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

Multi-Core Processor Memory Contention Benchmark Analysis Case Study

NASA Technical Reports Server (NTRS)

Simon, Tyler; McGalliard, James

2009-01-01

Multi-core processors dominate current mainframe, server, and high performance computing (HPC) systems. This paper provides synthetic kernel and natural benchmark results from an HPC system at the NASA Goddard Space Flight Center that illustrate the performance impacts of multi-core (dual- and quad-core) vs. single core processor systems. Analysis of processor design, application source code, and synthetic and natural test results all indicate that multi-core processors can suffer from significant memory subsystem contention compared to similar single-core processors.

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.

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

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

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.

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

Faillace, E.R.; Cheng, J.J.; Yu, C.

A series of benchmarking runs were conducted so that results obtained with the RESRAD code could be compared against those obtained with six pathway analysis models used to determine the radiation dose to an individual living on a radiologically contaminated site. The RESRAD computer code was benchmarked against five other computer codes - GENII-S, GENII, DECOM, PRESTO-EPA-CPG, and PATHRAE-EPA - and the uncodified methodology presented in the NUREG/CR-5512 report. Estimated doses for the external gamma pathway; the dust inhalation pathway; and the soil, food, and water ingestion pathways were calculated for each methodology by matching, to the extent possible, inputmore » parameters such as occupancy, shielding, and consumption factors.« less

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.

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

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

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.

Acoustic Source Bearing Estimation (ASBE) computer program development

NASA Technical Reports Server (NTRS)

Wiese, Michael R.

1987-01-01

A new bearing estimation algorithm (Acoustic Source Analysis Technique - ASAT) and an acoustic analysis computer program (Acoustic Source Bearing Estimation - ASBE) are described, which were developed by Computer Sciences Corporation for NASA Langley Research Center. The ASBE program is used by the Acoustics Division/Applied Acoustics Branch and the Instrument Research Division/Electro-Mechanical Instrumentation Branch to analyze acoustic data and estimate the azimuths from which the source signals radiated. Included are the input and output from a benchmark test case.

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...

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.

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.

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.

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.

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

Interfacing Computer Aided Parallelization and Performance Analysis

NASA Technical Reports Server (NTRS)

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

2003-01-01

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

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.

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

CPE--A New Perspective: The Impact of the Technology Revolution. Proceedings of the Computer Performance Evaluation Users Group Meeting (19th, San Francisco, California, October 25-28, 1983). Final Report. Reports on Computer Science and Technology.

ERIC Educational Resources Information Center

Mobray, Deborah, Ed.

Papers on local area networks (LANs), modelling techniques, software improvement, capacity planning, software engineering, microcomputers and end user computing, cost accounting and chargeback, configuration and performance management, and benchmarking presented at this conference include: (1) "Theoretical Performance Analysis of Virtual…

Towards accurate modeling of noncovalent interactions for protein rigidity analysis.

PubMed

Fox, Naomi; Streinu, Ileana

2013-01-01

Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future extensions. We have measured the gain in performance by comparing different modeling methods for noncovalent interactions. We showed that new criteria for modeling hydrogen bonds and hydrophobic interactions can significantly improve the results. The two new methods proposed here have been implemented and made publicly available in the current version of KINARI (v1.3), together with the benchmarking tools, which can be downloaded from our software's website, http://kinari.cs.umass.edu.

Towards accurate modeling of noncovalent interactions for protein rigidity analysis

PubMed Central

2013-01-01

Background Protein rigidity analysis is an efficient computational method for extracting flexibility information from static, X-ray crystallography protein data. Atoms and bonds are modeled as a mechanical structure and analyzed with a fast graph-based algorithm, producing a decomposition of the flexible molecule into interconnected rigid clusters. The result depends critically on noncovalent atomic interactions, primarily on how hydrogen bonds and hydrophobic interactions are computed and modeled. Ongoing research points to the stringent need for benchmarking rigidity analysis software systems, towards the goal of increasing their accuracy and validating their results, either against each other and against biologically relevant (functional) parameters. We propose two new methods for modeling hydrogen bonds and hydrophobic interactions that more accurately reflect a mechanical model, without being computationally more intensive. We evaluate them using a novel scoring method, based on the B-cubed score from the information retrieval literature, which measures how well two cluster decompositions match. Results To evaluate the modeling accuracy of KINARI, our pebble-game rigidity analysis system, we use a benchmark data set of 20 proteins, each with multiple distinct conformations deposited in the Protein Data Bank. Cluster decompositions for them were previously determined with the RigidFinder method from Gerstein's lab and validated against experimental data. When KINARI's default tuning parameters are used, an improvement of the B-cubed score over a crude baseline is observed in 30% of this data. With our new modeling options, improvements were observed in over 70% of the proteins in this data set. We investigate the sensitivity of the cluster decomposition score with case studies on pyruvate phosphate dikinase and calmodulin. Conclusion To substantially improve the accuracy of protein rigidity analysis systems, thorough benchmarking must be performed on all current systems and future extensions. We have measured the gain in performance by comparing different modeling methods for noncovalent interactions. We showed that new criteria for modeling hydrogen bonds and hydrophobic interactions can significantly improve the results. The two new methods proposed here have been implemented and made publicly available in the current version of KINARI (v1.3), together with the benchmarking tools, which can be downloaded from our software's website, http://kinari.cs.umass.edu. PMID:24564209

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.

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

Benchmarking undedicated cloud computing providers for analysis of genomic datasets.

PubMed

Yazar, Seyhan; Gooden, George E C; Mackey, David A; Hewitt, Alex W

2014-01-01

A major bottleneck in biological discovery is now emerging at the computational level. Cloud computing offers a dynamic means whereby small and medium-sized laboratories can rapidly adjust their computational capacity. We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets (E.coli CC102 strain and a Han Chinese male genome) and a standard bioinformatic pipeline on a Hadoop-based platform. Wall-clock time for complete assembly differed by 52.9% (95% CI: 27.5-78.2) for E.coli and 53.5% (95% CI: 34.4-72.6) for human genome, with GCE being more efficient than EMR. The cost of running this experiment on EMR and GCE differed significantly, with the costs on EMR being 257.3% (95% CI: 211.5-303.1) and 173.9% (95% CI: 134.6-213.1) more expensive for E.coli and human assemblies respectively. Thus, GCE was found to outperform EMR both in terms of cost and wall-clock time. Our findings confirm that cloud computing is an efficient and potentially cost-effective alternative for analysis of large genomic datasets. In addition to releasing our cost-effectiveness comparison, we present available ready-to-use scripts for establishing Hadoop instances with Ganglia monitoring on EC2 or GCE.

Benchmarking Undedicated Cloud Computing Providers for Analysis of Genomic Datasets

PubMed Central

Yazar, Seyhan; Gooden, George E. C.; Mackey, David A.; Hewitt, Alex W.

2014-01-01

A major bottleneck in biological discovery is now emerging at the computational level. Cloud computing offers a dynamic means whereby small and medium-sized laboratories can rapidly adjust their computational capacity. We benchmarked two established cloud computing services, Amazon Web Services Elastic MapReduce (EMR) on Amazon EC2 instances and Google Compute Engine (GCE), using publicly available genomic datasets (E.coli CC102 strain and a Han Chinese male genome) and a standard bioinformatic pipeline on a Hadoop-based platform. Wall-clock time for complete assembly differed by 52.9% (95% CI: 27.5–78.2) for E.coli and 53.5% (95% CI: 34.4–72.6) for human genome, with GCE being more efficient than EMR. The cost of running this experiment on EMR and GCE differed significantly, with the costs on EMR being 257.3% (95% CI: 211.5–303.1) and 173.9% (95% CI: 134.6–213.1) more expensive for E.coli and human assemblies respectively. Thus, GCE was found to outperform EMR both in terms of cost and wall-clock time. Our findings confirm that cloud computing is an efficient and potentially cost-effective alternative for analysis of large genomic datasets. In addition to releasing our cost-effectiveness comparison, we present available ready-to-use scripts for establishing Hadoop instances with Ganglia monitoring on EC2 or GCE. PMID:25247298

Molecular Isotopic Distribution Analysis (MIDAs) with Adjustable Mass Accuracy

NASA Astrophysics Data System (ADS)

Alves, Gelio; Ogurtsov, Aleksey Y.; Yu, Yi-Kuo

2014-01-01

In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

Molecular Isotopic Distribution Analysis (MIDAs) with adjustable mass accuracy.

PubMed

Alves, Gelio; Ogurtsov, Aleksey Y; Yu, Yi-Kuo

2014-01-01

In this paper, we present Molecular Isotopic Distribution Analysis (MIDAs), a new software tool designed to compute molecular isotopic distributions with adjustable accuracies. MIDAs offers two algorithms, one polynomial-based and one Fourier-transform-based, both of which compute molecular isotopic distributions accurately and efficiently. The polynomial-based algorithm contains few novel aspects, whereas the Fourier-transform-based algorithm consists mainly of improvements to other existing Fourier-transform-based algorithms. We have benchmarked the performance of the two algorithms implemented in MIDAs with that of eight software packages (BRAIN, Emass, Mercury, Mercury5, NeutronCluster, Qmass, JFC, IC) using a consensus set of benchmark molecules. Under the proposed evaluation criteria, MIDAs's algorithms, JFC, and Emass compute with comparable accuracy the coarse-grained (low-resolution) isotopic distributions and are more accurate than the other software packages. For fine-grained isotopic distributions, we compared IC, MIDAs's polynomial algorithm, and MIDAs's Fourier transform algorithm. Among the three, IC and MIDAs's polynomial algorithm compute isotopic distributions that better resemble their corresponding exact fine-grained (high-resolution) isotopic distributions. MIDAs can be accessed freely through a user-friendly web-interface at http://www.ncbi.nlm.nih.gov/CBBresearch/Yu/midas/index.html.

Uncertainty Quantification Techniques of SCALE/TSUNAMI

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

Rearden, Bradley T; Mueller, Don

2011-01-01

The Standardized Computer Analysis for Licensing Evaluation (SCALE) code system developed at Oak Ridge National Laboratory (ORNL) includes Tools for Sensitivity and Uncertainty Analysis Methodology Implementation (TSUNAMI). The TSUNAMI code suite can quantify the predicted change in system responses, such as k{sub eff}, reactivity differences, or ratios of fluxes or reaction rates, due to changes in the energy-dependent, nuclide-reaction-specific cross-section data. Where uncertainties in the neutron cross-section data are available, the sensitivity of the system to the cross-section data can be applied to propagate the uncertainties in the cross-section data to an uncertainty in the system response. Uncertainty quantification ismore » useful for identifying potential sources of computational biases and highlighting parameters important to code validation. Traditional validation techniques often examine one or more average physical parameters to characterize a system and identify applicable benchmark experiments. However, with TSUNAMI correlation coefficients are developed by propagating the uncertainties in neutron cross-section data to uncertainties in the computed responses for experiments and safety applications through sensitivity coefficients. The bias in the experiments, as a function of their correlation coefficient with the intended application, is extrapolated to predict the bias and bias uncertainty in the application through trending analysis or generalized linear least squares techniques, often referred to as 'data adjustment.' Even with advanced tools to identify benchmark experiments, analysts occasionally find that the application models include some feature or material for which adequately similar benchmark experiments do not exist to support validation. For example, a criticality safety analyst may want to take credit for the presence of fission products in spent nuclear fuel. In such cases, analysts sometimes rely on 'expert judgment' to select an additional administrative margin to account for gap in the validation data or to conclude that the impact on the calculated bias and bias uncertainty is negligible. As a result of advances in computer programs and the evolution of cross-section covariance data, analysts can use the sensitivity and uncertainty analysis tools in the TSUNAMI codes to estimate the potential impact on the application-specific bias and bias uncertainty resulting from nuclides not represented in available benchmark experiments. This paper presents the application of methods described in a companion paper.« less

Benchmarks for target tracking

NASA Astrophysics Data System (ADS)

Dunham, Darin T.; West, Philip D.

2011-09-01

The term benchmark originates from the chiseled horizontal marks that surveyors made, into which an angle-iron could be placed to bracket ("bench") a leveling rod, thus ensuring that the leveling rod can be repositioned in exactly the same place in the future. A benchmark in computer terms is the result of running a computer program, or a set of programs, in order to assess the relative performance of an object by running a number of standard tests and trials against it. This paper will discuss the history of simulation benchmarks that are being used by multiple branches of the military and agencies of the US government. These benchmarks range from missile defense applications to chemical biological situations. Typically, a benchmark is used with Monte Carlo runs in order to tease out how algorithms deal with variability and the range of possible inputs. We will also describe problems that can be solved by a benchmark.

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.

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.

Preliminary Results for the OECD/NEA Time Dependent Benchmark using Rattlesnake, Rattlesnake-IQS and TDKENO

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

DeHart, Mark D.; Mausolff, Zander; Weems, Zach

2016-08-01

One goal of the MAMMOTH M&S project is to validate the analysis capabilities within MAMMOTH. Historical data has shown limited value for validation of full three-dimensional (3D) multi-physics methods. Initial analysis considered the TREAT startup minimum critical core and one of the startup transient tests. At present, validation is focusing on measurements taken during the M8CAL test calibration series. These exercises will valuable in preliminary assessment of the ability of MAMMOTH to perform coupled multi-physics calculations; calculations performed to date are being used to validate the neutron transport solver Rattlesnake\\cite{Rattlesnake} and the fuels performance code BISON. Other validation projects outsidemore » of TREAT are available for single-physics benchmarking. Because the transient solution capability of Rattlesnake is one of the key attributes that makes it unique for TREAT transient simulations, validation of the transient solution of Rattlesnake using other time dependent kinetics benchmarks has considerable value. The Nuclear Energy Agency (NEA) of the Organization for Economic Cooperation and Development (OECD) has recently developed a computational benchmark for transient simulations. This benchmark considered both two-dimensional (2D) and 3D configurations for a total number of 26 different transients. All are negative reactivity insertions, typically returning to the critical state after some time.« less

Benchmark problems for numerical implementations of phase field models

DOE PAGES

Jokisaari, A. M.; Voorhees, P. W.; Guyer, J. E.; ...

2016-10-01

Here, we present the first set of benchmark problems for phase field models that are being developed by the Center for Hierarchical Materials Design (CHiMaD) and the National Institute of Standards and Technology (NIST). While many scientific research areas use a limited set of well-established software, the growing phase field community continues to develop a wide variety of codes and lacks benchmark problems to consistently evaluate the numerical performance of new implementations. Phase field modeling has become significantly more popular as computational power has increased and is now becoming mainstream, driving the need for benchmark problems to validate and verifymore » new implementations. We follow the example set by the micromagnetics community to develop an evolving set of benchmark problems that test the usability, computational resources, numerical capabilities and physical scope of phase field simulation codes. In this paper, we propose two benchmark problems that cover the physics of solute diffusion and growth and coarsening of a second phase via a simple spinodal decomposition model and a more complex Ostwald ripening model. We demonstrate the utility of benchmark problems by comparing the results of simulations performed with two different adaptive time stepping techniques, and we discuss the needs of future benchmark problems. The development of benchmark problems will enable the results of quantitative phase field models to be confidently incorporated into integrated computational materials science and engineering (ICME), an important goal of the Materials Genome Initiative.« 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.

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.

Benchmarking the MCNP code for Monte Carlo modelling of an in vivo neutron activation analysis system.

PubMed

Natto, S A; Lewis, D G; Ryde, S J

1998-01-01

The Monte Carlo computer code MCNP (version 4A) has been used to develop a personal computer-based model of the Swansea in vivo neutron activation analysis (IVNAA) system. The model included specification of the neutron source (252Cf), collimators, reflectors and shielding. The MCNP model was 'benchmarked' against fast neutron and thermal neutron fluence data obtained experimentally from the IVNAA system. The Swansea system allows two irradiation geometries using 'short' and 'long' collimators, which provide alternative dose rates for IVNAA. The data presented here relate to the short collimator, although results of similar accuracy were obtained using the long collimator. The fast neutron fluence was measured in air at a series of depths inside the collimator. The measurements agreed with the MCNP simulation within the statistical uncertainty (5-10%) of the calculations. The thermal neutron fluence was measured and calculated inside the cuboidal water phantom. The depth of maximum thermal fluence was 3.2 cm (measured) and 3.0 cm (calculated). The width of the 50% thermal fluence level across the phantom at its mid-depth was found to be the same by both MCNP and experiment. This benchmarking exercise has given us a high degree of confidence in MCNP as a tool for the design of IVNAA systems.

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.

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.

New Flutter Analysis Technique for Time-Domain Computational Aeroelasticity

NASA Technical Reports Server (NTRS)

Pak, Chan-Gi; Lung, Shun-Fat

2017-01-01

A new time-domain approach for computing flutter speed is presented. Based on the time-history result of aeroelastic simulation, the unknown unsteady aerodynamics model is estimated using a system identification technique. The full aeroelastic model is generated via coupling the estimated unsteady aerodynamic model with the known linear structure model. The critical dynamic pressure is computed and used in the subsequent simulation until the convergence of the critical dynamic pressure is achieved. The proposed method is applied to a benchmark cantilevered rectangular wing.

Benchmark problems and solutions

NASA Technical Reports Server (NTRS)

Tam, Christopher K. W.

1995-01-01

The scientific committee, after careful consideration, adopted six categories of benchmark problems for the workshop. These problems do not cover all the important computational issues relevant to Computational Aeroacoustics (CAA). The deciding factor to limit the number of categories to six was the amount of effort needed to solve these problems. For reference purpose, the benchmark problems are provided here. They are followed by the exact or approximate analytical solutions. At present, an exact solution for the Category 6 problem is not available.

Scalable and cost-effective NGS genotyping in the cloud.

PubMed

Souilmi, Yassine; Lancaster, Alex K; Jung, Jae-Yoon; Rizzo, Ettore; Hawkins, Jared B; Powles, Ryan; Amzazi, Saaïd; Ghazal, Hassan; Tonellato, Peter J; Wall, Dennis P

2015-10-15

While next-generation sequencing (NGS) costs have plummeted in recent years, cost and complexity of computation remain substantial barriers to the use of NGS in routine clinical care. The clinical potential of NGS will not be realized until robust and routine whole genome sequencing data can be accurately rendered to medically actionable reports within a time window of hours and at scales of economy in the 10's of dollars. We take a step towards addressing this challenge, by using COSMOS, a cloud-enabled workflow management system, to develop GenomeKey, an NGS whole genome analysis workflow. COSMOS implements complex workflows making optimal use of high-performance compute clusters. Here we show that the Amazon Web Service (AWS) implementation of GenomeKey via COSMOS provides a fast, scalable, and cost-effective analysis of both public benchmarking and large-scale heterogeneous clinical NGS datasets. Our systematic benchmarking reveals important new insights and considerations to produce clinical turn-around of whole genome analysis optimization and workflow management including strategic batching of individual genomes and efficient cluster resource configuration.

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

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.

RF transient analysis and stabilization of the phase and energy of the proposed PIP-II LINAC

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

Edelen, J. P.; Chase, B. E.

This paper describes a recent effort to develop and benchmark a simulation tool for the analysis of RF transients and their compensation in an H- linear accelerator. Existing tools in this area either focus on electron LINACs or lack fundamental details about the LLRF system that are necessary to provide realistic performance estimates. In our paper we begin with a discussion of our computational models followed by benchmarking with existing beam-dynamics codes and measured data. We then analyze the effect of RF transients and their compensation in the PIP-II LINAC, followed by an analysis of calibration errors and how amore » Newton’s Method based feedback scheme can be used to regulate the beam energy to within the specified limits.« less

Analysis of 100Mb/s Ethernet for the Whitney Commodity Computing Testbed

NASA Technical Reports Server (NTRS)

Fineberg, Samuel A.; Pedretti, Kevin T.; Kutler, Paul (Technical Monitor)

1997-01-01

We evaluate the performance of a Fast Ethernet network configured with a single large switch, a single hub, and a 4x4 2D torus topology in a testbed cluster of "commodity" Pentium Pro PCs. We also evaluated a mixed network composed of ethernet hubs and switches. An MPI collective communication benchmark, and the NAS Parallel Benchmarks version 2.2 (NPB2) show that the torus network performs best for all sizes that we were able to test (up to 16 nodes). For larger networks the ethernet switch outperforms the hub, though its performance is far less than peak. The hub/switch combination tests indicate that the NAS parallel benchmarks are relatively insensitive to hub densities of less than 7 nodes per hub.

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.

Second Computational Aeroacoustics (CAA) Workshop on Benchmark Problems

NASA Technical Reports Server (NTRS)

Tam, C. K. W. (Editor); Hardin, J. C. (Editor)

1997-01-01

The proceedings of the Second Computational Aeroacoustics (CAA) Workshop on Benchmark Problems held at Florida State University are the subject of this report. For this workshop, problems arising in typical industrial applications of CAA were chosen. Comparisons between numerical solutions and exact solutions are presented where possible.

Unstructured Adaptive (UA) NAS Parallel Benchmark. Version 1.0

NASA Technical Reports Server (NTRS)

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

2004-01-01

We present a complete specification of a new benchmark for measuring the performance of modern computer systems when solving scientific problems featuring irregular, dynamic memory accesses. It complements the existing NAS Parallel Benchmark suite. The benchmark involves the solution of a stylized heat transfer problem in a cubic domain, discretized on an adaptively refined, unstructured mesh.

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

Performance implications from sizing a VM on multi-core systems: A Data analytic application s view

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

Lim, Seung-Hwan; Horey, James L; Begoli, Edmon

In this paper, we present a quantitative performance analysis of data analytics applications running on multi-core virtual machines. Such environments form the core of cloud computing. In addition, data analytics applications, such as Cassandra and Hadoop, are becoming increasingly popular on cloud computing platforms. This convergence necessitates a better understanding of the performance and cost implications of such hybrid systems. For example, the very rst step in hosting applications in virtualized environments, requires the user to con gure the number of virtual processors and the size of memory. To understand performance implications of this step, we benchmarked three Yahoo Cloudmore » Serving Benchmark (YCSB) workloads in a virtualized multi-core environment. Our measurements indicate that the performance of Cassandra for YCSB workloads does not heavily depend on the processing capacity of a system, while the size of the data set is critical to performance relative to allocated memory. We also identi ed a strong relationship between the running time of workloads and various hardware events (last level cache loads, misses, and CPU migrations). From this analysis, we provide several suggestions to improve the performance of data analytics applications running on cloud computing environments.« less

Benchmark Comparison of Cloud Analytics Methods Applied to Earth Observations

NASA Technical Reports Server (NTRS)

Lynnes, Chris; Little, Mike; Huang, Thomas; Jacob, Joseph; Yang, Phil; Kuo, Kwo-Sen

2016-01-01

Cloud computing has the potential to bring high performance computing capabilities to the average science researcher. However, in order to take full advantage of cloud capabilities, the science data used in the analysis must often be reorganized. This typically involves sharding the data across multiple nodes to enable relatively fine-grained parallelism. This can be either via cloud-based file systems or cloud-enabled databases such as Cassandra, Rasdaman or SciDB. Since storing an extra copy of data leads to increased cost and data management complexity, NASA is interested in determining the benefits and costs of various cloud analytics methods for real Earth Observation cases. Accordingly, NASA's Earth Science Technology Office and Earth Science Data and Information Systems project have teamed with cloud analytics practitioners to run a benchmark comparison on cloud analytics methods using the same input data and analysis algorithms. We have particularly looked at analysis algorithms that work over long time series, because these are particularly intractable for many Earth Observation datasets which typically store data with one or just a few time steps per file. This post will present side-by-side cost and performance results for several common Earth observation analysis operations.

Benchmark Comparison of Cloud Analytics Methods Applied to Earth Observations

NASA Astrophysics Data System (ADS)

Lynnes, C.; Little, M. M.; Huang, T.; Jacob, J. C.; Yang, C. P.; Kuo, K. S.

2016-12-01

Cloud computing has the potential to bring high performance computing capabilities to the average science researcher. However, in order to take full advantage of cloud capabilities, the science data used in the analysis must often be reorganized. This typically involves sharding the data across multiple nodes to enable relatively fine-grained parallelism. This can be either via cloud-based filesystems or cloud-enabled databases such as Cassandra, Rasdaman or SciDB. Since storing an extra copy of data leads to increased cost and data management complexity, NASA is interested in determining the benefits and costs of various cloud analytics methods for real Earth Observation cases. Accordingly, NASA's Earth Science Technology Office and Earth Science Data and Information Systems project have teamed with cloud analytics practitioners to run a benchmark comparison on cloud analytics methods using the same input data and analysis algorithms. We have particularly looked at analysis algorithms that work over long time series, because these are particularly intractable for many Earth Observation datasets which typically store data with one or just a few time steps per file. This post will present side-by-side cost and performance results for several common Earth observation analysis operations.

Numerical Investigations of the Benchmark Supercritical Wing in Transonic Flow

NASA Technical Reports Server (NTRS)

Chwalowski, Pawel; Heeg, Jennifer; Biedron, Robert T.

2017-01-01

This paper builds on the computational aeroelastic results published previously and generated in support of the second Aeroelastic Prediction Workshop for the NASA Benchmark Supercritical Wing (BSCW) configuration. The computational results are obtained using FUN3D, an unstructured grid Reynolds-Averaged Navier-Stokes solver developed at the NASA Langley Research Center. The analysis results show the effects of the temporal and spatial resolution, the coupling scheme between the flow and the structural solvers, and the initial excitation conditions on the numerical flutter onset. Depending on the free stream condition and the angle of attack, the above parameters do affect the flutter onset. Two conditions are analyzed: Mach 0.74 with angle of attack 0 and Mach 0.85 with angle of attack 5. The results are presented in the form of the damping values computed from the wing pitch angle response as a function of the dynamic pressure or in the form of dynamic pressure as a function of the Mach number.

Translating an AI application from Lisp to Ada: A case study

NASA Technical Reports Server (NTRS)

Davis, Gloria J.

1991-01-01

A set of benchmarks was developed to test the performance of a newly designed computer executing both Lisp and Ada. Among these was AutoClassII -- a large Artificial Intelligence (AI) application written in Common Lisp. The extraction of a representative subset of this complex application was aided by a Lisp Code Analyzer (LCA). The LCA enabled rapid analysis of the code, putting it in a concise and functionally readable form. An equivalent benchmark was created in Ada through manual translation of the Lisp version. A comparison of the execution results of both programs across a variety of compiler-machine combinations indicate that line-by-line translation coupled with analysis of the initial code can produce relatively efficient and reusable target code.

The MCNP6 Analytic Criticality Benchmark Suite

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

Brown, Forrest B.

2016-06-16

Analytical benchmarks provide an invaluable tool for verifying computer codes used to simulate neutron transport. Several collections of analytical benchmark problems [1-4] are used routinely in the verification of production Monte Carlo codes such as MCNP® [5,6]. Verification of a computer code is a necessary prerequisite to the more complex validation process. The verification process confirms that a code performs its intended functions correctly. The validation process involves determining the absolute accuracy of code results vs. nature. In typical validations, results are computed for a set of benchmark experiments using a particular methodology (code, cross-section data with uncertainties, and modeling)more » and compared to the measured results from the set of benchmark experiments. The validation process determines bias, bias uncertainty, and possibly additional margins. Verification is generally performed by the code developers, while validation is generally performed by code users for a particular application space. The VERIFICATION_KEFF suite of criticality problems [1,2] was originally a set of 75 criticality problems found in the literature for which exact analytical solutions are available. Even though the spatial and energy detail is necessarily limited in analytical benchmarks, typically to a few regions or energy groups, the exact solutions obtained can be used to verify that the basic algorithms, mathematics, and methods used in complex production codes perform correctly. The present work has focused on revisiting this benchmark suite. A thorough review of the problems resulted in discarding some of them as not suitable for MCNP benchmarking. For the remaining problems, many of them were reformulated to permit execution in either multigroup mode or in the normal continuous-energy mode for MCNP. Execution of the benchmarks in continuous-energy mode provides a significant advance to MCNP verification methods.« less

Phase field benchmark problems for dendritic growth and linear elasticity

DOE PAGES

Jokisaari, Andrea M.; Voorhees, P. W.; Guyer, Jonathan E.; ...

2018-03-26

We present the second set of benchmark problems for phase field models that are being jointly developed by the Center for Hierarchical Materials Design (CHiMaD) and the National Institute of Standards and Technology (NIST) along with input from other members in the phase field community. As the integrated computational materials engineering (ICME) approach to materials design has gained traction, there is an increasing need for quantitative phase field results. New algorithms and numerical implementations increase computational capabilities, necessitating standard problems to evaluate their impact on simulated microstructure evolution as well as their computational performance. We propose one benchmark problem formore » solidifiication and dendritic growth in a single-component system, and one problem for linear elasticity via the shape evolution of an elastically constrained precipitate. We demonstrate the utility and sensitivity of the benchmark problems by comparing the results of 1) dendritic growth simulations performed with different time integrators and 2) elastically constrained precipitate simulations with different precipitate sizes, initial conditions, and elastic moduli. As a result, these numerical benchmark problems will provide a consistent basis for evaluating different algorithms, both existing and those to be developed in the future, for accuracy and computational efficiency when applied to simulate physics often incorporated in phase field models.« less

Phase field benchmark problems for dendritic growth and linear elasticity

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

Jokisaari, Andrea M.; Voorhees, P. W.; Guyer, Jonathan E.

We present the second set of benchmark problems for phase field models that are being jointly developed by the Center for Hierarchical Materials Design (CHiMaD) and the National Institute of Standards and Technology (NIST) along with input from other members in the phase field community. As the integrated computational materials engineering (ICME) approach to materials design has gained traction, there is an increasing need for quantitative phase field results. New algorithms and numerical implementations increase computational capabilities, necessitating standard problems to evaluate their impact on simulated microstructure evolution as well as their computational performance. We propose one benchmark problem formore » solidifiication and dendritic growth in a single-component system, and one problem for linear elasticity via the shape evolution of an elastically constrained precipitate. We demonstrate the utility and sensitivity of the benchmark problems by comparing the results of 1) dendritic growth simulations performed with different time integrators and 2) elastically constrained precipitate simulations with different precipitate sizes, initial conditions, and elastic moduli. As a result, these numerical benchmark problems will provide a consistent basis for evaluating different algorithms, both existing and those to be developed in the future, for accuracy and computational efficiency when applied to simulate physics often incorporated in phase field models.« less

Benchmarking fully analytic DFT force fields for vibrational spectroscopy: A study on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Cornaton, Yann

2018-05-01

This work presents an investigation of the theoretical predictions yielded by anharmonic force fields having the cubic and quartic force constants are computed analytically by means of density functional theory (DFT) using the recursive scheme developed by M. Ringholm et al. (J. Comput. Chem. 35 (2014) 622). Different functionals (namely B3LYP, PBE, PBE0 and PW86x) and basis sets were used for calculating the anharmonic vibrational spectra of two halomethanes. The benchmark analysis carried out demonstrates the reliability and overall good performances offered by hybrid approaches, where the harmonic data obtained at the coupled cluster with single and double excitations level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T), are combined with the fully analytic higher order force constants yielded by DFT functionals. These methods lead to reliable and computationally affordable calculations of anharmonic vibrational spectra with an accuracy comparable to that yielded by hybrid force fields having the anharmonic force fields computed at second order Møller-Plesset perturbation theory (MP2) level of theory using numerical differentiation but without the corresponding potential issues related to computational costs and numerical errors.

Supercomputing '91; Proceedings of the 4th Annual Conference on High Performance Computing, Albuquerque, NM, Nov. 18-22, 1991

NASA Technical Reports Server (NTRS)

1991-01-01

Various papers on supercomputing are presented. The general topics addressed include: program analysis/data dependence, memory access, distributed memory code generation, numerical algorithms, supercomputer benchmarks, latency tolerance, parallel programming, applications, processor design, networks, performance tools, mapping and scheduling, characterization affecting performance, parallelism packaging, computing climate change, combinatorial algorithms, hardware and software performance issues, system issues. (No individual items are abstracted in this volume)

Benchmarking and Modeling of a Conventional Mid-Size Car Using ALPHA (SAE Paper 2015-01-1140)

EPA Science Inventory

The Advanced Light-Duty Powertrain and Hybrid Analysis (ALPHA) modeling tool was created by EPA to estimate greenhouse gas (GHG) emissions of light-duty vehicles. ALPHA is a physics-based, forward-looking, full vehicle computer simulation capable of analyzing various vehicle type...

Identification of metabolic pathways using pathfinding approaches: a systematic review.

PubMed

Abd Algfoor, Zeyad; Shahrizal Sunar, Mohd; Abdullah, Afnizanfaizal; Kolivand, Hoshang

2017-03-01

Metabolic pathways have become increasingly available for various microorganisms. Such pathways have spurred the development of a wide array of computational tools, in particular, mathematical pathfinding approaches. This article can facilitate the understanding of computational analysis of metabolic pathways in genomics. Moreover, stoichiometric and pathfinding approaches in metabolic pathway analysis are discussed. Three major types of studies are elaborated: stoichiometric identification models, pathway-based graph analysis and pathfinding approaches in cellular metabolism. Furthermore, evaluation of the outcomes of the pathways with mathematical benchmarking metrics is provided. This review would lead to better comprehension of metabolism behaviors in living cells, in terms of computed pathfinding approaches. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

High Productivity Computing Systems Analysis and Performance

DTIC Science & Technology

2005-07-01

cubic grid Discrete Math Global Updates per second (GUP/S) RandomAccess Paper & Pencil Contact Bob Lucas (ISI) Multiple Precision none...can be found at the web site. One of the HPCchallenge codes, RandomAccess, is derived from the HPCS discrete math benchmarks that we released, and...Kernels Discrete Math … Graph Analysis … Linear Solvers … Signal Processi ng Execution Bounds Execution Indicators 6 Scalable Compact

StrAuto: automation and parallelization of STRUCTURE analysis.

PubMed

Chhatre, Vikram E; Emerson, Kevin J

2017-03-24

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

Third Computational Aeroacoustics (CAA) Workshop on Benchmark Problems

NASA Technical Reports Server (NTRS)

Dahl, Milo D. (Editor)

2000-01-01

The proceedings of the Third Computational Aeroacoustics (CAA) Workshop on Benchmark Problems cosponsored by the Ohio Aerospace Institute and the NASA Glenn Research Center are the subject of this report. Fan noise was the chosen theme for this workshop with representative problems encompassing four of the six benchmark problem categories. The other two categories were related to jet noise and cavity noise. For the first time in this series of workshops, the computational results for the cavity noise problem were compared to experimental data. All the other problems had exact solutions, which are included in this report. The Workshop included a panel discussion by representatives of industry. The participants gave their views on the status of applying computational aeroacoustics to solve practical industry related problems and what issues need to be addressed to make CAA a robust design tool.

Hardware accelerated high performance neutron transport computation based on AGENT methodology

NASA Astrophysics Data System (ADS)

Xiao, Shanjie

The spatial heterogeneity of the next generation Gen-IV nuclear reactor core designs brings challenges to the neutron transport analysis. The Arbitrary Geometry Neutron Transport (AGENT) AGENT code is a three-dimensional neutron transport analysis code being developed at the Laboratory for Neutronics and Geometry Computation (NEGE) at Purdue University. It can accurately describe the spatial heterogeneity in a hierarchical structure through the R-function solid modeler. The previous version of AGENT coupled the 2D transport MOC solver and the 1D diffusion NEM solver to solve the three dimensional Boltzmann transport equation. In this research, the 2D/1D coupling methodology was expanded to couple two transport solvers, the radial 2D MOC solver and the axial 1D MOC solver, for better accuracy. The expansion was benchmarked with the widely applied C5G7 benchmark models and two fast breeder reactor models, and showed good agreement with the reference Monte Carlo results. In practice, the accurate neutron transport analysis for a full reactor core is still time-consuming and thus limits its application. Therefore, another content of my research is focused on designing a specific hardware based on the reconfigurable computing technique in order to accelerate AGENT computations. It is the first time that the application of this type is used to the reactor physics and neutron transport for reactor design. The most time consuming part of the AGENT algorithm was identified. Moreover, the architecture of the AGENT acceleration system was designed based on the analysis. Through the parallel computation on the specially designed, highly efficient architecture, the acceleration design on FPGA acquires high performance at the much lower working frequency than CPUs. The whole design simulations show that the acceleration design would be able to speedup large scale AGENT computations about 20 times. The high performance AGENT acceleration system will drastically shortening the computation time for 3D full-core neutron transport analysis, making the AGENT methodology unique and advantageous, and thus supplies the possibility to extend the application range of neutron transport analysis in either industry engineering or academic research.

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

Benchmarking the efficiency of the Chilean water and sewerage companies: a double-bootstrap approach.

PubMed

Molinos-Senante, María; Donoso, Guillermo; Sala-Garrido, Ramon; Villegas, Andrés

2018-03-01

Benchmarking the efficiency of water companies is essential to set water tariffs and to promote their sustainability. In doing so, most of the previous studies have applied conventional data envelopment analysis (DEA) models. However, it is a deterministic method that does not allow to identify environmental factors influencing efficiency scores. To overcome this limitation, this paper evaluates the efficiency of a sample of Chilean water and sewerage companies applying a double-bootstrap DEA model. Results evidenced that the ranking of water and sewerage companies changes notably whether efficiency scores are computed applying conventional or double-bootstrap DEA models. Moreover, it was found that the percentage of non-revenue water and customer density are factors influencing the efficiency of Chilean water and sewerage companies. This paper illustrates the importance of using a robust and reliable method to increase the relevance of benchmarking tools.

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

MARC calculations for the second WIPP structural benchmark problem

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

Morgan, H.S.

1981-05-01

This report describes calculations made with the MARC structural finite element code for the second WIPP structural benchmark problem. Specific aspects of problem implementation such as element choice, slip line modeling, creep law implementation, and thermal-mechanical coupling are discussed in detail. Also included are the computational results specified in the benchmark problem formulation.

The Filament Sensor for Near Real-Time Detection of Cytoskeletal Fiber Structures

PubMed Central

Eltzner, Benjamin; Wollnik, Carina; Gottschlich, Carsten; Huckemann, Stephan; Rehfeldt, Florian

2015-01-01

A reliable extraction of filament data from microscopic images is of high interest in the analysis of acto-myosin structures as early morphological markers in mechanically guided differentiation of human mesenchymal stem cells and the understanding of the underlying fiber arrangement processes. In this paper, we propose the filament sensor (FS), a fast and robust processing sequence which detects and records location, orientation, length, and width for each single filament of an image, and thus allows for the above described analysis. The extraction of these features has previously not been possible with existing methods. We evaluate the performance of the proposed FS in terms of accuracy and speed in comparison to three existing methods with respect to their limited output. Further, we provide a benchmark dataset of real cell images along with filaments manually marked by a human expert as well as simulated benchmark images. The FS clearly outperforms existing methods in terms of computational runtime and filament extraction accuracy. The implementation of the FS and the benchmark database are available as open source. PMID:25996921

Analysis of 2D Torus and Hub Topologies of 100Mb/s Ethernet for the Whitney Commodity Computing Testbed

NASA Technical Reports Server (NTRS)

Pedretti, Kevin T.; Fineberg, Samuel A.; Kutler, Paul (Technical Monitor)

1997-01-01

A variety of different network technologies and topologies are currently being evaluated as part of the Whitney Project. This paper reports on the implementation and performance of a Fast Ethernet network configured in a 4x4 2D torus topology in a testbed cluster of 'commodity' Pentium Pro PCs. Several benchmarks were used for performance evaluation: an MPI point to point message passing benchmark, an MPI collective communication benchmark, and the NAS Parallel Benchmarks version 2.2 (NPB2). Our results show that for point to point communication on an unloaded network, the hub and 1 hop routes on the torus have about the same bandwidth and latency. However, the bandwidth decreases and the latency increases on the torus for each additional route hop. Collective communication benchmarks show that the torus provides roughly four times more aggregate bandwidth and eight times faster MPI barrier synchronizations than a hub based network for 16 processor systems. Finally, the SOAPBOX benchmarks, which simulate real-world CFD applications, generally demonstrated substantially better performance on the torus than on the hub. In the few cases the hub was faster, the difference was negligible. In total, our experimental results lead to the conclusion that for Fast Ethernet networks, the torus topology has better performance and scales better than a hub based network.

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.

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.

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.

Unstructured Finite Volume Computational Thermo-Fluid Dynamic Method for Multi-Disciplinary Analysis and Design Optimization

NASA Technical Reports Server (NTRS)

Majumdar, Alok; Schallhorn, Paul

1998-01-01

This paper describes a finite volume computational thermo-fluid dynamics method to solve for Navier-Stokes equations in conjunction with energy equation and thermodynamic equation of state in an unstructured coordinate system. The system of equations have been solved by a simultaneous Newton-Raphson method and compared with several benchmark solutions. Excellent agreements have been obtained in each case and the method has been found to be significantly faster than conventional Computational Fluid Dynamic(CFD) methods and therefore has the potential for implementation in Multi-Disciplinary analysis and design optimization in fluid and thermal systems. The paper also describes an algorithm of design optimization based on Newton-Raphson method which has been recently tested in a turbomachinery application.

Aerothermal modeling program, phase 1

NASA Technical Reports Server (NTRS)

Srinivasan, R.; Reynolds, R.; Ball, I.; Berry, R.; Johnson, K.; Mongia, H.

1983-01-01

Aerothermal submodels used in analytical combustor models are analyzed. The models described include turbulence and scalar transport, gaseous full combustion, spray evaporation/combustion, soot formation and oxidation, and radiation. The computational scheme is discussed in relation to boundary conditions and convergence criteria. Also presented is the data base for benchmark quality test cases and an analysis of simple flows.

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.

Development of Benchmark Examples for Delamination Onset and Fatigue Growth Prediction

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2011-01-01

An approach for assessing the delamination propagation and growth capabilities in commercial finite element codes was developed and demonstrated for the Virtual Crack Closure Technique (VCCT) implementations in ABAQUS. The Double Cantilever Beam (DCB) specimen was chosen as an example. First, benchmark results to assess delamination propagation capabilities under static loading were created using models simulating specimens with different delamination lengths. For each delamination length modeled, the load and displacement at the load point were monitored. The mixed-mode strain energy release rate components were calculated along the delamination front across the width of the specimen. A failure index was calculated by correlating the results with the mixed-mode failure criterion of the graphite/epoxy material. The calculated critical loads and critical displacements for delamination onset for each delamination length modeled were used as a benchmark. The load/displacement relationship computed during automatic propagation should closely match the benchmark case. Second, starting from an initially straight front, the delamination was allowed to propagate based on the algorithms implemented in the commercial finite element software. The load-displacement relationship obtained from the propagation analysis results and the benchmark results were compared. Good agreements could be achieved by selecting the appropriate input parameters, which were determined in an iterative procedure.

Covariance Applications in Criticality Safety, Light Water Reactor Analysis, and Spent Fuel Characterization

DOE PAGES

Williams, M. L.; Wiarda, D.; Ilas, G.; ...

2014-06-15

Recently, we processed a new covariance data library based on ENDF/B-VII.1 for the SCALE nuclear analysis code system. The multigroup covariance data are discussed here, along with testing and application results for critical benchmark experiments. Moreover, the cross section covariance library, along with covariances for fission product yields and decay data, is used to compute uncertainties in the decay heat produced by a burned reactor fuel assembly.

The benchmark aeroelastic models program: Description and highlights of initial results

NASA Technical Reports Server (NTRS)

Bennett, Robert M.; Eckstrom, Clinton V.; Rivera, Jose A., Jr.; Dansberry, Bryan E.; Farmer, Moses G.; Durham, Michael H.

1991-01-01

An experimental effort was implemented in aeroelasticity called the Benchmark Models Program. The primary purpose of this program is to provide the necessary data to evaluate computational fluid dynamic codes for aeroelastic analysis. It also focuses on increasing the understanding of the physics of unsteady flows and providing data for empirical design. An overview is given of this program and some results obtained in the initial tests are highlighted. The tests that were completed include measurement of unsteady pressures during flutter of rigid wing with a NACA 0012 airfoil section and dynamic response measurements of a flexible rectangular wing with a thick circular arc airfoil undergoing shock boundary layer oscillations.

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.

Benchmarking and performance analysis of the CM-2. [SIMD computer

NASA Technical Reports Server (NTRS)

Myers, David W.; Adams, George B., II

1988-01-01

A suite of benchmarking routines testing communication, basic arithmetic operations, and selected kernel algorithms written in LISP and PARIS was developed for the CM-2. Experiment runs are automated via a software framework that sequences individual tests, allowing for unattended overnight operation. Multiple measurements are made and treated statistically to generate well-characterized results from the noisy values given by cm:time. The results obtained provide a comparison with similar, but less extensive, testing done on a CM-1. Tests were chosen to aid the algorithmist in constructing fast, efficient, and correct code on the CM-2, as well as gain insight into what performance criteria are needed when evaluating parallel processing machines.

Airfoil Vibration Dampers program

NASA Technical Reports Server (NTRS)

Cook, Robert M.

1991-01-01

The Airfoil Vibration Damper program has consisted of an analysis phase and a testing phase. During the analysis phase, a state-of-the-art computer code was developed, which can be used to guide designers in the placement and sizing of friction dampers. The use of this computer code was demonstrated by performing representative analyses on turbine blades from the High Pressure Oxidizer Turbopump (HPOTP) and High Pressure Fuel Turbopump (HPFTP) of the Space Shuttle Main Engine (SSME). The testing phase of the program consisted of performing friction damping tests on two different cantilever beams. Data from these tests provided an empirical check on the accuracy of the computer code developed in the analysis phase. Results of the analysis and testing showed that the computer code can accurately predict the performance of friction dampers. In addition, a valuable set of friction damping data was generated, which can be used to aid in the design of friction dampers, as well as provide benchmark test cases for future code developers.

FX-87 performance measurements: data-flow implementation. Technical report

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

Hammel, R.T.; Gifford, D.K.

1988-11-01

This report documents a series of experiments performed to explore the thesis that the FX-87 effect system permits a compiler to schedule imperative programs (i.e., programs that may contain side-effects) for execution on a parallel computer. The authors analyze how much the FX-87 static effect system can improve the execution times of five benchmark programs on a parallel graph interpreter. Three of their benchmark programs do not use side-effects (factorial, fibonacci, and polynomial division) and thus did not have any effect-induced constraints. Their FX-87 performance was comparable to their performance in a purely functional language. Two of the benchmark programsmore » use side effects (DNA sequence matching and Scheme interpretation) and the compiler was able to use effect information to reduce their execution times by factors of 1.7 to 5.4 when compared with sequential execution times. These results support the thesis that a static effect system is a powerful tool for compilation to multiprocessor computers. However, the graph interpreter we used was based on unrealistic assumptions, and thus our results may not accurately reflect the performance of a practical FX-87 implementation. The results also suggest that conventional loop analysis would complement the FX-87 effect system« 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.

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.

FUN3D Analyses in Support of the Second Aeroelastic Prediction Workshop

NASA Technical Reports Server (NTRS)

Chwalowski, Pawel; Heeg, Jennifer

2016-01-01

This paper presents the computational aeroelastic results generated in support of the second Aeroelastic Prediction Workshop for the Benchmark Supercritical Wing (BSCW) configurations and compares them to the experimental data. The computational results are obtained using FUN3D, an unstructured grid Reynolds- Averaged Navier-Stokes solver developed at NASA Langley Research Center. The analysis results include aerodynamic coefficients and surface pressures obtained for steady-state, static aeroelastic equilibrium, and unsteady flow due to a pitching wing or flutter prediction. Frequency response functions of the pressure coefficients with respect to the angular displacement are computed and compared with the experimental data. The effects of spatial and temporal convergence on the computational results are examined.

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.

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.

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

Benchmark datasets for 3D MALDI- and DESI-imaging mass spectrometry.

PubMed

Oetjen, Janina; Veselkov, Kirill; Watrous, Jeramie; McKenzie, James S; Becker, Michael; Hauberg-Lotte, Lena; Kobarg, Jan Hendrik; Strittmatter, Nicole; Mróz, Anna K; Hoffmann, Franziska; Trede, Dennis; Palmer, Andrew; Schiffler, Stefan; Steinhorst, Klaus; Aichler, Michaela; Goldin, Robert; Guntinas-Lichius, Orlando; von Eggeling, Ferdinand; Thiele, Herbert; Maedler, Kathrin; Walch, Axel; Maass, Peter; Dorrestein, Pieter C; Takats, Zoltan; Alexandrov, Theodore

2015-01-01

Three-dimensional (3D) imaging mass spectrometry (MS) is an analytical chemistry technique for the 3D molecular analysis of a tissue specimen, entire organ, or microbial colonies on an agar plate. 3D-imaging MS has unique advantages over existing 3D imaging techniques, offers novel perspectives for understanding the spatial organization of biological processes, and has growing potential to be introduced into routine use in both biology and medicine. Owing to the sheer quantity of data generated, the visualization, analysis, and interpretation of 3D imaging MS data remain a significant challenge. Bioinformatics research in this field is hampered by the lack of publicly available benchmark datasets needed to evaluate and compare algorithms. High-quality 3D imaging MS datasets from different biological systems at several labs were acquired, supplied with overview images and scripts demonstrating how to read them, and deposited into MetaboLights, an open repository for metabolomics data. 3D imaging MS data were collected from five samples using two types of 3D imaging MS. 3D matrix-assisted laser desorption/ionization imaging (MALDI) MS data were collected from murine pancreas, murine kidney, human oral squamous cell carcinoma, and interacting microbial colonies cultured in Petri dishes. 3D desorption electrospray ionization (DESI) imaging MS data were collected from a human colorectal adenocarcinoma. With the aim to stimulate computational research in the field of computational 3D imaging MS, selected high-quality 3D imaging MS datasets are provided that could be used by algorithm developers as benchmark datasets.

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.

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.

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.

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

Computational singular perturbation analysis of stochastic chemical systems with stiffness

NASA Astrophysics Data System (ADS)

Wang, Lijin; Han, Xiaoying; Cao, Yanzhao; Najm, Habib N.

2017-04-01

Computational singular perturbation (CSP) is a useful method for analysis, reduction, and time integration of stiff ordinary differential equation systems. It has found dominant utility, in particular, in chemical reaction systems with a large range of time scales at continuum and deterministic level. On the other hand, CSP is not directly applicable to chemical reaction systems at micro or meso-scale, where stochasticity plays an non-negligible role and thus has to be taken into account. In this work we develop a novel stochastic computational singular perturbation (SCSP) analysis and time integration framework, and associated algorithm, that can be used to not only construct accurately and efficiently the numerical solutions to stiff stochastic chemical reaction systems, but also analyze the dynamics of the reduced stochastic reaction systems. The algorithm is illustrated by an application to a benchmark stochastic differential equation model, and numerical experiments are carried out to demonstrate the effectiveness of the construction.

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.

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

Fourth Computational Aeroacoustics (CAA) Workshop on Benchmark Problems

NASA Technical Reports Server (NTRS)

Dahl, Milo D. (Editor)

2004-01-01

This publication contains the proceedings of the Fourth Computational Aeroacoustics (CAA) Workshop on Benchmark Problems. In this workshop, as in previous workshops, the problems were devised to gauge the technological advancement of computational techniques to calculate all aspects of sound generation and propagation in air directly from the fundamental governing equations. A variety of benchmark problems have been previously solved ranging from simple geometries with idealized acoustic conditions to test the accuracy and effectiveness of computational algorithms and numerical boundary conditions; to sound radiation from a duct; to gust interaction with a cascade of airfoils; to the sound generated by a separating, turbulent viscous flow. By solving these and similar problems, workshop participants have shown the technical progress from the basic challenges to accurate CAA calculations to the solution of CAA problems of increasing complexity and difficulty. The fourth CAA workshop emphasized the application of CAA methods to the solution of realistic problems. The workshop was held at the Ohio Aerospace Institute in Cleveland, Ohio, on October 20 to 22, 2003. At that time, workshop participants presented their solutions to problems in one or more of five categories. Their solutions are presented in this proceedings along with the comparisons of their solutions to the benchmark solutions or experimental data. The five categories for the benchmark problems were as follows: Category 1:Basic Methods. The numerical computation of sound is affected by, among other issues, the choice of grid used and by the boundary conditions. Category 2:Complex Geometry. The ability to compute the sound in the presence of complex geometric surfaces is important in practical applications of CAA. Category 3:Sound Generation by Interacting With a Gust. The practical application of CAA for computing noise generated by turbomachinery involves the modeling of the noise source mechanism as a vortical gust interacting with an airfoil. Category 4:Sound Transmission and Radiation. Category 5:Sound Generation in Viscous Problems. Sound is generated under certain conditions by a viscous flow as the flow passes an object or a cavity.

MC21 analysis of the MIT PWR benchmark: Hot zero power results

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

Kelly Iii, D. J.; Aviles, B. N.; Herman, B. R.

2013-07-01

MC21 Monte Carlo results have been compared with hot zero power measurements from an operating pressurized water reactor (PWR), as specified in a new full core PWR performance benchmark from the MIT Computational Reactor Physics Group. Included in the comparisons are axially integrated full core detector measurements, axial detector profiles, control rod bank worths, and temperature coefficients. Power depressions from grid spacers are seen clearly in the MC21 results. Application of Coarse Mesh Finite Difference (CMFD) acceleration within MC21 has been accomplished, resulting in a significant reduction of inactive batches necessary to converge the fission source. CMFD acceleration has alsomore » been shown to work seamlessly with the Uniform Fission Site (UFS) variance reduction method. (authors)« less

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

Cloud-Based Evaluation of Anatomical Structure Segmentation and Landmark Detection Algorithms: VISCERAL Anatomy Benchmarks.

PubMed

Jimenez-Del-Toro, Oscar; Muller, Henning; Krenn, Markus; Gruenberg, Katharina; Taha, Abdel Aziz; Winterstein, Marianne; Eggel, Ivan; Foncubierta-Rodriguez, Antonio; Goksel, Orcun; Jakab, Andras; Kontokotsios, Georgios; Langs, Georg; Menze, Bjoern H; Salas Fernandez, Tomas; Schaer, Roger; Walleyo, Anna; Weber, Marc-Andre; Dicente Cid, Yashin; Gass, Tobias; Heinrich, Mattias; Jia, Fucang; Kahl, Fredrik; Kechichian, Razmig; Mai, Dominic; Spanier, Assaf B; Vincent, Graham; Wang, Chunliang; Wyeth, Daniel; Hanbury, Allan

2016-11-01

Variations in the shape and appearance of anatomical structures in medical images are often relevant radiological signs of disease. Automatic tools can help automate parts of this manual process. A cloud-based evaluation framework is presented in this paper including results of benchmarking current state-of-the-art medical imaging algorithms for anatomical structure segmentation and landmark detection: the VISCERAL Anatomy benchmarks. The algorithms are implemented in virtual machines in the cloud where participants can only access the training data and can be run privately by the benchmark administrators to objectively compare their performance in an unseen common test set. Overall, 120 computed tomography and magnetic resonance patient volumes were manually annotated to create a standard Gold Corpus containing a total of 1295 structures and 1760 landmarks. Ten participants contributed with automatic algorithms for the organ segmentation task, and three for the landmark localization task. Different algorithms obtained the best scores in the four available imaging modalities and for subsets of anatomical structures. The annotation framework, resulting data set, evaluation setup, results and performance analysis from the three VISCERAL Anatomy benchmarks are presented in this article. Both the VISCERAL data set and Silver Corpus generated with the fusion of the participant algorithms on a larger set of non-manually-annotated medical images are available to the research community.

The PAC-MAN model: Benchmark case for linear acoustics in computational physics

NASA Astrophysics Data System (ADS)

Ziegelwanger, Harald; Reiter, Paul

2017-10-01

Benchmark cases in the field of computational physics, on the one hand, have to contain a certain complexity to test numerical edge cases and, on the other hand, require the existence of an analytical solution, because an analytical solution allows the exact quantification of the accuracy of a numerical simulation method. This dilemma causes a need for analytical sound field formulations of complex acoustic problems. A well known example for such a benchmark case for harmonic linear acoustics is the ;Cat's Eye model;, which describes the three-dimensional sound field radiated from a sphere with a missing octant analytically. In this paper, a benchmark case for two-dimensional (2D) harmonic linear acoustic problems, viz., the ;PAC-MAN model;, is proposed. The PAC-MAN model describes the radiated and scattered sound field around an infinitely long cylinder with a cut out sector of variable angular width. While the analytical calculation of the 2D sound field allows different angular cut-out widths and arbitrarily positioned line sources, the computational cost associated with the solution of this problem is similar to a 1D problem because of a modal formulation of the sound field in the PAC-MAN model.

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.

Non-parametric correlative uncertainty quantification and sensitivity analysis: Application to a Langmuir bimolecular adsorption model

NASA Astrophysics Data System (ADS)

Feng, Jinchao; Lansford, Joshua; Mironenko, Alexander; Pourkargar, Davood Babaei; Vlachos, Dionisios G.; Katsoulakis, Markos A.

2018-03-01

We propose non-parametric methods for both local and global sensitivity analysis of chemical reaction models with correlated parameter dependencies. The developed mathematical and statistical tools are applied to a benchmark Langmuir competitive adsorption model on a close packed platinum surface, whose parameters, estimated from quantum-scale computations, are correlated and are limited in size (small data). The proposed mathematical methodology employs gradient-based methods to compute sensitivity indices. We observe that ranking influential parameters depends critically on whether or not correlations between parameters are taken into account. The impact of uncertainty in the correlation and the necessity of the proposed non-parametric perspective are demonstrated.

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

Three-dimensional viscous design methodology for advanced technology aircraft supersonic inlet systems

NASA Technical Reports Server (NTRS)

Anderson, B. H.

1983-01-01

A broad program to develop advanced, reliable, and user oriented three-dimensional viscous design techniques for supersonic inlet systems, and encourage their transfer into the general user community is discussed. Features of the program include: (1) develop effective methods of computing three-dimensional flows within a zonal modeling methodology; (2) ensure reasonable agreement between said analysis and selective sets of benchmark validation data; (3) develop user orientation into said analysis; and (4) explore and develop advanced numerical methodology.

Performance Comparison of Big Data Analytics With NEXUS and Giovanni

NASA Astrophysics Data System (ADS)

Jacob, J. C.; Huang, T.; Lynnes, C.

2016-12-01

NEXUS is an emerging data-intensive analysis framework developed with a new approach for handling science data that enables large-scale data analysis. It is available through open source. We compare performance of NEXUS and Giovanni for 3 statistics algorithms applied to NASA datasets. Giovanni is a statistics web service at NASA Distributed Active Archive Centers (DAACs). NEXUS is a cloud-computing environment developed at JPL and built on Apache Solr, Cassandra, and Spark. We compute global time-averaged map, correlation map, and area-averaged time series. The first two algorithms average over time to produce a value for each pixel in a 2-D map. The third algorithm averages spatially to produce a single value for each time step. This talk is our report on benchmark comparison findings that indicate 15x speedup with NEXUS over Giovanni to compute area-averaged time series of daily precipitation rate for the Tropical Rainfall Measuring Mission (TRMM with 0.25 degree spatial resolution) for the Continental United States over 14 years (2000-2014) with 64-way parallelism and 545 tiles per granule. 16-way parallelism with 16 tiles per granule worked best with NEXUS for computing an 18-year (1998-2015) TRMM daily precipitation global time averaged map (2.5 times speedup) and 18-year global map of correlation between TRMM daily precipitation and TRMM real time daily precipitation (7x speedup). These and other benchmark results will be presented along with key lessons learned in applying the NEXUS tiling approach to big data analytics in the cloud.

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

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.

I/O-Efficient Scientific Computation Using TPIE

NASA Technical Reports Server (NTRS)

Vengroff, Darren Erik; Vitter, Jeffrey Scott

1996-01-01

In recent years, input/output (I/O)-efficient algorithms for a wide variety of problems have appeared in the literature. However, systems specifically designed to assist programmers in implementing such algorithms have remained scarce. TPIE is a system designed to support I/O-efficient paradigms for problems from a variety of domains, including computational geometry, graph algorithms, and scientific computation. The TPIE interface frees programmers from having to deal not only with explicit read and write calls, but also the complex memory management that must be performed for I/O-efficient computation. In this paper we discuss applications of TPIE to problems in scientific computation. We discuss algorithmic issues underlying the design and implementation of the relevant components of TPIE and present performance results of programs written to solve a series of benchmark problems using our current TPIE prototype. Some of the benchmarks we present are based on the NAS parallel benchmarks while others are of our own creation. We demonstrate that the central processing unit (CPU) overhead required to manage I/O is small and that even with just a single disk, the I/O overhead of I/O-efficient computation ranges from negligible to the same order of magnitude as CPU time. We conjecture that if we use a number of disks in parallel this overhead can be all but eliminated.

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

Towards evidence-based computational statistics: lessons from clinical research on the role and design of real-data benchmark studies.

PubMed

Boulesteix, Anne-Laure; Wilson, Rory; Hapfelmeier, Alexander

2017-09-09

The goal of medical research is to develop interventions that are in some sense superior, with respect to patient outcome, to interventions currently in use. Similarly, the goal of research in methodological computational statistics is to develop data analysis tools that are themselves superior to the existing tools. The methodology of the evaluation of medical interventions continues to be discussed extensively in the literature and it is now well accepted that medicine should be at least partly "evidence-based". Although we statisticians are convinced of the importance of unbiased, well-thought-out study designs and evidence-based approaches in the context of clinical research, we tend to ignore these principles when designing our own studies for evaluating statistical methods in the context of our methodological research. In this paper, we draw an analogy between clinical trials and real-data-based benchmarking experiments in methodological statistical science, with datasets playing the role of patients and methods playing the role of medical interventions. Through this analogy, we suggest directions for improvement in the design and interpretation of studies which use real data to evaluate statistical methods, in particular with respect to dataset inclusion criteria and the reduction of various forms of bias. More generally, we discuss the concept of "evidence-based" statistical research, its limitations and its impact on the design and interpretation of real-data-based benchmark experiments. We suggest that benchmark studies-a method of assessment of statistical methods using real-world datasets-might benefit from adopting (some) concepts from evidence-based medicine towards the goal of more evidence-based statistical research.

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.

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

Computational Fluid Dynamics Technology for Hypersonic Applications

NASA Technical Reports Server (NTRS)

Gnoffo, Peter A.

2003-01-01

Several current challenges in computational fluid dynamics and aerothermodynamics for hypersonic vehicle applications are discussed. Example simulations are presented from code validation and code benchmarking efforts to illustrate capabilities and limitations. Opportunities to advance the state-of-art in algorithms, grid generation and adaptation, and code validation are identified. Highlights of diverse efforts to address these challenges are then discussed. One such effort to re-engineer and synthesize the existing analysis capability in LAURA, VULCAN, and FUN3D will provide context for these discussions. The critical (and evolving) role of agile software engineering practice in the capability enhancement process is also noted.

Summary of the Tandem Cylinder Solutions from the Benchmark Problems for Airframe Noise Computations-I Workshop

NASA Technical Reports Server (NTRS)

Lockard, David P.

2011-01-01

Fifteen submissions in the tandem cylinders category of the First Workshop on Benchmark problems for Airframe Noise Computations are summarized. Although the geometry is relatively simple, the problem involves complex physics. Researchers employed various block-structured, overset, unstructured and embedded Cartesian grid techniques and considerable computational resources to simulate the flow. The solutions are compared against each other and experimental data from 2 facilities. Overall, the simulations captured the gross features of the flow, but resolving all the details which would be necessary to compute the noise remains challenging. In particular, how to best simulate the effects of the experimental transition strip, and the associated high Reynolds number effects, was unclear. Furthermore, capturing the spanwise variation proved difficult.

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.

NAS Grid Benchmarks. 1.0

NASA Technical Reports Server (NTRS)

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

2002-01-01

We provide a paper-and-pencil specification of a benchmark suite for computational grids. It is based on the NAS (NASA Advanced Supercomputing) Parallel Benchmarks (NPB) and is called the NAS Grid Benchmarks (NGB). NGB problems are presented as data flow graphs encapsulating an instance of a slightly modified NPB task in each graph node, which communicates with other nodes by sending/receiving initialization data. Like NPB, NGB specifies several different classes (problem sizes). In this report we describe classes S, W, and A, and provide verification values for each. The implementor has the freedom to choose any language, grid environment, security model, fault tolerance/error correction mechanism, etc., as long as the resulting implementation passes the verification test and reports the turnaround time of the benchmark.

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-

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.

Computing sextic centrifugal distortion constants by DFT: A benchmark analysis on halogenated compounds

NASA Astrophysics Data System (ADS)

Pietropolli Charmet, Andrea; Stoppa, Paolo; Tasinato, Nicola; Giorgianni, Santi

2017-05-01

This work presents a benchmark study on the calculation of the sextic centrifugal distortion constants employing cubic force fields computed by means of density functional theory (DFT). For a set of semi-rigid halogenated organic compounds several functionals (B2PLYP, B3LYP, B3PW91, M06, M06-2X, O3LYP, X3LYP, ωB97XD, CAM-B3LYP, LC-ωPBE, PBE0, B97-1 and B97-D) were used for computing the sextic centrifugal distortion constants. The effects related to the size of basis sets and the performances of hybrid approaches, where the harmonic data obtained at higher level of electronic correlation are coupled with cubic force constants yielded by DFT functionals, are presented and discussed. The predicted values were compared to both the available data published in the literature and those obtained by calculations carried out at increasing level of electronic correlation: Hartree-Fock Self Consistent Field (HF-SCF), second order Møller-Plesset perturbation theory (MP2), and coupled-cluster single and double (CCSD) level of theory. Different hybrid approaches, having the cubic force field computed at DFT level of theory coupled to harmonic data computed at increasing level of electronic correlation (up to CCSD level of theory augmented by a perturbational estimate of the effects of connected triple excitations, CCSD(T)) were considered. The obtained results demonstrate that they can represent reliable and computationally affordable methods to predict sextic centrifugal terms with an accuracy almost comparable to that yielded by the more expensive anharmonic force fields fully computed at MP2 and CCSD levels of theory. In view of their reduced computational cost, these hybrid approaches pave the route to the study of more complex systems.

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.

[The QuIK-Registry of the German Society of Cardiologists in private practice: countrywide and benchmarking quality assurance in invasive cardiology].

PubMed

Albrecht, A; Levenson, B; Göhring, S; Haerer, W; Reifart, N; Ringwald, G; Troger, B

2009-10-01

QuIK is the German acronym for QUality Assurance in Invasive Cardiology. It describes the continuous project of an electronic data collection in Cardiac catheterization laboratories all over Germany. Mainly members of the German Society of Cardiologists in Private Practice (BNK) participate in this computer based project. Since 1996 data of diagnostic and interventional procedures are collected and send to a registry-center where a regular benchmarking analysis of the results is performed. Part of the project is a yearly auditing process including an on-site visit to the cath lab to guarantee for the reliability of information collected. Since 1996 about one million procedures have been documented. Georg Thieme Verlag KG Stuttgart , New York.

Turbulent Dispersion Modelling in a Complex Urban Environment - Data Analysis and Model Development

DTIC Science & Technology

2010-02-01

Technology Laboratory (Dstl) is used as a benchmark for comparison. Comparisons are also made with some more practically oriented computational fluid dynamics...predictions. To achieve clarity in the range of approaches available for practical models of con- taminant dispersion in urban areas, an overview of...complexity of those methods is simplified to a degree that allows straightforward practical implementation and application. Using these results as a

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.

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.

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

The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows.

PubMed

Bellec, Pierre; Lavoie-Courchesne, Sébastien; Dickinson, Phil; Lerch, Jason P; Zijdenbos, Alex P; Evans, Alan C

2012-01-01

The analysis of neuroimaging databases typically involves a large number of inter-connected steps called a pipeline. The pipeline system for Octave and Matlab (PSOM) is a flexible framework for the implementation of pipelines in the form of Octave or Matlab scripts. PSOM does not introduce new language constructs to specify the steps and structure of the workflow. All steps of analysis are instead described by a regular Matlab data structure, documenting their associated command and options, as well as their input, output, and cleaned-up files. The PSOM execution engine provides a number of automated services: (1) it executes jobs in parallel on a local computing facility as long as the dependencies between jobs allow for it and sufficient resources are available; (2) it generates a comprehensive record of the pipeline stages and the history of execution, which is detailed enough to fully reproduce the analysis; (3) if an analysis is started multiple times, it executes only the parts of the pipeline that need to be reprocessed. PSOM is distributed under an open-source MIT license and can be used without restriction for academic or commercial projects. The package has no external dependencies besides Matlab or Octave, is straightforward to install and supports of variety of operating systems (Linux, Windows, Mac). We ran several benchmark experiments on a public database including 200 subjects, using a pipeline for the preprocessing of functional magnetic resonance images (fMRI). The benchmark results showed that PSOM is a powerful solution for the analysis of large databases using local or distributed computing resources.

The pipeline system for Octave and Matlab (PSOM): a lightweight scripting framework and execution engine for scientific workflows

PubMed Central

Bellec, Pierre; Lavoie-Courchesne, Sébastien; Dickinson, Phil; Lerch, Jason P.; Zijdenbos, Alex P.; Evans, Alan C.

2012-01-01

The analysis of neuroimaging databases typically involves a large number of inter-connected steps called a pipeline. The pipeline system for Octave and Matlab (PSOM) is a flexible framework for the implementation of pipelines in the form of Octave or Matlab scripts. PSOM does not introduce new language constructs to specify the steps and structure of the workflow. All steps of analysis are instead described by a regular Matlab data structure, documenting their associated command and options, as well as their input, output, and cleaned-up files. The PSOM execution engine provides a number of automated services: (1) it executes jobs in parallel on a local computing facility as long as the dependencies between jobs allow for it and sufficient resources are available; (2) it generates a comprehensive record of the pipeline stages and the history of execution, which is detailed enough to fully reproduce the analysis; (3) if an analysis is started multiple times, it executes only the parts of the pipeline that need to be reprocessed. PSOM is distributed under an open-source MIT license and can be used without restriction for academic or commercial projects. The package has no external dependencies besides Matlab or Octave, is straightforward to install and supports of variety of operating systems (Linux, Windows, Mac). We ran several benchmark experiments on a public database including 200 subjects, using a pipeline for the preprocessing of functional magnetic resonance images (fMRI). The benchmark results showed that PSOM is a powerful solution for the analysis of large databases using local or distributed computing resources. PMID:22493575

Investigation of Storage Options for Scientific Computing on Grid and Cloud Facilities

NASA Astrophysics Data System (ADS)

Garzoglio, Gabriele

2012-12-01

In recent years, several new storage technologies, such as Lustre, Hadoop, OrangeFS, and BlueArc, have emerged. While several groups have run benchmarks to characterize them under a variety of configurations, more work is needed to evaluate these technologies for the use cases of scientific computing on Grid clusters and Cloud facilities. This paper discusses our evaluation of the technologies as deployed on a test bed at FermiCloud, one of the Fermilab infrastructure-as-a-service Cloud facilities. The test bed consists of 4 server-class nodes with 40 TB of disk space and up to 50 virtual machine clients, some running on the storage server nodes themselves. With this configuration, the evaluation compares the performance of some of these technologies when deployed on virtual machines and on “bare metal” nodes. In addition to running standard benchmarks such as IOZone to check the sanity of our installation, we have run I/O intensive tests using physics-analysis applications. This paper presents how the storage solutions perform in a variety of realistic use cases of scientific computing. One interesting difference among the storage systems tested is found in a decrease in total read throughput with increasing number of client processes, which occurs in some implementations but not others.

Hierarchical Kohonenen net for anomaly detection in network security.

PubMed

Sarasamma, Suseela T; Zhu, Qiuming A; Huff, Julie

2005-04-01

A novel multilevel hierarchical Kohonen Net (K-Map) for an intrusion detection system is presented. Each level of the hierarchical map is modeled as a simple winner-take-all K-Map. One significant advantage of this multilevel hierarchical K-Map is its computational efficiency. Unlike other statistical anomaly detection methods such as nearest neighbor approach, K-means clustering or probabilistic analysis that employ distance computation in the feature space to identify the outliers, our approach does not involve costly point-to-point computation in organizing the data into clusters. Another advantage is the reduced network size. We use the classification capability of the K-Map on selected dimensions of data set in detecting anomalies. Randomly selected subsets that contain both attacks and normal records from the KDD Cup 1999 benchmark data are used to train the hierarchical net. We use a confidence measure to label the clusters. Then we use the test set from the same KDD Cup 1999 benchmark to test the hierarchical net. We show that a hierarchical K-Map in which each layer operates on a small subset of the feature space is superior to a single-layer K-Map operating on the whole feature space in detecting a variety of attacks in terms of detection rate as well as false positive rate.

Investigation of storage options for scientific computing on Grid and Cloud facilities

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

Garzoglio, Gabriele

In recent years, several new storage technologies, such as Lustre, Hadoop, OrangeFS, and BlueArc, have emerged. While several groups have run benchmarks to characterize them under a variety of configurations, more work is needed to evaluate these technologies for the use cases of scientific computing on Grid clusters and Cloud facilities. This paper discusses our evaluation of the technologies as deployed on a test bed at FermiCloud, one of the Fermilab infrastructure-as-a-service Cloud facilities. The test bed consists of 4 server-class nodes with 40 TB of disk space and up to 50 virtual machine clients, some running on the storagemore » server nodes themselves. With this configuration, the evaluation compares the performance of some of these technologies when deployed on virtual machines and on bare metal nodes. In addition to running standard benchmarks such as IOZone to check the sanity of our installation, we have run I/O intensive tests using physics-analysis applications. This paper presents how the storage solutions perform in a variety of realistic use cases of scientific computing. One interesting difference among the storage systems tested is found in a decrease in total read throughput with increasing number of client processes, which occurs in some implementations but not others.« less

Benchmarking the ATLAS software through the Kit Validation engine

NASA Astrophysics Data System (ADS)

De Salvo, Alessandro; Brasolin, Franco

2010-04-01

The measurement of the experiment software performance is a very important metric in order to choose the most effective resources to be used and to discover the bottlenecks of the code implementation. In this work we present the benchmark techniques used to measure the ATLAS software performance through the ATLAS offline testing engine Kit Validation and the online portal Global Kit Validation. The performance measurements, the data collection, the online analysis and display of the results will be presented. The results of the measurement on different platforms and architectures will be shown, giving a full report on the CPU power and memory consumption of the Monte Carlo generation, simulation, digitization and reconstruction of the most CPU-intensive channels. The impact of the multi-core computing on the ATLAS software performance will also be presented, comparing the behavior of different architectures when increasing the number of concurrent processes. The benchmark techniques described in this paper have been used in the HEPiX group since the beginning of 2008 to help defining the performance metrics for the High Energy Physics applications, based on the real experiment software.

A determination of the external forces required to move the benchmark active controls testing model in pure plunge and pure pitch

NASA Technical Reports Server (NTRS)

Dcruz, Jonathan

1993-01-01

In view of the strong need for a well-documented set of experimental data which is suitable for the validation and/or calibration of modern Computational Fluid Dynamics codes, the Benchmark Models Program was initiated by the Structural Dynamics Division of the NASA Langley Research Center. One of the models in the program, the Benchmark Active Controls Testing Model, consists of a rigid wing of rectangular planform with a NACA 0012 profile and three control surfaces (a trailing-edge control surface, a lower-surface spoiler, and an upper-surface spoiler). The model is affixed to a flexible mount system which allows only plunging and/or pitching motion. An approximate analytical determination of the forces required to move this model, with its control surfaces fixed, in pure plunge and pure pitch at a number of test conditions is included. This provides a good indication of the type of actuator system required to generate the aerodynamic data resulting from pure plunging and pure pitching motion, in which much interest was expressed. The analysis makes use of previously obtained numerical results.

Benchmarking MARS (accident management software) with the Browns Ferry fire

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

Dawson, S.M.; Liu, L.Y.; Raines, J.C.

1992-01-01

The MAAP Accident Response System (MARS) is a userfriendly computer software developed to provide management and engineering staff with the most needed insights, during actual or simulated accidents, of the current and future conditions of the plant based on current plant data and its trends. To demonstrate the reliability of the MARS code in simulatng a plant transient, MARS is being benchmarked with the available reactor pressure vessel (RPV) pressure and level data from the Browns Ferry fire. The MRS software uses the Modular Accident Analysis Program (MAAP) code as its basis to calculate plant response under accident conditions. MARSmore » uses a limited set of plant data to initialize and track the accidnt progression. To perform this benchmark, a simulated set of plant data was constructed based on actual report data containing the information necessary to initialize MARS and keep track of plant system status throughout the accident progression. The initial Browns Ferry fire data were produced by performing a MAAP run to simulate the accident. The remaining accident simulation used actual plant data.« less

HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking.

PubMed

Lazaris, Charalampos; Kelly, Stephen; Ntziachristos, Panagiotis; Aifantis, Iannis; Tsirigos, Aristotelis

2017-01-05

Chromatin conformation capture techniques have evolved rapidly over the last few years and have provided new insights into genome organization at an unprecedented resolution. Analysis of Hi-C data is complex and computationally intensive involving multiple tasks and requiring robust quality assessment. This has led to the development of several tools and methods for processing Hi-C data. However, most of the existing tools do not cover all aspects of the analysis and only offer few quality assessment options. Additionally, availability of a multitude of tools makes scientists wonder how these tools and associated parameters can be optimally used, and how potential discrepancies can be interpreted and resolved. Most importantly, investigators need to be ensured that slight changes in parameters and/or methods do not affect the conclusions of their studies. To address these issues (compare, explore and reproduce), we introduce HiC-bench, a configurable computational platform for comprehensive and reproducible analysis of Hi-C sequencing data. HiC-bench performs all common Hi-C analysis tasks, such as alignment, filtering, contact matrix generation and normalization, identification of topological domains, scoring and annotation of specific interactions using both published tools and our own. We have also embedded various tasks that perform quality assessment and visualization. HiC-bench is implemented as a data flow platform with an emphasis on analysis reproducibility. Additionally, the user can readily perform parameter exploration and comparison of different tools in a combinatorial manner that takes into account all desired parameter settings in each pipeline task. This unique feature facilitates the design and execution of complex benchmark studies that may involve combinations of multiple tool/parameter choices in each step of the analysis. To demonstrate the usefulness of our platform, we performed a comprehensive benchmark of existing and new TAD callers exploring different matrix correction methods, parameter settings and sequencing depths. Users can extend our pipeline by adding more tools as they become available. HiC-bench consists an easy-to-use and extensible platform for comprehensive analysis of Hi-C datasets. We expect that it will facilitate current analyses and help scientists formulate and test new hypotheses in the field of three-dimensional genome organization.

Computational singular perturbation analysis of stochastic chemical systems with stiffness

DOE PAGES

Wang, Lijin; Han, Xiaoying; Cao, Yanzhao; ...

2017-01-25

Computational singular perturbation (CSP) is a useful method for analysis, reduction, and time integration of stiff ordinary differential equation systems. It has found dominant utility, in particular, in chemical reaction systems with a large range of time scales at continuum and deterministic level. On the other hand, CSP is not directly applicable to chemical reaction systems at micro or meso-scale, where stochasticity plays an non-negligible role and thus has to be taken into account. In this work we develop a novel stochastic computational singular perturbation (SCSP) analysis and time integration framework, and associated algorithm, that can be used to notmore » only construct accurately and efficiently the numerical solutions to stiff stochastic chemical reaction systems, but also analyze the dynamics of the reduced stochastic reaction systems. Furthermore, the algorithm is illustrated by an application to a benchmark stochastic differential equation model, and numerical experiments are carried out to demonstrate the effectiveness of the construction.« less

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.

Band structure analysis of leaky Bloch waves in 2D phononic crystal plates.

PubMed

Mazzotti, Matteo; Miniaci, Marco; Bartoli, Ivan

2017-02-01

A hybrid Finite Element-Plane Wave Expansion method is presented for the band structure analysis of phononic crystal plates with two dimensional lattice that are in contact with acoustic half-spaces. The method enables the computation of both real (propagative) and imaginary (attenuation) components of the Bloch wavenumber at any given frequency. Three numerical applications are presented: a benchmark dispersion analysis for an oil-loaded Titanium isotropic plate, the band structure analysis of a water-loaded Tungsten slab with square cylindrical cavities and a phononic crystal plate composed of Aurum cylinders embedded in an epoxy matrix. Copyright © 2016 Elsevier B.V. All rights reserved.

A solid reactor core thermal model for nuclear thermal rockets

NASA Astrophysics Data System (ADS)

Rider, William J.; Cappiello, Michael W.; Liles, Dennis R.

1991-01-01

A Helium/Hydrogen Cooled Reactor Analysis (HERA) computer code has been developed. HERA has the ability to model arbitrary geometries in three dimensions, which allows the user to easily analyze reactor cores constructed of prismatic graphite elements. The code accounts for heat generation in the fuel, control rods, and other structures; conduction and radiation across gaps; convection to the coolant; and a variety of boundary conditions. The numerical solution scheme has been optimized for vector computers, making long transient analyses economical. Time integration is either explicit or implicit, which allows the use of the model to accurately calculate both short- or long-term transients with an efficient use of computer time. Both the basic spatial and temporal integration schemes have been benchmarked against analytical solutions.

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.

Verification and benchmark testing of the NUFT computer code

NASA Astrophysics Data System (ADS)

Lee, K. H.; Nitao, J. J.; Kulshrestha, A.

1993-10-01

This interim report presents results of work completed in the ongoing verification and benchmark testing of the NUFT (Nonisothermal Unsaturated-saturated Flow and Transport) computer code. NUFT is a suite of multiphase, multicomponent models for numerical solution of thermal and isothermal flow and transport in porous media, with application to subsurface contaminant transport problems. The code simulates the coupled transport of heat, fluids, and chemical components, including volatile organic compounds. Grid systems may be cartesian or cylindrical, with one-, two-, or fully three-dimensional configurations possible. In this initial phase of testing, the NUFT code was used to solve seven one-dimensional unsaturated flow and heat transfer problems. Three verification and four benchmarking problems were solved. In the verification testing, excellent agreement was observed between NUFT results and the analytical or quasianalytical solutions. In the benchmark testing, results of code intercomparison were very satisfactory. From these testing results, it is concluded that the NUFT code is ready for application to field and laboratory problems similar to those addressed here. Multidimensional problems, including those dealing with chemical transport, will be addressed in a subsequent report.

The change of radial power factor distribution due to RCCA insertion at the first cycle core of AP1000

NASA Astrophysics Data System (ADS)

Susilo, J.; Suparlina, L.; Deswandri; Sunaryo, G. R.

2018-02-01

The using of a computer program for the PWR type core neutronic design parameters analysis has been carried out in some previous studies. These studies included a computer code validation on the neutronic parameters data values resulted from measurements and benchmarking calculation. In this study, the AP1000 first cycle core radial power peaking factor validation and analysis were performed using CITATION module of the SRAC2006 computer code. The computer code has been also validated with a good result to the criticality values of VERA benchmark core. The AP1000 core power distribution calculation has been done in two-dimensional X-Y geometry through ¼ section modeling. The purpose of this research is to determine the accuracy of the SRAC2006 code, and also the safety performance of the AP1000 core first cycle operating. The core calculations were carried out with the several conditions, those are without Rod Cluster Control Assembly (RCCA), by insertion of a single RCCA (AO, M1, M2, MA, MB, MC, MD) and multiple insertion RCCA (MA + MB, MA + MB + MC, MA + MB + MC + MD, and MA + MB + MC + MD + M1). The maximum power factor of the fuel rods value in the fuel assembly assumedapproximately 1.406. The calculation results analysis showed that the 2-dimensional CITATION module of SRAC2006 code is accurate in AP1000 power distribution calculation without RCCA and with MA+MB RCCA insertion.The power peaking factor on the first operating cycle of the AP1000 core without RCCA, as well as with single and multiple RCCA are still below in the safety limit values (less then about 1.798). So in terms of thermal power generated by the fuel assembly, then it can be considered that the AP100 core at the first operating cycle is safe.

Tools for 3D scientific visualization in computational aerodynamics

NASA Technical Reports Server (NTRS)

Bancroft, Gordon; Plessel, Todd; Merritt, Fergus; Watson, Val

1989-01-01

The purpose is to describe the tools and techniques in use at the NASA Ames Research Center for performing visualization of computational aerodynamics, for example visualization of flow fields from computer simulations of fluid dynamics about vehicles such as the Space Shuttle. The hardware used for visualization is a high-performance graphics workstation connected to a super computer with a high speed channel. At present, the workstation is a Silicon Graphics IRIS 3130, the supercomputer is a CRAY2, and the high speed channel is a hyperchannel. The three techniques used for visualization are post-processing, tracking, and steering. Post-processing analysis is done after the simulation. Tracking analysis is done during a simulation but is not interactive, whereas steering analysis involves modifying the simulation interactively during the simulation. Using post-processing methods, a flow simulation is executed on a supercomputer and, after the simulation is complete, the results of the simulation are processed for viewing. The software in use and under development at NASA Ames Research Center for performing these types of tasks in computational aerodynamics is described. Workstation performance issues, benchmarking, and high-performance networks for this purpose are also discussed as well as descriptions of other hardware for digital video and film recording.

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

Memory-Intensive Benchmarks: IRAM vs. Cache-Based Machines

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Gaeke, Brian R.; Husbands, Parry; Li, Xiaoye S.; Oliker, Leonid; Yelick, Katherine A.; Biegel, Bryan (Technical Monitor)

2002-01-01

The increasing gap between processor and memory performance has lead to new architectural models for memory-intensive applications. In this paper, we explore the performance of a set of memory-intensive benchmarks and use them to compare the performance of conventional cache-based microprocessors to a mixed logic and DRAM processor called VIRAM. The benchmarks are based on problem statements, rather than specific implementations, and in each case we explore the fundamental hardware requirements of the problem, as well as alternative algorithms and data structures that can help expose fine-grained parallelism or simplify memory access patterns. The benchmarks are characterized by their memory access patterns, their basic control structures, and the ratio of computation to memory operation.

Real-time radar signal processing using GPGPU (general-purpose graphic processing unit)

NASA Astrophysics Data System (ADS)

Kong, Fanxing; Zhang, Yan Rockee; Cai, Jingxiao; Palmer, Robert D.

2016-05-01

This study introduces a practical approach to develop real-time signal processing chain for general phased array radar on NVIDIA GPUs(Graphical Processing Units) using CUDA (Compute Unified Device Architecture) libraries such as cuBlas and cuFFT, which are adopted from open source libraries and optimized for the NVIDIA GPUs. The processed results are rigorously verified against those from the CPUs. Performance benchmarked in computation time with various input data cube sizes are compared across GPUs and CPUs. Through the analysis, it will be demonstrated that GPGPUs (General Purpose GPU) real-time processing of the array radar data is possible with relatively low-cost commercial GPUs.

Evaluation of Inelastic Constitutive Models for Nonlinear Structural Analysis

NASA Technical Reports Server (NTRS)

Kaufman, A.

1983-01-01

The influence of inelastic material models on computed stress-strain states, and therefore predicted lives, was studied for thermomechanically loaded structures. Nonlinear structural analyses were performed on a fatigue specimen which was subjected to thermal cycling in fluidized beds and on a mechanically load cycled benchmark notch specimen. Four incremental plasticity creep models (isotropic, kinematic, combined isotropic-kinematic, combined plus transient creep) were exercised. Of the plasticity models, kinematic hardening gave results most consistent with experimental observations. Life predictions using the computed strain histories at the critical location with a Strainrange Partitioning approach considerably overpredicted the crack initiation life of the thermal fatigue specimen.

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.

Customized recommendations for production management clusters of North American automatic milking systems.

PubMed

Tremblay, Marlène; Hess, Justin P; Christenson, Brock M; McIntyre, Kolby K; Smink, Ben; van der Kamp, Arjen J; de Jong, Lisanne G; Döpfer, Dörte

2016-07-01

Automatic milking systems (AMS) are implemented in a variety of situations and environments. Consequently, there is a need to characterize individual farming practices and regional challenges to streamline management advice and objectives for producers. Benchmarking is often used in the dairy industry to compare farms by computing percentile ranks of the production values of groups of farms. Grouping for conventional benchmarking is commonly limited to the use of a few factors such as farms' geographic region or breed of cattle. We hypothesized that herds' production data and management information could be clustered in a meaningful way using cluster analysis and that this clustering approach would yield better peer groups of farms than benchmarking methods based on criteria such as country, region, breed, or breed and region. By applying mixed latent-class model-based cluster analysis to 529 North American AMS dairy farms with respect to 18 significant risk factors, 6 clusters were identified. Each cluster (i.e., peer group) represented unique management styles, challenges, and production patterns. When compared with peer groups based on criteria similar to the conventional benchmarking standards, the 6 clusters better predicted milk produced (kilograms) per robot per day. Each cluster represented a unique management and production pattern that requires specialized advice. For example, cluster 1 farms were those that recently installed AMS robots, whereas cluster 3 farms (the most northern farms) fed high amounts of concentrates through the robot to compensate for low-energy feed in the bunk. In addition to general recommendations for farms within a cluster, individual farms can generate their own specific goals by comparing themselves to farms within their cluster. This is very comparable to benchmarking but adds the specific characteristics of the peer group, resulting in better farm management advice. The improvement that cluster analysis allows for is characterized by the multivariable approach and the fact that comparisons between production units can be accomplished within a cluster and between clusters as a choice. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

In Search of a Time Efficient Approach to Crack and Delamination Growth Predictions in Composites

NASA Technical Reports Server (NTRS)

Krueger, Ronald; Carvalho, Nelson

2016-01-01

Analysis benchmarking was used to assess the accuracy and time efficiency of algorithms suitable for automated delamination growth analysis. First, the Floating Node Method (FNM) was introduced and its combination with a simple exponential growth law (Paris Law) and Virtual Crack Closure technique (VCCT) was discussed. Implementation of the method into a user element (UEL) in Abaqus/Standard(Registered TradeMark) was also presented. For the assessment of growth prediction capabilities, an existing benchmark case based on the Double Cantilever Beam (DCB) specimen was briefly summarized. Additionally, the development of new benchmark cases based on the Mixed-Mode Bending (MMB) specimen to assess the growth prediction capabilities under mixed-mode I/II conditions was discussed in detail. A comparison was presented, in which the benchmark cases were used to assess the existing low-cycle fatigue analysis tool in Abaqus/Standard(Registered TradeMark) in comparison to the FNM-VCCT fatigue growth analysis implementation. The low-cycle fatigue analysis tool in Abaqus/Standard(Registered TradeMark) was able to yield results that were in good agreement with the DCB benchmark example. Results for the MMB benchmark cases, however, only captured the trend correctly. The user element (FNM-VCCT) always yielded results that were in excellent agreement with all benchmark cases, at a fraction of the analysis time. The ability to assess the implementation of two methods in one finite element code illustrated the value of establishing benchmark solutions.

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.

A Machine-to-Machine protocol benchmark for eHealth applications - Use case: Respiratory rehabilitation.

PubMed

Talaminos-Barroso, Alejandro; Estudillo-Valderrama, Miguel A; Roa, Laura M; Reina-Tosina, Javier; Ortega-Ruiz, Francisco

2016-06-01

M2M (Machine-to-Machine) communications represent one of the main pillars of the new paradigm of the Internet of Things (IoT), and is making possible new opportunities for the eHealth business. Nevertheless, the large number of M2M protocols currently available hinders the election of a suitable solution that satisfies the requirements that can demand eHealth applications. In the first place, to develop a tool that provides a benchmarking analysis in order to objectively select among the most relevant M2M protocols for eHealth solutions. In the second place, to validate the tool with a particular use case: the respiratory rehabilitation. A software tool, called Distributed Computing Framework (DFC), has been designed and developed to execute the benchmarking tests and facilitate the deployment in environments with a large number of machines, with independence of the protocol and performance metrics selected. DDS, MQTT, CoAP, JMS, AMQP and XMPP protocols were evaluated considering different specific performance metrics, including CPU usage, memory usage, bandwidth consumption, latency and jitter. The results obtained allowed to validate a case of use: respiratory rehabilitation of chronic obstructive pulmonary disease (COPD) patients in two scenarios with different types of requirement: Home-Based and Ambulatory. The results of the benchmark comparison can guide eHealth developers in the choice of M2M technologies. In this regard, the framework presented is a simple and powerful tool for the deployment of benchmark tests under specific environments and conditions. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

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.

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

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.

Pretest predictions of surface strain and fluid pressures in mercury targets undergoing thermal shock

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

Taleyarkhan, R.P.; Kim, S.H.; Haines, J.

The authors provide a perspective overview of pretest modeling and analysis work related to thermal shock effects in spallation neutron source targets that were designed for conducting thermal shock experiments at the Los Alamos Neutron Science Center (LANSCE). Data to be derived are to be used for benchmarking computational tools as well as to assess the efficacy of optical gauges for monitoring dynamic fluid pressures and phenomena such as the onset of cavitation.

Performance analysis of fusion nuclear-data benchmark experiments for light to heavy materials in MeV energy region with a neutron spectrum shifter

NASA Astrophysics Data System (ADS)

Murata, Isao; Ohta, Masayuki; Miyamaru, Hiroyuki; Kondo, Keitaro; Yoshida, Shigeo; Iida, Toshiyuki; Ochiai, Kentaro; Konno, Chikara

2011-10-01

Nuclear data are indispensable for development of fusion reactor candidate materials. However, benchmarking of the nuclear data in MeV energy region is not yet adequate. In the present study, benchmark performance in the MeV energy region was investigated theoretically for experiments by using a 14 MeV neutron source. We carried out a systematical analysis for light to heavy materials. As a result, the benchmark performance for the neutron spectrum was confirmed to be acceptable, while for gamma-rays it was not sufficiently accurate. Consequently, a spectrum shifter has to be applied. Beryllium had the best performance as a shifter. Moreover, a preliminary examination of whether it is really acceptable that only the spectrum before the last collision is considered in the benchmark performance analysis. It was pointed out that not only the last collision but also earlier collisions should be considered equally in the benchmark performance analysis.

Requirements for benchmarking personal image retrieval systems

NASA Astrophysics Data System (ADS)

Bouguet, Jean-Yves; Dulong, Carole; Kozintsev, Igor; Wu, Yi

2006-01-01

It is now common to have accumulated tens of thousands of personal ictures. Efficient access to that many pictures can only be done with a robust image retrieval system. This application is of high interest to Intel processor architects. It is highly compute intensive, and could motivate end users to upgrade their personal computers to the next generations of processors. A key question is how to assess the robustness of a personal image retrieval system. Personal image databases are very different from digital libraries that have been used by many Content Based Image Retrieval Systems.1 For example a personal image database has a lot of pictures of people, but a small set of different people typically family, relatives, and friends. Pictures are taken in a limited set of places like home, work, school, and vacation destination. The most frequent queries are searched for people, and for places. These attributes, and many others affect how a personal image retrieval system should be benchmarked, and benchmarks need to be different from existing ones based on art images, or medical images for examples. The attributes of the data set do not change the list of components needed for the benchmarking of such systems as specified in2: - data sets - query tasks - ground truth - evaluation measures - benchmarking events. This paper proposed a way to build these components to be representative of personal image databases, and of the corresponding usage models.

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.

Object-Oriented Implementation of the NAS Parallel Benchmarks using Charm++

NASA Technical Reports Server (NTRS)

Krishnan, Sanjeev; Bhandarkar, Milind; Kale, Laxmikant V.

1996-01-01

This report describes experiences with implementing the NAS Computational Fluid Dynamics benchmarks using a parallel object-oriented language, Charm++. Our main objective in implementing the NAS CFD kernel benchmarks was to develop a code that could be used to easily experiment with different domain decomposition strategies and dynamic load balancing. We also wished to leverage the object-orientation provided by the Charm++ parallel object-oriented language, to develop reusable abstractions that would simplify the process of developing parallel applications. We first describe the Charm++ parallel programming model and the parallel object array abstraction, then go into detail about each of the Scalar Pentadiagonal (SP) and Lower/Upper Triangular (LU) benchmarks, along with performance results. Finally we conclude with an evaluation of the methodology used.

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

Toward benchmarking in catalysis science: Best practices, challenges, and opportunities

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

Bligaard, Thomas; Bullock, R. Morris; Campbell, Charles T.

Benchmarking is a community-based and (preferably) community-driven activity involving consensus-based decisions on how to make reproducible, fair, and relevant assessments. In catalysis science, important catalyst performance metrics include activity, selectivity, and the deactivation profile, which enable comparisons between new and standard catalysts. Benchmarking also requires careful documentation, archiving, and sharing of methods and measurements, to ensure that the full value of research data can be realized. Beyond these goals, benchmarking presents unique opportunities to advance and accelerate understanding of complex reaction systems by combining and comparing experimental information from multiple, in situ and operando techniques with theoretical insights derived frommore » calculations characterizing model systems. This Perspective describes the origins and uses of benchmarking and its applications in computational catalysis, heterogeneous catalysis, molecular catalysis, and electrocatalysis. As a result, it also discusses opportunities and challenges for future developments in these fields.« less

Toward benchmarking in catalysis science: Best practices, challenges, and opportunities

DOE PAGES

Bligaard, Thomas; Bullock, R. Morris; Campbell, Charles T.; ...

2016-03-07

Benchmarking is a community-based and (preferably) community-driven activity involving consensus-based decisions on how to make reproducible, fair, and relevant assessments. In catalysis science, important catalyst performance metrics include activity, selectivity, and the deactivation profile, which enable comparisons between new and standard catalysts. Benchmarking also requires careful documentation, archiving, and sharing of methods and measurements, to ensure that the full value of research data can be realized. Beyond these goals, benchmarking presents unique opportunities to advance and accelerate understanding of complex reaction systems by combining and comparing experimental information from multiple, in situ and operando techniques with theoretical insights derived frommore » calculations characterizing model systems. This Perspective describes the origins and uses of benchmarking and its applications in computational catalysis, heterogeneous catalysis, molecular catalysis, and electrocatalysis. As a result, it also discusses opportunities and challenges for future developments in these fields.« less

Computational Investigation of In-Flight Temperature in Shaped Charge Jets and Explosively Formed Penetrators

NASA Astrophysics Data System (ADS)

Sable, Peter; Helminiak, Nathaniel; Harstad, Eric; Gullerud, Arne; Hollenshead, Jeromy; Hertel, Eugene; Sandia National Laboratories Collaboration; Marquette University Collaboration

2017-06-01

With the increasing use of hydrocodes in modeling and system design, experimental benchmarking of software has never been more important. While this has been a large area of focus since the inception of computational design, comparisons with temperature data are sparse due to experimental limitations. A novel temperature measurement technique, magnetic diffusion analysis, has enabled the acquisition of in-flight temperature measurements of hyper velocity projectiles. Using this, an AC-14 bare shaped charge and an LX-14 EFP, both with copper linings, were simulated using CTH to benchmark temperature against experimental results. Particular attention was given to the slug temperature profiles after separation, and the effect of varying equation-of-state and strength models. Simulations are in agreement with experimental, attaining better than 2% error between observed shaped charge temperatures. This varied notably depending on the strength model used. Similar observations were made simulating the EFP case, with a minimum 4% deviation. Jet structures compare well with radiographic images and are consistent with ALEGRA simulations previously conducted. Sandia is a multiprogram laboratory operated by Sandia Corporation, a Lockheed Martin Company, for the United States Department of Energy's National Nuclear Security Administration under contract DE-AC04-94AL85000.

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.

The effects of the physical and chemical properties of soils on the spectral reflectance of soils

NASA Technical Reports Server (NTRS)

Montgomery, O. L.; Baumgardner, M. F.

1974-01-01

The effects of organic matter, free iron oxides, texture, moisture content, and cation exchange capacity on the spectral reflectance of soils were investigated along with techniques for differentiating soil orders by computer analysis of multispectral data. By collecting soil samples of benchmark soils from the different climatic regions within the United States and using the extended wavelength field spectroradiometer to obtain reflectance values and curves for each sample, average curves were constructed for each soil order. Results indicate that multispectral analysis may be a valuable tool for delineating and quantifying differences between soils.

Elementary School Students' Science Talk Ability in Inquiry-Oriented Settings in Taiwan: Test Development, Verification, and Performance Benchmarks

ERIC Educational Resources Information Center

Lin, Sheau-Wen; Liu, Yu; Chen, Shin-Feng; Wang, Jing-Ru; Kao, Huey-Lien

2016-01-01

The purpose of this study was to develop a computer-based measure of elementary students' science talk and to report students' benchmarks. The development procedure had three steps: defining the framework of the test, collecting and identifying key reference sets of science talk, and developing and verifying the science talk instrument. The…

Bio-inspired benchmark generator for extracellular multi-unit recordings

PubMed Central

Mondragón-González, Sirenia Lizbeth; Burguière, Eric

2017-01-01

The analysis of multi-unit extracellular recordings of brain activity has led to the development of numerous tools, ranging from signal processing algorithms to electronic devices and applications. Currently, the evaluation and optimisation of these tools are hampered by the lack of ground-truth databases of neural signals. These databases must be parameterisable, easy to generate and bio-inspired, i.e. containing features encountered in real electrophysiological recording sessions. Towards that end, this article introduces an original computational approach to create fully annotated and parameterised benchmark datasets, generated from the summation of three components: neural signals from compartmental models and recorded extracellular spikes, non-stationary slow oscillations, and a variety of different types of artefacts. We present three application examples. (1) We reproduced in-vivo extracellular hippocampal multi-unit recordings from either tetrode or polytrode designs. (2) We simulated recordings in two different experimental conditions: anaesthetised and awake subjects. (3) Last, we also conducted a series of simulations to study the impact of different level of artefacts on extracellular recordings and their influence in the frequency domain. Beyond the results presented here, such a benchmark dataset generator has many applications such as calibration, evaluation and development of both hardware and software architectures. PMID:28233819

FDNS CFD Code Benchmark for RBCC Ejector Mode Operation

NASA Technical Reports Server (NTRS)

Holt, James B.; Ruf, Joe

1999-01-01

Computational Fluid Dynamics (CFD) analysis results are compared with benchmark quality test data from the Propulsion Engineering Research Center's (PERC) Rocket Based Combined Cycle (RBCC) experiments to verify fluid dynamic code and application procedures. RBCC engine flowpath development will rely on CFD applications to capture the multi-dimensional fluid dynamic interactions and to quantify their effect on the RBCC system performance. Therefore, the accuracy of these CFD codes must be determined through detailed comparisons with test data. The PERC experiments build upon the well-known 1968 rocket-ejector experiments of Odegaard and Stroup by employing advanced optical and laser based diagnostics to evaluate mixing and secondary combustion. The Finite Difference Navier Stokes (FDNS) code was used to model the fluid dynamics of the PERC RBCC ejector mode configuration. Analyses were performed for both Diffusion and Afterburning (DAB) and Simultaneous Mixing and Combustion (SMC) test conditions. Results from both the 2D and the 3D models are presented.

Binary Associative Memories as a Benchmark for Spiking Neuromorphic Hardware

PubMed Central

Stöckel, Andreas; Jenzen, Christoph; Thies, Michael; Rückert, Ulrich

2017-01-01

Large-scale neuromorphic hardware platforms, specialized computer systems for energy efficient simulation of spiking neural networks, are being developed around the world, for example as part of the European Human Brain Project (HBP). Due to conceptual differences, a universal performance analysis of these systems in terms of runtime, accuracy and energy efficiency is non-trivial, yet indispensable for further hard- and software development. In this paper we describe a scalable benchmark based on a spiking neural network implementation of the binary neural associative memory. We treat neuromorphic hardware and software simulators as black-boxes and execute exactly the same network description across all devices. Experiments on the HBP platforms under varying configurations of the associative memory show that the presented method allows to test the quality of the neuron model implementation, and to explain significant deviations from the expected reference output. PMID:28878642

Quantifying the quantum gate fidelity of single-atom spin qubits in silicon by randomized benchmarking.

PubMed

Muhonen, J T; Laucht, A; Simmons, S; Dehollain, J P; Kalra, R; Hudson, F E; Freer, S; Itoh, K M; Jamieson, D N; McCallum, J C; Dzurak, A S; Morello, A

2015-04-22

Building upon the demonstration of coherent control and single-shot readout of the electron and nuclear spins of individual (31)P atoms in silicon, we present here a systematic experimental estimate of quantum gate fidelities using randomized benchmarking of 1-qubit gates in the Clifford group. We apply this analysis to the electron and the ionized (31)P nucleus of a single P donor in isotopically purified (28)Si. We find average gate fidelities of 99.95% for the electron and 99.99% for the nuclear spin. These values are above certain error correction thresholds and demonstrate the potential of donor-based quantum computing in silicon. By studying the influence of the shape and power of the control pulses, we find evidence that the present limitation to the gate fidelity is mostly related to the external hardware and not the intrinsic behaviour of the qubit.

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.

Least-Squares Spectral Element Solutions to the CAA Workshop Benchmark Problems

NASA Technical Reports Server (NTRS)

Lin, Wen H.; Chan, Daniel C.

1997-01-01

This paper presents computed results for some of the CAA benchmark problems via the acoustic solver developed at Rocketdyne CFD Technology Center under the corporate agreement between Boeing North American, Inc. and NASA for the Aerospace Industry Technology Program. The calculations are considered as benchmark testing of the functionality, accuracy, and performance of the solver. Results of these computations demonstrate that the solver is capable of solving the propagation of aeroacoustic signals. Testing of sound generation and on more realistic problems is now pursued for the industrial applications of this solver. Numerical calculations were performed for the second problem of Category 1 of the current workshop problems for an acoustic pulse scattered from a rigid circular cylinder, and for two of the first CAA workshop problems, i. e., the first problem of Category 1 for the propagation of a linear wave and the first problem of Category 4 for an acoustic pulse reflected from a rigid wall in a uniform flow of Mach 0.5. The aim for including the last two problems in this workshop is to test the effectiveness of some boundary conditions set up in the solver. Numerical results of the last two benchmark problems have been compared with their corresponding exact solutions and the comparisons are excellent. This demonstrates the high fidelity of the solver in handling wave propagation problems. This feature lends the method quite attractive in developing a computational acoustic solver for calculating the aero/hydrodynamic noise in a violent flow environment.

An Application-Based Performance Characterization of the Columbia Supercluster

NASA Technical Reports Server (NTRS)

Biswas, Rupak; Djomehri, Jahed M.; Hood, Robert; Jin, Hoaqiang; Kiris, Cetin; Saini, Subhash

2005-01-01

Columbia is a 10,240-processor supercluster consisting of 20 Altix nodes with 512 processors each, and currently ranked as the second-fastest computer in the world. In this paper, we present the performance characteristics of Columbia obtained on up to four computing nodes interconnected via the InfiniBand and/or NUMAlink4 communication fabrics. We evaluate floating-point performance, memory bandwidth, message passing communication speeds, and compilers using a subset of the HPC Challenge benchmarks, and some of the NAS Parallel Benchmarks including the multi-zone versions. We present detailed performance results for three scientific applications of interest to NASA, one from molecular dynamics, and two from computational fluid dynamics. Our results show that both the NUMAlink4 and the InfiniBand hold promise for application scaling to a large number of processors.

Computation of elementary modes: a unifying framework and the new binary approach

PubMed Central

Gagneur, Julien; Klamt, Steffen

2004-01-01

Background Metabolic pathway analysis has been recognized as a central approach to the structural analysis of metabolic networks. The concept of elementary (flux) modes provides a rigorous formalism to describe and assess pathways and has proven to be valuable for many applications. However, computing elementary modes is a hard computational task. In recent years we assisted in a multiplication of algorithms dedicated to it. We require a summarizing point of view and a continued improvement of the current methods. Results We show that computing the set of elementary modes is equivalent to computing the set of extreme rays of a convex cone. This standard mathematical representation provides a unified framework that encompasses the most prominent algorithmic methods that compute elementary modes and allows a clear comparison between them. Taking lessons from this benchmark, we here introduce a new method, the binary approach, which computes the elementary modes as binary patterns of participating reactions from which the respective stoichiometric coefficients can be computed in a post-processing step. We implemented the binary approach in FluxAnalyzer 5.1, a software that is free for academics. The binary approach decreases the memory demand up to 96% without loss of speed giving the most efficient method available for computing elementary modes to date. Conclusions The equivalence between elementary modes and extreme ray computations offers opportunities for employing tools from polyhedral computation for metabolic pathway analysis. The new binary approach introduced herein was derived from this general theoretical framework and facilitates the computation of elementary modes in considerably larger networks. PMID:15527509

Benchmarking of Computational Models for NDE and SHM of Composites

NASA Technical Reports Server (NTRS)

Wheeler, Kevin; Leckey, Cara; Hafiychuk, Vasyl; Juarez, Peter; Timucin, Dogan; Schuet, Stefan; Hafiychuk, Halyna

2016-01-01

Ultrasonic wave phenomena constitute the leading physical mechanism for nondestructive evaluation (NDE) and structural health monitoring (SHM) of solid composite materials such as carbon-fiber-reinforced polymer (CFRP) laminates. Computational models of ultrasonic guided-wave excitation, propagation, scattering, and detection in quasi-isotropic laminates can be extremely valuable in designing practically realizable NDE and SHM hardware and software with desired accuracy, reliability, efficiency, and coverage. This paper presents comparisons of guided-wave simulations for CFRP composites implemented using three different simulation codes: two commercial finite-element analysis packages, COMSOL and ABAQUS, and a custom code implementing the Elastodynamic Finite Integration Technique (EFIT). Comparisons are also made to experimental laser Doppler vibrometry data and theoretical dispersion curves.

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.

Benchmark for Peak Detection Algorithms in Fiber Bragg Grating Interrogation and a New Neural Network for its Performance Improvement

PubMed Central

Negri, Lucas; Nied, Ademir; Kalinowski, Hypolito; Paterno, Aleksander

2011-01-01

This paper presents a benchmark for peak detection algorithms employed in fiber Bragg grating spectrometric interrogation systems. The accuracy, precision, and computational performance of currently used algorithms and those of a new proposed artificial neural network algorithm are compared. Centroid and gaussian fitting algorithms are shown to have the highest precision but produce systematic errors that depend on the FBG refractive index modulation profile. The proposed neural network displays relatively good precision with reduced systematic errors and improved computational performance when compared to other networks. Additionally, suitable algorithms may be chosen with the general guidelines presented. PMID:22163806

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

NASA Technical Reports Server (NTRS)

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

1998-01-01

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

Ongoing Analysis of Rocket Based Combined Cycle Engines by the Applied Fluid Dynamics Analysis Group at Marshall Space Flight Center

NASA Technical Reports Server (NTRS)

Ruf, Joseph; Holt, James B.; Canabal, Francisco

1999-01-01

This paper presents the status of analyses on three Rocket Based Combined Cycle configurations underway in the Applied Fluid Dynamics Analysis Group (TD64). TD64 is performing computational fluid dynamics analysis on a Penn State RBCC test rig, the proposed Draco axisymmetric RBCC engine and the Trailblazer engine. The intent of the analysis on the Penn State test rig is to benchmark the Finite Difference Navier Stokes code for ejector mode fluid dynamics. The Draco engine analysis is a trade study to determine the ejector mode performance as a function of three engine design variables. The Trailblazer analysis is to evaluate the nozzle performance in scramjet mode. Results to date of each analysis are presented.

A Benchmark Dataset for SSVEP-Based Brain-Computer Interfaces.

PubMed

Wang, Yijun; Chen, Xiaogang; Gao, Xiaorong; Gao, Shangkai

2017-10-01

This paper presents a benchmark steady-state visual evoked potential (SSVEP) dataset acquired with a 40-target brain- computer interface (BCI) speller. The dataset consists of 64-channel Electroencephalogram (EEG) data from 35 healthy subjects (8 experienced and 27 naïve) while they performed a cue-guided target selecting task. The virtual keyboard of the speller was composed of 40 visual flickers, which were coded using a joint frequency and phase modulation (JFPM) approach. The stimulation frequencies ranged from 8 Hz to 15.8 Hz with an interval of 0.2 Hz. The phase difference between two adjacent frequencies was . For each subject, the data included six blocks of 40 trials corresponding to all 40 flickers indicated by a visual cue in a random order. The stimulation duration in each trial was five seconds. The dataset can be used as a benchmark dataset to compare the methods for stimulus coding and target identification in SSVEP-based BCIs. Through offline simulation, the dataset can be used to design new system diagrams and evaluate their BCI performance without collecting any new data. The dataset also provides high-quality data for computational modeling of SSVEPs. The dataset is freely available fromhttp://bci.med.tsinghua.edu.cn/download.html.

Theory comparison and numerical benchmarking on neoclassical toroidal viscosity torque

NASA Astrophysics Data System (ADS)

Wang, Zhirui; Park, Jong-Kyu; Liu, Yueqiang; Logan, Nikolas; Kim, Kimin; Menard, Jonathan E.

2014-04-01

Systematic comparison and numerical benchmarking have been successfully carried out among three different approaches of neoclassical toroidal viscosity (NTV) theory and the corresponding codes: IPEC-PENT is developed based on the combined NTV theory but without geometric simplifications [Park et al., Phys. Rev. Lett. 102, 065002 (2009)]; MARS-Q includes smoothly connected NTV formula [Shaing et al., Nucl. Fusion 50, 025022 (2010)] based on Shaing's analytic formulation in various collisionality regimes; MARS-K, originally computing the drift kinetic energy, is upgraded to compute the NTV torque based on the equivalence between drift kinetic energy and NTV torque [J.-K. Park, Phys. Plasma 18, 110702 (2011)]. The derivation and numerical results both indicate that the imaginary part of drift kinetic energy computed by MARS-K is equivalent to the NTV torque in IPEC-PENT. In the benchmark of precession resonance between MARS-Q and MARS-K/IPEC-PENT, the agreement and correlation between the connected NTV formula and the combined NTV theory in different collisionality regimes are shown for the first time. Additionally, both IPEC-PENT and MARS-K indicate the importance of the bounce harmonic resonance which can greatly enhance the NTV torque when E ×B drift frequency reaches the bounce resonance condition.

An Approach for Assessing Delamination Propagation Capabilities in Commercial Finite Element Codes

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2007-01-01

An approach for assessing the delamination propagation capabilities in commercial finite element codes is presented and demonstrated for one code. For this investigation, the Double Cantilever Beam (DCB) specimen and the Single Leg Bending (SLB) specimen were chosen for full three-dimensional finite element simulations. First, benchmark results were created for both specimens. Second, starting from an initially straight front, the delamination was allowed to propagate. Good agreement between the load-displacement relationship obtained from the propagation analysis results and the benchmark results could be achieved by selecting the appropriate input parameters. Selecting the appropriate input parameters, however, was not straightforward and often required an iterative procedure. Qualitatively, the delamination front computed for the DCB specimen did not take the shape of a curved front as expected. However, the analysis of the SLB specimen yielded a curved front as may be expected from the distribution of the energy release rate and the failure index across the width of the specimen. Overall, the results are encouraging but further assessment on a structural level is required.

An Approach to Assess Delamination Propagation Simulation Capabilities in Commercial Finite Element Codes

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2008-01-01

An approach for assessing the delamination propagation simulation capabilities in commercial finite element codes is presented and demonstrated. For this investigation, the Double Cantilever Beam (DCB) specimen and the Single Leg Bending (SLB) specimen were chosen for full three-dimensional finite element simulations. First, benchmark results were created for both specimens. Second, starting from an initially straight front, the delamination was allowed to propagate. The load-displacement relationship and the total strain energy obtained from the propagation analysis results and the benchmark results were compared and good agreements could be achieved by selecting the appropriate input parameters. Selecting the appropriate input parameters, however, was not straightforward and often required an iterative procedure. Qualitatively, the delamination front computed for the DCB specimen did not take the shape of a curved front as expected. However, the analysis of the SLB specimen yielded a curved front as was expected from the distribution of the energy release rate and the failure index across the width of the specimen. Overall, the results are encouraging but further assessment on a structural level is required.

Radiant Energy Measurements from a Scaled Jet Engine Axisymmetric Exhaust Nozzle for a Baseline Code Validation Case

NASA Technical Reports Server (NTRS)

Baumeister, Joseph F.

1994-01-01

A non-flowing, electrically heated test rig was developed to verify computer codes that calculate radiant energy propagation from nozzle geometries that represent aircraft propulsion nozzle systems. Since there are a variety of analysis tools used to evaluate thermal radiation propagation from partially enclosed nozzle surfaces, an experimental benchmark test case was developed for code comparison. This paper briefly describes the nozzle test rig and the developed analytical nozzle geometry used to compare the experimental and predicted thermal radiation results. A major objective of this effort was to make available the experimental results and the analytical model in a format to facilitate conversion to existing computer code formats. For code validation purposes this nozzle geometry represents one validation case for one set of analysis conditions. Since each computer code has advantages and disadvantages based on scope, requirements, and desired accuracy, the usefulness of this single nozzle baseline validation case can be limited for some code comparisons.

Evaluation of the concrete shield compositions from the 2010 criticality accident alarm system benchmark experiments at the CEA Valduc SILENE facility

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

Miller, Thomas Martin; Celik, Cihangir; Dunn, Michael E

In October 2010, a series of benchmark experiments were conducted at the French Commissariat a l'Energie Atomique et aux Energies Alternatives (CEA) Valduc SILENE facility. These experiments were a joint effort between the United States Department of Energy Nuclear Criticality Safety Program and the CEA. The purpose of these experiments was to create three benchmarks for the verification and validation of radiation transport codes and evaluated nuclear data used in the analysis of criticality accident alarm systems. This series of experiments consisted of three single-pulsed experiments with the SILENE reactor. For the first experiment, the reactor was bare (unshielded), whereasmore » in the second and third experiments, it was shielded by lead and polyethylene, respectively. The polyethylene shield of the third experiment had a cadmium liner on its internal and external surfaces, which vertically was located near the fuel region of SILENE. During each experiment, several neutron activation foils and thermoluminescent dosimeters (TLDs) were placed around the reactor. Nearly half of the foils and TLDs had additional high-density magnetite concrete, high-density barite concrete, standard concrete, and/or BoroBond shields. CEA Saclay provided all the concrete, and the US Y-12 National Security Complex provided the BoroBond. Measurement data from the experiments were published at the 2011 International Conference on Nuclear Criticality (ICNC 2011) and the 2013 Nuclear Criticality Safety Division (NCSD 2013) topical meeting. Preliminary computational results for the first experiment were presented in the ICNC 2011 paper, which showed poor agreement between the computational results and the measured values of the foils shielded by concrete. Recently the hydrogen content, boron content, and density of these concrete shields were further investigated within the constraints of the previously available data. New computational results for the first experiment are now available that show much better agreement with the measured values.« less

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)

Scale-4 Analysis of Pressurized Water Reactor Critical Configurations: Volume 2-Sequoyah Unit 2 Cycle 3

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

Bowman, S.M.

1995-01-01

The requirements of ANSI/ANS 8.1 specify that calculational methods for away-from-reactor criticality safety analyses be validated against experimental measurements. If credit for the negative reactivity of the depleted (or spent) fuel isotopics is desired, it is necessary to benchmark computational methods against spent fuel critical configurations. This report summarizes a portion of the ongoing effort to benchmark away-from-reactor criticality analysis methods using critical configurations from commercial pressurized-water reactors. The analysis methodology selected for all the calculations reported herein is based on the codes and data provided in the SCALE-4 code system. The isotopic densities for the spent fuel assemblies inmore » the critical configurations were calculated using the SAS2H analytical sequence of the SCALE-4 system. The sources of data and the procedures for deriving SAS2H input parameters are described in detail. The SNIKR code module was used to extract the necessary isotopic densities from the SAS2H results and provide the data in the format required by the SCALE criticality analysis modules. The CSASN analytical sequence in SCALE-4 was used to perform resonance processing of the cross sections. The KENO V.a module of SCALE-4 was used to calculate the effective multiplication factor (k{sub eff}) of each case. The SCALE-4 27-group burnup library containing ENDF/B-IV (actinides) and ENDF/B-V (fission products) data was used for all the calculations. This volume of the report documents the SCALE system analysis of three reactor critical configurations for the Sequoyah Unit 2 Cycle 3. This unit and cycle were chosen because of the relevance in spent fuel benchmark applications: (1) the unit had a significantly long downtime of 2.7 years during the middle of cycle (MOC) 3, and (2) the core consisted entirely of burned fuel at the MOC restart. The first benchmark critical calculation was the MOC restart at hot, full-power (HFP) critical conditions. The other two benchmark critical calculations were the beginning-of-cycle (BOC) startup at both hot, zero-power (HZP) and HFP critical conditions. These latter calculations were used to check for consistency in the calculated results for different burnups and downtimes. The k{sub eff} results were in the range of 1.00014 to 1.00259 with a standard deviation of less than 0.001.« less

BIOSSES: a semantic sentence similarity estimation system for the biomedical domain.

PubMed

Sogancioglu, Gizem; Öztürk, Hakime; Özgür, Arzucan

2017-07-15

The amount of information available in textual format is rapidly increasing in the biomedical domain. Therefore, natural language processing (NLP) applications are becoming increasingly important to facilitate the retrieval and analysis of these data. Computing the semantic similarity between sentences is an important component in many NLP tasks including text retrieval and summarization. A number of approaches have been proposed for semantic sentence similarity estimation for generic English. However, our experiments showed that such approaches do not effectively cover biomedical knowledge and produce poor results for biomedical text. We propose several approaches for sentence-level semantic similarity computation in the biomedical domain, including string similarity measures and measures based on the distributed vector representations of sentences learned in an unsupervised manner from a large biomedical corpus. In addition, ontology-based approaches are presented that utilize general and domain-specific ontologies. Finally, a supervised regression based model is developed that effectively combines the different similarity computation metrics. A benchmark data set consisting of 100 sentence pairs from the biomedical literature is manually annotated by five human experts and used for evaluating the proposed methods. The experiments showed that the supervised semantic sentence similarity computation approach obtained the best performance (0.836 correlation with gold standard human annotations) and improved over the state-of-the-art domain-independent systems up to 42.6% in terms of the Pearson correlation metric. A web-based system for biomedical semantic sentence similarity computation, the source code, and the annotated benchmark data set are available at: http://tabilab.cmpe.boun.edu.tr/BIOSSES/ . gizemsogancioglu@gmail.com or arzucan.ozgur@boun.edu.tr. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

HyspIRI Low Latency Concept and Benchmarks

NASA Technical Reports Server (NTRS)

Mandl, Dan

2010-01-01

Topics include HyspIRI low latency data ops concept, HyspIRI data flow, ongoing efforts, experiment with Web Coverage Processing Service (WCPS) approach to injecting new algorithms into SensorWeb, low fidelity HyspIRI IPM testbed, compute cloud testbed, open cloud testbed environment, Global Lambda Integrated Facility (GLIF) and OCC collaboration with Starlight, delay tolerant network (DTN) protocol benchmarking, and EO-1 configuration for preliminary DTN prototype.

Availability of Neutronics Benchmarks in the ICSBEP and IRPhEP Handbooks for Computational Tools Testing

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

Bess, John D.; Briggs, J. Blair; Ivanova, Tatiana

2017-02-01

In the past several decades, numerous experiments have been performed worldwide to support reactor operations, measurements, design, and nuclear safety. Those experiments represent an extensive international investment in infrastructure, expertise, and cost, representing significantly valuable resources of data supporting past, current, and future research activities. Those valuable assets represent the basis for recording, development, and validation of our nuclear methods and integral nuclear data [1]. The loss of these experimental data, which has occurred all too much in the recent years, is tragic. The high cost to repeat many of these measurements can be prohibitive, if not impossible, to surmount.more » Two international projects were developed, and are under the direction of the Organisation for Co-operation and Development Nuclear Energy Agency (OECD NEA) to address the challenges of not just data preservation, but evaluation of the data to determine its merit for modern and future use. The International Criticality Safety Benchmark Evaluation Project (ICSBEP) was established to identify and verify comprehensive critical benchmark data sets; evaluate the data, including quantification of biases and uncertainties; compile the data and calculations in a standardized format; and formally document the effort into a single source of verified benchmark data [2]. Similarly, the International Reactor Physics Experiment Evaluation Project (IRPhEP) was established to preserve integral reactor physics experimental data, including separate or special effects data for nuclear energy and technology applications [3]. Annually, contributors from around the world continue to collaborate in the evaluation and review of select benchmark experiments for preservation and dissemination. The extensively peer-reviewed integral benchmark data can then be utilized to support nuclear design and safety analysts to validate the analytical tools, methods, and data needed for next-generation reactor design, safety analysis requirements, and all other front- and back-end activities contributing to the overall nuclear fuel cycle where quality neutronics calculations are paramount.« less

An integrated data envelopment analysis-artificial neural network approach for benchmarking of bank branches

NASA Astrophysics Data System (ADS)

Shokrollahpour, Elsa; Hosseinzadeh Lotfi, Farhad; Zandieh, Mostafa

2016-06-01

Efficiency and quality of services are crucial to today's banking industries. The competition in this section has become increasingly intense, as a result of fast improvements in Technology. Therefore, performance analysis of the banking sectors attracts more attention these days. Even though data envelopment analysis (DEA) is a pioneer approach in the literature as of an efficiency measurement tool and finding benchmarks, it is on the other hand unable to demonstrate the possible future benchmarks. The drawback to it could be that the benchmarks it provides us with, may still be less efficient compared to the more advanced future benchmarks. To cover for this weakness, artificial neural network is integrated with DEA in this paper to calculate the relative efficiency and more reliable benchmarks of one of the Iranian commercial bank branches. Therefore, each branch could have a strategy to improve the efficiency and eliminate the cause of inefficiencies based on a 5-year time forecast.

ViSAPy: a Python tool for biophysics-based generation of virtual spiking activity for evaluation of spike-sorting algorithms.

PubMed

Hagen, Espen; Ness, Torbjørn V; Khosrowshahi, Amir; Sørensen, Christina; Fyhn, Marianne; Hafting, Torkel; Franke, Felix; Einevoll, Gaute T

2015-04-30

New, silicon-based multielectrodes comprising hundreds or more electrode contacts offer the possibility to record spike trains from thousands of neurons simultaneously. This potential cannot be realized unless accurate, reliable automated methods for spike sorting are developed, in turn requiring benchmarking data sets with known ground-truth spike times. We here present a general simulation tool for computing benchmarking data for evaluation of spike-sorting algorithms entitled ViSAPy (Virtual Spiking Activity in Python). The tool is based on a well-established biophysical forward-modeling scheme and is implemented as a Python package built on top of the neuronal simulator NEURON and the Python tool LFPy. ViSAPy allows for arbitrary combinations of multicompartmental neuron models and geometries of recording multielectrodes. Three example benchmarking data sets are generated, i.e., tetrode and polytrode data mimicking in vivo cortical recordings and microelectrode array (MEA) recordings of in vitro activity in salamander retinas. The synthesized example benchmarking data mimics salient features of typical experimental recordings, for example, spike waveforms depending on interspike interval. ViSAPy goes beyond existing methods as it includes biologically realistic model noise, synaptic activation by recurrent spiking networks, finite-sized electrode contacts, and allows for inhomogeneous electrical conductivities. ViSAPy is optimized to allow for generation of long time series of benchmarking data, spanning minutes of biological time, by parallel execution on multi-core computers. ViSAPy is an open-ended tool as it can be generalized to produce benchmarking data or arbitrary recording-electrode geometries and with various levels of complexity. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

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.

Ongoing Analyses of Rocket Based Combined Cycle Engines by the Applied Fluid Dynamics Analysis Group at Marshall Space Flight Center

NASA Technical Reports Server (NTRS)

Ruf, Joseph H.; Holt, James B.; Canabal, Francisco

2001-01-01

This paper presents the status of analyses on three Rocket Based Combined Cycle (RBCC) configurations underway in the Applied Fluid Dynamics Analysis Group (TD64). TD64 is performing computational fluid dynamics (CFD) analysis on a Penn State RBCC test rig, the proposed Draco axisymmetric RBCC engine and the Trailblazer engine. The intent of the analysis on the Penn State test rig is to benchmark the Finite Difference Navier Stokes (FDNS) code for ejector mode fluid dynamics. The Draco analysis was a trade study to determine the ejector mode performance as a function of three engine design variables. The Trailblazer analysis is to evaluate the nozzle performance in scramjet mode. Results to date of each analysis are presented.

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

Sandor, Debra; Chung, Donald; Keyser, David

This report documents the CEMAC methodologies for developing and reporting annual global clean energy manufacturing benchmarks. The report reviews previously published manufacturing benchmark reports and foundational data, establishes a framework for benchmarking clean energy technologies, describes the CEMAC benchmark analysis methodologies, and describes the application of the methodologies to the manufacturing of four specific clean energy technologies.

Computational Modeling of Micro-Crack Induced Attenuation in CFRP Composites

NASA Technical Reports Server (NTRS)

Roberts, R. A.; Leckey, C. A. C.

2012-01-01

A computational study is performed to determine the contribution to ultrasound attenuation in carbon fiber reinforced polymer composite laminates of linear elastic scattering by matrix micro-cracking. Multiple scattering approximations are benchmarked against exact computational approaches. Results support linear scattering as the source of observed increased attenuation in the presence of micro-cracking.

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

Development of Benchmark Examples for Quasi-Static Delamination Propagation and Fatigue Growth Predictions

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2012-01-01

The development of benchmark examples for quasi-static delamination propagation and cyclic delamination onset and growth prediction is presented and demonstrated for Abaqus/Standard. The example is based on a finite element model of a Double-Cantilever Beam specimen. The example is independent of the analysis software used and allows the assessment of the automated delamination propagation, onset and growth prediction capabilities in commercial finite element codes based on the virtual crack closure technique (VCCT). First, a quasi-static benchmark example was created for the specimen. Second, based on the static results, benchmark examples for cyclic delamination growth were created. Third, the load-displacement relationship from a propagation analysis and the benchmark results were compared, and good agreement could be achieved by selecting the appropriate input parameters. Fourth, starting from an initially straight front, the delamination was allowed to grow under cyclic loading. The number of cycles to delamination onset and the number of cycles during delamination growth for each growth increment were obtained from the automated analysis and compared to the benchmark examples. Again, good agreement between the results obtained from the growth analysis and the benchmark results could be achieved by selecting the appropriate input parameters. The benchmarking procedure proved valuable by highlighting the issues associated with choosing the input parameters of the particular implementation. Selecting the appropriate input parameters, however, was not straightforward and often required an iterative procedure. Overall the results are encouraging, but further assessment for mixed-mode delamination is required.

Development of Benchmark Examples for Static Delamination Propagation and Fatigue Growth Predictions

NASA Technical Reports Server (NTRS)

Kruger, Ronald

2011-01-01

The development of benchmark examples for static delamination propagation and cyclic delamination onset and growth prediction is presented and demonstrated for a commercial code. The example is based on a finite element model of an End-Notched Flexure (ENF) specimen. The example is independent of the analysis software used and allows the assessment of the automated delamination propagation, onset and growth prediction capabilities in commercial finite element codes based on the virtual crack closure technique (VCCT). First, static benchmark examples were created for the specimen. Second, based on the static results, benchmark examples for cyclic delamination growth were created. Third, the load-displacement relationship from a propagation analysis and the benchmark results were compared, and good agreement could be achieved by selecting the appropriate input parameters. Fourth, starting from an initially straight front, the delamination was allowed to grow under cyclic loading. The number of cycles to delamination onset and the number of cycles during stable delamination growth for each growth increment were obtained from the automated analysis and compared to the benchmark examples. Again, good agreement between the results obtained from the growth analysis and the benchmark results could be achieved by selecting the appropriate input parameters. The benchmarking procedure proved valuable by highlighting the issues associated with the input parameters of the particular implementation. Selecting the appropriate input parameters, however, was not straightforward and often required an iterative procedure. Overall, the results are encouraging but further assessment for mixed-mode delamination is required.

Development and Application of Benchmark Examples for Mode II Static Delamination Propagation and Fatigue Growth Predictions

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2011-01-01

The development of benchmark examples for static delamination propagation and cyclic delamination onset and growth prediction is presented and demonstrated for a commercial code. The example is based on a finite element model of an End-Notched Flexure (ENF) specimen. The example is independent of the analysis software used and allows the assessment of the automated delamination propagation, onset and growth prediction capabilities in commercial finite element codes based on the virtual crack closure technique (VCCT). First, static benchmark examples were created for the specimen. Second, based on the static results, benchmark examples for cyclic delamination growth were created. Third, the load-displacement relationship from a propagation analysis and the benchmark results were compared, and good agreement could be achieved by selecting the appropriate input parameters. Fourth, starting from an initially straight front, the delamination was allowed to grow under cyclic loading. The number of cycles to delamination onset and the number of cycles during delamination growth for each growth increment were obtained from the automated analysis and compared to the benchmark examples. Again, good agreement between the results obtained from the growth analysis and the benchmark results could be achieved by selecting the appropriate input parameters. The benchmarking procedure proved valuable by highlighting the issues associated with choosing the input parameters of the particular implementation. Selecting the appropriate input parameters, however, was not straightforward and often required an iterative procedure. Overall the results are encouraging, but further assessment for mixed-mode delamination is required.

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/ .

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.

A Privacy-Preserving Platform for User-Centric Quantitative Benchmarking

NASA Astrophysics Data System (ADS)

Herrmann, Dominik; Scheuer, Florian; Feustel, Philipp; Nowey, Thomas; Federrath, Hannes

We propose a centralised platform for quantitative benchmarking of key performance indicators (KPI) among mutually distrustful organisations. Our platform offers users the opportunity to request an ad-hoc benchmarking for a specific KPI within a peer group of their choice. Architecture and protocol are designed to provide anonymity to its users and to hide the sensitive KPI values from other clients and the central server. To this end, we integrate user-centric peer group formation, exchangeable secure multi-party computation protocols, short-lived ephemeral key pairs as pseudonyms, and attribute certificates. We show by empirical evaluation of a prototype that the performance is acceptable for reasonably sized peer groups.

featsel: A framework for benchmarking of feature selection algorithms and cost functions

NASA Astrophysics Data System (ADS)

Reis, Marcelo S.; Estrela, Gustavo; Ferreira, Carlos Eduardo; Barrera, Junior

In this paper, we introduce featsel, a framework for benchmarking of feature selection algorithms and cost functions. This framework allows the user to deal with the search space as a Boolean lattice and has its core coded in C++ for computational efficiency purposes. Moreover, featsel includes Perl scripts to add new algorithms and/or cost functions, generate random instances, plot graphs and organize results into tables. Besides, this framework already comes with dozens of algorithms and cost functions for benchmarking experiments. We also provide illustrative examples, in which featsel outperforms the popular Weka workbench in feature selection procedures on data sets from the UCI Machine Learning Repository.

SU-D-BRD-03: A Gateway for GPU Computing in Cancer Radiotherapy Research

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

Jia, X; Folkerts, M; Shi, F

Purpose: Graphics Processing Unit (GPU) has become increasingly important in radiotherapy. However, it is still difficult for general clinical researchers to access GPU codes developed by other researchers, and for developers to objectively benchmark their codes. Moreover, it is quite often to see repeated efforts spent on developing low-quality GPU codes. The goal of this project is to establish an infrastructure for testing GPU codes, cross comparing them, and facilitating code distributions in radiotherapy community. Methods: We developed a system called Gateway for GPU Computing in Cancer Radiotherapy Research (GCR2). A number of GPU codes developed by our group andmore » other developers can be accessed via a web interface. To use the services, researchers first upload their test data or use the standard data provided by our system. Then they can select the GPU device on which the code will be executed. Our system offers all mainstream GPU hardware for code benchmarking purpose. After the code running is complete, the system automatically summarizes and displays the computing results. We also released a SDK to allow the developers to build their own algorithm implementation and submit their binary codes to the system. The submitted code is then systematically benchmarked using a variety of GPU hardware and representative data provided by our system. The developers can also compare their codes with others and generate benchmarking reports. Results: It is found that the developed system is fully functioning. Through a user-friendly web interface, researchers are able to test various GPU codes. Developers also benefit from this platform by comprehensively benchmarking their codes on various GPU platforms and representative clinical data sets. Conclusion: We have developed an open platform allowing the clinical researchers and developers to access the GPUs and GPU codes. This development will facilitate the utilization of GPU in radiation therapy field.« less

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

CLEAR: Cross-Layer Exploration for Architecting Resilience

DTIC Science & Technology

2017-03-01

benchmark analysis, also provides cost-effective solutions (~1% additional energy cost for the same 50× improvement). This paper addresses the...core (OoO-core) [Wang 04], across 18 benchmarks . Such extensive exploration enables us to conclusively answer the above cross-layer resilience...analysis of the effects of soft errors on application benchmarks , provides a highly effective soft error resilience approach. 3. The above

User and Performance Impacts from Franklin Upgrades

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

He, Yun

2009-05-10

The NERSC flagship computer Cray XT4 system"Franklin" has gone through three major upgrades: quad core upgrade, CLE 2.1 upgrade, and IO upgrade, during the past year. In this paper, we will discuss the various aspects of the user impacts such as user access, user environment, and user issues etc from these upgrades. The performance impacts on the kernel benchmarks and selected application benchmarks will also be presented.

Implementation of BT, SP, LU, and FT of NAS Parallel Benchmarks in Java

NASA Technical Reports Server (NTRS)

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

2000-01-01

A number of Java features make it an attractive but a debatable choice for High Performance Computing. We have implemented benchmarks working on single structured grid BT,SP,LU and FT in Java. The performance and scalability of the Java code shows that a significant improvement in Java compiler technology and in Java thread implementation are necessary for Java to compete with Fortran in HPC applications.

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.

Assessment of Static Delamination Propagation Capabilities in Commercial Finite Element Codes Using Benchmark Analysis

NASA Technical Reports Server (NTRS)

Orifici, Adrian C.; Krueger, Ronald

2010-01-01

With capabilities for simulating delamination growth in composite materials becoming available, the need for benchmarking and assessing these capabilities is critical. In this study, benchmark analyses were performed to assess the delamination propagation simulation capabilities of the VCCT implementations in Marc TM and MD NastranTM. Benchmark delamination growth results for Double Cantilever Beam, Single Leg Bending and End Notched Flexure specimens were generated using a numerical approach. This numerical approach was developed previously, and involves comparing results from a series of analyses at different delamination lengths to a single analysis with automatic crack propagation. Specimens were analyzed with three-dimensional and two-dimensional models, and compared with previous analyses using Abaqus . The results demonstrated that the VCCT implementation in Marc TM and MD Nastran(TradeMark) was capable of accurately replicating the benchmark delamination growth results and that the use of the numerical benchmarks offers advantages over benchmarking using experimental and analytical results.

Scalable randomized benchmarking of non-Clifford gates

NASA Astrophysics Data System (ADS)

Cross, Andrew; Magesan, Easwar; Bishop, Lev; Smolin, John; Gambetta, Jay

Randomized benchmarking is a widely used experimental technique to characterize the average error of quantum operations. Benchmarking procedures that scale to enable characterization of n-qubit circuits rely on efficient procedures for manipulating those circuits and, as such, have been limited to subgroups of the Clifford group. However, universal quantum computers require additional, non-Clifford gates to approximate arbitrary unitary transformations. We define a scalable randomized benchmarking procedure over n-qubit unitary matrices that correspond to protected non-Clifford gates for a class of stabilizer codes. We present efficient methods for representing and composing group elements, sampling them uniformly, and synthesizing corresponding poly (n) -sized circuits. The procedure provides experimental access to two independent parameters that together characterize the average gate fidelity of a group element. We acknowledge support from ARO under Contract W911NF-14-1-0124.

The EB Factory: Fundamental Stellar Astrophysics with Eclipsing Binary Stars Discovered by Kepler

NASA Astrophysics Data System (ADS)

Stassun, Keivan

Eclipsing binaries (EBs) are key laboratories for determining the fundamental properties of stars. EBs are therefore foundational objects for constraining stellar evolution models, which in turn are central to determinations of stellar mass functions, of exoplanet properties, and many other areas. The primary goal of this proposal is to mine the Kepler mission light curves for: (1) EBs that include a subgiant star, from which precise ages can be derived and which can thus serve as critically needed age benchmarks; and within these, (2) long-period EBs that include low-mass M stars or brown dwarfs, which are increa-singly becoming the focus of exoplanet searches, but for which there are the fewest available fundamental mass- radius-age benchmarks. A secondary goal of this proposal is to develop an end-to-end computational pipeline -- the Kepler EB Factory -- that allows automatic processing of Kepler light curves for EBs, from period finding, to object classification, to determination of EB physical properties for the most scientifically interesting EBs, and finally to accurate modeling of these EBs for detailed tests and benchmarking of theoretical stellar evolution models. We will integrate the most successful algorithms into a single, cohesive workflow environment, and apply this 'Kepler EB Factory' to the full public Kepler dataset to find and characterize new "benchmark grade" EBs, and will disseminate both the enhanced data products from this pipeline and the pipeline itself to the broader NASA science community. The proposed work responds directly to two of the defined Research Areas of the NASA Astrophysics Data Analysis Program (ADAP), specifically Research Area #2 (Stellar Astrophysics) and Research Area #9 (Astrophysical Databases). To be clear, our primary goal is the fundamental stellar astrophysics that will be enabled by the discovery and analysis of relatively rare, benchmark-grade EBs in the Kepler dataset. At the same time, to enable this goal will require bringing a suite of extant and new custom algorithms to bear on the Kepler data, and thus our development of the Kepler EB Factory represents a value-added product that will allow the widest scientific impact of the in-formation locked within the vast reservoir of the Kepler light curves.

Computer ray tracing speeds.

PubMed

Robb, P; Pawlowski, B

1990-05-01

The results of measuring the ray trace speed and compilation speed of thirty-nine computers in fifty-seven configurations, ranging from personal computers to super computers, are described. A correlation of ray trace speed has been made with the LINPACK benchmark which allows the ray trace speed to be estimated using LINPACK performance data. The results indicate that the latest generation of workstations, using CPUs based on RISC (Reduced Instruction Set Computer) technology, are as fast or faster than mainframe computers in compute-bound situations.

Joint estimation of motion and illumination change in a sequence of images

NASA Astrophysics Data System (ADS)

Koo, Ja-Keoung; Kim, Hyo-Hun; Hong, Byung-Woo

2015-09-01

We present an algorithm that simultaneously computes optical flow and estimates illumination change from an image sequence in a unified framework. We propose an energy functional consisting of conventional optical flow energy based on Horn-Schunck method and an additional constraint that is designed to compensate for illumination changes. Any undesirable illumination change that occurs in the imaging procedure in a sequence while the optical flow is being computed is considered a nuisance factor. In contrast to the conventional optical flow algorithm based on Horn-Schunck functional, which assumes the brightness constancy constraint, our algorithm is shown to be robust with respect to temporal illumination changes in the computation of optical flows. An efficient conjugate gradient descent technique is used in the optimization procedure as a numerical scheme. The experimental results obtained from the Middlebury benchmark dataset demonstrate the robustness and the effectiveness of our algorithm. In addition, comparative analysis of our algorithm and Horn-Schunck algorithm is performed on the additional test dataset that is constructed by applying a variety of synthetic bias fields to the original image sequences in the Middlebury benchmark dataset in order to demonstrate that our algorithm outperforms the Horn-Schunck algorithm. The superior performance of the proposed method is observed in terms of both qualitative visualizations and quantitative accuracy errors when compared to Horn-Schunck optical flow algorithm that easily yields poor results in the presence of small illumination changes leading to violation of the brightness constancy constraint.

TiD-Introducing and Benchmarking an Event-Delivery System for Brain-Computer Interfaces.

PubMed

Breitwieser, Christian; Tavella, Michele; Schreuder, Martijn; Cincotti, Febo; Leeb, Robert; Muller-Putz, Gernot R

2017-12-01

In this paper, we present and analyze an event distribution system for brain-computer interfaces. Events are commonly used to mark and describe incidents during an experiment and are therefore critical for later data analysis or immediate real-time processing. The presented approach, called Tools for brain-computer interaction interface D (TiD), delivers messages in XML format via a buslike system using transmission control protocol connections or shared memory. A dedicated server dispatches TiD messages to distributed or local clients. The TiD message is designed to be flexible and contains time stamps for event synchronization, whereas events describe incidents, which occur during an experiment. TiD was tested extensively toward stability and latency. The effect of an occurring event jitter was analyzed and benchmarked on a reference implementation under different conditions as gigabit and 100-Mb Ethernet or Wi-Fi with a different number of event receivers. A 3-dB signal attenuation, which occurs when averaging jitter influenced trials aligned by events, is starting to become visible at around 1-2 kHz in the case of a gigabit connection. Mean event distribution times across operating systems are ranging from 0.3 to 0.5ms for a gigabit network connection for 10 6 events. Results for other environmental conditions are available in this paper. References already using TiD for event distribution are provided showing the applicability of TiD for event delivery with distributed or local clients.

Can Humans Fly Action Understanding with Multiple Classes of Actors

DTIC Science & Technology

2015-06-08

recognition using structure from motion point clouds. In European Conference on Computer Vision, 2008. [5] R. Caruana. Multitask learning. Machine Learning...tonomous driving ? the kitti vision benchmark suite. In IEEE Conference on Computer Vision and Pattern Recognition, 2012. [12] L. Gorelick, M. Blank

Simple Benchmark Specifications for Space Radiation Protection

NASA Technical Reports Server (NTRS)

Singleterry, Robert C. Jr.; Aghara, Sukesh K.

2013-01-01

This report defines space radiation benchmark specifications. This specification starts with simple, monoenergetic, mono-directional particles on slabs and progresses to human models in spacecraft. This report specifies the models and sources needed to what the team performing the benchmark needs to produce in a report. Also included are brief descriptions of how OLTARIS, the NASA Langley website for space radiation analysis, performs its analysis.

Quantum computing applied to calculations of molecular energies: CH2 benchmark.

PubMed

Veis, Libor; Pittner, Jiří

2010-11-21

Quantum computers are appealing for their ability to solve some tasks much faster than their classical counterparts. It was shown in [Aspuru-Guzik et al., Science 309, 1704 (2005)] that they, if available, would be able to perform the full configuration interaction (FCI) energy calculations with a polynomial scaling. This is in contrast to conventional computers where FCI scales exponentially. We have developed a code for simulation of quantum computers and implemented our version of the quantum FCI algorithm. We provide a detailed description of this algorithm and the results of the assessment of its performance on the four lowest lying electronic states of CH(2) molecule. This molecule was chosen as a benchmark, since its two lowest lying (1)A(1) states exhibit a multireference character at the equilibrium geometry. It has been shown that with a suitably chosen initial state of the quantum register, one is able to achieve the probability amplification regime of the iterative phase estimation algorithm even in this case.

Large eddy simulation of the FDA benchmark nozzle for a Reynolds number of 6500.

PubMed

Janiga, Gábor

2014-04-01

This work investigates the flow in a benchmark nozzle model of an idealized medical device proposed by the FDA using computational fluid dynamics (CFD). It was in particular shown that a proper modeling of the transitional flow features is particularly challenging, leading to large discrepancies and inaccurate predictions from the different research groups using Reynolds-averaged Navier-Stokes (RANS) modeling. In spite of the relatively simple, axisymmetric computational geometry, the resulting turbulent flow is fairly complex and non-axisymmetric, in particular due to the sudden expansion. The resulting flow cannot be well predicted with simple modeling approaches. Due to the varying diameters and flow velocities encountered in the nozzle, different typical flow regions and regimes can be distinguished, from laminar to transitional and to weakly turbulent. The purpose of the present work is to re-examine the FDA-CFD benchmark nozzle model at a Reynolds number of 6500 using large eddy simulation (LES). The LES results are compared with published experimental data obtained by Particle Image Velocimetry (PIV) and an excellent agreement can be observed considering the temporally averaged flow velocities. Different flow regimes are characterized by computing the temporal energy spectra at different locations along the main axis. Copyright © 2014 Elsevier Ltd. All rights reserved.

Theory comparison and numerical benchmarking on neoclassical toroidal viscosity torque

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

Wang, Zhirui; Park, Jong-Kyu; Logan, Nikolas

Systematic comparison and numerical benchmarking have been successfully carried out among three different approaches of neoclassical toroidal viscosity (NTV) theory and the corresponding codes: IPEC-PENT is developed based on the combined NTV theory but without geometric simplifications [Park et al., Phys. Rev. Lett. 102, 065002 (2009)]; MARS-Q includes smoothly connected NTV formula [Shaing et al., Nucl. Fusion 50, 025022 (2010)] based on Shaing's analytic formulation in various collisionality regimes; MARS-K, originally computing the drift kinetic energy, is upgraded to compute the NTV torque based on the equivalence between drift kinetic energy and NTV torque [J.-K. Park, Phys. Plasma 18, 110702more » (2011)]. The derivation and numerical results both indicate that the imaginary part of drift kinetic energy computed by MARS-K is equivalent to the NTV torque in IPEC-PENT. In the benchmark of precession resonance between MARS-Q and MARS-K/IPEC-PENT, the agreement and correlation between the connected NTV formula and the combined NTV theory in different collisionality regimes are shown for the first time. Additionally, both IPEC-PENT and MARS-K indicate the importance of the bounce harmonic resonance which can greatly enhance the NTV torque when E×B drift frequency reaches the bounce resonance condition.« less

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.

Benchmarking Outpatient Rehabilitation Clinics Using Functional Status Outcomes.

PubMed

Gozalo, Pedro L; Resnik, Linda J; Silver, Benjamin

2016-04-01

To utilize functional status (FS) outcomes to benchmark outpatient therapy clinics. Outpatient therapy data from clinics using Focus on Therapeutic Outcomes (FOTO) assessments. Retrospective analysis of 538 clinics, involving 2,040 therapists and 90,392 patients admitted July 2006-June 2008. FS at discharge was modeled using hierarchical regression methods with patients nested within therapists within clinics. Separate models were estimated for all patients, for those with lumbar, and for those with shoulder impairments. All models risk-adjusted for intake FS, age, gender, onset, surgery count, functional comorbidity index, fear-avoidance level, and payer type. Inverse probability weighting adjusted for censoring. Functional status was captured using computer adaptive testing at intake and at discharge. Clinic and therapist effects explained 11.6 percent of variation in FS. Clinics ranked in the lowest quartile had significantly different outcomes than those in the highest quartile (p < .01). Clinics ranked similarly in lumbar and shoulder impairments (correlation = 0.54), but some clinics ranked in the highest quintile for one condition and in the lowest for the other. Benchmarking models based on validated FS measures clearly separated high-quality from low-quality clinics, and they could be used to inform value-based-payment policies. © Health Research and Educational Trust.

MEKS: A program for computation of inclusive jet cross sections at hadron colliders

NASA Astrophysics Data System (ADS)

Gao, Jun; Liang, Zhihua; Soper, Davison E.; Lai, Hung-Liang; Nadolsky, Pavel M.; Yuan, C.-P.

2013-06-01

EKS is a numerical program that predicts differential cross sections for production of single-inclusive hadronic jets and jet pairs at next-to-leading order (NLO) accuracy in a perturbative QCD calculation. We describe MEKS 1.0, an upgraded EKS program with increased numerical precision, suitable for comparisons to the latest experimental data from the Large Hadron Collider and Tevatron. The program integrates the regularized patron-level matrix elements over the kinematical phase space for production of two and three partons using the VEGAS algorithm. It stores the generated weighted events in finely binned two-dimensional histograms for fast offline analysis. A user interface allows one to customize computation of inclusive jet observables. Results of a benchmark comparison of the MEKS program and the commonly used FastNLO program are also documented. Program SummaryProgram title: MEKS 1.0 Catalogue identifier: AEOX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 9234 No. of bytes in distributed program, including test data, etc.: 51997 Distribution format: tar.gz Programming language: Fortran (main program), C (CUBA library and analysis program). Computer: All. Operating system: Any UNIX-like system. RAM: ˜300 MB Classification: 11.1. External routines: LHAPDF (https://lhapdf.hepforge.org/) Nature of problem: Computation of differential cross sections for inclusive production of single hadronic jets and jet pairs at next-to-leading order accuracy in perturbative quantum chromodynamics. Solution method: Upon subtraction of infrared singularities, the hard-scattering matrix elements are integrated over available phase space using an optimized VEGAS algorithm. Weighted events are generated and filled into a finely binned two-dimensional histogram, from which the final cross sections with typical experimental binning and cuts are computed by an independent analysis program. Monte Carlo sampling of event weights is tuned automatically to get better efficiency. Running time: Depends on details of the calculation and sought numerical accuracy. See benchmark performance in Section 4. The tests provided take approximately 27 min for the jetbin run and a few seconds for jetana.

International land Model Benchmarking (ILAMB) Package v002.00

DOE Data Explorer

Collier, Nathaniel [Oak Ridge National Laboratory; Hoffman, Forrest M. [Oak Ridge National Laboratory; Mu, Mingquan [University of California, Irvine; Randerson, James T. [University of California, Irvine; Riley, William J. [Lawrence Berkeley National Laboratory

2016-05-09

As a contribution to International Land Model Benchmarking (ILAMB) Project, we are providing new analysis approaches, benchmarking tools, and science leadership. The goal of ILAMB is to assess and improve the performance of land models through international cooperation and to inform the design of new measurement campaigns and field studies to reduce uncertainties associated with key biogeochemical processes and feedbacks. ILAMB is expected to be a primary analysis tool for CMIP6 and future model-data intercomparison experiments. This team has developed initial prototype benchmarking systems for ILAMB, which will be improved and extended to include ocean model metrics and diagnostics.

International land Model Benchmarking (ILAMB) Package v001.00

DOE Data Explorer

Mu, Mingquan [University of California, Irvine; Randerson, James T. [University of California, Irvine; Riley, William J. [Lawrence Berkeley National Laboratory; Hoffman, Forrest M. [Oak Ridge National Laboratory

2016-05-02

As a contribution to International Land Model Benchmarking (ILAMB) Project, we are providing new analysis approaches, benchmarking tools, and science leadership. The goal of ILAMB is to assess and improve the performance of land models through international cooperation and to inform the design of new measurement campaigns and field studies to reduce uncertainties associated with key biogeochemical processes and feedbacks. ILAMB is expected to be a primary analysis tool for CMIP6 and future model-data intercomparison experiments. This team has developed initial prototype benchmarking systems for ILAMB, which will be improved and extended to include ocean model metrics and diagnostics.

Benchmarking, benchmarks, or best practices? Applying quality improvement principles to decrease surgical turnaround time.

PubMed

Mitchell, L

1996-01-01

The processes of benchmarking, benchmark data comparative analysis, and study of best practices are distinctly different. The study of best practices is explained with an example based on the Arthur Andersen & Co. 1992 "Study of Best Practices in Ambulatory Surgery". The results of a national best practices study in ambulatory surgery were used to provide our quality improvement team with the goal of improving the turnaround time between surgical cases. The team used a seven-step quality improvement problem-solving process to improve the surgical turnaround time. The national benchmark for turnaround times between surgical cases in 1992 was 13.5 minutes. The initial turnaround time at St. Joseph's Medical Center was 19.9 minutes. After the team implemented solutions, the time was reduced to an average of 16.3 minutes, an 18% improvement. Cost-benefit analysis showed a potential enhanced revenue of approximately $300,000, or a potential savings of $10,119. Applying quality improvement principles to benchmarking, benchmarks, or best practices can improve process performance. Understanding which form of benchmarking the institution wishes to embark on will help focus a team and use appropriate resources. Communicating with professional organizations that have experience in benchmarking will save time and money and help achieve the desired results.

GraphBench

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

Sukumar, Sreenivas R.; Hong, Seokyong; Lee, Sangkeun

2016-06-01

GraphBench is a benchmark suite for graph pattern mining and graph analysis systems. The benchmark suite is a significant addition to conducting apples-apples comparison of graph analysis software (databases, in-memory tools, triple stores, etc.)

Decoys Selection in Benchmarking Datasets: Overview and Perspectives

PubMed Central

Réau, Manon; Langenfeld, Florent; Zagury, Jean-François; Lagarde, Nathalie; Montes, Matthieu

2018-01-01

Virtual Screening (VS) is designed to prospectively help identifying potential hits, i.e., compounds capable of interacting with a given target and potentially modulate its activity, out of large compound collections. Among the variety of methodologies, it is crucial to select the protocol that is the most adapted to the query/target system under study and that yields the most reliable output. To this aim, the performance of VS methods is commonly evaluated and compared by computing their ability to retrieve active compounds in benchmarking datasets. The benchmarking datasets contain a subset of known active compounds together with a subset of decoys, i.e., assumed non-active molecules. The composition of both the active and the decoy compounds subsets is critical to limit the biases in the evaluation of the VS methods. In this review, we focus on the selection of decoy compounds that has considerably changed over the years, from randomly selected compounds to highly customized or experimentally validated negative compounds. We first outline the evolution of decoys selection in benchmarking databases as well as current benchmarking databases that tend to minimize the introduction of biases, and secondly, we propose recommendations for the selection and the design of benchmarking datasets. PMID:29416509

Large-scale neural circuit mapping data analysis accelerated with the graphical processing unit (GPU).

PubMed

Shi, Yulin; Veidenbaum, Alexander V; Nicolau, Alex; Xu, Xiangmin

2015-01-15

Modern neuroscience research demands computing power. Neural circuit mapping studies such as those using laser scanning photostimulation (LSPS) produce large amounts of data and require intensive computation for post hoc processing and analysis. Here we report on the design and implementation of a cost-effective desktop computer system for accelerated experimental data processing with recent GPU computing technology. A new version of Matlab software with GPU enabled functions is used to develop programs that run on Nvidia GPUs to harness their parallel computing power. We evaluated both the central processing unit (CPU) and GPU-enabled computational performance of our system in benchmark testing and practical applications. The experimental results show that the GPU-CPU co-processing of simulated data and actual LSPS experimental data clearly outperformed the multi-core CPU with up to a 22× speedup, depending on computational tasks. Further, we present a comparison of numerical accuracy between GPU and CPU computation to verify the precision of GPU computation. In addition, we show how GPUs can be effectively adapted to improve the performance of commercial image processing software such as Adobe Photoshop. To our best knowledge, this is the first demonstration of GPU application in neural circuit mapping and electrophysiology-based data processing. Together, GPU enabled computation enhances our ability to process large-scale data sets derived from neural circuit mapping studies, allowing for increased processing speeds while retaining data precision. Copyright © 2014 Elsevier B.V. All rights reserved.

Large scale neural circuit mapping data analysis accelerated with the graphical processing unit (GPU)

PubMed Central

Shi, Yulin; Veidenbaum, Alexander V.; Nicolau, Alex; Xu, Xiangmin

2014-01-01

Background Modern neuroscience research demands computing power. Neural circuit mapping studies such as those using laser scanning photostimulation (LSPS) produce large amounts of data and require intensive computation for post-hoc processing and analysis. New Method Here we report on the design and implementation of a cost-effective desktop computer system for accelerated experimental data processing with recent GPU computing technology. A new version of Matlab software with GPU enabled functions is used to develop programs that run on Nvidia GPUs to harness their parallel computing power. Results We evaluated both the central processing unit (CPU) and GPU-enabled computational performance of our system in benchmark testing and practical applications. The experimental results show that the GPU-CPU co-processing of simulated data and actual LSPS experimental data clearly outperformed the multi-core CPU with up to a 22x speedup, depending on computational tasks. Further, we present a comparison of numerical accuracy between GPU and CPU computation to verify the precision of GPU computation. In addition, we show how GPUs can be effectively adapted to improve the performance of commercial image processing software such as Adobe Photoshop. Comparison with Existing Method(s) To our best knowledge, this is the first demonstration of GPU application in neural circuit mapping and electrophysiology-based data processing. Conclusions Together, GPU enabled computation enhances our ability to process large-scale data sets derived from neural circuit mapping studies, allowing for increased processing speeds while retaining data precision. PMID:25277633

Understanding the Performance and Potential of Cloud Computing for Scientific Applications

DOE PAGES

Sadooghi, Iman; Martin, Jesus Hernandez; Li, Tonglin; ...

2015-02-19

In this paper, commercial clouds bring a great opportunity to the scientific computing area. Scientific applications usually require significant resources, however not all scientists have access to sufficient high-end computing systems, may of which can be found in the Top500 list. Cloud Computing has gained the attention of scientists as a competitive resource to run HPC applications at a potentially lower cost. But as a different infrastructure, it is unclear whether clouds are capable of running scientific applications with a reasonable performance per money spent. This work studies the performance of public clouds and places this performance in context tomore » price. We evaluate the raw performance of different services of AWS cloud in terms of the basic resources, such as compute, memory, network and I/O. We also evaluate the performance of the scientific applications running in the cloud. This paper aims to assess the ability of the cloud to perform well, as well as to evaluate the cost of the cloud running scientific applications. We developed a full set of metrics and conducted a comprehensive performance evlauation over the Amazon cloud. We evaluated EC2, S3, EBS and DynamoDB among the many Amazon AWS services. We evaluated the memory sub-system performance with CacheBench, the network performance with iperf, processor and network performance with the HPL benchmark application, and shared storage with NFS and PVFS in addition to S3. We also evaluated a real scientific computing application through the Swift parallel scripting system at scale. Armed with both detailed benchmarks to gauge expected performance and a detailed monetary cost analysis, we expect this paper will be a recipe cookbook for scientists to help them decide where to deploy and run their scientific applications between public clouds, private clouds, or hybrid clouds.« less

Understanding the Performance and Potential of Cloud Computing for Scientific Applications

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

Sadooghi, Iman; Martin, Jesus Hernandez; Li, Tonglin

In this paper, commercial clouds bring a great opportunity to the scientific computing area. Scientific applications usually require significant resources, however not all scientists have access to sufficient high-end computing systems, may of which can be found in the Top500 list. Cloud Computing has gained the attention of scientists as a competitive resource to run HPC applications at a potentially lower cost. But as a different infrastructure, it is unclear whether clouds are capable of running scientific applications with a reasonable performance per money spent. This work studies the performance of public clouds and places this performance in context tomore » price. We evaluate the raw performance of different services of AWS cloud in terms of the basic resources, such as compute, memory, network and I/O. We also evaluate the performance of the scientific applications running in the cloud. This paper aims to assess the ability of the cloud to perform well, as well as to evaluate the cost of the cloud running scientific applications. We developed a full set of metrics and conducted a comprehensive performance evlauation over the Amazon cloud. We evaluated EC2, S3, EBS and DynamoDB among the many Amazon AWS services. We evaluated the memory sub-system performance with CacheBench, the network performance with iperf, processor and network performance with the HPL benchmark application, and shared storage with NFS and PVFS in addition to S3. We also evaluated a real scientific computing application through the Swift parallel scripting system at scale. Armed with both detailed benchmarks to gauge expected performance and a detailed monetary cost analysis, we expect this paper will be a recipe cookbook for scientists to help them decide where to deploy and run their scientific applications between public clouds, private clouds, or hybrid clouds.« less

Computational study of some fluoroquinolones: Structural, spectral and docking investigations

NASA Astrophysics Data System (ADS)

Sayin, Koray; Karakaş, Duran; Kariper, Sultan Erkan; Sayin, Tuba Alagöz

2018-03-01

Quantum chemical calculations are performed over norfloxacin, tosufloxacin and levofloxacin. The most stable structures for each molecule are determined by thermodynamic parameters. Then the best level for calculations is determined by benchmark analysis. M062X/6-31 + G(d) level is used in calculations. IR, UV-VIS and NMR spectrum are calculated and examined in detail. Some quantum chemical parameters are calculated and the tendency of activity is recommended. Additionally, molecular docking calculations are performed between related compounds and a protein (ID: 2J9N).

Crowdsourced estimation of cognitive decline and resilience in Alzheimer’s disease

PubMed Central

Allen, Genevera I; Amoroso, Nicola; Anghel, Catalina; Balagurusamy, Venkat; Bare, Christopher J; Beaton, Derek; Bellotti, Roberto; Bennett, David A; Boehme, Kevin; Boutros, Paul C; Caberlotto, Laura; Caloian, Cristian; Campbell, Frederick; Neto, Elias Chaibub; Chang, Yu-Chuan; Chen, Beibei; Chen, Chien-Yu; Chien, Ting-Ying; Clark, Tim; Das, Sudeshna; Davatzikos, Christos; Deng, Jieyao; Dillenberger, Donna; Dobson, Richard JB; Dong, Qilin; Doshi, Jimit; Duma, Denise; Errico, Rosangela; Erus, Guray; Everett, Evan; Fardo, David W; Friend, Stephen H; Fröhlich, Holger; Gan, Jessica; St George-Hyslop, Peter; Ghosh, Satrajit S; Glaab, Enrico; Green, Robert C; Guan, Yuanfang; Hong, Ming-Yi; Huang, Chao; Hwang, Jinseub; Ibrahim, Joseph; Inglese, Paolo; Jiang, Qijia; Katsumata, Yuriko; Kong, Dehan; Krause, Roland; Lalonde, Emilie; Lauria, Mario; Lee, Eunjee; Lin, Xihui; Liu, Zhandong; Livingstone, Julie; Logsdon, Benjamin A; Lovestone, Simon; Lyappan, Anandhi; Ma, Michelle; Malhotra, Ashutosh; Maxwell, Taylor J; Merrill, Emily; Nagorski, John; Namasivayam, Aishwarya; Narayan, Manjari; Naz, Mufassra; Newhouse, Stephen J; Norman, Thea C; Nurtdinov, Ramil N; Oyang, Yen-Jen; Pawitan, Yudi; Peng, Shengwen; Piccolo, Stephen R; Praveen, Paurush; Priami, Corrado; Sabelnykova, Veronica Y; Senger, Philipp; Shen, Xia; Simmons, Andrew; Sotiras, Aristeidis; Stolovitzky, Gustavo; Tangaro, Sabina; Tateo, Andrea; Tung, Yi-An; Tustison, Nicholas J; Varol, Erdem; Vradenburg, George; Weiner, Michael W; Xiao, Guanghua; Xie, Lei; Xie, Yang; Xu, Jia; Yang, Hojin; Zhan, Xiaowei; Zhou, Yunyun; Zhu, Fan; Zhu, Hongtu; Zhu, Shanfeng

2017-01-01

Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer’s Disease. The Alzheimer’s Disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer’s Disease based on high-dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for to prediction of cognitive performance. PMID:27079753

Cardiac image modelling: Breadth and depth in heart disease.

PubMed

Suinesiaputra, Avan; McCulloch, Andrew D; Nash, Martyn P; Pontre, Beau; Young, Alistair A

2016-10-01

With the advent of large-scale imaging studies and big health data, and the corresponding growth in analytics, machine learning and computational image analysis methods, there are now exciting opportunities for deepening our understanding of the mechanisms and characteristics of heart disease. Two emerging fields are computational analysis of cardiac remodelling (shape and motion changes due to disease) and computational analysis of physiology and mechanics to estimate biophysical properties from non-invasive imaging. Many large cohort studies now underway around the world have been specifically designed based on non-invasive imaging technologies in order to gain new information about the development of heart disease from asymptomatic to clinical manifestations. These give an unprecedented breadth to the quantification of population variation and disease development. Also, for the individual patient, it is now possible to determine biophysical properties of myocardial tissue in health and disease by interpreting detailed imaging data using computational modelling. For these population and patient-specific computational modelling methods to develop further, we need open benchmarks for algorithm comparison and validation, open sharing of data and algorithms, and demonstration of clinical efficacy in patient management and care. The combination of population and patient-specific modelling will give new insights into the mechanisms of cardiac disease, in particular the development of heart failure, congenital heart disease, myocardial infarction, contractile dysfunction and diastolic dysfunction. Copyright © 2016. Published by Elsevier B.V.

High Performance Computing at NASA

NASA Technical Reports Server (NTRS)

Bailey, David H.; Cooper, D. M. (Technical Monitor)

1994-01-01

The speaker will give an overview of high performance computing in the U.S. in general and within NASA in particular, including a description of the recently signed NASA-IBM cooperative agreement. The latest performance figures of various parallel systems on the NAS Parallel Benchmarks will be presented. The speaker was one of the authors of the NAS (National Aerospace Standards) Parallel Benchmarks, which are now widely cited in the industry as a measure of sustained performance on realistic high-end scientific applications. It will be shown that significant progress has been made by the highly parallel supercomputer industry during the past year or so, with several new systems, based on high-performance RISC processors, that now deliver superior performance per dollar compared to conventional supercomputers. Various pitfalls in reporting performance will be discussed. The speaker will then conclude by assessing the general state of the high performance computing field.

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.

The Equivalent Thermal Resistance of Tile Roofs with and without Batten Systems

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

Miller, William A

Clay and concrete tile roofs were installed on a fully instrumented attic test facility operating in East Tennessee s climate. Roof, attic and deck temperatures and heat flows were recorded for each of the tile roofs and also on an adjacent attic cavity covered with a conventionally pigmented and direct-nailed asphalt shingle roof. The data were used to benchmark a computer tool for simulation of roofs and attics and the tool used to develop an approach for computing an equivalent seasonal R-value for sub-tile venting. The approach computed equal heat fluxes through the ceilings of roofs having different combinations ofmore » surface radiation properties and or building constructions. A direct nailed shingle roof served as a control for estimating the equivalent thermal resistance of the air space. Simulations were benchmarked to data in the ASHRAE Fundamentals for the thermal resistance of inclined and closed air spaces.« less

Thought Experiment to Examine Benchmark Performance for Fusion Nuclear Data

NASA Astrophysics Data System (ADS)

Murata, Isao; Ohta, Masayuki; Kusaka, Sachie; Sato, Fuminobu; Miyamaru, Hiroyuki

2017-09-01

There are many benchmark experiments carried out so far with DT neutrons especially aiming at fusion reactor development. These integral experiments seemed vaguely to validate the nuclear data below 14 MeV. However, no precise studies exist now. The author's group thus started to examine how well benchmark experiments with DT neutrons can play a benchmarking role for energies below 14 MeV. Recently, as a next phase, to generalize the above discussion, the energy range was expanded to the entire region. In this study, thought experiments with finer energy bins have thus been conducted to discuss how to generally estimate performance of benchmark experiments. As a result of thought experiments with a point detector, the sensitivity for a discrepancy appearing in the benchmark analysis is "equally" due not only to contribution directly conveyed to the deterctor, but also due to indirect contribution of neutrons (named (A)) making neutrons conveying the contribution, indirect controbution of neutrons (B) making the neutrons (A) and so on. From this concept, it would become clear from a sensitivity analysis in advance how well and which energy nuclear data could be benchmarked with a benchmark experiment.

Computer simulation to predict energy use, greenhouse gas emissions and costs for production of fluid milk using alternative processing methods

USDA-ARS?s Scientific Manuscript database

Computer simulation is a useful tool for benchmarking the electrical and fuel energy consumption and water use in a fluid milk plant. In this study, a computer simulation model of the fluid milk process based on high temperature short time (HTST) pasteurization was extended to include models for pr...

Experimental flutter boundaries with unsteady pressure distributions for the NACA 0012 Benchmark Model

NASA Technical Reports Server (NTRS)

Rivera, Jose A., Jr.; Dansberry, Bryan E.; Farmer, Moses G.; Eckstrom, Clinton V.; Seidel, David A.; Bennett, Robert M.

1991-01-01

The Structural Dynamics Div. at NASA-Langley has started a wind tunnel activity referred to as the Benchmark Models Program. The objective is to acquire test data that will be useful for developing and evaluating aeroelastic type Computational Fluid Dynamics codes currently in use or under development. The progress is described which was achieved in testing the first model in the Benchmark Models Program. Experimental flutter boundaries are presented for a rigid semispan model (NACA 0012 airfoil section) mounted on a flexible mount system. Also, steady and unsteady pressure measurements taken at the flutter condition are presented. The pressure data were acquired over the entire model chord located at the 60 pct. span station.

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

Experimental power density distribution benchmark in the TRIGA Mark II reactor

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

Snoj, L.; Stancar, Z.; Radulovic, V.

2012-07-01

In order to improve the power calibration process and to benchmark the existing computational model of the TRIGA Mark II reactor at the Josef Stefan Inst. (JSI), a bilateral project was started as part of the agreement between the French Commissariat a l'energie atomique et aux energies alternatives (CEA) and the Ministry of higher education, science and technology of Slovenia. One of the objectives of the project was to analyze and improve the power calibration process of the JSI TRIGA reactor (procedural improvement and uncertainty reduction) by using absolutely calibrated CEA fission chambers (FCs). This is one of the fewmore » available power density distribution benchmarks for testing not only the fission rate distribution but also the absolute values of the fission rates. Our preliminary calculations indicate that the total experimental uncertainty of the measured reaction rate is sufficiently low that the experiments could be considered as benchmark experiments. (authors)« less

A Computational Fluid Dynamic Model for a Novel Flash Ironmaking Process

NASA Astrophysics Data System (ADS)

Perez-Fontes, Silvia E.; Sohn, Hong Yong; Olivas-Martinez, Miguel

A computational fluid dynamic model for a novel flash ironmaking process based on the direct gaseous reduction of iron oxide concentrates is presented. The model solves the three-dimensional governing equations including both gas-phase and gas-solid reaction kinetics. The turbulence-chemistry interaction in the gas-phase is modeled by the eddy dissipation concept incorporating chemical kinetics. The particle cloud model is used to track the particle phase in a Lagrangian framework. A nucleation and growth kinetics rate expression is adopted to calculate the reduction rate of magnetite concentrate particles. Benchmark experiments reported in the literature for a nonreacting swirling gas jet and a nonpremixed hydrogen jet flame were simulated for validation. The model predictions showed good agreement with measurements in terms of gas velocity, gas temperature and species concentrations. The relevance of the computational model for the analysis of a bench reactor operation and the design of an industrial-pilot plant is discussed.

diffuStats: an R package to compute diffusion-based scores on biological networks.

PubMed

Picart-Armada, Sergio; Thompson, Wesley K; Buil, Alfonso; Perera-Lluna, Alexandre

2018-02-01

Label propagation and diffusion over biological networks are a common mathematical formalism in computational biology for giving context to molecular entities and prioritizing novel candidates in the area of study. There are several choices in conceiving the diffusion process-involving the graph kernel, the score definitions and the presence of a posterior statistical normalization-which have an impact on the results. This manuscript describes diffuStats, an R package that provides a collection of graph kernels and diffusion scores, as well as a parallel permutation analysis for the normalized scores, that eases the computation of the scores and their benchmarking for an optimal choice. The R package diffuStats is publicly available in Bioconductor, https://bioconductor.org, under the GPL-3 license. sergi.picart@upc.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Construction and Utilization of a Beowulf Computing Cluster: A User's Perspective

NASA Technical Reports Server (NTRS)

Woods, Judy L.; West, Jeff S.; Sulyma, Peter R.

2000-01-01

Lockheed Martin Space Operations - Stennis Programs (LMSO) at the John C Stennis Space Center (NASA/SSC) has designed and built a Beowulf computer cluster which is owned by NASA/SSC and operated by LMSO. The design and construction of the cluster are detailed in this paper. The cluster is currently used for Computational Fluid Dynamics (CFD) simulations. The CFD codes in use and their applications are discussed. Examples of some of the work are also presented. Performance benchmark studies have been conducted for the CFD codes being run on the cluster. The results of two of the studies are presented and discussed. The cluster is not currently being utilized to its full potential; therefore, plans are underway to add more capabilities. These include the addition of structural, thermal, fluid, and acoustic Finite Element Analysis codes as well as real-time data acquisition and processing during test operations at NASA/SSC. These plans are discussed as well.

Design Choices for Thermofluid Flow Components and Systems that are Exported as Functional Mockup Units

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

Wetter, Michael; Fuchs, Marcus; Nouidui, Thierry

This paper discusses design decisions for exporting Modelica thermofluid flow components as Functional Mockup Units. The purpose is to provide guidelines that will allow building energy simulation programs and HVAC equipment manufacturers to effectively use FMUs for modeling of HVAC components and systems. We provide an analysis for direct input-output dependencies of such components and discuss how these dependencies can lead to algebraic loops that are formed when connecting thermofluid flow components. Based on this analysis, we provide recommendations that increase the computing efficiency of such components and systems that are formed by connecting multiple components. We explain what codemore » optimizations are lost when providing thermofluid flow components as FMUs rather than Modelica code. We present an implementation of a package for FMU export of such components, explain the rationale for selecting the connector variables of the FMUs and finally provide computing benchmarks for different design choices. It turns out that selecting temperature rather than specific enthalpy as input and output signals does not lead to a measurable increase in computing time, but selecting nine small FMUs rather than a large FMU increases computing time by 70%.« less

FDNS CFD Code Benchmark for RBCC Ejector Mode Operation: Continuing Toward Dual Rocket Effects

NASA Technical Reports Server (NTRS)

West, Jeff; Ruf, Joseph H.; Turner, James E. (Technical Monitor)

2000-01-01

Computational Fluid Dynamics (CFD) analysis results are compared with benchmark quality test data from the Propulsion Engineering Research Center's (PERC) Rocket Based Combined Cycle (RBCC) experiments to verify fluid dynamic code and application procedures. RBCC engine flowpath development will rely on CFD applications to capture the multi -dimensional fluid dynamic interactions and to quantify their effect on the RBCC system performance. Therefore, the accuracy of these CFD codes must be determined through detailed comparisons with test data. The PERC experiments build upon the well-known 1968 rocket-ejector experiments of Odegaard and Stroup by employing advanced optical and laser based diagnostics to evaluate mixing and secondary combustion. The Finite Difference Navier Stokes (FDNS) code [2] was used to model the fluid dynamics of the PERC RBCC ejector mode configuration. Analyses were performed for the Diffusion and Afterburning (DAB) test conditions at the 200-psia thruster operation point, Results with and without downstream fuel injection are presented.

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

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.

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.

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 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).

Modal analysis and acoustic transmission through offset-core honeycomb sandwich panels

NASA Astrophysics Data System (ADS)

Mathias, Adam Dustin

The work presented in this thesis is motivated by an earlier research that showed that double, offset-core honeycomb sandwich panels increased thermal resistance and, hence, decreased heat transfer through the panels. This result lead to the hypothesis that these panels could be used for acoustic insulation. Using commercial finite element modeling software, COMSOL Multiphysics, the acoustical properties, specifically the transmission loss across a variety of offset-core honeycomb sandwich panels, is studied for the case of a plane acoustic wave impacting the panel at normal incidence. The transmission loss results are compared with those of single-core honeycomb panels with the same cell sizes. The fundamental frequencies of the panels are also computed in an attempt to better understand the vibrational modes of these particular sandwich-structured panels. To ensure that the finite element analysis software is adequate for the task at hand, two relevant benchmark problems are solved and compared with theory. Results from these benchmark results compared well to those obtained from theory. Transmission loss results from the offset-core honeycomb sandwich panels show increased transmission loss, especially for large cell honeycombs when compared to single-core honeycomb panels.

Advances in molecular quantum chemistry contained in the Q-Chem 4 program package

NASA Astrophysics Data System (ADS)

Shao, Yihan; Gan, Zhengting; Epifanovsky, Evgeny; Gilbert, Andrew T. B.; Wormit, Michael; Kussmann, Joerg; Lange, Adrian W.; Behn, Andrew; Deng, Jia; Feng, Xintian; Ghosh, Debashree; Goldey, Matthew; Horn, Paul R.; Jacobson, Leif D.; Kaliman, Ilya; Khaliullin, Rustam Z.; Kuś, Tomasz; Landau, Arie; Liu, Jie; Proynov, Emil I.; Rhee, Young Min; Richard, Ryan M.; Rohrdanz, Mary A.; Steele, Ryan P.; Sundstrom, Eric J.; Woodcock, H. Lee, III; Zimmerman, Paul M.; Zuev, Dmitry; Albrecht, Ben; Alguire, Ethan; Austin, Brian; Beran, Gregory J. O.; Bernard, Yves A.; Berquist, Eric; Brandhorst, Kai; Bravaya, Ksenia B.; Brown, Shawn T.; Casanova, David; Chang, Chun-Min; Chen, Yunqing; Chien, Siu Hung; Closser, Kristina D.; Crittenden, Deborah L.; Diedenhofen, Michael; DiStasio, Robert A., Jr.; Do, Hainam; Dutoi, Anthony D.; Edgar, Richard G.; Fatehi, Shervin; Fusti-Molnar, Laszlo; Ghysels, An; Golubeva-Zadorozhnaya, Anna; Gomes, Joseph; Hanson-Heine, Magnus W. D.; Harbach, Philipp H. P.; Hauser, Andreas W.; Hohenstein, Edward G.; Holden, Zachary C.; Jagau, Thomas-C.; Ji, Hyunjun; Kaduk, Benjamin; Khistyaev, Kirill; Kim, Jaehoon; Kim, Jihan; King, Rollin A.; Klunzinger, Phil; Kosenkov, Dmytro; Kowalczyk, Tim; Krauter, Caroline M.; Lao, Ka Un; Laurent, Adèle D.; Lawler, Keith V.; Levchenko, Sergey V.; Lin, Ching Yeh; Liu, Fenglai; Livshits, Ester; Lochan, Rohini C.; Luenser, Arne; Manohar, Prashant; Manzer, Samuel F.; Mao, Shan-Ping; Mardirossian, Narbe; Marenich, Aleksandr V.; Maurer, Simon A.; Mayhall, Nicholas J.; Neuscamman, Eric; Oana, C. Melania; Olivares-Amaya, Roberto; O'Neill, Darragh P.; Parkhill, John A.; Perrine, Trilisa M.; Peverati, Roberto; Prociuk, Alexander; Rehn, Dirk R.; Rosta, Edina; Russ, Nicholas J.; Sharada, Shaama M.; Sharma, Sandeep; Small, David W.; Sodt, Alexander; Stein, Tamar; Stück, David; Su, Yu-Chuan; Thom, Alex J. W.; Tsuchimochi, Takashi; Vanovschi, Vitalii; Vogt, Leslie; Vydrov, Oleg; Wang, Tao; Watson, Mark A.; Wenzel, Jan; White, Alec; Williams, Christopher F.; Yang, Jun; Yeganeh, Sina; Yost, Shane R.; You, Zhi-Qiang; Zhang, Igor Ying; Zhang, Xing; Zhao, Yan; Brooks, Bernard R.; Chan, Garnet K. L.; Chipman, Daniel M.; Cramer, Christopher J.; Goddard, William A., III; Gordon, Mark S.; Hehre, Warren J.; Klamt, Andreas; Schaefer, Henry F., III; Schmidt, Michael W.; Sherrill, C. David; Truhlar, Donald G.; Warshel, Arieh; Xu, Xin; Aspuru-Guzik, Alán; Baer, Roi; Bell, Alexis T.; Besley, Nicholas A.; Chai, Jeng-Da; Dreuw, Andreas; Dunietz, Barry D.; Furlani, Thomas R.; Gwaltney, Steven R.; Hsu, Chao-Ping; Jung, Yousung; Kong, Jing; Lambrecht, Daniel S.; Liang, WanZhen; Ochsenfeld, Christian; Rassolov, Vitaly A.; Slipchenko, Lyudmila V.; Subotnik, Joseph E.; Van Voorhis, Troy; Herbert, John M.; Krylov, Anna I.; Gill, Peter M. W.; Head-Gordon, Martin

2015-01-01

A summary of the technical advances that are incorporated in the fourth major release of the Q-Chem quantum chemistry program is provided, covering approximately the last seven years. These include developments in density functional theory methods and algorithms, nuclear magnetic resonance (NMR) property evaluation, coupled cluster and perturbation theories, methods for electronically excited and open-shell species, tools for treating extended environments, algorithms for walking on potential surfaces, analysis tools, energy and electron transfer modelling, parallel computing capabilities, and graphical user interfaces. In addition, a selection of example case studies that illustrate these capabilities is given. These include extensive benchmarks of the comparative accuracy of modern density functionals for bonded and non-bonded interactions, tests of attenuated second order Møller-Plesset (MP2) methods for intermolecular interactions, a variety of parallel performance benchmarks, and tests of the accuracy of implicit solvation models. Some specific chemical examples include calculations on the strongly correlated Cr2 dimer, exploring zeolite-catalysed ethane dehydrogenation, energy decomposition analysis of a charged ter-molecular complex arising from glycerol photoionisation, and natural transition orbitals for a Frenkel exciton state in a nine-unit model of a self-assembling nanotube.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program

NASA Astrophysics Data System (ADS)

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A.

2017-12-01

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

PubMed

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

2017-12-28

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

ICT Proficiency and Gender: A Validation on Training and Development

ERIC Educational Resources Information Center

Lin, Shinyi; Shih, Tse-Hua; Lu, Ruiling

2013-01-01

Use of innovative learning/instruction mode, embedded in the Certification Pathway System (CPS) developed by Certiport TM, is geared toward Internet and Computing Benchmark & Mentor specifically for IC[superscript 3] certification. The Internet and Computing Core Certification (IC[superscript 3]), as an industry-based credentialing program,…

To Lease or Not To Lease.

ERIC Educational Resources Information Center

Hamilton, William A.

1998-01-01

Thanks to previous bond issues, the Walled Lake (Michigan) Schools had a well-defined technology plan featuring staff development, student performance benchmarks, and rooms of outdated computers. After three bond issues failed, the district adopted leasing as an alternative. Their present three-year contract supplies 154 used computers and a…

Visualization assisted by parallel processing

NASA Astrophysics Data System (ADS)

Lange, B.; Rey, H.; Vasques, X.; Puech, W.; Rodriguez, N.

2011-01-01

This paper discusses the experimental results of our visualization model for data extracted from sensors. The objective of this paper is to find a computationally efficient method to produce a real time rendering visualization for a large amount of data. We develop visualization method to monitor temperature variance of a data center. Sensors are placed on three layers and do not cover all the room. We use particle paradigm to interpolate data sensors. Particles model the "space" of the room. In this work we use a partition of the particle set, using two mathematical methods: Delaunay triangulation and Voronoý cells. Avis and Bhattacharya present these two algorithms in. Particles provide information on the room temperature at different coordinates over time. To locate and update particles data we define a computational cost function. To solve this function in an efficient way, we use a client server paradigm. Server computes data and client display this data on different kind of hardware. This paper is organized as follows. The first part presents related algorithm used to visualize large flow of data. The second part presents different platforms and methods used, which was evaluated in order to determine the better solution for the task proposed. The benchmark use the computational cost of our algorithm that formed based on located particles compared to sensors and on update of particles value. The benchmark was done on a personal computer using CPU, multi core programming, GPU programming and hybrid GPU/CPU. GPU programming method is growing in the research field; this method allows getting a real time rendering instates of a precompute rendering. For improving our results, we compute our algorithm on a High Performance Computing (HPC), this benchmark was used to improve multi-core method. HPC is commonly used in data visualization (astronomy, physic, etc) for improving the rendering and getting real-time.

EPA and EFSA approaches for Benchmark Dose modeling

EPA Science Inventory

Benchmark dose (BMD) modeling has become the preferred approach in the analysis of toxicological dose-response data for the purpose of deriving human health toxicity values. The software packages most often used are Benchmark Dose Software (BMDS, developed by EPA) and PROAST (de...

Design and Analysis of a Neuromemristive Reservoir Computing Architecture for Biosignal Processing

PubMed Central

Kudithipudi, Dhireesha; Saleh, Qutaiba; Merkel, Cory; Thesing, James; Wysocki, Bryant

2016-01-01

Reservoir computing (RC) is gaining traction in several signal processing domains, owing to its non-linear stateful computation, spatiotemporal encoding, and reduced training complexity over recurrent neural networks (RNNs). Previous studies have shown the effectiveness of software-based RCs for a wide spectrum of applications. A parallel body of work indicates that realizing RNN architectures using custom integrated circuits and reconfigurable hardware platforms yields significant improvements in power and latency. In this research, we propose a neuromemristive RC architecture, with doubly twisted toroidal structure, that is validated for biosignal processing applications. We exploit the device mismatch to implement the random weight distributions within the reservoir and propose mixed-signal subthreshold circuits for energy efficiency. A comprehensive analysis is performed to compare the efficiency of the neuromemristive RC architecture in both digital(reconfigurable) and subthreshold mixed-signal realizations. Both Electroencephalogram (EEG) and Electromyogram (EMG) biosignal benchmarks are used for validating the RC designs. The proposed RC architecture demonstrated an accuracy of 90 and 84% for epileptic seizure detection and EMG prosthetic finger control, respectively. PMID:26869876

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

DTIC Science & Technology

2017-04-13

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

Fingerprinting sea-level variations in response to continental ice loss: a benchmark exercise

NASA Astrophysics Data System (ADS)

Barletta, Valentina R.; Spada, Giorgio; Riva, Riccardo E. M.; James, Thomas S.; Simon, Karen M.; van der Wal, Wouter; Martinec, Zdenek; Klemann, Volker; Olsson, Per-Anders; Hagedoorn, Jan; Stocchi, Paolo; Vermeersen, Bert

2013-04-01

Understanding the response of the Earth to the waxing and waning ice sheets is crucial in various contexts, ranging from the interpretation of modern satellite geodetic measurements to the projections of future sea level trends in response to climate change. All the processes accompanying Glacial Isostatic Adjustment (GIA) can be described solving the so-called Sea Level Equation (SLE), an integral equation that accounts for the interactions between the ice sheets, the solid Earth, and the oceans. Modern approaches to the SLE are based on various techniques that range from purely analytical formulations to fully numerical methods. Here we present the results of a benchmark exercise of independently developed codes designed to solve the SLE. The study involves predictions of current sea level changes due to present-day ice mass loss. In spite of the differences in the methods employed, the comparison shows that a significant number of GIA modellers can reproduce their sea-level computations within 2% for well defined, large-scale present-day ice mass changes. Smaller and more detailed loads need further and dedicated benchmarking and high resolution computation. This study shows how the details of the implementation and the inputs specifications are an important, and often underappreciated, aspect. Hence this represents a step toward the assessment of reliability of sea level projections obtained with benchmarked SLE codes.

Parallel Algorithms for Monte Carlo Particle Transport Simulation on Exascale Computing Architectures

NASA Astrophysics Data System (ADS)

Romano, Paul Kollath

Monte Carlo particle transport methods are being considered as a viable option for high-fidelity simulation of nuclear reactors. While Monte Carlo methods offer several potential advantages over deterministic methods, there are a number of algorithmic shortcomings that would prevent their immediate adoption for full-core analyses. In this thesis, algorithms are proposed both to ameliorate the degradation in parallel efficiency typically observed for large numbers of processors and to offer a means of decomposing large tally data that will be needed for reactor analysis. A nearest-neighbor fission bank algorithm was proposed and subsequently implemented in the OpenMC Monte Carlo code. A theoretical analysis of the communication pattern shows that the expected cost is O( N ) whereas traditional fission bank algorithms are O(N) at best. The algorithm was tested on two supercomputers, the Intrepid Blue Gene/P and the Titan Cray XK7, and demonstrated nearly linear parallel scaling up to 163,840 processor cores on a full-core benchmark problem. An algorithm for reducing network communication arising from tally reduction was analyzed and implemented in OpenMC. The proposed algorithm groups only particle histories on a single processor into batches for tally purposes---in doing so it prevents all network communication for tallies until the very end of the simulation. The algorithm was tested, again on a full-core benchmark, and shown to reduce network communication substantially. A model was developed to predict the impact of load imbalances on the performance of domain decomposed simulations. The analysis demonstrated that load imbalances in domain decomposed simulations arise from two distinct phenomena: non-uniform particle densities and non-uniform spatial leakage. The dominant performance penalty for domain decomposition was shown to come from these physical effects rather than insufficient network bandwidth or high latency. The model predictions were verified with measured data from simulations in OpenMC on a full-core benchmark problem. Finally, a novel algorithm for decomposing large tally data was proposed, analyzed, and implemented/tested in OpenMC. The algorithm relies on disjoint sets of compute processes and tally servers. The analysis showed that for a range of parameters relevant to LWR analysis, the tally server algorithm should perform with minimal overhead. Tests were performed on Intrepid and Titan and demonstrated that the algorithm did indeed perform well over a wide range of parameters. (Copies available exclusively from MIT Libraries, libraries.mit.edu/docs - docs mit.edu)

Statistical Analysis of NAS Parallel Benchmarks and LINPACK Results

NASA Technical Reports Server (NTRS)

Meuer, Hans-Werner; Simon, Horst D.; Strohmeier, Erich; Lasinski, T. A. (Technical Monitor)

1994-01-01

In the last three years extensive performance data have been reported for parallel machines both based on the NAS Parallel Benchmarks, and on LINPACK. In this study we have used the reported benchmark results and performed a number of statistical experiments using factor, cluster, and regression analyses. In addition to the performance results of LINPACK and the eight NAS parallel benchmarks, we have also included peak performance of the machine, and the LINPACK n and n(sub 1/2) values. Some of the results and observations can be summarized as follows: 1) All benchmarks are strongly correlated with peak performance. 2) LINPACK and EP have each a unique signature. 3) The remaining NPB can grouped into three groups as follows: (CG and IS), (LU and SP), and (MG, FT, and BT). Hence three (or four with EP) benchmarks are sufficient to characterize the overall NPB performance. Our poster presentation will follow a standard poster format, and will present the data of our statistical analysis in detail.

Spatio-temporally resolved spectral measurements of laser-produced plasma and semiautomated spectral measurement-control and analysis software

NASA Astrophysics Data System (ADS)

Cao, S. Q.; Su, M. G.; Min, Q.; Sun, D. X.; O'Sullivan, G.; Dong, C. Z.

2018-02-01

A spatio-temporally resolved spectral measurement system of highly charged ions from laser-produced plasmas is presented. Corresponding semiautomated computer software for measurement control and spectral analysis has been written to achieve the best synchronicity possible among the instruments. This avoids the tedious comparative processes between experimental and theoretical results. To demonstrate the capabilities of this system, a series of spatio-temporally resolved experiments of laser-produced Al plasmas have been performed and applied to benchmark the software. The system is a useful tool for studying the spectral structures of highly charged ions and for evaluating the spatio-temporal evolution of laser-produced plasmas.

Higher-Order Adaptive Finite-Element Methods for Kohn-Sham Density Functional Theory

DTIC Science & Technology

2012-07-03

systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemi- cal accuracy...calculations. Further, we demonstrate the capability of the proposed approach to compute the electronic structure of materials systems contain- ing a...benchmark systems studied, we observe diminishing returns in computational savings beyond the sixth-order for accuracies commensurate with chemical accuracy

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.

Issues in benchmarking human reliability analysis methods : a literature review.

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

Lois, Erasmia; Forester, John Alan; Tran, Tuan Q.

There is a diversity of human reliability analysis (HRA) methods available for use in assessing human performance within probabilistic risk assessment (PRA). Due to the significant differences in the methods, including the scope, approach, and underlying models, there is a need for an empirical comparison investigating the validity and reliability of the methods. To accomplish this empirical comparison, a benchmarking study is currently underway that compares HRA methods with each other and against operator performance in simulator studies. In order to account for as many effects as possible in the construction of this benchmarking study, a literature review was conducted,more » reviewing past benchmarking studies in the areas of psychology and risk assessment. A number of lessons learned through these studies are presented in order to aid in the design of future HRA benchmarking endeavors.« less

Issues in Benchmarking Human Reliability Analysis Methods: A Literature Review

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

Ronald L. Boring; Stacey M. L. Hendrickson; John A. Forester

There is a diversity of human reliability analysis (HRA) methods available for use in assessing human performance within probabilistic risk assessments (PRA). Due to the significant differences in the methods, including the scope, approach, and underlying models, there is a need for an empirical comparison investigating the validity and reliability of the methods. To accomplish this empirical comparison, a benchmarking study comparing and evaluating HRA methods in assessing operator performance in simulator experiments is currently underway. In order to account for as many effects as possible in the construction of this benchmarking study, a literature review was conducted, reviewing pastmore » benchmarking studies in the areas of psychology and risk assessment. A number of lessons learned through these studies are presented in order to aid in the design of future HRA benchmarking endeavors.« less

Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data

PubMed Central

2014-01-01

Background The rapid evolution in high-throughput sequencing (HTS) technologies has opened up new perspectives in several research fields and led to the production of large volumes of sequence data. A fundamental step in HTS data analysis is the mapping of reads onto reference sequences. Choosing a suitable mapper for a given technology and a given application is a subtle task because of the difficulty of evaluating mapping algorithms. Results In this paper, we present a benchmark procedure to compare mapping algorithms used in HTS using both real and simulated datasets and considering four evaluation criteria: computational resource and time requirements, robustness of mapping, ability to report positions for reads in repetitive regions, and ability to retrieve true genetic variation positions. To measure robustness, we introduced a new definition for a correctly mapped read taking into account not only the expected start position of the read but also the end position and the number of indels and substitutions. We developed CuReSim, a new read simulator, that is able to generate customized benchmark data for any kind of HTS technology by adjusting parameters to the error types. CuReSim and CuReSimEval, a tool to evaluate the mapping quality of the CuReSim simulated reads, are freely available. We applied our benchmark procedure to evaluate 14 mappers in the context of whole genome sequencing of small genomes with Ion Torrent data for which such a comparison has not yet been established. Conclusions A benchmark procedure to compare HTS data mappers is introduced with a new definition for the mapping correctness as well as tools to generate simulated reads and evaluate mapping quality. The application of this procedure to Ion Torrent data from the whole genome sequencing of small genomes has allowed us to validate our benchmark procedure and demonstrate that it is helpful for selecting a mapper based on the intended application, questions to be addressed, and the technology used. This benchmark procedure can be used to evaluate existing or in-development mappers as well as to optimize parameters of a chosen mapper for any application and any sequencing platform. PMID:24708189

Benchmarking real-time RGBD odometry for light-duty UAVs

NASA Astrophysics Data System (ADS)

Willis, Andrew R.; Sahawneh, Laith R.; Brink, Kevin M.

2016-06-01

This article describes the theoretical and implementation challenges associated with generating 3D odometry estimates (delta-pose) from RGBD sensor data in real-time to facilitate navigation in cluttered indoor environments. The underlying odometry algorithm applies to general 6DoF motion; however, the computational platforms, trajectories, and scene content are motivated by their intended use on indoor, light-duty UAVs. Discussion outlines the overall software pipeline for sensor processing and details how algorithm choices for the underlying feature detection and correspondence computation impact the real-time performance and accuracy of the estimated odometry and associated covariance. This article also explores the consistency of odometry covariance estimates and the correlation between successive odometry estimates. The analysis is intended to provide users information needed to better leverage RGBD odometry within the constraints of their systems.

Three-dimensional turbopump flowfield analysis

NASA Technical Reports Server (NTRS)

Sharma, O. P.; Belford, K. A.; Ni, R. H.

1992-01-01

A program was conducted to develop a flow prediction method applicable to rocket turbopumps. The complex nature of a flowfield in turbopumps is described and examples of flowfields are discussed to illustrate that physics based models and analytical calculation procedures based on computational fluid dynamics (CFD) are needed to develop reliable design procedures for turbopumps. A CFD code developed at NASA ARC was used as the base code. The turbulence model and boundary conditions in the base code were modified, respectively, to: (1) compute transitional flows and account for extra rates of strain, e.g., rotation; and (2) compute surface heat transfer coefficients and allow computation through multistage turbomachines. Benchmark quality data from two and three-dimensional cascades were used to verify the code. The predictive capabilities of the present CFD code were demonstrated by computing the flow through a radial impeller and a multistage axial flow turbine. Results of the program indicate that the present code operated in a two-dimensional mode is a cost effective alternative to full three-dimensional calculations, and that it permits realistic predictions of unsteady loadings and losses for multistage machines.

Acceleration of High Angular Momentum Electron Repulsion Integrals and Integral Derivatives on Graphics Processing Units.

PubMed

Miao, Yipu; Merz, Kenneth M

2015-04-14

We present an efficient implementation of ab initio self-consistent field (SCF) energy and gradient calculations that run on Compute Unified Device Architecture (CUDA) enabled graphical processing units (GPUs) using recurrence relations. We first discuss the machine-generated code that calculates the electron-repulsion integrals (ERIs) for different ERI types. Next we describe the porting of the SCF gradient calculation to GPUs, which results in an acceleration of the computation of the first-order derivative of the ERIs. However, only s, p, and d ERIs and s and p derivatives could be executed simultaneously on GPUs using the current version of CUDA and generation of NVidia GPUs using a previously described algorithm [Miao and Merz J. Chem. Theory Comput. 2013, 9, 965-976.]. Hence, we developed an algorithm to compute f type ERIs and d type ERI derivatives on GPUs. Our benchmarks shows the performance GPU enable ERI and ERI derivative computation yielded speedups of 10-18 times relative to traditional CPU execution. An accuracy analysis using double-precision calculations demonstrates that the overall accuracy is satisfactory for most applications.

FDA Benchmark Medical Device Flow Models for CFD Validation.

PubMed

Malinauskas, Richard A; Hariharan, Prasanna; Day, Steven W; Herbertson, Luke H; Buesen, Martin; Steinseifer, Ulrich; Aycock, Kenneth I; Good, Bryan C; Deutsch, Steven; Manning, Keefe B; Craven, Brent A

Computational fluid dynamics (CFD) is increasingly being used to develop blood-contacting medical devices. However, the lack of standardized methods for validating CFD simulations and blood damage predictions limits its use in the safety evaluation of devices. Through a U.S. Food and Drug Administration (FDA) initiative, two benchmark models of typical device flow geometries (nozzle and centrifugal blood pump) were tested in multiple laboratories to provide experimental velocities, pressures, and hemolysis data to support CFD validation. In addition, computational simulations were performed by more than 20 independent groups to assess current CFD techniques. The primary goal of this article is to summarize the FDA initiative and to report recent findings from the benchmark blood pump model study. Discrepancies between CFD predicted velocities and those measured using particle image velocimetry most often occurred in regions of flow separation (e.g., downstream of the nozzle throat, and in the pump exit diffuser). For the six pump test conditions, 57% of the CFD predictions of pressure head were within one standard deviation of the mean measured values. Notably, only 37% of all CFD submissions contained hemolysis predictions. This project aided in the development of an FDA Guidance Document on factors to consider when reporting computational studies in medical device regulatory submissions. There is an accompanying podcast available for this article. Please visit the journal's Web site (www.asaiojournal.com) to listen.

Bond Dissociation Energies for Diatomic Molecules Containing 3d Transition Metals: Benchmark Scalar-Relativistic Coupled-Cluster Calculations for 20 Molecules

DOE PAGES

Cheng, Lan; Gauss, Jürgen; Ruscic, Branko; ...

2017-01-12

Benchmark scalar-relativistic coupled-cluster calculations for dissociation energies of the 20 diatomic molecules containing 3d transition metals in the 3dMLBE20 database ( J. Chem. Theory Comput. 2015, 11, 2036) are reported in this paper. Electron correlation and basis set effects are systematically studied. The agreement between theory and experiment is in general satisfactory. For a subset of 16 molecules, the standard deviation between computational and experimental values is 9 kJ/mol with the maximum deviation being 15 kJ/mol. The discrepancies between theory and experiment remain substantial (more than 20 kJ/mol) for VH, CrH, CoH, and FeH. To explore the source of themore » latter discrepancies, the analysis used to determine the experimental dissociation energies for VH and CrH is revisited. It is shown that, if improved values are used for the heterolytic C–H dissociation energies of di- and trimethylamine involved in the experimental determination, the experimental values for the dissociation energies of VH and CrH are increased by 18 kJ/mol, such that D 0(VH) = 223 ± 7 kJ/mol and D 0(CrH) = 204 ± 7 kJ/mol (or D e(VH) = 233 ± 7 kJ/mol and D e(CrH) = 214 ± 7 kJ/mol). Finally, the new experimental values agree quite well with the calculated values, showing the consistency of the computation and the measured reaction thresholds.« less

Evaluating the Information Power Grid using the NAS Grid Benchmarks

NASA Technical Reports Server (NTRS)

VanderWijngaartm Rob F.; Frumkin, Michael A.

2004-01-01

The NAS Grid Benchmarks (NGB) are a collection of synthetic distributed applications designed to rate the performance and functionality of computational grids. We compare several implementations of the NGB to determine programmability and efficiency of NASA's Information Power Grid (IPG), whose services are mostly based on the Globus Toolkit. We report on the overheads involved in porting existing NGB reference implementations to the IPG. No changes were made to the component tasks of the NGB can still be improved.

Computer System Resource Requirements of Novice Programming Students.

ERIC Educational Resources Information Center

Nutt, Gary J.

The characteristics of jobs that constitute the mix for lower division FORTRAN classes in a university were investigated. Samples of these programs were also benchmarked on a larger central site computer and two minicomputer systems. It was concluded that a carefully chosen minicomputer system could offer service at least the equivalent of the…

Benchmarking NWP Kernels on Multi- and Many-core Processors

NASA Astrophysics Data System (ADS)

Michalakes, J.; Vachharajani, M.

2008-12-01

Increased computing power for weather, climate, and atmospheric science has provided direct benefits for defense, agriculture, the economy, the environment, and public welfare and convenience. Today, very large clusters with many thousands of processors are allowing scientists to move forward with simulations of unprecedented size. But time-critical applications such as real-time forecasting or climate prediction need strong scaling: faster nodes and processors, not more of them. Moreover, the need for good cost- performance has never been greater, both in terms of performance per watt and per dollar. For these reasons, the new generations of multi- and many-core processors being mass produced for commercial IT and "graphical computing" (video games) are being scrutinized for their ability to exploit the abundant fine- grain parallelism in atmospheric models. We present results of our work to date identifying key computational kernels within the dynamics and physics of a large community NWP model, the Weather Research and Forecast (WRF) model. We benchmark and optimize these kernels on several different multi- and many-core processors. The goals are to (1) characterize and model performance of the kernels in terms of computational intensity, data parallelism, memory bandwidth pressure, memory footprint, etc. (2) enumerate and classify effective strategies for coding and optimizing for these new processors, (3) assess difficulties and opportunities for tool or higher-level language support, and (4) establish a continuing set of kernel benchmarks that can be used to measure and compare effectiveness of current and future designs of multi- and many-core processors for weather and climate applications.

A heterogeneous computing accelerated SCE-UA global optimization method using OpenMP, OpenCL, CUDA, and OpenACC.

PubMed

Kan, Guangyuan; He, Xiaoyan; Ding, Liuqian; Li, Jiren; Liang, Ke; Hong, Yang

2017-10-01

The shuffled complex evolution optimization developed at the University of Arizona (SCE-UA) has been successfully applied in various kinds of scientific and engineering optimization applications, such as hydrological model parameter calibration, for many years. The algorithm possesses good global optimality, convergence stability and robustness. However, benchmark and real-world applications reveal the poor computational efficiency of the SCE-UA. This research aims at the parallelization and acceleration of the SCE-UA method based on powerful heterogeneous computing technology. The parallel SCE-UA is implemented on Intel Xeon multi-core CPU (by using OpenMP and OpenCL) and NVIDIA Tesla many-core GPU (by using OpenCL, CUDA, and OpenACC). The serial and parallel SCE-UA were tested based on the Griewank benchmark function. Comparison results indicate the parallel SCE-UA significantly improves computational efficiency compared to the original serial version. The OpenCL implementation obtains the best overall acceleration results however, with the most complex source code. The parallel SCE-UA has bright prospects to be applied in real-world applications.

75 FR 82115 - Self-Regulatory Organizations; National Securities Clearing Corporation; Notice of Filing of...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-29

... to provide more efficient, cost-effective, and timely benchmarking and other market information about.... This market analysis (commonly referred to as ``benchmarking'') would allow users of this service to... determine to be most useful. The benchmarking portion of the service would provide information on an...

Implementation and validation of a conceptual benchmarking framework for patient blood management.

PubMed

Kastner, Peter; Breznik, Nada; Gombotz, Hans; Hofmann, Axel; Schreier, Günter

2015-01-01

Public health authorities and healthcare professionals are obliged to ensure high quality health service. Because of the high variability of the utilisation of blood and blood components, benchmarking is indicated in transfusion medicine. Implementation and validation of a benchmarking framework for Patient Blood Management (PBM) based on the report from the second Austrian Benchmark trial. Core modules for automatic report generation have been implemented with KNIME (Konstanz Information Miner) and validated by comparing the output with the results of the second Austrian benchmark trial. Delta analysis shows a deviation <0.1% for 95% (max. 1.4%). The framework provides a reliable tool for PBM benchmarking. The next step is technical integration with hospital information systems.

Sensitivity Analysis of Multidisciplinary Rotorcraft Simulations

NASA Technical Reports Server (NTRS)

Wang, Li; Diskin, Boris; Biedron, Robert T.; Nielsen, Eric J.; Bauchau, Olivier A.

2017-01-01

A multidisciplinary sensitivity analysis of rotorcraft simulations involving tightly coupled high-fidelity computational fluid dynamics and comprehensive analysis solvers is presented and evaluated. An unstructured sensitivity-enabled Navier-Stokes solver, FUN3D, and a nonlinear flexible multibody dynamics solver, DYMORE, are coupled to predict the aerodynamic loads and structural responses of helicopter rotor blades. A discretely-consistent adjoint-based sensitivity analysis available in FUN3D provides sensitivities arising from unsteady turbulent flows and unstructured dynamic overset meshes, while a complex-variable approach is used to compute DYMORE structural sensitivities with respect to aerodynamic loads. The multidisciplinary sensitivity analysis is conducted through integrating the sensitivity components from each discipline of the coupled system. Numerical results verify accuracy of the FUN3D/DYMORE system by conducting simulations for a benchmark rotorcraft test model and comparing solutions with established analyses and experimental data. Complex-variable implementation of sensitivity analysis of DYMORE and the coupled FUN3D/DYMORE system is verified by comparing with real-valued analysis and sensitivities. Correctness of adjoint formulations for FUN3D/DYMORE interfaces is verified by comparing adjoint-based and complex-variable sensitivities. Finally, sensitivities of the lift and drag functions obtained by complex-variable FUN3D/DYMORE simulations are compared with sensitivities computed by the multidisciplinary sensitivity analysis, which couples adjoint-based flow and grid sensitivities of FUN3D and FUN3D/DYMORE interfaces with complex-variable sensitivities of DYMORE structural responses.

Benchmarking hardware architecture candidates for the NFIRAOS real-time controller

NASA Astrophysics Data System (ADS)

Smith, Malcolm; Kerley, Dan; Herriot, Glen; Véran, Jean-Pierre

2014-07-01

As a part of the trade study for the Narrow Field Infrared Adaptive Optics System, the adaptive optics system for the Thirty Meter Telescope, we investigated the feasibility of performing real-time control computation using a Linux operating system and Intel Xeon E5 CPUs. We also investigated a Xeon Phi based architecture which allows higher levels of parallelism. This paper summarizes both the CPU based real-time controller architecture and the Xeon Phi based RTC. The Intel Xeon E5 CPU solution meets the requirements and performs the computation for one AO cycle in an average of 767 microseconds. The Xeon Phi solution did not meet the 1200 microsecond time requirement and also suffered from unpredictable execution times. More detailed benchmark results are reported for both architectures.

Development and Application of Benchmark Examples for Mixed-Mode I/II Quasi-Static Delamination Propagation Predictions

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2012-01-01

The development of benchmark examples for quasi-static delamination propagation prediction is presented and demonstrated for a commercial code. The examples are based on finite element models of the Mixed-Mode Bending (MMB) specimen. The examples are independent of the analysis software used and allow the assessment of the automated delamination propagation prediction capability in commercial finite element codes based on the virtual crack closure technique (VCCT). First, quasi-static benchmark examples were created for the specimen. Second, starting from an initially straight front, the delamination was allowed to propagate under quasi-static loading. Third, the load-displacement relationship from a propagation analysis and the benchmark results were compared, and good agreement could be achieved by selecting the appropriate input parameters. Good agreement between the results obtained from the automated propagation analysis and the benchmark results could be achieved by selecting input parameters that had previously been determined during analyses of mode I Double Cantilever Beam and mode II End Notched Flexure specimens. The benchmarking procedure proved valuable by highlighting the issues associated with choosing the input parameters of the particular implementation. Overall the results are encouraging, but further assessment for mixed-mode delamination fatigue onset and growth is required.

The Magellan Final Report on Cloud Computing

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

,; Coghlan, Susan; Yelick, Katherine

The goal of Magellan, a project funded through the U.S. Department of Energy (DOE) Office of Advanced Scientific Computing Research (ASCR), was to investigate the potential role of cloud computing in addressing the computing needs for the DOE Office of Science (SC), particularly related to serving the needs of mid- range computing and future data-intensive computing workloads. A set of research questions was formed to probe various aspects of cloud computing from performance, usability, and cost. To address these questions, a distributed testbed infrastructure was deployed at the Argonne Leadership Computing Facility (ALCF) and the National Energy Research Scientific Computingmore » Center (NERSC). The testbed was designed to be flexible and capable enough to explore a variety of computing models and hardware design points in order to understand the impact for various scientific applications. During the project, the testbed also served as a valuable resource to application scientists. Applications from a diverse set of projects such as MG-RAST (a metagenomics analysis server), the Joint Genome Institute, the STAR experiment at the Relativistic Heavy Ion Collider, and the Laser Interferometer Gravitational Wave Observatory (LIGO), were used by the Magellan project for benchmarking within the cloud, but the project teams were also able to accomplish important production science utilizing the Magellan cloud resources.« less

The International Conference on Vector and Parallel Computing (2nd)

DTIC Science & Technology

1989-01-17

Computation of the SVD of Bidiagonal Matrices" ...................................... 11 " Lattice QCD -As a Large Scale Scientific Computation...vectorizcd for the IBM 3090 Vector Facility. In addition, elapsed times " Lattice QCD -As a Large Scale Scientific have been reduced by using 3090...benchmarked Lattice QCD on a large number ofcompu- come from the wavefront solver routine. This was exten- ters: CrayX-MP and Cray 2 (vector

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

Performance Benchmark for a Prismatic Flow Solver

DTIC Science & Technology

2007-03-26

Gauss- Seidel (LU-SGS) implicit method is used for time integration to reduce the computational time. A one-equation turbulence model by Goldberg and...numerical flux computations. The Lower-Upper-Symmetric Gauss- Seidel (LU-SGS) implicit method [1] is used for time integration to reduce the...Sharov, D. and Nakahashi, K., “Reordering of Hybrid Unstructured Grids for Lower-Upper Symmetric Gauss- Seidel Computations,” AIAA Journal, Vol. 36

USAR Recruiting Success Factors.

DTIC Science & Technology

1987-12-01

scores, were used to predict production scores for each recruiter. Benchmark Achievement Scores (BAS) were computed by dividing total production bv...performance compnred to thil avigle would b ,’asl,_cr t.o compute . SAS correlated high y witi IIAS r .96 . so tihe two scores were practically equivalent...asked to make a sales pitch to a prospective enlistee about the benefits of Army life. Presen- tations were scored by computing the ratio of the

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.

BLENDING ANALYSIS FOR RADIOACTIVE SALT WASTE PROCESSING FACILITY

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

Lee, S.

2012-05-10

Savannah River National Laboratory (SRNL) evaluated methods to mix and blend the contents of the blend tanks to ensure the contents are properly blended before they are transferred from the blend tank such as Tank 21 and Tank 24 to the Salt Waste Processing Facility (SWPF) feed tank. The tank contents consist of three forms: dissolved salt solution, other waste salt solutions, and sludge containing settled solids. This paper focuses on developing the computational model and estimating the operation time of submersible slurry pump when the tank contents are adequately blended prior to their transfer to the SWPF facility. Amore » three-dimensional computational fluid dynamics approach was taken by using the full scale configuration of SRS Type-IV tank, Tank 21H. Major solid obstructions such as the tank wall boundary, the transfer pump column, and three slurry pump housings including one active and two inactive pumps were included in the mixing performance model. Basic flow pattern results predicted by the computational model were benchmarked against the SRNL test results and literature data. Tank 21 is a waste tank that is used to prepare batches of salt feed for SWPF. The salt feed must be a homogeneous solution satisfying the acceptance criterion of the solids entrainment during transfer operation. The work scope described here consists of two modeling areas. They are the steady state flow pattern calculations before the addition of acid solution for tank blending operation and the transient mixing analysis during miscible liquid blending operation. The transient blending calculations were performed by using the 95% homogeneity criterion for the entire liquid domain of the tank. The initial conditions for the entire modeling domain were based on the steady-state flow pattern results with zero second phase concentration. The performance model was also benchmarked against the SRNL test results and literature data.« less

A resource for benchmarking the usefulness of protein structure models.

PubMed

Carbajo, Daniel; Tramontano, Anna

2012-08-02

Increasingly, biologists and biochemists use computational tools to design experiments to probe the function of proteins and/or to engineer them for a variety of different purposes. The most effective strategies rely on the knowledge of the three-dimensional structure of the protein of interest. However it is often the case that an experimental structure is not available and that models of different quality are used instead. On the other hand, the relationship between the quality of a model and its appropriate use is not easy to derive in general, and so far it has been analyzed in detail only for specific application. This paper describes a database and related software tools that allow testing of a given structure based method on models of a protein representing different levels of accuracy. The comparison of the results of a computational experiment on the experimental structure and on a set of its decoy models will allow developers and users to assess which is the specific threshold of accuracy required to perform the task effectively. The ModelDB server automatically builds decoy models of different accuracy for a given protein of known structure and provides a set of useful tools for their analysis. Pre-computed data for a non-redundant set of deposited protein structures are available for analysis and download in the ModelDB database. IMPLEMENTATION, AVAILABILITY AND REQUIREMENTS: Project name: A resource for benchmarking the usefulness of protein structure models. Project home page: http://bl210.caspur.it/MODEL-DB/MODEL-DB_web/MODindex.php.Operating system(s): Platform independent. Programming language: Perl-BioPerl (program); mySQL, Perl DBI and DBD modules (database); php, JavaScript, Jmol scripting (web server). Other requirements: Java Runtime Environment v1.4 or later, Perl, BioPerl, CPAN modules, HHsearch, Modeller, LGA, NCBI Blast package, DSSP, Speedfill (Surfnet) and PSAIA. License: Free. Any restrictions to use by non-academics: No.

Neutron Activation and Thermoluminescent Detector Responses to a Bare Pulse of the CEA Valduc SILENE Critical Assembly

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

Miller, Thomas Martin; Celik, Cihangir; McMahan, Kimberly L.

This benchmark experiment was conducted as a joint venture between the US Department of Energy (DOE) and the French Commissariat à l'Energie Atomique (CEA). Staff at the Oak Ridge National Laboratory (ORNL) in the US and the Centre de Valduc in France planned this experiment. The experiment was conducted on October 11, 2010 in the SILENE critical assembly facility at Valduc. Several other organizations contributed to this experiment and the subsequent evaluation, including CEA Saclay, Lawrence Livermore National Laboratory (LLNL), the Y-12 National Security Complex (NSC), Babcock International Group in the United Kingdom, and Los Alamos National Laboratory (LANL). Themore » goal of this experiment was to measure neutron activation and thermoluminescent dosimeter (TLD) doses from a source similar to a fissile solution critical excursion. The resulting benchmark can be used for validation of computer codes and nuclear data libraries as required when performing analysis of criticality accident alarm systems (CAASs). A secondary goal of this experiment was to qualitatively test performance of two CAAS detectors similar to those currently and formerly in use in some US DOE facilities. The detectors tested were the CIDAS MkX and the Rocky Flats NCD-91. These detectors were being evaluated to determine whether they would alarm, so they were not expected to generate benchmark quality data.« less

QPROT: Statistical method for testing differential expression using protein-level intensity data in label-free quantitative proteomics.

PubMed

Choi, Hyungwon; Kim, Sinae; Fermin, Damian; Tsou, Chih-Chiang; Nesvizhskii, Alexey I

2015-11-03

We introduce QPROT, a statistical framework and computational tool for differential protein expression analysis using protein intensity data. QPROT is an extension of the QSPEC suite, originally developed for spectral count data, adapted for the analysis using continuously measured protein-level intensity data. QPROT offers a new intensity normalization procedure and model-based differential expression analysis, both of which account for missing data. Determination of differential expression of each protein is based on the standardized Z-statistic based on the posterior distribution of the log fold change parameter, guided by the false discovery rate estimated by a well-known Empirical Bayes method. We evaluated the classification performance of QPROT using the quantification calibration data from the clinical proteomic technology assessment for cancer (CPTAC) study and a recently published Escherichia coli benchmark dataset, with evaluation of FDR accuracy in the latter. QPROT is a statistical framework with computational software tool for comparative quantitative proteomics analysis. It features various extensions of QSPEC method originally built for spectral count data analysis, including probabilistic treatment of missing values in protein intensity data. With the increasing popularity of label-free quantitative proteomics data, the proposed method and accompanying software suite will be immediately useful for many proteomics laboratories. This article is part of a Special Issue entitled: Computational Proteomics. Copyright © 2015 Elsevier B.V. All rights reserved.

Simple techniques for improving deep neural network outcomes on commodity hardware

NASA Astrophysics Data System (ADS)

Colina, Nicholas Christopher A.; Perez, Carlos E.; Paraan, Francis N. C.

2017-08-01

We benchmark improvements in the performance of deep neural networks (DNN) on the MNIST data test upon imple-menting two simple modifications to the algorithm that have little overhead computational cost. First is GPU parallelization on a commodity graphics card, and second is initializing the DNN with random orthogonal weight matrices prior to optimization. Eigenspectra analysis of the weight matrices reveal that the initially orthogonal matrices remain nearly orthogonal after training. The probability distributions from which these orthogonal matrices are drawn are also shown to significantly affect the performance of these deep neural networks.

Crowdsourced estimation of cognitive decline and resilience in Alzheimer's disease.

PubMed

Allen, Genevera I; Amoroso, Nicola; Anghel, Catalina; Balagurusamy, Venkat; Bare, Christopher J; Beaton, Derek; Bellotti, Roberto; Bennett, David A; Boehme, Kevin L; Boutros, Paul C; Caberlotto, Laura; Caloian, Cristian; Campbell, Frederick; Chaibub Neto, Elias; Chang, Yu-Chuan; Chen, Beibei; Chen, Chien-Yu; Chien, Ting-Ying; Clark, Tim; Das, Sudeshna; Davatzikos, Christos; Deng, Jieyao; Dillenberger, Donna; Dobson, Richard J B; Dong, Qilin; Doshi, Jimit; Duma, Denise; Errico, Rosangela; Erus, Guray; Everett, Evan; Fardo, David W; Friend, Stephen H; Fröhlich, Holger; Gan, Jessica; St George-Hyslop, Peter; Ghosh, Satrajit S; Glaab, Enrico; Green, Robert C; Guan, Yuanfang; Hong, Ming-Yi; Huang, Chao; Hwang, Jinseub; Ibrahim, Joseph; Inglese, Paolo; Iyappan, Anandhi; Jiang, Qijia; Katsumata, Yuriko; Kauwe, John S K; Klein, Arno; Kong, Dehan; Krause, Roland; Lalonde, Emilie; Lauria, Mario; Lee, Eunjee; Lin, Xihui; Liu, Zhandong; Livingstone, Julie; Logsdon, Benjamin A; Lovestone, Simon; Ma, Tsung-Wei; Malhotra, Ashutosh; Mangravite, Lara M; Maxwell, Taylor J; Merrill, Emily; Nagorski, John; Namasivayam, Aishwarya; Narayan, Manjari; Naz, Mufassra; Newhouse, Stephen J; Norman, Thea C; Nurtdinov, Ramil N; Oyang, Yen-Jen; Pawitan, Yudi; Peng, Shengwen; Peters, Mette A; Piccolo, Stephen R; Praveen, Paurush; Priami, Corrado; Sabelnykova, Veronica Y; Senger, Philipp; Shen, Xia; Simmons, Andrew; Sotiras, Aristeidis; Stolovitzky, Gustavo; Tangaro, Sabina; Tateo, Andrea; Tung, Yi-An; Tustison, Nicholas J; Varol, Erdem; Vradenburg, George; Weiner, Michael W; Xiao, Guanghua; Xie, Lei; Xie, Yang; Xu, Jia; Yang, Hojin; Zhan, Xiaowei; Zhou, Yunyun; Zhu, Fan; Zhu, Hongtu; Zhu, Shanfeng

2016-06-01

Identifying accurate biomarkers of cognitive decline is essential for advancing early diagnosis and prevention therapies in Alzheimer's disease. The Alzheimer's disease DREAM Challenge was designed as a computational crowdsourced project to benchmark the current state-of-the-art in predicting cognitive outcomes in Alzheimer's disease based on high dimensional, publicly available genetic and structural imaging data. This meta-analysis failed to identify a meaningful predictor developed from either data modality, suggesting that alternate approaches should be considered for prediction of cognitive performance. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Towards a physical interpretation of the entropic lattice Boltzmann method

NASA Astrophysics Data System (ADS)

Malaspinas, Orestis; Deville, Michel; Chopard, Bastien

2008-12-01

The entropic lattice Boltzmann method (ELBM) is one among several different versions of the lattice Boltzmann method for the simulation of hydrodynamics. The collision term of the ELBM is characterized by a nonincreasing H function, guaranteed by a variable relaxation time. We propose here an analysis of the ELBM using the Chapman-Enskog expansion. We show that it can be interpreted as some kind of subgrid model, where viscosity correction scales like the strain rate tensor. We confirm our analytical results by the numerical computations of the relaxation time modifications on the two-dimensional dipole-wall interaction benchmark.

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.

Turnkey CAD/CAM selection and evaluation

NASA Technical Reports Server (NTRS)

Moody, T.

1980-01-01

The methodology to be followed in evaluating and selecting a computer system for manufacturing applications is discussed. Main frames and minicomputers are considered. Benchmark evaluations, demonstrations, and contract negotiations are discussed.

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.

Performance of Landslide-HySEA tsunami model for NTHMP benchmarking validation process

NASA Astrophysics Data System (ADS)

Macias, Jorge

2017-04-01

In its FY2009 Strategic Plan, the NTHMP required that all numerical tsunami inundation models be verified as accurate and consistent through a model benchmarking process. This was completed in 2011, but only for seismic tsunami sources and in a limited manner for idealized solid underwater landslides. Recent work by various NTHMP states, however, has shown that landslide tsunami hazard may be dominant along significant parts of the US coastline, as compared to hazards from other tsunamigenic sources. To perform the above-mentioned validation process, a set of candidate benchmarks were proposed. These benchmarks are based on a subset of available laboratory date 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. The Landslide-HySEA model has participated in the workshop that was organized at Texas A&M University - Galveston, on January 9-11, 2017. The aim of this presentation is to show some of the numerical results obtained for Landslide-HySEA in the framework of this benchmarking validation/verification effort. Acknowledgements. This research has been partially supported by the Junta de Andalucía research project TESELA (P11-RNM7069), the Spanish Government Research project SIMURISK (MTM2015-70490-C02-01-R) and Universidad de Málaga, Campus de Excelencia Internacional Andalucía Tech. The GPU computations were performed at the Unit of Numerical Methods (University of Malaga).

Benchmarking as a Global Strategy for Improving Instruction in Higher Education.

ERIC Educational Resources Information Center

Clark, Karen L.

This paper explores the concept of benchmarking in institutional research, a comparative analysis methodology designed to help colleges and universities increase their educational quality and delivery systems. The primary purpose of benchmarking is to compare an institution to its competitors in order to improve the product (in this case…

Benchmarking and beyond. Information trends in home care.

PubMed

Twiss, Amanda; Rooney, Heather; Lang, Christine

2002-11-01

With today's benchmarking concepts and tools, agencies have the unprecedented opportunity to use information as a strategic advantage. Because agencies are demanding more and better information, benchmark functionality has grown increasingly sophisticated. Agencies now require a new type of analysis, focused on high-level executive summaries while reducing the current "data overload."

Development and Application of Benchmark Examples for Mixed-Mode I/II Quasi-Static Delamination Propagation Predictions

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2012-01-01

The development of benchmark examples for quasi-static delamination propagation prediction is presented. The example is based on a finite element model of the Mixed-Mode Bending (MMB) specimen for 50% mode II. The benchmarking is demonstrated for Abaqus/Standard, however, the example is independent of the analysis software used and allows the assessment of the automated delamination propagation prediction capability in commercial finite element codes based on the virtual crack closure technique (VCCT). First, a quasi-static benchmark example was created for the specimen. Second, starting from an initially straight front, the delamination was allowed to propagate under quasi-static loading. Third, the load-displacement as well as delamination length versus applied load/displacement relationships from a propagation analysis and the benchmark results were compared, and good agreement could be achieved by selecting the appropriate input parameters. The benchmarking procedure proved valuable by highlighting the issues associated with choosing the input parameters of the particular implementation. Overall, the results are encouraging, but further assessment for mixed-mode delamination fatigue onset and growth is required.

Development and Applications of Benchmark Examples for Static Delamination Propagation Predictions

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2013-01-01

The development and application of benchmark examples for the assessment of quasistatic delamination propagation capabilities was demonstrated for ANSYS (TradeMark) and Abaqus/Standard (TradeMark). The examples selected were based on finite element models of Double Cantilever Beam (DCB) and Mixed-Mode Bending (MMB) specimens. First, quasi-static benchmark results were created based on an approach developed previously. Second, the delamination was allowed to propagate under quasi-static loading from its initial location using the automated procedure implemented in ANSYS (TradeMark) and Abaqus/Standard (TradeMark). Input control parameters were varied to study the effect on the computed delamination propagation. Overall, the benchmarking procedure proved valuable by highlighting the issues associated with choosing the appropriate input parameters for the VCCT implementations in ANSYS® and Abaqus/Standard®. However, further assessment for mixed-mode delamination fatigue onset and growth is required. Additionally studies should include the assessment of the propagation capabilities in more complex specimens and on a structural level.

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

Properties of model-averaged BMDLs: a study of model averaging in dichotomous response risk estimation.

PubMed

Wheeler, Matthew W; Bailer, A John

2007-06-01

Model averaging (MA) has been proposed as a method of accounting for model uncertainty in benchmark dose (BMD) estimation. The technique has been used to average BMD dose estimates derived from dichotomous dose-response experiments, microbial dose-response experiments, as well as observational epidemiological studies. While MA is a promising tool for the risk assessor, a previous study suggested that the simple strategy of averaging individual models' BMD lower limits did not yield interval estimators that met nominal coverage levels in certain situations, and this performance was very sensitive to the underlying model space chosen. We present a different, more computationally intensive, approach in which the BMD is estimated using the average dose-response model and the corresponding benchmark dose lower bound (BMDL) is computed by bootstrapping. This method is illustrated with TiO(2) dose-response rat lung cancer data, and then systematically studied through an extensive Monte Carlo simulation. The results of this study suggest that the MA-BMD, estimated using this technique, performs better, in terms of bias and coverage, than the previous MA methodology. Further, the MA-BMDL achieves nominal coverage in most cases, and is superior to picking the "best fitting model" when estimating the benchmark dose. Although these results show utility of MA for benchmark dose risk estimation, they continue to highlight the importance of choosing an adequate model space as well as proper model fit diagnostics.

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

Block-Parallel Data Analysis with DIY2

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

Morozov, Dmitriy; Peterka, Tom

DIY2 is a programming model and runtime for block-parallel analytics on distributed-memory machines. Its main abstraction is block-structured data parallelism: data are decomposed into blocks; blocks are assigned to processing elements (processes or threads); computation is described as iterations over these blocks, and communication between blocks is defined by reusable patterns. By expressing computation in this general form, the DIY2 runtime is free to optimize the movement of blocks between slow and fast memories (disk and flash vs. DRAM) and to concurrently execute blocks residing in memory with multiple threads. This enables the same program to execute in-core, out-of-core, serial,more » parallel, single-threaded, multithreaded, or combinations thereof. This paper describes the implementation of the main features of the DIY2 programming model and optimizations to improve performance. DIY2 is evaluated on benchmark test cases to establish baseline performance for several common patterns and on larger complete analysis codes running on large-scale HPC machines.« less

Parallel replica dynamics method for bistable stochastic reaction networks: Simulation and sensitivity analysis

NASA Astrophysics Data System (ADS)

Wang, Ting; Plecháč, Petr

2017-12-01

Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks. The proposed method uses parallel computing to accelerate the sampling of rare transitions. Furthermore, it can be combined with the path-space information bounds for parametric sensitivity analysis. With the proposed methodology, we study three bistable biological networks: the Schlögl model, the genetic switch network, and the enzymatic futile cycle network. We demonstrate the algorithmic speedup achieved in these numerical benchmarks. More significant acceleration is expected when multi-core or graphics processing unit computer architectures and programming tools such as CUDA are employed.

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.

Development of a Benchmark Example for Delamination Fatigue Growth Prediction

NASA Technical Reports Server (NTRS)

Krueger, Ronald

2010-01-01

The development of a benchmark example for cyclic delamination growth prediction is presented and demonstrated for a commercial code. The example is based on a finite element model of a Double Cantilever Beam (DCB) specimen, which is independent of the analysis software used and allows the assessment of the delamination growth prediction capabilities in commercial finite element codes. First, the benchmark result was created for the specimen. Second, starting from an initially straight front, the delamination was allowed to grow under cyclic loading in a finite element model of a commercial code. The number of cycles to delamination onset and the number of cycles during stable delamination growth for each growth increment were obtained from the analysis. In general, good agreement between the results obtained from the growth analysis and the benchmark results could be achieved by selecting the appropriate input parameters. Overall, the results are encouraging but further assessment for mixed-mode delamination is required

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

Friese, Ryan; Khemka, Bhavesh; Maciejewski, Anthony A

Rising costs of energy consumption and an ongoing effort for increases in computing performance are leading to a significant need for energy-efficient computing. Before systems such as supercomputers, servers, and datacenters can begin operating in an energy-efficient manner, the energy consumption and performance characteristics of the system must be analyzed. In this paper, we provide an analysis framework that will allow a system administrator to investigate the tradeoffs between system energy consumption and utility earned by a system (as a measure of system performance). We model these trade-offs as a bi-objective resource allocation problem. We use a popular multi-objective geneticmore » algorithm to construct Pareto fronts to illustrate how different resource allocations can cause a system to consume significantly different amounts of energy and earn different amounts of utility. We demonstrate our analysis framework using real data collected from online benchmarks, and further provide a method to create larger data sets that exhibit similar heterogeneity characteristics to real data sets. This analysis framework can provide system administrators with insight to make intelligent scheduling decisions based on the energy and utility needs of their systems.« less

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.

Pynamic: the Python Dynamic Benchmark

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

Lee, G L; Ahn, D H; de Supinksi, B R

2007-07-10

Python is widely used in scientific computing to facilitate application development and to support features such as computational steering. Making full use of some of Python's popular features, which improve programmer productivity, leads to applications that access extremely high numbers of dynamically linked libraries (DLLs). As a result, some important Python-based applications severely stress a system's dynamic linking and loading capabilities and also cause significant difficulties for most development environment tools, such as debuggers. Furthermore, using the Python paradigm for large scale MPI-based applications can create significant file IO and further stress tools and operating systems. In this paper, wemore » present Pynamic, the first benchmark program to support configurable emulation of a wide-range of the DLL usage of Python-based applications for large scale systems. Pynamic has already accurately reproduced system software and tool issues encountered by important large Python-based scientific applications on our supercomputers. Pynamic provided insight for our system software and tool vendors, and our application developers, into the impact of several design decisions. As we describe the Pynamic benchmark, we will highlight some of the issues discovered in our large scale system software and tools using Pynamic.« less

Benchmark radar targets for the validation of computational electromagnetics programs

NASA Technical Reports Server (NTRS)

Woo, Alex C.; Wang, Helen T. G.; Schuh, Michael J.; Sanders, Michael L.

1993-01-01

Results are presented of a set of computational electromagnetics validation measurements referring to three-dimensional perfectly conducting smooth targets, performed for the Electromagnetic Code Consortium. Plots are presented for both the low- and high-frequency measurements of the NASA almond, an ogive, a double ogive, a cone-sphere, and a cone-sphere with a gap.

Performance benchmark of LHCb code on state-of-the-art x86 architectures

NASA Astrophysics Data System (ADS)

Campora Perez, D. H.; Neufeld, N.; Schwemmer, R.

2015-12-01

For Run 2 of the LHC, LHCb is replacing a significant part of its event filter farm with new compute nodes. For the evaluation of the best performing solution, we have developed a method to convert our high level trigger application into a stand-alone, bootable benchmark image. With additional instrumentation we turned it into a self-optimising benchmark which explores techniques such as late forking, NUMA balancing and optimal number of threads, i.e. it automatically optimises box-level performance. We have run this procedure on a wide range of Haswell-E CPUs and numerous other architectures from both Intel and AMD, including also the latest Intel micro-blade servers. We present results in terms of performance, power consumption, overheads and relative cost.

Mean velocity and turbulence measurements in a 90 deg curved duct with thin inlet boundary layer

NASA Technical Reports Server (NTRS)

Crawford, R. A.; Peters, C. E.; Steinhoff, J.; Hornkohl, J. O.; Nourinejad, J.; Ramachandran, K.

1985-01-01

The experimental database established by this investigation of the flow in a large rectangular turning duct is of benchmark quality. The experimental Reynolds numbers, Deans numbers and boundary layer characteristics are significantly different from previous benchmark curved-duct experimental parameters. This investigation extends the experimental database to higher Reynolds number and thinner entrance boundary layers. The 5% to 10% thick boundary layers, based on duct half-width, results in a large region of near-potential flow in the duct core surrounded by developing boundary layers with large crossflows. The turbulent entrance boundary layer case at R sub ed = 328,000 provides an incompressible flowfield which approaches real turbine blade cascade characteristics. The results of this investigation provide a challenging benchmark database for computational fluid dynamics code development.

Information Literacy and Office Tool Competencies: A Benchmark Study

ERIC Educational Resources Information Center

Heinrichs, John H.; Lim, Jeen-Su

2010-01-01

Present information science literature recognizes the importance of information technology to achieve information literacy. The authors report the results of a benchmarking student survey regarding perceived functional skills and competencies in word-processing and presentation tools. They used analysis of variance and regression analysis to…

Benchmarking in Universities: League Tables Revisited

ERIC Educational Resources Information Center

Turner, David

2005-01-01

This paper examines the practice of benchmarking universities using a "league table" approach. Taking the example of the "Sunday Times University League Table", the author reanalyses the descriptive data on UK universities. Using a linear programming technique, data envelope analysis (DEA), the author uses the re-analysis to…

Accelerating next generation sequencing data analysis with system level optimizations.

PubMed

Kathiresan, Nagarajan; Temanni, Ramzi; Almabrazi, Hakeem; Syed, Najeeb; Jithesh, Puthen V; Al-Ali, Rashid

2017-08-22

Next generation sequencing (NGS) data analysis is highly compute intensive. In-memory computing, vectorization, bulk data transfer, CPU frequency scaling are some of the hardware features in the modern computing architectures. To get the best execution time and utilize these hardware features, it is necessary to tune the system level parameters before running the application. We studied the GATK-HaplotypeCaller which is part of common NGS workflows, that consume more than 43% of the total execution time. Multiple GATK 3.x versions were benchmarked and the execution time of HaplotypeCaller was optimized by various system level parameters which included: (i) tuning the parallel garbage collection and kernel shared memory to simulate in-memory computing, (ii) architecture-specific tuning in the PairHMM library for vectorization, (iii) including Java 1.8 features through GATK source code compilation and building a runtime environment for parallel sorting and bulk data transfer (iv) the default 'on-demand' mode of CPU frequency is over-clocked by using 'performance-mode' to accelerate the Java multi-threads. As a result, the HaplotypeCaller execution time was reduced by 82.66% in GATK 3.3 and 42.61% in GATK 3.7. Overall, the execution time of NGS pipeline was reduced to 70.60% and 34.14% for GATK 3.3 and GATK 3.7 respectively.

Hypersonic Experimental and Computational Capability, Improvement and Validation. Volume 2

NASA Technical Reports Server (NTRS)

Muylaert, Jean (Editor); Kumar, Ajay (Editor); Dujarric, Christian (Editor)

1998-01-01

The results of the phase 2 effort conducted under AGARD Working Group 18 on Hypersonic Experimental and Computational Capability, Improvement and Validation are presented in this report. The first volume, published in May 1996, mainly focused on the design methodology, plans and some initial results of experiments that had been conducted to serve as validation benchmarks. The current volume presents the detailed experimental and computational data base developed during this effort.

Scale/TSUNAMI Sensitivity Data for ICSBEP Evaluations

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

Rearden, Bradley T; Reed, Davis Allan; Lefebvre, Robert A

2011-01-01

The Tools for Sensitivity and Uncertainty Analysis Methodology Implementation (TSUNAMI) software developed at Oak Ridge National Laboratory (ORNL) as part of the Scale code system provide unique methods for code validation, gap analysis, and experiment design. For TSUNAMI analysis, sensitivity data are generated for each application and each existing or proposed experiment used in the assessment. The validation of diverse sets of applications requires potentially thousands of data files to be maintained and organized by the user, and a growing number of these files are available through the International Handbook of Evaluated Criticality Safety Benchmark Experiments (IHECSBE) distributed through themore » International Criticality Safety Benchmark Evaluation Program (ICSBEP). To facilitate the use of the IHECSBE benchmarks in rigorous TSUNAMI validation and gap analysis techniques, ORNL generated SCALE/TSUNAMI sensitivity data files (SDFs) for several hundred benchmarks for distribution with the IHECSBE. For the 2010 edition of IHECSBE, the sensitivity data were generated using 238-group cross-section data based on ENDF/B-VII.0 for 494 benchmark experiments. Additionally, ORNL has developed a quality assurance procedure to guide the generation of Scale inputs and sensitivity data, as well as a graphical user interface to facilitate the use of sensitivity data in identifying experiments and applying them in validation studies.« less

Aeroservoelastic and Flight Dynamics Analysis Using Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Arena, Andrew S., Jr.

1999-01-01

This document in large part is based on the Masters Thesis of Cole Stephens. The document encompasses a variety of technical and practical issues involved when using the STARS codes for Aeroservoelastic analysis of vehicles. The document covers in great detail a number of technical issues and step-by-step details involved in the simulation of a system where aerodynamics, structures and controls are tightly coupled. Comparisons are made to a benchmark experimental program conducted at NASA Langley. One of the significant advantages of the methodology detailed is that as a result of the technique used to accelerate the CFD-based simulation, a systems model is produced which is very useful for developing the control law strategy, and subsequent high-speed simulations.

A Consumer's Guide to Benchmark Dose Models: Results of U.S. EPA Testing of 14 Dichotomous, 8 Continuous, and 6 Developmental Models (Presentation)

EPA Science Inventory

Benchmark dose risk assessment software (BMDS) was designed by EPA to generate dose-response curves and facilitate the analysis, interpretation and synthesis of toxicological data. Partial results of QA/QC testing of the EPA benchmark dose software (BMDS) are presented. BMDS pr...

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

Employing Nested OpenMP for the Parallelization of Multi-Zone Computational Fluid Dynamics Applications

NASA Technical Reports Server (NTRS)

Ayguade, Eduard; Gonzalez, Marc; Martorell, Xavier; Jost, Gabriele

2004-01-01

In this paper we describe the parallelization of the multi-zone code versions of the NAS Parallel Benchmarks employing multi-level OpenMP parallelism. For our study we use the NanosCompiler, which supports nesting of OpenMP directives and provides clauses to control the grouping of threads, load balancing, and synchronization. We report the benchmark results, compare the timings with those of different hybrid parallelization paradigms and discuss OpenMP implementation issues which effect the performance of multi-level parallel applications.

Benchmark solutions for the galactic heavy-ion transport equations with energy and spatial coupling

NASA Technical Reports Server (NTRS)

Ganapol, Barry D.; Townsend, Lawrence W.; Lamkin, Stanley L.; Wilson, John W.

1991-01-01

Nontrivial benchmark solutions are developed for the galactic heavy ion transport equations in the straightahead approximation with energy and spatial coupling. Analytical representations of the ion fluxes are obtained for a variety of sources with the assumption that the nuclear interaction parameters are energy independent. The method utilizes an analytical LaPlace transform inversion to yield a closed form representation that is computationally efficient. The flux profiles are then used to predict ion dose profiles, which are important for shield design studies.

Diagnostic reference levels of paediatric computed tomography examinations performed at a dedicated Australian paediatric hospital.

PubMed

Bibbo, Giovanni; Brown, Scott; Linke, Rebecca

2016-08-01

Diagnostic Reference Levels (DRL) of procedures involving ionizing radiation are important tools to optimizing radiation doses delivered to patients and in identifying cases where the levels of doses are unusually high. This is particularly important for paediatric patients undergoing computed tomography (CT) examinations as these examinations are associated with relatively high-dose. Paediatric CT studies, performed at our institution from January 2010 to March 2014, have been retrospectively analysed to determine the 75th and 95th percentiles of both the volume computed tomography dose index (CTDIvol ) and dose-length product (DLP) for the most commonly performed studies to: establish local diagnostic reference levels for paediatric computed tomography examinations performed at our institution, benchmark our DRL with national and international published paediatric values, and determine the compliance of CT radiographer with established protocols. The derived local 75th percentile DRL have been found to be acceptable when compared with those published by the Australian National Radiation Dose Register and two national children's hospitals, and at the international level with the National Reference Doses for the UK. The 95th percentiles of CTDIvol for the various CT examinations have been found to be acceptable values for the CT scanner Dose-Check Notification. Benchmarking CT radiographers shows that they follow the set protocols for the various examinations without significant variations in the machine setting factors. The derivation of DRL has given us the tool to evaluate and improve the performance of our CT service by improved compliance and a reduction in radiation dose to our paediatric patients. We have also been able to benchmark our performance with similar national and international institutions. © 2016 The Royal Australian and New Zealand College of Radiologists.

A Combined Experimental and Computational Study on Selected Physical Properties of Aminosilicones

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

Perry, RJ; Genovese, SE; Farnum, RL

2014-01-29

A number of physical properties of aminosilicones have been determined experimentally and predicted computationally. It was found that COSMO-RS predicted the densities of the materials under study to within about 4% of the experimentally determined values. Vapor pressure measurements were performed, and all of the aminosilicones of interest were found to be significantly less volatile than the benchmark MEA material. COSMO-RS was reasonably accurate for predicting the vapor pressures for aminosilicones that were thermally stable. The heat capacities of all aminosilicones tested were between 2.0 and 2.3 J/(g.degrees C); again substantially lower than a benchmark 30% aqueous MEA solution. Surfacemore » energies for the aminosilicones were found to be 23.3-28.3 dyne/cm and were accurately predicted using the parachor method.« less

An efficient parallel algorithm for matrix-vector multiplication

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

Hendrickson, B.; Leland, R.; Plimpton, S.

The multiplication of a vector by a matrix is the kernel computation of many algorithms in scientific computation. A fast parallel algorithm for this calculation is therefore necessary if one is to make full use of the new generation of parallel supercomputers. This paper presents a high performance, parallel matrix-vector multiplication algorithm that is particularly well suited to hypercube multiprocessors. For an n x n matrix on p processors, the communication cost of this algorithm is O(n/[radical]p + log(p)), independent of the matrix sparsity pattern. The performance of the algorithm is demonstrated by employing it as the kernel in themore » well-known NAS conjugate gradient benchmark, where a run time of 6.09 seconds was observed. This is the best published performance on this benchmark achieved to date using a massively parallel supercomputer.« less

Five- and six-electron harmonium atoms: Highly accurate electronic properties and their application to benchmarking of approximate 1-matrix functionals

NASA Astrophysics Data System (ADS)

Cioslowski, Jerzy; Strasburger, Krzysztof

2018-04-01

Electronic properties of several states of the five- and six-electron harmonium atoms are obtained from large-scale calculations employing explicitly correlated basis functions. The high accuracy of the computed energies (including their components), natural spinorbitals, and their occupation numbers makes them suitable for testing, calibration, and benchmarking of approximate formalisms of quantum chemistry and solid state physics. In the case of the five-electron species, the availability of the new data for a wide range of the confinement strengths ω allows for confirmation and generalization of the previously reached conclusions concerning the performance of the presently known approximations for the electron-electron repulsion energy in terms of the 1-matrix that are at heart of the density matrix functional theory (DMFT). On the other hand, the properties of the three low-lying states of the six-electron harmonium atom, computed at ω = 500 and ω = 1000, uncover deficiencies of the 1-matrix functionals not revealed by previous studies. In general, the previously published assessment of the present implementations of DMFT being of poor accuracy is found to hold. Extending the present work to harmonically confined systems with even more electrons is most likely counterproductive as the steep increase in computational cost required to maintain sufficient accuracy of the calculated properties is not expected to be matched by the benefits of additional information gathered from the resulting benchmarks.

SU-E-T-148: Benchmarks and Pre-Treatment Reviews: A Study of Quality Assurance Effectiveness

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

Lowenstein, J; Nguyen, H; Roll, J

Purpose: To determine the impact benchmarks and pre-treatment reviews have on improving the quality of submitted clinical trial data. Methods: Benchmarks are used to evaluate a site’s ability to develop a treatment that meets a specific protocol’s treatment guidelines prior to placing their first patient on the protocol. A pre-treatment review is an actual patient placed on the protocol in which the dosimetry and contour volumes are evaluated to be per protocol guidelines prior to allowing the beginning of the treatment. A key component of these QA mechanisms is that sites are provided timely feedback to educate them on howmore » to plan per the protocol and prevent protocol deviations on patients accrued to a protocol. For both benchmarks and pre-treatment reviews a dose volume analysis (DVA) was performed using MIM softwareTM. For pre-treatment reviews a volume contour evaluation was also performed. Results: IROC Houston performed a QA effectiveness analysis of a protocol which required both benchmarks and pre-treatment reviews. In 70 percent of the patient cases submitted, the benchmark played an effective role in assuring that the pre-treatment review of the cases met protocol requirements. The 35 percent of sites failing the benchmark subsequently modified there planning technique to pass the benchmark before being allowed to submit a patient for pre-treatment review. However, in 30 percent of the submitted cases the pre-treatment review failed where the majority (71 percent) failed the DVA. 20 percent of sites submitting patients failed to correct their dose volume discrepancies indicated by the benchmark case. Conclusion: Benchmark cases and pre-treatment reviews can be an effective QA tool to educate sites on protocol guidelines and to minimize deviations. Without the benchmark cases it is possible that 65 percent of the cases undergoing a pre-treatment review would have failed to meet the protocols requirements.Support: U24-CA-180803.« less

Data-driven train set crash dynamics simulation

NASA Astrophysics Data System (ADS)

Tang, Zhao; Zhu, Yunrui; Nie, Yinyu; Guo, Shihui; Liu, Fengjia; Chang, Jian; Zhang, Jianjun

2017-02-01

Traditional finite element (FE) methods are arguably expensive in computation/simulation of the train crash. High computational cost limits their direct applications in investigating dynamic behaviours of an entire train set for crashworthiness design and structural optimisation. On the contrary, multi-body modelling is widely used because of its low computational cost with the trade-off in accuracy. In this study, a data-driven train crash modelling method is proposed to improve the performance of a multi-body dynamics simulation of train set crash without increasing the computational burden. This is achieved by the parallel random forest algorithm, which is a machine learning approach that extracts useful patterns of force-displacement curves and predicts a force-displacement relation in a given collision condition from a collection of offline FE simulation data on various collision conditions, namely different crash velocities in our analysis. Using the FE simulation results as a benchmark, we compared our method with traditional multi-body modelling methods and the result shows that our data-driven method improves the accuracy over traditional multi-body models in train crash simulation and runs at the same level of efficiency.

Computational techniques in gamma-ray skyshine analysis

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

George, D.L.

1988-12-01

Two computer codes were developed to analyze gamma-ray skyshine, the scattering of gamma photons by air molecules. A review of previous gamma-ray skyshine studies discusses several Monte Carlo codes, programs using a single-scatter model, and the MicroSkyshine program for microcomputers. A benchmark gamma-ray skyshine experiment performed at Kansas State University is also described. A single-scatter numerical model was presented which traces photons from the source to their first scatter, then applies a buildup factor along a direct path from the scattering point to a detector. The FORTRAN code SKY, developed with this model before the present study, was modified tomore » use Gauss quadrature, recent photon attenuation data and a more accurate buildup approximation. The resulting code, SILOGP, computes response from a point photon source on the axis of a silo, with and without concrete shielding over the opening. Another program, WALLGP, was developed using the same model to compute response from a point gamma source behind a perfectly absorbing wall, with and without shielding overhead. 29 refs., 48 figs., 13 tabs.« less

Computation of fluid and particle motion from a time-sequenced image pair: a global outlier identification approach.

PubMed

Ray, Nilanjan

2011-10-01

Fluid motion estimation from time-sequenced images is a significant image analysis task. Its application is widespread in experimental fluidics research and many related areas like biomedical engineering and atmospheric sciences. In this paper, we present a novel flow computation framework to estimate the flow velocity vectors from two consecutive image frames. In an energy minimization-based flow computation, we propose a novel data fidelity term, which: 1) can accommodate various measures, such as cross-correlation or sum of absolute or squared differences of pixel intensities between image patches; 2) has a global mechanism to control the adverse effect of outliers arising out of motion discontinuities, proximity of image borders; and 3) can go hand-in-hand with various spatial smoothness terms. Further, the proposed data term and related regularization schemes are both applicable to dense and sparse flow vector estimations. We validate these claims by numerical experiments on benchmark flow data sets. © 2011 IEEE

Flowfield Analysis of a Small Entry Probe (SPRITE) Tested in an Arc Jet

NASA Technical Reports Server (NTRS)

Prabhu, Dinesh K.

2011-01-01

Results of simulations of flow of an arc-heated stream around a 14-inch diameter 45 sphere-cone configuration are presented. Computations are first benchmarked against pressure and heat flux measurements made using copper slug calorimeters of different shapes and sizes. The influence of catalycity of copper on computed results is investigated. Good agreements between predictions and measurements are obtained by assuming the copper slug to be partially catalytic to atomic recombination. With total enthalpy estimates obtained from these preliminary computations, calculations are then performed for the test article, with the nozzle and test article considered as an integrated whole the same procedure adopted for calorimeter simulations. The resulting heat fluxes at select points on the test article (points at which fully instrumented plugs were placed) are used in material thermal response code calculations. Predicted time histories of temperature are compared against thermocouple data from the instrumented plugs, and recession determined. Good agreement is obtained for in-depth thermocouples.

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

Systematic chemical-genetic and chemical-chemical interaction datasets for prediction of compound synergism

PubMed Central

Wildenhain, Jan; Spitzer, Michaela; Dolma, Sonam; Jarvik, Nick; White, Rachel; Roy, Marcia; Griffiths, Emma; Bellows, David S.; Wright, Gerard D.; Tyers, Mike

2016-01-01

The network structure of biological systems suggests that effective therapeutic intervention may require combinations of agents that act synergistically. However, a dearth of systematic chemical combination datasets have limited the development of predictive algorithms for chemical synergism. Here, we report two large datasets of linked chemical-genetic and chemical-chemical interactions in the budding yeast Saccharomyces cerevisiae. We screened 5,518 unique compounds against 242 diverse yeast gene deletion strains to generate an extended chemical-genetic matrix (CGM) of 492,126 chemical-gene interaction measurements. This CGM dataset contained 1,434 genotype-specific inhibitors, termed cryptagens. We selected 128 structurally diverse cryptagens and tested all pairwise combinations to generate a benchmark dataset of 8,128 pairwise chemical-chemical interaction tests for synergy prediction, termed the cryptagen matrix (CM). An accompanying database resource called ChemGRID was developed to enable analysis, visualisation and downloads of all data. The CGM and CM datasets will facilitate the benchmarking of computational approaches for synergy prediction, as well as chemical structure-activity relationship models for anti-fungal drug discovery. PMID:27874849

Bias-Free Chemically Diverse Test Sets from Machine Learning.

PubMed

Swann, Ellen T; Fernandez, Michael; Coote, Michelle L; Barnard, Amanda S

2017-08-14

Current benchmarking methods in quantum chemistry rely on databases that are built using a chemist's intuition. It is not fully understood how diverse or representative these databases truly are. Multivariate statistical techniques like archetypal analysis and K-means clustering have previously been used to summarize large sets of nanoparticles however molecules are more diverse and not as easily characterized by descriptors. In this work, we compare three sets of descriptors based on the one-, two-, and three-dimensional structure of a molecule. Using data from the NIST Computational Chemistry Comparison and Benchmark Database and machine learning techniques, we demonstrate the functional relationship between these structural descriptors and the electronic energy of molecules. Archetypes and prototypes found with topological or Coulomb matrix descriptors can be used to identify smaller, statistically significant test sets that better capture the diversity of chemical space. We apply this same method to find a diverse subset of organic molecules to demonstrate how the methods can easily be reapplied to individual research projects. Finally, we use our bias-free test sets to assess the performance of density functional theory and quantum Monte Carlo methods.

Evaluation of Graph Pattern Matching Workloads in Graph Analysis Systems

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

Hong, Seokyong; Lee, Sangkeun; Lim, Seung-Hwan

2016-01-01

Graph analysis has emerged as a powerful method for data scientists to represent, integrate, query, and explore heterogeneous data sources. As a result, graph data management and mining became a popular area of research, and led to the development of plethora of systems in recent years. Unfortunately, the number of emerging graph analysis systems and the wide range of applications, coupled with a lack of apples-to-apples comparisons, make it difficult to understand the trade-offs between different systems and the graph operations for which they are designed. A fair comparison of these systems is a challenging task for the following reasons:more » multiple data models, non-standardized serialization formats, various query interfaces to users, and diverse environments they operate in. To address these key challenges, in this paper we present a new benchmark suite by extending the Lehigh University Benchmark (LUBM) to cover the most common capabilities of various graph analysis systems. We provide the design process of the benchmark, which generalizes the workflow for data scientists to conduct the desired graph analysis on different graph analysis systems. Equipped with this extended benchmark suite, we present performance comparison for nine subgraph pattern retrieval operations over six graph analysis systems, namely NetworkX, Neo4j, Jena, Titan, GraphX, and uRiKA. Through the proposed benchmark suite, this study reveals both quantitative and qualitative findings in (1) implications in loading data into each system; (2) challenges in describing graph patterns for each query interface; and (3) different sensitivity of each system to query selectivity. We envision that this study will pave the road for: (i) data scientists to select the suitable graph analysis systems, and (ii) data management system designers to advance graph analysis systems.« less

Application of an Upwind High Resolution Finite-Differencing Scheme and Multigrid Method in Steady-State Incompressible Flow Simulations

NASA Technical Reports Server (NTRS)

Yang, Cheng I.; Guo, Yan-Hu; Liu, C.- H.

1996-01-01

The analysis and design of a submarine propulsor requires the ability to predict the characteristics of both laminar and turbulent flows to a higher degree of accuracy. This report presents results of certain benchmark computations based on an upwind, high-resolution, finite-differencing Navier-Stokes solver. The purpose of the computations is to evaluate the ability, the accuracy and the performance of the solver in the simulation of detailed features of viscous flows. Features of interest include flow separation and reattachment, surface pressure and skin friction distributions. Those features are particularly relevant to the propulsor analysis. Test cases with a wide range of Reynolds numbers are selected; therefore, the effects of the convective and the diffusive terms of the solver can be evaluated separately. Test cases include flows over bluff bodies, such as circular cylinders and spheres, at various low Reynolds numbers, flows over a flat plate with and without turbulence effects, and turbulent flows over axisymmetric bodies with and without propulsor effects. Finally, to enhance the iterative solution procedure, a full approximation scheme V-cycle multigrid method is implemented. Preliminary results indicate that the method significantly reduces the computational effort.

Spatial Statistics for Tumor Cell Counting and Classification

NASA Astrophysics Data System (ADS)

Wirjadi, Oliver; Kim, Yoo-Jin; Breuel, Thomas

To count and classify cells in histological sections is a standard task in histology. One example is the grading of meningiomas, benign tumors of the meninges, which requires to assess the fraction of proliferating cells in an image. As this process is very time consuming when performed manually, automation is required. To address such problems, we propose a novel application of Markov point process methods in computer vision, leading to algorithms for computing the locations of circular objects in images. In contrast to previous algorithms using such spatial statistics methods in image analysis, the present one is fully trainable. This is achieved by combining point process methods with statistical classifiers. Using simulated data, the method proposed in this paper will be shown to be more accurate and more robust to noise than standard image processing methods. On the publicly available SIMCEP benchmark for cell image analysis algorithms, the cell count performance of the present paper is significantly more accurate than results published elsewhere, especially when cells form dense clusters. Furthermore, the proposed system performs as well as a state-of-the-art algorithm for the computer-aided histological grading of meningiomas when combined with a simple k-nearest neighbor classifier for identifying proliferating cells.

3D-Printed Tissue-Mimicking Phantoms for Medical Imaging and Computational Validation Applications

PubMed Central

Shahmirzadi, Danial; Li, Ronny X.; Doyle, Barry J.; Konofagou, Elisa E.; McGloughlin, Tim M.

2014-01-01

Abstract Abdominal aortic aneurysm (AAA) is a permanent, irreversible dilation of the distal region of the aorta. Recent efforts have focused on improved AAA screening and biomechanics-based failure prediction. Idealized and patient-specific AAA phantoms are often employed to validate numerical models and imaging modalities. To produce such phantoms, the investment casting process is frequently used, reconstructing the 3D vessel geometry from computed tomography patient scans. In this study the alternative use of 3D printing to produce phantoms is investigated. The mechanical properties of flexible 3D-printed materials are benchmarked against proven elastomers. We demonstrate the utility of this process with particular application to the emerging imaging modality of ultrasound-based pulse wave imaging, a noninvasive diagnostic methodology being developed to obtain regional vascular wall stiffness properties, differentiating normal and pathologic tissue in vivo. Phantom wall displacements under pulsatile loading conditions were observed, showing good correlation to fluid–structure interaction simulations and regions of peak wall stress predicted by finite element analysis. 3D-printed phantoms show a strong potential to improve medical imaging and computational analysis, potentially helping bridge the gap between experimental and clinical diagnostic tools. PMID:28804733

A Two-Step Approach to Uncertainty Quantification of Core Simulators

DOE PAGES

Yankov, Artem; Collins, Benjamin; Klein, Markus; ...

2012-01-01

For the multiple sources of error introduced into the standard computational regime for simulating reactor cores, rigorous uncertainty analysis methods are available primarily to quantify the effects of cross section uncertainties. Two methods for propagating cross section uncertainties through core simulators are the XSUSA statistical approach and the “two-step” method. The XSUSA approach, which is based on the SUSA code package, is fundamentally a stochastic sampling method. Alternatively, the two-step method utilizes generalized perturbation theory in the first step and stochastic sampling in the second step. The consistency of these two methods in quantifying uncertainties in the multiplication factor andmore » in the core power distribution was examined in the framework of phase I-3 of the OECD Uncertainty Analysis in Modeling benchmark. With the Three Mile Island Unit 1 core as a base model for analysis, the XSUSA and two-step methods were applied with certain limitations, and the results were compared to those produced by other stochastic sampling-based codes. Based on the uncertainty analysis results, conclusions were drawn as to the method that is currently more viable for computing uncertainties in burnup and transient calculations.« less

Developing a benchmark for emotional analysis of music

PubMed Central

Yang, Yi-Hsuan; Soleymani, Mohammad

2017-01-01

Music emotion recognition (MER) field rapidly expanded in the last decade. Many new methods and new audio features are developed to improve the performance of MER algorithms. However, it is very difficult to compare the performance of the new methods because of the data representation diversity and scarcity of publicly available data. In this paper, we address these problems by creating a data set and a benchmark for MER. The data set that we release, a MediaEval Database for Emotional Analysis in Music (DEAM), is the largest available data set of dynamic annotations (valence and arousal annotations for 1,802 songs and song excerpts licensed under Creative Commons with 2Hz time resolution). Using DEAM, we organized the ‘Emotion in Music’ task at MediaEval Multimedia Evaluation Campaign from 2013 to 2015. The benchmark attracted, in total, 21 active teams to participate in the challenge. We analyze the results of the benchmark: the winning algorithms and feature-sets. We also describe the design of the benchmark, the evaluation procedures and the data cleaning and transformations that we suggest. The results from the benchmark suggest that the recurrent neural network based approaches combined with large feature-sets work best for dynamic MER. PMID:28282400

Developing a benchmark for emotional analysis of music.

PubMed

Aljanaki, Anna; Yang, Yi-Hsuan; Soleymani, Mohammad

2017-01-01

Music emotion recognition (MER) field rapidly expanded in the last decade. Many new methods and new audio features are developed to improve the performance of MER algorithms. However, it is very difficult to compare the performance of the new methods because of the data representation diversity and scarcity of publicly available data. In this paper, we address these problems by creating a data set and a benchmark for MER. The data set that we release, a MediaEval Database for Emotional Analysis in Music (DEAM), is the largest available data set of dynamic annotations (valence and arousal annotations for 1,802 songs and song excerpts licensed under Creative Commons with 2Hz time resolution). Using DEAM, we organized the 'Emotion in Music' task at MediaEval Multimedia Evaluation Campaign from 2013 to 2015. The benchmark attracted, in total, 21 active teams to participate in the challenge. We analyze the results of the benchmark: the winning algorithms and feature-sets. We also describe the design of the benchmark, the evaluation procedures and the data cleaning and transformations that we suggest. The results from the benchmark suggest that the recurrent neural network based approaches combined with large feature-sets work best for dynamic MER.

An Application-Based Performance Evaluation of NASAs Nebula Cloud Computing Platform

NASA Technical Reports Server (NTRS)

Saini, Subhash; Heistand, Steve; Jin, Haoqiang; Chang, Johnny; Hood, Robert T.; Mehrotra, Piyush; Biswas, Rupak

2012-01-01

The high performance computing (HPC) community has shown tremendous interest in exploring cloud computing as it promises high potential. In this paper, we examine the feasibility, performance, and scalability of production quality scientific and engineering applications of interest to NASA on NASA's cloud computing platform, called Nebula, hosted at Ames Research Center. This work represents the comprehensive evaluation of Nebula using NUTTCP, HPCC, NPB, I/O, and MPI function benchmarks as well as four applications representative of the NASA HPC workload. Specifically, we compare Nebula performance on some of these benchmarks and applications to that of NASA s Pleiades supercomputer, a traditional HPC system. We also investigate the impact of virtIO and jumbo frames on interconnect performance. Overall results indicate that on Nebula (i) virtIO and jumbo frames improve network bandwidth by a factor of 5x, (ii) there is a significant virtualization layer overhead of about 10% to 25%, (iii) write performance is lower by a factor of 25x, (iv) latency for short MPI messages is very high, and (v) overall performance is 15% to 48% lower than that on Pleiades for NASA HPC applications. We also comment on the usability of the cloud platform.

Numerical Boundary Conditions for Computational Aeroacoustics Benchmark Problems

NASA Technical Reports Server (NTRS)

Tam, Chritsopher K. W.; Kurbatskii, Konstantin A.; Fang, Jun

1997-01-01

Category 1, Problems 1 and 2, Category 2, Problem 2, and Category 3, Problem 2 are solved computationally using the Dispersion-Relation-Preserving (DRP) scheme. All these problems are governed by the linearized Euler equations. The resolution requirements of the DRP scheme for maintaining low numerical dispersion and dissipation as well as accurate wave speeds in solving the linearized Euler equations are now well understood. As long as 8 or more mesh points per wavelength is employed in the numerical computation, high quality results are assured. For the first three categories of benchmark problems, therefore, the real challenge is to develop high quality numerical boundary conditions. For Category 1, Problems 1 and 2, it is the curved wall boundary conditions. For Category 2, Problem 2, it is the internal radiation boundary conditions inside the duct. For Category 3, Problem 2, they are the inflow and outflow boundary conditions upstream and downstream of the blade row. These are the foci of the present investigation. Special nonhomogeneous radiation boundary conditions that generate the incoming disturbances and at the same time allow the outgoing reflected or scattered acoustic disturbances to leave the computation domain without significant reflection are developed. Numerical results based on these boundary conditions are provided.

Commercial Building Energy Saver, Web App

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

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

The CBES App is a web-based toolkit for use by small businesses and building owners and operators of small and medium size commercial buildings to perform energy benchmarking and retrofit analysis for buildings. The CBES App analyzes the energy performance of user's building for pre-and posto-retrofit, in conjunction with user's input data, to identify recommended retrofit measures, energy savings and economic analysis for the selected measures. The CBES App provides energy benchmarking, including getting an EnergyStar score using EnergyStar API and benchmarking against California peer buildings using the EnergyIQ API. The retrofit analysis includes a preliminary analysis by looking upmore » retrofit measures from a pre-simulated database DEEP, and a detailed analysis creating and running EnergyPlus models to calculate energy savings of retrofit measures. The CBES App builds upon the LBNL CBES API.« less

A Bayesian Multinomial Probit MODEL FOR THE ANALYSIS OF PANEL CHOICE DATA.

PubMed

Fong, Duncan K H; Kim, Sunghoon; Chen, Zhe; DeSarbo, Wayne S

2016-03-01

A new Bayesian multinomial probit model is proposed for the analysis of panel choice data. Using a parameter expansion technique, we are able to devise a Markov Chain Monte Carlo algorithm to compute our Bayesian estimates efficiently. We also show that the proposed procedure enables the estimation of individual level coefficients for the single-period multinomial probit model even when the available prior information is vague. We apply our new procedure to consumer purchase data and reanalyze a well-known scanner panel dataset that reveals new substantive insights. In addition, we delineate a number of advantageous features of our proposed procedure over several benchmark models. Finally, through a simulation analysis employing a fractional factorial design, we demonstrate that the results from our proposed model are quite robust with respect to differing factors across various conditions.

Benchmarking the Importance and Use of Labor Market Surveys by Certified Rehabilitation Counselors

ERIC Educational Resources Information Center

Barros-Bailey, Mary; Saunders, Jodi L.

2013-01-01

The purpose of this research was to benchmark the importance and use of labor market survey (LMS) among U.S. certified rehabilitation counselors (CRCs). A secondary post hoc analysis of data collected via the "Rehabilitation Skills Inventory--Revised" for the 2011 Commission on Rehabilitation Counselor Certification job analysis resulted in…

Policy Analysis of the English Graduation Benchmark in Taiwan

ERIC Educational Resources Information Center

Shih, Chih-Min

2012-01-01

To nudge students to study English and to improve their English proficiency, many universities in Taiwan have imposed an English graduation benchmark on their students. This article reviews this policy, using the theoretic framework for education policy analysis proposed by Haddad and Demsky (1995). The author presents relevant research findings,…

The impact of a scheduling change on ninth grade high school performance on biology benchmark exams and the California Standards Test

NASA Astrophysics Data System (ADS)

Leonardi, Marcelo

The primary purpose of this study was to examine the impact of a scheduling change from a trimester 4x4 block schedule to a modified hybrid schedule on student achievement in ninth grade biology courses. This study examined the impact of the scheduling change on student achievement through teacher created benchmark assessments in Genetics, DNA, and Evolution and on the California Standardized Test in Biology. The secondary purpose of this study examined the ninth grade biology teacher perceptions of ninth grade biology student achievement. Using a mixed methods research approach, data was collected both quantitatively and qualitatively as aligned to research questions. Quantitative methods included gathering data from departmental benchmark exams and California Standardized Test in Biology and conducting multiple analysis of covariance and analysis of covariance to determine significance differences. Qualitative methods include journal entries questions and focus group interviews. The results revealed a statistically significant increase in scores on both the DNA and Evolution benchmark exams. DNA and Evolution benchmark exams showed significant improvements from a change in scheduling format. The scheduling change was responsible for 1.5% of the increase in DNA benchmark scores and 2% of the increase in Evolution benchmark scores. The results revealed a statistically significant decrease in scores on the Genetics Benchmark exam as a result of the scheduling change. The scheduling change was responsible for 1% of the decrease in Genetics benchmark scores. The results also revealed a statistically significant increase in scores on the CST Biology exam. The scheduling change was responsible for .7% of the increase in CST Biology scores. Results of the focus group discussions indicated that all teachers preferred the modified hybrid schedule over the trimester schedule and that it improved student achievement.

Evaluation of direct and indirect additive manufacture of maxillofacial prostheses.

PubMed

Eggbeer, Dominic; Bibb, Richard; Evans, Peter; Ji, Lu

2012-09-01

The efficacy of computer-aided technologies in the design and manufacture of maxillofacial prostheses has not been fully proven. This paper presents research into the evaluation of direct and indirect additive manufacture of a maxillofacial prosthesis against conventional laboratory-based techniques. An implant/magnet-retained nasal prosthesis case from a UK maxillofacial unit was selected as a case study. A benchmark prosthesis was fabricated using conventional laboratory-based techniques for comparison against additive manufactured prostheses. For the computer-aided workflow, photogrammetry, computer-aided design and additive manufacture (AM) methods were evaluated in direct prosthesis body fabrication and indirect production using an additively manufactured mould. Qualitative analysis of position, shape, colour and edge quality was undertaken. Mechanical testing to ISO standards was also used to compare the silicone rubber used in the conventional prosthesis with the AM material. Critical evaluation has shown that utilising a computer-aided work-flow can produce a prosthesis body that is comparable to that produced using existing best practice. Technical limitations currently prevent the direct fabrication method demonstrated in this paper from being clinically viable. This research helps prosthesis providers understand the application of a computer-aided approach and guides technology developers and researchers to address the limitations identified.

Analysis of impact of general-purpose graphics processor units in supersonic flow modeling

NASA Astrophysics Data System (ADS)

Emelyanov, V. N.; Karpenko, A. G.; Kozelkov, A. S.; Teterina, I. V.; Volkov, K. N.; Yalozo, A. V.

2017-06-01

Computational methods are widely used in prediction of complex flowfields associated with off-normal situations in aerospace engineering. Modern graphics processing units (GPU) provide architectures and new programming models that enable to harness their large processing power and to design computational fluid dynamics (CFD) simulations at both high performance and low cost. Possibilities of the use of GPUs for the simulation of external and internal flows on unstructured meshes are discussed. The finite volume method is applied to solve three-dimensional unsteady compressible Euler and Navier-Stokes equations on unstructured meshes with high resolution numerical schemes. CUDA technology is used for programming implementation of parallel computational algorithms. Solutions of some benchmark test cases on GPUs are reported, and the results computed are compared with experimental and computational data. Approaches to optimization of the CFD code related to the use of different types of memory are considered. Speedup of solution on GPUs with respect to the solution on central processor unit (CPU) is compared. Performance measurements show that numerical schemes developed achieve 20-50 speedup on GPU hardware compared to CPU reference implementation. The results obtained provide promising perspective for designing a GPU-based software framework for applications in CFD.

Evaluating the effects of dam breach methodologies on Consequence Estimation through Sensitivity Analysis

NASA Astrophysics Data System (ADS)

Kalyanapu, A. J.; Thames, B. A.

2013-12-01

Dam breach modeling often includes application of models that are sophisticated, yet computationally intensive to compute flood propagation at high temporal and spatial resolutions. This results in a significant need for computational capacity that requires development of newer flood models using multi-processor and graphics processing techniques. Recently, a comprehensive benchmark exercise titled the 12th Benchmark Workshop on Numerical Analysis of Dams, is organized by the International Commission on Large Dams (ICOLD) to evaluate the performance of these various tools used for dam break risk assessment. The ICOLD workshop is focused on estimating the consequences of failure of a hypothetical dam near a hypothetical populated area with complex demographics, and economic activity. The current study uses this hypothetical case study and focuses on evaluating the effects of dam breach methodologies on consequence estimation and analysis. The current study uses ICOLD hypothetical data including the topography, dam geometric and construction information, land use/land cover data along with socio-economic and demographic data. The objective of this study is to evaluate impacts of using four different dam breach methods on the consequence estimates used in the risk assessments. The four methodologies used are: i) Froehlich (1995), ii) MacDonald and Langridge-Monopolis 1984 (MLM), iii) Von Thun and Gillete 1990 (VTG), and iv) Froehlich (2008). To achieve this objective, three different modeling components were used. First, using the HEC-RAS v.4.1, dam breach discharge hydrographs are developed. These hydrographs are then provided as flow inputs into a two dimensional flood model named Flood2D-GPU, which leverages the computer's graphics card for much improved computational capabilities of the model input. Lastly, outputs from Flood2D-GPU, including inundated areas, depth grids, velocity grids, and flood wave arrival time grids, are input into HEC-FIA, which provides the consequence assessment for the solution to the problem statement. For the four breach methodologies, a sensitivity analysis of four breach parameters, breach side slope (SS), breach width (Wb), breach invert elevation (Elb), and time of failure (tf), is conducted. Up to, 68 simulations are computed to produce breach hydrographs in HEC-RAS for input into Flood2D-GPU. The Flood2D-GPU simulation results were then post-processed in HEC-FIA to evaluate: Total Population at Risk (PAR), 14-yr and Under PAR (PAR14-), 65-yr and Over PAR (PAR65+), Loss of Life (LOL) and Direct Economic Impact (DEI). The MLM approach resulted in wide variability in simulated minimum and maximum values of PAR, PAR 65+ and LOL estimates. For PAR14- and DEI, Froehlich (1995) resulted in lower values while MLM resulted in higher estimates. This preliminary study demonstrated the relative performance of four commonly used dam breach methodologies and their impacts on consequence estimation.

VMEbus based computer and real-time UNIX as infrastructure of DAQ

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

Yasu, Y.; Fujii, H.; Nomachi, M.

1994-12-31

This paper describes what the authors have constructed as the infrastructure of data acquisition system (DAQ). The paper reports recent developments concerned with HP VME board computer with LynxOS (HP742rt/HP-RT) and Alpha/OSF1 with VMEbus adapter. The paper also reports current status of developing a Benchmark Suite for Data Acquisition (DAQBENCH) for measuring not only the performance of VME/CAMAC access but also that of the context switching, the inter-process communications and so on, for various computers including Workstation-based systems and VME board computers.

Interactive visual optimization and analysis for RFID benchmarking.

PubMed

Wu, Yingcai; Chung, Ka-Kei; Qu, Huamin; Yuan, Xiaoru; Cheung, S C

2009-01-01

Radio frequency identification (RFID) is a powerful automatic remote identification technique that has wide applications. To facilitate RFID deployment, an RFID benchmarking instrument called aGate has been invented to identify the strengths and weaknesses of different RFID technologies in various environments. However, the data acquired by aGate are usually complex time varying multidimensional 3D volumetric data, which are extremely challenging for engineers to analyze. In this paper, we introduce a set of visualization techniques, namely, parallel coordinate plots, orientation plots, a visual history mechanism, and a 3D spatial viewer, to help RFID engineers analyze benchmark data visually and intuitively. With the techniques, we further introduce two workflow procedures (a visual optimization procedure for finding the optimum reader antenna configuration and a visual analysis procedure for comparing the performance and identifying the flaws of RFID devices) for the RFID benchmarking, with focus on the performance analysis of the aGate system. The usefulness and usability of the system are demonstrated in the user evaluation.

Automated Instrumentation, Monitoring and Visualization of PVM Programs Using AIMS

NASA Technical Reports Server (NTRS)

Mehra, Pankaj; VanVoorst, Brian; Yan, Jerry; Lum, Henry, Jr. (Technical Monitor)

1994-01-01

We present views and analysis of the execution of several PVM (Parallel Virtual Machine) codes for Computational Fluid Dynamics on a networks of Sparcstations, including: (1) NAS Parallel Benchmarks CG and MG; (2) a multi-partitioning algorithm for NAS Parallel Benchmark SP; and (3) an overset grid flowsolver. These views and analysis were obtained using our Automated Instrumentation and Monitoring System (AIMS) version 3.0, a toolkit for debugging the performance of PVM programs. We will describe the architecture, operation and application of AIMS. The AIMS toolkit contains: (1) Xinstrument, which can automatically instrument various computational and communication constructs in message-passing parallel programs; (2) Monitor, a library of runtime trace-collection routines; (3) VK (Visual Kernel), an execution-animation tool with source-code clickback; and (4) Tally, a tool for statistical analysis of execution profiles. Currently, Xinstrument can handle C and Fortran 77 programs using PVM 3.2.x; Monitor has been implemented and tested on Sun 4 systems running SunOS 4.1.2; and VK uses XIIR5 and Motif 1.2. Data and views obtained using AIMS clearly illustrate several characteristic features of executing parallel programs on networked workstations: (1) the impact of long message latencies; (2) the impact of multiprogramming overheads and associated load imbalance; (3) cache and virtual-memory effects; and (4) significant skews between workstation clocks. Interestingly, AIMS can compensate for constant skew (zero drift) by calibrating the skew between a parent and its spawned children. In addition, AIMS' skew-compensation algorithm can adjust timestamps in a way that eliminates physically impossible communications (e.g., messages going backwards in time). Our current efforts are directed toward creating new views to explain the observed performance of PVM programs. Some of the features planned for the near future include: (1) ConfigView, showing the physical topology of the virtual machine, inferred using specially formatted IP (Internet Protocol) packets: and (2) LoadView, synchronous animation of PVM-program execution and resource-utilization patterns.

Resources and costs for microbial sequence analysis evaluated using virtual machines and cloud computing.

PubMed

Angiuoli, Samuel V; White, James R; Matalka, Malcolm; White, Owen; Fricke, W Florian

2011-01-01

The widespread popularity of genomic applications is threatened by the "bioinformatics bottleneck" resulting from uncertainty about the cost and infrastructure needed to meet increasing demands for next-generation sequence analysis. Cloud computing services have been discussed as potential new bioinformatics support systems but have not been evaluated thoroughly. We present benchmark costs and runtimes for common microbial genomics applications, including 16S rRNA analysis, microbial whole-genome shotgun (WGS) sequence assembly and annotation, WGS metagenomics and large-scale BLAST. Sequence dataset types and sizes were selected to correspond to outputs typically generated by small- to midsize facilities equipped with 454 and Illumina platforms, except for WGS metagenomics where sampling of Illumina data was used. Automated analysis pipelines, as implemented in the CloVR virtual machine, were used in order to guarantee transparency, reproducibility and portability across different operating systems, including the commercial Amazon Elastic Compute Cloud (EC2), which was used to attach real dollar costs to each analysis type. We found considerable differences in computational requirements, runtimes and costs associated with different microbial genomics applications. While all 16S analyses completed on a single-CPU desktop in under three hours, microbial genome and metagenome analyses utilized multi-CPU support of up to 120 CPUs on Amazon EC2, where each analysis completed in under 24 hours for less than $60. Representative datasets were used to estimate maximum data throughput on different cluster sizes and to compare costs between EC2 and comparable local grid servers. Although bioinformatics requirements for microbial genomics depend on dataset characteristics and the analysis protocols applied, our results suggests that smaller sequencing facilities (up to three Roche/454 or one Illumina GAIIx sequencer) invested in 16S rRNA amplicon sequencing, microbial single-genome and metagenomics WGS projects can achieve cost-efficient bioinformatics support using CloVR in combination with Amazon EC2 as an alternative to local computing centers.

Resources and Costs for Microbial Sequence Analysis Evaluated Using Virtual Machines and Cloud Computing

PubMed Central

Angiuoli, Samuel V.; White, James R.; Matalka, Malcolm; White, Owen; Fricke, W. Florian

2011-01-01

Background The widespread popularity of genomic applications is threatened by the “bioinformatics bottleneck” resulting from uncertainty about the cost and infrastructure needed to meet increasing demands for next-generation sequence analysis. Cloud computing services have been discussed as potential new bioinformatics support systems but have not been evaluated thoroughly. Results We present benchmark costs and runtimes for common microbial genomics applications, including 16S rRNA analysis, microbial whole-genome shotgun (WGS) sequence assembly and annotation, WGS metagenomics and large-scale BLAST. Sequence dataset types and sizes were selected to correspond to outputs typically generated by small- to midsize facilities equipped with 454 and Illumina platforms, except for WGS metagenomics where sampling of Illumina data was used. Automated analysis pipelines, as implemented in the CloVR virtual machine, were used in order to guarantee transparency, reproducibility and portability across different operating systems, including the commercial Amazon Elastic Compute Cloud (EC2), which was used to attach real dollar costs to each analysis type. We found considerable differences in computational requirements, runtimes and costs associated with different microbial genomics applications. While all 16S analyses completed on a single-CPU desktop in under three hours, microbial genome and metagenome analyses utilized multi-CPU support of up to 120 CPUs on Amazon EC2, where each analysis completed in under 24 hours for less than $60. Representative datasets were used to estimate maximum data throughput on different cluster sizes and to compare costs between EC2 and comparable local grid servers. Conclusions Although bioinformatics requirements for microbial genomics depend on dataset characteristics and the analysis protocols applied, our results suggests that smaller sequencing facilities (up to three Roche/454 or one Illumina GAIIx sequencer) invested in 16S rRNA amplicon sequencing, microbial single-genome and metagenomics WGS projects can achieve cost-efficient bioinformatics support using CloVR in combination with Amazon EC2 as an alternative to local computing centers. PMID:22028928

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.

Variogram Analysis of Response surfaces (VARS): A New Framework for Global Sensitivity Analysis of Earth and Environmental Systems Models

NASA Astrophysics Data System (ADS)

Razavi, S.; Gupta, H. V.

2015-12-01

Earth and environmental systems models (EESMs) are continually growing in complexity and dimensionality with continuous advances in understanding and computing power. Complexity and dimensionality are manifested by introducing many different factors in EESMs (i.e., model parameters, forcings, boundary conditions, etc.) to be identified. Sensitivity Analysis (SA) provides an essential means for characterizing the role and importance of such factors in producing the model responses. However, conventional approaches to SA suffer from (1) an ambiguous characterization of sensitivity, and (2) poor computational efficiency, particularly as the problem dimension grows. Here, we present a new and general sensitivity analysis framework (called VARS), based on an analogy to 'variogram analysis', that provides an intuitive and comprehensive characterization of sensitivity across the full spectrum of scales in the factor space. We prove, theoretically, that Morris (derivative-based) and Sobol (variance-based) methods and their extensions are limiting cases of VARS, and that their SA indices can be computed as by-products of the VARS framework. We also present a practical strategy for the application of VARS to real-world problems, called STAR-VARS, including a new sampling strategy, called "star-based sampling". Our results across several case studies show the STAR-VARS approach to provide reliable and stable assessments of "global" sensitivity across the full range of scales in the factor space, while being at least 1-2 orders of magnitude more efficient than the benchmark Morris and Sobol approaches.

Evaluating virtual hosted desktops for graphics-intensive astronomy

NASA Astrophysics Data System (ADS)

Meade, B. F.; Fluke, C. J.

2018-04-01

Visualisation of data is critical to understanding astronomical phenomena. Today, many instruments produce datasets that are too big to be downloaded to a local computer, yet many of the visualisation tools used by astronomers are deployed only on desktop computers. Cloud computing is increasingly used to provide a computation and simulation platform in astronomy, but it also offers great potential as a visualisation platform. Virtual hosted desktops, with graphics processing unit (GPU) acceleration, allow interactive, graphics-intensive desktop applications to operate co-located with astronomy datasets stored in remote data centres. By combining benchmarking and user experience testing, with a cohort of 20 astronomers, we investigate the viability of replacing physical desktop computers with virtual hosted desktops. In our work, we compare two Apple MacBook computers (one old and one new, representing hardware and opposite ends of the useful lifetime) with two virtual hosted desktops: one commercial (Amazon Web Services) and one in a private research cloud (the Australian NeCTAR Research Cloud). For two-dimensional image-based tasks and graphics-intensive three-dimensional operations - typical of astronomy visualisation workflows - we found that benchmarks do not necessarily provide the best indication of performance. When compared to typical laptop computers, virtual hosted desktops can provide a better user experience, even with lower performing graphics cards. We also found that virtual hosted desktops are equally simple to use, provide greater flexibility in choice of configuration, and may actually be a more cost-effective option for typical usage profiles.

SP2Bench: A SPARQL Performance Benchmark

NASA Astrophysics Data System (ADS)

Schmidt, Michael; Hornung, Thomas; Meier, Michael; Pinkel, Christoph; Lausen, Georg

A meaningful analysis and comparison of both existing storage schemes for RDF data and evaluation approaches for SPARQL queries necessitates a comprehensive and universal benchmark platform. We present SP2Bench, a publicly available, language-specific performance benchmark for the SPARQL query language. SP2Bench is settled in the DBLP scenario and comprises a data generator for creating arbitrarily large DBLP-like documents and a set of carefully designed benchmark queries. The generated documents mirror vital key characteristics and social-world distributions encountered in the original DBLP data set, while the queries implement meaningful requests on top of this data, covering a variety of SPARQL operator constellations and RDF access patterns. In this chapter, we discuss requirements and desiderata for SPARQL benchmarks and present the SP2Bench framework, including its data generator, benchmark queries and performance metrics.

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.

Analytical theory of coherent synchrotron radiation wakefield of short bunches shielded by conducting parallel plates

NASA Astrophysics Data System (ADS)

Stupakov, Gennady; Zhou, Demin

2016-04-01

We develop a general model of coherent synchrotron radiation (CSR) impedance with shielding provided by two parallel conducting plates. This model allows us to easily reproduce all previously known analytical CSR wakes and to expand the analysis to situations not explored before. It reduces calculations of the impedance to taking integrals along the trajectory of the beam. New analytical results are derived for the radiation impedance with shielding for the following orbits: a kink, a bending magnet, a wiggler of finite length, and an infinitely long wiggler. All our formulas are benchmarked against numerical simulations with the CSRZ computer code.

Analytical theory of coherent synchrotron radiation wakefield of short bunches shielded by conducting parallel plates

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

Stupakov, Gennady; Zhou, Demin

2016-04-21

We develop a general model of coherent synchrotron radiation (CSR) impedance with shielding provided by two parallel conducting plates. This model allows us to easily reproduce all previously known analytical CSR wakes and to expand the analysis to situations not explored before. It reduces calculations of the impedance to taking integrals along the trajectory of the beam. New analytical results are derived for the radiation impedance with shielding for the following orbits: a kink, a bending magnet, a wiggler of finite length, and an infinitely long wiggler. All our formulas are benchmarked against numerical simulations with the CSRZ computer code.

SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes.

PubMed

Pruesse, Elmar; Peplies, Jörg; Glöckner, Frank Oliver

2012-07-15

In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck. This is especially troublesome for marker genes like the ribosomal RNA (rRNA) where already millions of sequences are publicly available and individual studies can easily produce hundreds of thousands of new sequences. Methods have been developed to cope with such numbers, but further improvements are needed to meet accuracy requirements. In this study, we present the SILVA Incremental Aligner (SINA) used to align the rRNA gene databases provided by the SILVA ribosomal RNA project. SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands. SINA was evaluated in comparison with the commonly used high throughput MSA programs PyNAST and mothur. The three BRAliBase III benchmark MSAs could be reproduced with 99.3, 97.6 and 96.1 accuracy. A larger benchmark MSA comprising 38 772 sequences could be reproduced with 98.9 and 99.3% accuracy using reference MSAs comprising 1000 and 5000 sequences. SINA was able to achieve higher accuracy than PyNAST and mothur in all performed benchmarks. Alignment of up to 500 sequences using the latest SILVA SSU/LSU Ref datasets as reference MSA is offered at http://www.arb-silva.de/aligner. This page also links to Linux binaries, user manual and tutorial. SINA is made available under a personal use license.

Preliminary Computational Analysis of the (HIRENASD) Configuration in Preparation for the Aeroelastic Prediction Workshop

NASA Technical Reports Server (NTRS)

Chwalowski, Pawel; Florance, Jennifer P.; Heeg, Jennifer; Wieseman, Carol D.; Perry, Boyd P.

2011-01-01

This paper presents preliminary computational aeroelastic analysis results generated in preparation for the first Aeroelastic Prediction Workshop (AePW). These results were produced using FUN3D software developed at NASA Langley and are compared against the experimental data generated during the HIgh REynolds Number Aero- Structural Dynamics (HIRENASD) Project. The HIRENASD wind-tunnel model was tested in the European Transonic Windtunnel in 2006 by Aachen University0s Department of Mechanics with funding from the German Research Foundation. The computational effort discussed here was performed (1) to obtain a preliminary assessment of the ability of the FUN3D code to accurately compute physical quantities experimentally measured on the HIRENASD model and (2) to translate the lessons learned from the FUN3D analysis of HIRENASD into a set of initial guidelines for the first AePW, which includes test cases for the HIRENASD model and its experimental data set. This paper compares the computational and experimental results obtained at Mach 0.8 for a Reynolds number of 7 million based on chord, corresponding to the HIRENASD test conditions No. 132 and No. 159. Aerodynamic loads and static aeroelastic displacements are compared at two levels of the grid resolution. Harmonic perturbation numerical results are compared with the experimental data using the magnitude and phase relationship between pressure coefficients and displacement. A dynamic aeroelastic numerical calculation is presented at one wind-tunnel condition in the form of the time history of the generalized displacements. Additional FUN3D validation results are also presented for the AGARD 445.6 wing data set. This wing was tested in the Transonic Dynamics Tunnel and is commonly used in the preliminary benchmarking of computational aeroelastic software.

Benchmarking Deep Learning Models on Large Healthcare Datasets.

PubMed

Purushotham, Sanjay; Meng, Chuizheng; Che, Zhengping; Liu, Yan

2018-06-04

Deep learning models (aka Deep Neural Networks) have revolutionized many fields including computer vision, natural language processing, speech recognition, and is being increasingly used in clinical healthcare applications. However, few works exist which have benchmarked the performance of the deep learning models with respect to the state-of-the-art machine learning models and prognostic scoring systems on publicly available healthcare datasets. In this paper, we present the benchmarking results for several clinical prediction tasks such as mortality prediction, length of stay prediction, and ICD-9 code group prediction using Deep Learning models, ensemble of machine learning models (Super Learner algorithm), SAPS II and SOFA scores. We used the Medical Information Mart for Intensive Care III (MIMIC-III) (v1.4) publicly available dataset, which includes all patients admitted to an ICU at the Beth Israel Deaconess Medical Center from 2001 to 2012, for the benchmarking tasks. Our results show that deep learning models consistently outperform all the other approaches especially when the 'raw' clinical time series data is used as input features to the models. Copyright © 2018 Elsevier Inc. All rights reserved.

Accelerating progress in Artificial General Intelligence: Choosing a benchmark for natural world interaction

NASA Astrophysics Data System (ADS)

Rohrer, Brandon

2010-12-01

Measuring progress in the field of Artificial General Intelligence (AGI) can be difficult without commonly accepted methods of evaluation. An AGI benchmark would allow evaluation and comparison of the many computational intelligence algorithms that have been developed. In this paper I propose that a benchmark for natural world interaction would possess seven key characteristics: fitness, breadth, specificity, low cost, simplicity, range, and task focus. I also outline two benchmark examples that meet most of these criteria. In the first, the direction task, a human coach directs a machine to perform a novel task in an unfamiliar environment. The direction task is extremely broad, but may be idealistic. In the second, the AGI battery, AGI candidates are evaluated based on their performance on a collection of more specific tasks. The AGI battery is designed to be appropriate to the capabilities of currently existing systems. Both the direction task and the AGI battery would require further definition before implementing. The paper concludes with a description of a task that might be included in the AGI battery: the search and retrieve task.

A review of the current state-of-the-art methodology for handling bias and uncertainty in performing criticality safety evaluations. Final report

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

Disney, R.K.

1994-10-01

The methodology for handling bias and uncertainty when calculational methods are used in criticality safety evaluations (CSE`s) is a rapidly evolving technology. The changes in the methodology are driven by a number of factors. One factor responsible for changes in the methodology for handling bias and uncertainty in CSE`s within the overview of the US Department of Energy (DOE) is a shift in the overview function from a ``site`` perception to a more uniform or ``national`` perception. Other causes for change or improvement in the methodology for handling calculational bias and uncertainty are; (1) an increased demand for benchmark criticalsmore » data to expand the area (range) of applicability of existing data, (2) a demand for new data to supplement existing benchmark criticals data, (3) the increased reliance on (or need for) computational benchmarks which supplement (or replace) experimental measurements in critical assemblies, and (4) an increased demand for benchmark data applicable to the expanded range of conditions and configurations encountered in DOE site restoration and remediation.« less

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

PredictSNP: Robust and Accurate Consensus Classifier for Prediction of Disease-Related Mutations

PubMed Central

Bendl, Jaroslav; Stourac, Jan; Salanda, Ondrej; Pavelka, Antonin; Wieben, Eric D.; Zendulka, Jaroslav; Brezovsky, Jan; Damborsky, Jiri

2014-01-01

Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp. PMID:24453961

Benchmark study for total enery electrons in thick slabs

NASA Technical Reports Server (NTRS)

Jun, I.

2002-01-01

The total energy deposition profiles when highenergy electrons impinge on a thick slab of elemental aluminum, copper, and tungsten have been computed using representative Monte Carlo codes (NOVICE, TIGER, MCNP), and compared in this paper.

Performance and scalability evaluation of "Big Memory" on Blue Gene Linux.

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

Yoshii, K.; Iskra, K.; Naik, H.

2011-05-01

We address memory performance issues observed in Blue Gene Linux and discuss the design and implementation of 'Big Memory' - an alternative, transparent memory space introduced to eliminate the memory performance issues. We evaluate the performance of Big Memory using custom memory benchmarks, NAS Parallel Benchmarks, and the Parallel Ocean Program, at a scale of up to 4,096 nodes. We find that Big Memory successfully resolves the performance issues normally encountered in Blue Gene Linux. For the ocean simulation program, we even find that Linux with Big Memory provides better scalability than does the lightweight compute node kernel designed solelymore » for high-performance applications. Originally intended exclusively for compute node tasks, our new memory subsystem dramatically improves the performance of certain I/O node applications as well. We demonstrate this performance using the central processor of the LOw Frequency ARray radio telescope as an example.« less

Accelerating execution of the integrated TIGER series Monte Carlo radiation transport codes

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

Smith, L.M.; Hochstedler, R.D.

1997-02-01

Execution of the integrated TIGER series (ITS) of coupled electron/photon Monte Carlo radiation transport codes has been accelerated by modifying the FORTRAN source code for more efficient computation. Each member code of ITS was benchmarked and profiled with a specific test case that directed the acceleration effort toward the most computationally intensive subroutines. Techniques for accelerating these subroutines included replacing linear search algorithms with binary versions, replacing the pseudo-random number generator, reducing program memory allocation, and proofing the input files for geometrical redundancies. All techniques produced identical or statistically similar results to the original code. Final benchmark timing of themore » accelerated code resulted in speed-up factors of 2.00 for TIGER (the one-dimensional slab geometry code), 1.74 for CYLTRAN (the two-dimensional cylindrical geometry code), and 1.90 for ACCEPT (the arbitrary three-dimensional geometry code).« less

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.

Exploring Infiniband Hardware Virtualization in OpenNebula towards Efficient High-Performance Computing

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

Pais Pitta de Lacerda Ruivo, Tiago; Bernabeu Altayo, Gerard; Garzoglio, Gabriele

2014-11-11

has been widely accepted that software virtualization has a big negative impact on high-performance computing (HPC) application performance. This work explores the potential use of Infiniband hardware virtualization in an OpenNebula cloud towards the efficient support of MPI-based workloads. We have implemented, deployed, and tested an Infiniband network on the FermiCloud private Infrastructure-as-a-Service (IaaS) cloud. To avoid software virtualization towards minimizing the virtualization overhead, we employed a technique called Single Root Input/Output Virtualization (SRIOV). Our solution spanned modifications to the Linux’s Hypervisor as well as the OpenNebula manager. We evaluated the performance of the hardware virtualization on up to 56more » virtual machines connected by up to 8 DDR Infiniband network links, with micro-benchmarks (latency and bandwidth) as well as w a MPI-intensive application (the HPL Linpack benchmark).« less

Benchmarks for time-domain simulation of sound propagation in soft-walled airways: Steady configurations

PubMed Central

Titze, Ingo R.; Palaparthi, Anil; Smith, Simeon L.

2014-01-01

Time-domain computer simulation of sound production in airways is a widely used tool, both for research and synthetic speech production technology. Speed of computation is generally the rationale for one-dimensional approaches to sound propagation and radiation. Transmission line and wave-reflection (scattering) algorithms are used to produce formant frequencies and bandwidths for arbitrarily shaped airways. Some benchmark graphs and tables are provided for formant frequencies and bandwidth calculations based on specific mathematical terms in the one-dimensional Navier–Stokes equation. Some rules are provided here for temporal and spatial discretization in terms of desired accuracy and stability of the solution. Kinetic losses, which have been difficult to quantify in frequency-domain simulations, are quantified here on the basis of the measurements of Scherer, Torkaman, Kucinschi, and Afjeh [(2010). J. Acoust. Soc. Am. 128(2), 828–838]. PMID:25480071

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.

Neutron Deep Penetration Calculations in Light Water with Monte Carlo TRIPOLI-4® Variance Reduction Techniques

NASA Astrophysics Data System (ADS)

Lee, Yi-Kang

2017-09-01

Nuclear decommissioning takes place in several stages due to the radioactivity in the reactor structure materials. A good estimation of the neutron activation products distributed in the reactor structure materials impacts obviously on the decommissioning planning and the low-level radioactive waste management. Continuous energy Monte-Carlo radiation transport code TRIPOLI-4 has been applied on radiation protection and shielding analyses. To enhance the TRIPOLI-4 application in nuclear decommissioning activities, both experimental and computational benchmarks are being performed. To calculate the neutron activation of the shielding and structure materials of nuclear facilities, the knowledge of 3D neutron flux map and energy spectra must be first investigated. To perform this type of neutron deep penetration calculations with the Monte Carlo transport code, variance reduction techniques are necessary in order to reduce the uncertainty of the neutron activation estimation. In this study, variance reduction options of the TRIPOLI-4 code were used on the NAIADE 1 light water shielding benchmark. This benchmark document is available from the OECD/NEA SINBAD shielding benchmark database. From this benchmark database, a simplified NAIADE 1 water shielding model was first proposed in this work in order to make the code validation easier. Determination of the fission neutron transport was performed in light water for penetration up to 50 cm for fast neutrons and up to about 180 cm for thermal neutrons. Measurement and calculation results were benchmarked. Variance reduction options and their performance were discussed and compared.

Visual Attention Modeling for Stereoscopic Video: A Benchmark and Computational Model.

PubMed

Fang, Yuming; Zhang, Chi; Li, Jing; Lei, Jianjun; Perreira Da Silva, Matthieu; Le Callet, Patrick

2017-10-01

In this paper, we investigate the visual attention modeling for stereoscopic video from the following two aspects. First, we build one large-scale eye tracking database as the benchmark of visual attention modeling for stereoscopic video. The database includes 47 video sequences and their corresponding eye fixation data. Second, we propose a novel computational model of visual attention for stereoscopic video based on Gestalt theory. In the proposed model, we extract the low-level features, including luminance, color, texture, and depth, from discrete cosine transform coefficients, which are used to calculate feature contrast for the spatial saliency computation. The temporal saliency is calculated by the motion contrast from the planar and depth motion features in the stereoscopic video sequences. The final saliency is estimated by fusing the spatial and temporal saliency with uncertainty weighting, which is estimated by the laws of proximity, continuity, and common fate in Gestalt theory. Experimental results show that the proposed method outperforms the state-of-the-art stereoscopic video saliency detection models on our built large-scale eye tracking database and one other database (DML-ITRACK-3D).

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.

Benchmarking the GW Approximation and Bethe–Salpeter Equation for Groups IB and IIB Atoms and Monoxides

DOE PAGES

Hung, Linda; Bruneval, Fabien; Baishya, Kopinjol; ...

2017-04-07

Energies from the GW approximation and the Bethe–Salpeter equation (BSE) are benchmarked against the excitation energies of transition-metal (Cu, Zn, Ag, and Cd) single atoms and monoxide anions. We demonstrate that best estimates of GW quasiparticle energies at the complete basis set limit should be obtained via extrapolation or closure relations, while numerically converged GW-BSE eigenvalues can be obtained on a finite basis set. Calculations using real-space wave functions and pseudopotentials are shown to give best-estimate GW energies that agree (up to the extrapolation error) with calculations using all-electron Gaussian basis sets. We benchmark the effects of a vertex approximationmore » (ΓLDA) and the mean-field starting point in GW and the BSE, performing computations using a real-space, transition-space basis and scalar-relativistic pseudopotentials. Here, while no variant of GW improves on perturbative G0W0 at predicting ionization energies, G0W0Γ LDA-BSE computations give excellent agreement with experimental absorption spectra as long as off-diagonal self-energy terms are included. We also present G0W0 quasiparticle energies for the CuO –, ZnO –, AgO –, and CdO – anions, in comparison to available anion photoelectron spectra.« less

The application of a Web-geographic information system for improving urban water cycle modelling.

PubMed

Mair, M; Mikovits, C; Sengthaler, M; Schöpf, M; Kinzel, H; Urich, C; Kleidorfer, M; Sitzenfrei, R; Rauch, W

2014-01-01

Research in urban water management has experienced a transition from traditional model applications to modelling water cycles as an integrated part of urban areas. This includes the interlinking of models of many research areas (e.g. urban development, socio-economy, urban water management). The integration and simulation is realized in newly developed frameworks (e.g. DynaMind and OpenMI) and often assumes a high knowledge in programming. This work presents a Web based urban water management modelling platform which simplifies the setup and usage of complex integrated models. The platform is demonstrated with a small application example on a case study within the Alpine region. The used model is a DynaMind model benchmarking the impact of newly connected catchments on the flooding behaviour of an existing combined sewer system. As a result the workflow of the user within a Web browser is demonstrated and benchmark results are shown. The presented platform hides implementation specific aspects behind Web services based technologies such that the user can focus on his main aim, which is urban water management modelling and benchmarking. Moreover, this platform offers a centralized data management, automatic software updates and access to high performance computers accessible with desktop computers and mobile devices.

Benchmarking the GW Approximation and Bethe–Salpeter Equation for Groups IB and IIB Atoms and Monoxides

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

Hung, Linda; Bruneval, Fabien; Baishya, Kopinjol

Energies from the GW approximation and the Bethe–Salpeter equation (BSE) are benchmarked against the excitation energies of transition-metal (Cu, Zn, Ag, and Cd) single atoms and monoxide anions. We demonstrate that best estimates of GW quasiparticle energies at the complete basis set limit should be obtained via extrapolation or closure relations, while numerically converged GW-BSE eigenvalues can be obtained on a finite basis set. Calculations using real-space wave functions and pseudopotentials are shown to give best-estimate GW energies that agree (up to the extrapolation error) with calculations using all-electron Gaussian basis sets. We benchmark the effects of a vertex approximationmore » (ΓLDA) and the mean-field starting point in GW and the BSE, performing computations using a real-space, transition-space basis and scalar-relativistic pseudopotentials. Here, while no variant of GW improves on perturbative G0W0 at predicting ionization energies, G0W0Γ LDA-BSE computations give excellent agreement with experimental absorption spectra as long as off-diagonal self-energy terms are included. We also present G0W0 quasiparticle energies for the CuO –, ZnO –, AgO –, and CdO – anions, in comparison to available anion photoelectron spectra.« less

Benchmarking to improve the quality of cystic fibrosis care.

PubMed

Schechter, Michael S

2012-11-01

Benchmarking involves the ascertainment of healthcare programs with most favorable outcomes as a means to identify and spread effective strategies for delivery of care. The recent interest in the development of patient registries for patients with cystic fibrosis (CF) has been fueled in part by an interest in using them to facilitate benchmarking. This review summarizes reports of how benchmarking has been operationalized in attempts to improve CF care. Although certain goals of benchmarking can be accomplished with an exclusive focus on registry data analysis, benchmarking programs in Germany and the United States have supplemented these data analyses with exploratory interactions and discussions to better understand successful approaches to care and encourage their spread throughout the care network. Benchmarking allows the discovery and facilitates the spread of effective approaches to care. It provides a pragmatic alternative to traditional research methods such as randomized controlled trials, providing insights into methods that optimize delivery of care and allowing judgments about the relative effectiveness of different therapeutic approaches.

Developing Student Character through Disciplinary Curricula: An Analysis of UK QAA Subject Benchmark Statements

ERIC Educational Resources Information Center

Quinlan, Kathleen M.

2016-01-01

What aspects of student character are expected to be developed through disciplinary curricula? This paper examines the UK written curriculum through an analysis of the Quality Assurance Agency's subject benchmark statements for the most popular subjects studied in the UK. It explores the language, principles and intended outcomes that suggest…

A BENCHMARKING ANALYSIS FOR FIVE RADIONUCLIDE VADOSE ZONE MODELS (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, AND CHAIN 2D) IN SOIL SCREENING LEVEL CALCULATIONS

EPA Science Inventory

Five radionuclide vadose zone models with different degrees of complexity (CHAIN, MULTIMED_DP, FECTUZ, HYDRUS, and CHAIN 2D) were selected for use in soil screening level (SSL) calculations. A benchmarking analysis between the models was conducted for a radionuclide (99Tc) rele...

The use of National Weather Service Data to Compute the Dose to the MEOI.

PubMed

Vickers, Linda

2018-05-01

The Turner method is the "benchmark method" for computing the stability class that is used to compute the X/Q (s m). The Turner method should be used to ascertain the validity of X/Q results determined by other methods. This paper used site-specific meteorological data obtained from the National Weather Service. The Turner method described herein is simple, quick, accurate, and transparent because all of the data, calculations, and results are visible for verification and validation with published literature.

Linear Scaling Density Functional Calculations with Gaussian Orbitals

NASA Technical Reports Server (NTRS)

Scuseria, Gustavo E.

1999-01-01

Recent advances in linear scaling algorithms that circumvent the computational bottlenecks of large-scale electronic structure simulations make it possible to carry out density functional calculations with Gaussian orbitals on molecules containing more than 1000 atoms and 15000 basis functions using current workstations and personal computers. This paper discusses the recent theoretical developments that have led to these advances and demonstrates in a series of benchmark calculations the present capabilities of state-of-the-art computational quantum chemistry programs for the prediction of molecular structure and properties.

Graph wavelet alignment kernels for drug virtual screening.

PubMed

Smalter, Aaron; Huan, Jun; Lushington, Gerald

2009-06-01

In this paper, we introduce a novel statistical modeling technique for target property prediction, with applications to virtual screening and drug design. In our method, we use graphs to model chemical structures and apply a wavelet analysis of graphs to summarize features capturing graph local topology. We design a novel graph kernel function to utilize the topology features to build predictive models for chemicals via Support Vector Machine classifier. We call the new graph kernel a graph wavelet-alignment kernel. We have evaluated the efficacy of the wavelet-alignment kernel using a set of chemical structure-activity prediction benchmarks. Our results indicate that the use of the kernel function yields performance profiles comparable to, and sometimes exceeding that of the existing state-of-the-art chemical classification approaches. In addition, our results also show that the use of wavelet functions significantly decreases the computational costs for graph kernel computation with more than ten fold speedup.

3D Space Radiation Transport in a Shielded ICRU Tissue Sphere

NASA Technical Reports Server (NTRS)

Wilson, John W.; Slaba, Tony C.; Badavi, Francis F.; Reddell, Brandon D.; Bahadori, Amir A.

2014-01-01

A computationally efficient 3DHZETRN code capable of simulating High Charge (Z) and Energy (HZE) and light ions (including neutrons) under space-like boundary conditions with enhanced neutron and light ion propagation was recently developed for a simple homogeneous shield object. Monte Carlo benchmarks were used to verify the methodology in slab and spherical geometry, and the 3D corrections were shown to provide significant improvement over the straight-ahead approximation in some cases. In the present report, the new algorithms with well-defined convergence criteria are extended to inhomogeneous media within a shielded tissue slab and a shielded tissue sphere and tested against Monte Carlo simulation to verify the solution methods. The 3D corrections are again found to more accurately describe the neutron and light ion fluence spectra as compared to the straight-ahead approximation. These computationally efficient methods provide a basis for software capable of space shield analysis and optimization.

Accurate multiple sequence-structure alignment of RNA sequences using combinatorial optimization.

PubMed

Bauer, Markus; Klau, Gunnar W; Reinert, Knut

2007-07-27

The discovery of functional non-coding RNA sequences has led to an increasing interest in algorithms related to RNA analysis. Traditional sequence alignment algorithms, however, fail at computing reliable alignments of low-homology RNA sequences. The spatial conformation of RNA sequences largely determines their function, and therefore RNA alignment algorithms have to take structural information into account. We present a graph-based representation for sequence-structure alignments, which we model as an integer linear program (ILP). We sketch how we compute an optimal or near-optimal solution to the ILP using methods from combinatorial optimization, and present results on a recently published benchmark set for RNA alignments. The implementation of our algorithm yields better alignments in terms of two published scores than the other programs that we tested: This is especially the case with an increasing number of input sequences. Our program LARA is freely available for academic purposes from http://www.planet-lisa.net.

High resolution propagation-based imaging system for in vivo dynamic computed tomography of lungs in small animals

NASA Astrophysics Data System (ADS)

Preissner, M.; Murrie, R. P.; Pinar, I.; Werdiger, F.; Carnibella, R. P.; Zosky, G. R.; Fouras, A.; Dubsky, S.

2018-04-01

We have developed an x-ray imaging system for in vivo four-dimensional computed tomography (4DCT) of small animals for pre-clinical lung investigations. Our customized laboratory facility is capable of high resolution in vivo imaging at high frame rates. Characterization using phantoms demonstrate a spatial resolution of slightly below 50 μm at imaging rates of 30 Hz, and the ability to quantify material density differences of at least 3%. We benchmark our system against existing small animal pre-clinical CT scanners using a quality factor that combines spatial resolution, image noise, dose and scan time. In vivo 4DCT images obtained on our system demonstrate resolution of important features such as blood vessels and small airways, of which the smallest discernible were measured as 55–60 μm in cross section. Quantitative analysis of the images demonstrate regional differences in ventilation between injured and healthy lungs.

Benchmark of FDNS CFD Code For Direct Connect RBCC Test Data

NASA Technical Reports Server (NTRS)

Ruf, J. H.

2000-01-01

Computational Fluid Dynamics (CFD) analysis results are compared with experimental data from the Pennsylvania State University's (PSU) Propulsion Engineering Research Center (PERC) rocket based combined cycle (RBCC) rocket-ejector experiments. The PERC RBCC experimental hardware was in a direct-connect configuration in diffusion and afterburning (DAB) operation. The objective of the present work was to validate the Finite Difference Navier Stokes (FDNS) CFD code for the rocket-ejector mode internal fluid mechanics and combustion phenomena. A second objective was determine the best application procedures to use FDNS as a predictive/engineering tool. Three-dimensional CFD analysis was performed. Solution methodology and grid requirements are discussed. CFD results are compared to experimental data for static pressure, Raman Spectroscopy species distribution data and RBCC net thrust and specified impulse.

Benchmark Comparison of Dual- and Quad-Core Processor Linux Clusters with Two Global Climate Modeling Workloads

NASA Technical Reports Server (NTRS)

McGalliard, James

2008-01-01

This viewgraph presentation details the science and systems environments that NASA High End computing program serves. Included is a discussion of the workload that is involved in the processing for the Global Climate Modeling. The Goddard Earth Observing System Model, Version 5 (GEOS-5) is a system of models integrated using the Earth System Modeling Framework (ESMF). The GEOS-5 system was used for the Benchmark tests, and the results of the tests are shown and discussed. Tests were also run for the Cubed Sphere system, results for these test are also shown.

Results of the 2013 UT modeling benchmark obtained with models implemented in CIVA

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

Toullelan, Gwénaël; Raillon, Raphaële; Chatillon, Sylvain

The 2013 Ultrasonic Testing (UT) modeling benchmark concerns direct echoes from side drilled holes (SDH), flat bottom holes (FBH) and corner echoes from backwall breaking artificial notches inspected with a matrix phased array probe. This communication presents the results obtained with the models implemented in the CIVA software: the pencilmodel is used to compute the field radiated by the probe, the Kirchhoff approximation is applied to predict the response of FBH and notches and the SOV (Separation Of Variables) model is used for the SDH responses. The comparison between simulated and experimental results are presented and discussed.

Turbofan forced mixer-nozzle internal flowfield. Volume 1: A benchmark experimental study

NASA Technical Reports Server (NTRS)

Paterson, R. W.

1982-01-01

An experimental investigation of the flow field within a model turbofan forced mixer nozzle is described. Velocity and thermodynamic state variable data for use in assessing the accuracy and assisting the further development of computational procedures for predicting the flow field within mixer nozzles are provided. Velocity and temperature data suggested that the nozzle mixing process was dominated by circulations (secondary flows) of a length scale on the order the lobe dimensions which were associated with strong radial velocities observed near the lobe exit plane. The 'benchmark' model mixer experiment conducted for code assessment purposes is discussed.

Benchmarking quantitative label-free LC-MS data processing workflows using a complex spiked proteomic standard dataset.

PubMed

Ramus, Claire; Hovasse, Agnès; Marcellin, Marlène; Hesse, Anne-Marie; Mouton-Barbosa, Emmanuelle; Bouyssié, David; Vaca, Sebastian; Carapito, Christine; Chaoui, Karima; Bruley, Christophe; Garin, Jérôme; Cianférani, Sarah; Ferro, Myriam; Van Dorssaeler, Alain; Burlet-Schiltz, Odile; Schaeffer, Christine; Couté, Yohann; Gonzalez de Peredo, Anne

2016-01-30

Proteomic workflows based on nanoLC-MS/MS data-dependent-acquisition analysis have progressed tremendously in recent years. High-resolution and fast sequencing instruments have enabled the use of label-free quantitative methods, based either on spectral counting or on MS signal analysis, which appear as an attractive way to analyze differential protein expression in complex biological samples. However, the computational processing of the data for label-free quantification still remains a challenge. Here, we used a proteomic standard composed of an equimolar mixture of 48 human proteins (Sigma UPS1) spiked at different concentrations into a background of yeast cell lysate to benchmark several label-free quantitative workflows, involving different software packages developed in recent years. This experimental design allowed to finely assess their performances in terms of sensitivity and false discovery rate, by measuring the number of true and false-positive (respectively UPS1 or yeast background proteins found as differential). The spiked standard dataset has been deposited to the ProteomeXchange repository with the identifier PXD001819 and can be used to benchmark other label-free workflows, adjust software parameter settings, improve algorithms for extraction of the quantitative metrics from raw MS data, or evaluate downstream statistical methods. Bioinformatic pipelines for label-free quantitative analysis must be objectively evaluated in their ability to detect variant proteins with good sensitivity and low false discovery rate in large-scale proteomic studies. This can be done through the use of complex spiked samples, for which the "ground truth" of variant proteins is known, allowing a statistical evaluation of the performances of the data processing workflow. We provide here such a controlled standard dataset and used it to evaluate the performances of several label-free bioinformatics tools (including MaxQuant, Skyline, MFPaQ, IRMa-hEIDI and Scaffold) in different workflows, for detection of variant proteins with different absolute expression levels and fold change values. The dataset presented here can be useful for tuning software tool parameters, and also testing new algorithms for label-free quantitative analysis, or for evaluation of downstream statistical methods. Copyright © 2015 Elsevier B.V. All rights reserved.

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

Benchmarking computational fluid dynamics models of lava flow simulation for hazard assessment, forecasting, and risk management

USGS Publications Warehouse

Dietterich, Hannah; Lev, Einat; Chen, Jiangzhi; Richardson, Jacob A.; Cashman, Katharine V.

2017-01-01

Numerical simulations of lava flow emplacement are valuable for assessing lava flow hazards, forecasting active flows, designing flow mitigation measures, interpreting past eruptions, and understanding the controls on lava flow behavior. Existing lava flow models vary in simplifying assumptions, physics, dimensionality, and the degree to which they have been validated against analytical solutions, experiments, and natural observations. In order to assess existing models and guide the development of new codes, we conduct a benchmarking study of computational fluid dynamics (CFD) models for lava flow emplacement, including VolcFlow, OpenFOAM, FLOW-3D, COMSOL, and MOLASSES. We model viscous, cooling, and solidifying flows over horizontal planes, sloping surfaces, and into topographic obstacles. We compare model results to physical observations made during well-controlled analogue and molten basalt experiments, and to analytical theory when available. Overall, the models accurately simulate viscous flow with some variability in flow thickness where flows intersect obstacles. OpenFOAM, COMSOL, and FLOW-3D can each reproduce experimental measurements of cooling viscous flows, and OpenFOAM and FLOW-3D simulations with temperature-dependent rheology match results from molten basalt experiments. We assess the goodness-of-fit of the simulation results and the computational cost. Our results guide the selection of numerical simulation codes for different applications, including inferring emplacement conditions of past lava flows, modeling the temporal evolution of ongoing flows during eruption, and probabilistic assessment of lava flow hazard prior to eruption. Finally, we outline potential experiments and desired key observational data from future flows that would extend existing benchmarking data sets.

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.

Benchmarking expert system tools

NASA Technical Reports Server (NTRS)

Riley, Gary

1988-01-01

As part of its evaluation of new technologies, the Artificial Intelligence Section of the Mission Planning and Analysis Div. at NASA-Johnson has made timing tests of several expert system building tools. Among the production systems tested were Automated Reasoning Tool, several versions of OPS5, and CLIPS (C Language Integrated Production System), an expert system builder developed by the AI section. Also included in the test were a Zetalisp version of the benchmark along with four versions of the benchmark written in Knowledge Engineering Environment, an object oriented, frame based expert system tool. The benchmarks used for testing are studied.

Generating Shifting Workloads to Benchmark Adaptability in Relational Database Systems

NASA Astrophysics Data System (ADS)

Rabl, Tilmann; Lang, Andreas; Hackl, Thomas; Sick, Bernhard; Kosch, Harald

A large body of research concerns the adaptability of database systems. Many commercial systems already contain autonomic processes that adapt configurations as well as data structures and data organization. Yet there is virtually no possibility for a just measurement of the quality of such optimizations. While standard benchmarks have been developed that simulate real-world database applications very precisely, none of them considers variations in workloads produced by human factors. Today’s benchmarks test the performance of database systems by measuring peak performance on homogeneous request streams. Nevertheless, in systems with user interaction access patterns are constantly shifting. We present a benchmark that simulates a web information system with interaction of large user groups. It is based on the analysis of a real online eLearning management system with 15,000 users. The benchmark considers the temporal dependency of user interaction. Main focus is to measure the adaptability of a database management system according to shifting workloads. We will give details on our design approach that uses sophisticated pattern analysis and data mining techniques.

A new numerical benchmark of a freshwater lens

NASA Astrophysics Data System (ADS)

Stoeckl, L.; Walther, M.; Graf, T.

2016-04-01

A numerical benchmark for 2-D variable-density flow and solute transport in a freshwater lens is presented. The benchmark is based on results of laboratory experiments conducted by Stoeckl and Houben (2012) using a sand tank on the meter scale. This benchmark describes the formation and degradation of a freshwater lens over time as it can be found under real-world islands. An error analysis gave the appropriate spatial and temporal discretization of 1 mm and 8.64 s, respectively. The calibrated parameter set was obtained using the parameter estimation tool PEST. Comparing density-coupled and density-uncoupled results showed that the freshwater-saltwater interface position is strongly dependent on density differences. A benchmark that adequately represents saltwater intrusion and that includes realistic features of coastal aquifers or freshwater lenses was lacking. This new benchmark was thus developed and is demonstrated to be suitable to test variable-density groundwater models applied to saltwater intrusion investigations.

Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization.

PubMed

Jia, Zhilong; Zhang, Xiang; Guan, Naiyang; Bo, Xiaochen; Barnes, Michael R; Luo, Zhigang

2015-01-01

RNA-sequencing is rapidly becoming the method of choice for studying the full complexity of transcriptomes, however with increasing dimensionality, accurate gene ranking is becoming increasingly challenging. This paper proposes an accurate and sensitive gene ranking method that implements discriminant non-negative matrix factorization (DNMF) for RNA-seq data. To the best of our knowledge, this is the first work to explore the utility of DNMF for gene ranking. When incorporating Fisher's discriminant criteria and setting the reduced dimension as two, DNMF learns two factors to approximate the original gene expression data, abstracting the up-regulated or down-regulated metagene by using the sample label information. The first factor denotes all the genes' weights of two metagenes as the additive combination of all genes, while the second learned factor represents the expression values of two metagenes. In the gene ranking stage, all the genes are ranked as a descending sequence according to the differential values of the metagene weights. Leveraging the nature of NMF and Fisher's criterion, DNMF can robustly boost the gene ranking performance. The Area Under the Curve analysis of differential expression analysis on two benchmarking tests of four RNA-seq data sets with similar phenotypes showed that our proposed DNMF-based gene ranking method outperforms other widely used methods. Moreover, the Gene Set Enrichment Analysis also showed DNMF outweighs others. DNMF is also computationally efficient, substantially outperforming all other benchmarked methods. Consequently, we suggest DNMF is an effective method for the analysis of differential gene expression and gene ranking for RNA-seq data.

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.

NACA0012 benchmark model experimental flutter results with unsteady pressure distributions

NASA Technical Reports Server (NTRS)

Rivera, Jose A., Jr.; Dansberry, Bryan E.; Bennett, Robert M.; Durham, Michael H.; Silva, Walter A.

1992-01-01

The Structural Dynamics Division at NASA Langley Research Center has started a wind tunnel activity referred to as the Benchmark Models Program. The primary objective of this program is to acquire measured dynamic instability and corresponding pressure data that will be useful for developing and evaluating aeroelastic type computational fluid dynamics codes currently in use or under development. The program is a multi-year activity that will involve testing of several different models to investigate various aeroelastic phenomena. This paper describes results obtained from a second wind tunnel test of the first model in the Benchmark Models Program. This first model consisted of a rigid semispan wing having a rectangular planform and a NACA 0012 airfoil shape which was mounted on a flexible two degree of freedom mount system. Experimental flutter boundaries and corresponding unsteady pressure distribution data acquired over two model chords located at the 60 and 95 percent span stations are presented.

Development of a CFD Code for Analysis of Fluid Dynamic Forces in Seals

NASA Technical Reports Server (NTRS)

Athavale, Mahesh M.; Przekwas, Andrzej J.; Singhal, Ashok K.

1991-01-01

The aim is to develop a 3-D computational fluid dynamics (CFD) code for the analysis of fluid flow in cylindrical seals and evaluation of the dynamic forces on the seals. This code is expected to serve as a scientific tool for detailed flow analysis as well as a check for the accuracy of the 2D industrial codes. The features necessary in the CFD code are outlined. The initial focus was to develop or modify and implement new techniques and physical models. These include collocated grid formulation, rotating coordinate frames and moving grid formulation. Other advanced numerical techniques include higher order spatial and temporal differencing and an efficient linear equation solver. These techniques were implemented in a 2D flow solver for initial testing. Several benchmark test cases were computed using the 2D code, and the results of these were compared to analytical solutions or experimental data to check the accuracy. Tests presented here include planar wedge flow, flow due to an enclosed rotor, and flow in a 2D seal with a whirling rotor. Comparisons between numerical and experimental results for an annular seal and a 7-cavity labyrinth seal are also included.

Computational scalability of large size image dissemination

NASA Astrophysics Data System (ADS)

Kooper, Rob; Bajcsy, Peter

2011-01-01

We have investigated the computational scalability of image pyramid building needed for dissemination of very large image data. The sources of large images include high resolution microscopes and telescopes, remote sensing and airborne imaging, and high resolution scanners. The term 'large' is understood from a user perspective which means either larger than a display size or larger than a memory/disk to hold the image data. The application drivers for our work are digitization projects such as the Lincoln Papers project (each image scan is about 100-150MB or about 5000x8000 pixels with the total number to be around 200,000) and the UIUC library scanning project for historical maps from 17th and 18th century (smaller number but larger images). The goal of our work is understand computational scalability of the web-based dissemination using image pyramids for these large image scans, as well as the preservation aspects of the data. We report our computational benchmarks for (a) building image pyramids to be disseminated using the Microsoft Seadragon library, (b) a computation execution approach using hyper-threading to generate image pyramids and to utilize the underlying hardware, and (c) an image pyramid preservation approach using various hard drive configurations of Redundant Array of Independent Disks (RAID) drives for input/output operations. The benchmarks are obtained with a map (334.61 MB, JPEG format, 17591x15014 pixels). The discussion combines the speed and preservation objectives.

International benchmarking of longitudinal train dynamics simulators: results

NASA Astrophysics Data System (ADS)

Wu, Qing; Spiryagin, Maksym; Cole, Colin; Chang, Chongyi; Guo, Gang; Sakalo, Alexey; Wei, Wei; Zhao, Xubao; Burgelman, Nico; Wiersma, Pier; Chollet, Hugues; Sebes, Michel; Shamdani, Amir; Melzi, Stefano; Cheli, Federico; di Gialleonardo, Egidio; Bosso, Nicola; Zampieri, Nicolò; Luo, Shihui; Wu, Honghua; Kaza, Guy-Léon

2018-03-01

This paper presents the results of the International Benchmarking of Longitudinal Train Dynamics Simulators which involved participation of nine simulators (TABLDSS, UM, CRE-LTS, TDEAS, PoliTo, TsDyn, CARS, BODYSIM and VOCO) from six countries. Longitudinal train dynamics results and computing time of four simulation cases are presented and compared. The results show that all simulators had basic agreement in simulations of locomotive forces, resistance forces and track gradients. The major differences among different simulators lie in the draft gear models. TABLDSS, UM, CRE-LTS, TDEAS, TsDyn and CARS had general agreement in terms of the in-train forces; minor differences exist as reflections of draft gear model variations. In-train force oscillations were observed in VOCO due to the introduction of wheel-rail contact. In-train force instabilities were sometimes observed in PoliTo and BODYSIM due to the velocity controlled transitional characteristics which could have generated unreasonable transitional stiffness. Regarding computing time per train operational second, the following list is in order of increasing computing speed: VOCO, TsDyn, PoliTO, CARS, BODYSIM, UM, TDEAS, CRE-LTS and TABLDSS (fastest); all simulators except VOCO, TsDyn and PoliTo achieved faster speeds than real-time simulations. Similarly, regarding computing time per integration step, the computing speeds in order are: CRE-LTS, VOCO, CARS, TsDyn, UM, TABLDSS and TDEAS (fastest).

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.

Feature Augmentation via Nonparametrics and Selection (FANS) in High-Dimensional Classification.

PubMed

Fan, Jianqing; Feng, Yang; Jiang, Jiancheng; Tong, Xin

We propose a high dimensional classification method that involves nonparametric feature augmentation. Knowing that marginal density ratios are the most powerful univariate classifiers, we use the ratio estimates to transform the original feature measurements. Subsequently, penalized logistic regression is invoked, taking as input the newly transformed or augmented features. This procedure trains models equipped with local complexity and global simplicity, thereby avoiding the curse of dimensionality while creating a flexible nonlinear decision boundary. The resulting method is called Feature Augmentation via Nonparametrics and Selection (FANS). We motivate FANS by generalizing the Naive Bayes model, writing the log ratio of joint densities as a linear combination of those of marginal densities. It is related to generalized additive models, but has better interpretability and computability. Risk bounds are developed for FANS. In numerical analysis, FANS is compared with competing methods, so as to provide a guideline on its best application domain. Real data analysis demonstrates that FANS performs very competitively on benchmark email spam and gene expression data sets. Moreover, FANS is implemented by an extremely fast algorithm through parallel computing.

Feature Augmentation via Nonparametrics and Selection (FANS) in High-Dimensional Classification

PubMed Central

Feng, Yang; Jiang, Jiancheng; Tong, Xin

2015-01-01

We propose a high dimensional classification method that involves nonparametric feature augmentation. Knowing that marginal density ratios are the most powerful univariate classifiers, we use the ratio estimates to transform the original feature measurements. Subsequently, penalized logistic regression is invoked, taking as input the newly transformed or augmented features. This procedure trains models equipped with local complexity and global simplicity, thereby avoiding the curse of dimensionality while creating a flexible nonlinear decision boundary. The resulting method is called Feature Augmentation via Nonparametrics and Selection (FANS). We motivate FANS by generalizing the Naive Bayes model, writing the log ratio of joint densities as a linear combination of those of marginal densities. It is related to generalized additive models, but has better interpretability and computability. Risk bounds are developed for FANS. In numerical analysis, FANS is compared with competing methods, so as to provide a guideline on its best application domain. Real data analysis demonstrates that FANS performs very competitively on benchmark email spam and gene expression data sets. Moreover, FANS is implemented by an extremely fast algorithm through parallel computing. PMID:27185970

The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code.

PubMed

Kunkel, Susanne; Schenck, Wolfram

2017-01-01

NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling.

The NEST Dry-Run Mode: Efficient Dynamic Analysis of Neuronal Network Simulation Code

PubMed Central

Kunkel, Susanne; Schenck, Wolfram

2017-01-01

NEST is a simulator for spiking neuronal networks that commits to a general purpose approach: It allows for high flexibility in the design of network models, and its applications range from small-scale simulations on laptops to brain-scale simulations on supercomputers. Hence, developers need to test their code for various use cases and ensure that changes to code do not impair scalability. However, running a full set of benchmarks on a supercomputer takes up precious compute-time resources and can entail long queuing times. Here, we present the NEST dry-run mode, which enables comprehensive dynamic code analysis without requiring access to high-performance computing facilities. A dry-run simulation is carried out by a single process, which performs all simulation steps except communication as if it was part of a parallel environment with many processes. We show that measurements of memory usage and runtime of neuronal network simulations closely match the corresponding dry-run data. Furthermore, we demonstrate the successful application of the dry-run mode in the areas of profiling and performance modeling. PMID:28701946

Approximation of traveling wave solutions in wall-bounded flows using resolvent modes

NASA Astrophysics Data System (ADS)

McKeon, Beverley; Graham, Michael; Moarref, Rashad; Park, Jae Sung; Sharma, Ati; Willis, Ashley

2014-11-01

Significant recent attention has been devoted to computing and understanding exact traveling wave solutions of the Navier-Stokes equations. These solutions can be interpreted as the state-space skeleton of turbulence and are attractive benchmarks for studying low-order models of wall turbulence. Here, we project such solutions onto the velocity response (or resolvent) modes supplied by the gain-based resolvent analysis outlined by McKeon & Sharma (JFM, 2010). We demonstrate that in both pipe (Pringle et al., Phil. Trans. R. Soc. A, 2009) and channel (Waleffe, JFM, 2001) flows, the solutions can be well-described by a small number of resolvent modes. Analysis of the nonlinear forcing modes sustaining these solutions reveals the importance of small amplitude forcing, consistent with the large amplifications admitted by the resolvent operator. We investigate the use of resolvent modes as computationally cheap ``seeds'' for the identification of further traveling wave solutions. The support of AFOSR under Grants FA9550-09-1-0701, FA9550-12-1-0469, FA9550-11-1-0094 and FA9550-14-1-0042 (program managers Rengasamy Ponnappan, Doug Smith and Gregg Abate) is gratefully acknowledged.

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

Experimental and computational surface and flow-field results for an all-body hypersonic aircraft

NASA Technical Reports Server (NTRS)

Lockman, William K.; Lawrence, Scott L.; Cleary, Joseph W.

1990-01-01

The objective of the present investigation is to establish a benchmark experimental data base for a generic hypersonic vehicle shape for validation and/or calibration of advanced computational fluid dynamics computer codes. This paper includes results from the comprehensive test program conducted in the NASA/Ames 3.5-foot Hypersonic Wind Tunnel for a generic all-body hypersonic aircraft model. Experimental and computational results on flow visualization, surface pressures, surface convective heat transfer, and pitot-pressure flow-field surveys are presented. Comparisons of the experimental results with computational results from an upwind parabolized Navier-Stokes code developed at Ames demonstrate the capabilities of this code.

Implementation of ADI: Schemes on MIMD parallel computers

NASA Technical Reports Server (NTRS)

Vanderwijngaart, Rob F.

1993-01-01

In order to simulate the effects of the impingement of hot exhaust jets of High Performance Aircraft on landing surfaces a multi-disciplinary computation coupling flow dynamics to heat conduction in the runway needs to be carried out. Such simulations, which are essentially unsteady, require very large computational power in order to be completed within a reasonable time frame of the order of an hour. Such power can be furnished by the latest generation of massively parallel computers. These remove the bottleneck of ever more congested data paths to one or a few highly specialized central processing units (CPU's) by having many off-the-shelf CPU's work independently on their own data, and exchange information only when needed. During the past year the first phase of this project was completed, in which the optimal strategy for mapping an ADI-algorithm for the three dimensional unsteady heat equation to a MIMD parallel computer was identified. This was done by implementing and comparing three different domain decomposition techniques that define the tasks for the CPU's in the parallel machine. These implementations were done for a Cartesian grid and Dirichlet boundary conditions. The most promising technique was then used to implement the heat equation solver on a general curvilinear grid with a suite of nontrivial boundary conditions. Finally, this technique was also used to implement the Scalar Penta-diagonal (SP) benchmark, which was taken from the NAS Parallel Benchmarks report. All implementations were done in the programming language C on the Intel iPSC/860 computer.

Atomic Physics Effects on Convergent, Child-Langmuir Ion Flow between Nearly Transparent Electrodes

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

Santarius, John F.; Emmert, Gilbert A.

Research during this project at the University of Wisconsin Fusion Technology Institute (UW FTI) on ion and neutral flow through an arbitrary, monotonic potential difference created by nearly transparent electrodes accomplished the following: (1) developed and implemented an integral equation approach for atomic physics effects in helium plasmas; (2) extended the analysis to coupled integral equations that treat atomic and molecular deuterium ions and neutrals; (3) implemented the key deuterium and helium atomic and molecular cross sections; (4) added negative ion production and related cross sections; and (5) benchmarked the code against experimental results. The analysis and codes treat themore » species D0, D20, D+, D2+, D3+, D and, separately at present, He0 and He+. Extensions enhanced the analysis and related computer codes to include He++ ions plus planar and cylindrical geometries.« less

Debris characterization diagnostic for the NIF

NASA Astrophysics Data System (ADS)

Miller, M. C.; Celeste, J. R.; Stoyer, M. A.; Suter, L. J.; Tobin, M. T.; Grun, J.; Davis, J. F.; Barnes, C. W.; Wilson, D. C.

2001-01-01

Generation of debris from targets and by x-ray ablation of surrounding materials will be a matter of concern for experimenters and National Ignition Facility (NIF) operations. Target chamber and final optics protection, for example debris shield damage, drive the interest for NIF operations. Experimenters are primarily concerned with diagnostic survivability, separation of mechanical versus radiation induced test object response in the case of effects tests, and radiation transport through the debris field when the net radiation output is used to benchmark computer codes. In addition, radiochemical analysis of activated capsule debris during ignition shots can provide a measure of the ablator <ρr>. Conceptual design of the Debris Monitor and Rad-Chem Station, one of the NIF core diagnostics, is presented. Methods of debris collection, particle size and mass analysis, impulse measurement, and radiochemical analysis are given. A description of recent experiments involving debris collection and impulse measurement on the OMEGA and Pharos lasers is also provided.

Spike sorting using locality preserving projection with gap statistics and landmark-based spectral clustering.

PubMed

Nguyen, Thanh; Khosravi, Abbas; Creighton, Douglas; Nahavandi, Saeid

2014-12-30

Understanding neural functions requires knowledge from analysing electrophysiological data. The process of assigning spikes of a multichannel signal into clusters, called spike sorting, is one of the important problems in such analysis. There have been various automated spike sorting techniques with both advantages and disadvantages regarding accuracy and computational costs. Therefore, developing spike sorting methods that are highly accurate and computationally inexpensive is always a challenge in the biomedical engineering practice. An automatic unsupervised spike sorting method is proposed in this paper. The method uses features extracted by the locality preserving projection (LPP) algorithm. These features afterwards serve as inputs for the landmark-based spectral clustering (LSC) method. Gap statistics (GS) is employed to evaluate the number of clusters before the LSC can be performed. The proposed LPP-LSC is highly accurate and computationally inexpensive spike sorting approach. LPP spike features are very discriminative; thereby boost the performance of clustering methods. Furthermore, the LSC method exhibits its efficiency when integrated with the cluster evaluator GS. The proposed method's accuracy is approximately 13% superior to that of the benchmark combination between wavelet transformation and superparamagnetic clustering (WT-SPC). Additionally, LPP-LSC computing time is six times less than that of the WT-SPC. LPP-LSC obviously demonstrates a win-win spike sorting solution meeting both accuracy and computational cost criteria. LPP and LSC are linear algorithms that help reduce computational burden and thus their combination can be applied into real-time spike analysis. Copyright © 2014 Elsevier B.V. All rights reserved.

Do Medicare Advantage Plans Minimize Costs? Investigating the Relationship Between Benchmarks, Costs, and Rebates.

PubMed

Zuckerman, Stephen; Skopec, Laura; Guterman, Stuart

2017-12-01

Medicare Advantage (MA), the program that allows people to receive their Medicare benefits through private health plans, uses a benchmark-and-bidding system to induce plans to provide benefits at lower costs. However, prior research suggests medical costs, profits, and other plan costs are not as low under this system as they might otherwise be. To examine how well the current system encourages MA plans to bid their lowest cost by examining the relationship between costs and bonuses (rebates) and the benchmarks Medicare uses in determining plan payments. Regression analysis using 2015 data for HMO and local PPO plans. Costs and rebates are higher for MA plans in areas with higher benchmarks, and plan costs vary less than benchmarks do. A one-dollar increase in benchmarks is associated with 32-cent-higher plan costs and a 52-cent-higher rebate, even when controlling for market and plan factors that can affect costs. This suggests the current benchmark-and-bidding system allows plans to bid higher than local input prices and other market conditions would seem to warrant. To incentivize MA plans to maximize efficiency and minimize costs, Medicare could change the way benchmarks are set or used.

Modernization at the Y-12 National Security Complex: A Case for Additional Experimental Benchmarks

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

Thornbury, M. L.; Juarez, C.; Krass, A. W.

Efforts are underway at the Y-12 National Security Complex (Y-12) to modernize the recovery, purification, and consolidation of un-irradiated, highly enriched uranium metal. Successful integration of advanced technology such as Electrorefining (ER) eliminates many of the intermediate chemistry systems and processes that are the current and historical basis of the nuclear fuel cycle at Y-12. The cost of operations, the inventory of hazardous chemicals, and the volume of waste are significantly reduced by ER. It also introduces unique material forms and compositions related to the chemistry of chloride salts for further consideration in safety analysis and engineering. The work hereinmore » briefly describes recent investigations of nuclear criticality for 235UO2Cl2 (uranyl chloride) and 6LiCl (lithium chloride) in aqueous solution. Of particular interest is the minimum critical mass of highly enriched uranium as a function of the molar ratio of 6Li to 235U. The work herein also briefly describes recent investigations of nuclear criticality for 235U metal reflected by salt mixtures of 6LiCl or 7LiCl (lithium chloride), KCl (potassium chloride), and 235UCl3 or 238UCl3 (uranium tri-chloride). Computational methods for analysis of nuclear criticality safety and published nuclear data are employed in the absence of directly relevant experimental criticality benchmarks.« less

A Numerical Simulator for Three-Dimensional Flows Through Vibrating Blade Rows

NASA Technical Reports Server (NTRS)

Chuang, H. Andrew; Verdon, Joseph M.

1998-01-01

The three-dimensional, multi-stage, unsteady, turbomachinery analysis, TURBO, has been extended to predict the aeroelastic and aeroacoustic response behaviors of a single blade row operating within a cylindrical annular duct. In particular, a blade vibration capability has been incorporated so that the TURBO analysis can be applied over a solution domain that deforms with a vibratory blade motion. Also, unsteady far-field conditions have been implemented to render the computational boundaries at inlet and exit transparent to outgoing unsteady disturbances. The modified TURBO analysis is applied herein to predict unsteady subsonic and transonic flows. The intent is to partially validate this nonlinear analysis for blade flutter applications, via numerical results for benchmark unsteady flows, and to demonstrate the analysis for a realistic fan rotor. For these purposes, we have considered unsteady subsonic flows through a 3D version of the 10th Standard Cascade, and unsteady transonic flows through the first stage rotor of the NASA Lewis, Rotor 67, two-stage fan.

A machine learning approach for automated assessment of retinal vasculature in the oxygen induced retinopathy model.

PubMed

Mazzaferri, Javier; Larrivée, Bruno; Cakir, Bertan; Sapieha, Przemyslaw; Costantino, Santiago

2018-03-02

Preclinical studies of vascular retinal diseases rely on the assessment of developmental dystrophies in the oxygen induced retinopathy rodent model. The quantification of vessel tufts and avascular regions is typically computed manually from flat mounted retinas imaged using fluorescent probes that highlight the vascular network. Such manual measurements are time-consuming and hampered by user variability and bias, thus a rapid and objective method is needed. Here, we introduce a machine learning approach to segment and characterize vascular tufts, delineate the whole vasculature network, and identify and analyze avascular regions. Our quantitative retinal vascular assessment (QuRVA) technique uses a simple machine learning method and morphological analysis to provide reliable computations of vascular density and pathological vascular tuft regions, devoid of user intervention within seconds. We demonstrate the high degree of error and variability of manual segmentations, and designed, coded, and implemented a set of algorithms to perform this task in a fully automated manner. We benchmark and validate the results of our analysis pipeline using the consensus of several manually curated segmentations using commonly used computer tools. The source code of our implementation is released under version 3 of the GNU General Public License ( https://www.mathworks.com/matlabcentral/fileexchange/65699-javimazzaf-qurva ).

The effects of Reynolds number, rotor incidence angle and surface roughness on the heat transfer distribution in a large-scale turbine rotor passage

NASA Technical Reports Server (NTRS)

Blair, M. F.

1991-01-01

A combined experimental and computational program was conducted to examine the heat transfer distribution in a turbine rotor passage geometrically similar to the Space Shuttle Main Engine (SSME) High Pressure Fuel Turbopump (HPFTP). Heat transfer was measured and computed for both the full span suction and pressure surfaces of the rotor airfoil as well as for the hub endwall surface. The objective of the program was to provide a benchmark-quality database for the assessment of rotor heat transfer computational techniques. The experimental portion of the study was conducted in a large scale, ambient temperature, rotating turbine model. The computational portion consisted of the application of a well-posed parabolized Navier-Stokes analysis of the calculation of the three-dimensional viscous flow through ducts simulating a gas turbine package. The results of this assessment indicate that the procedure has the potential to predict the aerodynamics and the heat transfer in a gas turbine passage and can be used to develop detailed three dimensional turbulence models for the prediction of skin friction and heat transfer in complex three dimensional flow passages.

FUN3D Analyses in Support of the First Aeroelastic Prediction Workshop

NASA Technical Reports Server (NTRS)

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

2013-01-01

This paper presents the computational aeroelastic results generated in support of the first Aeroelastic Prediction Workshop for the Benchmark Supercritical Wing (BSCW) and the HIgh REynolds Number AeroStructural Dynamics (HIRENASD) configurations and compares them to the experimental data. The computational results are obtained using FUN3D, an unstructured grid Reynolds-averaged Navier-Stokes solver developed at NASA Langley Research Center. The analysis results for both configurations include aerodynamic coefficients and surface pressures obtained for steady-state or static aeroelastic equilibrium (BSCW and HIRENASD, respectively) and for unsteady flow due to a pitching wing (BSCW) or modally-excited wing (HIRENASD). Frequency response functions of the pressure coefficients with respect to displacement are computed and compared with the experimental data. For the BSCW, the shock location is computed aft of the experimentally-located shock position. The pressure distribution upstream of this shock is in excellent agreement with the experimental data, but the pressure downstream of the shock in the separated flow region does not match as well. For HIRENASD, very good agreement between the numerical results and the experimental data is observed at the mid-span wing locations.

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.

Translational benchmark risk analysis

PubMed Central

Piegorsch, Walter W.

2010-01-01

Translational development – in the sense of translating a mature methodology from one area of application to another, evolving area – is discussed for the use of benchmark doses in quantitative risk assessment. Illustrations are presented with traditional applications of the benchmark paradigm in biology and toxicology, and also with risk endpoints that differ from traditional toxicological archetypes. It is seen that the benchmark approach can apply to a diverse spectrum of risk management settings. This suggests a promising future for this important risk-analytic tool. Extensions of the method to a wider variety of applications represent a significant opportunity for enhancing environmental, biomedical, industrial, and socio-economic risk assessments. PMID:20953283

Absolute Configuration of 3-METHYLCYCLOHEXANONE by Chiral Tag Rotational Spectroscopy and Vibrational Circular Dichroism

NASA Astrophysics Data System (ADS)

Evangelisti, Luca; Holdren, Martin S.; Mayer, Kevin J.; Smart, Taylor; West, Channing; Pate, Brooks

2017-06-01

The absolute configuration of 3-methylcyclohexanone was established by chiral tag rotational spectroscopy measurements using 3-butyn-2-ol as the tag partner. This molecule was chosen because it is a benchmark measurement for vibrational circular dichroism (VCD). A comparison of the analysis approaches of chiral tag rotational spectroscopy and VCD will be presented. One important issue in chiral analysis by both methods is the conformational flexibility of the molecule being analyzed. The analysis of conformational composition of samples will be illustrated. In this case, the high spectral resolution of molecular rotational spectroscopy and potential for spectral simplification by conformational cooling in the pulsed jet expansion are advantages for chiral tag spectroscopy. The computational chemistry requirements for the two methods will also be discussed. In this case, the need to perform conformer searches for weakly bound complexes and to perform reasonably high level quantum chemistry geometry optimizations on these complexes makes the computational time requirements less favorable for chiral tag rotational spectroscopy. Finally, the issue of reliability of the determination of the absolute configuration will be considered. In this case, rotational spectroscopy offers a "gold standard" analysis method through the determination of the ^{13}C-subsitution structure of the complex between 3-methylcyclohexanone and an enantiopure sample of the 3-butyn-2-ol tag.

Two new computational methods for universal DNA barcoding: a benchmark using barcode sequences of bacteria, archaea, animals, fungi, and land plants.

PubMed

Tanabe, Akifumi S; Toju, Hirokazu

2013-01-01

Taxonomic identification of biological specimens based on DNA sequence information (a.k.a. DNA barcoding) is becoming increasingly common in biodiversity science. Although several methods have been proposed, many of them are not universally applicable due to the need for prerequisite phylogenetic/machine-learning analyses, the need for huge computational resources, or the lack of a firm theoretical background. Here, we propose two new computational methods of DNA barcoding and show a benchmark for bacterial/archeal 16S, animal COX1, fungal internal transcribed spacer, and three plant chloroplast (rbcL, matK, and trnH-psbA) barcode loci that can be used to compare the performance of existing and new methods. The benchmark was performed under two alternative situations: query sequences were available in the corresponding reference sequence databases in one, but were not available in the other. In the former situation, the commonly used "1-nearest-neighbor" (1-NN) method, which assigns the taxonomic information of the most similar sequences in a reference database (i.e., BLAST-top-hit reference sequence) to a query, displays the highest rate and highest precision of successful taxonomic identification. However, in the latter situation, the 1-NN method produced extremely high rates of misidentification for all the barcode loci examined. In contrast, one of our new methods, the query-centric auto-k-nearest-neighbor (QCauto) method, consistently produced low rates of misidentification for all the loci examined in both situations. These results indicate that the 1-NN method is most suitable if the reference sequences of all potentially observable species are available in databases; otherwise, the QCauto method returns the most reliable identification results. The benchmark results also indicated that the taxon coverage of reference sequences is far from complete for genus or species level identification in all the barcode loci examined. Therefore, we need to accelerate the registration of reference barcode sequences to apply high-throughput DNA barcoding to genus or species level identification in biodiversity research.

Two New Computational Methods for Universal DNA Barcoding: A Benchmark Using Barcode Sequences of Bacteria, Archaea, Animals, Fungi, and Land Plants

PubMed Central

Tanabe, Akifumi S.; Toju, Hirokazu

2013-01-01

Taxonomic identification of biological specimens based on DNA sequence information (a.k.a. DNA barcoding) is becoming increasingly common in biodiversity science. Although several methods have been proposed, many of them are not universally applicable due to the need for prerequisite phylogenetic/machine-learning analyses, the need for huge computational resources, or the lack of a firm theoretical background. Here, we propose two new computational methods of DNA barcoding and show a benchmark for bacterial/archeal 16S, animal COX1, fungal internal transcribed spacer, and three plant chloroplast (rbcL, matK, and trnH-psbA) barcode loci that can be used to compare the performance of existing and new methods. The benchmark was performed under two alternative situations: query sequences were available in the corresponding reference sequence databases in one, but were not available in the other. In the former situation, the commonly used “1-nearest-neighbor” (1-NN) method, which assigns the taxonomic information of the most similar sequences in a reference database (i.e., BLAST-top-hit reference sequence) to a query, displays the highest rate and highest precision of successful taxonomic identification. However, in the latter situation, the 1-NN method produced extremely high rates of misidentification for all the barcode loci examined. In contrast, one of our new methods, the query-centric auto-k-nearest-neighbor (QCauto) method, consistently produced low rates of misidentification for all the loci examined in both situations. These results indicate that the 1-NN method is most suitable if the reference sequences of all potentially observable species are available in databases; otherwise, the QCauto method returns the most reliable identification results. The benchmark results also indicated that the taxon coverage of reference sequences is far from complete for genus or species level identification in all the barcode loci examined. Therefore, we need to accelerate the registration of reference barcode sequences to apply high-throughput DNA barcoding to genus or species level identification in biodiversity research. PMID:24204702

Re-analysis of Alaskan benchmark glacier mass-balance data using the index method

USGS Publications Warehouse

Van Beusekom, Ashely E.; O'Nell, Shad R.; March, Rod S.; Sass, Louis C.; Cox, Leif H.

2010-01-01

At Gulkana and Wolverine Glaciers, designated the Alaskan benchmark glaciers, we re-analyzed and re-computed the mass balance time series from 1966 to 2009 to accomplish our goal of making more robust time series. Each glacier's data record was analyzed with the same methods. For surface processes, we estimated missing information with an improved degree-day model. Degree-day models predict ablation from the sum of daily mean temperatures and an empirical degree-day factor. We modernized the traditional degree-day model and derived new degree-day factors in an effort to match the balance time series more closely. We estimated missing yearly-site data with a new balance gradient method. These efforts showed that an additional step needed to be taken at Wolverine Glacier to adjust for non-representative index sites. As with the previously calculated mass balances, the re-analyzed balances showed a continuing trend of mass loss. We noted that the time series, and thus our estimate of the cumulative mass loss over the period of record, was very sensitive to the data input, and suggest the need to add data-collection sites and modernize our weather stations.

Application configuration selection for energy-efficient execution on multicore systems

DOE PAGES

Wang, Shinan; Luo, Bing; Shi, Weisong; ...

2015-09-21

Balanced performance and energy consumption are incorporated in the design of modern computer systems. Several runtime factors, such as concurrency levels, thread mapping strategies, and dynamic voltage and frequency scaling (DVFS) should be considered in order to achieve optimal energy efficiency fora workload. Selecting appropriate run-time factors, however, is one of the most challenging tasks because the run-time factors are architecture-specific and workload-specific. And while most existing works concentrate on either static analysis of the workload or run-time prediction results, we present a hybrid two-step method that utilizes concurrency levels and DVFS settings to achieve the energy efficiency configuration formore » a worldoad. The experimental results based on a Xeon E5620 server with NPB and PARSEC benchmark suites show that the model is able to predict the energy efficient configuration accurately. On average, an additional 10% EDP (Energy Delay Product) saving is obtained by using run-time DVFS for the entire system. An off-line optimal solution is used to compare with the proposed scheme. Finally, the experimental results show that the average extra EDP saved by the optimal solution is within 5% on selective parallel benchmarks.« less

Hospital benchmarking: are U.S. eye hospitals ready?

PubMed

de Korne, Dirk F; van Wijngaarden, Jeroen D H; Sol, Kees J C A; Betz, Robert; Thomas, Richard C; Schein, Oliver D; Klazinga, Niek S

2012-01-01

Benchmarking is increasingly considered a useful management instrument to improve quality in health care, but little is known about its applicability in hospital settings. The aims of this study were to assess the applicability of a benchmarking project in U.S. eye hospitals and compare the results with an international initiative. We evaluated multiple cases by applying an evaluation frame abstracted from the literature to five U.S. eye hospitals that used a set of 10 indicators for efficiency benchmarking. Qualitative analysis entailed 46 semistructured face-to-face interviews with stakeholders, document analyses, and questionnaires. The case studies only partially met the conditions of the evaluation frame. Although learning and quality improvement were stated as overall purposes, the benchmarking initiative was at first focused on efficiency only. No ophthalmic outcomes were included, and clinicians were skeptical about their reporting relevance and disclosure. However, in contrast with earlier findings in international eye hospitals, all U.S. hospitals worked with internal indicators that were integrated in their performance management systems and supported benchmarking. Benchmarking can support performance management in individual hospitals. Having a certain number of comparable institutes provide similar services in a noncompetitive milieu seems to lay fertile ground for benchmarking. International benchmarking is useful only when these conditions are not met nationally. Although the literature focuses on static conditions for effective benchmarking, our case studies show that it is a highly iterative and learning process. The journey of benchmarking seems to be more important than the destination. Improving patient value (health outcomes per unit of cost) requires, however, an integrative perspective where clinicians and administrators closely cooperate on both quality and efficiency issues. If these worlds do not share such a relationship, the added "public" value of benchmarking in health care is questionable.

Assessing the Progress of Trapped-Ion Processors Towards Fault-Tolerant Quantum Computation

NASA Astrophysics Data System (ADS)

Bermudez, A.; Xu, X.; Nigmatullin, R.; O'Gorman, J.; Negnevitsky, V.; Schindler, P.; Monz, T.; Poschinger, U. G.; Hempel, C.; Home, J.; Schmidt-Kaler, F.; Biercuk, M.; Blatt, R.; Benjamin, S.; Müller, M.

2017-10-01

A quantitative assessment of the progress of small prototype quantum processors towards fault-tolerant quantum computation is a problem of current interest in experimental and theoretical quantum information science. We introduce a necessary and fair criterion for quantum error correction (QEC), which must be achieved in the development of these quantum processors before their sizes are sufficiently big to consider the well-known QEC threshold. We apply this criterion to benchmark the ongoing effort in implementing QEC with topological color codes using trapped-ion quantum processors and, more importantly, to guide the future hardware developments that will be required in order to demonstrate beneficial QEC with small topological quantum codes. In doing so, we present a thorough description of a realistic trapped-ion toolbox for QEC and a physically motivated error model that goes beyond standard simplifications in the QEC literature. We focus on laser-based quantum gates realized in two-species trapped-ion crystals in high-optical aperture segmented traps. Our large-scale numerical analysis shows that, with the foreseen technological improvements described here, this platform is a very promising candidate for fault-tolerant quantum computation.

Integrating the Apache Big Data Stack with HPC for Big Data

NASA Astrophysics Data System (ADS)

Fox, G. C.; Qiu, J.; Jha, S.

2014-12-01

There is perhaps a broad consensus as to important issues in practical parallel computing as applied to large scale simulations; this is reflected in supercomputer architectures, algorithms, libraries, languages, compilers and best practice for application development. However, the same is not so true for data intensive computing, even though commercially clouds devote much more resources to data analytics than supercomputers devote to simulations. We look at a sample of over 50 big data applications to identify characteristics of data intensive applications and to deduce needed runtime and architectures. We suggest a big data version of the famous Berkeley dwarfs and NAS parallel benchmarks and use these to identify a few key classes of hardware/software architectures. Our analysis builds on combining HPC and ABDS the Apache big data software stack that is well used in modern cloud computing. Initial results on clouds and HPC systems are encouraging. We propose the development of SPIDAL - Scalable Parallel Interoperable Data Analytics Library -- built on system aand data abstractions suggested by the HPC-ABDS architecture. We discuss how it can be used in several application areas including Polar Science.

Textual data compression in computational biology: a synopsis.

PubMed

Giancarlo, Raffaele; Scaturro, Davide; Utro, Filippo

2009-07-01

Textual data compression, and the associated techniques coming from information theory, are often perceived as being of interest for data communication and storage. However, they are also deeply related to classification and data mining and analysis. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison and reverse engineering of biological networks. The main focus of this review is on a systematic presentation of the key areas of bioinformatics and computational biology where compression has been used. When possible, a unifying organization of the main ideas and techniques is also provided. It goes without saying that most of the research results reviewed here offer software prototypes to the bioinformatics community. The Supplementary Material provides pointers to software and benchmark datasets for a range of applications of broad interest. In addition to provide reference to software, the Supplementary Material also gives a brief presentation of some fundamental results and techniques related to this paper. It is at: http://www.math.unipa.it/ approximately raffaele/suppMaterial/compReview/

Potential Deep Seated Landslide Mapping from Various Temporal Data - Benchmark, Aerial Photo, and SAR

NASA Astrophysics Data System (ADS)

Wang, Kuo-Lung; Lin, Jun-Tin; Lee, Yi-Hsuan; Lin, Meei-Ling; Chen, Chao-Wei; Liao, Ray-Tang; Chi, Chung-Chi; Lin, Hsi-Hung

2016-04-01

Landslide is always not hazard until mankind development in highly potential area. The study tries to map deep seated landslide before the initiation of landslide. Study area in central Taiwan is selected and the geological condition is quite unique, which is slate. Major direction of bedding in this area is northeast and the dip ranges from 30-75 degree to southeast. Several deep seated landslides were discovered in the same side of bedding from rainfall events. The benchmarks from 2002 ~ 2009 are in this study. However, the benchmarks were measured along Highway No. 14B and the road was constructed along the peak of mountains. Taiwan located between sea plates and continental plate. The elevation of mountains is rising according to most GPS and benchmarks in the island. The same trend is discovered from benchmarks in this area. But some benchmarks are located in landslide area thus the elevation is below average and event negative. The aerial photos from 1979 to 2007 are used for orthophoto generation. The changes of land use are obvious during 30 years and enlargement of river channel is also observed in this area. Both benchmarks and aerial photos have discovered landslide potential did exist this area but how big of landslide in not easy to define currently. Thus SAR data utilization is adopted in this case. DInSAR and SBAS sar analysis are used in this research and ALOS/PALSAR from 2006 to 2010 is adopted. DInSAR analysis shows that landslide is possible mapped but the error is not easy to reduce. The error is possibly form several conditions such as vegetation, clouds, vapor, etc. To conquer the problem, time series analysis, SBAS, is adopted in this research. The result of SBAS in this area shows that large deep seated landslides are easy mapped and the accuracy of vertical displacement is reasonable.

Benchmarking routine psychological services: a discussion of challenges and methods.

PubMed

Delgadillo, Jaime; McMillan, Dean; Leach, Chris; Lucock, Mike; Gilbody, Simon; Wood, Nick

2014-01-01

Policy developments in recent years have led to important changes in the level of access to evidence-based psychological treatments. Several methods have been used to investigate the effectiveness of these treatments in routine care, with different approaches to outcome definition and data analysis. To present a review of challenges and methods for the evaluation of evidence-based treatments delivered in routine mental healthcare. This is followed by a case example of a benchmarking method applied in primary care. High, average and poor performance benchmarks were calculated through a meta-analysis of published data from services working under the Improving Access to Psychological Therapies (IAPT) Programme in England. Pre-post treatment effect sizes (ES) and confidence intervals were estimated to illustrate a benchmarking method enabling services to evaluate routine clinical outcomes. High, average and poor performance ES for routine IAPT services were estimated to be 0.91, 0.73 and 0.46 for depression (using PHQ-9) and 1.02, 0.78 and 0.52 for anxiety (using GAD-7). Data from one specific IAPT service exemplify how to evaluate and contextualize routine clinical performance against these benchmarks. The main contribution of this report is to summarize key recommendations for the selection of an adequate set of psychometric measures, the operational definition of outcomes, and the statistical evaluation of clinical performance. A benchmarking method is also presented, which may enable a robust evaluation of clinical performance against national benchmarks. Some limitations concerned significant heterogeneity among data sources, and wide variations in ES and data completeness.

CERN Computing in Commercial Clouds

NASA Astrophysics Data System (ADS)

Cordeiro, C.; Field, L.; Garrido Bear, B.; Giordano, D.; Jones, B.; Keeble, O.; Manzi, A.; Martelli, E.; McCance, G.; Moreno-García, D.; Traylen, S.

2017-10-01

By the end of 2016 more than 10 Million core-hours of computing resources have been delivered by several commercial cloud providers to the four LHC experiments to run their production workloads, from simulation to full chain processing. In this paper we describe the experience gained at CERN in procuring and exploiting commercial cloud resources for the computing needs of the LHC experiments. The mechanisms used for provisioning, monitoring, accounting, alarming and benchmarking will be discussed, as well as the involvement of the LHC collaborations in terms of managing the workflows of the experiments within a multicloud environment.

Adding Fault Tolerance to NPB Benchmarks Using ULFM

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

Parchman, Zachary W; Vallee, Geoffroy R; Naughton III, Thomas J

2016-01-01

In the world of high-performance computing, fault tolerance and application resilience are becoming some of the primary concerns because of increasing hardware failures and memory corruptions. While the research community has been investigating various options, from system-level solutions to application-level solutions, standards such as the Message Passing Interface (MPI) are also starting to include such capabilities. The current proposal for MPI fault tolerant is centered around the User-Level Failure Mitigation (ULFM) concept, which provides means for fault detection and recovery of the MPI layer. This approach does not address application-level recovery, which is currently left to application developers. In thismore » work, we present a mod- ification of some of the benchmarks of the NAS parallel benchmark (NPB) to include support of the ULFM capabilities as well as application-level strategies and mechanisms for application-level failure recovery. As such, we present: (i) an application-level library to checkpoint and restore data, (ii) extensions of NPB benchmarks for fault tolerance based on different strategies, (iii) a fault injection tool, and (iv) some preliminary results that show the impact of such fault tolerant strategies on the application execution.« less

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.

Assessing the quality of GEOID12B model through field surveys

NASA Astrophysics Data System (ADS)

Elaksher, Ahmed; Kamtchang, Franck; Wegmann, Christian; Guerrero, Adalberto

2018-01-01

Elevation differences have been determined through conventional ground surveying techniques for over a century. Since the mid-80s GPS, GLONASS and other satellite systems have modernized the means by which elevation differences are observed. In this article, we assessed the quality of GEIOD12B through long-occupation GNSS static surveys. A set of NGS benchmarks was occupied for at least one hour using dual-frequency GNSS receivers. Collected measurements were processed using a single CORS station at most 24 kilometers from the benchmarks. Geoid undulation values were driven by subtracting measured ellipsoidal heights from the orthometric heights posted on the NGS website. To assess the quality of GEOID12B, we compared our computed vertical shifts at the benchmarks with those estimated from GEOID12B published by NGS. In addition, Kriging model was used to interpolate local maps for the geoid undulations from the benchmark heights. The maps were compared with corresponding parts of GEOID12B. No biases were detected in the results and only shifts due to random errors were found. Discrepancies in the range of ten centimetres were noticed between our geoid undulation and the values available from NGS.

Performance Evaluation and Benchmarking of Next Intelligent Systems

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

del Pobil, Angel; Madhavan, Raj; Bonsignorio, Fabio

Performance Evaluation and Benchmarking of Intelligent Systems presents research dedicated to the subject of performance evaluation and benchmarking of intelligent systems by drawing from the experiences and insights of leading experts gained both through theoretical development and practical implementation of intelligent systems in a variety of diverse application domains. This contributed volume offers a detailed and coherent picture of state-of-the-art, recent developments, and further research areas in intelligent systems. The chapters cover a broad range of applications, such as assistive robotics, planetary surveying, urban search and rescue, and line tracking for automotive assembly. Subsystems or components described in this bookmore » include human-robot interaction, multi-robot coordination, communications, perception, and mapping. Chapters are also devoted to simulation support and open source software for cognitive platforms, providing examples of the type of enabling underlying technologies that can help intelligent systems to propagate and increase in capabilities. Performance Evaluation and Benchmarking of Intelligent Systems serves as a professional reference for researchers and practitioners in the field. This book is also applicable to advanced courses for graduate level students and robotics professionals in a wide range of engineering and related disciplines including computer science, automotive, healthcare, manufacturing, and service robotics.« less

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.