising the space constituted by combining these techniques to find the most adequate combination has received less attention. In this paper, we propose exploring the heuristics space for the vertex coloring problem using evolutionary algorithms. We automatically generate three new algorithms by combining elementary heuristics. To evaluate the new algorithms, a computational experiment was performed that allowed comparing them numerically with existing heuristics. The obtained algorithms present an average 29.97% relative error, while four other heuristics selected from the literature present a 59.73% error, considering 29 of the more difficult instances in the DIMACS benchmark. PMID:23516506

Method and system for benchmarking computers

DOEpatents

Gustafson, John L.

1993-09-14

A testing system and method for benchmarking computer systems. The system includes a store containing a scalable set of tasks to be performed to produce a solution in ever-increasing degrees of resolution as a larger number of the tasks are performed. A timing and control module allots to each computer a fixed benchmarking interval in which to perform the stored tasks. Means are provided for determining, after completion of the benchmarking interval, the degree of progress through the scalable set of tasks and for producing a benchmarking rating relating to the degree of progress for each computer.

A Biogeography-Based Optimization Algorithm Hybridized with Tabu Search for the Quadratic Assignment Problem

PubMed Central

Lim, Wee Loon; Wibowo, Antoni; Desa, Mohammad Ishak; Haron, Habibollah

2016-01-01

The quadratic assignment problem (QAP) is an NP-hard combinatorial optimization problem with a wide variety of applications. Biogeography-based optimization (BBO), a relatively new optimization technique based on the biogeography concept, uses the idea of migration strategy of species to derive algorithm for solving optimization problems. It has been shown that BBO provides performance on a par with other optimization methods. A classical BBO algorithm employs the mutation operator as its diversification strategy. However, this process will often ruin the quality of solutions in QAP. In this paper, we propose a hybrid technique to overcome the weakness of classical BBO algorithm to solve QAP, by replacing the mutation operator with a tabu search procedure. Our experiments using the benchmark instances from QAPLIB show that the proposed hybrid method is able to find good solutions for them within reasonable computational times. Out of 61 benchmark instances tested, the proposed method is able to obtain the best known solutions for 57 of them. PMID:26819585

A Biogeography-Based Optimization Algorithm Hybridized with Tabu Search for the Quadratic Assignment Problem.

PubMed

Lim, Wee Loon; Wibowo, Antoni; Desa, Mohammad Ishak; Haron, Habibollah

2016-01-01

The quadratic assignment problem (QAP) is an NP-hard combinatorial optimization problem with a wide variety of applications. Biogeography-based optimization (BBO), a relatively new optimization technique based on the biogeography concept, uses the idea of migration strategy of species to derive algorithm for solving optimization problems. It has been shown that BBO provides performance on a par with other optimization methods. A classical BBO algorithm employs the mutation operator as its diversification strategy. However, this process will often ruin the quality of solutions in QAP. In this paper, we propose a hybrid technique to overcome the weakness of classical BBO algorithm to solve QAP, by replacing the mutation operator with a tabu search procedure. Our experiments using the benchmark instances from QAPLIB show that the proposed hybrid method is able to find good solutions for them within reasonable computational times. Out of 61 benchmark instances tested, the proposed method is able to obtain the best known solutions for 57 of them.

Numerical benchmarking of a Coarse-Mesh Transport (COMET) Method for medical physics applications

NASA Astrophysics Data System (ADS)

Blackburn, Megan Satterfield

2009-12-01

Radiation therapy has become a very import method for treating cancer patients. Thus, it is extremely important to accurately determine the location of energy deposition during these treatments, maximizing dose to the tumor region and minimizing it to healthy tissue. A Coarse-Mesh Transport Method (COMET) has been developed at the Georgia Institute of Technology in the Computational Reactor and Medical Physics Group for use very successfully with neutron transport to analyze whole-core criticality. COMET works by decomposing a large, heterogeneous system into a set of smaller fixed source problems. For each unique local problem that exists, a solution is obtained that we call a response function. These response functions are pre-computed and stored in a library for future use. The overall solution to the global problem can then be found by a linear superposition of these local problems. This method has now been extended to the transport of photons and electrons for use in medical physics problems to determine energy deposition from radiation therapy treatments. The main goal of this work was to develop benchmarks for testing in order to evaluate the COMET code to determine its strengths and weaknesses for these medical physics applications. For response function calculations, legendre polynomial expansions are necessary for space, angle, polar angle, and azimuthal angle. An initial sensitivity study was done to determine the best orders for future testing. After the expansion orders were found, three simple benchmarks were tested: a water phantom, a simplified lung phantom, and a non-clinical slab phantom. Each of these benchmarks was decomposed into 1cm x 1cm and 0.5cm x 0.5cm coarse meshes. Three more clinically relevant problems were developed from patient CT scans. These benchmarks modeled a lung patient, a prostate patient, and a beam re-entry situation. As before, the problems were divided into 1cm x 1cm, 0.5cm x 0.5cm, and 0.25cm x 0.25cm coarse mesh cases. Multiple beam energies were also tested for each case. The COMET solutions for each case were compared to a reference solution obtained by pure Monte Carlo results from EGSnrc. When comparing the COMET results to the reference cases, a pattern of differences appeared in each phantom case. It was found that better results were obtained for lower energy incident photon beams as well as for larger mesh sizes. Possible changes may need to be made with the expansion orders used for energy and angle to better model high energy secondary electrons. Heterogeneity also did not pose a problem for the COMET methodology. Heterogeneous results were found in a comparable amount of time to the homogeneous water phantom. The COMET results were typically found in minutes to hours of computational time, whereas the reference cases typically required hundreds or thousands of hours. A second sensitivity study was also performed on a more stringent problem and with smaller coarse meshes. Previously, the same expansion order was used for each incident photon beam energy so better comparisons could be made. From this second study, it was found that it is optimal to have different expansion orders based on the incident beam energy. Recommendations for future work with this method include more testing on higher expansion orders or possible code modification to better handle secondary electrons. The method also needs to handle more clinically relevant beam descriptions with an energy and angular distribution associated with it.

The ab-initio density matrix renormalization group in practice.

PubMed

Olivares-Amaya, Roberto; Hu, Weifeng; Nakatani, Naoki; Sharma, Sandeep; Yang, Jun; Chan, Garnet Kin-Lic

2015-01-21

The ab-initio density matrix renormalization group (DMRG) is a tool that can be applied to a wide variety of interesting problems in quantum chemistry. Here, we examine the density matrix renormalization group from the vantage point of the quantum chemistry user. What kinds of problems is the DMRG well-suited to? What are the largest systems that can be treated at practical cost? What sort of accuracies can be obtained, and how do we reason about the computational difficulty in different molecules? By examining a diverse benchmark set of molecules: π-electron systems, benchmark main-group and transition metal dimers, and the Mn-oxo-salen and Fe-porphine organometallic compounds, we provide some answers to these questions, and show how the density matrix renormalization group is used in practice.

Particle swarm optimization with recombination and dynamic linkage discovery.

PubMed

Chen, Ying-Ping; Peng, Wen-Chih; Jian, Ming-Chung

2007-12-01

In this paper, we try to improve the performance of the particle swarm optimizer by incorporating the linkage concept, which is an essential mechanism in genetic algorithms, and design a new linkage identification technique called dynamic linkage discovery to address the linkage problem in real-parameter optimization problems. Dynamic linkage discovery is a costless and effective linkage recognition technique that adapts the linkage configuration by employing only the selection operator without extra judging criteria irrelevant to the objective function. Moreover, a recombination operator that utilizes the discovered linkage configuration to promote the cooperation of particle swarm optimizer and dynamic linkage discovery is accordingly developed. By integrating the particle swarm optimizer, dynamic linkage discovery, and recombination operator, we propose a new hybridization of optimization methodologies called particle swarm optimization with recombination and dynamic linkage discovery (PSO-RDL). In order to study the capability of PSO-RDL, numerical experiments were conducted on a set of benchmark functions as well as on an important real-world application. The benchmark functions used in this paper were proposed in the 2005 Institute of Electrical and Electronics Engineers Congress on Evolutionary Computation. The experimental results on the benchmark functions indicate that PSO-RDL can provide a level of performance comparable to that given by other advanced optimization techniques. In addition to the benchmark, PSO-RDL was also used to solve the economic dispatch (ED) problem for power systems, which is a real-world problem and highly constrained. The results indicate that PSO-RDL can successfully solve the ED problem for the three-unit power system and obtain the currently known best solution for the 40-unit system.

Heuristic methods for the single machine scheduling problem with different ready times and a common due date

NASA Astrophysics Data System (ADS)

Birgin, Ernesto G.; Ronconi, Débora P.

2012-10-01

The single machine scheduling problem with a common due date and non-identical ready times for the jobs is examined in this work. Performance is measured by the minimization of the weighted sum of earliness and tardiness penalties of the jobs. Since this problem is NP-hard, the application of constructive heuristics that exploit specific characteristics of the problem to improve their performance is investigated. The proposed approaches are examined through a computational comparative study on a set of 280 benchmark test problems with up to 1000 jobs.

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

Bailey, David H.

The NAS Parallel Benchmarks (NPB) are a suite of parallel computer performance benchmarks. They were originally developed at the NASA Ames Research Center in 1991 to assess high-end parallel supercomputers. Although they are no longer used as widely as they once were for comparing high-end system performance, they continue to be studied and analyzed a great deal in the high-performance computing community. The acronym 'NAS' originally stood for the Numerical Aeronautical Simulation Program at NASA Ames. The name of this organization was subsequently changed to the Numerical Aerospace Simulation Program, and more recently to the NASA Advanced Supercomputing Center, althoughmore » the acronym remains 'NAS.' The developers of the original NPB suite were David H. Bailey, Eric Barszcz, John Barton, David Browning, Russell Carter, LeoDagum, Rod Fatoohi, Samuel Fineberg, Paul Frederickson, Thomas Lasinski, Rob Schreiber, Horst Simon, V. Venkatakrishnan and Sisira Weeratunga. The original NAS Parallel Benchmarks consisted of eight individual benchmark problems, each of which focused on some aspect of scientific computing. The principal focus was in computational aerophysics, although most of these benchmarks have much broader relevance, since in a much larger sense they are typical of many real-world scientific computing applications. The NPB suite grew out of the need for a more rational procedure to select new supercomputers for acquisition by NASA. The emergence of commercially available highly parallel computer systems in the late 1980s offered an attractive alternative to parallel vector supercomputers that had been the mainstay of high-end scientific computing. However, the introduction of highly parallel systems was accompanied by a regrettable level of hype, not only on the part of the commercial vendors but even, in some cases, by scientists using the systems. As a result, it was difficult to discern whether the new systems offered any fundamental performance advantage over vector supercomputers, and, if so, which of the parallel offerings would be most useful in real-world scientific computation. In part to draw attention to some of the performance reporting abuses prevalent at the time, the present author wrote a humorous essay 'Twelve Ways to Fool the Masses,' which described in a light-hearted way a number of the questionable ways in which both vendor marketing people and scientists were inflating and distorting their performance results. All of this underscored the need for an objective and scientifically defensible measure to compare performance on these systems.« less

The NAS parallel benchmarks

NASA Technical Reports Server (NTRS)

Bailey, David (Editor); Barton, John (Editor); Lasinski, Thomas (Editor); Simon, Horst (Editor)

1993-01-01

A new set of benchmarks was developed for the performance evaluation of highly parallel supercomputers. These benchmarks consist of a set of kernels, the 'Parallel Kernels,' and a simulated application benchmark. Together they mimic the computation and data movement characteristics of large scale computational fluid dynamics (CFD) applications. The principal distinguishing feature of these benchmarks is their 'pencil and paper' specification - all details of these benchmarks are specified only algorithmically. In this way many of the difficulties associated with conventional benchmarking approaches on highly parallel systems are avoided.

The Shortlist Method for fast computation of the Earth Mover's Distance and finding optimal solutions to transportation problems.

PubMed

Gottschlich, Carsten; Schuhmacher, Dominic

2014-01-01

Finding solutions to the classical transportation problem is of great importance, since this optimization problem arises in many engineering and computer science applications. Especially the Earth Mover's Distance is used in a plethora of applications ranging from content-based image retrieval, shape matching, fingerprint recognition, object tracking and phishing web page detection to computing color differences in linguistics and biology. Our starting point is the well-known revised simplex algorithm, which iteratively improves a feasible solution to optimality. The Shortlist Method that we propose substantially reduces the number of candidates inspected for improving the solution, while at the same time balancing the number of pivots required. Tests on simulated benchmarks demonstrate a considerable reduction in computation time for the new method as compared to the usual revised simplex algorithm implemented with state-of-the-art initialization and pivot strategies. As a consequence, the Shortlist Method facilitates the computation of large scale transportation problems in viable time. In addition we describe a novel method for finding an initial feasible solution which we coin Modified Russell's Method.

The Shortlist Method for Fast Computation of the Earth Mover's Distance and Finding Optimal Solutions to Transportation Problems

PubMed Central

Gottschlich, Carsten; Schuhmacher, Dominic

2014-01-01

Finding solutions to the classical transportation problem is of great importance, since this optimization problem arises in many engineering and computer science applications. Especially the Earth Mover's Distance is used in a plethora of applications ranging from content-based image retrieval, shape matching, fingerprint recognition, object tracking and phishing web page detection to computing color differences in linguistics and biology. Our starting point is the well-known revised simplex algorithm, which iteratively improves a feasible solution to optimality. The Shortlist Method that we propose substantially reduces the number of candidates inspected for improving the solution, while at the same time balancing the number of pivots required. Tests on simulated benchmarks demonstrate a considerable reduction in computation time for the new method as compared to the usual revised simplex algorithm implemented with state-of-the-art initialization and pivot strategies. As a consequence, the Shortlist Method facilitates the computation of large scale transportation problems in viable time. In addition we describe a novel method for finding an initial feasible solution which we coin Modified Russell's Method. PMID:25310106

Gust Acoustics Computation with a Space-Time CE/SE Parallel 3D Solver

NASA Technical Reports Server (NTRS)

Wang, X. Y.; Himansu, A.; Chang, S. C.; Jorgenson, P. C. E.; Reddy, D. R. (Technical Monitor)

2002-01-01

The benchmark Problem 2 in Category 3 of the Third Computational Aero-Acoustics (CAA) Workshop is solved using the space-time conservation element and solution element (CE/SE) method. This problem concerns the unsteady response of an isolated finite-span swept flat-plate airfoil bounded by two parallel walls to an incident gust. The acoustic field generated by the interaction of the gust with the flat-plate airfoil is computed by solving the 3D (three-dimensional) Euler equations in the time domain using a parallel version of a 3D CE/SE solver. The effect of the gust orientation on the far-field directivity is studied. Numerical solutions are presented and compared with analytical solutions, showing a reasonable agreement.

Implementing Scientific Simulation Codes Highly Tailored for Vector Architectures Using Custom Configurable Computing Machines

NASA Technical Reports Server (NTRS)

Rutishauser, David

2006-01-01

The motivation for this work comes from an observation that amidst the push for Massively Parallel (MP) solutions to high-end computing problems such as numerical physical simulations, large amounts of legacy code exist that are highly optimized for vector supercomputers. Because re-hosting legacy code often requires a complete re-write of the original code, which can be a very long and expensive effort, this work examines the potential to exploit reconfigurable computing machines in place of a vector supercomputer to implement an essentially unmodified legacy source code. Custom and reconfigurable computing resources could be used to emulate an original application's target platform to the extent required to achieve high performance. To arrive at an architecture that delivers the desired performance subject to limited resources involves solving a multi-variable optimization problem with constraints. Prior research in the area of reconfigurable computing has demonstrated that designing an optimum hardware implementation of a given application under hardware resource constraints is an NP-complete problem. The premise of the approach is that the general issue of applying reconfigurable computing resources to the implementation of an application, maximizing the performance of the computation subject to physical resource constraints, can be made a tractable problem by assuming a computational paradigm, such as vector processing. This research contributes a formulation of the problem and a methodology to design a reconfigurable vector processing implementation of a given application that satisfies a performance metric. A generic, parametric, architectural framework for vector processing implemented in reconfigurable logic is developed as a target for a scheduling/mapping algorithm that maps an input computation to a given instance of the architecture. This algorithm is integrated with an optimization framework to arrive at a specification of the architecture parameters that attempts to minimize execution time, while staying within resource constraints. The flexibility of using a custom reconfigurable implementation is exploited in a unique manner to leverage the lessons learned in vector supercomputer development. The vector processing framework is tailored to the application, with variable parameters that are fixed in traditional vector processing. Benchmark data that demonstrates the functionality and utility of the approach is presented. The benchmark data includes an identified bottleneck in a real case study example vector code, the NASA Langley Terminal Area Simulation System (TASS) application.

PDS: A Performance Database Server

DOE PAGES

Berry, Michael W.; Dongarra, Jack J.; Larose, Brian H.; ...

1994-01-01

The process of gathering, archiving, and distributing computer benchmark data is a cumbersome task usually performed by computer users and vendors with little coordination. Most important, there is no publicly available central depository of performance data for all ranges of machines from personal computers to supercomputers. We present an Internet-accessible performance database server (PDS) that can be used to extract current benchmark data and literature. As an extension to the X-Windows-based user interface (Xnetlib) to the Netlib archival system, PDS provides an on-line catalog of public domain computer benchmarks such as the LINPACK benchmark, Perfect benchmarks, and the NAS parallelmore » benchmarks. PDS does not reformat or present the benchmark data in any way that conflicts with the original methodology of any particular benchmark; it is thereby devoid of any subjective interpretations of machine performance. We believe that all branches (research laboratories, academia, and industry) of the general computing community can use this facility to archive performance metrics and make them readily available to the public. PDS can provide a more manageable approach to the development and support of a large dynamic database of published performance metrics.« less

Performance Comparison of NAMI DANCE and FLOW-3D® Models in Tsunami Propagation, Inundation and Currents using NTHMP Benchmark Problems

NASA Astrophysics Data System (ADS)

Velioglu Sogut, Deniz; Yalciner, Ahmet Cevdet

2018-06-01

Field observations provide valuable data regarding nearshore tsunami impact, yet only in inundation areas where tsunami waves have already flooded. Therefore, tsunami modeling is essential to understand tsunami behavior and prepare for tsunami inundation. It is necessary that all numerical models used in tsunami emergency planning be subject to benchmark tests for validation and verification. This study focuses on two numerical codes, NAMI DANCE and FLOW-3D®, for validation and performance comparison. NAMI DANCE is an in-house tsunami numerical model developed by the Ocean Engineering Research Center of Middle East Technical University, Turkey and Laboratory of Special Research Bureau for Automation of Marine Research, Russia. FLOW-3D® is a general purpose computational fluid dynamics software, which was developed by scientists who pioneered in the design of the Volume-of-Fluid technique. The codes are validated and their performances are compared via analytical, experimental and field benchmark problems, which are documented in the ``Proceedings and Results of the 2011 National Tsunami Hazard Mitigation Program (NTHMP) Model Benchmarking Workshop'' and the ``Proceedings and Results of the NTHMP 2015 Tsunami Current Modeling Workshop". The variations between the numerical solutions of these two models are evaluated through statistical error analysis.

The NAS parallel benchmarks

NASA Technical Reports Server (NTRS)

Bailey, D. H.; Barszcz, E.; Barton, J. T.; Carter, R. L.; Lasinski, T. A.; Browning, D. S.; Dagum, L.; Fatoohi, R. A.; Frederickson, P. O.; Schreiber, R. S.

1991-01-01

A new set of benchmarks has been developed for the performance evaluation of highly parallel supercomputers in the framework of the NASA Ames Numerical Aerodynamic Simulation (NAS) Program. These consist of five 'parallel kernel' benchmarks and three 'simulated application' benchmarks. Together they mimic the computation and data movement characteristics of large-scale computational fluid dynamics applications. The principal distinguishing feature of these benchmarks is their 'pencil and paper' specification-all details of these benchmarks are specified only algorithmically. In this way many of the difficulties associated with conventional benchmarking approaches on highly parallel systems are avoided.

The Suite for Embedded Applications and Kernels

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

2016-05-10

Many applications of high performance embedded computing are limited by performance or power bottlenecks. We havedesigned SEAK, a new benchmark suite, (a) to capture these bottlenecks in a way that encourages creative solutions to these bottlenecks? and (b) to facilitate rigorous, objective, end-user evaluation for their solutions. To avoid biasing solutions toward existing algorithms, SEAK benchmarks use a mission-centric (abstracted from a particular algorithm) andgoal-oriented (functional) specification. To encourage solutions that are any combination of software or hardware, we use an end-user blackbox evaluation that can capture tradeoffs between performance, power, accuracy, size, and weight. The tradeoffs are especially informativemore » for procurement decisions. We call our benchmarks future proof because each mission-centric interface and evaluation remains useful despite shifting algorithmic preferences. It is challenging to create both concise and precise goal-oriented specifications for mission-centric problems. This paper describes the SEAK benchmark suite and presents an evaluation of sample solutions that highlights power and performance tradeoffs.« less

Validation of tsunami inundation model TUNA-RP using OAR-PMEL-135 benchmark problem set

NASA Astrophysics Data System (ADS)

Koh, H. L.; Teh, S. Y.; Tan, W. K.; Kh'ng, X. Y.

2017-05-01

A standard set of benchmark problems, known as OAR-PMEL-135, is developed by the US National Tsunami Hazard Mitigation Program for tsunami inundation model validation. Any tsunami inundation model must be tested for its accuracy and capability using this standard set of benchmark problems before it can be gainfully used for inundation simulation. The authors have previously developed an in-house tsunami inundation model known as TUNA-RP. This inundation model solves the two-dimensional nonlinear shallow water equations coupled with a wet-dry moving boundary algorithm. This paper presents the validation of TUNA-RP against the solutions provided in the OAR-PMEL-135 benchmark problem set. This benchmark validation testing shows that TUNA-RP can indeed perform inundation simulation with accuracy consistent with that in the tested benchmark problem set.

A new numerical benchmark for variably saturated variable-density flow and transport in porous media

NASA Astrophysics Data System (ADS)

Guevara, Carlos; Graf, Thomas

2016-04-01

In subsurface hydrological systems, spatial and temporal variations in solute concentration and/or temperature may affect fluid density and viscosity. These variations could lead to potentially unstable situations, in which a dense fluid overlies a less dense fluid. These situations could produce instabilities that appear as dense plume fingers migrating downwards counteracted by vertical upwards flow of freshwater (Simmons et al., Transp. Porous Medium, 2002). As a result of unstable variable-density flow, solute transport rates are increased over large distances and times as compared to constant-density flow. The numerical simulation of variable-density flow in saturated and unsaturated media requires corresponding benchmark problems against which a computer model is validated (Diersch and Kolditz, Adv. Water Resour, 2002). Recorded data from a laboratory-scale experiment of variable-density flow and solute transport in saturated and unsaturated porous media (Simmons et al., Transp. Porous Medium, 2002) is used to define a new numerical benchmark. The HydroGeoSphere code (Therrien et al., 2004) coupled with PEST (www.pesthomepage.org) are used to obtain an optimized parameter set capable of adequately representing the data set by Simmons et al., (2002). Fingering in the numerical model is triggered using random hydraulic conductivity fields. Due to the inherent randomness, a large number of simulations were conducted in this study. The optimized benchmark model adequately predicts the plume behavior and the fate of solutes. This benchmark is useful for model verification of variable-density flow problems in saturated and/or unsaturated media.

New core-reflector boundary conditions for transient nodal reactor calculations

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

Lee, E.K.; Kim, C.H.; Joo, H.K.

1995-09-01

New core-reflector boundary conditions designed for the exclusion of the reflector region in transient nodal reactor calculations are formulated. Spatially flat frequency approximations for the temporal neutron behavior and two types of transverse leakage approximations in the reflector region are introduced to solve the transverse-integrated time-dependent one-dimensional diffusion equation and then to obtain relationships between net current and flux at the core-reflector interfaces. To examine the effectiveness of new core-reflector boundary conditions in transient nodal reactor computations, nodal expansion method (NEM) computations with and without explicit representation of the reflector are performed for Laboratorium fuer Reaktorregelung und Anlagen (LRA) boilingmore » water reactor (BWR) and Nuclear Energy Agency Committee on Reactor Physics (NEACRP) pressurized water reactor (PWR) rod ejection kinetics benchmark problems. Good agreement between two NEM computations is demonstrated in all the important transient parameters of two benchmark problems. A significant amount of CPU time saving is also demonstrated with the boundary condition model with transverse leakage (BCMTL) approximations in the reflector region. In the three-dimensional LRA BWR, the BCMTL and the explicit reflector model computations differ by {approximately}4% in transient peak power density while the BCMTL results in >40% of CPU time saving by excluding both the axial and the radial reflector regions from explicit computational nodes. In the NEACRP PWR problem, which includes six different transient cases, the largest difference is 24.4% in the transient maximum power in the one-node-per-assembly B1 transient results. This difference in the transient maximum power of the B1 case is shown to reduce to 11.7% in the four-node-per-assembly computations. As for the computing time, BCMTL is shown to reduce the CPU time >20% in all six transient cases of the NEACRP PWR.« less

Improved Quasi-Newton method via PSB update for solving systems of nonlinear equations

NASA Astrophysics Data System (ADS)

Mamat, Mustafa; Dauda, M. K.; Waziri, M. Y.; Ahmad, Fadhilah; Mohamad, Fatma Susilawati

2016-10-01

The Newton method has some shortcomings which includes computation of the Jacobian matrix which may be difficult or even impossible to compute and solving the Newton system in every iteration. Also, the common setback with some quasi-Newton methods is that they need to compute and store an n × n matrix at each iteration, this is computationally costly for large scale problems. To overcome such drawbacks, an improved Method for solving systems of nonlinear equations via PSB (Powell-Symmetric-Broyden) update is proposed. In the proposed method, the approximate Jacobian inverse Hk of PSB is updated and its efficiency has improved thereby require low memory storage, hence the main aim of this paper. The preliminary numerical results show that the proposed method is practically efficient when applied on some benchmark problems.

There is no one-size-fits-all product for InSAR; on the inclusion of contextual information for geodetically-proof InSAR data products

NASA Astrophysics Data System (ADS)

Hanssen, R. F.

2017-12-01

In traditional geodesy, one is interested in determining the coordinates, or the change in coordinates, of predefined benchmarks. These benchmarks are clearly identifiable and are especially established to be representative of the signal of interest. This holds, e.g., for leveling benchmarks, for triangulation/trilateration benchmarks, and for GNSS benchmarks. The desired coordinates are not identical to the basic measurements, and need to be estimated using robust estimation procedures, where the stochastic nature of the measurements is taken into account. For InSAR, however, the `benchmarks' are not predefined. In fact, usually we do not know where an effective benchmark is located, even though we can determine its dynamic behavior pretty well. This poses several significant problems. First, we cannot describe the quality of the measurements, unless we already know the dynamic behavior of the benchmark. Second, if we don't know the quality of the measurements, we cannot compute the quality of the estimated parameters. Third, rather harsh assumptions need to be made to produce a result. These (usually implicit) assumptions differ between processing operators and the used software, and are severely affected by the amount of available data. Fourth, the `relative' nature of the final estimates is usually not explicitly stated, which is particularly problematic for non-expert users. Finally, whereas conventional geodesy applies rigorous testing to check for measurement or model errors, this is hardly ever done in InSAR-geodesy. These problems make it rather impossible to provide a precise, reliable, repeatable, and `universal' InSAR product or service. Here we evaluate the requirements and challenges to move towards InSAR as a geodetically-proof product. In particular this involves the explicit inclusion of contextual information, as well as InSAR procedures, standards and a technical protocol, supported by the International Association of Geodesy and the international scientific community.

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed with an emphasis on recent developments, such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is found that new developments in methodology, combined with improvements in computer hardware, are leading to unprecedented accuracy in solving problems in spectroscopy.

The application of ab initio calculations to molecular spectroscopy

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.

1989-01-01

The state of the art in ab initio molecular structure calculations is reviewed, with an emphasis on recent developments such as full configuration-interaction benchmark calculations and atomic natural orbital basis sets. It is shown that new developments in methodology combined with improvements in computer hardware are leading to unprecedented accuracy in solving problems in spectroscopy.

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.

Hierarchical Artificial Bee Colony Algorithm for RFID Network Planning Optimization

PubMed Central

Ma, Lianbo; Chen, Hanning; Hu, Kunyuan; Zhu, Yunlong

2014-01-01

This paper presents a novel optimization algorithm, namely, hierarchical artificial bee colony optimization, called HABC, to tackle the radio frequency identification network planning (RNP) problem. In the proposed multilevel model, the higher-level species can be aggregated by the subpopulations from lower level. In the bottom level, each subpopulation employing the canonical ABC method searches the part-dimensional optimum in parallel, which can be constructed into a complete solution for the upper level. At the same time, the comprehensive learning method with crossover and mutation operators is applied to enhance the global search ability between species. Experiments are conducted on a set of 10 benchmark optimization problems. The results demonstrate that the proposed HABC obtains remarkable performance on most chosen benchmark functions when compared to several successful swarm intelligence and evolutionary algorithms. Then HABC is used for solving the real-world RNP problem on two instances with different scales. Simulation results show that the proposed algorithm is superior for solving RNP, in terms of optimization accuracy and computation robustness. PMID:24592200

Hierarchical artificial bee colony algorithm for RFID network planning optimization.

PubMed

Ma, Lianbo; Chen, Hanning; Hu, Kunyuan; Zhu, Yunlong

2014-01-01

This paper presents a novel optimization algorithm, namely, hierarchical artificial bee colony optimization, called HABC, to tackle the radio frequency identification network planning (RNP) problem. In the proposed multilevel model, the higher-level species can be aggregated by the subpopulations from lower level. In the bottom level, each subpopulation employing the canonical ABC method searches the part-dimensional optimum in parallel, which can be constructed into a complete solution for the upper level. At the same time, the comprehensive learning method with crossover and mutation operators is applied to enhance the global search ability between species. Experiments are conducted on a set of 10 benchmark optimization problems. The results demonstrate that the proposed HABC obtains remarkable performance on most chosen benchmark functions when compared to several successful swarm intelligence and evolutionary algorithms. Then HABC is used for solving the real-world RNP problem on two instances with different scales. Simulation results show that the proposed algorithm is superior for solving RNP, in terms of optimization accuracy and computation robustness.

Performance evaluation of firefly algorithm with variation in sorting for non-linear benchmark problems

NASA Astrophysics Data System (ADS)

Umbarkar, A. J.; Balande, U. T.; Seth, P. D.

2017-06-01

The field of nature inspired computing and optimization techniques have evolved to solve difficult optimization problems in diverse fields of engineering, science and technology. The firefly attraction process is mimicked in the algorithm for solving optimization problems. In Firefly Algorithm (FA) sorting of fireflies is done by using sorting algorithm. The original FA is proposed with bubble sort for ranking the fireflies. In this paper, the quick sort replaces bubble sort to decrease the time complexity of FA. The dataset used is unconstrained benchmark functions from CEC 2005 [22]. The comparison of FA using bubble sort and FA using quick sort is performed with respect to best, worst, mean, standard deviation, number of comparisons and execution time. The experimental result shows that FA using quick sort requires less number of comparisons but requires more execution time. The increased number of fireflies helps to converge into optimal solution whereas by varying dimension for algorithm performed better at a lower dimension than higher dimension.

A hybrid heuristic for the multiple choice multidimensional knapsack problem

NASA Astrophysics Data System (ADS)

Mansi, Raïd; Alves, Cláudio; Valério de Carvalho, J. M.; Hanafi, Saïd

2013-08-01

In this article, a new solution approach for the multiple choice multidimensional knapsack problem is described. The problem is a variant of the multidimensional knapsack problem where items are divided into classes, and exactly one item per class has to be chosen. Both problems are NP-hard. However, the multiple choice multidimensional knapsack problem appears to be more difficult to solve in part because of its choice constraints. Many real applications lead to very large scale multiple choice multidimensional knapsack problems that can hardly be addressed using exact algorithms. A new hybrid heuristic is proposed that embeds several new procedures for this problem. The approach is based on the resolution of linear programming relaxations of the problem and reduced problems that are obtained by fixing some variables of the problem. The solutions of these problems are used to update the global lower and upper bounds for the optimal solution value. A new strategy for defining the reduced problems is explored, together with a new family of cuts and a reformulation procedure that is used at each iteration to improve the performance of the heuristic. An extensive set of computational experiments is reported for benchmark instances from the literature and for a large set of hard instances generated randomly. The results show that the approach outperforms other state-of-the-art methods described so far, providing the best known solution for a significant number of benchmark instances.

Accurate quantum chemical calculations

NASA Technical Reports Server (NTRS)

Bauschlicher, Charles W., Jr.; Langhoff, Stephen R.; Taylor, Peter R.

1989-01-01

An important goal of quantum chemical calculations is to provide an understanding of chemical bonding and molecular electronic structure. A second goal, the prediction of energy differences to chemical accuracy, has been much harder to attain. First, the computational resources required to achieve such accuracy are very large, and second, it is not straightforward to demonstrate that an apparently accurate result, in terms of agreement with experiment, does not result from a cancellation of errors. Recent advances in electronic structure methodology, coupled with the power of vector supercomputers, have made it possible to solve a number of electronic structure problems exactly using the full configuration interaction (FCI) method within a subspace of the complete Hilbert space. These exact results can be used to benchmark approximate techniques that are applicable to a wider range of chemical and physical problems. The methodology of many-electron quantum chemistry is reviewed. Methods are considered in detail for performing FCI calculations. The application of FCI methods to several three-electron problems in molecular physics are discussed. A number of benchmark applications of FCI wave functions are described. Atomic basis sets and the development of improved methods for handling very large basis sets are discussed: these are then applied to a number of chemical and spectroscopic problems; to transition metals; and to problems involving potential energy surfaces. Although the experiences described give considerable grounds for optimism about the general ability to perform accurate calculations, there are several problems that have proved less tractable, at least with current computer resources, and these and possible solutions are discussed.

Spherical Harmonic Solutions to the 3D Kobayashi Benchmark Suite

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

Brown, P.N.; Chang, B.; Hanebutte, U.R.

1999-12-29

Spherical harmonic solutions of order 5, 9 and 21 on spatial grids containing up to 3.3 million cells are presented for the Kobayashi benchmark suite. This suite of three problems with simple geometry of pure absorber with large void region was proposed by Professor Kobayashi at an OECD/NEA meeting in 1996. Each of the three problems contains a source, a void and a shield region. Problem 1 can best be described as a box in a box problem, where a source region is surrounded by a square void region which itself is embedded in a square shield region. Problems 2more » and 3 represent a shield with a void duct. Problem 2 having a straight and problem 3 a dog leg shaped duct. A pure absorber and a 50% scattering case are considered for each of the three problems. The solutions have been obtained with Ardra, a scalable, parallel neutron transport code developed at Lawrence Livermore National Laboratory (LLNL). The Ardra code takes advantage of a two-level parallelization strategy, which combines message passing between processing nodes and thread based parallelism amongst processors on each node. All calculations were performed on the IBM ASCI Blue-Pacific computer at LLNL.« less

GLAD: a system for developing and deploying large-scale bioinformatics grid.

PubMed

Teo, Yong-Meng; Wang, Xianbing; Ng, Yew-Kwong

2005-03-01

Grid computing is used to solve large-scale bioinformatics problems with gigabytes database by distributing the computation across multiple platforms. Until now in developing bioinformatics grid applications, it is extremely tedious to design and implement the component algorithms and parallelization techniques for different classes of problems, and to access remotely located sequence database files of varying formats across the grid. In this study, we propose a grid programming toolkit, GLAD (Grid Life sciences Applications Developer), which facilitates the development and deployment of bioinformatics applications on a grid. GLAD has been developed using ALiCE (Adaptive scaLable Internet-based Computing Engine), a Java-based grid middleware, which exploits the task-based parallelism. Two bioinformatics benchmark applications, such as distributed sequence comparison and distributed progressive multiple sequence alignment, have been developed using GLAD.

Importance of inlet boundary conditions for numerical simulation of combustor flows

NASA Technical Reports Server (NTRS)

Sturgess, G. J.; Syed, S. A.; Mcmanus, K. R.

1983-01-01

Fluid dynamic computer codes for the mathematical simulation of problems in gas turbine engine combustion systems are required as design and diagnostic tools. To eventually achieve a performance standard with these codes of more than qualitative accuracy it is desirable to use benchmark experiments for validation studies. Typical of the fluid dynamic computer codes being developed for combustor simulations is the TEACH (Teaching Elliptic Axisymmetric Characteristics Heuristically) solution procedure. It is difficult to find suitable experiments which satisfy the present definition of benchmark quality. For the majority of the available experiments there is a lack of information concerning the boundary conditions. A standard TEACH-type numerical technique is applied to a number of test-case experiments. It is found that numerical simulations of gas turbine combustor-relevant flows can be sensitive to the plane at which the calculations start and the spatial distributions of inlet quantities for swirling flows.

A novel artificial fish swarm algorithm for solving large-scale reliability-redundancy application problem.

PubMed

He, Qiang; Hu, Xiangtao; Ren, Hong; Zhang, Hongqi

2015-11-01

A novel artificial fish swarm algorithm (NAFSA) is proposed for solving large-scale reliability-redundancy allocation problem (RAP). In NAFSA, the social behaviors of fish swarm are classified in three ways: foraging behavior, reproductive behavior, and random behavior. The foraging behavior designs two position-updating strategies. And, the selection and crossover operators are applied to define the reproductive ability of an artificial fish. For the random behavior, which is essentially a mutation strategy, the basic cloud generator is used as the mutation operator. Finally, numerical results of four benchmark problems and a large-scale RAP are reported and compared. NAFSA shows good performance in terms of computational accuracy and computational efficiency for large scale RAP. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Computing eigenfunctions and eigenvalues of boundary-value problems with the orthogonal spectral renormalization method

NASA Astrophysics Data System (ADS)

Cartarius, Holger; Musslimani, Ziad H.; Schwarz, Lukas; Wunner, Günter

2018-03-01

The spectral renormalization method was introduced in 2005 as an effective way to compute ground states of nonlinear Schrödinger and Gross-Pitaevskii type equations. In this paper, we introduce an orthogonal spectral renormalization (OSR) method to compute ground and excited states (and their respective eigenvalues) of linear and nonlinear eigenvalue problems. The implementation of the algorithm follows four simple steps: (i) reformulate the underlying eigenvalue problem as a fixed-point equation, (ii) introduce a renormalization factor that controls the convergence properties of the iteration, (iii) perform a Gram-Schmidt orthogonalization process in order to prevent the iteration from converging to an unwanted mode, and (iv) compute the solution sought using a fixed-point iteration. The advantages of the OSR scheme over other known methods (such as Newton's and self-consistency) are (i) it allows the flexibility to choose large varieties of initial guesses without diverging, (ii) it is easy to implement especially at higher dimensions, and (iii) it can easily handle problems with complex and random potentials. The OSR method is implemented on benchmark Hermitian linear and nonlinear eigenvalue problems as well as linear and nonlinear non-Hermitian PT -symmetric models.

A comparative study of upwind and MacCormack schemes for CAA benchmark problems

NASA Technical Reports Server (NTRS)

Viswanathan, K.; Sankar, L. N.

1995-01-01

In this study, upwind schemes and MacCormack schemes are evaluated as to their suitability for aeroacoustic applications. The governing equations are cast in a curvilinear coordinate system and discretized using finite volume concepts. A flux splitting procedure is used for the upwind schemes, where the signals crossing the cell faces are grouped into two categories: signals that bring information from outside into the cell, and signals that leave the cell. These signals may be computed in several ways, with the desired spatial and temporal accuracy achieved by choosing appropriate interpolating polynomials. The classical MacCormack schemes employed here are fourth order accurate in time and space. Results for categories 1, 4, and 6 of the workshop's benchmark problems are presented. Comparisons are also made with the exact solutions, where available. The main conclusions of this study are finally presented.

Benchmarking gate-based quantum computers

NASA Astrophysics Data System (ADS)

Michielsen, Kristel; Nocon, Madita; Willsch, Dennis; Jin, Fengping; Lippert, Thomas; De Raedt, Hans

2017-11-01

With the advent of public access to small gate-based quantum processors, it becomes necessary to develop a benchmarking methodology such that independent researchers can validate the operation of these processors. We explore the usefulness of a number of simple quantum circuits as benchmarks for gate-based quantum computing devices and show that circuits performing identity operations are very simple, scalable and sensitive to gate errors and are therefore very well suited for this task. We illustrate the procedure by presenting benchmark results for the IBM Quantum Experience, a cloud-based platform for gate-based quantum computing.

Benchmarking Multilayer-HySEA model for landslide generated tsunami. HTHMP validation process.

NASA Astrophysics Data System (ADS)

Macias, J.; Escalante, C.; Castro, M. J.

2017-12-01

Landslide tsunami hazard may be dominant along significant parts of the coastline around the world, in particular in the USA, as compared to hazards from other tsunamigenic sources. This fact motivated NTHMP about the need of benchmarking models for landslide generated tsunamis, following the same methodology already used for standard tsunami models when the source is seismic. To perform the above-mentioned validation process, a set of candidate benchmarks were proposed. These benchmarks are based on a subset of available laboratory data sets for solid slide experiments and deformable slide experiments, and include both submarine and subaerial slides. A benchmark based on a historic field event (Valdez, AK, 1964) close the list of proposed benchmarks. A total of 7 benchmarks. The Multilayer-HySEA model including non-hydrostatic effects has been used to perform all the benchmarking problems dealing with laboratory experiments proposed in the workshop that was organized at Texas A&M University - Galveston, on January 9-11, 2017 by NTHMP. The aim of this presentation is to show some of the latest numerical results obtained with the Multilayer-HySEA (non-hydrostatic) model in the framework of this validation effort.Acknowledgements. This research has been partially supported by the Spanish Government Research project SIMURISK (MTM2015-70490-C02-01-R) and University of Malaga, Campus de Excelencia Internacional Andalucía Tech. The GPU computations were performed at the Unit of Numerical Methods (University of Malaga).

Benchmarking multimedia performance

NASA Astrophysics Data System (ADS)

Zandi, Ahmad; Sudharsanan, Subramania I.

1998-03-01

With the introduction of faster processors and special instruction sets tailored to multimedia, a number of exciting applications are now feasible on the desktops. Among these is the DVD playback consisting, among other things, of MPEG-2 video and Dolby digital audio or MPEG-2 audio. Other multimedia applications such as video conferencing and speech recognition are also becoming popular on computer systems. In view of this tremendous interest in multimedia, a group of major computer companies have formed, Multimedia Benchmarks Committee as part of Standard Performance Evaluation Corp. to address the performance issues of multimedia applications. The approach is multi-tiered with three tiers of fidelity from minimal to full compliant. In each case the fidelity of the bitstream reconstruction as well as quality of the video or audio output are measured and the system is classified accordingly. At the next step the performance of the system is measured. In many multimedia applications such as the DVD playback the application needs to be run at a specific rate. In this case the measurement of the excess processing power, makes all the difference. All these make a system level, application based, multimedia benchmark very challenging. Several ideas and methodologies for each aspect of the problems will be presented and analyzed.

Optimally stopped variational quantum algorithms

NASA Astrophysics Data System (ADS)

Vinci, Walter; Shabani, Alireza

2018-04-01

Quantum processors promise a paradigm shift in high-performance computing which needs to be assessed by accurate benchmarking measures. In this article, we introduce a benchmark for the variational quantum algorithm (VQA), recently proposed as a heuristic algorithm for small-scale quantum processors. In VQA, a classical optimization algorithm guides the processor's quantum dynamics to yield the best solution for a given problem. A complete assessment of the scalability and competitiveness of VQA should take into account both the quality and the time of dynamics optimization. The method of optimal stopping, employed here, provides such an assessment by explicitly including time as a cost factor. Here, we showcase this measure for benchmarking VQA as a solver for some quadratic unconstrained binary optimization. Moreover, we show that a better choice for the cost function of the classical routine can significantly improve the performance of the VQA algorithm and even improve its scaling properties.

A note on bound constraints handling for the IEEE CEC'05 benchmark function suite.

PubMed

Liao, Tianjun; Molina, Daniel; de Oca, Marco A Montes; Stützle, Thomas

2014-01-01

The benchmark functions and some of the algorithms proposed for the special session on real parameter optimization of the 2005 IEEE Congress on Evolutionary Computation (CEC'05) have played and still play an important role in the assessment of the state of the art in continuous optimization. In this article, we show that if bound constraints are not enforced for the final reported solutions, state-of-the-art algorithms produce infeasible best candidate solutions for the majority of functions of the IEEE CEC'05 benchmark function suite. This occurs even though the optima of the CEC'05 functions are within the specified bounds. This phenomenon has important implications on algorithm comparisons, and therefore on algorithm designs. This article's goal is to draw the attention of the community to the fact that some authors might have drawn wrong conclusions from experiments using the CEC'05 problems.

a Proposed Benchmark Problem for Scatter Calculations in Radiographic Modelling

NASA Astrophysics Data System (ADS)

Jaenisch, G.-R.; Bellon, C.; Schumm, A.; Tabary, J.; Duvauchelle, Ph.

2009-03-01

Code Validation is a permanent concern in computer modelling, and has been addressed repeatedly in eddy current and ultrasonic modeling. A good benchmark problem is sufficiently simple to be taken into account by various codes without strong requirements on geometry representation capabilities, focuses on few or even a single aspect of the problem at hand to facilitate interpretation and to avoid that compound errors compensate themselves, yields a quantitative result and is experimentally accessible. In this paper we attempt to address code validation for one aspect of radiographic modeling, the scattered radiation prediction. Many NDT applications can not neglect scattered radiation, and the scatter calculation thus is important to faithfully simulate the inspection situation. Our benchmark problem covers the wall thickness range of 10 to 50 mm for single wall inspections, with energies ranging from 100 to 500 keV in the first stage, and up to 1 MeV with wall thicknesses up to 70 mm in the extended stage. A simple plate geometry is sufficient for this purpose, and the scatter data is compared on a photon level, without a film model, which allows for comparisons with reference codes like MCNP. We compare results of three Monte Carlo codes (McRay, Sindbad and Moderato) as well as an analytical first order scattering code (VXI), and confront them to results obtained with MCNP. The comparison with an analytical scatter model provides insights into the application domain where this kind of approach can successfully replace Monte-Carlo calculations.

Patch planting of hard spin-glass problems: Getting ready for the next generation of optimization approaches

NASA Astrophysics Data System (ADS)

Wang, Wenlong; Mandrà, Salvatore; Katzgraber, Helmut

We propose a patch planting heuristic that allows us to create arbitrarily-large Ising spin-glass instances on any topology and with any type of disorder, and where the exact ground-state energy of the problem is known by construction. By breaking up the problem into patches that can be treated either with exact or heuristic solvers, we can reconstruct the optimum of the original, considerably larger, problem. The scaling of the computational complexity of these instances with various patch numbers and sizes is investigated and compared with random instances using population annealing Monte Carlo and quantum annealing on the D-Wave 2X quantum annealer. The method can be useful for benchmarking of novel computing technologies and algorithms. NSF-DMR-1208046 and the Office of the Director of National Intelligence (ODNI), Intelligence Advanced Research Projects Activity (IARPA), via MIT Lincoln Laboratory Air Force Contract No. FA8721-05-C-0002.

A set partitioning reformulation for the multiple-choice multidimensional knapsack problem

NASA Astrophysics Data System (ADS)

Voß, Stefan; Lalla-Ruiz, Eduardo

2016-05-01

The Multiple-choice Multidimensional Knapsack Problem (MMKP) is a well-known ?-hard combinatorial optimization problem that has received a lot of attention from the research community as it can be easily translated to several real-world problems arising in areas such as allocating resources, reliability engineering, cognitive radio networks, cloud computing, etc. In this regard, an exact model that is able to provide high-quality feasible solutions for solving it or being partially included in algorithmic schemes is desirable. The MMKP basically consists of finding a subset of objects that maximizes the total profit while observing some capacity restrictions. In this article a reformulation of the MMKP as a set partitioning problem is proposed to allow for new insights into modelling the MMKP. The computational experimentation provides new insights into the problem itself and shows that the new model is able to improve on the best of the known results for some of the most common benchmark instances.

Multiscale computations with a wavelet-adaptive algorithm

NASA Astrophysics Data System (ADS)

Rastigejev, Yevgenii Anatolyevich

A wavelet-based adaptive multiresolution algorithm for the numerical solution of multiscale problems governed by partial differential equations is introduced. The main features of the method include fast algorithms for the calculation of wavelet coefficients and approximation of derivatives on nonuniform stencils. The connection between the wavelet order and the size of the stencil is established. The algorithm is based on the mathematically well established wavelet theory. This allows us to provide error estimates of the solution which are used in conjunction with an appropriate threshold criteria to adapt the collocation grid. The efficient data structures for grid representation as well as related computational algorithms to support grid rearrangement procedure are developed. The algorithm is applied to the simulation of phenomena described by Navier-Stokes equations. First, we undertake the study of the ignition and subsequent viscous detonation of a H2 : O2 : Ar mixture in a one-dimensional shock tube. Subsequently, we apply the algorithm to solve the two- and three-dimensional benchmark problem of incompressible flow in a lid-driven cavity at large Reynolds numbers. For these cases we show that solutions of comparable accuracy as the benchmarks are obtained with more than an order of magnitude reduction in degrees of freedom. The simulations show the striking ability of the algorithm to adapt to a solution having different scales at different spatial locations so as to produce accurate results at a relatively low computational cost.

47 CFR 69.108 - Transport rate benchmark.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Transport rate benchmark. 69.108 Section 69.108... Computation of Charges § 69.108 Transport rate benchmark. (a) For transport charges computed in accordance... interoffice transmission using the telephone company's DS1 special access rates. (b) Initial transport rates...

47 CFR 69.108 - Transport rate benchmark.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Transport rate benchmark. 69.108 Section 69.108... Computation of Charges § 69.108 Transport rate benchmark. (a) For transport charges computed in accordance... interoffice transmission using the telephone company's DS1 special access rates. (b) Initial transport rates...

Analytic Approximations to the Free Boundary and Multi-dimensional Problems in Financial Derivatives Pricing

NASA Astrophysics Data System (ADS)

Lau, Chun Sing

This thesis studies two types of problems in financial derivatives pricing. The first type is the free boundary problem, which can be formulated as a partial differential equation (PDE) subject to a set of free boundary condition. Although the functional form of the free boundary condition is given explicitly, the location of the free boundary is unknown and can only be determined implicitly by imposing continuity conditions on the solution. Two specific problems are studied in details, namely the valuation of fixed-rate mortgages and CEV American options. The second type is the multi-dimensional problem, which involves multiple correlated stochastic variables and their governing PDE. One typical problem we focus on is the valuation of basket-spread options, whose underlying asset prices are driven by correlated geometric Brownian motions (GBMs). Analytic approximate solutions are derived for each of these three problems. For each of the two free boundary problems, we propose a parametric moving boundary to approximate the unknown free boundary, so that the original problem transforms into a moving boundary problem which can be solved analytically. The governing parameter of the moving boundary is determined by imposing the first derivative continuity condition on the solution. The analytic form of the solution allows the price and the hedging parameters to be computed very efficiently. When compared against the benchmark finite-difference method, the computational time is significantly reduced without compromising the accuracy. The multi-stage scheme further allows the approximate results to systematically converge to the benchmark results as one recasts the moving boundary into a piecewise smooth continuous function. For the multi-dimensional problem, we generalize the Kirk (1995) approximate two-asset spread option formula to the case of multi-asset basket-spread option. Since the final formula is in closed form, all the hedging parameters can also be derived in closed form. Numerical examples demonstrate that the pricing and hedging errors are in general less than 1% relative to the benchmark prices obtained by numerical integration or Monte Carlo simulation. By exploiting an explicit relationship between the option price and the underlying probability distribution, we further derive an approximate distribution function for the general basket-spread variable. It can be used to approximate the transition probability distribution of any linear combination of correlated GBMs. Finally, an implicit perturbation is applied to reduce the pricing errors by factors of up to 100. When compared against the existing methods, the basket-spread option formula coupled with the implicit perturbation turns out to be one of the most robust and accurate approximation methods.

On the isotropic Raman spectrum of Ar2 and how to benchmark ab initio calculations of small atomic clusters: Paradox lost.

PubMed

Chrysos, Michael; Dixneuf, Sophie; Rachet, Florent

2015-07-14

This is the long-overdue answer to the discrepancies observed between theory and experiment in Ar2 regarding both the isotropic Raman spectrum and the second refractivity virial coefficient, BR [Gaye et al., Phys. Rev. A 55, 3484 (1997)]. At the origin of this progress is the advent (posterior to 1997) of advanced computational methods for weakly interconnected neutral species at close separations. Here, we report agreement between the previously taken Raman measurements and quantum lineshapes now computed with the employ of large-scale CCSD or smartly constructed MP2 induced-polarizability data. By using these measurements as a benchmark tool, we assess the degree of performance of various other ab initio computed data for the mean polarizability α, and we show that an excellent agreement with the most recently measured value of BR is reached. We propose an even more refined model for α, which is solution of the inverse-scattering problem and whose lineshape matches exactly the measured spectrum over the entire frequency-shift range probed.

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

Frayce, D.; Khayat, R.E.; Derdouri, A.

The dual reciprocity boundary element method (DRBEM) is implemented to solve three-dimensional transient heat conduction problems in the presence of arbitrary sources, typically as these problems arise in materials processing. The DRBEM has a major advantage over conventional BEM, since it avoids the computation of volume integrals. These integrals stem from transient, nonlinear, and/or source terms. Thus there is no need to discretize the inner domain, since only a number of internal points are needed for the computation. The validity of the method is assessed upon comparison with results from benchmark problems where analytical solutions exist. There is generally goodmore » agreement. Comparison against finite element results is also favorable. Calculations are carried out in order to assess the influence of the number and location of internal nodes. The influence of the ratio of the numbers of internal to boundary nodes is also examined.« less

Adiabatic Quantum Computation with Neutral Cesium

NASA Astrophysics Data System (ADS)

Hankin, Aaron; Parazzoli, L.; Chou, Chin-Wen; Jau, Yuan-Yu; Burns, George; Young, Amber; Kemme, Shanalyn; Ferdinand, Andrew; Biedermann, Grant; Landahl, Andrew; Ivan H. Deutsch Collaboration; Mark Saffman Collaboration

2013-05-01

We are implementing a new platform for adiabatic quantum computation (AQC) based on trapped neutral atoms whose coupling is mediated by the dipole-dipole interactions of Rydberg states. Ground state cesium atoms are dressed by laser fields in a manner conditional on the Rydberg blockade mechanism, thereby providing the requisite entangling interactions. As a benchmark we study a Quadratic Unconstrained Binary Optimization (QUBO) problem whose solution is found in the ground state spin configuration of an Ising-like model. University of New Mexico: Ivan H. Deutsch, Tyler Keating, Krittika Goyal.

Benchmark Lisp And Ada Programs

NASA Technical Reports Server (NTRS)

Davis, Gloria; Galant, David; Lim, Raymond; Stutz, John; Gibson, J.; Raghavan, B.; Cheesema, P.; Taylor, W.

1992-01-01

Suite of nonparallel benchmark programs, ELAPSE, designed for three tests: comparing efficiency of computer processing via Lisp vs. Ada; comparing efficiencies of several computers processing via Lisp; or comparing several computers processing via Ada. Tests efficiency which computer executes routines in each language. Available for computer equipped with validated Ada compiler and/or Common Lisp system.

Skipping Strategy (SS) for Initial Population of Job-Shop Scheduling Problem

NASA Astrophysics Data System (ADS)

Abdolrazzagh-Nezhad, M.; Nababan, E. B.; Sarim, H. M.

2018-03-01

Initial population in job-shop scheduling problem (JSSP) is an essential step to obtain near optimal solution. Techniques used to solve JSSP are computationally demanding. Skipping strategy (SS) is employed to acquire initial population after sequence of job on machine and sequence of operations (expressed in Plates-jobs and mPlates-jobs) are determined. The proposed technique is applied to benchmark datasets and the results are compared to that of other initialization techniques. It is shown that the initial population obtained from the SS approach could generate optimal solution.

Development of a Computer-based Benchmarking and Analytical Tool. Benchmarking and Energy & Water Savings Tool in Dairy Plants (BEST-Dairy)

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

Xu, Tengfang; Flapper, Joris; Ke, Jing

The overall goal of the project is to develop a computer-based benchmarking and energy and water savings tool (BEST-Dairy) for use in the California dairy industry – including four dairy processes – cheese, fluid milk, butter, and milk powder.

Analysis of a benchmark suite to evaluate mixed numeric and symbolic processing

NASA Technical Reports Server (NTRS)

Ragharan, Bharathi; Galant, David

1992-01-01

The suite of programs that formed the benchmark for a proposed advanced computer is described and analyzed. The features of the processor and its operating system that are tested by the benchmark are discussed. The computer codes and the supporting data for the analysis are given as appendices.

A benchmark for subduction zone modeling

NASA Astrophysics Data System (ADS)

van Keken, P.; King, S.; Peacock, S.

2003-04-01

Our understanding of subduction zones hinges critically on the ability to discern its thermal structure and dynamics. Computational modeling has become an essential complementary approach to observational and experimental studies. The accurate modeling of subduction zones is challenging due to the unique geometry, complicated rheological description and influence of fluid and melt formation. The complicated physics causes problems for the accurate numerical solution of the governing equations. As a consequence it is essential for the subduction zone community to be able to evaluate the ability and limitations of various modeling approaches. The participants of a workshop on the modeling of subduction zones, held at the University of Michigan at Ann Arbor, MI, USA in 2002, formulated a number of case studies to be developed into a benchmark similar to previous mantle convection benchmarks (Blankenbach et al., 1989; Busse et al., 1991; Van Keken et al., 1997). Our initial benchmark focuses on the dynamics of the mantle wedge and investigates three different rheologies: constant viscosity, diffusion creep, and dislocation creep. In addition we investigate the ability of codes to accurate model dynamic pressure and advection dominated flows. Proceedings of the workshop and the formulation of the benchmark are available at www.geo.lsa.umich.edu/~keken/subduction02.html We strongly encourage interested research groups to participate in this benchmark. At Nice 2003 we will provide an update and first set of benchmark results. Interested researchers are encouraged to contact one of the authors for further details.

BODYFIT-1FE: a computer code for three-dimensional steady-state/transient single-phase rod-bundle thermal-hydraulic analysis. Draft report

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

Chen, B.C.J.; Sha, W.T.; Doria, M.L.

1980-11-01

The governing equations, i.e., conservation equations for mass, momentum, and energy, are solved as a boundary-value problem in space and an initial-value problem in time. BODYFIT-1FE code uses the technique of boundary-fitted coordinate systems where all the physical boundaries are transformed to be coincident with constant coordinate lines in the transformed space. By using this technique, one can prescribe boundary conditions accurately without interpolation. The transformed governing equations in terms of the boundary-fitted coordinates are then solved by using implicit cell-by-cell procedure with a choice of either central or upwind convective derivatives. It is a true benchmark rod-bundle code withoutmore » invoking any assumptions in the case of laminar flow. However, for turbulent flow, some empiricism must be employed due to the closure problem of turbulence modeling. The detailed velocity and temperature distributions calculated from the code can be used to benchmark and calibrate empirical coefficients employed in subchannel codes and porous-medium analyses.« less

Helmholtz and parabolic equation solutions to a benchmark problem in ocean acoustics.

PubMed

Larsson, Elisabeth; Abrahamsson, Leif

2003-05-01

The Helmholtz equation (HE) describes wave propagation in applications such as acoustics and electromagnetics. For realistic problems, solving the HE is often too expensive. Instead, approximations like the parabolic wave equation (PE) are used. For low-frequency shallow-water environments, one persistent problem is to assess the accuracy of the PE model. In this work, a recently developed HE solver that can handle a smoothly varying bathymetry, variable material properties, and layered materials, is used for an investigation of the errors in PE solutions. In the HE solver, a preconditioned Krylov subspace method is applied to the discretized equations. The preconditioner combines domain decomposition and fast transform techniques. A benchmark problem with upslope-downslope propagation over a penetrable lossy seamount is solved. The numerical experiments show that, for the same bathymetry, a soft and slow bottom gives very similar HE and PE solutions, whereas the PE model is far from accurate for a hard and fast bottom. A first attempt to estimate the error is made by computing the relative deviation from the energy balance for the PE solution. This measure gives an indication of the magnitude of the error, but cannot be used as a strict error bound.

A semi-implicit level set method for multiphase flows and fluid-structure interaction problems

NASA Astrophysics Data System (ADS)

Cottet, Georges-Henri; Maitre, Emmanuel

2016-06-01

In this paper we present a novel semi-implicit time-discretization of the level set method introduced in [8] for fluid-structure interaction problems. The idea stems from a linear stability analysis derived on a simplified one-dimensional problem. The semi-implicit scheme relies on a simple filter operating as a pre-processing on the level set function. It applies to multiphase flows driven by surface tension as well as to fluid-structure interaction problems. The semi-implicit scheme avoids the stability constraints that explicit scheme need to satisfy and reduces significantly the computational cost. It is validated through comparisons with the original explicit scheme and refinement studies on two-dimensional benchmarks.

A Modified Artificial Bee Colony Algorithm for p-Center Problems

PubMed Central

Yurtkuran, Alkın

2014-01-01

The objective of the p-center problem is to locate p-centers on a network such that the maximum of the distances from each node to its nearest center is minimized. The artificial bee colony algorithm is a swarm-based meta-heuristic algorithm that mimics the foraging behavior of honey bee colonies. This study proposes a modified ABC algorithm that benefits from a variety of search strategies to balance exploration and exploitation. Moreover, random key-based coding schemes are used to solve the p-center problem effectively. The proposed algorithm is compared to state-of-the-art techniques using different benchmark problems, and computational results reveal that the proposed approach is very efficient. PMID:24616648

Parallel 3D Mortar Element Method for Adaptive Nonconforming Meshes

NASA Technical Reports Server (NTRS)

Feng, Huiyu; Mavriplis, Catherine; VanderWijngaart, Rob; Biswas, Rupak

2004-01-01

High order methods are frequently used in computational simulation for their high accuracy. An efficient way to avoid unnecessary computation in smooth regions of the solution is to use adaptive meshes which employ fine grids only in areas where they are needed. Nonconforming spectral elements allow the grid to be flexibly adjusted to satisfy the computational accuracy requirements. The method is suitable for computational simulations of unsteady problems with very disparate length scales or unsteady moving features, such as heat transfer, fluid dynamics or flame combustion. In this work, we select the Mark Element Method (MEM) to handle the non-conforming interfaces between elements. A new technique is introduced to efficiently implement MEM in 3-D nonconforming meshes. By introducing an "intermediate mortar", the proposed method decomposes the projection between 3-D elements and mortars into two steps. In each step, projection matrices derived in 2-D are used. The two-step method avoids explicitly forming/deriving large projection matrices for 3-D meshes, and also helps to simplify the implementation. This new technique can be used for both h- and p-type adaptation. This method is applied to an unsteady 3-D moving heat source problem. With our new MEM implementation, mesh adaptation is able to efficiently refine the grid near the heat source and coarsen the grid once the heat source passes. The savings in computational work resulting from the dynamic mesh adaptation is demonstrated by the reduction of the the number of elements used and CPU time spent. MEM and mesh adaptation, respectively, bring irregularity and dynamics to the computer memory access pattern. Hence, they provide a good way to gauge the performance of computer systems when running scientific applications whose memory access patterns are irregular and unpredictable. We select a 3-D moving heat source problem as the Unstructured Adaptive (UA) grid benchmark, a new component of the NAS Parallel Benchmarks (NPB). In this paper, we present some interesting performance results of ow OpenMP parallel implementation on different architectures such as the SGI Origin2000, SGI Altix, and Cray MTA-2.

Advanced Computational Methods for Security Constrained Financial Transmission Rights

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

Kalsi, Karanjit; Elbert, Stephen T.; Vlachopoulou, Maria

Financial Transmission Rights (FTRs) are financial insurance tools to help power market participants reduce price risks associated with transmission congestion. FTRs are issued based on a process of solving a constrained optimization problem with the objective to maximize the FTR social welfare under power flow security constraints. Security constraints for different FTR categories (monthly, seasonal or annual) are usually coupled and the number of constraints increases exponentially with the number of categories. Commercial software for FTR calculation can only provide limited categories of FTRs due to the inherent computational challenges mentioned above. In this paper, first an innovative mathematical reformulationmore » of the FTR problem is presented which dramatically improves the computational efficiency of optimization problem. After having re-formulated the problem, a novel non-linear dynamic system (NDS) approach is proposed to solve the optimization problem. The new formulation and performance of the NDS solver is benchmarked against widely used linear programming (LP) solvers like CPLEX™ and tested on both standard IEEE test systems and large-scale systems using data from the Western Electricity Coordinating Council (WECC). The performance of the NDS is demonstrated to be comparable and in some cases is shown to outperform the widely used CPLEX algorithms. The proposed formulation and NDS based solver is also easily parallelizable enabling further computational improvement.« less

A Multifunctional Interface Method for Coupling Finite Element and Finite Difference Methods: Two-Dimensional Scalar-Field Problems

NASA Technical Reports Server (NTRS)

Ransom, Jonathan B.

2002-01-01

A multifunctional interface method with capabilities for variable-fidelity modeling and multiple method analysis is presented. The methodology provides an effective capability by which domains with diverse idealizations can be modeled independently to exploit the advantages of one approach over another. The multifunctional method is used to couple independently discretized subdomains, and it is used to couple the finite element and the finite difference methods. The method is based on a weighted residual variational method and is presented for two-dimensional scalar-field problems. A verification test problem and a benchmark application are presented, and the computational implications are discussed.

Parallelization of Unsteady Adaptive Mesh Refinement for Unstructured Navier-Stokes Solvers

NASA Technical Reports Server (NTRS)

Schwing, Alan M.; Nompelis, Ioannis; Candler, Graham V.

2014-01-01

This paper explores the implementation of the MPI parallelization in a Navier-Stokes solver using adaptive mesh re nement. Viscous and inviscid test problems are considered for the purpose of benchmarking, as are implicit and explicit time advancement methods. The main test problem for comparison includes e ects from boundary layers and other viscous features and requires a large number of grid points for accurate computation. Ex- perimental validation against double cone experiments in hypersonic ow are shown. The adaptive mesh re nement shows promise for a staple test problem in the hypersonic com- munity. Extension to more advanced techniques for more complicated ows is described.

Pattern-set generation algorithm for the one-dimensional multiple stock sizes cutting stock problem

NASA Astrophysics Data System (ADS)

Cui, Yaodong; Cui, Yi-Ping; Zhao, Zhigang

2015-09-01

A pattern-set generation algorithm (PSG) for the one-dimensional multiple stock sizes cutting stock problem (1DMSSCSP) is presented. The solution process contains two stages. In the first stage, the PSG solves the residual problems repeatedly to generate the patterns in the pattern set, where each residual problem is solved by the column-generation approach, and each pattern is generated by solving a single large object placement problem. In the second stage, the integer linear programming model of the 1DMSSCSP is solved using a commercial solver, where only the patterns in the pattern set are considered. The computational results of benchmark instances indicate that the PSG outperforms existing heuristic algorithms and rivals the exact algorithm in solution quality.

Benchmarking neuromorphic vision: lessons learnt from computer vision

PubMed Central

Tan, Cheston; Lallee, Stephane; Orchard, Garrick

2015-01-01

Neuromorphic Vision sensors have improved greatly since the first silicon retina was presented almost three decades ago. They have recently matured to the point where they are commercially available and can be operated by laymen. However, despite improved availability of sensors, there remains a lack of good datasets, while algorithms for processing spike-based visual data are still in their infancy. On the other hand, frame-based computer vision algorithms are far more mature, thanks in part to widely accepted datasets which allow direct comparison between algorithms and encourage competition. We are presented with a unique opportunity to shape the development of Neuromorphic Vision benchmarks and challenges by leveraging what has been learnt from the use of datasets in frame-based computer vision. Taking advantage of this opportunity, in this paper we review the role that benchmarks and challenges have played in the advancement of frame-based computer vision, and suggest guidelines for the creation of Neuromorphic Vision benchmarks and challenges. We also discuss the unique challenges faced when benchmarking Neuromorphic Vision algorithms, particularly when attempting to provide direct comparison with frame-based computer vision. PMID:26528120

Benchmark dataset for undirected and Mixed Capacitated Arc Routing Problems under Time restrictions with Intermediate Facilities.

PubMed

Willemse, Elias J; Joubert, Johan W

2016-09-01

In this article we present benchmark datasets for the Mixed Capacitated Arc Routing Problem under Time restrictions with Intermediate Facilities (MCARPTIF). The problem is a generalisation of the Capacitated Arc Routing Problem (CARP), and closely represents waste collection routing. Four different test sets are presented, each consisting of multiple instance files, and which can be used to benchmark different solution approaches for the MCARPTIF. An in-depth description of the datasets can be found in "Constructive heuristics for the Mixed Capacity Arc Routing Problem under Time Restrictions with Intermediate Facilities" (Willemseand Joubert, 2016) [2] and "Splitting procedures for the Mixed Capacitated Arc Routing Problem under Time restrictions with Intermediate Facilities" (Willemseand Joubert, in press) [4]. The datasets are publicly available from "Library of benchmark test sets for variants of the Capacitated Arc Routing Problem under Time restrictions with Intermediate Facilities" (Willemse and Joubert, 2016) [3].

Global height datum unification: a new approach in gravity potential space

NASA Astrophysics Data System (ADS)

Ardalan, A. A.; Safari, A.

2005-12-01

The problem of “global height datum unification” is solved in the gravity potential space based on: (1) high-resolution local gravity field modeling, (2) geocentric coordinates of the reference benchmark, and (3) a known value of the geoid’s potential. The high-resolution local gravity field model is derived based on a solution of the fixed-free two-boundary-value problem of the Earth’s gravity field using (a) potential difference values (from precise leveling), (b) modulus of the gravity vector (from gravimetry), (c) astronomical longitude and latitude (from geodetic astronomy and/or combination of (GNSS) Global Navigation Satellite System observations with total station measurements), (d) and satellite altimetry. Knowing the height of the reference benchmark in the national height system and its geocentric GNSS coordinates, and using the derived high-resolution local gravity field model, the gravity potential value of the zero point of the height system is computed. The difference between the derived gravity potential value of the zero point of the height system and the geoid’s potential value is computed. This potential difference gives the offset of the zero point of the height system from geoid in the “potential space”, which is transferred into “geometry space” using the transformation formula derived in this paper. The method was applied to the computation of the offset of the zero point of the Iranian height datum from the geoid’s potential value W 0=62636855.8 m2/s2. According to the geometry space computations, the height datum of Iran is 0.09 m below the geoid.

Heterogeneous Distributed Computing for Computational Aerosciences

NASA Technical Reports Server (NTRS)

Sunderam, Vaidy S.

1998-01-01

The research supported under this award focuses on heterogeneous distributed computing for high-performance applications, with particular emphasis on computational aerosciences. The overall goal of this project was to and investigate issues in, and develop solutions to, efficient execution of computational aeroscience codes in heterogeneous concurrent computing environments. In particular, we worked in the context of the PVM[1] system and, subsequent to detailed conversion efforts and performance benchmarking, devising novel techniques to increase the efficacy of heterogeneous networked environments for computational aerosciences. Our work has been based upon the NAS Parallel Benchmark suite, but has also recently expanded in scope to include the NAS I/O benchmarks as specified in the NHT-1 document. In this report we summarize our research accomplishments under the auspices of the grant.

Benchmark solution of the dynamic response of a spherical shell at finite strain

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

Versino, Daniele; Brock, Jerry S.

2016-09-28

Our paper describes the development of high fidelity solutions for the study of homogeneous (elastic and inelastic) spherical shells subject to dynamic loading and undergoing finite deformations. The goal of the activity is to provide high accuracy results that can be used as benchmark solutions for the verification of computational physics codes. Furthermore, the equilibrium equations for the geometrically non-linear problem are solved through mode expansion of the displacement field and the boundary conditions are enforced in a strong form. Time integration is performed through high-order implicit Runge–Kutta schemes. Finally, we evaluate accuracy and convergence of the proposed method bymore » means of numerical examples with finite deformations and material non-linearities and inelasticity.« less

Lagrangian Descriptors: A Method for Revealing Phase Space Structures of General Time Dependent Dynamical Systems

NASA Astrophysics Data System (ADS)

Mancho, Ana M.; Wiggins, Stephen; Curbelo, Jezabel; Mendoza, Carolina

2013-11-01

Lagrangian descriptors are a recent technique which reveals geometrical structures in phase space and which are valid for aperiodically time dependent dynamical systems. We discuss a general methodology for constructing them and we discuss a ``heuristic argument'' that explains why this method is successful. We support this argument by explicit calculations on a benchmark problem. Several other benchmark examples are considered that allow us to assess the performance of Lagrangian descriptors with both finite time Lyapunov exponents (FTLEs) and finite time averages of certain components of the vector field (``time averages''). In all cases Lagrangian descriptors are shown to be both more accurate and computationally efficient than these methods. We thank CESGA for computing facilities. This research was supported by MINECO grants: MTM2011-26696, I-Math C3-0104, ICMAT Severo Ochoa project SEV-2011-0087, and CSIC grant OCEANTECH. SW acknowledges the support of the ONR (Grant No. N00014-01-1-0769).

Lattice Boltzmann and Navier-Stokes Cartesian CFD Approaches for Airframe Noise Predictions

NASA Technical Reports Server (NTRS)

Barad, Michael F.; Kocheemoolayil, Joseph G.; Kiris, Cetin C.

2017-01-01

Lattice Boltzmann (LB) and compressible Navier-Stokes (NS) equations based computational fluid dynamics (CFD) approaches are compared for simulating airframe noise. Both LB and NS CFD approaches are implemented within the Launch Ascent and Vehicle Aerodynamics (LAVA) framework. Both schemes utilize the same underlying Cartesian structured mesh paradigm with provision for local adaptive grid refinement and sub-cycling in time. We choose a prototypical massively separated, wake-dominated flow ideally suited for Cartesian-grid based approaches in this study - The partially-dressed, cavity-closed nose landing gear (PDCC-NLG) noise problem from AIAA's Benchmark problems for Airframe Noise Computations (BANC) series of workshops. The relative accuracy and computational efficiency of the two approaches are systematically compared. Detailed comments are made on the potential held by LB to significantly reduce time-to-solution for a desired level of accuracy within the context of modeling airframes noise from first principles.

Cooperative parallel adaptive neighbourhood search for the disjunctively constrained knapsack problem

NASA Astrophysics Data System (ADS)

Quan, Zhe; Wu, Lei

2017-09-01

This article investigates the use of parallel computing for solving the disjunctively constrained knapsack problem. The proposed parallel computing model can be viewed as a cooperative algorithm based on a multi-neighbourhood search. The cooperation system is composed of a team manager and a crowd of team members. The team members aim at applying their own search strategies to explore the solution space. The team manager collects the solutions from the members and shares the best one with them. The performance of the proposed method is evaluated on a group of benchmark data sets. The results obtained are compared to those reached by the best methods from the literature. The results show that the proposed method is able to provide the best solutions in most cases. In order to highlight the robustness of the proposed parallel computing model, a new set of large-scale instances is introduced. Encouraging results have been obtained.

An Intelligent Model for Pairs Trading Using Genetic Algorithms.

PubMed

Huang, Chien-Feng; Hsu, Chi-Jen; Chen, Chi-Chung; Chang, Bao Rong; Li, Chen-An

2015-01-01

Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice.

An Intelligent Model for Pairs Trading Using Genetic Algorithms

PubMed Central

Hsu, Chi-Jen; Chen, Chi-Chung; Li, Chen-An

2015-01-01

Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice. PMID:26339236

Performance Characteristics of the Multi-Zone NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Jin, Haoqiang; VanderWijngaart, Rob F.

2003-01-01

We describe a new suite of computational benchmarks that models applications featuring multiple levels of parallelism. Such parallelism is often available in realistic flow computations on systems of grids, but had not previously been captured in bench-marks. The new suite, named NPB Multi-Zone, is extended from the NAS Parallel Benchmarks suite, and involves solving the application benchmarks LU, BT and SP on collections of loosely coupled discretization meshes. The solutions on the meshes are updated independently, but after each time step they exchange boundary value information. This strategy provides relatively easily exploitable coarse-grain parallelism between meshes. Three reference implementations are available: one serial, one hybrid using the Message Passing Interface (MPI) and OpenMP, and another hybrid using a shared memory multi-level programming model (SMP+OpenMP). We examine the effectiveness of hybrid parallelization paradigms in these implementations on three different parallel computers. We also use an empirical formula to investigate the performance characteristics of the multi-zone benchmarks.

Benchmarking for Bayesian Reinforcement Learning

PubMed Central

Ernst, Damien; Couëtoux, Adrien

2016-01-01

In the Bayesian Reinforcement Learning (BRL) setting, agents try to maximise the collected rewards while interacting with their environment while using some prior knowledge that is accessed beforehand. Many BRL algorithms have already been proposed, but the benchmarks used to compare them are only relevant for specific cases. The paper addresses this problem, and provides a new BRL comparison methodology along with the corresponding open source library. In this methodology, a comparison criterion that measures the performance of algorithms on large sets of Markov Decision Processes (MDPs) drawn from some probability distributions is defined. In order to enable the comparison of non-anytime algorithms, our methodology also includes a detailed analysis of the computation time requirement of each algorithm. Our library is released with all source code and documentation: it includes three test problems, each of which has two different prior distributions, and seven state-of-the-art RL algorithms. Finally, our library is illustrated by comparing all the available algorithms and the results are discussed. PMID:27304891

Benchmarking for Bayesian Reinforcement Learning.

PubMed

Castronovo, Michael; Ernst, Damien; Couëtoux, Adrien; Fonteneau, Raphael

2016-01-01

In the Bayesian Reinforcement Learning (BRL) setting, agents try to maximise the collected rewards while interacting with their environment while using some prior knowledge that is accessed beforehand. Many BRL algorithms have already been proposed, but the benchmarks used to compare them are only relevant for specific cases. The paper addresses this problem, and provides a new BRL comparison methodology along with the corresponding open source library. In this methodology, a comparison criterion that measures the performance of algorithms on large sets of Markov Decision Processes (MDPs) drawn from some probability distributions is defined. In order to enable the comparison of non-anytime algorithms, our methodology also includes a detailed analysis of the computation time requirement of each algorithm. Our library is released with all source code and documentation: it includes three test problems, each of which has two different prior distributions, and seven state-of-the-art RL algorithms. Finally, our library is illustrated by comparing all the available algorithms and the results are discussed.

Cove benchmark calculations using SAGUARO and FEMTRAN

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

Eaton, R.R.; Martinez, M.J.

1986-10-01

Three small-scale, time-dependent, benchmarking calculations have been made using the finite element codes SAGUARO, to determine hydraulic head and water velocity profiles, and FEMTRAN, to predict the solute transport. Sand and hard rock porous materials were used. Time scales for the problems, which ranged from tens of hours to thousands of years, have posed no particular diffculty for the two codes. Studies have been performed to determine the effects of computational mesh, boundary conditions, velocity formulation and SAGUARO/FEMTRAN code-coupling on water and solute transport. Results showed that mesh refinement improved mass conservation. Varying the drain-tile size in COVE 1N hadmore » a weak effect on the rate at which the tile field drained. Excellent agreement with published COVE 1N data was obtained for the hydrological field and reasonable agreement for the solute-concentration predictions. The question remains whether these types of calculations can be carried out on repository-scale problems using material characteristic curves representing tuff with fractures.« less

Solutions of the benchmark problems by the dispersion-relation-preserving scheme

NASA Technical Reports Server (NTRS)

Tam, Christopher K. W.; Shen, H.; Kurbatskii, K. A.; Auriault, L.

1995-01-01

The 7-point stencil Dispersion-Relation-Preserving scheme of Tam and Webb is used to solve all the six categories of the CAA benchmark problems. The purpose is to show that the scheme is capable of solving linear, as well as nonlinear aeroacoustics problems accurately. Nonlinearities, inevitably, lead to the generation of spurious short wave length numerical waves. Often, these spurious waves would overwhelm the entire numerical solution. In this work, the spurious waves are removed by the addition of artificial selective damping terms to the discretized equations. Category 3 problems are for testing radiation and outflow boundary conditions. In solving these problems, the radiation and outflow boundary conditions of Tam and Webb are used. These conditions are derived from the asymptotic solutions of the linearized Euler equations. Category 4 problems involved solid walls. Here, the wall boundary conditions for high-order schemes of Tam and Dong are employed. These conditions require the use of one ghost value per boundary point per physical boundary condition. In the second problem of this category, the governing equations, when written in cylindrical coordinates, are singular along the axis of the radial coordinate. The proper boundary conditions at the axis are derived by applying the limiting process of r approaches 0 to the governing equations. The Category 5 problem deals with the numerical noise issue. In the present approach, the time-independent mean flow solution is computed first. Once the residual drops to the machine noise level, the incident sound wave is turned on gradually. The solution is marched in time until a time-periodic state is reached. No exact solution is known for the Category 6 problem. Because of this, the problem is formulated in two totally different ways, first as a scattering problem then as a direct simulation problem. There is good agreement between the two numerical solutions. This offers confidence in the computed results. Both formulations are solved as initial value problems. As such, no Kutta condition is required at the trailing edge of the airfoil.

Assessment of different radiative transfer equation solvers for combined natural convection and radiation heat transfer problems

NASA Astrophysics Data System (ADS)

Sun, Yujia; Zhang, Xiaobing; Howell, John R.

2017-06-01

This work investigates the performance of the DOM, FVM, P1, SP3 and P3 methods for 2D combined natural convection and radiation heat transfer for an absorbing, emitting medium. The Monte Carlo method is used to solve the RTE coupled with the energy equation, and its results are used as benchmark solutions. Effects of the Rayleigh number, Planck number and optical thickness are considered, all covering several orders of magnitude. Temperature distributions, heat transfer rate and computational performance in terms of accuracy and computing time are presented and analyzed.

An Absorbing Boundary Condition for the Lattice Boltzmann Method Based on the Perfectly Matched Layer

PubMed Central

Najafi-Yazdi, A.; Mongeau, L.

2012-01-01

The Lattice Boltzmann Method (LBM) is a well established computational tool for fluid flow simulations. This method has been recently utilized for low Mach number computational aeroacoustics. Robust and nonreflective boundary conditions, similar to those used in Navier-Stokes solvers, are needed for LBM-based aeroacoustics simulations. The goal of the present study was to develop an absorbing boundary condition based on the perfectly matched layer (PML) concept for LBM. The derivation of formulations for both two and three dimensional problems are presented. The macroscopic behavior of the new formulation is discussed. The new formulation was tested using benchmark acoustic problems. The perfectly matched layer concept appears to be very well suited for LBM, and yielded very low acoustic reflection factor. PMID:23526050

A comparative study of computational solutions to flow over a backward-facing step

NASA Technical Reports Server (NTRS)

Mizukami, M.; Georgiadis, N. J.; Cannon, M. R.

1993-01-01

A comparative study was conducted for computational fluid dynamic solutions to flow over a backward-facing step. This flow is a benchmark problem, with a simple geometry, but involves complicated flow physics such as free shear layers, reattaching flow, recirculation, and high turbulence intensities. Three Reynolds-averaged Navier-Stokes flow solvers with k-epsilon turbulence models were used, each using a different solution algorithm: finite difference, finite element, and hybrid finite element - finite difference. Comparisons were made with existing experimental data. Results showed that velocity profiles and reattachment lengths were predicted reasonably well by all three methods, while the skin friction coefficients were more difficult to predict accurately. It was noted that, in general, selecting an appropriate solver for each problem to be considered is important.

Optimally Stopped Optimization

NASA Astrophysics Data System (ADS)

Vinci, Walter; Lidar, Daniel

We combine the fields of heuristic optimization and optimal stopping. We propose a strategy for benchmarking randomized optimization algorithms that minimizes the expected total cost for obtaining a good solution with an optimal number of calls to the solver. To do so, rather than letting the objective function alone define a cost to be minimized, we introduce a further cost-per-call of the algorithm. We show that this problem can be formulated using optimal stopping theory. The expected cost is a flexible figure of merit for benchmarking probabilistic solvers that can be computed when the optimal solution is not known, and that avoids the biases and arbitrariness that affect other measures. The optimal stopping formulation of benchmarking directly leads to a real-time, optimal-utilization strategy for probabilistic optimizers with practical impact. We apply our formulation to benchmark the performance of a D-Wave 2X quantum annealer and the HFS solver, a specialized classical heuristic algorithm designed for low tree-width graphs. On a set of frustrated-loop instances with planted solutions defined on up to N = 1098 variables, the D-Wave device is between one to two orders of magnitude faster than the HFS solver.

Geant4 Computing Performance Benchmarking and Monitoring

DOE PAGES

Dotti, Andrea; Elvira, V. Daniel; Folger, Gunter; ...

2015-12-23

Performance evaluation and analysis of large scale computing applications is essential for optimal use of resources. As detector simulation is one of the most compute intensive tasks and Geant4 is the simulation toolkit most widely used in contemporary high energy physics (HEP) experiments, it is important to monitor Geant4 through its development cycle for changes in computing performance and to identify problems and opportunities for code improvements. All Geant4 development and public releases are being profiled with a set of applications that utilize different input event samples, physics parameters, and detector configurations. Results from multiple benchmarking runs are compared tomore » previous public and development reference releases to monitor CPU and memory usage. Observed changes are evaluated and correlated with code modifications. Besides the full summary of call stack and memory footprint, a detailed call graph analysis is available to Geant4 developers for further analysis. The set of software tools used in the performance evaluation procedure, both in sequential and multi-threaded modes, include FAST, IgProf and Open|Speedshop. In conclusion, the scalability of the CPU time and memory performance in multi-threaded application is evaluated by measuring event throughput and memory gain as a function of the number of threads for selected event samples.« less

Evolutionary algorithms for the optimal management of coastal groundwater: A comparative study toward future challenges

NASA Astrophysics Data System (ADS)

Ketabchi, Hamed; Ataie-Ashtiani, Behzad

2015-01-01

This paper surveys the literature associated with the application of evolutionary algorithms (EAs) in coastal groundwater management problems (CGMPs). This review demonstrates that previous studies were mostly relied on the application of limited and particular EAs, mainly genetic algorithm (GA) and its variants, to a number of specific problems. The exclusive investigation of these problems is often not the representation of the variety of feasible processes may be occurred in coastal aquifers. In this study, eight EAs are evaluated for CGMPs. The considered EAs are: GA, continuous ant colony optimization (CACO), particle swarm optimization (PSO), differential evolution (DE), artificial bee colony optimization (ABC), harmony search (HS), shuffled complex evolution (SCE), and simplex simulated annealing (SIMPSA). The first application of PSO, ABC, HS, and SCE in CGMPs is reported here. Moreover, the four benchmark problems with different degree of difficulty and variety are considered to address the important issues of groundwater resources in coastal regions. Hence, the wide ranges of popular objective functions and constraints with the number of decision variables ranging from 4 to 15 are included. These benchmark problems are applied in the combined simulation-optimization model to examine the optimization scenarios. Some preliminary experiments are performed to select the most efficient parameters values for EAs to set a fair comparison. The specific capabilities of each EA toward CGMPs in terms of results quality and required computational time are compared. The evaluation of the results highlights EA's applicability in CGMPs, besides the remarkable strengths and weaknesses of them. The comparisons show that SCE, CACO, and PSO yield superior solutions among the EAs according to the quality of solutions whereas ABC presents the poor performance. CACO provides the better solutions (up to 17%) than the worst EA (ABC) for the problem with the highest decision variables and more complexity. In terms of computational time, PSO and SIMPSA are the fastest. SCE needs the highest computational time, even up to four times in comparison to the fastest EAs. CACO and PSO can be recommended for application in CGMPs, in terms of both abovementioned criteria.

An iterative bidirectional heuristic placement algorithm for solving the two-dimensional knapsack packing problem

NASA Astrophysics Data System (ADS)

Shiangjen, Kanokwatt; Chaijaruwanich, Jeerayut; Srisujjalertwaja, Wijak; Unachak, Prakarn; Somhom, Samerkae

2018-02-01

This article presents an efficient heuristic placement algorithm, namely, a bidirectional heuristic placement, for solving the two-dimensional rectangular knapsack packing problem. The heuristic demonstrates ways to maximize space utilization by fitting the appropriate rectangle from both sides of the wall of the current residual space layer by layer. The iterative local search along with a shift strategy is developed and applied to the heuristic to balance the exploitation and exploration tasks in the solution space without the tuning of any parameters. The experimental results on many scales of packing problems show that this approach can produce high-quality solutions for most of the benchmark datasets, especially for large-scale problems, within a reasonable duration of computational time.

Developing a Shuffled Complex-Self Adaptive Hybrid Evolution (SC-SAHEL) Framework for Water Resources Management and Water-Energy System Optimization

NASA Astrophysics Data System (ADS)

Rahnamay Naeini, M.; Sadegh, M.; AghaKouchak, A.; Hsu, K. L.; Sorooshian, S.; Yang, T.

2017-12-01

Meta-Heuristic optimization algorithms have gained a great deal of attention in a wide variety of fields. Simplicity and flexibility of these algorithms, along with their robustness, make them attractive tools for solving optimization problems. Different optimization methods, however, hold algorithm-specific strengths and limitations. Performance of each individual algorithm obeys the "No-Free-Lunch" theorem, which means a single algorithm cannot consistently outperform all possible optimization problems over a variety of problems. From users' perspective, it is a tedious process to compare, validate, and select the best-performing algorithm for a specific problem or a set of test cases. In this study, we introduce a new hybrid optimization framework, entitled Shuffled Complex-Self Adaptive Hybrid EvoLution (SC-SAHEL), which combines the strengths of different evolutionary algorithms (EAs) in a parallel computing scheme, and allows users to select the most suitable algorithm tailored to the problem at hand. The concept of SC-SAHEL is to execute different EAs as separate parallel search cores, and let all participating EAs to compete during the course of the search. The newly developed SC-SAHEL algorithm is designed to automatically select, the best performing algorithm for the given optimization problem. This algorithm is rigorously effective in finding the global optimum for several strenuous benchmark test functions, and computationally efficient as compared to individual EAs. We benchmark the proposed SC-SAHEL algorithm over 29 conceptual test functions, and two real-world case studies - one hydropower reservoir model and one hydrological model (SAC-SMA). Results show that the proposed framework outperforms individual EAs in an absolute majority of the test problems, and can provide competitive results to the fittest EA algorithm with more comprehensive information during the search. The proposed framework is also flexible for merging additional EAs, boundary-handling techniques, and sampling schemes, and has good potential to be used in Water-Energy system optimal operation and management.

Benchmarked analyses of gamma skyshine using MORSE-CGA-PC and the DABL69 cross-section set

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

Reichert, P.T.; Golshani, M.

1991-01-01

Design for gamma-ray skyshine is a common consideration for a variety of nuclear and accelerator facilities. Many of these designs can benefit from a more accurate and complete treatment than can be provided by simple skyshine analysis tools. Those methods typically require a number of conservative, simplifying assumptions in modeling the radiation source and shielding geometry. This paper considers the benchmarking of one analytical option. The MORSE-CGA Monte Carlo radiation transport code system provides the capability for detailed treatment of virtually any source and shielding geometry. Unfortunately, the mainframe computer costs of MORSE-CGA analyses can prevent cost-effective application to smallmore » projects. For this reason, the MORSE-CGA system was converted to run on IBM personal computer (PC)-compatible computers using the Intel 80386 or 80486 microprocessors. The DLC-130/DABL69 cross-section set (46n,23g) was chosen as the most suitable, readily available, broad-group library. The most important reason is the relatively high (P{sub 5}) Legendre order of expansion for angular distribution. This is likely to be beneficial in the deep-penetration conditions modeled in some skyshine problems.« less

Benchmarking Strategies for Measuring the Quality of Healthcare: Problems and Prospects

PubMed Central

Lovaglio, Pietro Giorgio

2012-01-01

Over the last few years, increasing attention has been directed toward the problems inherent to measuring the quality of healthcare and implementing benchmarking strategies. Besides offering accreditation and certification processes, recent approaches measure the performance of healthcare institutions in order to evaluate their effectiveness, defined as the capacity to provide treatment that modifies and improves the patient's state of health. This paper, dealing with hospital effectiveness, focuses on research methods for effectiveness analyses within a strategy comparing different healthcare institutions. The paper, after having introduced readers to the principle debates on benchmarking strategies, which depend on the perspective and type of indicators used, focuses on the methodological problems related to performing consistent benchmarking analyses. Particularly, statistical methods suitable for controlling case-mix, analyzing aggregate data, rare events, and continuous outcomes measured with error are examined. Specific challenges of benchmarking strategies, such as the risk of risk adjustment (case-mix fallacy, underreporting, risk of comparing noncomparable hospitals), selection bias, and possible strategies for the development of consistent benchmarking analyses, are discussed. Finally, to demonstrate the feasibility of the illustrated benchmarking strategies, an application focused on determining regional benchmarks for patient satisfaction (using 2009 Lombardy Region Patient Satisfaction Questionnaire) is proposed. PMID:22666140

Benchmarking strategies for measuring the quality of healthcare: problems and prospects.

PubMed

Lovaglio, Pietro Giorgio

2012-01-01

Over the last few years, increasing attention has been directed toward the problems inherent to measuring the quality of healthcare and implementing benchmarking strategies. Besides offering accreditation and certification processes, recent approaches measure the performance of healthcare institutions in order to evaluate their effectiveness, defined as the capacity to provide treatment that modifies and improves the patient's state of health. This paper, dealing with hospital effectiveness, focuses on research methods for effectiveness analyses within a strategy comparing different healthcare institutions. The paper, after having introduced readers to the principle debates on benchmarking strategies, which depend on the perspective and type of indicators used, focuses on the methodological problems related to performing consistent benchmarking analyses. Particularly, statistical methods suitable for controlling case-mix, analyzing aggregate data, rare events, and continuous outcomes measured with error are examined. Specific challenges of benchmarking strategies, such as the risk of risk adjustment (case-mix fallacy, underreporting, risk of comparing noncomparable hospitals), selection bias, and possible strategies for the development of consistent benchmarking analyses, are discussed. Finally, to demonstrate the feasibility of the illustrated benchmarking strategies, an application focused on determining regional benchmarks for patient satisfaction (using 2009 Lombardy Region Patient Satisfaction Questionnaire) is proposed.

Within-Group Effect-Size Benchmarks for Problem-Solving Therapy for Depression in Adults

ERIC Educational Resources Information Center

Rubin, Allen; Yu, Miao

2017-01-01

This article provides benchmark data on within-group effect sizes from published randomized clinical trials that supported the efficacy of problem-solving therapy (PST) for depression among adults. Benchmarks are broken down by type of depression (major or minor), type of outcome measure (interview or self-report scale), whether PST was provided…

Semiclassical approach to finite-temperature quantum annealing with trapped ions

NASA Astrophysics Data System (ADS)

Raventós, David; Graß, Tobias; Juliá-Díaz, Bruno; Lewenstein, Maciej

2018-05-01

Recently it has been demonstrated that an ensemble of trapped ions may serve as a quantum annealer for the number-partitioning problem [Nat. Commun. 7, 11524 (2016), 10.1038/ncomms11524]. This hard computational problem may be addressed by employing a tunable spin-glass architecture. Following the proposal of the trapped-ion annealer, we study here its robustness against thermal effects; that is, we investigate the role played by thermal phonons. For the efficient description of the system, we use a semiclassical approach, and benchmark it against the exact quantum evolution. The aim is to understand better and characterize how the quantum device approaches a solution of an otherwise difficult to solve NP-hard problem.

Numerical Solution of Optimal Control Problem under SPDE Constraints

DTIC Science & Technology

2011-10-14

Faure and Sobol sequences are used to evaluate high dimensional integrals, and the errors in the numerical results for over 30 dimensions become quite...sequence; right: 1000 points of dimension 26 and 27 projection for optimal Kronecker sequence. benchmark Faure and Sobol methods. 2.2 High order...J. Goodman and J. O’Rourke, Handbook of discrete and computational geome- try, CRC Press, Inc., (2004). [5] S. Joe and F. Kuo, Constructing Sobol

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC, year 2 quarter 1 progress report.

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

Lottes, S.A.; Bojanowski, C.; Shen, J.

2012-04-09

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water effects on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to improve design allowing for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, CFD analysis of the operation of the wind tunnel in the TFHRC wind engineering laboratory. This quarterly report documents technical progress on the project tasks for the period of October through December 2011.« less

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC, year 2 quarter 2 progress report

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

Lottes, S.A.; Bojanowski, C.; Shen, J.

2012-06-28

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water effects on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to improve design allowing for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, CFD analysis of the operation of the wind tunnel in the TFHRC wind engineering laboratory. This quarterly report documents technical progress on the project tasks for the period of January through March 2012.« less

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC, year 1 quarter 3 progress report.

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

Lottes, S.A.; Kulak, R.F.; Bojanowski, C.

2011-08-26

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water loads on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to assess them for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, vehicle stability under high wind loading, and the use of electromagnetic shock absorbers to improve vehicle stability under high wind conditions. This quarterly report documents technical progress on the project tasks for the period of April through June 2011.« less

Benchmarking Memory Performance with the Data Cube Operator

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Shabanov, Leonid V.

2004-01-01

Data movement across a computer memory hierarchy and across computational grids is known to be a limiting factor for applications processing large data sets. We use the Data Cube Operator on an Arithmetic Data Set, called ADC, to benchmark capabilities of computers and of computational grids to handle large distributed data sets. We present a prototype implementation of a parallel algorithm for computation of the operatol: The algorithm follows a known approach for computing views from the smallest parent. The ADC stresses all levels of grid memory and storage by producing some of 2d views of an Arithmetic Data Set of d-tuples described by a small number of integers. We control data intensity of the ADC by selecting the tuple parameters, the sizes of the views, and the number of realized views. Benchmarking results of memory performance of a number of computer architectures and of a small computational grid are presented.

Approximate l-fold cross-validation with Least Squares SVM and Kernel Ridge Regression

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

Edwards, Richard E; Zhang, Hao; Parker, Lynne Edwards

2013-01-01

Kernel methods have difficulties scaling to large modern data sets. The scalability issues are based on computational and memory requirements for working with a large matrix. These requirements have been addressed over the years by using low-rank kernel approximations or by improving the solvers scalability. However, Least Squares Support VectorMachines (LS-SVM), a popular SVM variant, and Kernel Ridge Regression still have several scalability issues. In particular, the O(n^3) computational complexity for solving a single model, and the overall computational complexity associated with tuning hyperparameters are still major problems. We address these problems by introducing an O(n log n) approximate l-foldmore » cross-validation method that uses a multi-level circulant matrix to approximate the kernel. In addition, we prove our algorithm s computational complexity and present empirical runtimes on data sets with approximately 1 million data points. We also validate our approximate method s effectiveness at selecting hyperparameters on real world and standard benchmark data sets. Lastly, we provide experimental results on using a multi-level circulant kernel approximation to solve LS-SVM problems with hyperparameters selected using our method.« less

Computational ecology as an emerging science

PubMed Central

Petrovskii, Sergei; Petrovskaya, Natalia

2012-01-01

It has long been recognized that numerical modelling and computer simulations can be used as a powerful research tool to understand, and sometimes to predict, the tendencies and peculiarities in the dynamics of populations and ecosystems. It has been, however, much less appreciated that the context of modelling and simulations in ecology is essentially different from those that normally exist in other natural sciences. In our paper, we review the computational challenges arising in modern ecology in the spirit of computational mathematics, i.e. with our main focus on the choice and use of adequate numerical methods. Somewhat paradoxically, the complexity of ecological problems does not always require the use of complex computational methods. This paradox, however, can be easily resolved if we recall that application of sophisticated computational methods usually requires clear and unambiguous mathematical problem statement as well as clearly defined benchmark information for model validation. At the same time, many ecological problems still do not have mathematically accurate and unambiguous description, and available field data are often very noisy, and hence it can be hard to understand how the results of computations should be interpreted from the ecological viewpoint. In this scientific context, computational ecology has to deal with a new paradigm: conventional issues of numerical modelling such as convergence and stability become less important than the qualitative analysis that can be provided with the help of computational techniques. We discuss this paradigm by considering computational challenges arising in several specific ecological applications. PMID:23565336

Implementation of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan (Technical Monitor)

2002-01-01

Several features make Java an attractive choice for High Performance Computing (HPC). In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for CFD applications.

Benchmarking--Measuring and Comparing for Continuous Improvement.

ERIC Educational Resources Information Center

Henczel, Sue

2002-01-01

Discussion of benchmarking focuses on the use of internal and external benchmarking by special librarians. Highlights include defining types of benchmarking; historical development; benefits, including efficiency, improved performance, increased competitiveness, and better decision making; problems, including inappropriate adaptation; developing a…

Differential Cloud Particles Evolution Algorithm Based on Data-Driven Mechanism for Applications of ANN

PubMed Central

2017-01-01

Computational scientists have designed many useful algorithms by exploring a biological process or imitating natural evolution. These algorithms can be used to solve engineering optimization problems. Inspired by the change of matter state, we proposed a novel optimization algorithm called differential cloud particles evolution algorithm based on data-driven mechanism (CPDD). In the proposed algorithm, the optimization process is divided into two stages, namely, fluid stage and solid stage. The algorithm carries out the strategy of integrating global exploration with local exploitation in fluid stage. Furthermore, local exploitation is carried out mainly in solid stage. The quality of the solution and the efficiency of the search are influenced greatly by the control parameters. Therefore, the data-driven mechanism is designed for obtaining better control parameters to ensure good performance on numerical benchmark problems. In order to verify the effectiveness of CPDD, numerical experiments are carried out on all the CEC2014 contest benchmark functions. Finally, two application problems of artificial neural network are examined. The experimental results show that CPDD is competitive with respect to other eight state-of-the-art intelligent optimization algorithms. PMID:28761438

Shift Verification and Validation

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

Pandya, Tara M.; Evans, Thomas M.; Davidson, Gregory G

2016-09-07

This documentation outlines the verification and validation of Shift for the Consortium for Advanced Simulation of Light Water Reactors (CASL). Five main types of problems were used for validation: small criticality benchmark problems; full-core reactor benchmarks for light water reactors; fixed-source coupled neutron-photon dosimetry benchmarks; depletion/burnup benchmarks; and full-core reactor performance benchmarks. We compared Shift results to measured data and other simulated Monte Carlo radiation transport code results, and found very good agreement in a variety of comparison measures. These include prediction of critical eigenvalue, radial and axial pin power distributions, rod worth, leakage spectra, and nuclide inventories over amore » burn cycle. Based on this validation of Shift, we are confident in Shift to provide reference results for CASL benchmarking.« less

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC. Quarterly report January through March 2011. Year 1 Quarter 2 progress report.

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

Lottes, S. A.; Kulak, R. F.; Bojanowski, C.

2011-05-19

This project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at the Turner-Fairbank Highway Research Center for a period of five years, beginning in October 2010. The analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focusmore » of the project are wind and water loads on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to assess them for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, vehicle stability under high wind loading, and the use of electromagnetic shock absorbers to improve vehicle stability under high wind conditions. This quarterly report documents technical progress on the project tasks for the period of January through March 2011.« less

Benchmarking high performance computing architectures with CMS’ skeleton framework

NASA Astrophysics Data System (ADS)

Sexton-Kennedy, E.; Gartung, P.; Jones, C. D.

2017-10-01

In 2012 CMS evaluated which underlying concurrency technology would be the best to use for its multi-threaded framework. The available technologies were evaluated on the high throughput computing systems dominating the resources in use at that time. A skeleton framework benchmarking suite that emulates the tasks performed within a CMSSW application was used to select Intel’s Thread Building Block library, based on the measured overheads in both memory and CPU on the different technologies benchmarked. In 2016 CMS will get access to high performance computing resources that use new many core architectures; machines such as Cori Phase 1&2, Theta, Mira. Because of this we have revived the 2012 benchmark to test it’s performance and conclusions on these new architectures. This talk will discuss the results of this exercise.

A Parallel Processing Algorithm for Remote Sensing Classification

NASA Technical Reports Server (NTRS)

Gualtieri, J. Anthony

2005-01-01

A current thread in parallel computation is the use of cluster computers created by networking a few to thousands of commodity general-purpose workstation-level commuters using the Linux operating system. For example on the Medusa cluster at NASA/GSFC, this provides for super computing performance, 130 G(sub flops) (Linpack Benchmark) at moderate cost, $370K. However, to be useful for scientific computing in the area of Earth science, issues of ease of programming, access to existing scientific libraries, and portability of existing code need to be considered. In this paper, I address these issues in the context of tools for rendering earth science remote sensing data into useful products. In particular, I focus on a problem that can be decomposed into a set of independent tasks, which on a serial computer would be performed sequentially, but with a cluster computer can be performed in parallel, giving an obvious speedup. To make the ideas concrete, I consider the problem of classifying hyperspectral imagery where some ground truth is available to train the classifier. In particular I will use the Support Vector Machine (SVM) approach as applied to hyperspectral imagery. The approach will be to introduce notions about parallel computation and then to restrict the development to the SVM problem. Pseudocode (an outline of the computation) will be described and then details specific to the implementation will be given. Then timing results will be reported to show what speedups are possible using parallel computation. The paper will close with a discussion of the results.

Implementation of NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

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

2000-01-01

A number of features make Java an attractive but a debatable choice for High Performance Computing (HPC). In order to gauge the applicability of Java to the Computational Fluid Dynamics (CFD) we have implemented NAS Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would move Java closer to Fortran in the competition for CFD applications.

Benchmark Problems for Spacecraft Formation Flying Missions

NASA Technical Reports Server (NTRS)

Carpenter, J. Russell; Leitner, Jesse A.; Burns, Richard D.; Folta, David C.

2003-01-01

To provide high-level focus to distributed space system flight dynamics and control research, several benchmark problems are suggested. These problems are not specific to any current or proposed mission, but instead are intended to capture high-level features that would be generic to many similar missions.

A One-group, One-dimensional Transport Benchmark in Cylindrical Geometry

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

Barry Ganapol; Abderrafi M. Ougouag

A 1-D, 1-group computational benchmark in cylndrical geometry is described. This neutron transport benchmark is useful for evaluating reactor concepts that possess azimuthal symmetry such as a pebble-bed reactor.

A proposed benchmark problem for cargo nuclear threat monitoring

NASA Astrophysics Data System (ADS)

Wesley Holmes, Thomas; Calderon, Adan; Peeples, Cody R.; Gardner, Robin P.

2011-10-01

There is currently a great deal of technical and political effort focused on reducing the risk of potential attacks on the United States involving radiological dispersal devices or nuclear weapons. This paper proposes a benchmark problem for gamma-ray and X-ray cargo monitoring with results calculated using MCNP5, v1.51. The primary goal is to provide a benchmark problem that will allow researchers in this area to evaluate Monte Carlo models for both speed and accuracy in both forward and inverse calculational codes and approaches for nuclear security applications. A previous benchmark problem was developed by one of the authors (RPG) for two similar oil well logging problems (Gardner and Verghese, 1991, [1]). One of those benchmarks has recently been used by at least two researchers in the nuclear threat area to evaluate the speed and accuracy of Monte Carlo codes combined with variance reduction techniques. This apparent need has prompted us to design this benchmark problem specifically for the nuclear threat researcher. This benchmark consists of conceptual design and preliminary calculational results using gamma-ray interactions on a system containing three thicknesses of three different shielding materials. A point source is placed inside the three materials lead, aluminum, and plywood. The first two materials are in right circular cylindrical form while the third is a cube. The entire system rests on a sufficiently thick lead base so as to reduce undesired scattering events. The configuration was arranged in such a manner that as gamma-ray moves from the source outward it first passes through the lead circular cylinder, then the aluminum circular cylinder, and finally the wooden cube before reaching the detector. A 2 in.×4 in.×16 in. box style NaI (Tl) detector was placed 1 m from the point source located in the center with the 4 in.×16 in. side facing the system. The two sources used in the benchmark are 137Cs and 235U.

Research on computer systems benchmarking

NASA Technical Reports Server (NTRS)

Smith, Alan Jay (Principal Investigator)

1996-01-01

This grant addresses the topic of research on computer systems benchmarking and is more generally concerned with performance issues in computer systems. This report reviews work in those areas during the period of NASA support under this grant. The bulk of the work performed concerned benchmarking and analysis of CPUs, compilers, caches, and benchmark programs. The first part of this work concerned the issue of benchmark performance prediction. A new approach to benchmarking and machine characterization was reported, using a machine characterizer that measures the performance of a given system in terms of a Fortran abstract machine. Another report focused on analyzing compiler performance. The performance impact of optimization in the context of our methodology for CPU performance characterization was based on the abstract machine model. Benchmark programs are analyzed in another paper. A machine-independent model of program execution was developed to characterize both machine performance and program execution. By merging these machine and program characterizations, execution time can be estimated for arbitrary machine/program combinations. The work was continued into the domain of parallel and vector machines, including the issue of caches in vector processors and multiprocessors. All of the afore-mentioned accomplishments are more specifically summarized in this report, as well as those smaller in magnitude supported by this grant.

Analytical three-dimensional neutron transport benchmarks for verification of nuclear engineering codes. Final report

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

Ganapol, B.D.; Kornreich, D.E.

Because of the requirement of accountability and quality control in the scientific world, a demand for high-quality analytical benchmark calculations has arisen in the neutron transport community. The intent of these benchmarks is to provide a numerical standard to which production neutron transport codes may be compared in order to verify proper operation. The overall investigation as modified in the second year renewal application includes the following three primary tasks. Task 1 on two dimensional neutron transport is divided into (a) single medium searchlight problem (SLP) and (b) two-adjacent half-space SLP. Task 2 on three-dimensional neutron transport covers (a) pointmore » source in arbitrary geometry, (b) single medium SLP, and (c) two-adjacent half-space SLP. Task 3 on code verification, includes deterministic and probabilistic codes. The primary aim of the proposed investigation was to provide a suite of comprehensive two- and three-dimensional analytical benchmarks for neutron transport theory applications. This objective has been achieved. The suite of benchmarks in infinite media and the three-dimensional SLP are a relatively comprehensive set of one-group benchmarks for isotropically scattering media. Because of time and resource limitations, the extensions of the benchmarks to include multi-group and anisotropic scattering are not included here. Presently, however, enormous advances in the solution for the planar Green`s function in an anisotropically scattering medium have been made and will eventually be implemented in the two- and three-dimensional solutions considered under this grant. Of particular note in this work are the numerical results for the three-dimensional SLP, which have never before been presented. The results presented were made possible only because of the tremendous advances in computing power that have occurred during the past decade.« less

Demonstration of Qubit Operations Below a Rigorous Fault Tolerance Threshold With Gate Set Tomography (Open Access, Publisher’s Version)

DTIC Science & Technology

2017-02-15

Maunz2 Quantum information processors promise fast algorithms for problems inaccessible to classical computers. But since qubits are noisy and error-prone...information processors have been demonstrated experimentally using superconducting circuits1–3, electrons in semiconductors4–6, trapped atoms and...qubit quantum information processor has been realized14, and single- qubit gates have demonstrated randomized benchmarking (RB) infidelities as low as 10

Benchmark Computation and Finite Element Performance Evaluation for a Rhombic Plate Bending Problem

DTIC Science & Technology

1987-09-01

Physical Science and Technology University of Maryland, College Park, MD 20742, USA and Dip. Matematica - Universita di Pavia - 27100 Pavia - ITALY DTIC...University of Maryland, College Park,, MD 20742, USA , and Dip. Matematica - Universita di Pavia - 27100 Pavia - ITALY SFor Oe" -- 4- I , CA& 11 --l...drawn when based on the state of the art of both theoretical and experience field. The reliability has to be understood not only with respect to a

A Message Passing Approach to Side Chain Positioning with Applications in Protein Docking Refinement *

PubMed Central

Moghadasi, Mohammad; Kozakov, Dima; Mamonov, Artem B.; Vakili, Pirooz; Vajda, Sandor; Paschalidis, Ioannis Ch.

2013-01-01

We introduce a message-passing algorithm to solve the Side Chain Positioning (SCP) problem. SCP is a crucial component of protein docking refinement, which is a key step of an important class of problems in computational structural biology called protein docking. We model SCP as a combinatorial optimization problem and formulate it as a Maximum Weighted Independent Set (MWIS) problem. We then employ a modified and convergent belief-propagation algorithm to solve a relaxation of MWIS and develop randomized estimation heuristics that use the relaxed solution to obtain an effective MWIS feasible solution. Using a benchmark set of protein complexes we demonstrate that our approach leads to more accurate docking predictions compared to a baseline algorithm that does not solve the SCP. PMID:23515575

Hybrid discrete ordinates and characteristics method for solving the linear Boltzmann equation

NASA Astrophysics Data System (ADS)

Yi, Ce

With the ability of computer hardware and software increasing rapidly, deterministic methods to solve the linear Boltzmann equation (LBE) have attracted some attention for computational applications in both the nuclear engineering and medical physics fields. Among various deterministic methods, the discrete ordinates method (SN) and the method of characteristics (MOC) are two of the most widely used methods. The SN method is the traditional approach to solve the LBE for its stability and efficiency. While the MOC has some advantages in treating complicated geometries. However, in 3-D problems requiring a dense discretization grid in phase space (i.e., a large number of spatial meshes, directions, or energy groups), both methods could suffer from the need for large amounts of memory and computation time. In our study, we developed a new hybrid algorithm by combing the two methods into one code, TITAN. The hybrid approach is specifically designed for application to problems containing low scattering regions. A new serial 3-D time-independent transport code has been developed. Under the hybrid approach, the preferred method can be applied in different regions (blocks) within the same problem model. Since the characteristics method is numerically more efficient in low scattering media, the hybrid approach uses a block-oriented characteristics solver in low scattering regions, and a block-oriented SN solver in the remainder of the physical model. In the TITAN code, a physical problem model is divided into a number of coarse meshes (blocks) in Cartesian geometry. Either the characteristics solver or the SN solver can be chosen to solve the LBE within a coarse mesh. A coarse mesh can be filled with fine meshes or characteristic rays depending on the solver assigned to the coarse mesh. Furthermore, with its object-oriented programming paradigm and layered code structure, TITAN allows different individual spatial meshing schemes and angular quadrature sets for each coarse mesh. Two quadrature types (level-symmetric and Legendre-Chebyshev quadrature) along with the ordinate splitting techniques (rectangular splitting and PN-TN splitting) are implemented. In the S N solver, we apply a memory-efficient 'front-line' style paradigm to handle the fine mesh interface fluxes. In the characteristics solver, we have developed a novel 'backward' ray-tracing approach, in which a bi-linear interpolation procedure is used on the incoming boundaries of a coarse mesh. A CPU-efficient scattering kernel is shared in both solvers within the source iteration scheme. Angular and spatial projection techniques are developed to transfer the angular fluxes on the interfaces of coarse meshes with different discretization grids. The performance of the hybrid algorithm is tested in a number of benchmark problems in both nuclear engineering and medical physics fields. Among them are the Kobayashi benchmark problems and a computational tomography (CT) device model. We also developed an extra sweep procedure with the fictitious quadrature technique to calculate angular fluxes along directions of interest. The technique is applied in a single photon emission computed tomography (SPECT) phantom model to simulate the SPECT projection images. The accuracy and efficiency of the TITAN code are demonstrated in these benchmarks along with its scalability. A modified version of the characteristics solver is integrated in the PENTRAN code and tested within the parallel engine of PENTRAN. The limitations on the hybrid algorithm are also studied.

Using domain decomposition in the multigrid NAS parallel benchmark on the Fujitsu VPP500

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

Wang, J.C.H.; Lung, H.; Katsumata, Y.

1995-12-01

In this paper, we demonstrate how domain decomposition can be applied to the multigrid algorithm to convert the code for MPP architectures. We also discuss the performance and scalability of this implementation on the new product line of Fujitsu`s vector parallel computer, VPP500. This computer has Fujitsu`s well-known vector processor as the PE each rated at 1.6 C FLOPS. The high speed crossbar network rated at 800 MB/s provides the inter-PE communication. The results show that the physical domain decomposition is the best way to solve MG problems on VPP500.

Fast Boundary Element Method for acoustics with the Sparse Cardinal Sine Decomposition

NASA Astrophysics Data System (ADS)

Alouges, François; Aussal, Matthieu; Parolin, Emile

2017-07-01

This paper presents the newly proposed method Sparse Cardinal Sine Decomposition that allows fast convolution on unstructured grids. We focus on its use when coupled with finite element techniques to solve acoustic problems with the (compressed) Boundary Element Method. In addition, we also compare the computational performances of two equivalent Matlab® and Python implementations of the method. We show validation test cases in order to assess the precision of the approach. Eventually, the performance of the method is illustrated by the computation of the acoustic target strength of a realistic submarine from the Benchmark Target Strength Simulation international workshop.

Lecture Notes on Criticality Safety Validation Using MCNP & Whisper

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

Brown, Forrest B.; Rising, Michael Evan; Alwin, Jennifer Louise

Training classes for nuclear criticality safety, MCNP documentation. The need for, and problems surrounding, validation of computer codes and data area considered first. Then some background for MCNP & Whisper is given--best practices for Monte Carlo criticality calculations, neutron spectra, S(α,β) thermal neutron scattering data, nuclear data sensitivities, covariance data, and correlation coefficients. Whisper is computational software designed to assist the nuclear criticality safety analyst with validation studies with the Monte Carlo radiation transport package MCNP. Whisper's methodology (benchmark selection – C k's, weights; extreme value theory – bias, bias uncertainty; MOS for nuclear data uncertainty – GLLS) and usagemore » are discussed.« less

Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems

PubMed Central

Rodriguez-Fernandez, Maria; Egea, Jose A; Banga, Julio R

2006-01-01

Background We consider the problem of parameter estimation (model calibration) in nonlinear dynamic models of biological systems. Due to the frequent ill-conditioning and multi-modality of many of these problems, traditional local methods usually fail (unless initialized with very good guesses of the parameter vector). In order to surmount these difficulties, global optimization (GO) methods have been suggested as robust alternatives. Currently, deterministic GO methods can not solve problems of realistic size within this class in reasonable computation times. In contrast, certain types of stochastic GO methods have shown promising results, although the computational cost remains large. Rodriguez-Fernandez and coworkers have presented hybrid stochastic-deterministic GO methods which could reduce computation time by one order of magnitude while guaranteeing robustness. Our goal here was to further reduce the computational effort without loosing robustness. Results We have developed a new procedure based on the scatter search methodology for nonlinear optimization of dynamic models of arbitrary (or even unknown) structure (i.e. black-box models). In this contribution, we describe and apply this novel metaheuristic, inspired by recent developments in the field of operations research, to a set of complex identification problems and we make a critical comparison with respect to the previous (above mentioned) successful methods. Conclusion Robust and efficient methods for parameter estimation are of key importance in systems biology and related areas. The new metaheuristic presented in this paper aims to ensure the proper solution of these problems by adopting a global optimization approach, while keeping the computational effort under reasonable values. This new metaheuristic was applied to a set of three challenging parameter estimation problems of nonlinear dynamic biological systems, outperforming very significantly all the methods previously used for these benchmark problems. PMID:17081289

Novel metaheuristic for parameter estimation in nonlinear dynamic biological systems.

PubMed

Rodriguez-Fernandez, Maria; Egea, Jose A; Banga, Julio R

2006-11-02

We consider the problem of parameter estimation (model calibration) in nonlinear dynamic models of biological systems. Due to the frequent ill-conditioning and multi-modality of many of these problems, traditional local methods usually fail (unless initialized with very good guesses of the parameter vector). In order to surmount these difficulties, global optimization (GO) methods have been suggested as robust alternatives. Currently, deterministic GO methods can not solve problems of realistic size within this class in reasonable computation times. In contrast, certain types of stochastic GO methods have shown promising results, although the computational cost remains large. Rodriguez-Fernandez and coworkers have presented hybrid stochastic-deterministic GO methods which could reduce computation time by one order of magnitude while guaranteeing robustness. Our goal here was to further reduce the computational effort without loosing robustness. We have developed a new procedure based on the scatter search methodology for nonlinear optimization of dynamic models of arbitrary (or even unknown) structure (i.e. black-box models). In this contribution, we describe and apply this novel metaheuristic, inspired by recent developments in the field of operations research, to a set of complex identification problems and we make a critical comparison with respect to the previous (above mentioned) successful methods. Robust and efficient methods for parameter estimation are of key importance in systems biology and related areas. The new metaheuristic presented in this paper aims to ensure the proper solution of these problems by adopting a global optimization approach, while keeping the computational effort under reasonable values. This new metaheuristic was applied to a set of three challenging parameter estimation problems of nonlinear dynamic biological systems, outperforming very significantly all the methods previously used for these benchmark problems.

Systematic and efficient side chain optimization for molecular docking using a cheapest-path procedure.

PubMed

Schumann, Marcel; Armen, Roger S

2013-05-30

Molecular docking of small-molecules is an important procedure for computer-aided drug design. Modeling receptor side chain flexibility is often important or even crucial, as it allows the receptor to adopt new conformations as induced by ligand binding. However, the accurate and efficient incorporation of receptor side chain flexibility has proven to be a challenge due to the huge computational complexity required to adequately address this problem. Here we describe a new docking approach with a very fast, graph-based optimization algorithm for assignment of the near-optimal set of residue rotamers. We extensively validate our approach using the 40 DUD target benchmarks commonly used to assess virtual screening performance and demonstrate a large improvement using the developed side chain optimization over rigid receptor docking (average ROC AUC of 0.693 vs. 0.623). Compared to numerous benchmarks, the overall performance is better than nearly all other commonly used procedures. Furthermore, we provide a detailed analysis of the level of receptor flexibility observed in docking results for different classes of residues and elucidate potential avenues for further improvement. Copyright © 2013 Wiley Periodicals, Inc.

Validation of numerical codes for impact and explosion cratering: Impacts on strengthless and metal targets

NASA Astrophysics Data System (ADS)

Pierazzo, E.; Artemieva, N.; Asphaug, E.; Baldwin, E. C.; Cazamias, J.; Coker, R.; Collins, G. S.; Crawford, D. A.; Davison, T.; Elbeshausen, D.; Holsapple, K. A.; Housen, K. R.; Korycansky, D. G.; Wünnemann, K.

2008-12-01

Over the last few decades, rapid improvement of computer capabilities has allowed impact cratering to be modeled with increasing complexity and realism, and has paved the way for a new era of numerical modeling of the impact process, including full, three-dimensional (3D) simulations. When properly benchmarked and validated against observation, computer models offer a powerful tool for understanding the mechanics of impact crater formation. This work presents results from the first phase of a project to benchmark and validate shock codes. A variety of 2D and 3D codes were used in this study, from commercial products like AUTODYN, to codes developed within the scientific community like SOVA, SPH, ZEUS-MP, iSALE, and codes developed at U.S. National Laboratories like CTH, SAGE/RAGE, and ALE3D. Benchmark calculations of shock wave propagation in aluminum-on-aluminum impacts were performed to examine the agreement between codes for simple idealized problems. The benchmark simulations show that variability in code results is to be expected due to differences in the underlying solution algorithm of each code, artificial stability parameters, spatial and temporal resolution, and material models. Overall, the inter-code variability in peak shock pressure as a function of distance is around 10 to 20%. In general, if the impactor is resolved by at least 20 cells across its radius, the underestimation of peak shock pressure due to spatial resolution is less than 10%. In addition to the benchmark tests, three validation tests were performed to examine the ability of the codes to reproduce the time evolution of crater radius and depth observed in vertical laboratory impacts in water and two well-characterized aluminum alloys. Results from these calculations are in good agreement with experiments. There appears to be a general tendency of shock physics codes to underestimate the radius of the forming crater. Overall, the discrepancy between the model and experiment results is between 10 and 20%, similar to the inter-code variability.

Confronting Decision Cliffs: Diagnostic Assessment of Multi-Objective Evolutionary Algorithms' Performance for Addressing Uncertain Environmental Thresholds

NASA Astrophysics Data System (ADS)

Ward, V. L.; Singh, R.; Reed, P. M.; Keller, K.

2014-12-01

As water resources problems typically involve several stakeholders with conflicting objectives, multi-objective evolutionary algorithms (MOEAs) are now key tools for understanding management tradeoffs. Given the growing complexity of water planning problems, it is important to establish if an algorithm can consistently perform well on a given class of problems. This knowledge allows the decision analyst to focus on eliciting and evaluating appropriate problem formulations. This study proposes a multi-objective adaptation of the classic environmental economics "Lake Problem" as a computationally simple but mathematically challenging MOEA benchmarking problem. The lake problem abstracts a fictional town on a lake which hopes to maximize its economic benefit without degrading the lake's water quality to a eutrophic (polluted) state through excessive phosphorus loading. The problem poses the challenge of maintaining economic activity while confronting the uncertainty of potentially crossing a nonlinear and potentially irreversible pollution threshold beyond which the lake is eutrophic. Objectives for optimization are maximizing economic benefit from lake pollution, maximizing water quality, maximizing the reliability of remaining below the environmental threshold, and minimizing the probability that the town will have to drastically change pollution policies in any given year. The multi-objective formulation incorporates uncertainty with a stochastic phosphorus inflow abstracting non-point source pollution. We performed comprehensive diagnostics using 6 algorithms: Borg, MOEAD, eMOEA, eNSGAII, GDE3, and NSGAII to ascertain their controllability, reliability, efficiency, and effectiveness. The lake problem abstracts elements of many current water resources and climate related management applications where there is the potential for crossing irreversible, nonlinear thresholds. We show that many modern MOEAs can fail on this test problem, indicating its suitability as a useful and nontrivial benchmarking problem.

The Earthquake Source Inversion Validation (SIV) - Project: Summary, Status, Outlook

NASA Astrophysics Data System (ADS)

Mai, P. M.

2017-12-01

Finite-fault earthquake source inversions infer the (time-dependent) displacement on the rupture surface from geophysical data. The resulting earthquake source models document the complexity of the rupture process. However, this kinematic source inversion is ill-posed and returns non-unique solutions, as seen for instance in multiple source models for the same earthquake, obtained by different research teams, that often exhibit remarkable dissimilarities. To address the uncertainties in earthquake-source inversions and to understand strengths and weaknesses of various methods, the Source Inversion Validation (SIV) project developed a set of forward-modeling exercises and inversion benchmarks. Several research teams then use these validation exercises to test their codes and methods, but also to develop and benchmark new approaches. In this presentation I will summarize the SIV strategy, the existing benchmark exercises and corresponding results. Using various waveform-misfit criteria and newly developed statistical comparison tools to quantify source-model (dis)similarities, the SIV platforms is able to rank solutions and identify particularly promising source inversion approaches. Existing SIV exercises (with related data and descriptions) and all computational tools remain available via the open online collaboration platform; additional exercises and benchmark tests will be uploaded once they are fully developed. I encourage source modelers to use the SIV benchmarks for developing and testing new methods. The SIV efforts have already led to several promising new techniques for tackling the earthquake-source imaging problem. I expect that future SIV benchmarks will provide further innovations and insights into earthquake source kinematics that will ultimately help to better understand the dynamics of the rupture process.

Benchmarking high performance computing architectures with CMS’ skeleton framework

DOE PAGES

Sexton-Kennedy, E.; Gartung, P.; Jones, C. D.

2017-11-23

Here, in 2012 CMS evaluated which underlying concurrency technology would be the best to use for its multi-threaded framework. The available technologies were evaluated on the high throughput computing systems dominating the resources in use at that time. A skeleton framework benchmarking suite that emulates the tasks performed within a CMSSW application was used to select Intel’s Thread Building Block library, based on the measured overheads in both memory and CPU on the different technologies benchmarked. In 2016 CMS will get access to high performance computing resources that use new many core architectures; machines such as Cori Phase 1&2, Theta,more » Mira. Because of this we have revived the 2012 benchmark to test it’s performance and conclusions on these new architectures. This talk will discuss the results of this exercise.« less

Benchmarking high performance computing architectures with CMS’ skeleton framework

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

Sexton-Kennedy, E.; Gartung, P.; Jones, C. D.

Here, in 2012 CMS evaluated which underlying concurrency technology would be the best to use for its multi-threaded framework. The available technologies were evaluated on the high throughput computing systems dominating the resources in use at that time. A skeleton framework benchmarking suite that emulates the tasks performed within a CMSSW application was used to select Intel’s Thread Building Block library, based on the measured overheads in both memory and CPU on the different technologies benchmarked. In 2016 CMS will get access to high performance computing resources that use new many core architectures; machines such as Cori Phase 1&2, Theta,more » Mira. Because of this we have revived the 2012 benchmark to test it’s performance and conclusions on these new architectures. This talk will discuss the results of this exercise.« less

A PSO-Based Hybrid Metaheuristic for Permutation Flowshop Scheduling Problems

PubMed Central

Zhang, Le; Wu, Jinnan

2014-01-01

This paper investigates the permutation flowshop scheduling problem (PFSP) with the objectives of minimizing the makespan and the total flowtime and proposes a hybrid metaheuristic based on the particle swarm optimization (PSO). To enhance the exploration ability of the hybrid metaheuristic, a simulated annealing hybrid with a stochastic variable neighborhood search is incorporated. To improve the search diversification of the hybrid metaheuristic, a solution replacement strategy based on the pathrelinking is presented to replace the particles that have been trapped in local optimum. Computational results on benchmark instances show that the proposed PSO-based hybrid metaheuristic is competitive with other powerful metaheuristics in the literature. PMID:24672389

A PSO-based hybrid metaheuristic for permutation flowshop scheduling problems.

PubMed

Zhang, Le; Wu, Jinnan

2014-01-01

This paper investigates the permutation flowshop scheduling problem (PFSP) with the objectives of minimizing the makespan and the total flowtime and proposes a hybrid metaheuristic based on the particle swarm optimization (PSO). To enhance the exploration ability of the hybrid metaheuristic, a simulated annealing hybrid with a stochastic variable neighborhood search is incorporated. To improve the search diversification of the hybrid metaheuristic, a solution replacement strategy based on the pathrelinking is presented to replace the particles that have been trapped in local optimum. Computational results on benchmark instances show that the proposed PSO-based hybrid metaheuristic is competitive with other powerful metaheuristics in the literature.

Improved Fractal Space Filling Curves Hybrid Optimization Algorithm for Vehicle Routing Problem.

PubMed

Yue, Yi-xiang; Zhang, Tong; Yue, Qun-xing

2015-01-01

Vehicle Routing Problem (VRP) is one of the key issues in optimization of modern logistics system. In this paper, a modified VRP model with hard time window is established and a Hybrid Optimization Algorithm (HOA) based on Fractal Space Filling Curves (SFC) method and Genetic Algorithm (GA) is introduced. By incorporating the proposed algorithm, SFC method can find an initial and feasible solution very fast; GA is used to improve the initial solution. Thereafter, experimental software was developed and a large number of experimental computations from Solomon's benchmark have been studied. The experimental results demonstrate the feasibility and effectiveness of the HOA.

Auction dynamics: A volume constrained MBO scheme

NASA Astrophysics Data System (ADS)

Jacobs, Matt; Merkurjev, Ekaterina; Esedoǧlu, Selim

2018-02-01

We show how auction algorithms, originally developed for the assignment problem, can be utilized in Merriman, Bence, and Osher's threshold dynamics scheme to simulate multi-phase motion by mean curvature in the presence of equality and inequality volume constraints on the individual phases. The resulting algorithms are highly efficient and robust, and can be used in simulations ranging from minimal partition problems in Euclidean space to semi-supervised machine learning via clustering on graphs. In the case of the latter application, numerous experimental results on benchmark machine learning datasets show that our approach exceeds the performance of current state-of-the-art methods, while requiring a fraction of the computation time.

Improved Fractal Space Filling Curves Hybrid Optimization Algorithm for Vehicle Routing Problem

PubMed Central

Yue, Yi-xiang; Zhang, Tong; Yue, Qun-xing

2015-01-01

Vehicle Routing Problem (VRP) is one of the key issues in optimization of modern logistics system. In this paper, a modified VRP model with hard time window is established and a Hybrid Optimization Algorithm (HOA) based on Fractal Space Filling Curves (SFC) method and Genetic Algorithm (GA) is introduced. By incorporating the proposed algorithm, SFC method can find an initial and feasible solution very fast; GA is used to improve the initial solution. Thereafter, experimental software was developed and a large number of experimental computations from Solomon's benchmark have been studied. The experimental results demonstrate the feasibility and effectiveness of the HOA. PMID:26167171

HPGMG 1.0: A Benchmark for Ranking High Performance Computing Systems

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

Adams, Mark; Brown, Jed; Shalf, John

2014-05-05

This document provides an overview of the benchmark ? HPGMG ? for ranking large scale general purpose computers for use on the Top500 list [8]. We provide a rationale for the need for a replacement for the current metric HPL, some background of the Top500 list and the challenges of developing such a metric; we discuss our design philosophy and methodology, and an overview of the specification of the benchmark. The primary documentation with maintained details on the specification can be found at hpgmg.org and the Wiki and benchmark code itself can be found in the repository https://bitbucket.org/hpgmg/hpgmg.

Merton's problem for an investor with a benchmark in a Barndorff-Nielsen and Shephard market.

PubMed

Lennartsson, Jan; Lindberg, Carl

2015-01-01

To try to outperform an externally given benchmark with known weights is the most common equity mandate in the financial industry. For quantitative investors, this task is predominantly approached by optimizing their portfolios consecutively over short time horizons with one-period models. We seek in this paper to provide a theoretical justification to this practice when the underlying market is of Barndorff-Nielsen and Shephard type. This is done by verifying that an investor who seeks to maximize her expected terminal exponential utility of wealth in excess of her benchmark will in fact use an optimal portfolio equivalent to the one-period Markowitz mean-variance problem in continuum under the corresponding Black-Scholes market. Further, we can represent the solution to the optimization problem as in Feynman-Kac form. Hence, the problem, and its solution, is analogous to Merton's classical portfolio problem, with the main difference that Merton maximizes expected utility of terminal wealth, not wealth in excess of a benchmark.

High-performance conjugate-gradient benchmark: A new metric for ranking high-performance computing systems

DOE PAGES

Dongarra, Jack; Heroux, Michael A.; Luszczek, Piotr

2015-08-17

Here, we describe a new high-performance conjugate-gradient (HPCG) benchmark. HPCG is composed of computations and data-access patterns commonly found in scientific applications. HPCG strives for a better correlation to existing codes from the computational science domain and to be representative of their performance. Furthermore, HPCG is meant to help drive the computer system design and implementation in directions that will better impact future performance improvement.

A self-adaptive memeplexes robust search scheme for solving stochastic demands vehicle routing problem

NASA Astrophysics Data System (ADS)

Chen, Xianshun; Feng, Liang; Ong, Yew Soon

2012-07-01

In this article, we proposed a self-adaptive memeplex robust search (SAMRS) for finding robust and reliable solutions that are less sensitive to stochastic behaviours of customer demands and have low probability of route failures, respectively, in vehicle routing problem with stochastic demands (VRPSD). In particular, the contribution of this article is three-fold. First, the proposed SAMRS employs the robust solution search scheme (RS 3) as an approximation of the computationally intensive Monte Carlo simulation, thus reducing the computation cost of fitness evaluation in VRPSD, while directing the search towards robust and reliable solutions. Furthermore, a self-adaptive individual learning based on the conceptual modelling of memeplex is introduced in the SAMRS. Finally, SAMRS incorporates a gene-meme co-evolution model with genetic and memetic representation to effectively manage the search for solutions in VRPSD. Extensive experimental results are then presented for benchmark problems to demonstrate that the proposed SAMRS serves as an efficable means of generating high-quality robust and reliable solutions in VRPSD.

Graph Matching: Relax at Your Own Risk.

PubMed

Lyzinski, Vince; Fishkind, Donniell E; Fiori, Marcelo; Vogelstein, Joshua T; Priebe, Carey E; Sapiro, Guillermo

2016-01-01

Graph matching-aligning a pair of graphs to minimize their edge disagreements-has received wide-spread attention from both theoretical and applied communities over the past several decades, including combinatorics, computer vision, and connectomics. Its attention can be partially attributed to its computational difficulty. Although many heuristics have previously been proposed in the literature to approximately solve graph matching, very few have any theoretical support for their performance. A common technique is to relax the discrete problem to a continuous problem, therefore enabling practitioners to bring gradient-descent-type algorithms to bear. We prove that an indefinite relaxation (when solved exactly) almost always discovers the optimal permutation, while a common convex relaxation almost always fails to discover the optimal permutation. These theoretical results suggest that initializing the indefinite algorithm with the convex optimum might yield improved practical performance. Indeed, experimental results illuminate and corroborate these theoretical findings, demonstrating that excellent results are achieved in both benchmark and real data problems by amalgamating the two approaches.

Computational Hemodynamic Simulation of Human Circulatory System under Altered Gravity

NASA Technical Reports Server (NTRS)

Kim. Chang Sung; Kiris, Cetin; Kwak, Dochan

2003-01-01

A computational hemodynamics approach is presented to simulate the blood flow through the human circulatory system under altered gravity conditions. Numerical techniques relevant to hemodynamics issues are introduced to non-Newtonian modeling for flow characteristics governed by red blood cells, distensible wall motion due to the heart pulse, and capillary bed modeling for outflow boundary conditions. Gravitational body force terms are added to the Navier-Stokes equations to study the effects of gravity on internal flows. Six-type gravity benchmark problems are originally presented to provide the fundamental understanding of gravitational effects on the human circulatory system. For code validation, computed results are compared with steady and unsteady experimental data for non-Newtonian flows in a carotid bifurcation model and a curved circular tube, respectively. This computational approach is then applied to the blood circulation in the human brain as a target problem. A three-dimensional, idealized Circle of Willis configuration is developed with minor arteries truncated based on anatomical data. Demonstrated is not only the mechanism of the collateral circulation but also the effects of gravity on the distensible wall motion and resultant flow patterns.

Aerothermal environment induced by mismatch at the SSME main combustion chamber-nozzle joint

NASA Technical Reports Server (NTRS)

Mcconnaughey, H. V.; O'Farrell, J. M.; Olive, T. A.; Brown, G. B.; Holt, J. B.

1990-01-01

The computational study reported here is motivated by a Space Shuttle main engine hardware problem detected in post-flight and post-test inspections. Of interest are the potential for hot gas ingestion into the joint (G15) at the main combustion chamber-to-nozzle interface and the effect of particular goemetric nonuniformities on that gas ingestion. The flowfield in the G15 region involves supersonic flow past a rounded forward facing step preceded by a deep narrow cavity. This paper describes the physical problem associated with joint G15 and computational investigations of the G15 aerothermal environment. The associated flowfield was simulated in two and three space dimensions using the United Solutions Algorithm (USA) computational fluid dynamics code series. A benchmark calculation of experimentally measured supersonic flow over of a square cavity was performed to demonstrate the accuracy of the USA code in analyzing flows similar to the G15 computational flowfield. The G15 results demonstrate the mechanism for hot gas ingestion into the joint and reveal the sensitivity to salient geometric nonuniformities.

Accuracy of a simplified method for shielded gamma-ray skyshine sources

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

Bassett, M.S.; Shultis, J.K.

1989-11-01

Rigorous transport or Monte Carlo methods for estimating far-field gamma-ray skyshine doses generally are computationally intensive. consequently, several simplified techniques such as point-kernel methods and methods based on beam response functions have been proposed. For unshielded skyshine sources, these simplified methods have been shown to be quite accurate from comparisons to benchmark problems and to benchmark experimental results. For shielded sources, the simplified methods typically use exponential attenuation and photon buildup factors to describe the effect of the shield. However, the energy and directional redistribution of photons scattered in the shield is usually ignored, i.e., scattered photons are assumed tomore » emerge from the shield with the same energy and direction as the uncollided photons. The accuracy of this shield treatment is largely unknown due to the paucity of benchmark results for shielded sources. In this paper, the validity of such a shield treatment is assessed by comparison to a composite method, which accurately calculates the energy and angular distribution of photons penetrating the shield.« less

A novel heuristic algorithm for capacitated vehicle routing problem

NASA Astrophysics Data System (ADS)

Kır, Sena; Yazgan, Harun Reşit; Tüncel, Emre

2017-09-01

The vehicle routing problem with the capacity constraints was considered in this paper. It is quite difficult to achieve an optimal solution with traditional optimization methods by reason of the high computational complexity for large-scale problems. Consequently, new heuristic or metaheuristic approaches have been developed to solve this problem. In this paper, we constructed a new heuristic algorithm based on the tabu search and adaptive large neighborhood search (ALNS) with several specifically designed operators and features to solve the capacitated vehicle routing problem (CVRP). The effectiveness of the proposed algorithm was illustrated on the benchmark problems. The algorithm provides a better performance on large-scaled instances and gained advantage in terms of CPU time. In addition, we solved a real-life CVRP using the proposed algorithm and found the encouraging results by comparison with the current situation that the company is in.

A modified genetic algorithm with fuzzy roulette wheel selection for job-shop scheduling problems

NASA Astrophysics Data System (ADS)

Thammano, Arit; Teekeng, Wannaporn

2015-05-01

The job-shop scheduling problem is one of the most difficult production planning problems. Since it is in the NP-hard class, a recent trend in solving the job-shop scheduling problem is shifting towards the use of heuristic and metaheuristic algorithms. This paper proposes a novel metaheuristic algorithm, which is a modification of the genetic algorithm. This proposed algorithm introduces two new concepts to the standard genetic algorithm: (1) fuzzy roulette wheel selection and (2) the mutation operation with tabu list. The proposed algorithm has been evaluated and compared with several state-of-the-art algorithms in the literature. The experimental results on 53 JSSPs show that the proposed algorithm is very effective in solving the combinatorial optimization problems. It outperforms all state-of-the-art algorithms on all benchmark problems in terms of the ability to achieve the optimal solution and the computational time.

Module discovery by exhaustive search for densely connected, co-expressed regions in biomolecular interaction networks.

PubMed

Colak, Recep; Moser, Flavia; Chu, Jeffrey Shih-Chieh; Schönhuth, Alexander; Chen, Nansheng; Ester, Martin

2010-10-25

Computational prediction of functionally related groups of genes (functional modules) from large-scale data is an important issue in computational biology. Gene expression experiments and interaction networks are well studied large-scale data sources, available for many not yet exhaustively annotated organisms. It has been well established, when analyzing these two data sources jointly, modules are often reflected by highly interconnected (dense) regions in the interaction networks whose participating genes are co-expressed. However, the tractability of the problem had remained unclear and methods by which to exhaustively search for such constellations had not been presented. We provide an algorithmic framework, referred to as Densely Connected Biclustering (DECOB), by which the aforementioned search problem becomes tractable. To benchmark the predictive power inherent to the approach, we computed all co-expressed, dense regions in physical protein and genetic interaction networks from human and yeast. An automatized filtering procedure reduces our output which results in smaller collections of modules, comparable to state-of-the-art approaches. Our results performed favorably in a fair benchmarking competition which adheres to standard criteria. We demonstrate the usefulness of an exhaustive module search, by using the unreduced output to more quickly perform GO term related function prediction tasks. We point out the advantages of our exhaustive output by predicting functional relationships using two examples. We demonstrate that the computation of all densely connected and co-expressed regions in interaction networks is an approach to module discovery of considerable value. Beyond confirming the well settled hypothesis that such co-expressed, densely connected interaction network regions reflect functional modules, we open up novel computational ways to comprehensively analyze the modular organization of an organism based on prevalent and largely available large-scale datasets. Software and data sets are available at http://www.sfu.ca/~ester/software/DECOB.zip.

A comparison of fitness-case sampling methods for genetic programming

NASA Astrophysics Data System (ADS)

Martínez, Yuliana; Naredo, Enrique; Trujillo, Leonardo; Legrand, Pierrick; López, Uriel

2017-11-01

Genetic programming (GP) is an evolutionary computation paradigm for automatic program induction. GP has produced impressive results but it still needs to overcome some practical limitations, particularly its high computational cost, overfitting and excessive code growth. Recently, many researchers have proposed fitness-case sampling methods to overcome some of these problems, with mixed results in several limited tests. This paper presents an extensive comparative study of four fitness-case sampling methods, namely: Interleaved Sampling, Random Interleaved Sampling, Lexicase Selection and Keep-Worst Interleaved Sampling. The algorithms are compared on 11 symbolic regression problems and 11 supervised classification problems, using 10 synthetic benchmarks and 12 real-world data-sets. They are evaluated based on test performance, overfitting and average program size, comparing them with a standard GP search. Comparisons are carried out using non-parametric multigroup tests and post hoc pairwise statistical tests. The experimental results suggest that fitness-case sampling methods are particularly useful for difficult real-world symbolic regression problems, improving performance, reducing overfitting and limiting code growth. On the other hand, it seems that fitness-case sampling cannot improve upon GP performance when considering supervised binary classification.

PMLB: a large benchmark suite for machine learning evaluation and comparison.

PubMed

Olson, Randal S; La Cava, William; Orzechowski, Patryk; Urbanowicz, Ryan J; Moore, Jason H

2017-01-01

The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world and simulated benchmark datasets have emerged from different sources, but their organization and adoption as standards have been inconsistent. As such, selecting and curating specific benchmarks remains an unnecessary burden on machine learning practitioners and data scientists. The present study introduces an accessible, curated, and developing public benchmark resource to facilitate identification of the strengths and weaknesses of different machine learning methodologies. We compare meta-features among the current set of benchmark datasets in this resource to characterize the diversity of available data. Finally, we apply a number of established machine learning methods to the entire benchmark suite and analyze how datasets and algorithms cluster in terms of performance. From this study, we find that existing benchmarks lack the diversity to properly benchmark machine learning algorithms, and there are several gaps in benchmarking problems that still need to be considered. This work represents another important step towards understanding the limitations of popular benchmarking suites and developing a resource that connects existing benchmarking standards to more diverse and efficient standards in the future.

On the impact of approximate computation in an analog DeSTIN architecture.

PubMed

Young, Steven; Lu, Junjie; Holleman, Jeremy; Arel, Itamar

2014-05-01

Deep machine learning (DML) holds the potential to revolutionize machine learning by automating rich feature extraction, which has become the primary bottleneck of human engineering in pattern recognition systems. However, the heavy computational burden renders DML systems implemented on conventional digital processors impractical for large-scale problems. The highly parallel computations required to implement large-scale deep learning systems are well suited to custom hardware. Analog computation has demonstrated power efficiency advantages of multiple orders of magnitude relative to digital systems while performing nonideal computations. In this paper, we investigate typical error sources introduced by analog computational elements and their impact on system-level performance in DeSTIN--a compositional deep learning architecture. These inaccuracies are evaluated on a pattern classification benchmark, clearly demonstrating the robustness of the underlying algorithm to the errors introduced by analog computational elements. A clear understanding of the impacts of nonideal computations is necessary to fully exploit the efficiency of analog circuits.

A decade of aeroacoustic research at NASA Ames Research Center

NASA Technical Reports Server (NTRS)

Schmitz, Frederic H.; Mosher, M.; Kitaplioglu, Cahit; Cross, J.; Chang, I.

1988-01-01

The rotorcraft aeroacoustic research accomplishments of the past decade at Ames Research Center are reviewed. These include an extensive sequence of flight, ground, and wind tunnel tests that have utilized the facilities to guide and pioneer theoretical research. Many of these experiments were of benchmark quality. The experiments were used to isolate the inadequacies of linear theory in high-speed impulsive noise research, have led to the development of theoretical approaches, and have guided the emerging discipline of computational fluid dynamics to rotorcraft aeroacoustic problems.

Biclustering as a method for RNA local multiple sequence alignment.

PubMed

Wang, Shu; Gutell, Robin R; Miranker, Daniel P

2007-12-15

Biclustering is a clustering method that simultaneously clusters both the domain and range of a relation. A challenge in multiple sequence alignment (MSA) is that the alignment of sequences is often intended to reveal groups of conserved functional subsequences. Simultaneously, the grouping of the sequences can impact the alignment; precisely the kind of dual situation biclustering is intended to address. We define a representation of the MSA problem enabling the application of biclustering algorithms. We develop a computer program for local MSA, BlockMSA, that combines biclustering with divide-and-conquer. BlockMSA simultaneously finds groups of similar sequences and locally aligns subsequences within them. Further alignment is accomplished by dividing both the set of sequences and their contents. The net result is both a multiple sequence alignment and a hierarchical clustering of the sequences. BlockMSA was tested on the subsets of the BRAliBase 2.1 benchmark suite that display high variability and on an extension to that suite to larger problem sizes. Also, alignments were evaluated of two large datasets of current biological interest, T box sequences and Group IC1 Introns. The results were compared with alignments computed by ClustalW, MAFFT, MUCLE and PROBCONS alignment programs using Sum of Pairs (SPS) and Consensus Count. Results for the benchmark suite are sensitive to problem size. On problems of 15 or greater sequences, BlockMSA is consistently the best. On none of the problems in the test suite are there appreciable differences in scores among BlockMSA, MAFFT and PROBCONS. On the T box sequences, BlockMSA does the most faithful job of reproducing known annotations. MAFFT and PROBCONS do not. On the Intron sequences, BlockMSA, MAFFT and MUSCLE are comparable at identifying conserved regions. BlockMSA is implemented in Java. Source code and supplementary datasets are available at http://aug.csres.utexas.edu/msa/

Characterization of robotics parallel algorithms and mapping onto a reconfigurable SIMD machine

NASA Technical Reports Server (NTRS)

Lee, C. S. G.; Lin, C. T.

1989-01-01

The kinematics, dynamics, Jacobian, and their corresponding inverse computations are six essential problems in the control of robot manipulators. Efficient parallel algorithms for these computations are discussed and analyzed. Their characteristics are identified and a scheme on the mapping of these algorithms to a reconfigurable parallel architecture is presented. Based on the characteristics including type of parallelism, degree of parallelism, uniformity of the operations, fundamental operations, data dependencies, and communication requirement, it is shown that most of the algorithms for robotic computations possess highly regular properties and some common structures, especially the linear recursive structure. Moreover, they are well-suited to be implemented on a single-instruction-stream multiple-data-stream (SIMD) computer with reconfigurable interconnection network. The model of a reconfigurable dual network SIMD machine with internal direct feedback is introduced. A systematic procedure internal direct feedback is introduced. A systematic procedure to map these computations to the proposed machine is presented. A new scheduling problem for SIMD machines is investigated and a heuristic algorithm, called neighborhood scheduling, that reorders the processing sequence of subtasks to reduce the communication time is described. Mapping results of a benchmark algorithm are illustrated and discussed.

A formative evaluation of CU-SeeMe

NASA Astrophysics Data System (ADS)

Bibeau, Michael

1995-02-01

CU-SeeMe is a video conferencing software package that was designed and programmed at Cornell University. The program works with the TCP/IP network protocol and allows two or more parties to conduct a real-time video conference with full audio support. In this paper we evaluate CU-SeeMe through the process of Formative Evaluation. We first perform a Critical Review of the software using a subset of the Smith and Mosier Guidelines for Human-Computer Interaction. Next, we empirically review the software interface through a series of benchmark tests that are derived directly from a set of scenarios. The scenarios attempt to model real world situations that might be encountered by an individual in the target user class. Designing benchmark tasks becomes a natural and straightforward process when they are derived from the scenario set. Empirical measures are taken for each task, including completion times and error counts. These measures are accompanied by critical incident analysis 2 7 13 which serves to identify problems with the interface and the cognitive roots of those problems. The critical incidents reported by participants are accompanied by explanations of what caused the problem and why This helps in the process of formulating solutions for observed usability problems. All the testing results are combined in the Appendix in an illustrated partial redesign of the CU-SeeMe Interface.

Benchmarking on Tsunami Currents with ComMIT

NASA Astrophysics Data System (ADS)

Sharghi vand, N.; Kanoglu, U.

2015-12-01

There were no standards for the validation and verification of tsunami numerical models before 2004 Indian Ocean tsunami. Even, number of numerical models has been used for inundation mapping effort, evaluation of critical structures, etc. without validation and verification. After 2004, NOAA Center for Tsunami Research (NCTR) established standards for the validation and verification of tsunami numerical models (Synolakis et al. 2008 Pure Appl. Geophys. 165, 2197-2228), which will be used evaluation of critical structures such as nuclear power plants against tsunami attack. NCTR presented analytical, experimental and field benchmark problems aimed to estimate maximum runup and accepted widely by the community. Recently, benchmark problems were suggested by the US National Tsunami Hazard Mitigation Program Mapping & Modeling Benchmarking Workshop: Tsunami Currents on February 9-10, 2015 at Portland, Oregon, USA (http://nws.weather.gov/nthmp/index.html). These benchmark problems concentrated toward validation and verification of tsunami numerical models on tsunami currents. Three of the benchmark problems were: current measurement of the Japan 2011 tsunami in Hilo Harbor, Hawaii, USA and in Tauranga Harbor, New Zealand, and single long-period wave propagating onto a small-scale experimental model of the town of Seaside, Oregon, USA. These benchmark problems were implemented in the Community Modeling Interface for Tsunamis (ComMIT) (Titov et al. 2011 Pure Appl. Geophys. 168, 2121-2131), which is a user-friendly interface to the validated and verified Method of Splitting Tsunami (MOST) (Titov and Synolakis 1995 J. Waterw. Port Coastal Ocean Eng. 121, 308-316) model and is developed by NCTR. The modeling results are compared with the required benchmark data, providing good agreements and results are discussed. Acknowledgment: The research leading to these results has received funding from the European Union's Seventh Framework Programme (FP7/2007-2013) under grant agreement no 603839 (Project ASTARTE - Assessment, Strategy and Risk Reduction for Tsunamis in Europe)

Solving bi-level optimization problems in engineering design using kriging models

NASA Astrophysics Data System (ADS)

Xia, Yi; Liu, Xiaojie; Du, Gang

2018-05-01

Stackelberg game-theoretic approaches are applied extensively in engineering design to handle distributed collaboration decisions. Bi-level genetic algorithms (BLGAs) and response surfaces have been used to solve the corresponding bi-level programming models. However, the computational costs for BLGAs often increase rapidly with the complexity of lower-level programs, and optimal solution functions sometimes cannot be approximated by response surfaces. This article proposes a new method, namely the optimal solution function approximation by kriging model (OSFAKM), in which kriging models are used to approximate the optimal solution functions. A detailed example demonstrates that OSFAKM can obtain better solutions than BLGAs and response surface-based methods, and at the same time reduce the workload of computation remarkably. Five benchmark problems and a case study of the optimal design of a thin-walled pressure vessel are also presented to illustrate the feasibility and potential of the proposed method for bi-level optimization in engineering design.

Fully Decentralized Semi-supervised Learning via Privacy-preserving Matrix Completion.

PubMed

Fierimonte, Roberto; Scardapane, Simone; Uncini, Aurelio; Panella, Massimo

2016-08-26

Distributed learning refers to the problem of inferring a function when the training data are distributed among different nodes. While significant work has been done in the contexts of supervised and unsupervised learning, the intermediate case of Semi-supervised learning in the distributed setting has received less attention. In this paper, we propose an algorithm for this class of problems, by extending the framework of manifold regularization. The main component of the proposed algorithm consists of a fully distributed computation of the adjacency matrix of the training patterns. To this end, we propose a novel algorithm for low-rank distributed matrix completion, based on the framework of diffusion adaptation. Overall, the distributed Semi-supervised algorithm is efficient and scalable, and it can preserve privacy by the inclusion of flexible privacy-preserving mechanisms for similarity computation. The experimental results and comparison on a wide range of standard Semi-supervised benchmarks validate our proposal.

Testing New Programming Paradigms with NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Jin, H.; Frumkin, M.; Schultz, M.; Yan, J.

2000-01-01

Over the past decade, high performance computing has evolved rapidly, not only in hardware architectures but also with increasing complexity of real applications. Technologies have been developing to aim at scaling up to thousands of processors on both distributed and shared memory systems. Development of parallel programs on these computers is always a challenging task. Today, writing parallel programs with message passing (e.g. MPI) is the most popular way of achieving scalability and high performance. However, writing message passing programs is difficult and error prone. Recent years new effort has been made in defining new parallel programming paradigms. The best examples are: HPF (based on data parallelism) and OpenMP (based on shared memory parallelism). Both provide simple and clear extensions to sequential programs, thus greatly simplify the tedious tasks encountered in writing message passing programs. HPF is independent of memory hierarchy, however, due to the immaturity of compiler technology its performance is still questionable. Although use of parallel compiler directives is not new, OpenMP offers a portable solution in the shared-memory domain. Another important development involves the tremendous progress in the internet and its associated technology. Although still in its infancy, Java promisses portability in a heterogeneous environment and offers possibility to "compile once and run anywhere." In light of testing these new technologies, we implemented new parallel versions of the NAS Parallel Benchmarks (NPBs) with HPF and OpenMP directives, and extended the work with Java and Java-threads. The purpose of this study is to examine the effectiveness of alternative programming paradigms. NPBs consist of five kernels and three simulated applications that mimic the computation and data movement of large scale computational fluid dynamics (CFD) applications. We started with the serial version included in NPB2.3. Optimization of memory and cache usage was applied to several benchmarks, noticeably BT and SP, resulting in better sequential performance. In order to overcome the lack of an HPF performance model and guide the development of the HPF codes, we employed an empirical performance model for several primitives found in the benchmarks. We encountered a few limitations of HPF, such as lack of supporting the "REDISTRIBUTION" directive and no easy way to handle irregular computation. The parallelization with OpenMP directives was done at the outer-most loop level to achieve the largest granularity. The performance of six HPF and OpenMP benchmarks is compared with their MPI counterparts for the Class-A problem size in the figure in next page. These results were obtained on an SGI Origin2000 (195MHz) with MIPSpro-f77 compiler 7.2.1 for OpenMP and MPI codes and PGI pghpf-2.4.3 compiler with MPI interface for HPF programs.

Higher-order adaptive finite-element methods for Kohn–Sham density functional theory

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

Motamarri, P.; Nowak, M.R.; Leiter, K.

2013-11-15

We present an efficient computational approach to perform real-space electronic structure calculations using an adaptive higher-order finite-element discretization of Kohn–Sham density-functional theory (DFT). To this end, we develop an a priori mesh-adaption technique to construct a close to optimal finite-element discretization of the problem. We further propose an efficient solution strategy for solving the discrete eigenvalue problem by using spectral finite-elements in conjunction with Gauss–Lobatto quadrature, and a Chebyshev acceleration technique for computing the occupied eigenspace. The proposed approach has been observed to provide a staggering 100–200-fold computational advantage over the solution of a generalized eigenvalue problem. Using the proposedmore » solution procedure, we investigate the computational efficiency afforded by higher-order finite-element discretizations of the Kohn–Sham DFT problem. Our studies suggest that staggering computational savings—of the order of 1000-fold—relative to linear finite-elements can be realized, for both all-electron and local pseudopotential calculations, by using higher-order finite-element discretizations. On all the benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy, suggesting that the hexic spectral-element may be an optimal choice for the finite-element discretization of the Kohn–Sham DFT problem. A comparative study of the computational efficiency of the proposed higher-order finite-element discretizations suggests that the performance of finite-element basis is competing with the plane-wave discretization for non-periodic local pseudopotential calculations, and compares to the Gaussian basis for all-electron calculations to within an order of magnitude. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of a metallic system containing 1688 atoms using modest computational resources, and good scalability of the present implementation up to 192 processors.« less

A suite of benchmark and challenge problems for enhanced geothermal systems

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

White, Mark; Fu, Pengcheng; McClure, Mark

A diverse suite of numerical simulators is currently being applied to predict or understand the performance of enhanced geothermal systems (EGS). To build confidence and identify critical development needs for these analytical tools, the United States Department of Energy, Geothermal Technologies Office sponsored a Code Comparison Study (GTO-CCS), with participants from universities, industry, and national laboratories. A principal objective for the study was to create a community forum for improvement and verification of numerical simulators for EGS modeling. Teams participating in the study were those representing U.S. national laboratories, universities, and industries, and each team brought unique numerical simulation capabilitiesmore » to bear on the problems. Two classes of problems were developed during the study, benchmark problems and challenge problems. The benchmark problems were structured to test the ability of the collection of numerical simulators to solve various combinations of coupled thermal, hydrologic, geomechanical, and geochemical processes. This class of problems was strictly defined in terms of properties, driving forces, initial conditions, and boundary conditions. The challenge problems were based on the enhanced geothermal systems research conducted at Fenton Hill, near Los Alamos, New Mexico, between 1974 and 1995. The problems involved two phases of research, stimulation, development, and circulation in two separate reservoirs. The challenge problems had specific questions to be answered via numerical simulation in three topical areas: 1) reservoir creation/stimulation, 2) reactive and passive transport, and 3) thermal recovery. Whereas the benchmark class of problems were designed to test capabilities for modeling coupled processes under strictly specified conditions, the stated objective for the challenge class of problems was to demonstrate what new understanding of the Fenton Hill experiments could be realized via the application of modern numerical simulation tools by recognized expert practitioners. We present the suite of benchmark and challenge problems developed for the GTO-CCS, providing problem descriptions and sample solutions.« less

Multi-Constituent Simulation of Thrombus Deposition

NASA Astrophysics Data System (ADS)

Wu, Wei-Tao; Jamiolkowski, Megan A.; Wagner, William R.; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F.

2017-02-01

In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The transport and reactions of 10 chemical and biological species are incorporated using a system of coupled convection-reaction-diffusion (CRD) equations to represent three processes in thrombus formation: initiation, propagation and stabilization. Computational fluid dynamic (CFD) simulations using the libraries of OpenFOAM were performed for two illustrative benchmark problems: in vivo thrombus growth in an injured blood vessel and in vitro thrombus deposition in micro-channels (1.5 mm × 1.6 mm × 0.1 mm) with small crevices (125 μm × 75 μm and 125 μm × 137 μm). For both problems, the simulated thrombus deposition agreed very well with experimental observations, both spatially and temporally. Based on the success with these two benchmark problems, which have very different flow conditions and biological environments, we believe that the current model will provide useful insight into the genesis of thrombosis in blood-wetted devices, and provide a tool for the design of less thrombogenic devices.

Multi-Constituent Simulation of Thrombus Deposition

PubMed Central

Wu, Wei-Tao; Jamiolkowski, Megan A.; Wagner, William R.; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F.

2017-01-01

In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The transport and reactions of 10 chemical and biological species are incorporated using a system of coupled convection-reaction-diffusion (CRD) equations to represent three processes in thrombus formation: initiation, propagation and stabilization. Computational fluid dynamic (CFD) simulations using the libraries of OpenFOAM were performed for two illustrative benchmark problems: in vivo thrombus growth in an injured blood vessel and in vitro thrombus deposition in micro-channels (1.5 mm × 1.6 mm × 0.1 mm) with small crevices (125 μm × 75 μm and 125 μm × 137 μm). For both problems, the simulated thrombus deposition agreed very well with experimental observations, both spatially and temporally. Based on the success with these two benchmark problems, which have very different flow conditions and biological environments, we believe that the current model will provide useful insight into the genesis of thrombosis in blood-wetted devices, and provide a tool for the design of less thrombogenic devices. PMID:28218279

Multi-Constituent Simulation of Thrombus Deposition.

PubMed

Wu, Wei-Tao; Jamiolkowski, Megan A; Wagner, William R; Aubry, Nadine; Massoudi, Mehrdad; Antaki, James F

2017-02-20

In this paper, we present a spatio-temporal mathematical model for simulating the formation and growth of a thrombus. Blood is treated as a multi-constituent mixture comprised of a linear fluid phase and a thrombus (solid) phase. The transport and reactions of 10 chemical and biological species are incorporated using a system of coupled convection-reaction-diffusion (CRD) equations to represent three processes in thrombus formation: initiation, propagation and stabilization. Computational fluid dynamic (CFD) simulations using the libraries of OpenFOAM were performed for two illustrative benchmark problems: in vivo thrombus growth in an injured blood vessel and in vitro thrombus deposition in micro-channels (1.5 mm × 1.6 mm × 0.1 mm) with small crevices (125 μm × 75 μm and 125 μm × 137 μm). For both problems, the simulated thrombus deposition agreed very well with experimental observations, both spatially and temporally. Based on the success with these two benchmark problems, which have very different flow conditions and biological environments, we believe that the current model will provide useful insight into the genesis of thrombosis in blood-wetted devices, and provide a tool for the design of less thrombogenic devices.

On the Performance of Linear Decreasing Inertia Weight Particle Swarm Optimization for Global Optimization

PubMed Central

Arasomwan, Martins Akugbe; Adewumi, Aderemi Oluyinka

2013-01-01

Linear decreasing inertia weight (LDIW) strategy was introduced to improve on the performance of the original particle swarm optimization (PSO). However, linear decreasing inertia weight PSO (LDIW-PSO) algorithm is known to have the shortcoming of premature convergence in solving complex (multipeak) optimization problems due to lack of enough momentum for particles to do exploitation as the algorithm approaches its terminal point. Researchers have tried to address this shortcoming by modifying LDIW-PSO or proposing new PSO variants. Some of these variants have been claimed to outperform LDIW-PSO. The major goal of this paper is to experimentally establish the fact that LDIW-PSO is very much efficient if its parameters are properly set. First, an experiment was conducted to acquire a percentage value of the search space limits to compute the particle velocity limits in LDIW-PSO based on commonly used benchmark global optimization problems. Second, using the experimentally obtained values, five well-known benchmark optimization problems were used to show the outstanding performance of LDIW-PSO over some of its competitors which have in the past claimed superiority over it. Two other recent PSO variants with different inertia weight strategies were also compared with LDIW-PSO with the latter outperforming both in the simulation experiments conducted. PMID:24324383

Application of Jacobian-free Newton–Krylov method in implicitly solving two-fluid six-equation two-phase flow problems: Implementation, validation and benchmark

DOE PAGES

Zou, Ling; Zhao, Haihua; Zhang, Hongbin

2016-03-09

This work represents a first-of-its-kind successful application to employ advanced numerical methods in solving realistic two-phase flow problems with two-fluid six-equation two-phase flow model. These advanced numerical methods include high-resolution spatial discretization scheme with staggered grids (high-order) fully implicit time integration schemes, and Jacobian-free Newton–Krylov (JFNK) method as the nonlinear solver. The computer code developed in this work has been extensively validated with existing experimental flow boiling data in vertical pipes and rod bundles, which cover wide ranges of experimental conditions, such as pressure, inlet mass flux, wall heat flux and exit void fraction. Additional code-to-code benchmark with the RELAP5-3Dmore » code further verifies the correct code implementation. The combined methods employed in this work exhibit strong robustness in solving two-phase flow problems even when phase appearance (boiling) and realistic discrete flow regimes are considered. Transitional flow regimes used in existing system analysis codes, normally introduced to overcome numerical difficulty, were completely removed in this work. As a result, this in turn provides the possibility to utilize more sophisticated flow regime maps in the future to further improve simulation accuracy.« less

Biomimicry of symbiotic multi-species coevolution for discrete and continuous optimization in RFID networks.

PubMed

Lin, Na; Chen, Hanning; Jing, Shikai; Liu, Fang; Liang, Xiaodan

2017-03-01

In recent years, symbiosis as a rich source of potential engineering applications and computational model has attracted more and more attentions in the adaptive complex systems and evolution computing domains. Inspired by different symbiotic coevolution forms in nature, this paper proposed a series of multi-swarm particle swarm optimizers called PS 2 Os, which extend the single population particle swarm optimization (PSO) algorithm to interacting multi-swarms model by constructing hierarchical interaction topologies and enhanced dynamical update equations. According to different symbiotic interrelationships, four versions of PS 2 O are initiated to mimic mutualism, commensalism, predation, and competition mechanism, respectively. In the experiments, with five benchmark problems, the proposed algorithms are proved to have considerable potential for solving complex optimization problems. The coevolutionary dynamics of symbiotic species in each PS 2 O version are also studied respectively to demonstrate the heterogeneity of different symbiotic interrelationships that effect on the algorithm's performance. Then PS 2 O is used for solving the radio frequency identification (RFID) network planning (RNP) problem with a mixture of discrete and continuous variables. Simulation results show that the proposed algorithm outperforms the reference algorithms for planning RFID networks, in terms of optimization accuracy and computation robustness.

An Integrated Method Based on PSO and EDA for the Max-Cut Problem.

PubMed

Lin, Geng; Guan, Jian

2016-01-01

The max-cut problem is NP-hard combinatorial optimization problem with many real world applications. In this paper, we propose an integrated method based on particle swarm optimization and estimation of distribution algorithm (PSO-EDA) for solving the max-cut problem. The integrated algorithm overcomes the shortcomings of particle swarm optimization and estimation of distribution algorithm. To enhance the performance of the PSO-EDA, a fast local search procedure is applied. In addition, a path relinking procedure is developed to intensify the search. To evaluate the performance of PSO-EDA, extensive experiments were carried out on two sets of benchmark instances with 800 to 20,000 vertices from the literature. Computational results and comparisons show that PSO-EDA significantly outperforms the existing PSO-based and EDA-based algorithms for the max-cut problem. Compared with other best performing algorithms, PSO-EDA is able to find very competitive results in terms of solution quality.

Benchmarking the SPHINX and CTH shock physics codes for three problems in ballistics

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

Wilson, L.T.; Hertel, E.; Schwalbe, L.

1998-02-01

The CTH Eulerian hydrocode, and the SPHINX smooth particle hydrodynamics (SPH) code were used to model a shock tube, two long rod penetrations into semi-infinite steel targets, and a long rod penetration into a spaced plate array. The results were then compared to experimental data. Both SPHINX and CTH modeled the one-dimensional shock tube problem well. Both codes did a reasonable job in modeling the outcome of the axisymmetric rod impact problem. Neither code correctly reproduced the depth of penetration in both experiments. In the 3-D problem, both codes reasonably replicated the penetration of the rod through the first plate.more » After this, however, the predictions of both codes began to diverge from the results seen in the experiment. In terms of computer resources, the run times are problem dependent, and are discussed in the text.« less

Mixed Arlequin method for multiscale poromechanics problems: Mixed Arlequin method for multiscale poromechanics problems

DOE PAGES

Sun, WaiChing; Cai, Zhijun; Choo, Jinhyun

2016-11-18

An Arlequin poromechanics model is introduced to simulate the hydro-mechanical coupling effects of fluid-infiltrated porous media across different spatial scales within a concurrent computational framework. A two-field poromechanics problem is first recast as the twofold saddle point of an incremental energy functional. We then introduce Lagrange multipliers and compatibility energy functionals to enforce the weak compatibility of hydro-mechanical responses in the overlapped domain. Here, to examine the numerical stability of this hydro-mechanical Arlequin model, we derive a necessary condition for stability, the twofold inf–sup condition for multi-field problems, and establish a modified inf–sup test formulated in the product space ofmore » the solution field. We verify the implementation of the Arlequin poromechanics model through benchmark problems covering the entire range of drainage conditions. Finally, through these numerical examples, we demonstrate the performance, robustness, and numerical stability of the Arlequin poromechanics model.« less

On solving three-dimensional open-dimension rectangular packing problems

NASA Astrophysics Data System (ADS)

Junqueira, Leonardo; Morabito, Reinaldo

2017-05-01

In this article, a recently proposed three-dimensional open-dimension rectangular packing problem is considered, in which the objective is to find a minimal volume rectangular container that packs a set of rectangular boxes. The literature has tackled small-sized instances of this problem by means of optimization solvers, position-free mixed-integer programming (MIP) formulations and piecewise linearization approaches. In this study, the problem is alternatively addressed by means of grid-based position MIP formulations, whereas still considering optimization solvers and the same piecewise linearization techniques. A comparison of the computational performance of both models is then presented, when tested with benchmark problem instances and with new instances, and it is shown that the grid-based position MIP formulation can be competitive, depending on the characteristics of the instances. The grid-based position MIP formulation is also embedded with real-world practical constraints, such as cargo stability, and results are additionally presented.

Prediction of Sound Waves Propagating Through a Nozzle Without/With a Shock Wave Using the Space-Time CE/SE Method

NASA Technical Reports Server (NTRS)

Wang, Xiao-Yen; Chang, Sin-Chung; Jorgenson, Philip C. E.

2000-01-01

The benchmark problems in Category 1 (Internal Propagation) of the third Computational Aeroacoustics (CAA) Work-shop sponsored by NASA Glenn Research Center are solved using the space-time conservation element and solution element (CE/SE) method. The first problem addresses the propagation of sound waves through a nearly choked transonic nozzle. The second one concerns shock-sound interaction in a supersonic nozzle. A quasi one-dimension CE/SE Euler solver for a nonuniform mesh is developed and employed to solve both problems. Numerical solutions are compared with the analytical solution for both problems. It is demonstrated that the CE/SE method is capable of solving aeroacoustic problems with/without shock waves in a simple way. Furthermore, the simple nonreflecting boundary condition used in the CE/SE method which is not based on the characteristic theory works very well.

Genetic Algorithm for Traveling Salesman Problem with Modified Cycle Crossover Operator

PubMed Central

Mohamd Shoukry, Alaa; Gani, Showkat

2017-01-01

Genetic algorithms are evolutionary techniques used for optimization purposes according to survival of the fittest idea. These methods do not ensure optimal solutions; however, they give good approximation usually in time. The genetic algorithms are useful for NP-hard problems, especially the traveling salesman problem. The genetic algorithm depends on selection criteria, crossover, and mutation operators. To tackle the traveling salesman problem using genetic algorithms, there are various representations such as binary, path, adjacency, ordinal, and matrix representations. In this article, we propose a new crossover operator for traveling salesman problem to minimize the total distance. This approach has been linked with path representation, which is the most natural way to represent a legal tour. Computational results are also reported with some traditional path representation methods like partially mapped and order crossovers along with new cycle crossover operator for some benchmark TSPLIB instances and found improvements. PMID:29209364

Genetic Algorithm for Traveling Salesman Problem with Modified Cycle Crossover Operator.

PubMed

Hussain, Abid; Muhammad, Yousaf Shad; Nauman Sajid, M; Hussain, Ijaz; Mohamd Shoukry, Alaa; Gani, Showkat

2017-01-01

Genetic algorithms are evolutionary techniques used for optimization purposes according to survival of the fittest idea. These methods do not ensure optimal solutions; however, they give good approximation usually in time. The genetic algorithms are useful for NP-hard problems, especially the traveling salesman problem. The genetic algorithm depends on selection criteria, crossover, and mutation operators. To tackle the traveling salesman problem using genetic algorithms, there are various representations such as binary, path, adjacency, ordinal, and matrix representations. In this article, we propose a new crossover operator for traveling salesman problem to minimize the total distance. This approach has been linked with path representation, which is the most natural way to represent a legal tour. Computational results are also reported with some traditional path representation methods like partially mapped and order crossovers along with new cycle crossover operator for some benchmark TSPLIB instances and found improvements.

Improved teaching-learning-based and JAYA optimization algorithms for solving flexible flow shop scheduling problems

NASA Astrophysics Data System (ADS)

Buddala, Raviteja; Mahapatra, Siba Sankar

2017-11-01

Flexible flow shop (or a hybrid flow shop) scheduling problem is an extension of classical flow shop scheduling problem. In a simple flow shop configuration, a job having `g' operations is performed on `g' operation centres (stages) with each stage having only one machine. If any stage contains more than one machine for providing alternate processing facility, then the problem becomes a flexible flow shop problem (FFSP). FFSP which contains all the complexities involved in a simple flow shop and parallel machine scheduling problems is a well-known NP-hard (Non-deterministic polynomial time) problem. Owing to high computational complexity involved in solving these problems, it is not always possible to obtain an optimal solution in a reasonable computation time. To obtain near-optimal solutions in a reasonable computation time, a large variety of meta-heuristics have been proposed in the past. However, tuning algorithm-specific parameters for solving FFSP is rather tricky and time consuming. To address this limitation, teaching-learning-based optimization (TLBO) and JAYA algorithm are chosen for the study because these are not only recent meta-heuristics but they do not require tuning of algorithm-specific parameters. Although these algorithms seem to be elegant, they lose solution diversity after few iterations and get trapped at the local optima. To alleviate such drawback, a new local search procedure is proposed in this paper to improve the solution quality. Further, mutation strategy (inspired from genetic algorithm) is incorporated in the basic algorithm to maintain solution diversity in the population. Computational experiments have been conducted on standard benchmark problems to calculate makespan and computational time. It is found that the rate of convergence of TLBO is superior to JAYA. From the results, it is found that TLBO and JAYA outperform many algorithms reported in the literature and can be treated as efficient methods for solving the FFSP.

A New Soft Computing Method for K-Harmonic Means Clustering.

PubMed

Yeh, Wei-Chang; Jiang, Yunzhi; Chen, Yee-Fen; Chen, Zhe

2016-01-01

The K-harmonic means clustering algorithm (KHM) is a new clustering method used to group data such that the sum of the harmonic averages of the distances between each entity and all cluster centroids is minimized. Because it is less sensitive to initialization than K-means (KM), many researchers have recently been attracted to studying KHM. In this study, the proposed iSSO-KHM is based on an improved simplified swarm optimization (iSSO) and integrates a variable neighborhood search (VNS) for KHM clustering. As evidence of the utility of the proposed iSSO-KHM, we present extensive computational results on eight benchmark problems. From the computational results, the comparison appears to support the superiority of the proposed iSSO-KHM over previously developed algorithms for all experiments in the literature.

Documentation of probabilistic fracture mechanics codes used for reactor pressure vessels subjected to pressurized thermal shock loading: Parts 1 and 2. Final report

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

Balkey, K.; Witt, F.J.; Bishop, B.A.

1995-06-01

Significant attention has been focused on the issue of reactor vessel pressurized thermal shock (PTS) for many years. Pressurized thermal shock transient events are characterized by a rapid cooldown at potentially high pressure levels that could lead to a reactor vessel integrity concern for some pressurized water reactors. As a result of regulatory and industry efforts in the early 1980`s, a probabilistic risk assessment methodology has been established to address this concern. Probabilistic fracture mechanics analyses are performed as part of this methodology to determine conditional probability of significant flaw extension for given pressurized thermal shock events. While recent industrymore » efforts are underway to benchmark probabilistic fracture mechanics computer codes that are currently used by the nuclear industry, Part I of this report describes the comparison of two independent computer codes used at the time of the development of the original U.S. Nuclear Regulatory Commission (NRC) pressurized thermal shock rule. The work that was originally performed in 1982 and 1983 to compare the U.S. NRC - VISA and Westinghouse (W) - PFM computer codes has been documented and is provided in Part I of this report. Part II of this report describes the results of more recent industry efforts to benchmark PFM computer codes used by the nuclear industry. This study was conducted as part of the USNRC-EPRI Coordinated Research Program for reviewing the technical basis for pressurized thermal shock (PTS) analyses of the reactor pressure vessel. The work focused on the probabilistic fracture mechanics (PFM) analysis codes and methods used to perform the PTS calculations. An in-depth review of the methodologies was performed to verify the accuracy and adequacy of the various different codes. The review was structured around a series of benchmark sample problems to provide a specific context for discussion and examination of the fracture mechanics methodology.« less

Four-Nozzle Benchmark Wind Tunnel Model USA Code Solutions for Simulation of Multiple Rocket Base Flow Recirculation at 145,000 Feet Altitude

NASA Technical Reports Server (NTRS)

Dougherty, N. S.; Johnson, S. L.

1993-01-01

Multiple rocket exhaust plume interactions at high altitudes can produce base flow recirculation with attendant alteration of the base pressure coefficient and increased base heating. A search for a good wind tunnel benchmark problem to check grid clustering technique and turbulence modeling turned up the experiment done at AEDC in 1961 by Goethert and Matz on a 4.25-in. diameter domed missile base model with four rocket nozzles. This wind tunnel model with varied external bleed air flow for the base flow wake produced measured p/p(sub ref) at the center of the base as high as 3.3 due to plume flow recirculation back onto the base. At that time in 1961, relatively inexpensive experimentation with air at gamma = 1.4 and nozzle A(sub e)/A of 10.6 and theta(sub n) = 7.55 deg with P(sub c) = 155 psia simulated a LO2/LH2 rocket exhaust plume with gamma = 1.20, A(sub e)/A of 78 and P(sub c) about 1,000 psia. An array of base pressure taps on the aft dome gave a clear measurement of the plume recirculation effects at p(infinity) = 4.76 psfa corresponding to 145,000 ft altitude. Our CFD computations of the flow field with direct comparison of computed-versus-measured base pressure distribution (across the dome) provide detailed information on velocities and particle traces as well eddy viscosity in the base and nozzle region. The solution was obtained using a six-zone mesh with 284,000 grid points for one quadrant taking advantage of symmetry. Results are compared using a zero-equation algebraic and a one-equation pointwise R(sub t) turbulence model (work in progress). Good agreement with the experimental pressure data was obtained with both; and this benchmark showed the importance of: (1) proper grid clustering and (2) proper choice of turbulence modeling for rocket plume problems/recirculation at high altitude.

Sensitivity Analysis of OECD Benchmark Tests in BISON

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

Swiler, Laura Painton; Gamble, Kyle; Schmidt, Rodney C.

2015-09-01

This report summarizes a NEAMS (Nuclear Energy Advanced Modeling and Simulation) project focused on sensitivity analysis of a fuels performance benchmark problem. The benchmark problem was defined by the Uncertainty Analysis in Modeling working group of the Nuclear Science Committee, part of the Nuclear Energy Agency of the Organization for Economic Cooperation and Development (OECD ). The benchmark problem involv ed steady - state behavior of a fuel pin in a Pressurized Water Reactor (PWR). The problem was created in the BISON Fuels Performance code. Dakota was used to generate and analyze 300 samples of 17 input parameters defining coremore » boundary conditions, manuf acturing tolerances , and fuel properties. There were 24 responses of interest, including fuel centerline temperatures at a variety of locations and burnup levels, fission gas released, axial elongation of the fuel pin, etc. Pearson and Spearman correlatio n coefficients and Sobol' variance - based indices were used to perform the sensitivity analysis. This report summarizes the process and presents results from this study.« less

Analyzing the BBOB results by means of benchmarking concepts.

PubMed

Mersmann, O; Preuss, M; Trautmann, H; Bischl, B; Weihs, C

2015-01-01

We present methods to answer two basic questions that arise when benchmarking optimization algorithms. The first one is: which algorithm is the "best" one? and the second one is: which algorithm should I use for my real-world problem? Both are connected and neither is easy to answer. We present a theoretical framework for designing and analyzing the raw data of such benchmark experiments. This represents a first step in answering the aforementioned questions. The 2009 and 2010 BBOB benchmark results are analyzed by means of this framework and we derive insight regarding the answers to the two questions. Furthermore, we discuss how to properly aggregate rankings from algorithm evaluations on individual problems into a consensus, its theoretical background and which common pitfalls should be avoided. Finally, we address the grouping of test problems into sets with similar optimizer rankings and investigate whether these are reflected by already proposed test problem characteristics, finding that this is not always the case.

Numerical study of base pressure characteristic curve for a four-engine clustered nozzle configuration

NASA Astrophysics Data System (ADS)

Wang, Ten-See

1993-07-01

Excessive base heating has been a problem for many launch vehicles. For certain designs such as the direct dump of turbine exhaust in the nozzle section and at the nozzle lip of the Space Transportation Systems Engine (STME), the potential burning of the turbine exhaust in the base region has caused tremendous concern. Two conventional approaches have been considered for predicting the base environment: (1) empirical approach, and (2) experimental approach. The empirical approach uses a combination of data correlations and semi-theoretical calculations. It works best for linear problems, simple physics and geometry. However, it is highly suspicious when complex geometry and flow physics are involved, especially when the subject is out of historical database. The experimental approach is often used to establish database for engineering analysis. However, it is qualitative at best for base flow problems. Other criticisms include the inability to simulate forebody boundary layer correctly, the interference effect from tunnel walls, and the inability to scale all pertinent parameters. Furthermore, there is a contention that the information extrapolated from subscale tests with combustion is not conservative. One potential alternative to the conventional methods is computational fluid dynamics (CFD), which has none of the above restrictions and is becoming more feasible due to maturing algorithms and advancing computer technology. It provides more details of the flowfield and is only limited by computer resources. However, it has its share of criticisms as a predictive tool for base environment. One major concern is that CFD has not been extensively tested for base flow problems. It is therefore imperative that CFD be assessed and benchmarked satisfactorily for base flows. In this study, the turbulent base flowfield of a experimental investigation for a four-engine clustered nozzle is numerically benchmarked using a pressure based CFD method. Since the cold air was the medium, accurate prediction of the base pressure distributions at high altitudes is the primary goal. Other factors which may influence the numerical results such as the effects of grid density, turbulence model, differencing scheme, and boundary conditions are also being addressed.

Numerical Study of Base Pressure Characteristic Curve for a Four-Engine Clustered Nozzle Configuration

NASA Technical Reports Server (NTRS)

Wang, Ten-See

1993-01-01

Excessive base heating has been a problem for many launch vehicles. For certain designs such as the direct dump of turbine exhaust in the nozzle section and at the nozzle lip of the Space Transportation Systems Engine (STME), the potential burning of the turbine exhaust in the base region has caused tremendous concern. Two conventional approaches have been considered for predicting the base environment: (1) empirical approach, and (2) experimental approach. The empirical approach uses a combination of data correlations and semi-theoretical calculations. It works best for linear problems, simple physics and geometry. However, it is highly suspicious when complex geometry and flow physics are involved, especially when the subject is out of historical database. The experimental approach is often used to establish database for engineering analysis. However, it is qualitative at best for base flow problems. Other criticisms include the inability to simulate forebody boundary layer correctly, the interference effect from tunnel walls, and the inability to scale all pertinent parameters. Furthermore, there is a contention that the information extrapolated from subscale tests with combustion is not conservative. One potential alternative to the conventional methods is computational fluid dynamics (CFD), which has none of the above restrictions and is becoming more feasible due to maturing algorithms and advancing computer technology. It provides more details of the flowfield and is only limited by computer resources. However, it has its share of criticisms as a predictive tool for base environment. One major concern is that CFD has not been extensively tested for base flow problems. It is therefore imperative that CFD be assessed and benchmarked satisfactorily for base flows. In this study, the turbulent base flowfield of a experimental investigation for a four-engine clustered nozzle is numerically benchmarked using a pressure based CFD method. Since the cold air was the medium, accurate prediction of the base pressure distributions at high altitudes is the primary goal. Other factors which may influence the numerical results such as the effects of grid density, turbulence model, differencing scheme, and boundary conditions are also being addressed. Preliminary results of the computed base pressure agreed reasonably well with that of the measurement. Basic base flow features such as the reverse jet, wall jet, recompression shock, and static pressure field in plane of impingement have been captured.

Computational mechanics research and support for aerodynamics and hydraulics at TFHRC year 1 quarter 4 progress report.

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

Lottes, S.A.; Kulak, R.F.; Bojanowski, C.

2011-12-09

The computational fluid dynamics (CFD) and computational structural mechanics (CSM) focus areas at Argonne's Transportation Research and Analysis Computing Center (TRACC) initiated a project to support and compliment the experimental programs at the Turner-Fairbank Highway Research Center (TFHRC) with high performance computing based analysis capabilities in August 2010. The project was established with a new interagency agreement between the Department of Energy and the Department of Transportation to provide collaborative research, development, and benchmarking of advanced three-dimensional computational mechanics analysis methods to the aerodynamics and hydraulics laboratories at TFHRC for a period of five years, beginning in October 2010. Themore » analysis methods employ well-benchmarked and supported commercial computational mechanics software. Computational mechanics encompasses the areas of Computational Fluid Dynamics (CFD), Computational Wind Engineering (CWE), Computational Structural Mechanics (CSM), and Computational Multiphysics Mechanics (CMM) applied in Fluid-Structure Interaction (FSI) problems. The major areas of focus of the project are wind and water effects on bridges - superstructure, deck, cables, and substructure (including soil), primarily during storms and flood events - and the risks that these loads pose to structural failure. For flood events at bridges, another major focus of the work is assessment of the risk to bridges caused by scour of stream and riverbed material away from the foundations of a bridge. Other areas of current research include modeling of flow through culverts to assess them for fish passage, modeling of the salt spray transport into bridge girders to address suitability of using weathering steel in bridges, CFD analysis of the operation of the wind tunnel in the TFCHR wind engineering laboratory, vehicle stability under high wind loading, and the use of electromagnetic shock absorbers to improve vehicle stability under high wind conditions. This quarterly report documents technical progress on the project tasks for the period of July through September 2011.« less

A hybrid CS-SA intelligent approach to solve uncertain dynamic facility layout problems considering dependency of demands

NASA Astrophysics Data System (ADS)

Moslemipour, Ghorbanali

2018-07-01

This paper aims at proposing a quadratic assignment-based mathematical model to deal with the stochastic dynamic facility layout problem. In this problem, product demands are assumed to be dependent normally distributed random variables with known probability density function and covariance that change from period to period at random. To solve the proposed model, a novel hybrid intelligent algorithm is proposed by combining the simulated annealing and clonal selection algorithms. The proposed model and the hybrid algorithm are verified and validated using design of experiment and benchmark methods. The results show that the hybrid algorithm has an outstanding performance from both solution quality and computational time points of view. Besides, the proposed model can be used in both of the stochastic and deterministic situations.

Thermo-hydro-mechanical-chemical processes in fractured-porous media: Benchmarks and examples

NASA Astrophysics Data System (ADS)

Kolditz, O.; Shao, H.; Görke, U.; Kalbacher, T.; Bauer, S.; McDermott, C. I.; Wang, W.

2012-12-01

The book comprises an assembly of benchmarks and examples for porous media mechanics collected over the last twenty years. Analysis of thermo-hydro-mechanical-chemical (THMC) processes is essential to many applications in environmental engineering, such as geological waste deposition, geothermal energy utilisation, carbon capture and storage, water resources management, hydrology, even climate change. In order to assess the feasibility as well as the safety of geotechnical applications, process-based modelling is the only tool to put numbers, i.e. to quantify future scenarios. This charges a huge responsibility concerning the reliability of computational tools. Benchmarking is an appropriate methodology to verify the quality of modelling tools based on best practices. Moreover, benchmarking and code comparison foster community efforts. The benchmark book is part of the OpenGeoSys initiative - an open source project to share knowledge and experience in environmental analysis and scientific computation.

Numerical Analysis of Base Flowfield for a Four-Engine Clustered Nozzle Configuration

NASA Technical Reports Server (NTRS)

Wang, Ten-See

1995-01-01

Excessive base heating has been a problem for many launch vehicles. For certain designs such as the direct dump of turbine exhaust inside and at the lip of the nozzle, the potential burning of the turbine exhaust in the base region can be of great concern. Accurate prediction of the base environment at altitudes is therefore very important during the vehicle design phase. Otherwise, undesirable consequences may occur. In this study, the turbulent base flowfield of a cold flow experimental investigation for a four-engine clustered nozzle was numerically benchmarked using a pressure-based computational fluid dynamics (CFD) method. This is a necessary step before the benchmarking of hot flow and combustion flow tests can be considered. Since the medium was unheated air, reasonable prediction of the base pressure distribution at high altitude was the main goal. Several physical phenomena pertaining to the multiengine clustered nozzle base flow physics were deduced from the analysis.

Study of blood flow in several benchmark micro-channels using a two-fluid approach.

PubMed

Wu, Wei-Tao; Yang, Fang; Antaki, James F; Aubry, Nadine; Massoudi, Mehrdad

2015-10-01

It is known that in a vessel whose characteristic dimension (e.g., its diameter) is in the range of 20 to 500 microns, blood behaves as a non-Newtonian fluid, exhibiting complex phenomena, such as shear-thinning, stress relaxation, and also multi-component behaviors, such as the Fahraeus effect, plasma-skimming, etc. For describing these non-Newtonian and multi-component characteristics of blood, using the framework of mixture theory, a two-fluid model is applied, where the plasma is treated as a Newtonian fluid and the red blood cells (RBCs) are treated as shear-thinning fluid. A computational fluid dynamic (CFD) simulation incorporating the constitutive model was implemented using OpenFOAM® in which benchmark problems including a sudden expansion and various driven slots and crevices were studied numerically. The numerical results exhibited good agreement with the experimental observations with respect to both the velocity field and the volume fraction distribution of RBCs.

From honeybees to Internet servers: biomimicry for distributed management of Internet hosting centers.

PubMed

Nakrani, Sunil; Tovey, Craig

2007-12-01

An Internet hosting center hosts services on its server ensemble. The center must allocate servers dynamically amongst services to maximize revenue earned from hosting fees. The finite server ensemble, unpredictable request arrival behavior and server reallocation cost make server allocation optimization difficult. Server allocation closely resembles honeybee forager allocation amongst flower patches to optimize nectar influx. The resemblance inspires a honeybee biomimetic algorithm. This paper describes details of the honeybee self-organizing model in terms of information flow and feedback, analyzes the homology between the two problems and derives the resulting biomimetic algorithm for hosting centers. The algorithm is assessed for effectiveness and adaptiveness by comparative testing against benchmark and conventional algorithms. Computational results indicate that the new algorithm is highly adaptive to widely varying external environments and quite competitive against benchmark assessment algorithms. Other swarm intelligence applications are briefly surveyed, and some general speculations are offered regarding their various degrees of success.

Astronomy education and the Astrophysics Source Code Library

NASA Astrophysics Data System (ADS)

Allen, Alice; Nemiroff, Robert J.

2016-01-01

The Astrophysics Source Code Library (ASCL) is an online registry of source codes used in refereed astrophysics research. It currently lists nearly 1,200 codes and covers all aspects of computational astrophysics. How can this resource be of use to educators and to the graduate students they mentor? The ASCL serves as a discovery tool for codes that can be used for one's own research. Graduate students can also investigate existing codes to see how common astronomical problems are approached numerically in practice, and use these codes as benchmarks for their own solutions to these problems. Further, they can deepen their knowledge of software practices and techniques through examination of others' codes.

Combined AIE/EBE/GMRES approach to incompressible flows. [Adaptive Implicit-Explicit/Grouped Element-by-Element/Generalized Minimum Residuals

NASA Technical Reports Server (NTRS)

Liou, J.; Tezduyar, T. E.

1990-01-01

Adaptive implicit-explicit (AIE), grouped element-by-element (GEBE), and generalized minimum residuals (GMRES) solution techniques for incompressible flows are combined. In this approach, the GEBE and GMRES iteration methods are employed to solve the equation systems resulting from the implicitly treated elements, and therefore no direct solution effort is involved. The benchmarking results demonstrate that this approach can substantially reduce the CPU time and memory requirements in large-scale flow problems. Although the description of the concepts and the numerical demonstration are based on the incompressible flows, the approach presented here is applicable to larger class of problems in computational mechanics.

Next Generation Distributed Computing for Cancer Research

PubMed Central

Agarwal, Pankaj; Owzar, Kouros

2014-01-01

Advances in next generation sequencing (NGS) and mass spectrometry (MS) technologies have provided many new opportunities and angles for extending the scope of translational cancer research while creating tremendous challenges in data management and analysis. The resulting informatics challenge is invariably not amenable to the use of traditional computing models. Recent advances in scalable computing and associated infrastructure, particularly distributed computing for Big Data, can provide solutions for addressing these challenges. In this review, the next generation of distributed computing technologies that can address these informatics problems is described from the perspective of three key components of a computational platform, namely computing, data storage and management, and networking. A broad overview of scalable computing is provided to set the context for a detailed description of Hadoop, a technology that is being rapidly adopted for large-scale distributed computing. A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop. Finally, Hadoop is compared with a number of other current technologies for distributed computing. PMID:25983539

Next generation distributed computing for cancer research.

PubMed

Agarwal, Pankaj; Owzar, Kouros

2014-01-01

Advances in next generation sequencing (NGS) and mass spectrometry (MS) technologies have provided many new opportunities and angles for extending the scope of translational cancer research while creating tremendous challenges in data management and analysis. The resulting informatics challenge is invariably not amenable to the use of traditional computing models. Recent advances in scalable computing and associated infrastructure, particularly distributed computing for Big Data, can provide solutions for addressing these challenges. In this review, the next generation of distributed computing technologies that can address these informatics problems is described from the perspective of three key components of a computational platform, namely computing, data storage and management, and networking. A broad overview of scalable computing is provided to set the context for a detailed description of Hadoop, a technology that is being rapidly adopted for large-scale distributed computing. A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop. Finally, Hadoop is compared with a number of other current technologies for distributed computing.

Quantum and classical dynamics in adiabatic computation

NASA Astrophysics Data System (ADS)

Crowley, P. J. D.; Äńurić, T.; Vinci, W.; Warburton, P. A.; Green, A. G.

2014-10-01

Adiabatic transport provides a powerful way to manipulate quantum states. By preparing a system in a readily initialized state and then slowly changing its Hamiltonian, one may achieve quantum states that would otherwise be inaccessible. Moreover, a judicious choice of final Hamiltonian whose ground state encodes the solution to a problem allows adiabatic transport to be used for universal quantum computation. However, the dephasing effects of the environment limit the quantum correlations that an open system can support and degrade the power of such adiabatic computation. We quantify this effect by allowing the system to evolve over a restricted set of quantum states, providing a link between physically inspired classical optimization algorithms and quantum adiabatic optimization. This perspective allows us to develop benchmarks to bound the quantum correlations harnessed by an adiabatic computation. We apply these to the D-Wave Vesuvius machine with revealing—though inconclusive—results.

Computational Prediction of miRNA Genes from Small RNA Sequencing Data

PubMed Central

Kang, Wenjing; Friedländer, Marc R.

2015-01-01

Next-generation sequencing now for the first time allows researchers to gage the depth and variation of entire transcriptomes. However, now as rare transcripts can be detected that are present in cells at single copies, more advanced computational tools are needed to accurately annotate and profile them. microRNAs (miRNAs) are 22 nucleotide small RNAs (sRNAs) that post-transcriptionally reduce the output of protein coding genes. They have established roles in numerous biological processes, including cancers and other diseases. During miRNA biogenesis, the sRNAs are sequentially cleaved from precursor molecules that have a characteristic hairpin RNA structure. The vast majority of new miRNA genes that are discovered are mined from small RNA sequencing (sRNA-seq), which can detect more than a billion RNAs in a single run. However, given that many of the detected RNAs are degradation products from all types of transcripts, the accurate identification of miRNAs remain a non-trivial computational problem. Here, we review the tools available to predict animal miRNAs from sRNA sequencing data. We present tools for generalist and specialist use cases, including prediction from massively pooled data or in species without reference genome. We also present wet-lab methods used to validate predicted miRNAs, and approaches to computationally benchmark prediction accuracy. For each tool, we reference validation experiments and benchmarking efforts. Last, we discuss the future of the field. PMID:25674563

Aircraft Engine Gas Path Diagnostic Methods: Public Benchmarking Results

NASA Technical Reports Server (NTRS)

Simon, Donald L.; Borguet, Sebastien; Leonard, Olivier; Zhang, Xiaodong (Frank)

2013-01-01

Recent technology reviews have identified the need for objective assessments of aircraft engine health management (EHM) technologies. To help address this issue, a gas path diagnostic benchmark problem has been created and made publicly available. This software tool, referred to as the Propulsion Diagnostic Method Evaluation Strategy (ProDiMES), has been constructed based on feedback provided by the aircraft EHM community. It provides a standard benchmark problem enabling users to develop, evaluate and compare diagnostic methods. This paper will present an overview of ProDiMES along with a description of four gas path diagnostic methods developed and applied to the problem. These methods, which include analytical and empirical diagnostic techniques, will be described and associated blind-test-case metric results will be presented and compared. Lessons learned along with recommendations for improving the public benchmarking processes will also be presented and discussed.

Benchmarking Brain-Computer Interfaces Outside the Laboratory: The Cybathlon 2016

PubMed Central

Novak, Domen; Sigrist, Roland; Gerig, Nicolas J.; Wyss, Dario; Bauer, René; Götz, Ulrich; Riener, Robert

2018-01-01

This paper presents a new approach to benchmarking brain-computer interfaces (BCIs) outside the lab. A computer game was created that mimics a real-world application of assistive BCIs, with the main outcome metric being the time needed to complete the game. This approach was used at the Cybathlon 2016, a competition for people with disabilities who use assistive technology to achieve tasks. The paper summarizes the technical challenges of BCIs, describes the design of the benchmarking game, then describes the rules for acceptable hardware, software and inclusion of human pilots in the BCI competition at the Cybathlon. The 11 participating teams, their approaches, and their results at the Cybathlon are presented. Though the benchmarking procedure has some limitations (for instance, we were unable to identify any factors that clearly contribute to BCI performance), it can be successfully used to analyze BCI performance in realistic, less structured conditions. In the future, the parameters of the benchmarking game could be modified to better mimic different applications (e.g., the need to use some commands more frequently than others). Furthermore, the Cybathlon has the potential to showcase such devices to the general public. PMID:29375294

AltiVec performance increases for autonomous robotics for the MARSSCAPE architecture program

NASA Astrophysics Data System (ADS)

Gothard, Benny M.

2002-02-01

One of the main tall poles that must be overcome to develop a fully autonomous vehicle is the inability of the computer to understand its surrounding environment to a level that is required for the intended task. The military mission scenario requires a robot to interact in a complex, unstructured, dynamic environment. Reference A High Fidelity Multi-Sensor Scene Understanding System for Autonomous Navigation The Mobile Autonomous Robot Software Self Composing Adaptive Programming Environment (MarsScape) perception research addresses three aspects of the problem; sensor system design, processing architectures, and algorithm enhancements. A prototype perception system has been demonstrated on robotic High Mobility Multi-purpose Wheeled Vehicle and All Terrain Vehicle testbeds. This paper addresses the tall pole of processing requirements and the performance improvements based on the selected MarsScape Processing Architecture. The processor chosen is the Motorola Altivec-G4 Power PC(PPC) (1998 Motorola, Inc.), a highly parallized commercial Single Instruction Multiple Data processor. Both derived perception benchmarks and actual perception subsystems code will be benchmarked and compared against previous Demo II-Semi-autonomous Surrogate Vehicle processing architectures along with desktop Personal Computers(PC). Performance gains are highlighted with progress to date, and lessons learned and future directions are described.

Development of a Computing Cluster At the University of Richmond

NASA Astrophysics Data System (ADS)

Carbonneau, J.; Gilfoyle, G. P.; Bunn, E. F.

2010-11-01

The University of Richmond has developed a computing cluster to support the massive simulation and data analysis requirements for programs in intermediate-energy nuclear physics, and cosmology. It is a 20-node, 240-core system running Red Hat Enterprise Linux 5. We have built and installed the physics software packages (Geant4, gemc, MADmap...) and developed shell and Perl scripts for running those programs on the remote nodes. The system has a theoretical processing peak of about 2500 GFLOPS. Testing with the High Performance Linpack (HPL) benchmarking program (one of the standard benchmarks used by the TOP500 list of fastest supercomputers) resulted in speeds of over 900 GFLOPS. The difference between the maximum and measured speeds is due to limitations in the communication speed among the nodes; creating a bottleneck for large memory problems. As HPL sends data between nodes, the gigabit Ethernet connection cannot keep up with the processing power. We will show how both the theoretical and actual performance of the cluster compares with other current and past clusters, as well as the cost per GFLOP. We will also examine the scaling of the performance when distributed to increasing numbers of nodes.

Exploiting the Dynamics of Soft Materials for Machine Learning

PubMed Central

Hauser, Helmut; Li, Tao; Pfeifer, Rolf

2018-01-01

Abstract Soft materials are increasingly utilized for various purposes in many engineering applications. These materials have been shown to perform a number of functions that were previously difficult to implement using rigid materials. Here, we argue that the diverse dynamics generated by actuating soft materials can be effectively used for machine learning purposes. This is demonstrated using a soft silicone arm through a technique of multiplexing, which enables the rich transient dynamics of the soft materials to be fully exploited as a computational resource. The computational performance of the soft silicone arm is examined through two standard benchmark tasks. Results show that the soft arm compares well to or even outperforms conventional machine learning techniques under multiple conditions. We then demonstrate that this system can be used for the sensory time series prediction problem for the soft arm itself, which suggests its immediate applicability to a real-world machine learning problem. Our approach, on the one hand, represents a radical departure from traditional computational methods, whereas on the other hand, it fits nicely into a more general perspective of computation by way of exploiting the properties of physical materials in the real world. PMID:29708857

Exploiting the Dynamics of Soft Materials for Machine Learning.

PubMed

Nakajima, Kohei; Hauser, Helmut; Li, Tao; Pfeifer, Rolf

2018-06-01

Soft materials are increasingly utilized for various purposes in many engineering applications. These materials have been shown to perform a number of functions that were previously difficult to implement using rigid materials. Here, we argue that the diverse dynamics generated by actuating soft materials can be effectively used for machine learning purposes. This is demonstrated using a soft silicone arm through a technique of multiplexing, which enables the rich transient dynamics of the soft materials to be fully exploited as a computational resource. The computational performance of the soft silicone arm is examined through two standard benchmark tasks. Results show that the soft arm compares well to or even outperforms conventional machine learning techniques under multiple conditions. We then demonstrate that this system can be used for the sensory time series prediction problem for the soft arm itself, which suggests its immediate applicability to a real-world machine learning problem. Our approach, on the one hand, represents a radical departure from traditional computational methods, whereas on the other hand, it fits nicely into a more general perspective of computation by way of exploiting the properties of physical materials in the real world.

Learning-based computing techniques in geoid modeling for precise height transformation

NASA Astrophysics Data System (ADS)

Erol, B.; Erol, S.

2013-03-01

Precise determination of local geoid is of particular importance for establishing height control in geodetic GNSS applications, since the classical leveling technique is too laborious. A geoid model can be accurately obtained employing properly distributed benchmarks having GNSS and leveling observations using an appropriate computing algorithm. Besides the classical multivariable polynomial regression equations (MPRE), this study attempts an evaluation of learning based computing algorithms: artificial neural networks (ANNs), adaptive network-based fuzzy inference system (ANFIS) and especially the wavelet neural networks (WNNs) approach in geoid surface approximation. These algorithms were developed parallel to advances in computer technologies and recently have been used for solving complex nonlinear problems of many applications. However, they are rather new in dealing with precise modeling problem of the Earth gravity field. In the scope of the study, these methods were applied to Istanbul GPS Triangulation Network data. The performances of the methods were assessed considering the validation results of the geoid models at the observation points. In conclusion the ANFIS and WNN revealed higher prediction accuracies compared to ANN and MPRE methods. Beside the prediction capabilities, these methods were also compared and discussed from the practical point of view in conclusions.

A Fluid Structure Algorithm with Lagrange Multipliers to Model Free Swimming

NASA Astrophysics Data System (ADS)

Sahin, Mehmet; Dilek, Ezgi

2017-11-01

A new monolithic approach is prosed to solve the fluid-structure interaction (FSI) problem with Lagrange multipliers in order to model free swimming/flying. In the present approach, the fluid domain is modeled by the incompressible Navier-Stokes equations and discretized using an Arbitrary Lagrangian-Eulerian (ALE) formulation based on the stable side-centered unstructured finite volume method. The solid domain is modeled by the constitutive laws for the nonlinear Saint Venant-Kirchhoff material and the classical Galerkin finite element method is used to discretize the governing equations in a Lagrangian frame. In order to impose the body motion/deformation, the distance between the constraint pair nodes is imposed using the Lagrange multipliers, which is independent from the frame of reference. The resulting algebraic linear equations are solved in a fully coupled manner using a dual approach (null space method). The present numerical algorithm is initially validated for the classical FSI benchmark problems and then applied to the free swimming of three linked ellipses. The authors are grateful for the use of the computing resources provided by the National Center for High Performance Computing (UYBHM) under Grant Number 10752009 and the computing facilities at TUBITAK-ULAKBIM, High Performance and Grid Computing Center.

Advanced Computational Methods for Security Constrained Financial Transmission Rights: Structure and Parallelism

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

Elbert, Stephen T.; Kalsi, Karanjit; Vlachopoulou, Maria

Financial Transmission Rights (FTRs) help power market participants reduce price risks associated with transmission congestion. FTRs are issued based on a process of solving a constrained optimization problem with the objective to maximize the FTR social welfare under power flow security constraints. Security constraints for different FTR categories (monthly, seasonal or annual) are usually coupled and the number of constraints increases exponentially with the number of categories. Commercial software for FTR calculation can only provide limited categories of FTRs due to the inherent computational challenges mentioned above. In this paper, a novel non-linear dynamical system (NDS) approach is proposed tomore » solve the optimization problem. The new formulation and performance of the NDS solver is benchmarked against widely used linear programming (LP) solvers like CPLEX™ and tested on large-scale systems using data from the Western Electricity Coordinating Council (WECC). The NDS is demonstrated to outperform the widely used CPLEX algorithms while exhibiting superior scalability. Furthermore, the NDS based solver can be easily parallelized which results in significant computational improvement.« less

Application of Fast Multipole Methods to the NASA Fast Scattering Code

NASA Technical Reports Server (NTRS)

Dunn, Mark H.; Tinetti, Ana F.

2008-01-01

The NASA Fast Scattering Code (FSC) is a versatile noise prediction program designed to conduct aeroacoustic noise reduction studies. The equivalent source method is used to solve an exterior Helmholtz boundary value problem with an impedance type boundary condition. The solution process in FSC v2.0 requires direct manipulation of a large, dense system of linear equations, limiting the applicability of the code to small scales and/or moderate excitation frequencies. Recent advances in the use of Fast Multipole Methods (FMM) for solving scattering problems, coupled with sparse linear algebra techniques, suggest that a substantial reduction in computer resource utilization over conventional solution approaches can be obtained. Implementation of the single level FMM (SLFMM) and a variant of the Conjugate Gradient Method (CGM) into the FSC is discussed in this paper. The culmination of this effort, FSC v3.0, was used to generate solutions for three configurations of interest. Benchmarking against previously obtained simulations indicate that a twenty-fold reduction in computational memory and up to a four-fold reduction in computer time have been achieved on a single processor.

Benchmarking Ligand-Based Virtual High-Throughput Screening with the PubChem Database

PubMed Central

Butkiewicz, Mariusz; Lowe, Edward W.; Mueller, Ralf; Mendenhall, Jeffrey L.; Teixeira, Pedro L.; Weaver, C. David; Meiler, Jens

2013-01-01

With the rapidly increasing availability of High-Throughput Screening (HTS) data in the public domain, such as the PubChem database, methods for ligand-based computer-aided drug discovery (LB-CADD) have the potential to accelerate and reduce the cost of probe development and drug discovery efforts in academia. We assemble nine data sets from realistic HTS campaigns representing major families of drug target proteins for benchmarking LB-CADD methods. Each data set is public domain through PubChem and carefully collated through confirmation screens validating active compounds. These data sets provide the foundation for benchmarking a new cheminformatics framework BCL::ChemInfo, which is freely available for non-commercial use. Quantitative structure activity relationship (QSAR) models are built using Artificial Neural Networks (ANNs), Support Vector Machines (SVMs), Decision Trees (DTs), and Kohonen networks (KNs). Problem-specific descriptor optimization protocols are assessed including Sequential Feature Forward Selection (SFFS) and various information content measures. Measures of predictive power and confidence are evaluated through cross-validation, and a consensus prediction scheme is tested that combines orthogonal machine learning algorithms into a single predictor. Enrichments ranging from 15 to 101 for a TPR cutoff of 25% are observed. PMID:23299552

Model Prediction Results for 2007 Ultrasonic Benchmark Problems

NASA Astrophysics Data System (ADS)

Kim, Hak-Joon; Song, Sung-Jin

2008-02-01

The World Federation of NDE Centers (WFNDEC) has addressed two types of problems for the 2007 ultrasonic benchmark problems: prediction of side-drilled hole responses with 45° and 60° refracted shear waves, and effects of surface curvatures on the ultrasonic responses of flat-bottomed hole. To solve this year's ultrasonic benchmark problems, we applied multi-Gaussian beam models for calculation of ultrasonic beam fields and the Kirchhoff approximation and the separation of variables method for calculation of far-field scattering amplitudes of flat-bottomed holes and side-drilled holes respectively In this paper, we present comparison results of model predictions to experiments for side-drilled holes and discuss effect of interface curvatures on ultrasonic responses by comparison of peak-to-peak amplitudes of flat-bottomed hole responses with different sizes and interface curvatures.

A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design.

PubMed

Ó Conchúir, Shane; Barlow, Kyle A; Pache, Roland A; Ollikainen, Noah; Kundert, Kale; O'Meara, Matthew J; Smith, Colin A; Kortemme, Tanja

2015-01-01

The development and validation of computational macromolecular modeling and design methods depend on suitable benchmark datasets and informative metrics for comparing protocols. In addition, if a method is intended to be adopted broadly in diverse biological applications, there needs to be information on appropriate parameters for each protocol, as well as metrics describing the expected accuracy compared to experimental data. In certain disciplines, there exist established benchmarks and public resources where experts in a particular methodology are encouraged to supply their most efficient implementation of each particular benchmark. We aim to provide such a resource for protocols in macromolecular modeling and design. We present a freely accessible web resource (https://kortemmelab.ucsf.edu/benchmarks) to guide the development of protocols for protein modeling and design. The site provides benchmark datasets and metrics to compare the performance of a variety of modeling protocols using different computational sampling methods and energy functions, providing a "best practice" set of parameters for each method. Each benchmark has an associated downloadable benchmark capture archive containing the input files, analysis scripts, and tutorials for running the benchmark. The captures may be run with any suitable modeling method; we supply command lines for running the benchmarks using the Rosetta software suite. We have compiled initial benchmarks for the resource spanning three key areas: prediction of energetic effects of mutations, protein design, and protein structure prediction, each with associated state-of-the-art modeling protocols. With the help of the wider macromolecular modeling community, we hope to expand the variety of benchmarks included on the website and continue to evaluate new iterations of current methods as they become available.

Unequal-area, fixed-shape facility layout problems using the firefly algorithm

NASA Astrophysics Data System (ADS)

Ingole, Supriya; Singh, Dinesh

2017-07-01

In manufacturing industries, the facility layout design is a very important task, as it is concerned with the overall manufacturing cost and profit of the industry. The facility layout problem (FLP) is solved by arranging the departments or facilities of known dimensions on the available floor space. The objective of this article is to implement the firefly algorithm (FA) for solving unequal-area, fixed-shape FLPs and optimizing the costs of total material handling and transportation between the facilities. The FA is a nature-inspired algorithm and can be used for combinatorial optimization problems. Benchmark problems from the previous literature are solved using the FA. To check its effectiveness, it is implemented to solve large-sized FLPs. Computational results obtained using the FA show that the algorithm is less time consuming and the total layout costs for FLPs are better than the best results achieved so far.

Restarting and recentering genetic algorithm variations for DNA fragment assembly: The necessity of a multi-strategy approach.

PubMed

Hughes, James Alexander; Houghten, Sheridan; Ashlock, Daniel

2016-12-01

DNA Fragment assembly - an NP-Hard problem - is one of the major steps in of DNA sequencing. Multiple strategies have been used for this problem, including greedy graph-based algorithms, deBruijn graphs, and the overlap-layout-consensus approach. This study focuses on the overlap-layout-consensus approach. Heuristics and computational intelligence methods are combined to exploit their respective benefits. These algorithm combinations were able to produce high quality results surpassing the best results obtained by a number of competitive algorithms specially designed and tuned for this problem on thirteen of sixteen popular benchmarks. This work also reinforces the necessity of using multiple search strategies as it is clearly observed that algorithm performance is dependent on problem instance; without a deeper look into many searches, top solutions could be missed entirely. Copyright © 2016. Published by Elsevier Ireland Ltd.

Fourier-Accelerated Nodal Solvers (FANS) for homogenization problems

NASA Astrophysics Data System (ADS)

Leuschner, Matthias; Fritzen, Felix

2017-11-01

Fourier-based homogenization schemes are useful to analyze heterogeneous microstructures represented by 2D or 3D image data. These iterative schemes involve discrete periodic convolutions with global ansatz functions (mostly fundamental solutions). The convolutions are efficiently computed using the fast Fourier transform. FANS operates on nodal variables on regular grids and converges to finite element solutions. Compared to established Fourier-based methods, the number of convolutions is reduced by FANS. Additionally, fast iterations are possible by assembling the stiffness matrix. Due to the related memory requirement, the method is best suited for medium-sized problems. A comparative study involving established Fourier-based homogenization schemes is conducted for a thermal benchmark problem with a closed-form solution. Detailed technical and algorithmic descriptions are given for all methods considered in the comparison. Furthermore, many numerical examples focusing on convergence properties for both thermal and mechanical problems, including also plasticity, are presented.

A Benchmarking Initiative for Reactive Transport Modeling Applied to Subsurface Environmental Applications

NASA Astrophysics Data System (ADS)

Steefel, C. I.

2015-12-01

Over the last 20 years, we have seen the evolution of multicomponent reactive transport modeling and the expanding range and increasing complexity of subsurface environmental applications it is being used to address. Reactive transport modeling is being asked to provide accurate assessments of engineering performance and risk for important issues with far-reaching consequences. As a result, the complexity and detail of subsurface processes, properties, and conditions that can be simulated have significantly expanded. Closed form solutions are necessary and useful, but limited to situations that are far simpler than typical applications that combine many physical and chemical processes, in many cases in coupled form. In the absence of closed form and yet realistic solutions for complex applications, numerical benchmark problems with an accepted set of results will be indispensable to qualifying codes for various environmental applications. The intent of this benchmarking exercise, now underway for more than five years, is to develop and publish a set of well-described benchmark problems that can be used to demonstrate simulator conformance with norms established by the subsurface science and engineering community. The objective is not to verify this or that specific code--the reactive transport codes play a supporting role in this regard—but rather to use the codes to verify that a common solution of the problem can be achieved. Thus, the objective of each of the manuscripts is to present an environmentally-relevant benchmark problem that tests the conceptual model capabilities, numerical implementation, process coupling, and accuracy. The benchmark problems developed to date include 1) microbially-mediated reactions, 2) isotopes, 3) multi-component diffusion, 4) uranium fate and transport, 5) metal mobility in mining affected systems, and 6) waste repositories and related aspects.

Efficiently modeling neural networks on massively parallel computers

NASA Technical Reports Server (NTRS)

Farber, Robert M.

1993-01-01

Neural networks are a very useful tool for analyzing and modeling complex real world systems. Applying neural network simulations to real world problems generally involves large amounts of data and massive amounts of computation. To efficiently handle the computational requirements of large problems, we have implemented at Los Alamos a highly efficient neural network compiler for serial computers, vector computers, vector parallel computers, and fine grain SIMD computers such as the CM-2 connection machine. This paper describes the mapping used by the compiler to implement feed-forward backpropagation neural networks for a SIMD (Single Instruction Multiple Data) architecture parallel computer. Thinking Machines Corporation has benchmarked our code at 1.3 billion interconnects per second (approximately 3 gigaflops) on a 64,000 processor CM-2 connection machine (Singer 1990). This mapping is applicable to other SIMD computers and can be implemented on MIMD computers such as the CM-5 connection machine. Our mapping has virtually no communications overhead with the exception of the communications required for a global summation across the processors (which has a sub-linear runtime growth on the order of O(log(number of processors)). We can efficiently model very large neural networks which have many neurons and interconnects and our mapping can extend to arbitrarily large networks (within memory limitations) by merging the memory space of separate processors with fast adjacent processor interprocessor communications. This paper will consider the simulation of only feed forward neural network although this method is extendable to recurrent networks.

Simulation of biochemical reactions with time-dependent rates by the rejection-based algorithm

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

Thanh, Vo Hong, E-mail: vo@cosbi.eu; Priami, Corrado, E-mail: priami@cosbi.eu; Department of Mathematics, University of Trento, Trento

We address the problem of simulating biochemical reaction networks with time-dependent rates and propose a new algorithm based on our rejection-based stochastic simulation algorithm (RSSA) [Thanh et al., J. Chem. Phys. 141(13), 134116 (2014)]. The computation for selecting next reaction firings by our time-dependent RSSA (tRSSA) is computationally efficient. Furthermore, the generated trajectory is exact by exploiting the rejection-based mechanism. We benchmark tRSSA on different biological systems with varying forms of reaction rates to demonstrate its applicability and efficiency. We reveal that for nontrivial cases, the selection of reaction firings in existing algorithms introduces approximations because the integration of reactionmore » rates is very computationally demanding and simplifying assumptions are introduced. The selection of the next reaction firing by our approach is easier while preserving the exactness.« less

Improving Multi-Objective Management of Water Quality Tipping Points: Revisiting the Classical Shallow Lake Problem

NASA Astrophysics Data System (ADS)

Quinn, J. D.; Reed, P. M.; Keller, K.

2015-12-01

Recent multi-objective extensions of the classical shallow lake problem are useful for exploring the conceptual and computational challenges that emerge when managing irreversible water quality tipping points. Building on this work, we explore a four objective version of the lake problem where a hypothetical town derives economic benefits from polluting a nearby lake, but at the risk of irreversibly tipping the lake into a permanently polluted state. The trophic state of the lake exhibits non-linear threshold dynamics; below some critical phosphorus (P) threshold it is healthy and oligotrophic, but above this threshold it is irreversibly eutrophic. The town must decide how much P to discharge each year, a decision complicated by uncertainty in the natural P inflow to the lake. The shallow lake problem provides a conceptually rich set of dynamics, low computational demands, and a high level of mathematical difficulty. These properties maximize its value for benchmarking the relative merits and limitations of emerging decision support frameworks, such as Direct Policy Search (DPS). Here, we explore the use of DPS as a formal means of developing robust environmental pollution control rules that effectively account for deeply uncertain system states and conflicting objectives. The DPS reformulation of the shallow lake problem shows promise in formalizing pollution control triggers and signposts, while dramatically reducing the computational complexity of the multi-objective pollution control problem. More broadly, the insights from the DPS variant of the shallow lake problem formulated in this study bridge emerging work related to socio-ecological systems management, tipping points, robust decision making, and robust control.

Delivering Science on Day One

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

Williams, Timothy J.

2016-03-01

While benchmarking software is useful for testing the performance limits and stability of Argonne National Laboratory’s new Theta supercomputer, there is no substitute for running real applications to explore the system’s potential. The Argonne Leadership Computing Facility’s Theta Early Science Program, modeled after its highly successful code migration program for the Mira supercomputer, has one primary aim: to deliver science on day one. Here is a closer look at the type of science problems that will be getting early access to Theta, a next-generation machine being rolled out this year.

Making Benchmark Testing Work

ERIC Educational Resources Information Center

Herman, Joan L.; Baker, Eva L.

2005-01-01

Many schools are moving to develop benchmark tests to monitor their students' progress toward state standards throughout the academic year. Benchmark tests can provide the ongoing information that schools need to guide instructional programs and to address student learning problems. The authors discuss six criteria that educators can use to…

Parallelized modelling and solution scheme for hierarchically scaled simulations

NASA Technical Reports Server (NTRS)

Padovan, Joe

1995-01-01

This two-part paper presents the results of a benchmarked analytical-numerical investigation into the operational characteristics of a unified parallel processing strategy for implicit fluid mechanics formulations. This hierarchical poly tree (HPT) strategy is based on multilevel substructural decomposition. The Tree morphology is chosen to minimize memory, communications and computational effort. The methodology is general enough to apply to existing finite difference (FD), finite element (FEM), finite volume (FV) or spectral element (SE) based computer programs without an extensive rewrite of code. In addition to finding large reductions in memory, communications, and computational effort associated with a parallel computing environment, substantial reductions are generated in the sequential mode of application. Such improvements grow with increasing problem size. Along with a theoretical development of general 2-D and 3-D HPT, several techniques for expanding the problem size that the current generation of computers are capable of solving, are presented and discussed. Among these techniques are several interpolative reduction methods. It was found that by combining several of these techniques that a relatively small interpolative reduction resulted in substantial performance gains. Several other unique features/benefits are discussed in this paper. Along with Part 1's theoretical development, Part 2 presents a numerical approach to the HPT along with four prototype CFD applications. These demonstrate the potential of the HPT strategy.

Adiabatic Quantum Computing via the Rydberg Blockade

NASA Astrophysics Data System (ADS)

Keating, Tyler; Goyal, Krittika; Deutsch, Ivan

2012-06-01

We study an architecture for implementing adiabatic quantum computation with trapped neutral atoms. Ground state atoms are dressed by laser fields in a manner conditional on the Rydberg blockade mechanism, thereby providing the requisite entangling interactions. As a benchmark we study the performance of a Quadratic Unconstrained Binary Optimization (QUBO) problem whose solution is found in the ground state spin configuration of an Ising-like model. We model a realistic architecture, including the effects of magnetic level structure, with qubits encoded into the clock states of ^133Cs, effective B-fields implemented through microwaves and light shifts, and atom-atom coupling achieved by excitation to a high-lying Rydberg level. Including the fundamental effects of photon scattering we find a high fidelity for the two-qubit implementation.

Computers for real time flight simulation: A market survey

NASA Technical Reports Server (NTRS)

Bekey, G. A.; Karplus, W. J.

1977-01-01

An extensive computer market survey was made to determine those available systems suitable for current and future flight simulation studies at Ames Research Center. The primary requirement is for the computation of relatively high frequency content (5 Hz) math models representing powered lift flight vehicles. The Rotor Systems Research Aircraft (RSRA) was used as a benchmark vehicle for computation comparison studies. The general nature of helicopter simulations and a description of the benchmark model are presented, and some of the sources of simulation difficulties are examined. A description of various applicable computer architectures is presented, along with detailed discussions of leading candidate systems and comparisons between them.

Modeling Cardiac Electrophysiology at the Organ Level in the Peta FLOPS Computing Age

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

Mitchell, Lawrence; Bishop, Martin; Hoetzl, Elena

2010-09-30

Despite a steep increase in available compute power, in-silico experimentation with highly detailed models of the heart remains to be challenging due to the high computational cost involved. It is hoped that next generation high performance computing (HPC) resources lead to significant reductions in execution times to leverage a new class of in-silico applications. However, performance gains with these new platforms can only be achieved by engaging a much larger number of compute cores, necessitating strongly scalable numerical techniques. So far strong scalability has been demonstrated only for a moderate number of cores, orders of magnitude below the range requiredmore » to achieve the desired performance boost.In this study, strong scalability of currently used techniques to solve the bidomain equations is investigated. Benchmark results suggest that scalability is limited to 512-4096 cores within the range of relevant problem sizes even when systems are carefully load-balanced and advanced IO strategies are employed.« less

A CUMULATIVE MIGRATION METHOD FOR COMPUTING RIGOROUS TRANSPORT CROSS SECTIONS AND DIFFUSION COEFFICIENTS FOR LWR LATTICES WITH MONTE CARLO

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

Zhaoyuan Liu; Kord Smith; Benoit Forget

2016-05-01

A new method for computing homogenized assembly neutron transport cross sections and dif- fusion coefficients that is both rigorous and computationally efficient is proposed in this paper. In the limit of a homogeneous hydrogen slab, the new method is equivalent to the long-used, and only-recently-published CASMO transport method. The rigorous method is used to demonstrate the sources of inaccuracy in the commonly applied “out-scatter” transport correction. It is also demonstrated that the newly developed method is directly applicable to lattice calculations per- formed by Monte Carlo and is capable of computing rigorous homogenized transport cross sections for arbitrarily heterogeneous lattices.more » Comparisons of several common transport cross section ap- proximations are presented for a simple problem of infinite medium hydrogen. The new method has also been applied in computing 2-group diffusion data for an actual PWR lattice from BEAVRS benchmark.« less

Benchmarking: A Process for Improvement.

ERIC Educational Resources Information Center

Peischl, Thomas M.

One problem with the outcome-based measures used in higher education is that they measure quantity but not quality. Benchmarking, or the use of some external standard of quality to measure tasks, processes, and outputs, is partially solving that difficulty. Benchmarking allows for the establishment of a systematic process to indicate if outputs…

Solution of the neutronics code dynamic benchmark by finite element method

NASA Astrophysics Data System (ADS)

Avvakumov, A. V.; Vabishchevich, P. N.; Vasilev, A. O.; Strizhov, V. F.

2016-10-01

The objective is to analyze the dynamic benchmark developed by Atomic Energy Research for the verification of best-estimate neutronics codes. The benchmark scenario includes asymmetrical ejection of a control rod in a water-type hexagonal reactor at hot zero power. A simple Doppler feedback mechanism assuming adiabatic fuel temperature heating is proposed. The finite element method on triangular calculation grids is used to solve the three-dimensional neutron kinetics problem. The software has been developed using the engineering and scientific calculation library FEniCS. The matrix spectral problem is solved using the scalable and flexible toolkit SLEPc. The solution accuracy of the dynamic benchmark is analyzed by condensing calculation grid and varying degree of finite elements.

Learning of state-space models with highly informative observations: A tempered sequential Monte Carlo solution

NASA Astrophysics Data System (ADS)

Svensson, Andreas; Schön, Thomas B.; Lindsten, Fredrik

2018-05-01

Probabilistic (or Bayesian) modeling and learning offers interesting possibilities for systematic representation of uncertainty using probability theory. However, probabilistic learning often leads to computationally challenging problems. Some problems of this type that were previously intractable can now be solved on standard personal computers thanks to recent advances in Monte Carlo methods. In particular, for learning of unknown parameters in nonlinear state-space models, methods based on the particle filter (a Monte Carlo method) have proven very useful. A notoriously challenging problem, however, still occurs when the observations in the state-space model are highly informative, i.e. when there is very little or no measurement noise present, relative to the amount of process noise. The particle filter will then struggle in estimating one of the basic components for probabilistic learning, namely the likelihood p (data | parameters). To this end we suggest an algorithm which initially assumes that there is substantial amount of artificial measurement noise present. The variance of this noise is sequentially decreased in an adaptive fashion such that we, in the end, recover the original problem or possibly a very close approximation of it. The main component in our algorithm is a sequential Monte Carlo (SMC) sampler, which gives our proposed method a clear resemblance to the SMC2 method. Another natural link is also made to the ideas underlying the approximate Bayesian computation (ABC). We illustrate it with numerical examples, and in particular show promising results for a challenging Wiener-Hammerstein benchmark problem.

Implicit time-integration method for simultaneous solution of a coupled non-linear system

NASA Astrophysics Data System (ADS)

Watson, Justin Kyle

Historically large physical problems have been divided into smaller problems based on the physics involved. This is no different in reactor safety analysis. The problem of analyzing a nuclear reactor for design basis accidents is performed by a handful of computer codes each solving a portion of the problem. The reactor thermal hydraulic response to an event is determined using a system code like TRAC RELAP Advanced Computational Engine (TRACE). The core power response to the same accident scenario is determined using a core physics code like Purdue Advanced Core Simulator (PARCS). Containment response to the reactor depressurization in a Loss Of Coolant Accident (LOCA) type event is calculated by a separate code. Sub-channel analysis is performed with yet another computer code. This is just a sample of the computer codes used to solve the overall problems of nuclear reactor design basis accidents. Traditionally each of these codes operates independently from each other using only the global results from one calculation as boundary conditions to another. Industry's drive to uprate power for reactors has motivated analysts to move from a conservative approach to design basis accident towards a best estimate method. To achieve a best estimate calculation efforts have been aimed at coupling the individual physics models to improve the accuracy of the analysis and reduce margins. The current coupling techniques are sequential in nature. During a calculation time-step data is passed between the two codes. The individual codes solve their portion of the calculation and converge to a solution before the calculation is allowed to proceed to the next time-step. This thesis presents a fully implicit method of simultaneous solving the neutron balance equations, heat conduction equations and the constitutive fluid dynamics equations. It discusses the problems involved in coupling different physics phenomena within multi-physics codes and presents a solution to these problems. The thesis also outlines the basic concepts behind the nodal balance equations, heat transfer equations and the thermal hydraulic equations, which will be coupled to form a fully implicit nonlinear system of equations. The coupling of separate physics models to solve a larger problem and improve accuracy and efficiency of a calculation is not a new idea, however implementing them in an implicit manner and solving the system simultaneously is. Also the application to reactor safety codes is new and has not be done with thermal hydraulics and neutronics codes on realistic applications in the past. The coupling technique described in this thesis is applicable to other similar coupled thermal hydraulic and core physics reactor safety codes. This technique is demonstrated using coupled input decks to show that the system is solved correctly and then verified by using two derivative test problems based on international benchmark problems the OECD/NRC Three mile Island (TMI) Main Steam Line Break (MSLB) problem (representative of pressurized water reactor analysis) and the OECD/NRC Peach Bottom (PB) Turbine Trip (TT) benchmark (representative of boiling water reactor analysis).

Aeroelasticity Benchmark Assessment: Subsonic Fixed Wing Program

NASA Technical Reports Server (NTRS)

Florance, Jennifer P.; Chwalowski, Pawel; Wieseman, Carol D.

2010-01-01

The fundamental technical challenge in computational aeroelasticity is the accurate prediction of unsteady aerodynamic phenomena and the effect on the aeroelastic response of a vehicle. Currently, a benchmarking standard for use in validating the accuracy of computational aeroelasticity codes does not exist. Many aeroelastic data sets have been obtained in wind-tunnel and flight testing throughout the world; however, none have been globally presented or accepted as an ideal data set. There are numerous reasons for this. One reason is that often, such aeroelastic data sets focus on the aeroelastic phenomena alone (flutter, for example) and do not contain associated information such as unsteady pressures and time-correlated structural dynamic deflections. Other available data sets focus solely on the unsteady pressures and do not address the aeroelastic phenomena. Other discrepancies can include omission of relevant data, such as flutter frequency and / or the acquisition of only qualitative deflection data. In addition to these content deficiencies, all of the available data sets present both experimental and computational technical challenges. Experimental issues include facility influences, nonlinearities beyond those being modeled, and data processing. From the computational perspective, technical challenges include modeling geometric complexities, coupling between the flow and the structure, grid issues, and boundary conditions. The Aeroelasticity Benchmark Assessment task seeks to examine the existing potential experimental data sets and ultimately choose the one that is viewed as the most suitable for computational benchmarking. An initial computational evaluation of that configuration will then be performed using the Langley-developed computational fluid dynamics (CFD) software FUN3D1 as part of its code validation process. In addition to the benchmarking activity, this task also includes an examination of future research directions. Researchers within the Aeroelasticity Branch will examine other experimental efforts within the Subsonic Fixed Wing (SFW) program (such as testing of the NASA Common Research Model (CRM)) and other NASA programs and assess aeroelasticity issues and research topics.

A Methodology for Benchmarking Relational Database Machines,

DTIC Science & Technology

1984-01-01

user benchmarks is to compare the multiple users to the best-case performance The data for each query classification coll and the performance...called a benchmark. The term benchmark originates from the markers used by sur - veyors in establishing common reference points for their measure...formatted databases. In order to further simplify the problem, we restrict our study to those DBMs which support the relational model. A sur - vey

ogs6 - a new concept for porous-fractured media simulations

NASA Astrophysics Data System (ADS)

Naumov, Dmitri; Bilke, Lars; Fischer, Thomas; Rink, Karsten; Wang, Wenqing; Watanabe, Norihiro; Kolditz, Olaf

2015-04-01

OpenGeoSys (OGS) is a scientific open-source initiative for numerical simulation of thermo-hydro-mechanical/chemical (THMC) processes in porous and fractured media, continuously developed since the mid-eighties. The basic concept is to provide a flexible numerical framework for solving coupled multi-field problems. OGS is targeting mainly on applications in environmental geoscience, e.g. in the fields of contaminant hydrology, water resources management, waste deposits, or geothermal energy systems, but it has also been successfully applied to new topics in energy storage recently. OGS is actively participating several international benchmarking initiatives, e.g. DECOVALEX (waste management), CO2BENCH (CO2 storage and sequestration), SeSBENCH (reactive transport processes) and HM-Intercomp (coupled hydrosystems). Despite the broad applicability of OGS in geo-, hydro- and energy-sciences, several shortcomings became obvious concerning the computational efficiency as well as the code structure became too sophisticated for further efficient development. OGS-5 was designed for object-oriented FEM applications. However, in many multi-field problems a certain flexibility of tailored numerical schemes is essential. Therefore, a new concept was designed to overcome existing bottlenecks. The paradigms for ogs6 are: - Flexibility of numerical schemes (FEM#FVM#FDM), - Computational efficiency (PetaScale ready), - Developer- and user-friendly. ogs6 has a module-oriented architecture based on thematic libraries (e.g. MeshLib, NumLib) on the large scale and uses object-oriented approach for the small scale interfaces. Usage of a linear algebra library (Eigen3) for the mathematical operations together with the ISO C++11 standard increases the expressiveness of the code and makes it more developer-friendly. The new C++ standard also makes the template meta-programming technique code used for compile-time optimizations more compact. We have transitioned the main code development to the GitHub code hosting system (https://github.com/ufz/ogs). The very flexible revision control system Git in combination with issue tracking, developer feedback and the code review options improve the code quality and the development process in general. The continuous testing procedure of the benchmarks as it was established for OGS-5 is maintained. Additionally unit testing, which is automatically triggered by any code changes, is executed by two continuous integration frameworks (Jenkins CI, Travis CI) which build and test the code on different operating systems (Windows, Linux, Mac OS), in multiple configurations and with different compilers (GCC, Clang, Visual Studio). To improve the testing possibilities further, XML based file input formats are introduced helping with automatic validation of the user contributed benchmarks. The first ogs6 prototype version 6.0.1 has been implemented for solving generic elliptic problems. Next steps are envisaged to transient, non-linear and coupled problems. Literature: [1] Kolditz O, Shao H, Wang W, Bauer S (eds) (2014): Thermo-Hydro-Mechanical-Chemical Processes in Fractured Porous Media: Modelling and Benchmarking - Closed Form Solutions. In: Terrestrial Environmental Sciences, Vol. 1, Springer, Heidelberg, ISBN 978-3-319-11893-2, 315pp. http://www.springer.com/earth+sciences+and+geography/geology/book/978-3-319-11893-2 [2] Naumov D (2015): Computational Fluid Dynamics in Unconsolidated Sediments: Model Generation and Discrete Flow Simulations, PhD thesis, Technische Universität Dresden.

Creation of problem-dependent Doppler-broadened cross sections in the KENO Monte Carlo code

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

Hart, Shane W. D.; Celik, Cihangir; Maldonado, G. Ivan

2015-11-06

In this paper, we introduce a quick method for improving the accuracy of Monte Carlo simulations by generating one- and two-dimensional cross sections at a user-defined temperature before performing transport calculations. A finite difference method is used to Doppler-broaden cross sections to the desired temperature, and unit-base interpolation is done to generate the probability distributions for double differential two-dimensional thermal moderator cross sections at any arbitrarily user-defined temperature. The accuracy of these methods is tested using a variety of contrived problems. In addition, various benchmarks at elevated temperatures are modeled, and results are compared with benchmark results. Lastly, the problem-dependentmore » cross sections are observed to produce eigenvalue estimates that are closer to the benchmark results than those without the problem-dependent cross sections.« less

On the inflation of poro-hyperelastic annuli

NASA Astrophysics Data System (ADS)

Selvadurai, A. P. S.; Suvorov, A. P.

2017-10-01

The paper presents the radially and spherically symmetric problems associated with the inflation of poro-hyperelastic regions. The theory of poro-hyperelasticity is a convenient framework for modelling the mechanical behaviour of highly deformable materials in which the pore space is saturated with fluids. Including the coupled mechanical responses of both the hyperelastic porous skeleton and the fluid is regarded as an important consideration for the application of the results, particularly to soft tissues encountered in biomechanical applications. The analytical solutions for radially and spherically symmetric problems involving annular domains are used to benchmark the accuracy of a standard computational approach. The paper also generates results applicable to the hyperelastic solutions when coupling is eliminated through the presence of a highly permeable pore structure.

Atomization simulations using an Eulerian-VOF-Lagrangian method

NASA Technical Reports Server (NTRS)

Chen, Yen-Sen; Shang, Huan-Min; Liaw, Paul; Chen, C. P.

1994-01-01

This paper summarizes the technical development and validation of a multiphase computational fluid dynamics (CFD) numerical method using the volume-of-fluid (VOF) model and a Lagrangian tracking model which can be employed to analyze general multiphase flow problems with free surface mechanism. The gas-liquid interface mass, momentum and energy conservations are modeled by continuum surface mechanisms. A new solution method is developed such that the present VOF model can be applied for all-speed flow regimes. The objectives of the present study are to develop and verify the fractional volume-of-fluid cell partitioning approach into a predictor-corrector algorithm and to demonstrate the effectiveness of the present innovative approach by simulating benchmark problems including the coaxial jet atomization.

Final Report

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

Hollingsworth, Jeff

2014-07-31

The purpose of this project was to develop tools and techniques to improve the ability of computational scientists to investigate and correct problems (bugs) in their programs. Specifically, the University of Maryland component of this project focused on the problems associated with the finite number of bits available in a computer to represent numeric values. In large scale scientific computation, numbers are frequently added to and multiplied with each other billions of times. Thus even small errors due to the representation of numbers can accumulate into big errors. However, using too many bits to represent a number results in additionalmore » computation, memory, and energy costs. Thus it is critical to find the right size for numbers. This project focused on several aspects of this general problem. First, we developed a tool to look for cancelations, the catastrophic loss of precision in numbers due to the addition of two numbers whose actual values are close to each other, but whose representation in a computer is identical or nearly so. Second, we developed a suite of tools to allow programmers to identify exactly how much precision is required for each operation in their program. This tool allows programmers to both verify that enough precision is available, but more importantly find cases where extra precision could be eliminated to allow the program to use less memory, computer time, or energy. These tools use advanced binary modification techniques to allow the analysis of actual optimized code. The system, called Craft, has been applied to a number of benchmarks and real applications.« less

Benchmarking infrastructure for mutation text mining

PubMed Central

2014-01-01

Background Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation text mining systems. Results We propose a community-oriented annotation and benchmarking infrastructure to support development, testing, benchmarking, and comparison of mutation text mining systems. The design is based on semantic standards, where RDF is used to represent annotations, an OWL ontology provides an extensible schema for the data and SPARQL is used to compute various performance metrics, so that in many cases no programming is needed to analyze results from a text mining system. While large benchmark corpora for biological entity and relation extraction are focused mostly on genes, proteins, diseases, and species, our benchmarking infrastructure fills the gap for mutation information. The core infrastructure comprises (1) an ontology for modelling annotations, (2) SPARQL queries for computing performance metrics, and (3) a sizeable collection of manually curated documents, that can support mutation grounding and mutation impact extraction experiments. Conclusion We have developed the principal infrastructure for the benchmarking of mutation text mining tasks. The use of RDF and OWL as the representation for corpora ensures extensibility. The infrastructure is suitable for out-of-the-box use in several important scenarios and is ready, in its current state, for initial community adoption. PMID:24568600

Benchmarking infrastructure for mutation text mining.

PubMed

Klein, Artjom; Riazanov, Alexandre; Hindle, Matthew M; Baker, Christopher Jo

2014-02-25

Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation text mining systems. We propose a community-oriented annotation and benchmarking infrastructure to support development, testing, benchmarking, and comparison of mutation text mining systems. The design is based on semantic standards, where RDF is used to represent annotations, an OWL ontology provides an extensible schema for the data and SPARQL is used to compute various performance metrics, so that in many cases no programming is needed to analyze results from a text mining system. While large benchmark corpora for biological entity and relation extraction are focused mostly on genes, proteins, diseases, and species, our benchmarking infrastructure fills the gap for mutation information. The core infrastructure comprises (1) an ontology for modelling annotations, (2) SPARQL queries for computing performance metrics, and (3) a sizeable collection of manually curated documents, that can support mutation grounding and mutation impact extraction experiments. We have developed the principal infrastructure for the benchmarking of mutation text mining tasks. The use of RDF and OWL as the representation for corpora ensures extensibility. The infrastructure is suitable for out-of-the-box use in several important scenarios and is ready, in its current state, for initial community adoption.

BACT Simulation User Guide (Version 7.0)

NASA Technical Reports Server (NTRS)

Waszak, Martin R.

1997-01-01

This report documents the structure and operation of a simulation model of the Benchmark Active Control Technology (BACT) Wind-Tunnel Model. The BACT system was designed, built, and tested at NASA Langley Research Center as part of the Benchmark Models Program and was developed to perform wind-tunnel experiments to obtain benchmark quality data to validate computational fluid dynamics and computational aeroelasticity codes, to verify the accuracy of current aeroservoelasticity design and analysis tools, and to provide an active controls testbed for evaluating new and innovative control algorithms for flutter suppression and gust load alleviation. The BACT system has been especially valuable as a control system testbed.

Deterministically estimated fission source distributions for Monte Carlo k-eigenvalue problems

DOE PAGES

Biondo, Elliott D.; Davidson, Gregory G.; Pandya, Tara M.; ...

2018-04-30

The standard Monte Carlo (MC) k-eigenvalue algorithm involves iteratively converging the fission source distribution using a series of potentially time-consuming inactive cycles before quantities of interest can be tallied. One strategy for reducing the computational time requirements of these inactive cycles is the Sourcerer method, in which a deterministic eigenvalue calculation is performed to obtain an improved initial guess for the fission source distribution. This method has been implemented in the Exnihilo software suite within SCALE using the SPNSPN or SNSN solvers in Denovo and the Shift MC code. The efficacy of this method is assessed with different Denovo solutionmore » parameters for a series of typical k-eigenvalue problems including small criticality benchmarks, full-core reactors, and a fuel cask. Here it is found that, in most cases, when a large number of histories per cycle are required to obtain a detailed flux distribution, the Sourcerer method can be used to reduce the computational time requirements of the inactive cycles.« less

Potential of minicomputer/array-processor system for nonlinear finite-element analysis

NASA Technical Reports Server (NTRS)

Strohkorb, G. A.; Noor, A. K.

1983-01-01

The potential of using a minicomputer/array-processor system for the efficient solution of large-scale, nonlinear, finite-element problems is studied. A Prime 750 is used as the host computer, and a software simulator residing on the Prime is employed to assess the performance of the Floating Point Systems AP-120B array processor. Major hardware characteristics of the system such as virtual memory and parallel and pipeline processing are reviewed, and the interplay between various hardware components is examined. Effective use of the minicomputer/array-processor system for nonlinear analysis requires the following: (1) proper selection of the computational procedure and the capability to vectorize the numerical algorithms; (2) reduction of input-output operations; and (3) overlapping host and array-processor operations. A detailed discussion is given of techniques to accomplish each of these tasks. Two benchmark problems with 1715 and 3230 degrees of freedom, respectively, are selected to measure the anticipated gain in speed obtained by using the proposed algorithms on the array processor.

Deterministically estimated fission source distributions for Monte Carlo k-eigenvalue problems

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

Biondo, Elliott D.; Davidson, Gregory G.; Pandya, Tara M.

The standard Monte Carlo (MC) k-eigenvalue algorithm involves iteratively converging the fission source distribution using a series of potentially time-consuming inactive cycles before quantities of interest can be tallied. One strategy for reducing the computational time requirements of these inactive cycles is the Sourcerer method, in which a deterministic eigenvalue calculation is performed to obtain an improved initial guess for the fission source distribution. This method has been implemented in the Exnihilo software suite within SCALE using the SPNSPN or SNSN solvers in Denovo and the Shift MC code. The efficacy of this method is assessed with different Denovo solutionmore » parameters for a series of typical k-eigenvalue problems including small criticality benchmarks, full-core reactors, and a fuel cask. Here it is found that, in most cases, when a large number of histories per cycle are required to obtain a detailed flux distribution, the Sourcerer method can be used to reduce the computational time requirements of the inactive cycles.« less

Improved Ant Colony Clustering Algorithm and Its Performance Study

PubMed Central

Gao, Wei

2016-01-01

Clustering analysis is used in many disciplines and applications; it is an important tool that descriptively identifies homogeneous groups of objects based on attribute values. The ant colony clustering algorithm is a swarm-intelligent method used for clustering problems that is inspired by the behavior of ant colonies that cluster their corpses and sort their larvae. A new abstraction ant colony clustering algorithm using a data combination mechanism is proposed to improve the computational efficiency and accuracy of the ant colony clustering algorithm. The abstraction ant colony clustering algorithm is used to cluster benchmark problems, and its performance is compared with the ant colony clustering algorithm and other methods used in existing literature. Based on similar computational difficulties and complexities, the results show that the abstraction ant colony clustering algorithm produces results that are not only more accurate but also more efficiently determined than the ant colony clustering algorithm and the other methods. Thus, the abstraction ant colony clustering algorithm can be used for efficient multivariate data clustering. PMID:26839533

Benchmarking a Visual-Basic based multi-component one-dimensional reactive transport modeling tool

NASA Astrophysics Data System (ADS)

Torlapati, Jagadish; Prabhakar Clement, T.

2013-01-01

We present the details of a comprehensive numerical modeling tool, RT1D, which can be used for simulating biochemical and geochemical reactive transport problems. The code can be run within the standard Microsoft EXCEL Visual Basic platform, and it does not require any additional software tools. The code can be easily adapted by others for simulating different types of laboratory-scale reactive transport experiments. We illustrate the capabilities of the tool by solving five benchmark problems with varying levels of reaction complexity. These literature-derived benchmarks are used to highlight the versatility of the code for solving a variety of practical reactive transport problems. The benchmarks are described in detail to provide a comprehensive database, which can be used by model developers to test other numerical codes. The VBA code presented in the study is a practical tool that can be used by laboratory researchers for analyzing both batch and column datasets within an EXCEL platform.

Critical Assessment of Metagenome Interpretation – a benchmark of computational metagenomics software

PubMed Central

Sczyrba, Alexander; Hofmann, Peter; Belmann, Peter; Koslicki, David; Janssen, Stefan; Dröge, Johannes; Gregor, Ivan; Majda, Stephan; Fiedler, Jessika; Dahms, Eik; Bremges, Andreas; Fritz, Adrian; Garrido-Oter, Ruben; Jørgensen, Tue Sparholt; Shapiro, Nicole; Blood, Philip D.; Gurevich, Alexey; Bai, Yang; Turaev, Dmitrij; DeMaere, Matthew Z.; Chikhi, Rayan; Nagarajan, Niranjan; Quince, Christopher; Meyer, Fernando; Balvočiūtė, Monika; Hansen, Lars Hestbjerg; Sørensen, Søren J.; Chia, Burton K. H.; Denis, Bertrand; Froula, Jeff L.; Wang, Zhong; Egan, Robert; Kang, Dongwan Don; Cook, Jeffrey J.; Deltel, Charles; Beckstette, Michael; Lemaitre, Claire; Peterlongo, Pierre; Rizk, Guillaume; Lavenier, Dominique; Wu, Yu-Wei; Singer, Steven W.; Jain, Chirag; Strous, Marc; Klingenberg, Heiner; Meinicke, Peter; Barton, Michael; Lingner, Thomas; Lin, Hsin-Hung; Liao, Yu-Chieh; Silva, Genivaldo Gueiros Z.; Cuevas, Daniel A.; Edwards, Robert A.; Saha, Surya; Piro, Vitor C.; Renard, Bernhard Y.; Pop, Mihai; Klenk, Hans-Peter; Göker, Markus; Kyrpides, Nikos C.; Woyke, Tanja; Vorholt, Julia A.; Schulze-Lefert, Paul; Rubin, Edward M.; Darling, Aaron E.; Rattei, Thomas; McHardy, Alice C.

2018-01-01

In metagenome analysis, computational methods for assembly, taxonomic profiling and binning are key components facilitating downstream biological data interpretation. However, a lack of consensus about benchmarking datasets and evaluation metrics complicates proper performance assessment. The Critical Assessment of Metagenome Interpretation (CAMI) challenge has engaged the global developer community to benchmark their programs on datasets of unprecedented complexity and realism. Benchmark metagenomes were generated from ~700 newly sequenced microorganisms and ~600 novel viruses and plasmids, including genomes with varying degrees of relatedness to each other and to publicly available ones and representing common experimental setups. Across all datasets, assembly and genome binning programs performed well for species represented by individual genomes, while performance was substantially affected by the presence of related strains. Taxonomic profiling and binning programs were proficient at high taxonomic ranks, with a notable performance decrease below the family level. Parameter settings substantially impacted performances, underscoring the importance of program reproducibility. While highlighting current challenges in computational metagenomics, the CAMI results provide a roadmap for software selection to answer specific research questions. PMID:28967888

Introduction to the IWA task group on biofilm modeling.

PubMed

Noguera, D R; Morgenroth, E

2004-01-01

An International Water Association (IWA) Task Group on Biofilm Modeling was created with the purpose of comparatively evaluating different biofilm modeling approaches. The task group developed three benchmark problems for this comparison, and used a diversity of modeling techniques that included analytical, pseudo-analytical, and numerical solutions to the biofilm problems. Models in one, two, and three dimensional domains were also compared. The first benchmark problem (BM1) described a monospecies biofilm growing in a completely mixed reactor environment and had the purpose of comparing the ability of the models to predict substrate fluxes and concentrations for a biofilm system of fixed total biomass and fixed biomass density. The second problem (BM2) represented a situation in which substrate mass transport by convection was influenced by the hydrodynamic conditions of the liquid in contact with the biofilm. The third problem (BM3) was designed to compare the ability of the models to simulate multispecies and multisubstrate biofilms. These three benchmark problems allowed identification of the specific advantages and disadvantages of each modeling approach. A detailed presentation of the comparative analyses for each problem is provided elsewhere in these proceedings.

A coarse-grid projection method for accelerating incompressible flow computations

NASA Astrophysics Data System (ADS)

San, Omer; Staples, Anne E.

2013-01-01

We present a coarse-grid projection (CGP) method for accelerating incompressible flow computations, which is applicable to methods involving Poisson equations as incompressibility constraints. The CGP methodology is a modular approach that facilitates data transfer with simple interpolations and uses black-box solvers for the Poisson and advection-diffusion equations in the flow solver. After solving the Poisson equation on a coarsened grid, an interpolation scheme is used to obtain the fine data for subsequent time stepping on the full grid. A particular version of the method is applied here to the vorticity-stream function, primitive variable, and vorticity-velocity formulations of incompressible Navier-Stokes equations. We compute several benchmark flow problems on two-dimensional Cartesian and non-Cartesian grids, as well as a three-dimensional flow problem. The method is found to accelerate these computations while retaining a level of accuracy close to that of the fine resolution field, which is significantly better than the accuracy obtained for a similar computation performed solely using a coarse grid. A linear acceleration rate is obtained for all the cases we consider due to the linear-cost elliptic Poisson solver used, with reduction factors in computational time between 2 and 42. The computational savings are larger when a suboptimal Poisson solver is used. We also find that the computational savings increase with increasing distortion ratio on non-Cartesian grids, making the CGP method a useful tool for accelerating generalized curvilinear incompressible flow solvers.

BENCHMARK DOSE TECHNICAL GUIDANCE DOCUMENT ...

EPA Pesticide Factsheets

The purpose of this document is to provide guidance for the Agency on the application of the benchmark dose approach in determining the point of departure (POD) for health effects data, whether a linear or nonlinear low dose extrapolation is used. The guidance includes discussion on computation of benchmark doses and benchmark concentrations (BMDs and BMCs) and their lower confidence limits, data requirements, dose-response analysis, and reporting requirements. This guidance is based on today's knowledge and understanding, and on experience gained in using this approach.

Benchmark Problems for Space Mission Formation Flying

NASA Technical Reports Server (NTRS)

Carpenter, J. Russell; Leitner, Jesse A.; Folta, David C.; Burns, Richard

2003-01-01

To provide a high-level focus to distributed space system flight dynamics and control research, several benchmark problems are suggested for space mission formation flying. The problems cover formation flying in low altitude, near-circular Earth orbit, high altitude, highly elliptical Earth orbits, and large amplitude lissajous trajectories about co-linear libration points of the Sun-Earth/Moon system. These problems are not specific to any current or proposed mission, but instead are intended to capture high-level features that would be generic to many similar missions that are of interest to various agencies.

Simplified Numerical Analysis of ECT Probe - Eddy Current Benchmark Problem 3

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

Sikora, R.; Chady, T.; Gratkowski, S.

2005-04-09

In this paper a third eddy current benchmark problem is considered. The objective of the benchmark is to determine optimal operating frequency and size of the pancake coil designated for testing tubes made of Inconel. It can be achieved by maximization of the change in impedance of the coil due to a flaw. Approximation functions of the probe (coil) characteristic were developed and used in order to reduce number of required calculations. It results in significant speed up of the optimization process. An optimal testing frequency and size of the probe were achieved as a final result of the calculation.

Benchmarking Gas Path Diagnostic Methods: A Public Approach

NASA Technical Reports Server (NTRS)

Simon, Donald L.; Bird, Jeff; Davison, Craig; Volponi, Al; Iverson, R. Eugene

2008-01-01

Recent technology reviews have identified the need for objective assessments of engine health management (EHM) technology. The need is two-fold: technology developers require relevant data and problems to design and validate new algorithms and techniques while engine system integrators and operators need practical tools to direct development and then evaluate the effectiveness of proposed solutions. This paper presents a publicly available gas path diagnostic benchmark problem that has been developed by the Propulsion and Power Systems Panel of The Technical Cooperation Program (TTCP) to help address these needs. The problem is coded in MATLAB (The MathWorks, Inc.) and coupled with a non-linear turbofan engine simulation to produce "snap-shot" measurements, with relevant noise levels, as if collected from a fleet of engines over their lifetime of use. Each engine within the fleet will experience unique operating and deterioration profiles, and may encounter randomly occurring relevant gas path faults including sensor, actuator and component faults. The challenge to the EHM community is to develop gas path diagnostic algorithms to reliably perform fault detection and isolation. An example solution to the benchmark problem is provided along with associated evaluation metrics. A plan is presented to disseminate this benchmark problem to the engine health management technical community and invite technology solutions.

Multi-Complementary Model for Long-Term Tracking

PubMed Central

Zhang, Deng; Zhang, Junchang; Xia, Chenyang

2018-01-01

In recent years, video target tracking algorithms have been widely used. However, many tracking algorithms do not achieve satisfactory performance, especially when dealing with problems such as object occlusions, background clutters, motion blur, low illumination color images, and sudden illumination changes in real scenes. In this paper, we incorporate an object model based on contour information into a Staple tracker that combines the correlation filter model and color model to greatly improve the tracking robustness. Since each model is responsible for tracking specific features, the three complementary models combine for more robust tracking. In addition, we propose an efficient object detection model with contour and color histogram features, which has good detection performance and better detection efficiency compared to the traditional target detection algorithm. Finally, we optimize the traditional scale calculation, which greatly improves the tracking execution speed. We evaluate our tracker on the Object Tracking Benchmarks 2013 (OTB-13) and Object Tracking Benchmarks 2015 (OTB-15) benchmark datasets. With the OTB-13 benchmark datasets, our algorithm is improved by 4.8%, 9.6%, and 10.9% on the success plots of OPE, TRE and SRE, respectively, in contrast to another classic LCT (Long-term Correlation Tracking) algorithm. On the OTB-15 benchmark datasets, when compared with the LCT algorithm, our algorithm achieves 10.4%, 12.5%, and 16.1% improvement on the success plots of OPE, TRE, and SRE, respectively. At the same time, it needs to be emphasized that, due to the high computational efficiency of the color model and the object detection model using efficient data structures, and the speed advantage of the correlation filters, our tracking algorithm could still achieve good tracking speed. PMID:29425170

A study of workstation computational performance for real-time flight simulation

NASA Technical Reports Server (NTRS)

Maddalon, Jeffrey M.; Cleveland, Jeff I., II

1995-01-01

With recent advances in microprocessor technology, some have suggested that modern workstations provide enough computational power to properly operate a real-time simulation. This paper presents the results of a computational benchmark, based on actual real-time flight simulation code used at Langley Research Center, which was executed on various workstation-class machines. The benchmark was executed on different machines from several companies including: CONVEX Computer Corporation, Cray Research, Digital Equipment Corporation, Hewlett-Packard, Intel, International Business Machines, Silicon Graphics, and Sun Microsystems. The machines are compared by their execution speed, computational accuracy, and porting effort. The results of this study show that the raw computational power needed for real-time simulation is now offered by workstations.

Application of a screening method in assessing occupational safety and health of computer workstations.

PubMed

Niskanen, Toivo; Lehtelä, Jouni; Länsikallio, Riina

2014-01-01

Employers and workers need concrete guidance to plan and implement changes in the ergonomics of computer workstations. The Näppärä method is a screening tool for identifying problems requiring further assessment and corrective actions. The aim of this study was to assess the work of occupational safety and health (OSH) government inspectors who used Näppärä as part of their OSH enforcement inspections (430 assessments) related to computer work. The modifications in workstation ergonomics involved mainly adjustments to the screen, mouse, keyboard, forearm supports, and chair. One output of the assessment is an index indicating the percentage of compliance items. This method can be considered as exposure assessment and ergonomics intervention used as a benchmark for the level of ergonomics. Future research can examine whether the effectiveness of participatory ergonomics interventions should be investigated with Näppärä.

Review and standardization of cell phone exposure calculations using the SAM phantom and anatomically correct head models.

PubMed

Beard, Brian B; Kainz, Wolfgang

2004-10-13

We reviewed articles using computational RF dosimetry to compare the Specific Anthropomorphic Mannequin (SAM) to anatomically correct models of the human head. Published conclusions based on such comparisons have varied widely. We looked for reasons that might cause apparently similar comparisons to produce dissimilar results. We also looked at the information needed to adequately compare the results of computational RF dosimetry studies. We concluded studies were not comparable because of differences in definitions, models, and methodology. Therefore we propose a protocol, developed by an IEEE standards group, as an initial step in alleviating this problem. The protocol calls for a benchmark validation study comparing the SAM phantom to two anatomically correct models of the human head. It also establishes common definitions and reporting requirements that will increase the comparability of all computational RF dosimetry studies of the human head.

NASA Astrophysics Data System (ADS)

Knosp, B.; Neely, S.; Zimdars, P.; Mills, B.; Vance, N.

2007-12-01

The Microwave Limb Sounder (MLS) Science Computing Facility (SCF) stores over 50 terabytes of data, has over 240 computer processing hosts, and 64 users from around the world. These resources are spread over three primary geographical locations - the Jet Propulsion Laboratory (JPL), Raytheon RIS, and New Mexico Institute of Mining and Technology (NMT). A need for a grid network system was identified and defined to solve the problem of users competing for finite, and increasingly scarce, MLS SCF computing resources. Using Sun's Grid Engine software, a grid network was successfully created in a development environment that connected the JPL and Raytheon sites, established master and slave hosts, and demonstrated that transfer queues for jobs can work among multiple clusters in the same grid network. This poster will first describe MLS SCF resources and the lessons that were learned in the design and development phase of this project. It will then go on to discuss the test environment and plans for deployment by highlighting benchmarks and user experiences.

Review and standardization of cell phone exposure calculations using the SAM phantom and anatomically correct head models

PubMed Central

Beard, Brian B; Kainz, Wolfgang

2004-01-01

We reviewed articles using computational RF dosimetry to compare the Specific Anthropomorphic Mannequin (SAM) to anatomically correct models of the human head. Published conclusions based on such comparisons have varied widely. We looked for reasons that might cause apparently similar comparisons to produce dissimilar results. We also looked at the information needed to adequately compare the results of computational RF dosimetry studies. We concluded studies were not comparable because of differences in definitions, models, and methodology. Therefore we propose a protocol, developed by an IEEE standards group, as an initial step in alleviating this problem. The protocol calls for a benchmark validation study comparing the SAM phantom to two anatomically correct models of the human head. It also establishes common definitions and reporting requirements that will increase the comparability of all computational RF dosimetry studies of the human head. PMID:15482601

Firefly algorithm for cardinality constrained mean-variance portfolio optimization problem with entropy diversity constraint.

PubMed

Bacanin, Nebojsa; Tuba, Milan

2014-01-01

Portfolio optimization (selection) problem is an important and hard optimization problem that, with the addition of necessary realistic constraints, becomes computationally intractable. Nature-inspired metaheuristics are appropriate for solving such problems; however, literature review shows that there are very few applications of nature-inspired metaheuristics to portfolio optimization problem. This is especially true for swarm intelligence algorithms which represent the newer branch of nature-inspired algorithms. No application of any swarm intelligence metaheuristics to cardinality constrained mean-variance (CCMV) portfolio problem with entropy constraint was found in the literature. This paper introduces modified firefly algorithm (FA) for the CCMV portfolio model with entropy constraint. Firefly algorithm is one of the latest, very successful swarm intelligence algorithm; however, it exhibits some deficiencies when applied to constrained problems. To overcome lack of exploration power during early iterations, we modified the algorithm and tested it on standard portfolio benchmark data sets used in the literature. Our proposed modified firefly algorithm proved to be better than other state-of-the-art algorithms, while introduction of entropy diversity constraint further improved results.

Firefly Algorithm for Cardinality Constrained Mean-Variance Portfolio Optimization Problem with Entropy Diversity Constraint

PubMed Central

2014-01-01

Portfolio optimization (selection) problem is an important and hard optimization problem that, with the addition of necessary realistic constraints, becomes computationally intractable. Nature-inspired metaheuristics are appropriate for solving such problems; however, literature review shows that there are very few applications of nature-inspired metaheuristics to portfolio optimization problem. This is especially true for swarm intelligence algorithms which represent the newer branch of nature-inspired algorithms. No application of any swarm intelligence metaheuristics to cardinality constrained mean-variance (CCMV) portfolio problem with entropy constraint was found in the literature. This paper introduces modified firefly algorithm (FA) for the CCMV portfolio model with entropy constraint. Firefly algorithm is one of the latest, very successful swarm intelligence algorithm; however, it exhibits some deficiencies when applied to constrained problems. To overcome lack of exploration power during early iterations, we modified the algorithm and tested it on standard portfolio benchmark data sets used in the literature. Our proposed modified firefly algorithm proved to be better than other state-of-the-art algorithms, while introduction of entropy diversity constraint further improved results. PMID:24991645

Analysing the performance of personal computers based on Intel microprocessors for sequence aligning bioinformatics applications.

PubMed

Nair, Pradeep S; John, Eugene B

2007-01-01

Aligning specific sequences against a very large number of other sequences is a central aspect of bioinformatics. With the widespread availability of personal computers in biology laboratories, sequence alignment is now often performed locally. This makes it necessary to analyse the performance of personal computers for sequence aligning bioinformatics benchmarks. In this paper, we analyse the performance of a personal computer for the popular BLAST and FASTA sequence alignment suites. Results indicate that these benchmarks have a large number of recurring operations and use memory operations extensively. It seems that the performance can be improved with a bigger L1-cache.

Evaluation of Cache-based Superscalar and Cacheless Vector Architectures for Scientific Computations

NASA Technical Reports Server (NTRS)

Oliker, Leonid; Carter, Jonathan; Shalf, John; Skinner, David; Ethier, Stephane; Biswas, Rupak; Djomehri, Jahed; VanderWijngaart, Rob

2003-01-01

The growing gap between sustained and peak performance for scientific applications has become a well-known problem in high performance computing. The recent development of parallel vector systems offers the potential to bridge this gap for a significant number of computational science codes and deliver a substantial increase in computing capabilities. This paper examines the intranode performance of the NEC SX6 vector processor and the cache-based IBM Power3/4 superscalar architectures across a number of key scientific computing areas. First, we present the performance of a microbenchmark suite that examines a full spectrum of low-level machine characteristics. Next, we study the behavior of the NAS Parallel Benchmarks using some simple optimizations. Finally, we evaluate the perfor- mance of several numerical codes from key scientific computing domains. Overall results demonstrate that the SX6 achieves high performance on a large fraction of our application suite and in many cases significantly outperforms the RISC-based architectures. However, certain classes of applications are not easily amenable to vectorization and would likely require extensive reengineering of both algorithm and implementation to utilize the SX6 effectively.

Implementing Cognitive Strategy Instruction across the School: The Benchmark Manual for Teachers.

ERIC Educational Resources Information Center

Gaskins, Irene; Elliot, Thorne

Improving reading instruction has been the primary focus at the Benchmark School in Media, Pennsylvania. This book describes the various phases of Benchmark's development of a program to create strategic learners, thinkers, and problem solvers across the curriculum. The goal is to provide teachers and administrators with a handbook that can be…

Adaptive unified continuum FEM modeling of a 3D FSI benchmark problem.

PubMed

Jansson, Johan; Degirmenci, Niyazi Cem; Hoffman, Johan

2017-09-01

In this paper, we address a 3D fluid-structure interaction benchmark problem that represents important characteristics of biomedical modeling. We present a goal-oriented adaptive finite element methodology for incompressible fluid-structure interaction based on a streamline diffusion-type stabilization of the balance equations for mass and momentum for the entire continuum in the domain, which is implemented in the Unicorn/FEniCS software framework. A phase marker function and its corresponding transport equation are introduced to select the constitutive law, where the mesh tracks the discontinuous fluid-structure interface. This results in a unified simulation method for fluids and structures. We present detailed results for the benchmark problem compared with experiments, together with a mesh convergence study. Copyright © 2016 John Wiley & Sons, Ltd.

Study of blood flow in several benchmark micro-channels using a two-fluid approach

PubMed Central

Wu, Wei-Tao; Yang, Fang; Antaki, James F.; Aubry, Nadine; Massoudi, Mehrdad

2015-01-01

It is known that in a vessel whose characteristic dimension (e.g., its diameter) is in the range of 20 to 500 microns, blood behaves as a non-Newtonian fluid, exhibiting complex phenomena, such as shear-thinning, stress relaxation, and also multi-component behaviors, such as the Fahraeus effect, plasma-skimming, etc. For describing these non-Newtonian and multi-component characteristics of blood, using the framework of mixture theory, a two-fluid model is applied, where the plasma is treated as a Newtonian fluid and the red blood cells (RBCs) are treated as shear-thinning fluid. A computational fluid dynamic (CFD) simulation incorporating the constitutive model was implemented using OpenFOAM® in which benchmark problems including a sudden expansion and various driven slots and crevices were studied numerically. The numerical results exhibited good agreement with the experimental observations with respect to both the velocity field and the volume fraction distribution of RBCs. PMID:26240438

Moving template analysis of crack growth. 1: Procedure development

NASA Astrophysics Data System (ADS)

Padovan, Joe; Guo, Y. H.

1994-06-01

Based on a moving template procedure, this two part series will develop a method to follow the crack tip physics in a self-adaptive manner which provides a uniformly accurate prediction of crack growth. For multiple crack environments, this is achieved by attaching a moving template to each crack tip. The templates are each individually oriented to follow the associated growth orientation and rate. In this part, the essentials of the procedure are derived for application to fatigue crack environments. Overall the scheme derived possesses several hierarchical levels, i.e. the global model, the interpolatively tied moving template, and a multilevel element death option to simulate the crack wake. To speed up computation, the hierarchical polytree scheme is used to reorganize the global stiffness inversion process. In addition to developing the various features of the scheme, the accuracy of predictions for various crack lengths is also benchmarked. Part 2 extends the scheme to multiple crack problems. Extensive benchmarking is also presented to verify the scheme.

Benchmarking: contexts and details matter.

PubMed

Zheng, Siyuan

2017-07-05

Benchmarking is an essential step in the development of computational tools. We take this opportunity to pitch in our opinions on tool benchmarking, in light of two correspondence articles published in Genome Biology.Please see related Li et al. and Newman et al. correspondence articles: www.dx.doi.org/10.1186/s13059-017-1256-5 and www.dx.doi.org/10.1186/s13059-017-1257-4.

Biased ART: a neural architecture that shifts attention toward previously disregarded features following an incorrect prediction.

PubMed

Carpenter, Gail A; Gaddam, Sai Chaitanya

2010-04-01

Memories in Adaptive Resonance Theory (ART) networks are based on matched patterns that focus attention on those portions of bottom-up inputs that match active top-down expectations. While this learning strategy has proved successful for both brain models and applications, computational examples show that attention to early critical features may later distort memory representations during online fast learning. For supervised learning, biased ARTMAP (bARTMAP) solves the problem of over-emphasis on early critical features by directing attention away from previously attended features after the system makes a predictive error. Small-scale, hand-computed analog and binary examples illustrate key model dynamics. Two-dimensional simulation examples demonstrate the evolution of bARTMAP memories as they are learned online. Benchmark simulations show that featural biasing also improves performance on large-scale examples. One example, which predicts movie genres and is based, in part, on the Netflix Prize database, was developed for this project. Both first principles and consistent performance improvements on all simulation studies suggest that featural biasing should be incorporated by default in all ARTMAP systems. Benchmark datasets and bARTMAP code are available from the CNS Technology Lab Website: http://techlab.bu.edu/bART/. Copyright 2009 Elsevier Ltd. All rights reserved.

A broad-group cross-section library based on ENDF/B-VII.0 for fast neutron dosimetry Applications

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

Alpan, F.A.

2011-07-01

A new ENDF/B-VII.0-based coupled 44-neutron, 20-gamma-ray-group cross-section library was developed to investigate the latest evaluated nuclear data file (ENDF) ,in comparison to ENDF/B-VI.3 used in BUGLE-96, as well as to generate an objective-specific library. The objectives selected for this work consisted of dosimetry calculations for in-vessel and ex-vessel reactor locations, iron atom displacement calculations for reactor internals and pressure vessel, and {sup 58}Ni(n,{gamma}) calculation that is important for gas generation in the baffle plate. The new library was generated based on the contribution and point-wise cross-section-driven (CPXSD) methodology and was applied to one of the most widely used benchmarks, themore » Oak Ridge National Laboratory Pool Critical Assembly benchmark problem. In addition to the new library, BUGLE-96 and an ENDF/B-VII.0-based coupled 47-neutron, 20-gamma-ray-group cross-section library was generated and used with both SNLRML and IRDF dosimetry cross sections to compute reaction rates. All reaction rates computed by the multigroup libraries are within {+-} 20 % of measurement data and meet the U. S. Nuclear Regulatory Commission acceptance criterion for reactor vessel neutron exposure evaluations specified in Regulatory Guide 1.190. (authors)« less

Benchmarking of Neutron Production of Heavy-Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Benchmarking of Heavy Ion Transport Codes

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

Remec, Igor; Ronningen, Reginald M.; Heilbronn, Lawrence

Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in designing and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondary neutron production. Results are encouraging; however, further improvements in models andmore » codes and additional benchmarking are required.« less

Sequoia Messaging Rate Benchmark

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

Friedley, Andrew

2008-01-22

The purpose of this benchmark is to measure the maximal message rate of a single compute node. The first num_cores ranks are expected to reside on the 'core' compute node for which message rate is being tested. After that, the next num_nbors ranks are neighbors for the first core rank, the next set of num_nbors ranks are neighbors for the second core rank, and so on. For example, testing an 8-core node (num_cores = 8) with 4 neighbors (num_nbors = 4) requires 8 + 8 * 4 - 40 ranks. The first 8 of those 40 ranks are expected tomore » be on the 'core' node being benchmarked, while the rest of the ranks are on separate nodes.« less

Quantum annealing for the number-partitioning problem using a tunable spin glass of ions

PubMed Central

Graß, Tobias; Raventós, David; Juliá-Díaz, Bruno; Gogolin, Christian; Lewenstein, Maciej

2016-01-01

Exploiting quantum properties to outperform classical ways of information processing is an outstanding goal of modern physics. A promising route is quantum simulation, which aims at implementing relevant and computationally hard problems in controllable quantum systems. Here we demonstrate that in a trapped ion setup, with present day technology, it is possible to realize a spin model of the Mattis-type that exhibits spin glass phases. Our method produces the glassy behaviour without the need for any disorder potential, just by controlling the detuning of the spin-phonon coupling. Applying a transverse field, the system can be used to benchmark quantum annealing strategies which aim at reaching the ground state of the spin glass starting from the paramagnetic phase. In the vicinity of a phonon resonance, the problem maps onto number partitioning, and instances which are difficult to address classically can be implemented. PMID:27230802

Resource-constrained scheduling with hard due windows and rejection penalties

NASA Astrophysics Data System (ADS)

Garcia, Christopher

2016-09-01

This work studies a scheduling problem where each job must be either accepted and scheduled to complete within its specified due window, or rejected altogether. Each job has a certain processing time and contributes a certain profit if accepted or penalty cost if rejected. There is a set of renewable resources, and no resource limit can be exceeded at any time. Each job requires a certain amount of each resource when processed, and the objective is to maximize total profit. A mixed-integer programming formulation and three approximation algorithms are presented: a priority rule heuristic, an algorithm based on the metaheuristic for randomized priority search and an evolutionary algorithm. Computational experiments comparing these four solution methods were performed on a set of generated benchmark problems covering a wide range of problem characteristics. The evolutionary algorithm outperformed the other methods in most cases, often significantly, and never significantly underperformed any method.

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.

The Edge-Disjoint Path Problem on Random Graphs by Message-Passing.

PubMed

Altarelli, Fabrizio; Braunstein, Alfredo; Dall'Asta, Luca; De Bacco, Caterina; Franz, Silvio

2015-01-01

We present a message-passing algorithm to solve a series of edge-disjoint path problems on graphs based on the zero-temperature cavity equations. Edge-disjoint paths problems are important in the general context of routing, that can be defined by incorporating under a unique framework both traffic optimization and total path length minimization. The computation of the cavity equations can be performed efficiently by exploiting a mapping of a generalized edge-disjoint path problem on a star graph onto a weighted maximum matching problem. We perform extensive numerical simulations on random graphs of various types to test the performance both in terms of path length minimization and maximization of the number of accommodated paths. In addition, we test the performance on benchmark instances on various graphs by comparison with state-of-the-art algorithms and results found in the literature. Our message-passing algorithm always outperforms the others in terms of the number of accommodated paths when considering non trivial instances (otherwise it gives the same trivial results). Remarkably, the largest improvement in performance with respect to the other methods employed is found in the case of benchmarks with meshes, where the validity hypothesis behind message-passing is expected to worsen. In these cases, even though the exact message-passing equations do not converge, by introducing a reinforcement parameter to force convergence towards a sub optimal solution, we were able to always outperform the other algorithms with a peak of 27% performance improvement in terms of accommodated paths. On random graphs, we numerically observe two separated regimes: one in which all paths can be accommodated and one in which this is not possible. We also investigate the behavior of both the number of paths to be accommodated and their minimum total length.

The Edge-Disjoint Path Problem on Random Graphs by Message-Passing

PubMed Central

2015-01-01

We present a message-passing algorithm to solve a series of edge-disjoint path problems on graphs based on the zero-temperature cavity equations. Edge-disjoint paths problems are important in the general context of routing, that can be defined by incorporating under a unique framework both traffic optimization and total path length minimization. The computation of the cavity equations can be performed efficiently by exploiting a mapping of a generalized edge-disjoint path problem on a star graph onto a weighted maximum matching problem. We perform extensive numerical simulations on random graphs of various types to test the performance both in terms of path length minimization and maximization of the number of accommodated paths. In addition, we test the performance on benchmark instances on various graphs by comparison with state-of-the-art algorithms and results found in the literature. Our message-passing algorithm always outperforms the others in terms of the number of accommodated paths when considering non trivial instances (otherwise it gives the same trivial results). Remarkably, the largest improvement in performance with respect to the other methods employed is found in the case of benchmarks with meshes, where the validity hypothesis behind message-passing is expected to worsen. In these cases, even though the exact message-passing equations do not converge, by introducing a reinforcement parameter to force convergence towards a sub optimal solution, we were able to always outperform the other algorithms with a peak of 27% performance improvement in terms of accommodated paths. On random graphs, we numerically observe two separated regimes: one in which all paths can be accommodated and one in which this is not possible. We also investigate the behavior of both the number of paths to be accommodated and their minimum total length. PMID:26710102

Reference Solutions for Benchmark Turbulent Flows in Three Dimensions

NASA Technical Reports Server (NTRS)

Diskin, Boris; Thomas, James L.; Pandya, Mohagna J.; Rumsey, Christopher L.

2016-01-01

A grid convergence study is performed to establish benchmark solutions for turbulent flows in three dimensions (3D) in support of turbulence-model verification campaign at the Turbulence Modeling Resource (TMR) website. The three benchmark cases are subsonic flows around a 3D bump and a hemisphere-cylinder configuration and a supersonic internal flow through a square duct. Reference solutions are computed for Reynolds Averaged Navier Stokes equations with the Spalart-Allmaras turbulence model using a linear eddy-viscosity model for the external flows and a nonlinear eddy-viscosity model based on a quadratic constitutive relation for the internal flow. The study involves three widely-used practical computational fluid dynamics codes developed and supported at NASA Langley Research Center: FUN3D, USM3D, and CFL3D. Reference steady-state solutions computed with these three codes on families of consistently refined grids are presented. Grid-to-grid and code-to-code variations are described in detail.

Unstructured Adaptive Meshes: Bad for Your Memory?

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Feng, Hui-Yu; VanderWijngaart, Rob

2003-01-01

This viewgraph presentation explores the need for a NASA Advanced Supercomputing (NAS) parallel benchmark for problems with irregular dynamical memory access. This benchmark is important and necessary because: 1) Problems with localized error source benefit from adaptive nonuniform meshes; 2) Certain machines perform poorly on such problems; 3) Parallel implementation may provide further performance improvement but is difficult. Some examples of problems which use irregular dynamical memory access include: 1) Heat transfer problem; 2) Heat source term; 3) Spectral element method; 4) Base functions; 5) Elemental discrete equations; 6) Global discrete equations. Nonconforming Mesh and Mortar Element Method are covered in greater detail in this presentation.

Accelerating cardiac bidomain simulations using graphics processing units.

PubMed

Neic, A; Liebmann, M; Hoetzl, E; Mitchell, L; Vigmond, E J; Haase, G; Plank, G

2012-08-01

Anatomically realistic and biophysically detailed multiscale computer models of the heart are playing an increasingly important role in advancing our understanding of integrated cardiac function in health and disease. Such detailed simulations, however, are computationally vastly demanding, which is a limiting factor for a wider adoption of in-silico modeling. While current trends in high-performance computing (HPC) hardware promise to alleviate this problem, exploiting the potential of such architectures remains challenging since strongly scalable algorithms are necessitated to reduce execution times. Alternatively, acceleration technologies such as graphics processing units (GPUs) are being considered. While the potential of GPUs has been demonstrated in various applications, benefits in the context of bidomain simulations where large sparse linear systems have to be solved in parallel with advanced numerical techniques are less clear. In this study, the feasibility of multi-GPU bidomain simulations is demonstrated by running strong scalability benchmarks using a state-of-the-art model of rabbit ventricles. The model is spatially discretized using the finite element methods (FEM) on fully unstructured grids. The GPU code is directly derived from a large pre-existing code, the Cardiac Arrhythmia Research Package (CARP), with very minor perturbation of the code base. Overall, bidomain simulations were sped up by a factor of 11.8 to 16.3 in benchmarks running on 6-20 GPUs compared to the same number of CPU cores. To match the fastest GPU simulation which engaged 20 GPUs, 476 CPU cores were required on a national supercomputing facility.

Accelerating Cardiac Bidomain Simulations Using Graphics Processing Units

PubMed Central

Neic, Aurel; Liebmann, Manfred; Hoetzl, Elena; Mitchell, Lawrence; Vigmond, Edward J.; Haase, Gundolf

2013-01-01

Anatomically realistic and biophysically detailed multiscale computer models of the heart are playing an increasingly important role in advancing our understanding of integrated cardiac function in health and disease. Such detailed simulations, however, are computationally vastly demanding, which is a limiting factor for a wider adoption of in-silico modeling. While current trends in high-performance computing (HPC) hardware promise to alleviate this problem, exploiting the potential of such architectures remains challenging since strongly scalable algorithms are necessitated to reduce execution times. Alternatively, acceleration technologies such as graphics processing units (GPUs) are being considered. While the potential of GPUs has been demonstrated in various applications, benefits in the context of bidomain simulations where large sparse linear systems have to be solved in parallel with advanced numerical techniques are less clear. In this study, the feasibility of multi-GPU bidomain simulations is demonstrated by running strong scalability benchmarks using a state-of-the-art model of rabbit ventricles. The model is spatially discretized using the finite element methods (FEM) on fully unstructured grids. The GPU code is directly derived from a large pre-existing code, the Cardiac Arrhythmia Research Package (CARP), with very minor perturbation of the code base. Overall, bidomain simulations were sped up by a factor of 11.8 to 16.3 in benchmarks running on 6–20 GPUs compared to the same number of CPU cores. To match the fastest GPU simulation which engaged 20GPUs, 476 CPU cores were required on a national supercomputing facility. PMID:22692867

Dynamic vehicle routing with time windows in theory and practice.

PubMed

Yang, Zhiwei; van Osta, Jan-Paul; van Veen, Barry; van Krevelen, Rick; van Klaveren, Richard; Stam, Andries; Kok, Joost; Bäck, Thomas; Emmerich, Michael

2017-01-01

The vehicle routing problem is a classical combinatorial optimization problem. This work is about a variant of the vehicle routing problem with dynamically changing orders and time windows. In real-world applications often the demands change during operation time. New orders occur and others are canceled. In this case new schedules need to be generated on-the-fly. Online optimization algorithms for dynamical vehicle routing address this problem but so far they do not consider time windows. Moreover, to match the scenarios found in real-world problems adaptations of benchmarks are required. In this paper, a practical problem is modeled based on the procedure of daily routing of a delivery company. New orders by customers are introduced dynamically during the working day and need to be integrated into the schedule. A multiple ant colony algorithm combined with powerful local search procedures is proposed to solve the dynamic vehicle routing problem with time windows. The performance is tested on a new benchmark based on simulations of a working day. The problems are taken from Solomon's benchmarks but a certain percentage of the orders are only revealed to the algorithm during operation time. Different versions of the MACS algorithm are tested and a high performing variant is identified. Finally, the algorithm is tested in situ: In a field study, the algorithm schedules a fleet of cars for a surveillance company. We compare the performance of the algorithm to that of the procedure used by the company and we summarize insights gained from the implementation of the real-world study. The results show that the multiple ant colony algorithm can get a much better solution on the academic benchmark problem and also can be integrated in a real-world environment.

MODFLOW-2000, the U.S. Geological Survey Modular Ground-Water Model--Documentation of the SEAWAT-2000 Version with the Variable-Density Flow Process (VDF) and the Integrated MT3DMS Transport Process (IMT)

USGS Publications Warehouse

Langevin, Christian D.; Shoemaker, W. Barclay; Guo, Weixing

2003-01-01

SEAWAT-2000 is the latest release of the SEAWAT computer program for simulation of three-dimensional, variable-density, transient ground-water flow in porous media. SEAWAT-2000 was designed by combining a modified version of MODFLOW-2000 and MT3DMS into a single computer program. The code was developed using the MODFLOW-2000 concept of a process, which is defined as ?part of the code that solves a fundamental equation by a specified numerical method.? SEAWAT-2000 contains all of the processes distributed with MODFLOW-2000 and also includes the Variable-Density Flow Process (as an alternative to the constant-density Ground-Water Flow Process) and the Integrated MT3DMS Transport Process. Processes may be active or inactive, depending on simulation objectives; however, not all processes are compatible. For example, the Sensitivity and Parameter Estimation Processes are not compatible with the Variable-Density Flow and Integrated MT3DMS Transport Processes. The SEAWAT-2000 computer code was tested with the common variable-density benchmark problems and also with problems representing evaporation from a salt lake and rotation of immiscible fluids.

Molecular simulation of small Knudsen number flows

NASA Astrophysics Data System (ADS)

Fei, Fei; Fan, Jing

2012-11-01

The direct simulation Monte Carlo (DSMC) method is a powerful particle-based method for modeling gas flows. It works well for relatively large Knudsen (Kn) numbers, typically larger than 0.01, but quickly becomes computationally intensive as Kn decreases due to its time step and cell size limitations. An alternative approach was proposed to relax or remove these limitations, based on replacing pairwise collisions with a stochastic model corresponding to the Fokker-Planck equation [J. Comput. Phys., 229, 1077 (2010); J. Fluid Mech., 680, 574 (2011)]. Similar to the DSMC method, the downside of that approach suffers from computationally statistical noise. To solve the problem, a diffusion-based information preservation (D-IP) method has been developed. The main idea is to track the motion of a simulated molecule from the diffusive standpoint, and obtain the flow velocity and temperature through sampling and averaging the IP quantities. To validate the idea and the corresponding model, several benchmark problems with Kn ˜ 10-3-10-4 have been investigated. It is shown that the IP calculations are not only accurate, but also efficient because they make possible using a time step and cell size over an order of magnitude larger than the mean collision time and mean free path, respectively.

Simulations & Measurements of Airframe Noise: A BANC Workshops Perspective

NASA Technical Reports Server (NTRS)

Choudhari, Meelan; Lockard, David

2016-01-01

Airframe noise corresponds to the acoustic radiation due to turbulent flow in the vicinity of airframe components such as high-lift devices and landing gears. Since 2010, the American Institute of Aeronautics and Astronautics has organized an ongoing series of workshops devoted to Benchmark Problems for Airframe Noise Computations (BANC). The BANC workshops are aimed at enabling a systematic progress in the understanding and high-fidelity predictions of airframe noise via collaborative investigations that integrate computational fluid dynamics, computational aeroacoustics, and in depth measurements targeting a selected set of canonical yet realistic configurations that advance the current state-of-the-art in multiple respects. Unique features of the BANC Workshops include: intrinsically multi-disciplinary focus involving both fluid dynamics and aeroacoustics, holistic rather than predictive emphasis, concurrent, long term evolution of experiments and simulations with a powerful interplay between the two, and strongly integrative nature by virtue of multi-team, multi-facility, multiple-entry measurements. This paper illustrates these features in the context of the BANC problem categories and outlines some of the challenges involved and how they were addressed. A brief summary of the BANC effort, including its technical objectives, strategy, and selective outcomes thus far is also included.

MIP models for connected facility location: A theoretical and computational study☆

PubMed Central

Gollowitzer, Stefan; Ljubić, Ivana

2011-01-01

This article comprises the first theoretical and computational study on mixed integer programming (MIP) models for the connected facility location problem (ConFL). ConFL combines facility location and Steiner trees: given a set of customers, a set of potential facility locations and some inter-connection nodes, ConFL searches for the minimum-cost way of assigning each customer to exactly one open facility, and connecting the open facilities via a Steiner tree. The costs needed for building the Steiner tree, facility opening costs and the assignment costs need to be minimized. We model ConFL using seven compact and three mixed integer programming formulations of exponential size. We also show how to transform ConFL into the Steiner arborescence problem. A full hierarchy between the models is provided. For two exponential size models we develop a branch-and-cut algorithm. An extensive computational study is based on two benchmark sets of randomly generated instances with up to 1300 nodes and 115,000 edges. We empirically compare the presented models with respect to the quality of obtained bounds and the corresponding running time. We report optimal values for all but 16 instances for which the obtained gaps are below 0.6%. PMID:25009366

Determining Wheel-Soil Interaction Loads Using a Meshfree Finite Element Approach Assisting Future Missions with Rover Wheel Design

NASA Technical Reports Server (NTRS)

Contreras, Michael T.; Peng, Chia-Yen; Wang, Dongdong; Chen, Jiun-Shyan

2012-01-01

A wheel experiencing sinkage and slippage events poses a high risk to rover missions as evidenced by recent mobility challenges on the Mars Exploration Rover (MER) project. Because several factors contribute to wheel sinkage and slippage conditions such as soil composition, large deformation soil behavior, wheel geometry, nonlinear contact forces, terrain irregularity, etc., there are significant benefits to modeling these events to a sufficient degree of complexity. For the purposes of modeling wheel sinkage and slippage at an engineering scale, meshfree finite element approaches enable simulations that capture sufficient detail of wheel-soil interaction while remaining computationally feasible. This study demonstrates some of the large deformation modeling capability of meshfree methods and the realistic solutions obtained by accounting for the soil material properties. A benchmark wheel-soil interaction problem is developed and analyzed using a specific class of meshfree methods called Reproducing Kernel Particle Method (RKPM). The benchmark problem is also analyzed using a commercially available finite element approach with Lagrangian meshing for comparison. RKPM results are comparable to classical pressure-sinkage terramechanics relationships proposed by Bekker-Wong. Pending experimental calibration by future work, the meshfree modeling technique will be a viable simulation tool for trade studies assisting rover wheel design.

Divide et impera: subgoaling reduces the complexity of probabilistic inference and problem solving

PubMed Central

Maisto, Domenico; Donnarumma, Francesco; Pezzulo, Giovanni

2015-01-01

It has long been recognized that humans (and possibly other animals) usually break problems down into smaller and more manageable problems using subgoals. Despite a general consensus that subgoaling helps problem solving, it is still unclear what the mechanisms guiding online subgoal selection are during the solution of novel problems for which predefined solutions are not available. Under which conditions does subgoaling lead to optimal behaviour? When is subgoaling better than solving a problem from start to finish? Which is the best number and sequence of subgoals to solve a given problem? How are these subgoals selected during online inference? Here, we present a computational account of subgoaling in problem solving. Following Occam's razor, we propose that good subgoals are those that permit planning solutions and controlling behaviour using less information resources, thus yielding parsimony in inference and control. We implement this principle using approximate probabilistic inference: subgoals are selected using a sampling method that considers the descriptive complexity of the resulting sub-problems. We validate the proposed method using a standard reinforcement learning benchmark (four-rooms scenario) and show that the proposed method requires less inferential steps and permits selecting more compact control programs compared to an equivalent procedure without subgoaling. Furthermore, we show that the proposed method offers a mechanistic explanation of the neuronal dynamics found in the prefrontal cortex of monkeys that solve planning problems. Our computational framework provides a novel integrative perspective on subgoaling and its adaptive advantages for planning, control and learning, such as for example lowering cognitive effort and working memory load. PMID:25652466

Issues in Benchmark Metric Selection

NASA Astrophysics Data System (ADS)

Crolotte, Alain

It is true that a metric can influence a benchmark but will esoteric metrics create more problems than they will solve? We answer this question affirmatively by examining the case of the TPC-D metric which used the much debated geometric mean for the single-stream test. We will show how a simple choice influenced the benchmark and its conduct and, to some extent, DBMS development. After examining other alternatives our conclusion is that the “real” measure for a decision-support benchmark is the arithmetic mean.

Fast Eigensolver for Computing 3D Earth's Normal Modes

NASA Astrophysics Data System (ADS)

Shi, J.; De Hoop, M. V.; Li, R.; Xi, Y.; Saad, Y.

2017-12-01

We present a novel parallel computational approach to compute Earth's normal modes. We discretize Earth via an unstructured tetrahedral mesh and apply the continuous Galerkin finite element method to the elasto-gravitational system. To resolve the eigenvalue pollution issue, following the analysis separating the seismic point spectrum, we utilize explicitly a representation of the displacement for describing the oscillations of the non-seismic modes in the fluid outer core. Effectively, we separate out the essential spectrum which is naturally related to the Brunt-Väisälä frequency. We introduce two Lanczos approaches with polynomial and rational filtering for solving this generalized eigenvalue problem in prescribed intervals. The polynomial filtering technique only accesses the matrix pair through matrix-vector products and is an ideal candidate for solving three-dimensional large-scale eigenvalue problems. The matrix-free scheme allows us to deal with fluid separation and self-gravitation in an efficient way, while the standard shift-and-invert method typically needs an explicit shifted matrix and its factorization. The rational filtering method converges much faster than the standard shift-and-invert procedure when computing all the eigenvalues inside an interval. Both two Lanczos approaches solve for the internal eigenvalues extremely accurately, comparing with the standard eigensolver. In our computational experiments, we compare our results with the radial earth model benchmark, and visualize the normal modes using vector plots to illustrate the properties of the displacements in different modes.

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

DOE PAGES

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto; ...

2017-09-15

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

Modelling low Reynolds number vortex-induced vibration problems with a fixed mesh fluid-solid interaction formulation

NASA Astrophysics Data System (ADS)

González Cornejo, Felipe A.; Cruchaga, Marcela A.; Celentano, Diego J.

2017-11-01

The present work reports a fluid-rigid solid interaction formulation described within the framework of a fixed-mesh technique. The numerical analysis is focussed on the study of a vortex-induced vibration (VIV) of a circular cylinder at low Reynolds number. The proposed numerical scheme encompasses the fluid dynamics computation in an Eulerian domain where the body is embedded using a collection of markers to describe its shape, and the rigid solid's motion is obtained with the well-known Newton's law. The body's velocity is imposed on the fluid domain through a penalty technique on the embedded fluid-solid interface. The fluid tractions acting on the solid are computed from the fluid dynamic solution of the flow around the body. The resulting forces are considered to solve the solid motion. The numerical code is validated by contrasting the obtained results with those reported in the literature using different approaches for simulating the flow past a fixed circular cylinder as a benchmark problem. Moreover, a mesh convergence analysis is also done providing a satisfactory response. In particular, a VIV problem is analyzed, emphasizing the description of the synchronization phenomenon.

ELSI: A unified software interface for Kohn-Sham electronic structure solvers

NASA Astrophysics Data System (ADS)

Yu, Victor Wen-zhe; Corsetti, Fabiano; García, Alberto; Huhn, William P.; Jacquelin, Mathias; Jia, Weile; Lange, Björn; Lin, Lin; Lu, Jianfeng; Mi, Wenhui; Seifitokaldani, Ali; Vázquez-Mayagoitia, Álvaro; Yang, Chao; Yang, Haizhao; Blum, Volker

2018-01-01

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aims to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. Comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.

Computational and analytical comparison of flux discretizations for the semiconductor device equations beyond Boltzmann statistics

NASA Astrophysics Data System (ADS)

Farrell, Patricio; Koprucki, Thomas; Fuhrmann, Jürgen

2017-10-01

We compare three thermodynamically consistent numerical fluxes known in the literature, appearing in a Voronoï finite volume discretization of the van Roosbroeck system with general charge carrier statistics. Our discussion includes an extension of the Scharfetter-Gummel scheme to non-Boltzmann (e.g. Fermi-Dirac) statistics. It is based on the analytical solution of a two-point boundary value problem obtained by projecting the continuous differential equation onto the interval between neighboring collocation points. Hence, it serves as a reference flux. The exact solution of the boundary value problem can be approximated by computationally cheaper fluxes which modify certain physical quantities. One alternative scheme averages the nonlinear diffusion (caused by the non-Boltzmann nature of the problem), another one modifies the effective density of states. To study the differences between these three schemes, we analyze the Taylor expansions, derive an error estimate, visualize the flux error and show how the schemes perform for a carefully designed p-i-n benchmark simulation. We present strong evidence that the flux discretization based on averaging the nonlinear diffusion has an edge over the scheme based on modifying the effective density of states.

Modified artificial bee colony for the vehicle routing problems with time windows.

PubMed

Alzaqebah, Malek; Abdullah, Salwani; Jawarneh, Sana

2016-01-01

The natural behaviour of the honeybee has attracted the attention of researchers in recent years and several algorithms have been developed that mimic swarm behaviour to solve optimisation problems. This paper introduces an artificial bee colony (ABC) algorithm for the vehicle routing problem with time windows (VRPTW). A Modified ABC algorithm is proposed to improve the solution quality of the original ABC. The high exploration ability of the ABC slows-down its convergence speed, which may due to the mechanism used by scout bees in replacing abandoned (unimproved) solutions with new ones. In the Modified ABC a list of abandoned solutions is used by the scout bees to memorise the abandoned solutions, then the scout bees select a solution from the list based on roulette wheel selection and replace by a new solution with random routs selected from the best solution. The performance of the Modified ABC is evaluated on Solomon benchmark datasets and compared with the original ABC. The computational results demonstrate that the Modified ABC outperforms the original ABC also produce good solutions when compared with the best-known results in the literature. Computational investigations show that the proposed algorithm is a good and promising approach for the VRPTW.

Wavenumber-extended high-order oscillation control finite volume schemes for multi-dimensional aeroacoustic computations

NASA Astrophysics Data System (ADS)

Kim, Sungtae; Lee, Soogab; Kim, Kyu Hong

2008-04-01

A new numerical method toward accurate and efficient aeroacoustic computations of multi-dimensional compressible flows has been developed. The core idea of the developed scheme is to unite the advantages of the wavenumber-extended optimized scheme and M-AUSMPW+/MLP schemes by predicting a physical distribution of flow variables more accurately in multi-space dimensions. The wavenumber-extended optimization procedure for the finite volume approach based on the conservative requirement is newly proposed for accuracy enhancement, which is required to capture the acoustic portion of the solution in the smooth region. Furthermore, the new distinguishing mechanism which is based on the Gibbs phenomenon in discontinuity, between continuous and discontinuous regions is introduced to eliminate the excessive numerical dissipation in the continuous region by the restricted application of MLP according to the decision of the distinguishing function. To investigate the effectiveness of the developed method, a sequence of benchmark simulations such as spherical wave propagation, nonlinear wave propagation, shock tube problem and vortex preservation test problem are executed. Also, throughout more realistic shock-vortex interaction and muzzle blast flow problems, the utility of the new method for aeroacoustic applications is verified by comparing with the previous numerical or experimental results.

ELSI: A unified software interface for Kohn–Sham electronic structure solvers

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

Yu, Victor Wen-zhe; Corsetti, Fabiano; Garcia, Alberto

Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current electronic structure codes, based on similar matrix expressions, and by high-performance computation. We here present a unified software interface, ELSI, to access different strategies that address the Kohn-Sham eigenvalue problem. Currently supported algorithms include the dense generalized eigensolver library ELPA, the orbital minimization method implemented in libOMM, and the pole expansion and selected inversion (PEXSI) approach with lower computational complexity for semilocal density functionals. The ELSI interface aimsmore » to simplify the implementation and optimal use of the different strategies, by offering (a) a unified software framework designed for the electronic structure solvers in Kohn-Sham density-functional theory; (b) reasonable default parameters for a chosen solver; (c) automatic conversion between input and internal working matrix formats, and in the future (d) recommendation of the optimal solver depending on the specific problem. As a result, comparative benchmarks are shown for system sizes up to 11,520 atoms (172,800 basis functions) on distributed memory supercomputing architectures.« less

Implementation of Finite Volume based Navier Stokes Algorithm Within General Purpose Flow Network Code

NASA Technical Reports Server (NTRS)

Schallhorn, Paul; Majumdar, Alok

2012-01-01

This paper describes a finite volume based numerical algorithm that allows multi-dimensional computation of fluid flow within a system level network flow analysis. There are several thermo-fluid engineering problems where higher fidelity solutions are needed that are not within the capacity of system level codes. The proposed algorithm will allow NASA's Generalized Fluid System Simulation Program (GFSSP) to perform multi-dimensional flow calculation within the framework of GFSSP s typical system level flow network consisting of fluid nodes and branches. The paper presents several classical two-dimensional fluid dynamics problems that have been solved by GFSSP's multi-dimensional flow solver. The numerical solutions are compared with the analytical and benchmark solution of Poiseulle, Couette and flow in a driven cavity.

Execution models for mapping programs onto distributed memory parallel computers

NASA Technical Reports Server (NTRS)

Sussman, Alan

1992-01-01

The problem of exploiting the parallelism available in a program to efficiently employ the resources of the target machine is addressed. The problem is discussed in the context of building a mapping compiler for a distributed memory parallel machine. The paper describes using execution models to drive the process of mapping a program in the most efficient way onto a particular machine. Through analysis of the execution models for several mapping techniques for one class of programs, we show that the selection of the best technique for a particular program instance can make a significant difference in performance. On the other hand, the results of benchmarks from an implementation of a mapping compiler show that our execution models are accurate enough to select the best mapping technique for a given program.

Weak Galerkin finite element methods for Darcy flow: Anisotropy and heterogeneity

NASA Astrophysics Data System (ADS)

Lin, Guang; Liu, Jiangguo; Mu, Lin; Ye, Xiu

2014-11-01

This paper presents a family of weak Galerkin finite element methods (WGFEMs) for Darcy flow computation. The WGFEMs are new numerical methods that rely on the novel concept of discrete weak gradients. The WGFEMs solve for pressure unknowns both in element interiors and on the mesh skeleton. The numerical velocity is then obtained from the discrete weak gradient of the numerical pressure. The new methods are quite different than many existing numerical methods in that they are locally conservative by design, the resulting discrete linear systems are symmetric and positive-definite, and there is no need for tuning problem-dependent penalty factors. We test the WGFEMs on benchmark problems to demonstrate the strong potential of these new methods in handling strong anisotropy and heterogeneity in Darcy flow.

Numerical modeling of spray combustion with an advanced VOF method

NASA Technical Reports Server (NTRS)

Chen, Yen-Sen; Shang, Huan-Min; Shih, Ming-Hsin; Liaw, Paul

1995-01-01

This paper summarizes the technical development and validation of a multiphase computational fluid dynamics (CFD) numerical method using the volume-of-fluid (VOF) model and a Lagrangian tracking model which can be employed to analyze general multiphase flow problems with free surface mechanism. The gas-liquid interface mass, momentum and energy conservation relationships are modeled by continuum surface mechanisms. A new solution method is developed such that the present VOF model can be applied for all-speed flow regimes. The objectives of the present study are to develop and verify the fractional volume-of-fluid cell partitioning approach into a predictor-corrector algorithm and to demonstrate the effectiveness of the present approach by simulating benchmark problems including laminar impinging jets, shear coaxial jet atomization and shear coaxial spray combustion flows.

Benchmarking the Use of a Rapid Response Team by Surgical Services at a Tertiary Care Hospital

PubMed Central

Barocas, Daniel A; Kulahalli, Chirag S; Ehrenfeld, Jesse M; Kapu, April N; Penson, David F; You, Chaochen (Chad); Weavind, Lisa; Dmochowski, Roger

2015-01-01

BACKGROUND Rapid response teams (RRT) are used to prevent adverse events in patients with acute clinical deterioration, and to save costs of unnecessary transfer in patients with lower-acuity problems. However, determining the optimal use of RRT services is challenging. One method of benchmarking performance is to determine whether a department's event rate is commensurate with its volume and acuity. STUDY DESIGN Using admissions between 2009 and 2011 to 18 distinct surgical services at a tertiary care center, we developed logistic regression models to predict RRT activation, accounting for days at-risk for RRT and patient acuity, using claims modifiers for risk of mortality (ROM) and severity of illness (SOI). The model was used to compute observed-to-expected (O/E) RRT use by service. RESULTS Of 45,651 admissions, 728 (1.6%, or 3.2 per 1,000 inpatient days) resulted in 1 or more RRT activations. Use varied widely across services (0.4% to 6.2% of admissions; 1.39 to 8.73 per 1,000 inpatient days, unadjusted). In the multivariable model, the greatest contributors to the likelihood of RRT were days at risk, SOI, and ROM. The O/E RRT use ranged from 0.32 to 2.82 across services, with 8 services having an observed value that was significantly higher or lower than predicted by the model. CONCLUSIONS We developed a tool for identifying outlying use of an important institutional medical resource. The O/E computation provides a starting point for further investigation into the reasons for variability among services, and a benchmark for quality and process improvement efforts in patient safety. PMID:24275072

Higher Education Ranking and Leagues Tables: Lessons Learned from Benchmarking

ERIC Educational Resources Information Center

Proulx, Roland

2007-01-01

The paper intends to contribute to the debate on ranking and league tables by adopting a critical approach to ranking methodologies from the point of view of a university benchmarking exercise. The absence of a strict benchmarking exercise in the ranking process has been, in the opinion of the author, one of the major problems encountered in the…

Efficient constraint handling in electromagnetism-like algorithm for traveling salesman problem with time windows.

PubMed

Yurtkuran, Alkın; Emel, Erdal

2014-01-01

The traveling salesman problem with time windows (TSPTW) is a variant of the traveling salesman problem in which each customer should be visited within a given time window. In this paper, we propose an electromagnetism-like algorithm (EMA) that uses a new constraint handling technique to minimize the travel cost in TSPTW problems. The EMA utilizes the attraction-repulsion mechanism between charged particles in a multidimensional space for global optimization. This paper investigates the problem-specific constraint handling capability of the EMA framework using a new variable bounding strategy, in which real-coded particle's boundary constraints associated with the corresponding time windows of customers, is introduced and combined with the penalty approach to eliminate infeasibilities regarding time window violations. The performance of the proposed algorithm and the effectiveness of the constraint handling technique have been studied extensively, comparing it to that of state-of-the-art metaheuristics using several sets of benchmark problems reported in the literature. The results of the numerical experiments show that the EMA generates feasible and near-optimal results within shorter computational times compared to the test algorithms.

Efficient Constraint Handling in Electromagnetism-Like Algorithm for Traveling Salesman Problem with Time Windows

PubMed Central

Yurtkuran, Alkın

2014-01-01

The traveling salesman problem with time windows (TSPTW) is a variant of the traveling salesman problem in which each customer should be visited within a given time window. In this paper, we propose an electromagnetism-like algorithm (EMA) that uses a new constraint handling technique to minimize the travel cost in TSPTW problems. The EMA utilizes the attraction-repulsion mechanism between charged particles in a multidimensional space for global optimization. This paper investigates the problem-specific constraint handling capability of the EMA framework using a new variable bounding strategy, in which real-coded particle's boundary constraints associated with the corresponding time windows of customers, is introduced and combined with the penalty approach to eliminate infeasibilities regarding time window violations. The performance of the proposed algorithm and the effectiveness of the constraint handling technique have been studied extensively, comparing it to that of state-of-the-art metaheuristics using several sets of benchmark problems reported in the literature. The results of the numerical experiments show that the EMA generates feasible and near-optimal results within shorter computational times compared to the test algorithms. PMID:24723834

Verification of cardiac mechanics software: benchmark problems and solutions for testing active and passive material behaviour.

PubMed

Land, Sander; Gurev, Viatcheslav; Arens, Sander; Augustin, Christoph M; Baron, Lukas; Blake, Robert; Bradley, Chris; Castro, Sebastian; Crozier, Andrew; Favino, Marco; Fastl, Thomas E; Fritz, Thomas; Gao, Hao; Gizzi, Alessio; Griffith, Boyce E; Hurtado, Daniel E; Krause, Rolf; Luo, Xiaoyu; Nash, Martyn P; Pezzuto, Simone; Plank, Gernot; Rossi, Simone; Ruprecht, Daniel; Seemann, Gunnar; Smith, Nicolas P; Sundnes, Joakim; Rice, J Jeremy; Trayanova, Natalia; Wang, Dafang; Jenny Wang, Zhinuo; Niederer, Steven A

2015-12-08

Models of cardiac mechanics are increasingly used to investigate cardiac physiology. These models are characterized by a high level of complexity, including the particular anisotropic material properties of biological tissue and the actively contracting material. A large number of independent simulation codes have been developed, but a consistent way of verifying the accuracy and replicability of simulations is lacking. To aid in the verification of current and future cardiac mechanics solvers, this study provides three benchmark problems for cardiac mechanics. These benchmark problems test the ability to accurately simulate pressure-type forces that depend on the deformed objects geometry, anisotropic and spatially varying material properties similar to those seen in the left ventricle and active contractile forces. The benchmark was solved by 11 different groups to generate consensus solutions, with typical differences in higher-resolution solutions at approximately 0.5%, and consistent results between linear, quadratic and cubic finite elements as well as different approaches to simulating incompressible materials. Online tools and solutions are made available to allow these tests to be effectively used in verification of future cardiac mechanics software.

Performance and Scalability of the NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

Frumkin, Michael A.; Schultz, Matthew; Jin, Haoqiang; Yan, Jerry; Biegel, Bryan A. (Technical Monitor)

2002-01-01

Several features make Java an attractive choice for scientific applications. In order to gauge the applicability of Java to Computational Fluid Dynamics (CFD), we have implemented the NAS (NASA Advanced Supercomputing) Parallel Benchmarks in Java. The performance and scalability of the benchmarks point out the areas where improvement in Java compiler technology and in Java thread implementation would position Java closer to Fortran in the competition for scientific applications.

Benchmarking hypercube hardware and software

NASA Technical Reports Server (NTRS)

Grunwald, Dirk C.; Reed, Daniel A.

1986-01-01

It was long a truism in computer systems design that balanced systems achieve the best performance. Message passing parallel processors are no different. To quantify the balance of a hypercube design, an experimental methodology was developed and the associated suite of benchmarks was applied to several existing hypercubes. The benchmark suite includes tests of both processor speed in the absence of internode communication and message transmission speed as a function of communication patterns.

Evaluation of the ACEC Benchmark Suite for Real-Time Applications

DTIC Science & Technology

1990-07-23

1.0 benchmark suite waSanalyzed with respect to its measuring of Ada real-time features such as tasking, memory management, input/output, scheduling...and delay statement, Chapter 13 features , pragmas, interrupt handling, subprogram overhead, numeric computations etc. For most of the features that...meant for programming real-time systems. The ACEC benchmarks have been analyzed extensively with respect to their measuring of Ada real-time features

Studies in nonlinear problems of energy. Final report

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

Matkowsky, B.J.

1998-12-01

The author completed a successful research program on Nonlinear Problems of Energy, with emphasis on combustion and flame propagation. A total of 183 papers associated with the grant has appeared in the literature, and the efforts have twice been recognized by DOE`s Basic Science Division for Top Accomplishment. In the research program the author concentrated on modeling, analysis and computation of combustion phenomena, with particular emphasis on the transition from laminar to turbulent combustion. Thus he investigated the nonlinear dynamics and pattern formation in the successive stages of transition. He described the stability of combustion waves, and transitions to wavesmore » exhibiting progressively higher degrees of spatio-temporal complexity. Combustion waves are characterized by large activation energies, so that chemical reactions are significant only in thin layers, termed reaction zones. In the limit of infinite activation energy, the zones shrink to moving surfaces, termed fronts, which must be found during the course of the analysis, so that the problems are moving free boundary problems. The analytical studies were carried out for the limiting case with fronts, while the numerical studies were carried out for the case of finite, though large, activation energy. Accurate resolution of the solution in the reaction zone(s) is essential, otherwise false predictions of dynamical behavior are possible. Since the reaction zones move, and their location is not known a-priori, the author has developed adaptive pseudo-spectral methods, which have proven to be very useful for the accurate, efficient computation of solutions of combustion, and other, problems. The approach is based on a combination of analytical and numerical methods. The numerical computations built on and extended the information obtained analytically. Furthermore, the solutions obtained analytically served as benchmarks for testing the accuracy of the solutions determined computationally. Finally, the computational results suggested new analysis to be considered. A cumulative list of publications citing the grant make up the contents of this report.« less

Solving Fractional Programming Problems based on Swarm Intelligence

NASA Astrophysics Data System (ADS)

Raouf, Osama Abdel; Hezam, Ibrahim M.

2014-04-01

This paper presents a new approach to solve Fractional Programming Problems (FPPs) based on two different Swarm Intelligence (SI) algorithms. The two algorithms are: Particle Swarm Optimization, and Firefly Algorithm. The two algorithms are tested using several FPP benchmark examples and two selected industrial applications. The test aims to prove the capability of the SI algorithms to solve any type of FPPs. The solution results employing the SI algorithms are compared with a number of exact and metaheuristic solution methods used for handling FPPs. Swarm Intelligence can be denoted as an effective technique for solving linear or nonlinear, non-differentiable fractional objective functions. Problems with an optimal solution at a finite point and an unbounded constraint set, can be solved using the proposed approach. Numerical examples are given to show the feasibility, effectiveness, and robustness of the proposed algorithm. The results obtained using the two SI algorithms revealed the superiority of the proposed technique among others in computational time. A better accuracy was remarkably observed in the solution results of the industrial application problems.

A comparison of skyshine computational methods.

PubMed

Hertel, Nolan E; Sweezy, Jeremy E; Shultis, J Kenneth; Warkentin, J Karl; Rose, Zachary J

2005-01-01

A variety of methods employing radiation transport and point-kernel codes have been used to model two skyshine problems. The first problem is a 1 MeV point source of photons on the surface of the earth inside a 2 m tall and 1 m radius silo having black walls. The skyshine radiation downfield from the point source was estimated with and without a 30-cm-thick concrete lid on the silo. The second benchmark problem is to estimate the skyshine radiation downfield from 12 cylindrical canisters emplaced in a low-level radioactive waste trench. The canisters are filled with ion-exchange resin with a representative radionuclide loading, largely 60Co, 134Cs and 137Cs. The solution methods include use of the MCNP code to solve the problem by directly employing variance reduction techniques, the single-scatter point kernel code GGG-GP, the QADMOD-GP point kernel code, the COHORT Monte Carlo code, the NAC International version of the SKYSHINE-III code, the KSU hybrid method and the associated KSU skyshine codes.

Qualifying for the Green500: Experience with the newest generation of supercomputers at LANL

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

Yilk, Todd

The High Performance Computing Division of Los Alamos National Laboratory recently brought four new supercomputing platforms on line: Trinity with separate partitions built around the Haswell and Knights Landing CPU architectures for capability computing and Grizzly, Fire, and Ice for capacity computing applications. The power monitoring infrastructure of these machines is significantly enhanced over previous supercomputing generations at LANL and all were qualified at the highest level of the Green500 benchmark. Here, this paper discusses supercomputing at LANL, the Green500 benchmark, and notes on our experience meeting the Green500's reporting requirements.

Qualifying for the Green500: Experience with the newest generation of supercomputers at LANL

DOE PAGES

Yilk, Todd

2018-02-17

The High Performance Computing Division of Los Alamos National Laboratory recently brought four new supercomputing platforms on line: Trinity with separate partitions built around the Haswell and Knights Landing CPU architectures for capability computing and Grizzly, Fire, and Ice for capacity computing applications. The power monitoring infrastructure of these machines is significantly enhanced over previous supercomputing generations at LANL and all were qualified at the highest level of the Green500 benchmark. Here, this paper discusses supercomputing at LANL, the Green500 benchmark, and notes on our experience meeting the Green500's reporting requirements.

High-Accuracy Finite Element Method: Benchmark Calculations

NASA Astrophysics Data System (ADS)

Gusev, Alexander; Vinitsky, Sergue; Chuluunbaatar, Ochbadrakh; Chuluunbaatar, Galmandakh; Gerdt, Vladimir; Derbov, Vladimir; Góźdź, Andrzej; Krassovitskiy, Pavel

2018-02-01

We describe a new high-accuracy finite element scheme with simplex elements for solving the elliptic boundary-value problems and show its efficiency on benchmark solutions of the Helmholtz equation for the triangle membrane and hypercube.

Synapse-Centric Mapping of Cortical Models to the SpiNNaker Neuromorphic Architecture

PubMed Central

Knight, James C.; Furber, Steve B.

2016-01-01

While the adult human brain has approximately 8.8 × 1010 neurons, this number is dwarfed by its 1 × 1015 synapses. From the point of view of neuromorphic engineering and neural simulation in general this makes the simulation of these synapses a particularly complex problem. SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Current solutions for simulating spiking neural networks on SpiNNaker are heavily inspired by work on distributed high-performance computing. However, while SpiNNaker shares many characteristics with such distributed systems, its component nodes have much more limited resources and, as the system lacks global synchronization, the computation performed on each node must complete within a fixed time step. We first analyze the performance of the current SpiNNaker neural simulation software and identify several problems that occur when it is used to simulate networks of the type often used to model the cortex which contain large numbers of sparsely connected synapses. We then present a new, more flexible approach for mapping the simulation of such networks to SpiNNaker which solves many of these problems. Finally we analyze the performance of our new approach using both benchmarks, designed to represent cortical connectivity, and larger, functional cortical models. In a benchmark network where neurons receive input from 8000 STDP synapses, our new approach allows 4× more neurons to be simulated on each SpiNNaker core than has been previously possible. We also demonstrate that the largest plastic neural network previously simulated on neuromorphic hardware can be run in real time using our new approach: double the speed that was previously achieved. Additionally this network contains two types of plastic synapse which previously had to be trained separately but, using our new approach, can be trained simultaneously. PMID:27683540

System identification using Nuclear Norm & Tabu Search optimization

NASA Astrophysics Data System (ADS)

Ahmed, Asif A.; Schoen, Marco P.; Bosworth, Ken W.

2018-01-01

In recent years, subspace System Identification (SI) algorithms have seen increased research, stemming from advanced minimization methods being applied to the Nuclear Norm (NN) approach in system identification. These minimization algorithms are based on hard computing methodologies. To the authors’ knowledge, as of now, there has been no work reported that utilizes soft computing algorithms to address the minimization problem within the nuclear norm SI framework. A linear, time-invariant, discrete time system is used in this work as the basic model for characterizing a dynamical system to be identified. The main objective is to extract a mathematical model from collected experimental input-output data. Hankel matrices are constructed from experimental data, and the extended observability matrix is employed to define an estimated output of the system. This estimated output and the actual - measured - output are utilized to construct a minimization problem. An embedded rank measure assures minimum state realization outcomes. Current NN-SI algorithms employ hard computing algorithms for minimization. In this work, we propose a simple Tabu Search (TS) algorithm for minimization. TS algorithm based SI is compared with the iterative Alternating Direction Method of Multipliers (ADMM) line search optimization based NN-SI. For comparison, several different benchmark system identification problems are solved by both approaches. Results show improved performance of the proposed SI-TS algorithm compared to the NN-SI ADMM algorithm.

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

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

Madduri, Kamesh; Ediger, David; Jiang, Karl

2009-02-15

We present a new lock-free parallel algorithm for computing betweenness centralityof massive small-world networks. With minor changes to the data structures, ouralgorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in HPCS SSCA#2, a benchmark extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the Threadstorm processor, and a single-socket Sun multicore server with the UltraSPARC T2 processor. For a small-world network of 134 millionmore » vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.« less

A Faster Parallel Algorithm and Efficient Multithreaded Implementations for Evaluating Betweenness Centrality on Massive Datasets

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

Madduri, Kamesh; Ediger, David; Jiang, Karl

2009-05-29

We present a new lock-free parallel algorithm for computing betweenness centrality of massive small-world networks. With minor changes to the data structures, our algorithm also achieves better spatial cache locality compared to previous approaches. Betweenness centrality is a key algorithm kernel in the HPCS SSCA#2 Graph Analysis benchmark, which has been extensively used to evaluate the performance of emerging high-performance computing architectures for graph-theoretic computations. We design optimized implementations of betweenness centrality and the SSCA#2 benchmark for two hardware multithreaded systems: a Cray XMT system with the ThreadStorm processor, and a single-socket Sun multicore server with the UltraSparc T2 processor.more » For a small-world network of 134 million vertices and 1.073 billion edges, the 16-processor XMT system and the 8-core Sun Fire T5120 server achieve TEPS scores (an algorithmic performance count for the SSCA#2 benchmark) of 160 million and 90 million respectively, which corresponds to more than a 2X performance improvement over the previous parallel implementations. To better characterize the performance of these multithreaded systems, we correlate the SSCA#2 performance results with data from the memory-intensive STREAM and RandomAccess benchmarks. Finally, we demonstrate the applicability of our implementation to analyze massive real-world datasets by computing approximate betweenness centrality for a large-scale IMDb movie-actor network.« less

A new approach to three-dimensional neutron transport solution based on the method of characteristics and linear axial approximation

NASA Astrophysics Data System (ADS)

Zheng, Youqi; Choi, Sooyoung; Lee, Deokjung

2017-12-01

A new approach based on the method of characteristics (MOC) is proposed to solve the neutron transport equation. A new three-dimensional (3D) spatial discretization is applied to avoid the instability issue of the transverse leakage iteration of the traditional 2D/1D approach. In this new approach, the axial and radial variables are discretized in two different ways: the linear expansion is performed in the axial direction, then, the 3D solution of the angular flux is transformed to be the planar solution of 2D angular expansion moments, which are solved by the planar MOC sweeping. Based on the boundary and interface continuity conditions, the 2D expansion moment solution is equivalently transformed to be the solution of the axially averaged angular flux. Using the piecewise averaged angular flux at the top and bottom surfaces of 3D meshes, the planes are coupled to give the 3D angular flux distribution. The 3D CMFD linear system is established from the surface net current of every 3D pin-mesh to accelerate the convergence of power iteration. The STREAM code is extended to be capable of handling 3D problems based on the new approach. Several benchmarks are tested to verify its feasibility and accuracy, including the 3D homogeneous benchmarks and heterogeneous benchmarks. The computational sensitivity is discussed. The results show good accuracy in all tests. With the CMFD acceleration, the convergence is stable. In addition, a pin-cell problem with void gap is calculated. This shows the advantage compared to the traditional 2D/1D MOC methods.

Benchmarking of neutron production of heavy-ion transport codes

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

Remec, I.; Ronningen, R. M.; Heilbronn, L.

Document available in abstract form only, full text of document follows: Accurate prediction of radiation fields generated by heavy ion interactions is important in medical applications, space missions, and in design and operation of rare isotope research facilities. In recent years, several well-established computer codes in widespread use for particle and radiation transport calculations have been equipped with the capability to simulate heavy ion transport and interactions. To assess and validate these capabilities, we performed simulations of a series of benchmark-quality heavy ion experiments with the computer codes FLUKA, MARS15, MCNPX, and PHITS. We focus on the comparisons of secondarymore » neutron production. Results are encouraging; however, further improvements in models and codes and additional benchmarking are required. (authors)« less

The effects of perceived USB-delay for sensor and embedded system development.

PubMed

Du, J; Kade, D; Gerdtman, C; Ozcan, O; Linden, M

2016-08-01

Perceiving delay in computer input devices is a problem which gets even more eminent when being used in healthcare applications and/or in small, embedded systems. Therefore, the amount of delay found as acceptable when using computer input devices was investigated in this paper. A device was developed to perform a benchmark test for the perception of delay. The delay can be set from 0 to 999 milliseconds (ms) between a receiving computer and an available USB-device. The USB-device can be a mouse, a keyboard or some other type of USB-connected input device. Feedback from performed user tests with 36 people form the basis for the determination of time limitations for the USB data processing in microprocessors and embedded systems without users' noticing the delay. For this paper, tests were performed with a personal computer and a common computer mouse, testing the perception of delays between 0 and 500 ms. The results of our user tests show that perceived delays up to 150 ms were acceptable and delays larger than 300 ms were not acceptable at all.

Development of a particle method of characteristics (PMOC) for one-dimensional shock waves

NASA Astrophysics Data System (ADS)

Hwang, Y.-H.

2018-03-01

In the present study, a particle method of characteristics is put forward to simulate the evolution of one-dimensional shock waves in barotropic gaseous, closed-conduit, open-channel, and two-phase flows. All these flow phenomena can be described with the same set of governing equations. The proposed scheme is established based on the characteristic equations and formulated by assigning the computational particles to move along the characteristic curves. Both the right- and left-running characteristics are traced and represented by their associated computational particles. It inherits the computational merits from the conventional method of characteristics (MOC) and moving particle method, but without their individual deficiencies. In addition, special particles with dual states deduced to the enforcement of the Rankine-Hugoniot relation are deliberately imposed to emulate the shock structure. Numerical tests are carried out by solving some benchmark problems, and the computational results are compared with available analytical solutions. From the derivation procedure and obtained computational results, it is concluded that the proposed PMOC will be a useful tool to replicate one-dimensional shock waves.

Simulating Hydrologic Flow and Reactive Transport with PFLOTRAN and PETSc on Emerging Fine-Grained Parallel Computer Architectures

NASA Astrophysics Data System (ADS)

Mills, R. T.; Rupp, K.; Smith, B. F.; Brown, J.; Knepley, M.; Zhang, H.; Adams, M.; Hammond, G. E.

2017-12-01

As the high-performance computing community pushes towards the exascale horizon, power and heat considerations have driven the increasing importance and prevalence of fine-grained parallelism in new computer architectures. High-performance computing centers have become increasingly reliant on GPGPU accelerators and "manycore" processors such as the Intel Xeon Phi line, and 512-bit SIMD registers have even been introduced in the latest generation of Intel's mainstream Xeon server processors. The high degree of fine-grained parallelism and more complicated memory hierarchy considerations of such "manycore" processors present several challenges to existing scientific software. Here, we consider how the massively parallel, open-source hydrologic flow and reactive transport code PFLOTRAN - and the underlying Portable, Extensible Toolkit for Scientific Computation (PETSc) library on which it is built - can best take advantage of such architectures. We will discuss some key features of these novel architectures and our code optimizations and algorithmic developments targeted at them, and present experiences drawn from working with a wide range of PFLOTRAN benchmark problems on these architectures.

Performance of Multi-chaotic PSO on a shifted benchmark functions set

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

Pluhacek, Michal; Senkerik, Roman; Zelinka, Ivan

2015-03-10

In this paper the performance of Multi-chaotic PSO algorithm is investigated using two shifted benchmark functions. The purpose of shifted benchmark functions is to simulate the time-variant real-world problems. The results of chaotic PSO are compared with canonical version of the algorithm. It is concluded that using the multi-chaotic approach can lead to better results in optimization of shifted functions.

ELAPSE - NASA AMES LISP AND ADA BENCHMARK SUITE: EFFICIENCY OF LISP AND ADA PROCESSING - A SYSTEM EVALUATION

NASA Technical Reports Server (NTRS)

Davis, G. J.

1994-01-01

One area of research of the Information Sciences Division at NASA Ames Research Center is devoted to the analysis and enhancement of processors and advanced computer architectures, specifically in support of automation and robotic systems. To compare systems' abilities to efficiently process Lisp and Ada, scientists at Ames Research Center have developed a suite of non-parallel benchmarks called ELAPSE. The benchmark suite was designed to test a single computer's efficiency as well as alternate machine comparisons on Lisp, and/or Ada languages. ELAPSE tests the efficiency with which a machine can execute the various routines in each environment. The sample routines are based on numeric and symbolic manipulations and include two-dimensional fast Fourier transformations, Cholesky decomposition and substitution, Gaussian elimination, high-level data processing, and symbol-list references. Also included is a routine based on a Bayesian classification program sorting data into optimized groups. The ELAPSE benchmarks are available for any computer with a validated Ada compiler and/or Common Lisp system. Of the 18 routines that comprise ELAPSE, provided within this package are 14 developed or translated at Ames. The others are readily available through literature. The benchmark that requires the most memory is CHOLESKY.ADA. Under VAX/VMS, CHOLESKY.ADA requires 760K of main memory. ELAPSE is available on either two 5.25 inch 360K MS-DOS format diskettes (standard distribution) or a 9-track 1600 BPI ASCII CARD IMAGE format magnetic tape. The contents of the diskettes are compressed using the PKWARE archiving tools. The utility to unarchive the files, PKUNZIP.EXE, is included. The ELAPSE benchmarks were written in 1990. VAX and VMS are trademarks of Digital Equipment Corporation. MS-DOS is a registered trademark of Microsoft Corporation.

How to benchmark methods for structure-based virtual screening of large compound libraries.

PubMed

Christofferson, Andrew J; Huang, Niu

2012-01-01

Structure-based virtual screening is a useful computational technique for ligand discovery. To systematically evaluate different docking approaches, it is important to have a consistent benchmarking protocol that is both relevant and unbiased. Here, we describe the designing of a benchmarking data set for docking screen assessment, a standard docking screening process, and the analysis and presentation of the enrichment of annotated ligands among a background decoy database.

Benchmarking image fusion system design parameters

NASA Astrophysics Data System (ADS)

Howell, Christopher L.

2013-06-01

A clear and absolute method for discriminating between image fusion algorithm performances is presented. This method can effectively be used to assist in the design and modeling of image fusion systems. Specifically, it is postulated that quantifying human task performance using image fusion should be benchmarked to whether the fusion algorithm, at a minimum, retained the performance benefit achievable by each independent spectral band being fused. The established benchmark would then clearly represent the threshold that a fusion system should surpass to be considered beneficial to a particular task. A genetic algorithm is employed to characterize the fused system parameters using a Matlab® implementation of NVThermIP as the objective function. By setting the problem up as a mixed-integer constraint optimization problem, one can effectively look backwards through the image acquisition process: optimizing fused system parameters by minimizing the difference between modeled task difficulty measure and the benchmark task difficulty measure. The results of an identification perception experiment are presented, where human observers were asked to identify a standard set of military targets, and used to demonstrate the effectiveness of the benchmarking process.

Bin packing problem solution through a deterministic weighted finite automaton

NASA Astrophysics Data System (ADS)

Zavala-Díaz, J. C.; Pérez-Ortega, J.; Martínez-Rebollar, A.; Almanza-Ortega, N. N.; Hidalgo-Reyes, M.

2016-06-01

In this article the solution of Bin Packing problem of one dimension through a weighted finite automaton is presented. Construction of the automaton and its application to solve three different instances, one synthetic data and two benchmarks are presented: N1C1W1_A.BPP belonging to data set Set_1; and BPP13.BPP belonging to hard28. The optimal solution of synthetic data is obtained. In the first benchmark the solution obtained is one more container than the ideal number of containers and in the second benchmark the solution is two more containers than the ideal solution (approximately 2.5%). The runtime in all three cases was less than one second.

Spherical harmonic results for the 3D Kobayashi Benchmark suite

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

Brown, P N; Chang, B; Hanebutte, U R

1999-03-02

Spherical harmonic solutions are presented for the Kobayashi benchmark suite. The results were obtained with Ardra, a scalable, parallel neutron transport code developed at Lawrence Livermore National Laboratory (LLNL). The calculations were performed on the IBM ASCI Blue-Pacific computer at LLNL.

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.

Graph 500 on OpenSHMEM: Using a Practical Survey of Past Work to Motivate Novel Algorithmic Developments

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

Grossman, Max; Pritchard Jr., Howard Porter; Budimlic, Zoran

2016-12-22

Graph500 [14] is an effort to offer a standardized benchmark across large-scale distributed platforms which captures the behavior of common communicationbound graph algorithms. Graph500 differs from other large-scale benchmarking efforts (such as HPL [6] or HPGMG [7]) primarily in the irregularity of its computation and data access patterns. The core computational kernel of Graph500 is a breadth-first search (BFS) implemented on an undirected graph. The output of Graph500 is a spanning tree of the input graph, usually represented by a predecessor mapping for every node in the graph. The Graph500 benchmark defines several pre-defined input sizes for implementers to testmore » against. This report summarizes investigation into implementing the Graph500 benchmark on OpenSHMEM, and focuses on first building a strong and practical understanding of the strengths and limitations of past work before proposing and developing novel extensions.« less

Towards unbiased benchmarking of evolutionary and hybrid algorithms for real-valued optimisation

NASA Astrophysics Data System (ADS)

MacNish, Cara

2007-12-01

Randomised population-based algorithms, such as evolutionary, genetic and swarm-based algorithms, and their hybrids with traditional search techniques, have proven successful and robust on many difficult real-valued optimisation problems. This success, along with the readily applicable nature of these techniques, has led to an explosion in the number of algorithms and variants proposed. In order for the field to advance it is necessary to carry out effective comparative evaluations of these algorithms, and thereby better identify and understand those properties that lead to better performance. This paper discusses the difficulties of providing benchmarking of evolutionary and allied algorithms that is both meaningful and logistically viable. To be meaningful the benchmarking test must give a fair comparison that is free, as far as possible, from biases that favour one style of algorithm over another. To be logistically viable it must overcome the need for pairwise comparison between all the proposed algorithms. To address the first problem, we begin by attempting to identify the biases that are inherent in commonly used benchmarking functions. We then describe a suite of test problems, generated recursively as self-similar or fractal landscapes, designed to overcome these biases. For the second, we describe a server that uses web services to allow researchers to 'plug in' their algorithms, running on their local machines, to a central benchmarking repository.

Alternative Modal Basis Selection Procedures For Reduced-Order Nonlinear Random Response Simulation

NASA Technical Reports Server (NTRS)

Przekop, Adam; Guo, Xinyun; Rizi, Stephen A.

2012-01-01

Three procedures to guide selection of an efficient modal basis in a nonlinear random response analysis are examined. One method is based only on proper orthogonal decomposition, while the other two additionally involve smooth orthogonal decomposition. Acoustic random response problems are employed to assess the performance of the three modal basis selection approaches. A thermally post-buckled beam exhibiting snap-through behavior, a shallowly curved arch in the auto-parametric response regime and a plate structure are used as numerical test articles. The results of a computationally taxing full-order analysis in physical degrees of freedom are taken as the benchmark for comparison with the results from the three reduced-order analyses. For the cases considered, all three methods are shown to produce modal bases resulting in accurate and computationally efficient reduced-order nonlinear simulations.

Determination and correction of persistent biases in quantum annealers

PubMed Central

Perdomo-Ortiz, Alejandro; O’Gorman, Bryan; Fluegemann, Joseph; Biswas, Rupak; Smelyanskiy, Vadim N.

2016-01-01

Calibration of quantum computers is essential to the effective utilisation of their quantum resources. Specifically, the performance of quantum annealers is likely to be significantly impaired by noise in their programmable parameters, effectively misspecification of the computational problem to be solved, often resulting in spurious suboptimal solutions. We developed a strategy to determine and correct persistent, systematic biases between the actual values of the programmable parameters and their user-specified values. We applied the recalibration strategy to two D-Wave Two quantum annealers, one at NASA Ames Research Center in Moffett Field, California, and another at D-Wave Systems in Burnaby, Canada. We show that the recalibration procedure not only reduces the magnitudes of the biases in the programmable parameters but also enhances the performance of the device on a set of random benchmark instances. PMID:26783120

Empirical comparison of local structural similarity indices for collaborative-filtering-based recommender systems

NASA Astrophysics Data System (ADS)

Zhang, Qian-Ming; Shang, Ming-Sheng; Zeng, Wei; Chen, Yong; Lü, Linyuan

2010-08-01

Collaborative filtering is one of the most successful recommendation techniques, which can effectively predict the possible future likes of users based on their past preferences. The key problem of this method is how to define the similarity between users. A standard approach is using the correlation between the ratings that two users give to a set of objects, such as Cosine index and Pearson correlation coefficient. However, the costs of computing this kind of indices are relatively high, and thus it is impossible to be applied in the huge-size systems. To solve this problem, in this paper, we introduce six local-structure-based similarity indices and compare their performances with the above two benchmark indices. Experimental results on two data sets demonstrate that the structure-based similarity indices overall outperform the Pearson correlation coefficient. When the data is dense, the structure-based indices can perform competitively good as Cosine index, while with lower computational complexity. Furthermore, when the data is sparse, the structure-based indices give even better results than Cosine index.

Scalability of surrogate-assisted multi-objective optimization of antenna structures exploiting variable-fidelity electromagnetic simulation models

NASA Astrophysics Data System (ADS)

Koziel, Slawomir; Bekasiewicz, Adrian

2016-10-01

Multi-objective optimization of antenna structures is a challenging task owing to the high computational cost of evaluating the design objectives as well as the large number of adjustable parameters. Design speed-up can be achieved by means of surrogate-based optimization techniques. In particular, a combination of variable-fidelity electromagnetic (EM) simulations, design space reduction techniques, response surface approximation models and design refinement methods permits identification of the Pareto-optimal set of designs within a reasonable timeframe. Here, a study concerning the scalability of surrogate-assisted multi-objective antenna design is carried out based on a set of benchmark problems, with the dimensionality of the design space ranging from six to 24 and a CPU cost of the EM antenna model from 10 to 20 min per simulation. Numerical results indicate that the computational overhead of the design process increases more or less quadratically with the number of adjustable geometric parameters of the antenna structure at hand, which is a promising result from the point of view of handling even more complex problems.

A computer code for multiphase all-speed transient flows in complex geometries. MAST version 1.0

NASA Technical Reports Server (NTRS)

Chen, C. P.; Jiang, Y.; Kim, Y. M.; Shang, H. M.

1991-01-01

The operation of the MAST code, which computes transient solutions to the multiphase flow equations applicable to all-speed flows, is described. Two-phase flows are formulated based on the Eulerian-Lagrange scheme in which the continuous phase is described by the Navier-Stokes equation (or Reynolds equations for turbulent flows). Dispersed phase is formulated by a Lagrangian tracking scheme. The numerical solution algorithms utilized for fluid flows is a newly developed pressure-implicit algorithm based on the operator-splitting technique in generalized nonorthogonal coordinates. This operator split allows separate operation on each of the variable fields to handle pressure-velocity coupling. The obtained pressure correction equation has the hyperbolic nature and is effective for Mach numbers ranging from the incompressible limit to supersonic flow regimes. The present code adopts a nonstaggered grid arrangement; thus, the velocity components and other dependent variables are collocated at the same grid. A sequence of benchmark-quality problems, including incompressible, subsonic, transonic, supersonic, gas-droplet two-phase flows, as well as spray-combustion problems, were performed to demonstrate the robustness and accuracy of the present code.

Revisiting Yasinsky and Henry`s benchmark using modern nodal codes

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

Feltus, M.A.; Becker, M.W.

1995-12-31

The numerical experiments analyzed by Yasinsky and Henry are quite trivial by comparison with today`s standards because they used the finite difference code WIGLE for their benchmark. Also, this problem is a simple slab (one-dimensional) case with no feedback mechanisms. This research attempts to obtain STAR (Ref. 2) and NEM (Ref. 3) code results in order to produce a more modern kinetics benchmark with results comparable WIGLE.

Enhanced Verification Test Suite for Physics Simulation Codes

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

Kamm, J R; Brock, J S; Brandon, S T

2008-10-10

This document discusses problems with which to augment, in quantity and in quality, the existing tri-laboratory suite of verification problems used by Los Alamos National Laboratory (LANL), Lawrence Livermore National Laboratory (LLNL), and Sandia National Laboratories (SNL). The purpose of verification analysis is demonstrate whether the numerical results of the discretization algorithms in physics and engineering simulation codes provide correct solutions of the corresponding continuum equations. The key points of this document are: (1) Verification deals with mathematical correctness of the numerical algorithms in a code, while validation deals with physical correctness of a simulation in a regime of interest.more » This document is about verification. (2) The current seven-problem Tri-Laboratory Verification Test Suite, which has been used for approximately five years at the DOE WP laboratories, is limited. (3) Both the methodology for and technology used in verification analysis have evolved and been improved since the original test suite was proposed. (4) The proposed test problems are in three basic areas: (a) Hydrodynamics; (b) Transport processes; and (c) Dynamic strength-of-materials. (5) For several of the proposed problems we provide a 'strong sense verification benchmark', consisting of (i) a clear mathematical statement of the problem with sufficient information to run a computer simulation, (ii) an explanation of how the code result and benchmark solution are to be evaluated, and (iii) a description of the acceptance criterion for simulation code results. (6) It is proposed that the set of verification test problems with which any particular code be evaluated include some of the problems described in this document. Analysis of the proposed verification test problems constitutes part of a necessary--but not sufficient--step that builds confidence in physics and engineering simulation codes. More complicated test cases, including physics models of greater sophistication or other physics regimes (e.g., energetic material response, magneto-hydrodynamics), would represent a scientifically desirable complement to the fundamental test cases discussed in this report. The authors believe that this document can be used to enhance the verification analyses undertaken at the DOE WP Laboratories and, thus, to improve the quality, credibility, and usefulness of the simulation codes that are analyzed with these problems.« less

A benchmark study of the sea-level equation in GIA modelling

NASA Astrophysics Data System (ADS)

Martinec, Zdenek; Klemann, Volker; van der Wal, Wouter; Riva, Riccardo; Spada, Giorgio; Simon, Karen; Blank, Bas; Sun, Yu; Melini, Daniele; James, Tom; Bradley, Sarah

2017-04-01

The sea-level load in glacial isostatic adjustment (GIA) is described by the so called sea-level equation (SLE), which represents the mass redistribution between ice sheets and oceans on a deforming earth. Various levels of complexity of SLE have been proposed in the past, ranging from a simple mean global sea level (the so-called eustatic sea level) to the load with a deforming ocean bottom, migrating coastlines and a changing shape of the geoid. Several approaches to solve the SLE have been derived, from purely analytical formulations to fully numerical methods. Despite various teams independently investigating GIA, there has been no systematic intercomparison amongst the solvers through which the methods may be validated. The goal of this paper is to present a series of benchmark experiments designed for testing and comparing numerical implementations of the SLE. Our approach starts with simple load cases even though the benchmark will not result in GIA predictions for a realistic loading scenario. In the longer term we aim for a benchmark with a realistic loading scenario, and also for benchmark solutions with rotational feedback. The current benchmark uses an earth model for which Love numbers have been computed and benchmarked in Spada et al (2011). In spite of the significant differences in the numerical methods employed, the test computations performed so far show a satisfactory agreement between the results provided by the participants. The differences found can often be attributed to the different approximations inherent to the various algorithms. Literature G. Spada, V. R. Barletta, V. Klemann, R. E. M. Riva, Z. Martinec, P. Gasperini, B. Lund, D. Wolf, L. L. A. Vermeersen, and M. A. King, 2011. A benchmark study for glacial isostatic adjustment codes. Geophys. J. Int. 185: 106-132 doi:10.1111/j.1365-

Parameterized Micro-benchmarking: An Auto-tuning Approach for Complex Applications

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

Ma, Wenjing; Krishnamoorthy, Sriram; Agrawal, Gagan

2012-05-15

Auto-tuning has emerged as an important practical method for creating highly optimized implementations of key computational kernels and applications. However, the growing complexity of architectures and applications is creating new challenges for auto-tuning. Complex applications can involve a prohibitively large search space that precludes empirical auto-tuning. Similarly, architectures are becoming increasingly complicated, making it hard to model performance. In this paper, we focus on the challenge to auto-tuning presented by applications with a large number of kernels and kernel instantiations. While these kernels may share a somewhat similar pattern, they differ considerably in problem sizes and the exact computation performed.more » We propose and evaluate a new approach to auto-tuning which we refer to as parameterized micro-benchmarking. It is an alternative to the two existing classes of approaches to auto-tuning: analytical model-based and empirical search-based. Particularly, we argue that the former may not be able to capture all the architectural features that impact performance, whereas the latter might be too expensive for an application that has several different kernels. In our approach, different expressions in the application, different possible implementations of each expression, and the key architectural features, are used to derive a simple micro-benchmark and a small parameter space. This allows us to learn the most significant features of the architecture that can impact the choice of implementation for each kernel. We have evaluated our approach in the context of GPU implementations of tensor contraction expressions encountered in excited state calculations in quantum chemistry. We have focused on two aspects of GPUs that affect tensor contraction execution: memory access patterns and kernel consolidation. Using our parameterized micro-benchmarking approach, we obtain a speedup of up to 2 over the version that used default optimizations, but no auto-tuning. We demonstrate that observations made from microbenchmarks match the behavior seen from real expressions. In the process, we make important observations about the memory hierarchy of two of the most recent NVIDIA GPUs, which can be used in other optimization frameworks as well.« less

Predicting Cost/Performance Trade-Offs for Whitney: A Commodity Computing Cluster

NASA Technical Reports Server (NTRS)

Becker, Jeffrey C.; Nitzberg, Bill; VanderWijngaart, Rob F.; Kutler, Paul (Technical Monitor)

1997-01-01

Recent advances in low-end processor and network technology have made it possible to build a "supercomputer" out of commodity components. We develop simple models of the NAS Parallel Benchmarks version 2 (NPB 2) to explore the cost/performance trade-offs involved in building a balanced parallel computer supporting a scientific workload. We develop closed form expressions detailing the number and size of messages sent by each benchmark. Coupling these with measured single processor performance, network latency, and network bandwidth, our models predict benchmark performance to within 30%. A comparison based on total system cost reveals that current commodity technology (200 MHz Pentium Pros with 100baseT Ethernet) is well balanced for the NPBs up to a total system cost of around $1,000,000.

RISC Processors and High Performance Computing

NASA Technical Reports Server (NTRS)

Bailey, David H.; Saini, Subhash; Craw, James M. (Technical Monitor)

1995-01-01

This tutorial will discuss the top five RISC microprocessors and the parallel systems in which they are used. It will provide a unique cross-machine comparison not available elsewhere. The effective performance of these processors will be compared by citing standard benchmarks in the context of real applications. The latest NAS Parallel Benchmarks, both absolute performance and performance per dollar, will be listed. The next generation of the NPB will be described. The tutorial will conclude with a discussion of future directions in the field. Technology Transfer Considerations: All of these computer systems are commercially available internationally. Information about these processors is available in the public domain, mostly from the vendors themselves. The NAS Parallel Benchmarks and their results have been previously approved numerous times for public release, beginning back in 1991.

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

Perumalla, Kalyan S.; Yoginath, Srikanth B.

Problems such as fault tolerance and scalable synchronization can be efficiently solved using reversibility of applications. Making applications reversible by relying on computation rather than on memory is ideal for large scale parallel computing, especially for the next generation of supercomputers in which memory is expensive in terms of latency, energy, and price. In this direction, a case study is presented here in reversing a computational core, namely, Basic Linear Algebra Subprograms, which is widely used in scientific applications. A new Reversible BLAS (RBLAS) library interface has been designed, and a prototype has been implemented with two modes: (1) amore » memory-mode in which reversibility is obtained by checkpointing to memory in forward and restoring from memory in reverse, and (2) a computational-mode in which nothing is saved in the forward, but restoration is done entirely via inverse computation in reverse. The article is focused on detailed performance benchmarking to evaluate the runtime dynamics and performance effects, comparing reversible computation with checkpointing on both traditional CPU platforms and recent GPU accelerator platforms. For BLAS Level-1 subprograms, data indicates over an order of magnitude better speed of reversible computation compared to checkpointing. For BLAS Level-2 and Level-3, a more complex tradeoff is observed between reversible computation and checkpointing, depending on computational and memory complexities of the subprograms.« less

Divide et impera: subgoaling reduces the complexity of probabilistic inference and problem solving.

PubMed

Maisto, Domenico; Donnarumma, Francesco; Pezzulo, Giovanni

2015-03-06

It has long been recognized that humans (and possibly other animals) usually break problems down into smaller and more manageable problems using subgoals. Despite a general consensus that subgoaling helps problem solving, it is still unclear what the mechanisms guiding online subgoal selection are during the solution of novel problems for which predefined solutions are not available. Under which conditions does subgoaling lead to optimal behaviour? When is subgoaling better than solving a problem from start to finish? Which is the best number and sequence of subgoals to solve a given problem? How are these subgoals selected during online inference? Here, we present a computational account of subgoaling in problem solving. Following Occam's razor, we propose that good subgoals are those that permit planning solutions and controlling behaviour using less information resources, thus yielding parsimony in inference and control. We implement this principle using approximate probabilistic inference: subgoals are selected using a sampling method that considers the descriptive complexity of the resulting sub-problems. We validate the proposed method using a standard reinforcement learning benchmark (four-rooms scenario) and show that the proposed method requires less inferential steps and permits selecting more compact control programs compared to an equivalent procedure without subgoaling. Furthermore, we show that the proposed method offers a mechanistic explanation of the neuronal dynamics found in the prefrontal cortex of monkeys that solve planning problems. Our computational framework provides a novel integrative perspective on subgoaling and its adaptive advantages for planning, control and learning, such as for example lowering cognitive effort and working memory load. © 2015 The Author(s) Published by the Royal Society. All rights reserved.

Weak Galerkin finite element methods for Darcy flow: Anisotropy and heterogeneity

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

Lin, Guang; Liu, Jiangguo; Mu, Lin

2014-11-01

This paper presents a family of weak Galerkin finite element methods (WGFEMs) for Darcy flow computation. The WGFEMs are new numerical methods that rely on the novel concept of discrete weak gradients. The WGFEMs solve for pressure unknowns both in element interiors and on the mesh skeleton. The numerical velocity is then obtained from the discrete weak gradient of the numerical pressure. The new methods are quite different than many existing numerical methods in that they are locally conservative by design, the resulting discrete linear systems are symmetric and positive-definite, and there is no need for tuning problem-dependent penalty factors.more » We test the WGFEMs on benchmark problems to demonstrate the strong potential of these new methods in handling strong anisotropy and heterogeneity in Darcy flow.« less

Discriminatively learning for representing local image features with quadruplet model

NASA Astrophysics Data System (ADS)

Zhang, Da-long; Zhao, Lei; Xu, Duan-qing; Lu, Dong-ming

2017-11-01

Traditional hand-crafted features for representing local image patches are evolving into current data-driven and learning-based image feature, but learning a robust and discriminative descriptor which is capable of controlling various patch-level computer vision tasks is still an open problem. In this work, we propose a novel deep convolutional neural network (CNN) to learn local feature descriptors. We utilize the quadruplets with positive and negative training samples, together with a constraint to restrict the intra-class variance, to learn good discriminative CNN representations. Compared with previous works, our model reduces the overlap in feature space between corresponding and non-corresponding patch pairs, and mitigates margin varying problem caused by commonly used triplet loss. We demonstrate that our method achieves better embedding result than some latest works, like PN-Net and TN-TG, on benchmark dataset.

Genetic Parallel Programming: design and implementation.

PubMed

Cheang, Sin Man; Leung, Kwong Sak; Lee, Kin Hong

2006-01-01

This paper presents a novel Genetic Parallel Programming (GPP) paradigm for evolving parallel programs running on a Multi-Arithmetic-Logic-Unit (Multi-ALU) Processor (MAP). The MAP is a Multiple Instruction-streams, Multiple Data-streams (MIMD), general-purpose register machine that can be implemented on modern Very Large-Scale Integrated Circuits (VLSIs) in order to evaluate genetic programs at high speed. For human programmers, writing parallel programs is more difficult than writing sequential programs. However, experimental results show that GPP evolves parallel programs with less computational effort than that of their sequential counterparts. It creates a new approach to evolving a feasible problem solution in parallel program form and then serializes it into a sequential program if required. The effectiveness and efficiency of GPP are investigated using a suite of 14 well-studied benchmark problems. Experimental results show that GPP speeds up evolution substantially.

A Novel Consensus-Based Particle Swarm Optimization-Assisted Trust-Tech Methodology for Large-Scale Global Optimization.

PubMed

Zhang, Yong-Feng; Chiang, Hsiao-Dong

2017-09-01

A novel three-stage methodology, termed the "consensus-based particle swarm optimization (PSO)-assisted Trust-Tech methodology," to find global optimal solutions for nonlinear optimization problems is presented. It is composed of Trust-Tech methods, consensus-based PSO, and local optimization methods that are integrated to compute a set of high-quality local optimal solutions that can contain the global optimal solution. The proposed methodology compares very favorably with several recently developed PSO algorithms based on a set of small-dimension benchmark optimization problems and 20 large-dimension test functions from the CEC 2010 competition. The analytical basis for the proposed methodology is also provided. Experimental results demonstrate that the proposed methodology can rapidly obtain high-quality optimal solutions that can contain the global optimal solution. The scalability of the proposed methodology is promising.

Development of a Quantitative Decision Metric for Selecting the Most Suitable Discretization Method for SN Transport Problems

NASA Astrophysics Data System (ADS)

Schunert, Sebastian

In this work we develop a quantitative decision metric for spatial discretization methods of the SN equations. The quantitative decision metric utilizes performance data from selected test problems for computing a fitness score that is used for the selection of the most suitable discretization method for a particular SN transport application. The fitness score is aggregated as a weighted geometric mean of single performance indicators representing various performance aspects relevant to the user. Thus, the fitness function can be adjusted to the particular needs of the code practitioner by adding/removing single performance indicators or changing their importance via the supplied weights. Within this work a special, broad class of methods is considered, referred to as nodal methods. This class is naturally comprised of the DGFEM methods of all function space families. Within this work it is also shown that the Higher Order Diamond Difference (HODD) method is a nodal method. Building on earlier findings that the Arbitrarily High Order Method of the Nodal type (AHOTN) is also a nodal method, a generalized finite-element framework is created to yield as special cases various methods that were developed independently using profoundly different formalisms. A selection of test problems related to a certain performance aspect are considered: an Method of Manufactured Solutions (MMS) test suite for assessing accuracy and execution time, Lathrop's test problem for assessing resilience against occurrence of negative fluxes, and a simple, homogeneous cube test problem to verify if a method possesses the thick diffusive limit. The contending methods are implemented as efficiently as possible under a common SN transport code framework to level the playing field for a fair comparison of their computational load. Numerical results are presented for all three test problems and a qualitative rating of each method's performance is provided for each aspect: accuracy/efficiency, resilience against negative fluxes, and possession of the thick diffusion limit, separately. The choice of the most efficient method depends on the utilized error norm: in Lp error norms higher order methods such as the AHOTN method of order three perform best, while for computing integral quantities the linear nodal (LN) method is most efficient. The most resilient method against occurrence of negative fluxes is the simple corner balance (SCB) method. A validation of the quantitative decision metric is performed based on the NEA box-inbox suite of test problems. The validation exercise comprises two stages: first prediction of the contending methods' performance via the decision metric and second computing the actual scores based on data obtained from the NEA benchmark problem. The comparison of predicted and actual scores via a penalty function (ratio of predicted best performer's score to actual best score) completes the validation exercise. It is found that the decision metric is capable of very accurate predictions (penalty < 10%) in more than 83% of the considered cases and features penalties up to 20% for the remaining cases. An exception to this rule is the third test case NEA-III intentionally set up to incorporate a poor match of the benchmark with the "data" problems. However, even under these worst case conditions the decision metric's suggestions are never detrimental. Suggestions for improving the decision metric's accuracy are to increase the pool of employed data, to refine the mapping of a given configuration to a case in the database, and to better characterize the desired target quantities.

A Lagrangian model for the age of tracer in surface water

NASA Astrophysics Data System (ADS)

Ding, Yu; Liu, Haifei; Yi, Yujun

The age of tracer is a spatio-temporal scale, indicating the transition time of solute particles, which is helpful to monitor and manage the pollutant leakage accidents. In this study, an effective Lagrangian model for the age of tracer is developed based on the lattice Boltzmann method in D2Q5 lattices. A tracer age problem in an asymmetrical circular reservoir is then employed as a benchmark test to verify this method. Then it is applied to computing the age of tracers under two different reservoir operation schemes in the Danjiangkou Reservoir, the drinking water source for the Middle Route of South-to-North Water Transfer Project.

Uncertainty propagation of p-boxes using sparse polynomial chaos expansions

NASA Astrophysics Data System (ADS)

Schöbi, Roland; Sudret, Bruno

2017-06-01

In modern engineering, physical processes are modelled and analysed using advanced computer simulations, such as finite element models. Furthermore, concepts of reliability analysis and robust design are becoming popular, hence, making efficient quantification and propagation of uncertainties an important aspect. In this context, a typical workflow includes the characterization of the uncertainty in the input variables. In this paper, input variables are modelled by probability-boxes (p-boxes), accounting for both aleatory and epistemic uncertainty. The propagation of p-boxes leads to p-boxes of the output of the computational model. A two-level meta-modelling approach is proposed using non-intrusive sparse polynomial chaos expansions to surrogate the exact computational model and, hence, to facilitate the uncertainty quantification analysis. The capabilities of the proposed approach are illustrated through applications using a benchmark analytical function and two realistic engineering problem settings. They show that the proposed two-level approach allows for an accurate estimation of the statistics of the response quantity of interest using a small number of evaluations of the exact computational model. This is crucial in cases where the computational costs are dominated by the runs of high-fidelity computational models.

Uncertainty propagation of p-boxes using sparse polynomial chaos expansions

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

Schöbi, Roland, E-mail: schoebi@ibk.baug.ethz.ch; Sudret, Bruno, E-mail: sudret@ibk.baug.ethz.ch

2017-06-15

In modern engineering, physical processes are modelled and analysed using advanced computer simulations, such as finite element models. Furthermore, concepts of reliability analysis and robust design are becoming popular, hence, making efficient quantification and propagation of uncertainties an important aspect. In this context, a typical workflow includes the characterization of the uncertainty in the input variables. In this paper, input variables are modelled by probability-boxes (p-boxes), accounting for both aleatory and epistemic uncertainty. The propagation of p-boxes leads to p-boxes of the output of the computational model. A two-level meta-modelling approach is proposed using non-intrusive sparse polynomial chaos expansions tomore » surrogate the exact computational model and, hence, to facilitate the uncertainty quantification analysis. The capabilities of the proposed approach are illustrated through applications using a benchmark analytical function and two realistic engineering problem settings. They show that the proposed two-level approach allows for an accurate estimation of the statistics of the response quantity of interest using a small number of evaluations of the exact computational model. This is crucial in cases where the computational costs are dominated by the runs of high-fidelity computational models.« less

Adaptiveness in monotone pseudo-Boolean optimization and stochastic neural computation.

PubMed

Grossi, Giuliano

2009-08-01

Hopfield neural network (HNN) is a nonlinear computational model successfully applied in finding near-optimal solutions of several difficult combinatorial problems. In many cases, the network energy function is obtained through a learning procedure so that its minima are states falling into a proper subspace (feasible region) of the search space. However, because of the network nonlinearity, a number of undesirable local energy minima emerge from the learning procedure, significantly effecting the network performance. In the neural model analyzed here, we combine both a penalty and a stochastic process in order to enhance the performance of a binary HNN. The penalty strategy allows us to gradually lead the search towards states representing feasible solutions, so avoiding oscillatory behaviors or asymptotically instable convergence. Presence of stochastic dynamics potentially prevents the network to fall into shallow local minima of the energy function, i.e., quite far from global optimum. Hence, for a given fixed network topology, the desired final distribution on the states can be reached by carefully modulating such process. The model uses pseudo-Boolean functions both to express problem constraints and cost function; a combination of these two functions is then interpreted as energy of the neural network. A wide variety of NP-hard problems fall in the class of problems that can be solved by the model at hand, particularly those having a monotonic quadratic pseudo-Boolean function as constraint function. That is, functions easily derived by closed algebraic expressions representing the constraint structure and easy (polynomial time) to maximize. We show the asymptotic convergence properties of this model characterizing its state space distribution at thermal equilibrium in terms of Markov chain and give evidence of its ability to find high quality solutions on benchmarks and randomly generated instances of two specific problems taken from the computational graph theory.

Grid-converged solution and analysis of the unsteady viscous flow in a two-dimensional shock tube

NASA Astrophysics Data System (ADS)

Zhou, Guangzhao; Xu, Kun; Liu, Feng

2018-01-01

The flow in a shock tube is extremely complex with dynamic multi-scale structures of sharp fronts, flow separation, and vortices due to the interaction of the shock wave, the contact surface, and the boundary layer over the side wall of the tube. Prediction and understanding of the complex fluid dynamics are of theoretical and practical importance. It is also an extremely challenging problem for numerical simulation, especially at relatively high Reynolds numbers. Daru and Tenaud ["Evaluation of TVD high resolution schemes for unsteady viscous shocked flows," Comput. Fluids 30, 89-113 (2001)] proposed a two-dimensional model problem as a numerical test case for high-resolution schemes to simulate the flow field in a square closed shock tube. Though many researchers attempted this problem using a variety of computational methods, there is not yet an agreed-upon grid-converged solution of the problem at the Reynolds number of 1000. This paper presents a rigorous grid-convergence study and the resulting grid-converged solutions for this problem by using a newly developed, efficient, and high-order gas-kinetic scheme. Critical data extracted from the converged solutions are documented as benchmark data. The complex fluid dynamics of the flow at Re = 1000 are discussed and analyzed in detail. Major phenomena revealed by the numerical computations include the downward concentration of the fluid through the curved shock, the formation of the vortices, the mechanism of the shock wave bifurcation, the structure of the jet along the bottom wall, and the Kelvin-Helmholtz instability near the contact surface. Presentation and analysis of those flow processes provide important physical insight into the complex flow physics occurring in a shock tube.

Application of learning to rank to protein remote homology detection.

PubMed

Liu, Bin; Chen, Junjie; Wang, Xiaolong

2015-11-01

Protein remote homology detection is one of the fundamental problems in computational biology, aiming to find protein sequences in a database of known structures that are evolutionarily related to a given query protein. Some computational methods treat this problem as a ranking problem and achieve the state-of-the-art performance, such as PSI-BLAST, HHblits and ProtEmbed. This raises the possibility to combine these methods to improve the predictive performance. In this regard, we are to propose a new computational method called ProtDec-LTR for protein remote homology detection, which is able to combine various ranking methods in a supervised manner via using the Learning to Rank (LTR) algorithm derived from natural language processing. Experimental results on a widely used benchmark dataset showed that ProtDec-LTR can achieve an ROC1 score of 0.8442 and an ROC50 score of 0.9023 outperforming all the individual predictors and some state-of-the-art methods. These results indicate that it is correct to treat protein remote homology detection as a ranking problem, and predictive performance improvement can be achieved by combining different ranking approaches in a supervised manner via using LTR. For users' convenience, the software tools of three basic ranking predictors and Learning to Rank algorithm were provided at http://bioinformatics.hitsz.edu.cn/ProtDec-LTR/home/ bliu@insun.hit.edu.cn Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Benchmarking the Collocation Stand-Alone Library and Toolkit (CSALT)

NASA Technical Reports Server (NTRS)

Hughes, Steven; Knittel, Jeremy; Shoan, Wendy; Kim, Youngkwang; Conway, Claire; Conway, Darrel J.

2017-01-01

This paper describes the processes and results of Verification and Validation (VV) efforts for the Collocation Stand Alone Library and Toolkit (CSALT). We describe the test program and environments, the tools used for independent test data, and comparison results. The VV effort employs classical problems with known analytic solutions, solutions from other available software tools, and comparisons to benchmarking data available in the public literature. Presenting all test results are beyond the scope of a single paper. Here we present high-level test results for a broad range of problems, and detailed comparisons for selected problems.

Benchmarking the Collocation Stand-Alone Library and Toolkit (CSALT)

NASA Technical Reports Server (NTRS)

Hughes, Steven; Knittel, Jeremy; Shoan, Wendy (Compiler); Kim, Youngkwang; Conway, Claire (Compiler); Conway, Darrel

2017-01-01

This paper describes the processes and results of Verification and Validation (V&V) efforts for the Collocation Stand Alone Library and Toolkit (CSALT). We describe the test program and environments, the tools used for independent test data, and comparison results. The V&V effort employs classical problems with known analytic solutions, solutions from other available software tools, and comparisons to benchmarking data available in the public literature. Presenting all test results are beyond the scope of a single paper. Here we present high-level test results for a broad range of problems, and detailed comparisons for selected problems.

Efficiently characterizing the total error in quantum circuits

NASA Astrophysics Data System (ADS)

Carignan-Dugas, Arnaud; Wallman, Joel J.; Emerson, Joseph

A promising technological advancement meant to enlarge our computational means is the quantum computer. Such a device would harvest the quantum complexity of the physical world in order to unfold concrete mathematical problems more efficiently. However, the errors emerging from the implementation of quantum operations are likewise quantum, and hence share a similar level of intricacy. Fortunately, randomized benchmarking protocols provide an efficient way to characterize the operational noise within quantum devices. The resulting figures of merit, like the fidelity and the unitarity, are typically attached to a set of circuit components. While important, this doesn't fulfill the main goal: determining if the error rate of the total circuit is small enough in order to trust its outcome. In this work, we fill the gap by providing an optimal bound on the total fidelity of a circuit in terms of component-wise figures of merit. Our bound smoothly interpolates between the classical regime, in which the error rate grows linearly in the circuit's length, and the quantum regime, which can naturally allow quadratic growth. Conversely, our analysis substantially improves the bounds on single circuit element fidelities obtained through techniques such as interleaved randomized benchmarking. This research was supported by the U.S. Army Research Office through Grant W911NF- 14-1-0103, CIFAR, the Government of Ontario, and the Government of Canada through NSERC and Industry Canada.

Pc as Physics Computer for Lhc ?

NASA Astrophysics Data System (ADS)

Jarp, Sverre; Simmins, Antony; Tang, Hong; Yaari, R.

In the last five years, we have seen RISC workstations take over the computing scene that was once controlled by mainframes and supercomputers. In this paper we will argue that the same phenomenon might happen again. A project, active since March this year in the Physics Data Processing group, of CERN's CN division is described where ordinary desktop PCs running Windows (NT and 3.11) have been used for creating an environment for running large LHC batch jobs (initially the DICE simulation job of Atlas). The problems encountered in porting both the CERN library and the specific Atlas codes are described together with some encouraging benchmark results when comparing to existing RISC workstations in use by the Atlas collaboration. The issues of establishing the batch environment (Batch monitor, staging software, etc.) are also covered. Finally a quick extrapolation of commodity computing power available in the future is touched upon to indicate what kind of cost envelope could be sufficient for the simulation farms required by the LHC experiments.

A spectral approach for discrete dislocation dynamics simulations of nanoindentation

NASA Astrophysics Data System (ADS)

Bertin, Nicolas; Glavas, Vedran; Datta, Dibakar; Cai, Wei

2018-07-01

We present a spectral approach to perform nanoindentation simulations using three-dimensional nodal discrete dislocation dynamics. The method relies on a two step approach. First, the contact problem between an indenter of arbitrary shape and an isotropic elastic half-space is solved using a spectral iterative algorithm, and the contact pressure is fully determined on the half-space surface. The contact pressure is then used as a boundary condition of the spectral solver to determine the resulting stress field produced in the simulation volume. In both stages, the mechanical fields are decomposed into Fourier modes and are efficiently computed using fast Fourier transforms. To further improve the computational efficiency, the method is coupled with a subcycling integrator and a special approach is devised to approximate the displacement field associated with surface steps. As a benchmark, the method is used to compute the response of an elastic half-space using different types of indenter. An example of a dislocation dynamics nanoindentation simulation with complex initial microstructure is presented.

Verification assessment of piston boundary conditions for Lagrangian simulation of compressible flow similarity solutions

DOE PAGES

Ramsey, Scott D.; Ivancic, Philip R.; Lilieholm, Jennifer F.

2015-12-10

This work is concerned with the use of similarity solutions of the compressible flow equations as benchmarks or verification test problems for finite-volume compressible flow simulation software. In practice, this effort can be complicated by the infinite spatial/temporal extent of many candidate solutions or “test problems.” Methods can be devised with the intention of ameliorating this inconsistency with the finite nature of computational simulation; the exact strategy will depend on the code and problem archetypes under investigation. For example, self-similar shock wave propagation can be represented in Lagrangian compressible flow simulations as rigid boundary-driven flow, even if no such “piston”more » is present in the counterpart mathematical similarity solution. The purpose of this work is to investigate in detail the methodology of representing self-similar shock wave propagation as a piston-driven flow in the context of various test problems featuring simple closed-form solutions of infinite spatial/temporal extent. The closed-form solutions allow for the derivation of similarly closed-form piston boundary conditions (BCs) for use in Lagrangian compressible flow solvers. Finally, the consequences of utilizing these BCs (as opposed to directly initializing the self-similar solution in a computational spatial grid) are investigated in terms of common code verification analysis metrics (e.g., shock strength/position errors and global convergence rates).« less

Verification assessment of piston boundary conditions for Lagrangian simulation of compressible flow similarity solutions

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

Ramsey, Scott D.; Ivancic, Philip R.; Lilieholm, Jennifer F.

This work is concerned with the use of similarity solutions of the compressible flow equations as benchmarks or verification test problems for finite-volume compressible flow simulation software. In practice, this effort can be complicated by the infinite spatial/temporal extent of many candidate solutions or “test problems.” Methods can be devised with the intention of ameliorating this inconsistency with the finite nature of computational simulation; the exact strategy will depend on the code and problem archetypes under investigation. For example, self-similar shock wave propagation can be represented in Lagrangian compressible flow simulations as rigid boundary-driven flow, even if no such “piston”more » is present in the counterpart mathematical similarity solution. The purpose of this work is to investigate in detail the methodology of representing self-similar shock wave propagation as a piston-driven flow in the context of various test problems featuring simple closed-form solutions of infinite spatial/temporal extent. The closed-form solutions allow for the derivation of similarly closed-form piston boundary conditions (BCs) for use in Lagrangian compressible flow solvers. Finally, the consequences of utilizing these BCs (as opposed to directly initializing the self-similar solution in a computational spatial grid) are investigated in terms of common code verification analysis metrics (e.g., shock strength/position errors and global convergence rates).« less

Acceleration of the Smith-Waterman algorithm using single and multiple graphics processors

NASA Astrophysics Data System (ADS)

Khajeh-Saeed, Ali; Poole, Stephen; Blair Perot, J.

2010-06-01

Finding regions of similarity between two very long data streams is a computationally intensive problem referred to as sequence alignment. Alignment algorithms must allow for imperfect sequence matching with different starting locations and some gaps and errors between the two data sequences. Perhaps the most well known application of sequence matching is the testing of DNA or protein sequences against genome databases. The Smith-Waterman algorithm is a method for precisely characterizing how well two sequences can be aligned and for determining the optimal alignment of those two sequences. Like many applications in computational science, the Smith-Waterman algorithm is constrained by the memory access speed and can be accelerated significantly by using graphics processors (GPUs) as the compute engine. In this work we show that effective use of the GPU requires a novel reformulation of the Smith-Waterman algorithm. The performance of this new version of the algorithm is demonstrated using the SSCA#1 (Bioinformatics) benchmark running on one GPU and on up to four GPUs executing in parallel. The results indicate that for large problems a single GPU is up to 45 times faster than a CPU for this application, and the parallel implementation shows linear speed up on up to 4 GPUs.

A diffusive information preservation method for small Knudsen number flows

NASA Astrophysics Data System (ADS)

Fei, Fei; Fan, Jing

2013-06-01

The direct simulation Monte Carlo (DSMC) method is a powerful particle-based method for modeling gas flows. It works well for relatively large Knudsen (Kn) numbers, typically larger than 0.01, but quickly becomes computationally intensive as Kn decreases due to its time step and cell size limitations. An alternative approach was proposed to relax or remove these limitations, based on replacing pairwise collisions with a stochastic model corresponding to the Fokker-Planck equation [J. Comput. Phys., 229, 1077 (2010); J. Fluid Mech., 680, 574 (2011)]. Similar to the DSMC method, the downside of that approach suffers from computationally statistical noise. To solve the problem, a diffusion-based information preservation (D-IP) method has been developed. The main idea is to track the motion of a simulated molecule from the diffusive standpoint, and obtain the flow velocity and temperature through sampling and averaging the IP quantities. To validate the idea and the corresponding model, several benchmark problems with Kn ˜ 10-3-10-4 have been investigated. It is shown that the IP calculations are not only accurate, but also efficient because they make possible using a time step and cell size over an order of magnitude larger than the mean collision time and mean free path, respectively.

Fine-grained parallelism accelerating for RNA secondary structure prediction with pseudoknots based on FPGA.

PubMed

Xia, Fei; Jin, Guoqing

2014-06-01

PKNOTS is a most famous benchmark program and has been widely used to predict RNA secondary structure including pseudoknots. It adopts the standard four-dimensional (4D) dynamic programming (DP) method and is the basis of many variants and improved algorithms. Unfortunately, the O(N(6)) computing requirements and complicated data dependency greatly limits the usefulness of PKNOTS package with the explosion in gene database size. In this paper, we present a fine-grained parallel PKNOTS package and prototype system for accelerating RNA folding application based on FPGA chip. We adopted a series of storage optimization strategies to resolve the "Memory Wall" problem. We aggressively exploit parallel computing strategies to improve computational efficiency. We also propose several methods that collectively reduce the storage requirements for FPGA on-chip memory. To the best of our knowledge, our design is the first FPGA implementation for accelerating 4D DP problem for RNA folding application including pseudoknots. The experimental results show a factor of more than 50x average speedup over the PKNOTS-1.08 software running on a PC platform with Intel Core2 Q9400 Quad CPU for input RNA sequences. However, the power consumption of our FPGA accelerator is only about 50% of the general-purpose micro-processors.

A Survey on the Feasibility of Sound Classification on Wireless Sensor Nodes

PubMed Central

Salomons, Etto L.; Havinga, Paul J. M.

2015-01-01

Wireless sensor networks are suitable to gain context awareness for indoor environments. As sound waves form a rich source of context information, equipping the nodes with microphones can be of great benefit. The algorithms to extract features from sound waves are often highly computationally intensive. This can be problematic as wireless nodes are usually restricted in resources. In order to be able to make a proper decision about which features to use, we survey how sound is used in the literature for global sound classification, age and gender classification, emotion recognition, person verification and identification and indoor and outdoor environmental sound classification. The results of the surveyed algorithms are compared with respect to accuracy and computational load. The accuracies are taken from the surveyed papers; the computational loads are determined by benchmarking the algorithms on an actual sensor node. We conclude that for indoor context awareness, the low-cost algorithms for feature extraction perform equally well as the more computationally-intensive variants. As the feature extraction still requires a large amount of processing time, we present four possible strategies to deal with this problem. PMID:25822142

Groundwater flow with energy transport and water-ice phase change: Numerical simulations, benchmarks, and application to freezing in peat bogs

USGS Publications Warehouse

McKenzie, J.M.; Voss, C.I.; Siegel, D.I.

2007-01-01

In northern peatlands, subsurface ice formation is an important process that can control heat transport, groundwater flow, and biological activity. Temperature was measured over one and a half years in a vertical profile in the Red Lake Bog, Minnesota. To successfully simulate the transport of heat within the peat profile, the U.S. Geological Survey's SUTRA computer code was modified. The modified code simulates fully saturated, coupled porewater-energy transport, with freezing and melting porewater, and includes proportional heat capacity and thermal conductivity of water and ice, decreasing matrix permeability due to ice formation, and latent heat. The model is verified by correctly simulating the Lunardini analytical solution for ice formation in a porous medium with a mixed ice-water zone. The modified SUTRA model correctly simulates the temperature and ice distributions in the peat bog. Two possible benchmark problems for groundwater and energy transport with ice formation and melting are proposed that may be used by other researchers for code comparison. ?? 2006 Elsevier Ltd. All rights reserved.

Benchmarking FEniCS for mantle convection simulations

NASA Astrophysics Data System (ADS)

Vynnytska, L.; Rognes, M. E.; Clark, S. R.

2013-01-01

This paper evaluates the usability of the FEniCS Project for mantle convection simulations by numerical comparison to three established benchmarks. The benchmark problems all concern convection processes in an incompressible fluid induced by temperature or composition variations, and cover three cases: (i) steady-state convection with depth- and temperature-dependent viscosity, (ii) time-dependent convection with constant viscosity and internal heating, and (iii) a Rayleigh-Taylor instability. These problems are modeled by the Stokes equations for the fluid and advection-diffusion equations for the temperature and composition. The FEniCS Project provides a novel platform for the automated solution of differential equations by finite element methods. In particular, it offers a significant flexibility with regard to modeling and numerical discretization choices; we have here used a discontinuous Galerkin method for the numerical solution of the advection-diffusion equations. Our numerical results are in agreement with the benchmarks, and demonstrate the applicability of both the discontinuous Galerkin method and FEniCS for such applications.

A Deep Penetration Problem Calculation Using AETIUS:An Easy Modeling Discrete Ordinates Transport Code UsIng Unstructured Tetrahedral Mesh, Shared Memory Parallel

NASA Astrophysics Data System (ADS)

KIM, Jong Woon; LEE, Young-Ouk

2017-09-01

As computing power gets better and better, computer codes that use a deterministic method seem to be less useful than those using the Monte Carlo method. In addition, users do not like to think about space, angles, and energy discretization for deterministic codes. However, a deterministic method is still powerful in that we can obtain a solution of the flux throughout the problem, particularly as when particles can barely penetrate, such as in a deep penetration problem with small detection volumes. Recently, a new state-of-the-art discrete-ordinates code, ATTILA, was developed and has been widely used in several applications. ATTILA provides the capabilities to solve geometrically complex 3-D transport problems by using an unstructured tetrahedral mesh. Since 2009, we have been developing our own code by benchmarking ATTILA. AETIUS is a discrete ordinates code that uses an unstructured tetrahedral mesh such as ATTILA. For pre- and post- processing, Gmsh is used to generate an unstructured tetrahedral mesh by importing a CAD file (*.step) and visualizing the calculation results of AETIUS. Using a CAD tool, the geometry can be modeled very easily. In this paper, we describe a brief overview of AETIUS and provide numerical results from both AETIUS and a Monte Carlo code, MCNP5, in a deep penetration problem with small detection volumes. The results demonstrate the effectiveness and efficiency of AETIUS for such calculations.

A blended continuous–discontinuous finite element method for solving the multi-fluid plasma model

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

Sousa, E.M., E-mail: sousae@uw.edu; Shumlak, U., E-mail: shumlak@uw.edu

The multi-fluid plasma model represents electrons, multiple ion species, and multiple neutral species as separate fluids that interact through short-range collisions and long-range electromagnetic fields. The model spans a large range of temporal and spatial scales, which renders the model stiff and presents numerical challenges. To address the large range of timescales, a blended continuous and discontinuous Galerkin method is proposed, where the massive ion and neutral species are modeled using an explicit discontinuous Galerkin method while the electrons and electromagnetic fields are modeled using an implicit continuous Galerkin method. This approach is able to capture large-gradient ion and neutralmore » physics like shock formation, while resolving high-frequency electron dynamics in a computationally efficient manner. The details of the Blended Finite Element Method (BFEM) are presented. The numerical method is benchmarked for accuracy and tested using two-fluid one-dimensional soliton problem and electromagnetic shock problem. The results are compared to conventional finite volume and finite element methods, and demonstrate that the BFEM is particularly effective in resolving physics in stiff problems involving realistic physical parameters, including realistic electron mass and speed of light. The benefit is illustrated by computing a three-fluid plasma application that demonstrates species separation in multi-component plasmas.« less

On robust parameter estimation in brain-computer interfacing

NASA Astrophysics Data System (ADS)

Samek, Wojciech; Nakajima, Shinichi; Kawanabe, Motoaki; Müller, Klaus-Robert

2017-12-01

Objective. The reliable estimation of parameters such as mean or covariance matrix from noisy and high-dimensional observations is a prerequisite for successful application of signal processing and machine learning algorithms in brain-computer interfacing (BCI). This challenging task becomes significantly more difficult if the data set contains outliers, e.g. due to subject movements, eye blinks or loose electrodes, as they may heavily bias the estimation and the subsequent statistical analysis. Although various robust estimators have been developed to tackle the outlier problem, they ignore important structural information in the data and thus may not be optimal. Typical structural elements in BCI data are the trials consisting of a few hundred EEG samples and indicating the start and end of a task. Approach. This work discusses the parameter estimation problem in BCI and introduces a novel hierarchical view on robustness which naturally comprises different types of outlierness occurring in structured data. Furthermore, the class of minimum divergence estimators is reviewed and a robust mean and covariance estimator for structured data is derived and evaluated with simulations and on a benchmark data set. Main results. The results show that state-of-the-art BCI algorithms benefit from robustly estimated parameters. Significance. Since parameter estimation is an integral part of various machine learning algorithms, the presented techniques are applicable to many problems beyond BCI.

Performance Benchmarking of tsunami-HySEA for NTHMP Inundation Mapping Activities

NASA Astrophysics Data System (ADS)

González Vida, Jose M.; Castro, Manuel J.; Ortega Acosta, Sergio; Macías, Jorge; Millán, Alejandro

2016-04-01

According to the 2006 USA Tsunami Warning and Education Act, the tsunami inundation models used in the National Tsunami Hazard Mitigation Program (NTHMP) projects must be validated against some existing standard problems (see [OAR-PMEL-135], [Proceedings of the 2011 NTHMP Model Benchmarking Workshop]). These Benchmark Problems (BPs) cover different tsunami processes related to the inundation stage that the models must meet to achieve the NTHMP Mapping and Modeling Subcommittee (MMS) approval. Tsunami-HySEA solves the two-dimensional shallow-water system using a high-order path-conservative finite volume method. Values of h, qx and qy in each grid cell represent cell averages of the water depth and momentum components. The numerical scheme is conservative for both mass and momentum in flat bathymetries, and, in general, is mass preserving for arbitrary bathymetries. Tsunami-HySEA implements a PVM-type method that uses the fastest and the slowest wave speeds, similar to HLL method (see [Castro et al, 2012]). A general overview of the derivation of the high order methods is performed in [Castro et al, 2009]. For very big domains, Tsunami-HySEA also implements a two-step scheme similar to leap-frog for the propagation step and a second-order TVD-WAF flux-limiter scheme described in [de la Asunción et al, 2013] for the inundation step. Here, we present the results obtained by the model tsunami-HySEA against the proposed BPs. BP1: Solitary wave on a simple beach (non-breaking - analytic experiment). BP4: Solitary wave on a simple beach (breaking - laboratory experiment). BP6: Solitary wave on a conical island (laboratory experiment). BP7 - Runup on Monai Valley beach (laboratory experiment) and BP9: Okushiri Island tsunami (field experiment). The analysis and results of Tsunami-HySEA model are presented, concluding that the model meets the required objectives for all the BP proposed. References - Castro M.J., E.D. Fernández, A.M. Ferreiro, A. García, C. Parés (2009). High order extension of Roe schemes for two dimensional nonconservative hyperbolic systems. J. Sci. Comput. 39(1), 67-114. - Castro M.J., E.D. Fernández-Nieto (2012). A class of computationally fast first order finite volume solvers: PVM methods. SIAM J. Sci. Comput. 34, A2173-2196. - de la Asunción M., M.J. Castro, E.D. Fernández-Nieto, J.M. Mantas, et al. Efficient GPU implementation of a two waves TVD-WAF method for the two-dimensional one layer shallow water system on structured meshes (2013). Computers & Fluids 80, 441-452. - OAR PMEL-135. Synolakis, C.E., E.N. Bernard, V.V. Titov, U. Kânoǧlu, and F.I. González (2007). Standards, criteria, and procedures for NOAA evaluation of tsunami numerical models. NOAA Tech. Memo. NOAA/Pacific Marine Environmental Laboratory, Seattle, WA, 55 pp. - Proceedings and results of the 2011 NTHMP Model Benchmarking Workshop. NOAA Special Report. July 2012. Acknowledgements This research has been partially supported by the Junta de Andalucía research project TESELA (P11-RNM7069), the Spanish Government Research project DAIFLUID (MTM2012-38383-C02-01) and the Unit of Numerical Methods (UNM) of the Research Support Central Services (SCAI) of the University of Málaga.

TRUST. I. A 3D externally illuminated slab benchmark for dust radiative transfer

NASA Astrophysics Data System (ADS)

Gordon, K. D.; Baes, M.; Bianchi, S.; Camps, P.; Juvela, M.; Kuiper, R.; Lunttila, T.; Misselt, K. A.; Natale, G.; Robitaille, T.; Steinacker, J.

2017-07-01

Context. The radiative transport of photons through arbitrary three-dimensional (3D) structures of dust is a challenging problem due to the anisotropic scattering of dust grains and strong coupling between different spatial regions. The radiative transfer problem in 3D is solved using Monte Carlo or Ray Tracing techniques as no full analytic solution exists for the true 3D structures. Aims: We provide the first 3D dust radiative transfer benchmark composed of a slab of dust with uniform density externally illuminated by a star. This simple 3D benchmark is explicitly formulated to provide tests of the different components of the radiative transfer problem including dust absorption, scattering, and emission. Methods: The details of the external star, the slab itself, and the dust properties are provided. This benchmark includes models with a range of dust optical depths fully probing cases that are optically thin at all wavelengths to optically thick at most wavelengths. The dust properties adopted are characteristic of the diffuse Milky Way interstellar medium. This benchmark includes solutions for the full dust emission including single photon (stochastic) heating as well as two simplifying approximations: One where all grains are considered in equilibrium with the radiation field and one where the emission is from a single effective grain with size-distribution-averaged properties. A total of six Monte Carlo codes and one Ray Tracing code provide solutions to this benchmark. Results: The solution to this benchmark is given as global spectral energy distributions (SEDs) and images at select diagnostic wavelengths from the ultraviolet through the infrared. Comparison of the results revealed that the global SEDs are consistent on average to a few percent for all but the scattered stellar flux at very high optical depths. The image results are consistent within 10%, again except for the stellar scattered flux at very high optical depths. The lack of agreement between different codes of the scattered flux at high optical depths is quantified for the first time. Convergence tests using one of the Monte Carlo codes illustrate the sensitivity of the solutions to various model parameters. Conclusions: We provide the first 3D dust radiative transfer benchmark and validate the accuracy of this benchmark through comparisons between multiple independent codes and detailed convergence tests.

3D hierarchical interface-enriched finite element method: Implementation and applications

NASA Astrophysics Data System (ADS)

Soghrati, Soheil; Ahmadian, Hossein

2015-10-01

A hierarchical interface-enriched finite element method (HIFEM) is proposed for the mesh-independent treatment of 3D problems with intricate morphologies. The HIFEM implements a recursive algorithm for creating enrichment functions that capture gradient discontinuities in nonconforming finite elements cut by arbitrary number and configuration of materials interfaces. The method enables the mesh-independent simulation of multiphase problems with materials interfaces that are in close proximity or contact while providing a straightforward general approach for evaluating the enrichments. In this manuscript, we present a detailed discussion on the implementation issues and required computational geometry considerations associated with the HIFEM approximation of thermal and mechanical responses of 3D problems. A convergence study is provided to investigate the accuracy and convergence rate of the HIFEM and compare them with standard FEM benchmark solutions. We will also demonstrate the application of this mesh-independent method for simulating the thermal and mechanical responses of two composite materials systems with complex microstructures.

Classification of adaptive memetic algorithms: a comparative study.

PubMed

Ong, Yew-Soon; Lim, Meng-Hiot; Zhu, Ning; Wong, Kok-Wai

2006-02-01

Adaptation of parameters and operators represents one of the recent most important and promising areas of research in evolutionary computations; it is a form of designing self-configuring algorithms that acclimatize to suit the problem in hand. Here, our interests are on a recent breed of hybrid evolutionary algorithms typically known as adaptive memetic algorithms (MAs). One unique feature of adaptive MAs is the choice of local search methods or memes and recent studies have shown that this choice significantly affects the performances of problem searches. In this paper, we present a classification of memes adaptation in adaptive MAs on the basis of the mechanism used and the level of historical knowledge on the memes employed. Then the asymptotic convergence properties of the adaptive MAs considered are analyzed according to the classification. Subsequently, empirical studies on representatives of adaptive MAs for different type-level meme adaptations using continuous benchmark problems indicate that global-level adaptive MAs exhibit better search performances. Finally we conclude with some promising research directions in the area.

An iterated local search algorithm for the team orienteering problem with variable profits

NASA Astrophysics Data System (ADS)

Gunawan, Aldy; Ng, Kien Ming; Kendall, Graham; Lai, Junhan

2018-07-01

The orienteering problem (OP) is a routing problem that has numerous applications in various domains such as logistics and tourism. The objective is to determine a subset of vertices to visit for a vehicle so that the total collected score is maximized and a given time budget is not exceeded. The extensive application of the OP has led to many different variants, including the team orienteering problem (TOP) and the team orienteering problem with time windows. The TOP extends the OP by considering multiple vehicles. In this article, the team orienteering problem with variable profits (TOPVP) is studied. The main characteristic of the TOPVP is that the amount of score collected from a visited vertex depends on the duration of stay on that vertex. A mathematical programming model for the TOPVP is first presented and an algorithm based on iterated local search (ILS) that is able to solve modified benchmark instances is then proposed. It is concluded that ILS produces solutions which are comparable to those obtained by the commercial solver CPLEX for smaller instances. For the larger instances, ILS obtains good-quality solutions that have significantly better objective value than those found by CPLEX under reasonable computational times.

A Simple Graphical Method for Quantification of Disaster Management Surge Capacity Using Computer Simulation and Process-control Tools.

PubMed

Franc, Jeffrey Michael; Ingrassia, Pier Luigi; Verde, Manuela; Colombo, Davide; Della Corte, Francesco

2015-02-01

Surge capacity, or the ability to manage an extraordinary volume of patients, is fundamental for hospital management of mass-casualty incidents. However, quantification of surge capacity is difficult and no universal standard for its measurement has emerged, nor has a standardized statistical method been advocated. As mass-casualty incidents are rare, simulation may represent a viable alternative to measure surge capacity. Hypothesis/Problem The objective of the current study was to develop a statistical method for the quantification of surge capacity using a combination of computer simulation and simple process-control statistical tools. Length-of-stay (LOS) and patient volume (PV) were used as metrics. The use of this method was then demonstrated on a subsequent computer simulation of an emergency department (ED) response to a mass-casualty incident. In the derivation phase, 357 participants in five countries performed 62 computer simulations of an ED response to a mass-casualty incident. Benchmarks for ED response were derived from these simulations, including LOS and PV metrics for triage, bed assignment, physician assessment, and disposition. In the application phase, 13 students of the European Master in Disaster Medicine (EMDM) program completed the same simulation scenario, and the results were compared to the standards obtained in the derivation phase. Patient-volume metrics included number of patients to be triaged, assigned to rooms, assessed by a physician, and disposed. Length-of-stay metrics included median time to triage, room assignment, physician assessment, and disposition. Simple graphical methods were used to compare the application phase group to the derived benchmarks using process-control statistical tools. The group in the application phase failed to meet the indicated standard for LOS from admission to disposition decision. This study demonstrates how simulation software can be used to derive values for objective benchmarks of ED surge capacity using PV and LOS metrics. These objective metrics can then be applied to other simulation groups using simple graphical process-control tools to provide a numeric measure of surge capacity. Repeated use in simulations of actual EDs may represent a potential means of objectively quantifying disaster management surge capacity. It is hoped that the described statistical method, which is simple and reusable, will be useful for investigators in this field to apply to their own research.

NAS Parallel Benchmarks. 2.4

NASA Technical Reports Server (NTRS)

VanderWijngaart, Rob; Biegel, Bryan A. (Technical Monitor)

2002-01-01

We describe a new problem size, called Class D, for the NAS Parallel Benchmarks (NPB), whose MPI source code implementation is being released as NPB 2.4. A brief rationale is given for how the new class is derived. We also describe the modifications made to the MPI (Message Passing Interface) implementation to allow the new class to be run on systems with 32-bit integers, and with moderate amounts of memory. Finally, we give the verification values for the new problem size.

A benchmarking tool to evaluate computer tomography perfusion infarct core predictions against a DWI standard.

PubMed

Cereda, Carlo W; Christensen, Søren; Campbell, Bruce Cv; Mishra, Nishant K; Mlynash, Michael; Levi, Christopher; Straka, Matus; Wintermark, Max; Bammer, Roland; Albers, Gregory W; Parsons, Mark W; Lansberg, Maarten G

2016-10-01

Differences in research methodology have hampered the optimization of Computer Tomography Perfusion (CTP) for identification of the ischemic core. We aim to optimize CTP core identification using a novel benchmarking tool. The benchmarking tool consists of an imaging library and a statistical analysis algorithm to evaluate the performance of CTP. The tool was used to optimize and evaluate an in-house developed CTP-software algorithm. Imaging data of 103 acute stroke patients were included in the benchmarking tool. Median time from stroke onset to CT was 185 min (IQR 180-238), and the median time between completion of CT and start of MRI was 36 min (IQR 25-79). Volumetric accuracy of the CTP-ROIs was optimal at an rCBF threshold of <38%; at this threshold, the mean difference was 0.3 ml (SD 19.8 ml), the mean absolute difference was 14.3 (SD 13.7) ml, and CTP was 67% sensitive and 87% specific for identification of DWI positive tissue voxels. The benchmarking tool can play an important role in optimizing CTP software as it provides investigators with a novel method to directly compare the performance of alternative CTP software packages. © The Author(s) 2015.

Assessment of composite motif discovery methods.

PubMed

Klepper, Kjetil; Sandve, Geir K; Abul, Osman; Johansen, Jostein; Drablos, Finn

2008-02-26

Computational discovery of regulatory elements is an important area of bioinformatics research and more than a hundred motif discovery methods have been published. Traditionally, most of these methods have addressed the problem of single motif discovery - discovering binding motifs for individual transcription factors. In higher organisms, however, transcription factors usually act in combination with nearby bound factors to induce specific regulatory behaviours. Hence, recent focus has shifted from single motifs to the discovery of sets of motifs bound by multiple cooperating transcription factors, so called composite motifs or cis-regulatory modules. Given the large number and diversity of methods available, independent assessment of methods becomes important. Although there have been several benchmark studies of single motif discovery, no similar studies have previously been conducted concerning composite motif discovery. We have developed a benchmarking framework for composite motif discovery and used it to evaluate the performance of eight published module discovery tools. Benchmark datasets were constructed based on real genomic sequences containing experimentally verified regulatory modules, and the module discovery programs were asked to predict both the locations of these modules and to specify the single motifs involved. To aid the programs in their search, we provided position weight matrices corresponding to the binding motifs of the transcription factors involved. In addition, selections of decoy matrices were mixed with the genuine matrices on one dataset to test the response of programs to varying levels of noise. Although some of the methods tested tended to score somewhat better than others overall, there were still large variations between individual datasets and no single method performed consistently better than the rest in all situations. The variation in performance on individual datasets also shows that the new benchmark datasets represents a suitable variety of challenges to most methods for module discovery.

SIGACE Code for Generating High-Temperature ACE Files; Validation and Benchmarking

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

Sharma, Amit R.; Ganesan, S.; Trkov, A.

2005-05-24

A code named SIGACE has been developed as a tool for MCNP users within the scope of a research contract awarded by the Nuclear Data Section of the International Atomic Energy Agency (IAEA) (Ref: 302-F4-IND-11566 B5-IND-29641). A new recipe has been evolved for generating high-temperature ACE files for use with the MCNP code. Under this scheme the low-temperature ACE file is first converted to an ENDF formatted file using the ACELST code and then Doppler broadened, essentially limited to the data in the resolved resonance region, to any desired higher temperature using SIGMA1. The SIGACE code then generates a high-temperaturemore » ACE file for use with the MCNP code. A thinning routine has also been introduced in the SIGACE code for reducing the size of the ACE files. The SIGACE code and the recipe for generating ACE files at higher temperatures has been applied to the SEFOR fast reactor benchmark problem (sodium-cooled fast reactor benchmark described in ENDF-202/BNL-19302, 1974 document). The calculated Doppler coefficient is in good agreement with the experimental value. A similar calculation using ACE files generated directly with the NJOY system also agrees with our SIGACE computed results. The SIGACE code and the recipe is further applied to study the numerical benchmark configuration of selected idealized PWR pin cell configurations with five different fuel enrichments as reported by Mosteller and Eisenhart. The SIGACE code that has been tested with several FENDL/MC files will be available, free of cost, upon request, from the Nuclear Data Section of the IAEA.« less

Processor Emulator with Benchmark Applications

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

Lloyd, G. Scott; Pearce, Roger; Gokhale, Maya

2015-11-13

A processor emulator and a suite of benchmark applications have been developed to assist in characterizing the performance of data-centric workloads on current and future computer architectures. Some of the applications have been collected from other open source projects. For more details on the emulator and an example of its usage, see reference [1].

Probabilistic performance estimators for computational chemistry methods: The empirical cumulative distribution function of absolute errors

NASA Astrophysics Data System (ADS)

Pernot, Pascal; Savin, Andreas

2018-06-01

Benchmarking studies in computational chemistry use reference datasets to assess the accuracy of a method through error statistics. The commonly used error statistics, such as the mean signed and mean unsigned errors, do not inform end-users on the expected amplitude of prediction errors attached to these methods. We show that, the distributions of model errors being neither normal nor zero-centered, these error statistics cannot be used to infer prediction error probabilities. To overcome this limitation, we advocate for the use of more informative statistics, based on the empirical cumulative distribution function of unsigned errors, namely, (1) the probability for a new calculation to have an absolute error below a chosen threshold and (2) the maximal amplitude of errors one can expect with a chosen high confidence level. Those statistics are also shown to be well suited for benchmarking and ranking studies. Moreover, the standard error on all benchmarking statistics depends on the size of the reference dataset. Systematic publication of these standard errors would be very helpful to assess the statistical reliability of benchmarking conclusions.

First benchmark of the Unstructured Grid Adaptation Working Group

NASA Technical Reports Server (NTRS)

Ibanez, Daniel; Barral, Nicolas; Krakos, Joshua; Loseille, Adrien; Michal, Todd; Park, Mike

2017-01-01

Unstructured grid adaptation is a technology that holds the potential to improve the automation and accuracy of computational fluid dynamics and other computational disciplines. Difficulty producing the highly anisotropic elements necessary for simulation on complex curved geometries that satisfies a resolution request has limited this technology's widespread adoption. The Unstructured Grid Adaptation Working Group is an open gathering of researchers working on adapting simplicial meshes to conform to a metric field. Current members span a wide range of institutions including academia, industry, and national laboratories. The purpose of this group is to create a common basis for understanding and improving mesh adaptation. We present our first major contribution: a common set of benchmark cases, including input meshes and analytic metric specifications, that are publicly available to be used for evaluating any mesh adaptation code. We also present the results of several existing codes on these benchmark cases, to illustrate their utility in identifying key challenges common to all codes and important differences between available codes. Future directions are defined to expand this benchmark to mature the technology necessary to impact practical simulation workflows.

Optimization of a solid-state electron spin qubit using Gate Set Tomography

DOE PAGES

Dehollain, Juan P.; Muhonen, Juha T.; Blume-Kohout, Robin J.; ...

2016-10-13

Here, state of the art qubit systems are reaching the gate fidelities required for scalable quantum computation architectures. Further improvements in the fidelity of quantum gates demands characterization and benchmarking protocols that are efficient, reliable and extremely accurate. Ideally, a benchmarking protocol should also provide information on how to rectify residual errors. Gate Set Tomography (GST) is one such protocol designed to give detailed characterization of as-built qubits. We implemented GST on a high-fidelity electron-spin qubit confined by a single 31P atom in 28Si. The results reveal systematic errors that a randomized benchmarking analysis could measure but not identify, whereasmore » GST indicated the need for improved calibration of the length of the control pulses. After introducing this modification, we measured a new benchmark average gate fidelity of 99.942(8)%, an improvement on the previous value of 99.90(2)%. Furthermore, GST revealed high levels of non-Markovian noise in the system, which will need to be understood and addressed when the qubit is used within a fault-tolerant quantum computation scheme.« less

Driver's workload comparison in waste collection vehicle routing problem

NASA Astrophysics Data System (ADS)

Benjamin, Aida Mauziah; Abdul-Rahman, Syariza

2016-10-01

This paper compares the workload of the drivers for a waste collection benchmark problem. The problem involves ten data sets with different number of customers to be served and different number of disposal facilities available. Previous studies proposed a heuristic algorithm, namely Different Initial Customer (DIC) to solve the problem by constructing initial vehicles routes for the drivers with two main objectives; to minimize the total distance travelled and to minimize the total number of vehicles needed to collect the waste. The results from DIC compared well with other solutions in the literature. However, the balance of the workload among the vehicle drivers is not considered in the solutions. Thus in this paper, we evaluate the quality of the solutions in terms of the total number of customers served by each driver. Then the computational result is compared in terms of the total distance travelled which have been presented in a previous study. Comparison results show that the workload of the drivers are unbalance in terms of these two factors that may cause dissatisfaction among the drivers as well as to the managament.

Demonstration of qubit operations below a rigorous fault tolerance threshold with gate set tomography

DOE PAGES

Blume-Kohout, Robin; Gamble, John King; Nielsen, Erik; ...

2017-02-15

Quantum information processors promise fast algorithms for problems inaccessible to classical computers. But since qubits are noisy and error-prone, they will depend on fault-tolerant quantum error correction (FTQEC) to compute reliably. Quantum error correction can protect against general noise if—and only if—the error in each physical qubit operation is smaller than a certain threshold. The threshold for general errors is quantified by their diamond norm. Until now, qubits have been assessed primarily by randomized benchmarking, which reports a different error rate that is not sensitive to all errors, and cannot be compared directly to diamond norm thresholds. Finally, we usemore » gate set tomography to completely characterize operations on a trapped-Yb +-ion qubit and demonstrate with greater than 95% confidence that they satisfy a rigorous threshold for FTQEC (diamond norm ≤6.7 × 10 -4).« less

A Commodity Computing Cluster

NASA Astrophysics Data System (ADS)

Teuben, P. J.; Wolfire, M. G.; Pound, M. W.; Mundy, L. G.

We have assembled a cluster of Intel-Pentium based PCs running Linux to compute a large set of Photodissociation Region (PDR) and Dust Continuum models. For various reasons the cluster is heterogeneous, currently ranging from a single Pentium-II 333 MHz to dual Pentium-III 450 MHz CPU machines. Although this will be sufficient for our ``embarrassingly parallelizable problem'' it may present some challenges for as yet unplanned future use. In addition the cluster was used to construct a MIRIAD benchmark, and compared to equivalent Ultra-Sparc based workstations. Currently the cluster consists of 8 machines, 14 CPUs, 50GB of disk-space, and a total peak speed of 5.83 GHz, or about 1.5 Gflops. The total cost of this cluster has been about $12,000, including all cabling, networking equipment, rack, and a CD-R backup system. The URL for this project is http://dustem.astro.umd.edu.

Demonstration of qubit operations below a rigorous fault tolerance threshold with gate set tomography

PubMed Central

Blume-Kohout, Robin; Gamble, John King; Nielsen, Erik; Rudinger, Kenneth; Mizrahi, Jonathan; Fortier, Kevin; Maunz, Peter

2017-01-01

Quantum information processors promise fast algorithms for problems inaccessible to classical computers. But since qubits are noisy and error-prone, they will depend on fault-tolerant quantum error correction (FTQEC) to compute reliably. Quantum error correction can protect against general noise if—and only if—the error in each physical qubit operation is smaller than a certain threshold. The threshold for general errors is quantified by their diamond norm. Until now, qubits have been assessed primarily by randomized benchmarking, which reports a different error rate that is not sensitive to all errors, and cannot be compared directly to diamond norm thresholds. Here we use gate set tomography to completely characterize operations on a trapped-Yb+-ion qubit and demonstrate with greater than 95% confidence that they satisfy a rigorous threshold for FTQEC (diamond norm ≤6.7 × 10−4). PMID:28198466

Demonstration of qubit operations below a rigorous fault tolerance threshold with gate set tomography

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

Blume-Kohout, Robin; Gamble, John King; Nielsen, Erik

Quantum information processors promise fast algorithms for problems inaccessible to classical computers. But since qubits are noisy and error-prone, they will depend on fault-tolerant quantum error correction (FTQEC) to compute reliably. Quantum error correction can protect against general noise if—and only if—the error in each physical qubit operation is smaller than a certain threshold. The threshold for general errors is quantified by their diamond norm. Until now, qubits have been assessed primarily by randomized benchmarking, which reports a different error rate that is not sensitive to all errors, and cannot be compared directly to diamond norm thresholds. Finally, we usemore » gate set tomography to completely characterize operations on a trapped-Yb +-ion qubit and demonstrate with greater than 95% confidence that they satisfy a rigorous threshold for FTQEC (diamond norm ≤6.7 × 10 -4).« less

Computational Performance of a Parallelized Three-Dimensional High-Order Spectral Element Toolbox

NASA Astrophysics Data System (ADS)

Bosshard, Christoph; Bouffanais, Roland; Clémençon, Christian; Deville, Michel O.; Fiétier, Nicolas; Gruber, Ralf; Kehtari, Sohrab; Keller, Vincent; Latt, Jonas

In this paper, a comprehensive performance review of an MPI-based high-order three-dimensional spectral element method C++ toolbox is presented. The focus is put on the performance evaluation of several aspects with a particular emphasis on the parallel efficiency. The performance evaluation is analyzed with help of a time prediction model based on a parameterization of the application and the hardware resources. A tailor-made CFD computation benchmark case is introduced and used to carry out this review, stressing the particular interest for clusters with up to 8192 cores. Some problems in the parallel implementation have been detected and corrected. The theoretical complexities with respect to the number of elements, to the polynomial degree, and to communication needs are correctly reproduced. It is concluded that this type of code has a nearly perfect speed up on machines with thousands of cores, and is ready to make the step to next-generation petaflop machines.

Benchmark solutions for the galactic ion transport equations: Energy and spatially dependent problems

NASA Technical Reports Server (NTRS)

Ganapol, Barry D.; Townsend, Lawrence W.; Wilson, John W.

1989-01-01

Nontrivial benchmark solutions are developed for the galactic ion transport (GIT) equations in the straight-ahead approximation. These equations are used to predict potential radiation hazards in the upper atmosphere and in space. Two levels of difficulty are considered: (1) energy independent, and (2) spatially independent. The analysis emphasizes analytical methods never before applied to the GIT equations. Most of the representations derived have been numerically implemented and compared to more approximate calculations. Accurate ion fluxes are obtained (3 to 5 digits) for nontrivial sources. For monoenergetic beams, both accurate doses and fluxes are found. The benchmarks presented are useful in assessing the accuracy of transport algorithms designed to accommodate more complex radiation protection problems. In addition, these solutions can provide fast and accurate assessments of relatively simple shield configurations.

A novel discrete PSO algorithm for solving job shop scheduling problem to minimize makespan

NASA Astrophysics Data System (ADS)

Rameshkumar, K.; Rajendran, C.

2018-02-01

In this work, a discrete version of PSO algorithm is proposed to minimize the makespan of a job-shop. A novel schedule builder has been utilized to generate active schedules. The discrete PSO is tested using well known benchmark problems available in the literature. The solution produced by the proposed algorithms is compared with best known solution published in the literature and also compared with hybrid particle swarm algorithm and variable neighborhood search PSO algorithm. The solution construction methodology adopted in this study is found to be effective in producing good quality solutions for the various benchmark job-shop scheduling problems.

Finite Element Modeling of the World Federation's Second MFL Benchmark Problem

NASA Astrophysics Data System (ADS)

Zeng, Zhiwei; Tian, Yong; Udpa, Satish; Udpa, Lalita

2004-02-01

This paper presents results obtained by simulating the second magnetic flux leakage benchmark problem proposed by the World Federation of NDE Centers. The geometry consists of notches machined on the internal and external surfaces of a rotating steel pipe that is placed between two yokes that are part of a magnetic circuit energized by an electromagnet. The model calculates the radial component of the leaked field at specific positions. The nonlinear material property of the ferromagnetic pipe is taken into account in simulating the problem. The velocity effect caused by the rotation of the pipe is, however, ignored for reasons of simplicity.

Benchmark Evaluation of Start-Up and Zero-Power Measurements at the High-Temperature Engineering Test Reactor

DOE PAGES

Bess, John D.; Fujimoto, Nozomu

2014-10-09

Benchmark models were developed to evaluate six cold-critical and two warm-critical, zero-power measurements of the HTTR. Additional measurements of a fully-loaded subcritical configuration, core excess reactivity, shutdown margins, six isothermal temperature coefficients, and axial reaction-rate distributions were also evaluated as acceptable benchmark experiments. Insufficient information is publicly available to develop finely-detailed models of the HTTR as much of the design information is still proprietary. However, the uncertainties in the benchmark models are judged to be of sufficient magnitude to encompass any biases and bias uncertainties incurred through the simplification process used to develop the benchmark models. Dominant uncertainties in themore » experimental keff for all core configurations come from uncertainties in the impurity content of the various graphite blocks that comprise the HTTR. Monte Carlo calculations of keff are between approximately 0.9 % and 2.7 % greater than the benchmark values. Reevaluation of the HTTR models as additional information becomes available could improve the quality of this benchmark and possibly reduce the computational biases. High-quality characterization of graphite impurities would significantly improve the quality of the HTTR benchmark assessment. Simulation of the other reactor physics measurements are in good agreement with the benchmark experiment values. The complete benchmark evaluation details are available in the 2014 edition of the International Handbook of Evaluated Reactor Physics Benchmark Experiments.« less

HPC on Competitive Cloud Resources

NASA Astrophysics Data System (ADS)

Bientinesi, Paolo; Iakymchuk, Roman; Napper, Jeff

Computing as a utility has reached the mainstream. Scientists can now easily rent time on large commercial clusters that can be expanded and reduced on-demand in real-time. However, current commercial cloud computing performance falls short of systems specifically designed for scientific applications. Scientific computing needs are quite different from those of the web applications that have been the focus of cloud computing vendors. In this chapter we demonstrate through empirical evaluation the computational efficiency of high-performance numerical applications in a commercial cloud environment when resources are shared under high contention. Using the Linpack benchmark as a case study, we show that cache utilization becomes highly unpredictable and similarly affects computation time. For some problems, not only is it more efficient to underutilize resources, but the solution can be reached sooner in realtime (wall-time). We also show that the smallest, cheapest (64-bit) instance on the studied environment is the best for price to performance ration. In light of the high-contention we witness, we believe that alternative definitions of efficiency for commercial cloud environments should be introduced where strong performance guarantees do not exist. Concepts like average, expected performance and execution time, expected cost to completion, and variance measures--traditionally ignored in the high-performance computing context--now should complement or even substitute the standard definitions of efficiency.

Space Object Collision Probability via Monte Carlo on the Graphics Processing Unit

NASA Astrophysics Data System (ADS)

Vittaldev, Vivek; Russell, Ryan P.

2017-09-01

Fast and accurate collision probability computations are essential for protecting space assets. Monte Carlo (MC) simulation is the most accurate but computationally intensive method. A Graphics Processing Unit (GPU) is used to parallelize the computation and reduce the overall runtime. Using MC techniques to compute the collision probability is common in literature as the benchmark. An optimized implementation on the GPU, however, is a challenging problem and is the main focus of the current work. The MC simulation takes samples from the uncertainty distributions of the Resident Space Objects (RSOs) at any time during a time window of interest and outputs the separations at closest approach. Therefore, any uncertainty propagation method may be used and the collision probability is automatically computed as a function of RSO collision radii. Integration using a fixed time step and a quartic interpolation after every Runge Kutta step ensures that no close approaches are missed. Two orders of magnitude speedups over a serial CPU implementation are shown, and speedups improve moderately with higher fidelity dynamics. The tool makes the MC approach tractable on a single workstation, and can be used as a final product, or for verifying surrogate and analytical collision probability methods.

Architectures for Quantum Simulation Showing a Quantum Speedup

NASA Astrophysics Data System (ADS)

Bermejo-Vega, Juan; Hangleiter, Dominik; Schwarz, Martin; Raussendorf, Robert; Eisert, Jens

2018-04-01

One of the main aims in the field of quantum simulation is to achieve a quantum speedup, often referred to as "quantum computational supremacy," referring to the experimental realization of a quantum device that computationally outperforms classical computers. In this work, we show that one can devise versatile and feasible schemes of two-dimensional, dynamical, quantum simulators showing such a quantum speedup, building on intermediate problems involving nonadaptive, measurement-based, quantum computation. In each of the schemes, an initial product state is prepared, potentially involving an element of randomness as in disordered models, followed by a short-time evolution under a basic translationally invariant Hamiltonian with simple nearest-neighbor interactions and a mere sampling measurement in a fixed basis. The correctness of the final-state preparation in each scheme is fully efficiently certifiable. We discuss experimental necessities and possible physical architectures, inspired by platforms of cold atoms in optical lattices and a number of others, as well as specific assumptions that enter the complexity-theoretic arguments. This work shows that benchmark settings exhibiting a quantum speedup may require little control, in contrast to universal quantum computing. Thus, our proposal puts a convincing experimental demonstration of a quantum speedup within reach in the near term.

Evaluating the Efficacy of the Cloud for Cluster Computation

NASA Technical Reports Server (NTRS)

Knight, David; Shams, Khawaja; Chang, George; Soderstrom, Tom

2012-01-01

Computing requirements vary by industry, and it follows that NASA and other research organizations have computing demands that fall outside the mainstream. While cloud computing made rapid inroads for tasks such as powering web applications, performance issues on highly distributed tasks hindered early adoption for scientific computation. One venture to address this problem is Nebula, NASA's homegrown cloud project tasked with delivering science-quality cloud computing resources. However, another industry development is Amazon's high-performance computing (HPC) instances on Elastic Cloud Compute (EC2) that promises improved performance for cluster computation. This paper presents results from a series of benchmarks run on Amazon EC2 and discusses the efficacy of current commercial cloud technology for running scientific applications across a cluster. In particular, a 240-core cluster of cloud instances achieved 2 TFLOPS on High-Performance Linpack (HPL) at 70% of theoretical computational performance. The cluster's local network also demonstrated sub-100 ?s inter-process latency with sustained inter-node throughput in excess of 8 Gbps. Beyond HPL, a real-world Hadoop image processing task from NASA's Lunar Mapping and Modeling Project (LMMP) was run on a 29 instance cluster to process lunar and Martian surface images with sizes on the order of tens of gigapixels. These results demonstrate that while not a rival of dedicated supercomputing clusters, commercial cloud technology is now a feasible option for moderately demanding scientific workloads.

A Hidden Markov Model Approach to the Problem of Heuristic Selection in Hyper-Heuristics with a Case Study in High School Timetabling Problems.

PubMed

Kheiri, Ahmed; Keedwell, Ed

2017-01-01

Operations research is a well-established field that uses computational systems to support decisions in business and public life. Good solutions to operations research problems can make a large difference to the efficient running of businesses and organisations and so the field often searches for new methods to improve these solutions. The high school timetabling problem is an example of an operations research problem and is a challenging task which requires assigning events and resources to time slots subject to a set of constraints. In this article, a new sequence-based selection hyper-heuristic is presented that produces excellent results on a suite of high school timetabling problems. In this study, we present an easy-to-implement, easy-to-maintain, and effective sequence-based selection hyper-heuristic to solve high school timetabling problems using a benchmark of unified real-world instances collected from different countries. We show that with sequence-based methods, it is possible to discover new best known solutions for a number of the problems in the timetabling domain. Through this investigation, the usefulness of sequence-based selection hyper-heuristics has been demonstrated and the capability of these methods has been shown to exceed the state of the art.

Clear, Complete, and Justified Problem Formulations for Aquatic Life Benchmark Values: Specifying the Dimensions

EPA Science Inventory

Nations that develop water quality benchmark values have relied primarily on standard data and methods. However, experience with chemicals such as Se, ammonia, and tributyltin has shown that standard methods do not adequately address some taxa, modes of exposure and effects. Deve...

CLEAR, COMPLETE, AND JUSTIFIED PROBLEM FORMULATIONS FOR AQUATIC LIFE BENCHMARK VALUES: SPECIFYING THE DIMENSIONS

EPA Science Inventory

Nations that develop water quality benchmark values have relied primarily on standard data and methods. However, experience with chemicals such as Se, ammonia, and tributyltin has shown that standard methods do not adequately address some taxa, modes of exposure and effects. Deve...

Surrogate model approach for improving the performance of reactive transport simulations

NASA Astrophysics Data System (ADS)

Jatnieks, Janis; De Lucia, Marco; Sips, Mike; Dransch, Doris

2016-04-01

Reactive transport models can serve a large number of important geoscientific applications involving underground resources in industry and scientific research. It is common for simulation of reactive transport to consist of at least two coupled simulation models. First is a hydrodynamics simulator that is responsible for simulating the flow of groundwaters and transport of solutes. Hydrodynamics simulators are well established technology and can be very efficient. When hydrodynamics simulations are performed without coupled geochemistry, their spatial geometries can span millions of elements even when running on desktop workstations. Second is a geochemical simulation model that is coupled to the hydrodynamics simulator. Geochemical simulation models are much more computationally costly. This is a problem that makes reactive transport simulations spanning millions of spatial elements very difficult to achieve. To address this problem we propose to replace the coupled geochemical simulation model with a surrogate model. A surrogate is a statistical model created to include only the necessary subset of simulator complexity for a particular scenario. To demonstrate the viability of such an approach we tested it on a popular reactive transport benchmark problem that involves 1D Calcite transport. This is a published benchmark problem (Kolditz, 2012) for simulation models and for this reason we use it to test the surrogate model approach. To do this we tried a number of statistical models available through the caret and DiceEval packages for R, to be used as surrogate models. These were trained on randomly sampled subset of the input-output data from the geochemical simulation model used in the original reactive transport simulation. For validation we use the surrogate model to predict the simulator output using the part of sampled input data that was not used for training the statistical model. For this scenario we find that the multivariate adaptive regression splines (MARS) method provides the best trade-off between speed and accuracy. This proof-of-concept forms an essential step towards building an interactive visual analytics system to enable user-driven systematic creation of geochemical surrogate models. Such a system shall enable reactive transport simulations with unprecedented spatial and temporal detail to become possible. References: Kolditz, O., Görke, U.J., Shao, H. and Wang, W., 2012. Thermo-hydro-mechanical-chemical processes in porous media: benchmarks and examples (Vol. 86). Springer Science & Business Media.

Coalescent: an open-science framework for importance sampling in coalescent theory.

PubMed

Tewari, Susanta; Spouge, John L

2015-01-01

Background. In coalescent theory, computer programs often use importance sampling to calculate likelihoods and other statistical quantities. An importance sampling scheme can exploit human intuition to improve statistical efficiency of computations, but unfortunately, in the absence of general computer frameworks on importance sampling, researchers often struggle to translate new sampling schemes computationally or benchmark against different schemes, in a manner that is reliable and maintainable. Moreover, most studies use computer programs lacking a convenient user interface or the flexibility to meet the current demands of open science. In particular, current computer frameworks can only evaluate the efficiency of a single importance sampling scheme or compare the efficiencies of different schemes in an ad hoc manner. Results. We have designed a general framework (http://coalescent.sourceforge.net; language: Java; License: GPLv3) for importance sampling that computes likelihoods under the standard neutral coalescent model of a single, well-mixed population of constant size over time following infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. For a given dataset, it computes the likelihood and provides the maximum likelihood estimate of the mutation parameter. Well-known benchmarks in the coalescent literature validate the accuracy of the framework. The framework provides an intuitive user interface with minimal clutter. For performance, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework reliable and maintainable. Conclusions. In coalescent theory, many studies of computational efficiency consider only effective sample size. Here, we evaluate proposals in the coalescent literature, to discover that the order of efficiency among the three importance sampling schemes changes when one considers running time as well as effective sample size. We also describe a computational technique called "just-in-time delegation" available to improve the trade-off between running time and precision by constructing improved importance sampling schemes from existing ones. Thus, our systems approach is a potential solution to the "2(8) programs problem" highlighted by Felsenstein, because it provides the flexibility to include or exclude various features of similar coalescent models or importance sampling schemes.

Benchmark Problems of the Geothermal Technologies Office Code Comparison Study

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

White, Mark D.; Podgorney, Robert; Kelkar, Sharad M.

A diverse suite of numerical simulators is currently being applied to predict or understand the performance of enhanced geothermal systems (EGS). To build confidence and identify critical development needs for these analytical tools, the United States Department of Energy, Geothermal Technologies Office has sponsored a Code Comparison Study (GTO-CCS), with participants from universities, industry, and national laboratories. A principal objective for the study was to create a community forum for improvement and verification of numerical simulators for EGS modeling. Teams participating in the study were those representing U.S. national laboratories, universities, and industries, and each team brought unique numerical simulationmore » capabilities to bear on the problems. Two classes of problems were developed during the study, benchmark problems and challenge problems. The benchmark problems were structured to test the ability of the collection of numerical simulators to solve various combinations of coupled thermal, hydrologic, geomechanical, and geochemical processes. This class of problems was strictly defined in terms of properties, driving forces, initial conditions, and boundary conditions. Study participants submitted solutions to problems for which their simulation tools were deemed capable or nearly capable. Some participating codes were originally developed for EGS applications whereas some others were designed for different applications but can simulate processes similar to those in EGS. Solution submissions from both were encouraged. In some cases, participants made small incremental changes to their numerical simulation codes to address specific elements of the problem, and in other cases participants submitted solutions with existing simulation tools, acknowledging the limitations of the code. The challenge problems were based on the enhanced geothermal systems research conducted at Fenton Hill, near Los Alamos, New Mexico, between 1974 and 1995. The problems involved two phases of research, stimulation, development, and circulation in two separate reservoirs. The challenge problems had specific questions to be answered via numerical simulation in three topical areas: 1) reservoir creation/stimulation, 2) reactive and passive transport, and 3) thermal recovery. Whereas the benchmark class of problems were designed to test capabilities for modeling coupled processes under strictly specified conditions, the stated objective for the challenge class of problems was to demonstrate what new understanding of the Fenton Hill experiments could be realized via the application of modern numerical simulation tools by recognized expert practitioners.« less

Simultaneous delivery time and aperture shape optimization for the volumetric-modulated arc therapy (VMAT) treatment planning problem

NASA Astrophysics Data System (ADS)

Mahnam, Mehdi; Gendreau, Michel; Lahrichi, Nadia; Rousseau, Louis-Martin

2017-07-01

In this paper, we propose a novel heuristic algorithm for the volumetric-modulated arc therapy treatment planning problem, optimizing the trade-off between delivery time and treatment quality. We present a new mixed integer programming model in which the multi-leaf collimator leaf positions, gantry speed, and dose rate are determined simultaneously. Our heuristic is based on column generation; the aperture configuration is modeled in the columns and the dose distribution and time restriction in the rows. To reduce the number of voxels and increase the efficiency of the master model, we aggregate similar voxels using a clustering technique. The efficiency of the algorithm and the treatment quality are evaluated on a benchmark clinical prostate cancer case. The computational results show that a high-quality treatment is achievable using a four-thread CPU. Finally, we analyze the effects of the various parameters and two leaf-motion strategies.

A Least-Squares Finite Element Method for Electromagnetic Scattering Problems

NASA Technical Reports Server (NTRS)

Wu, Jie; Jiang, Bo-nan

1996-01-01

The least-squares finite element method (LSFEM) is applied to electromagnetic scattering and radar cross section (RCS) calculations. In contrast to most existing numerical approaches, in which divergence-free constraints are omitted, the LSFF-M directly incorporates two divergence equations in the discretization process. The importance of including the divergence equations is demonstrated by showing that otherwise spurious solutions with large divergence occur near the scatterers. The LSFEM is based on unstructured grids and possesses full flexibility in handling complex geometry and local refinement Moreover, the LSFEM does not require any special handling, such as upwinding, staggered grids, artificial dissipation, flux-differencing, etc. Implicit time discretization is used and the scheme is unconditionally stable. By using a matrix-free iterative method, the computational cost and memory requirement for the present scheme is competitive with other approaches. The accuracy of the LSFEM is verified by several benchmark test problems.

Improved Bat Algorithm Applied to Multilevel Image Thresholding

PubMed Central

2014-01-01

Multilevel image thresholding is a very important image processing technique that is used as a basis for image segmentation and further higher level processing. However, the required computational time for exhaustive search grows exponentially with the number of desired thresholds. Swarm intelligence metaheuristics are well known as successful and efficient optimization methods for intractable problems. In this paper, we adjusted one of the latest swarm intelligence algorithms, the bat algorithm, for the multilevel image thresholding problem. The results of testing on standard benchmark images show that the bat algorithm is comparable with other state-of-the-art algorithms. We improved standard bat algorithm, where our modifications add some elements from the differential evolution and from the artificial bee colony algorithm. Our new proposed improved bat algorithm proved to be better than five other state-of-the-art algorithms, improving quality of results in all cases and significantly improving convergence speed. PMID:25165733

Eigenvalue routines in NASTRAN: A comparison with the Block Lanczos method

NASA Technical Reports Server (NTRS)

Tischler, V. A.; Venkayya, Vipperla B.

1993-01-01

The NASA STRuctural ANalysis (NASTRAN) program is one of the most extensively used engineering applications software in the world. It contains a wealth of matrix operations and numerical solution techniques, and they were used to construct efficient eigenvalue routines. The purpose of this paper is to examine the current eigenvalue routines in NASTRAN and to make efficiency comparisons with a more recent implementation of the Block Lanczos algorithm by Boeing Computer Services (BCS). This eigenvalue routine is now available in the BCS mathematics library as well as in several commercial versions of NASTRAN. In addition, CRAY maintains a modified version of this routine on their network. Several example problems, with a varying number of degrees of freedom, were selected primarily for efficiency bench-marking. Accuracy is not an issue, because they all gave comparable results. The Block Lanczos algorithm was found to be extremely efficient, in particular, for very large size problems.

Accelerated Path-following Iterative Shrinkage Thresholding Algorithm with Application to Semiparametric Graph Estimation

PubMed Central

Zhao, Tuo; Liu, Han

2016-01-01

We propose an accelerated path-following iterative shrinkage thresholding algorithm (APISTA) for solving high dimensional sparse nonconvex learning problems. The main difference between APISTA and the path-following iterative shrinkage thresholding algorithm (PISTA) is that APISTA exploits an additional coordinate descent subroutine to boost the computational performance. Such a modification, though simple, has profound impact: APISTA not only enjoys the same theoretical guarantee as that of PISTA, i.e., APISTA attains a linear rate of convergence to a unique sparse local optimum with good statistical properties, but also significantly outperforms PISTA in empirical benchmarks. As an application, we apply APISTA to solve a family of nonconvex optimization problems motivated by estimating sparse semiparametric graphical models. APISTA allows us to obtain new statistical recovery results which do not exist in the existing literature. Thorough numerical results are provided to back up our theory. PMID:28133430

Clomp

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

Gylenhaal, J.; Bronevetsky, G.

2007-05-25

CLOMP is the C version of the Livermore OpenMP benchmark deeloped to measure OpenMP overheads and other performance impacts due to threading (like NUMA memory layouts, memory contention, cache effects, etc.) in order to influence future system design. Current best-in-class implementations of OpenMP have overheads at least ten times larger than is required by many of our applications for effective use of OpenMP. This benchmark shows the significant negative performance impact of these relatively large overheads and of other thread effects. The CLOMP benchmark highly configurable to allow a variety of problem sizes and threading effects to be studied andmore » it carefully checks its results to catch many common threading errors. This benchmark is expected to be included as part of the Sequoia Benchmark suite for the Sequoia procurement.« less

Building Bridges Between Geoscience and Data Science through Benchmark Data Sets

NASA Astrophysics Data System (ADS)

Thompson, D. R.; Ebert-Uphoff, I.; Demir, I.; Gel, Y.; Hill, M. C.; Karpatne, A.; Güereque, M.; Kumar, V.; Cabral, E.; Smyth, P.

2017-12-01

The changing nature of observational field data demands richer and more meaningful collaboration between data scientists and geoscientists. Thus, among other efforts, the Working Group on Case Studies of the NSF-funded RCN on Intelligent Systems Research To Support Geosciences (IS-GEO) is developing a framework to strengthen such collaborations through the creation of benchmark datasets. Benchmark datasets provide an interface between disciplines without requiring extensive background knowledge. The goals are to create (1) a means for two-way communication between geoscience and data science researchers; (2) new collaborations, which may lead to new approaches for data analysis in the geosciences; and (3) a public, permanent repository of complex data sets, representative of geoscience problems, useful to coordinate efforts in research and education. The group identified 10 key elements and characteristics for ideal benchmarks. High impact: A problem with high potential impact. Active research area: A group of geoscientists should be eager to continue working on the topic. Challenge: The problem should be challenging for data scientists. Data science generality and versatility: It should stimulate development of new general and versatile data science methods. Rich information content: Ideally the data set provides stimulus for analysis at many different levels. Hierarchical problem statement: A hierarchy of suggested analysis tasks, from relatively straightforward to open-ended tasks. Means for evaluating success: Data scientists and geoscientists need means to evaluate whether the algorithms are successful and achieve intended purpose. Quick start guide: Introduction for data scientists on how to easily read the data to enable rapid initial data exploration. Geoscience context: Summary for data scientists of the specific data collection process, instruments used, any pre-processing and the science questions to be answered. Citability: A suitable identifier to facilitate tracking the use of the benchmark later on, e.g. allowing search engines to find all research papers using it. A first sample benchmark developed in collaboration with the Jet Propulsion Laboratory (JPL) deals with the automatic analysis of imaging spectrometer data to detect significant methane sources in the atmosphere.

An impatient evolutionary algorithm with probabilistic tabu search for unified solution of some NP-hard problems in graph and set theory via clique finding.

PubMed

Guturu, Parthasarathy; Dantu, Ram

2008-06-01

Many graph- and set-theoretic problems, because of their tremendous application potential and theoretical appeal, have been well investigated by the researchers in complexity theory and were found to be NP-hard. Since the combinatorial complexity of these problems does not permit exhaustive searches for optimal solutions, only near-optimal solutions can be explored using either various problem-specific heuristic strategies or metaheuristic global-optimization methods, such as simulated annealing, genetic algorithms, etc. In this paper, we propose a unified evolutionary algorithm (EA) to the problems of maximum clique finding, maximum independent set, minimum vertex cover, subgraph and double subgraph isomorphism, set packing, set partitioning, and set cover. In the proposed approach, we first map these problems onto the maximum clique-finding problem (MCP), which is later solved using an evolutionary strategy. The proposed impatient EA with probabilistic tabu search (IEA-PTS) for the MCP integrates the best features of earlier successful approaches with a number of new heuristics that we developed to yield a performance that advances the state of the art in EAs for the exploration of the maximum cliques in a graph. Results of experimentation with the 37 DIMACS benchmark graphs and comparative analyses with six state-of-the-art algorithms, including two from the smaller EA community and four from the larger metaheuristics community, indicate that the IEA-PTS outperforms the EAs with respect to a Pareto-lexicographic ranking criterion and offers competitive performance on some graph instances when individually compared to the other heuristic algorithms. It has also successfully set a new benchmark on one graph instance. On another benchmark suite called Benchmarks with Hidden Optimal Solutions, IEA-PTS ranks second, after a very recent algorithm called COVER, among its peers that have experimented with this suite.

Benchmark On Sensitivity Calculation (Phase III)

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

Ivanova, Tatiana; Laville, Cedric; Dyrda, James

2012-01-01

The sensitivities of the keff eigenvalue to neutron cross sections have become commonly used in similarity studies and as part of the validation algorithm for criticality safety assessments. To test calculations of the sensitivity coefficients, a benchmark study (Phase III) has been established by the OECD-NEA/WPNCS/EG UACSA (Expert Group on Uncertainty Analysis for Criticality Safety Assessment). This paper presents some sensitivity results generated by the benchmark participants using various computational tools based upon different computational methods: SCALE/TSUNAMI-3D and -1D, MONK, APOLLO2-MORET 5, DRAGON-SUSD3D and MMKKENO. The study demonstrates the performance of the tools. It also illustrates how model simplifications impactmore » the sensitivity results and demonstrates the importance of 'implicit' (self-shielding) sensitivities. This work has been a useful step towards verification of the existing and developed sensitivity analysis methods.« less

Anharmonic Vibrational Spectroscopy on Metal Transition Complexes

NASA Astrophysics Data System (ADS)

Latouche, Camille; Bloino, Julien; Barone, Vincenzo

2014-06-01

Advances in hardware performance and the availability of efficient and reliable computational models have made possible the application of computational spectroscopy to ever larger molecular systems. The systematic interpretation of experimental data and the full characterization of complex molecules can then be facilitated. Focusing on vibrational spectroscopy, several approaches have been proposed to simulate spectra beyond the double harmonic approximation, so that more details become available. However, a routine use of such tools requires the preliminary definition of a valid protocol with the most appropriate combination of electronic structure and nuclear calculation models. Several benchmark of anharmonic calculations frequency have been realized on organic molecules. Nevertheless, benchmarks of organometallics or inorganic metal complexes at this level are strongly lacking despite the interest of these systems due to their strong emission and vibrational properties. Herein we report the benchmark study realized with anharmonic calculations on simple metal complexes, along with some pilot applications on systems of direct technological or biological interest.

Numerical aspects in modeling high Deborah number flow and elastic instability

NASA Astrophysics Data System (ADS)

Kwon, Youngdon

2014-05-01

Investigating highly nonlinear viscoelastic flow in 2D domain, we explore problem as well as property possibly inherent in the streamline upwinding technique (SUPG) and then present various results of elastic instability. The mathematically stable Leonov model written in tensor-logarithmic formulation is employed in the framework of finite element method for spatial discretization of several representative problem domains. For enhancement of computation speed, decoupled integration scheme is applied for shear thinning and Boger-type fluids. From the analysis of 4:1 contraction flow at low and moderate values of the Deborah number (De) the solution with SUPG method does not show noticeable difference from the one by the computation without upwinding. On the other hand, in the flow regime of high De, especially in the state of elastic instability the SUPG significantly distorts the flow field and the result differs considerably from the solution acquired straightforwardly. When the strength of elastic flow and thus the nonlinearity further increase, the computational scheme with upwinding fails to converge and evolutionary solution does not become available any more. All this result suggests that extreme care has to be taken on occasions where upwinding is applied, and one has to first of all prove validity of this algorithm in the case of high nonlinearity. On the contrary, the straightforward computation with no upwinding can efficiently model representative phenomena of elastic instability in such benchmark problems as 4:1 contraction flow, flow over a circular cylinder and flow over asymmetric array of cylinders. Asymmetry of the flow field occurring in the symmetric domain, enhanced spatial and temporal fluctuation of dynamic variables and flow effects caused by extension hardening are properly described in this study.

Benchmarking in national health service procurement in Scotland.

PubMed

Walker, Scott; Masson, Ron; Telford, Ronnie; White, David

2007-11-01

The paper reports the results of a study on benchmarking activities undertaken by the procurement organization within the National Health Service (NHS) in Scotland, namely National Procurement (previously Scottish Healthcare Supplies Contracts Branch). NHS performance is of course politically important, and benchmarking is increasingly seen as a means to improve performance, so the study was carried out to determine if the current benchmarking approaches could be enhanced. A review of the benchmarking activities used by the private sector, local government and NHS organizations was carried out to establish a framework of the motivations, benefits, problems and costs associated with benchmarking. This framework was used to carry out the research through case studies and a questionnaire survey of NHS procurement organizations both in Scotland and other parts of the UK. Nine of the 16 Scottish Health Boards surveyed reported carrying out benchmarking during the last three years. The findings of the research were that there were similarities in approaches between local government and NHS Scotland Health, but differences between NHS Scotland and other UK NHS procurement organizations. Benefits were seen as significant and it was recommended that National Procurement should pursue the formation of a benchmarking group with members drawn from NHS Scotland and external benchmarking bodies to establish measures to be used in benchmarking across the whole of NHS Scotland.

Evaluation of CHO Benchmarks on the Arria 10 FPGA using Intel FPGA SDK for OpenCL

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

Jin, Zheming; Yoshii, Kazutomo; Finkel, Hal

The OpenCL standard is an open programming model for accelerating algorithms on heterogeneous computing system. OpenCL extends the C-based programming language for developing portable codes on different platforms such as CPU, Graphics processing units (GPUs), Digital Signal Processors (DSPs) and Field Programmable Gate Arrays (FPGAs). The Intel FPGA SDK for OpenCL is a suite of tools that allows developers to abstract away the complex FPGA-based development flow for a high-level software development flow. Users can focus on the design of hardware-accelerated kernel functions in OpenCL and then direct the tools to generate the low-level FPGA implementations. The approach makes themore » FPGA-based development more accessible to software users as the needs for hybrid computing using CPUs and FPGAs are increasing. It can also significantly reduce the hardware development time as users can evaluate different ideas with high-level language without deep FPGA domain knowledge. Benchmarking of OpenCL-based framework is an effective way for analyzing the performance of system by studying the execution of the benchmark applications. CHO is a suite of benchmark applications that provides support for OpenCL [1]. The authors presented CHO as an OpenCL port of the CHStone benchmark. Using Altera OpenCL (AOCL) compiler to synthesize the benchmark applications, they listed the resource usage and performance of each kernel that can be successfully synthesized by the compiler. In this report, we evaluate the resource usage and performance of the CHO benchmark applications using the Intel FPGA SDK for OpenCL and Nallatech 385A FPGA board that features an Arria 10 FPGA device. The focus of the report is to have a better understanding of the resource usage and performance of the kernel implementations using Arria-10 FPGA devices compared to Stratix-5 FPGA devices. In addition, we also gain knowledge about the limitations of the current compiler when it fails to synthesize a benchmark application.« less

Information processing using a single dynamical node as complex system

PubMed Central

Appeltant, L.; Soriano, M.C.; Van der Sande, G.; Danckaert, J.; Massar, S.; Dambre, J.; Schrauwen, B.; Mirasso, C.R.; Fischer, I.

2011-01-01

Novel methods for information processing are highly desired in our information-driven society. Inspired by the brain's ability to process information, the recently introduced paradigm known as 'reservoir computing' shows that complex networks can efficiently perform computation. Here we introduce a novel architecture that reduces the usually required large number of elements to a single nonlinear node with delayed feedback. Through an electronic implementation, we experimentally and numerically demonstrate excellent performance in a speech recognition benchmark. Complementary numerical studies also show excellent performance for a time series prediction benchmark. These results prove that delay-dynamical systems, even in their simplest manifestation, can perform efficient information processing. This finding paves the way to feasible and resource-efficient technological implementations of reservoir computing. PMID:21915110

Towards the Solution of the Many-Electron Problem in Real Materials: Equation of State of the Hydrogen Chain with State-of-the-Art Many-Body Methods

DOE PAGES

Motta, Mario; Ceperley, David M.; Chan, Garnet Kin-Lic; ...

2017-09-28

We present numerical results for the equation of state of an infinite chain of hydrogen atoms. A variety of modern many-body methods are employed, with exhaustive cross-checks and validation. Approaches for reaching the continuous space limit and the thermodynamic limit are investigated, proposed, and tested. The detailed comparisons provide a benchmark for assessing the current state of the art in many-body computation, and for the development of new methods. The ground-state energy per atom in the linear chain is accurately determined versus bond length, with a confidence bound given on all uncertainties.

Performance Review of Harmony Search, Differential Evolution and Particle Swarm Optimization

NASA Astrophysics Data System (ADS)

Mohan Pandey, Hari

2017-08-01

Metaheuristic algorithms are effective in the design of an intelligent system. These algorithms are widely applied to solve complex optimization problems, including image processing, big data analytics, language processing, pattern recognition and others. This paper presents a performance comparison of three meta-heuristic algorithms, namely Harmony Search, Differential Evolution, and Particle Swarm Optimization. These algorithms are originated altogether from different fields of meta-heuristics yet share a common objective. The standard benchmark functions are used for the simulation. Statistical tests are conducted to derive a conclusion on the performance. The key motivation to conduct this research is to categorize the computational capabilities, which might be useful to the researchers.

Augmented Lagrange Programming Neural Network for Localization Using Time-Difference-of-Arrival Measurements.

PubMed

Han, Zifa; Leung, Chi Sing; So, Hing Cheung; Constantinides, Anthony George

2017-08-15

A commonly used measurement model for locating a mobile source is time-difference-of-arrival (TDOA). As each TDOA measurement defines a hyperbola, it is not straightforward to compute the mobile source position due to the nonlinear relationship in the measurements. This brief exploits the Lagrange programming neural network (LPNN), which provides a general framework to solve nonlinear constrained optimization problems, for the TDOA-based localization. The local stability of the proposed LPNN solution is also analyzed. Simulation results are included to evaluate the localization accuracy of the LPNN scheme by comparing with the state-of-the-art methods and the optimality benchmark of Cramér-Rao lower bound.

Flight program language requirements. Volume 2: Requirements and evaluations

NASA Technical Reports Server (NTRS)

1972-01-01

The efforts and results are summarized for a study to establish requirements for a flight programming language for future onboard computer applications. Several different languages were available as potential candidates for future NASA flight programming efforts. The study centered around an evaluation of the four most pertinent existing aerospace languages. Evaluation criteria were established, and selected kernels from the current Saturn 5 and Skylab flight programs were used as benchmark problems for sample coding. An independent review of the language specifications incorporated anticipated future programming requirements into the evaluation. A set of detailed language requirements was synthesized from these activities. The details of program language requirements and of the language evaluations are described.

Towards the Solution of the Many-Electron Problem in Real Materials: Equation of State of the Hydrogen Chain with State-of-the-Art Many-Body Methods

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

Motta, Mario; Ceperley, David M.; Chan, Garnet Kin-Lic

We present numerical results for the equation of state of an infinite chain of hydrogen atoms. A variety of modern many-body methods are employed, with exhaustive cross-checks and validation. Approaches for reaching the continuous space limit and the thermodynamic limit are investigated, proposed, and tested. The detailed comparisons provide a benchmark for assessing the current state of the art in many-body computation, and for the development of new methods. The ground-state energy per atom in the linear chain is accurately determined versus bond length, with a confidence bound given on all uncertainties.

Stagnation Point Nonequilibrium Radiative Heating and the Influence of Energy Exchange Models

NASA Technical Reports Server (NTRS)

Hartung, Lin C.; Mitcheltree, Robert A.; Gnoffo, Peter A.

1991-01-01

A nonequilibrium radiative heating prediction method has been used to evaluate several energy exchange models used in nonequilibrium computational fluid dynamics methods. The radiative heating measurements from the FIRE II flight experiment supply an experimental benchmark against which different formulations for these exchange models can be judged. The models which predict the lowest radiative heating are found to give the best agreement with the flight data. Examination of the spectral distribution of radiation indicates that despite close agreement of the total radiation, many of the models examined predict excessive molecular radiation. It is suggested that a study of the nonequilibrium chemical kinetics may lead to a correction for this problem.

Role of CFD in propulsion design - Government perspective

NASA Technical Reports Server (NTRS)

Schutzenhofer, L. A.; Mcconnaughey, H. V.; Mcconnaughey, P. K.

1990-01-01

Various aspects of computational fluid dynamics (CFD), as it relates to design applications in rocket propulsion activities from the government perspective, are discussed. Specific examples are given that demonstrate the application of CFD to support hardware development activities, such as Space Shuttle Main Engine flight issues, and the associated teaming strategy used for solving such problems. In addition, select examples that delineate the motivation, methods of approach, goals and key milestones for several space flight progams are cited. An approach is described toward applying CFD in the design environment from the government perspective. A discussion of benchmark validation, advanced technology hardware concepts, accomplishments, needs, future applications, and near-term expectations from the flight-center perspective is presented.

Towards reversible basic linear algebra subprograms: A performance study

DOE PAGES

Perumalla, Kalyan S.; Yoginath, Srikanth B.

2014-12-06

Problems such as fault tolerance and scalable synchronization can be efficiently solved using reversibility of applications. Making applications reversible by relying on computation rather than on memory is ideal for large scale parallel computing, especially for the next generation of supercomputers in which memory is expensive in terms of latency, energy, and price. In this direction, a case study is presented here in reversing a computational core, namely, Basic Linear Algebra Subprograms, which is widely used in scientific applications. A new Reversible BLAS (RBLAS) library interface has been designed, and a prototype has been implemented with two modes: (1) amore » memory-mode in which reversibility is obtained by checkpointing to memory in forward and restoring from memory in reverse, and (2) a computational-mode in which nothing is saved in the forward, but restoration is done entirely via inverse computation in reverse. The article is focused on detailed performance benchmarking to evaluate the runtime dynamics and performance effects, comparing reversible computation with checkpointing on both traditional CPU platforms and recent GPU accelerator platforms. For BLAS Level-1 subprograms, data indicates over an order of magnitude better speed of reversible computation compared to checkpointing. For BLAS Level-2 and Level-3, a more complex tradeoff is observed between reversible computation and checkpointing, depending on computational and memory complexities of the subprograms.« less

Comparison of Origin 2000 and Origin 3000 Using NAS Parallel Benchmarks

NASA Technical Reports Server (NTRS)

Turney, Raymond D.

2001-01-01

This report describes results of benchmark tests on the Origin 3000 system currently being installed at the NASA Ames National Advanced Supercomputing facility. This machine will ultimately contain 1024 R14K processors. The first part of the system, installed in November, 2000 and named mendel, is an Origin 3000 with 128 R12K processors. For comparison purposes, the tests were also run on lomax, an Origin 2000 with R12K processors. The BT, LU, and SP application benchmarks in the NAS Parallel Benchmark Suite and the kernel benchmark FT were chosen to determine system performance and measure the impact of changes on the machine as it evolves. Having been written to measure performance on Computational Fluid Dynamics applications, these benchmarks are assumed appropriate to represent the NAS workload. Since the NAS runs both message passing (MPI) and shared-memory, compiler directive type codes, both MPI and OpenMP versions of the benchmarks were used. The MPI versions used were the latest official release of the NAS Parallel Benchmarks, version 2.3. The OpenMP versiqns used were PBN3b2, a beta version that is in the process of being released. NPB 2.3 and PBN 3b2 are technically different benchmarks, and NPB results are not directly comparable to PBN results.

Microbially Mediated Kinetic Sulfur Isotope Fractionation: Reactive Transport Modeling Benchmark

NASA Astrophysics Data System (ADS)

Wanner, C.; Druhan, J. L.; Cheng, Y.; Amos, R. T.; Steefel, C. I.; Ajo Franklin, J. B.

2014-12-01

Microbially mediated sulfate reduction is a ubiquitous process in many subsurface systems. Isotopic fractionation is characteristic of this anaerobic process, since sulfate reducing bacteria (SRB) favor the reduction of the lighter sulfate isotopologue (S32O42-) over the heavier isotopologue (S34O42-). Detection of isotopic shifts have been utilized as a proxy for the onset of sulfate reduction in subsurface systems such as oil reservoirs and aquifers undergoing uranium bioremediation. Reactive transport modeling (RTM) of kinetic sulfur isotope fractionation has been applied to field and laboratory studies. These RTM approaches employ different mathematical formulations in the representation of kinetic sulfur isotope fractionation. In order to test the various formulations, we propose a benchmark problem set for the simulation of kinetic sulfur isotope fractionation during microbially mediated sulfate reduction. The benchmark problem set is comprised of four problem levels and is based on a recent laboratory column experimental study of sulfur isotope fractionation. Pertinent processes impacting sulfur isotopic composition such as microbial sulfate reduction and dispersion are included in the problem set. To date, participating RTM codes are: CRUNCHTOPE, TOUGHREACT, MIN3P and THE GEOCHEMIST'S WORKBENCH. Preliminary results from various codes show reasonable agreement for the problem levels simulating sulfur isotope fractionation in 1D.

Full dimensional (15-dimensional) quantum-dynamical simulation of the protonated water-dimer III: Mixed Jacobi-valence parametrization and benchmark results for the zero point energy, vibrationally excited states, and infrared spectrum.

PubMed

Vendrell, Oriol; Brill, Michael; Gatti, Fabien; Lauvergnat, David; Meyer, Hans-Dieter

2009-06-21

Quantum dynamical calculations are reported for the zero point energy, several low-lying vibrational states, and the infrared spectrum of the H(5)O(2)(+) cation. The calculations are performed by the multiconfiguration time-dependent Hartree (MCTDH) method. A new vector parametrization based on a mixed Jacobi-valence description of the system is presented. With this parametrization the potential energy surface coupling is reduced with respect to a full Jacobi description, providing a better convergence of the n-mode representation of the potential. However, new coupling terms appear in the kinetic energy operator. These terms are derived and discussed. A mode-combination scheme based on six combined coordinates is used, and the representation of the 15-dimensional potential in terms of a six-combined mode cluster expansion including up to some 7-dimensional grids is discussed. A statistical analysis of the accuracy of the n-mode representation of the potential at all orders is performed. Benchmark, fully converged results are reported for the zero point energy, which lie within the statistical uncertainty of the reference diffusion Monte Carlo result for this system. Some low-lying vibrationally excited eigenstates are computed by block improved relaxation, illustrating the applicability of the approach to large systems. Benchmark calculations of the linear infrared spectrum are provided, and convergence with increasing size of the time-dependent basis and as a function of the order of the n-mode representation is studied. The calculations presented here make use of recent developments in the parallel version of the MCTDH code, which are briefly discussed. We also show that the infrared spectrum can be computed, to a very good approximation, within D(2d) symmetry, instead of the G(16) symmetry used before, in which the complete rotation of one water molecule with respect to the other is allowed, thus simplifying the dynamical problem.

Benchmark tests on the digital equipment corporation Alpha AXP 21164-based AlphaServer 8400, including a comparison of optimized vector and superscalar processing

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

Wasserman, H.J.

1996-02-01

The second generation of the Digital Equipment Corp. (DEC) DECchip Alpha AXP microprocessor is referred to as the 21164. From the viewpoint of numerically-intensive computing, the primary difference between it and its predecessor, the 21064, is that the 21164 has twice the multiply/add throughput per clock period (CP), a maximum of two floating point operations (FLOPS) per CP vs. one for 21064. The AlphaServer 8400 is a shared-memory multiprocessor server system that can accommodate up to 12 CPUs and up to 14 GB of memory. In this report we will compare single processor performance of the 8400 system with thatmore » of the International Business Machines Corp. (IBM) RISC System/6000 POWER-2 microprocessor running at 66 MHz, the Silicon Graphics, Inc. (SGI) MIPS R8000 microprocessor running at 75 MHz, and the Cray Research, Inc. CRAY J90. The performance comparison is based on a set of Fortran benchmark codes that represent a portion of the Los Alamos National Laboratory supercomputer workload. The advantage of using these codes, is that the codes also span a wide range of computational characteristics, such as vectorizability, problem size, and memory access pattern. The primary disadvantage of using them is that detailed, quantitative analysis of performance behavior of all codes on all machines is difficult. One important addition to the benchmark set appears for the first time in this report. Whereas the older version was written for a vector processor, the newer version is more optimized for microprocessor architectures. Therefore, we have for the first time, an opportunity to measure performance on a single application using implementations that expose the respective strengths of vector and superscalar architecture. All results in this report are from single processors. A subsequent article will explore shared-memory multiprocessing performance of the 8400 system.« less