Verification Test Suite for Physics Simulation Codes

Brock, Jerry S.; Kamm, James R.; Rider, William J.; Brandon, S; Woodward, Carol S.; Knupp, Patrick; Trucano, Timothy Guy

doi:10.2172/898449

Cited by 5 publications

(5 citation statements)

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“…There exists an agreed-upon set of problems used by the Laboratories for verification purposes. This set of seven problems [Bro06] forms a nominal basis with which to assess code capabilities. In recent years, verification analysis capabilities have matured significantly, enabling augmentation of the test suite.…”

Section: Verification Test Problemsmentioning

confidence: 99%

Enhanced Verification Test Suite for Physics Simulation Codes

Kamm¹,

Brock²,

Brandon³

et al. 2008

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Section: Verification Test Problemsmentioning

confidence: 99%

Enhanced Verification Test Suite for Physics Simulation Codes

Kamm¹,

Brock²,

Brandon³

et al. 2008

Self Cite

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“…Therefore, verification represents a fundamental and necessary part of the development, assessment, and application of simulation software for physics and engineering. An agreed-upon set of seven problems [Bro06] used by the LANL, LLNL, and SNL forms a nominal basis for current, mutually undertaken verification purposes.…”

Section: Discussionmentioning

confidence: 99%

“…This set of seven problems [Bro06] forms a nominal basis with which to assess code capabilities. In recent years, verification analysis capabilities have matured significantly, enabling augmentation of the test suite.…”

Section: Verification Test Problemsmentioning

confidence: 99%

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Enhanced verification test suite for physics simulation codes

Kamm¹,

Brock²,

Brandon³

et al. 2008

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Executive SummaryThis document discusses problems with which to augment, in quantity and in quality, the existing tri-laboratory suite of verification problems used by Los Alamos National Laboratory (LANL), Lawrence Livermore National Laboratory (LLNL), and Sandia National Laboratories (SNL). The purpose of verification analysis is demonstrate whether the numerical results of the discretization algorithms in physics and engineering simulation codes provide correct solutions of the corresponding continuum equations. The key points of this document are:• Verification deals with mathematical correctness of the numerical algorithms in a code, while validation deals with physical correctness of a simulation in a regime of interest. This document is about verification.• The current seven-problem Tri-Laboratory Verification Test Suite, which has been used for approximately five years at the DOE WP laboratories, is limited.• Both the methodology for and technology used in verification analysis have evolved and been improved since the original test suite was proposed.• The proposed test problems are in three basic areas:1. Hydrodynamics 2. Transport processes 3. Dynamic strength-of-materials• For several of the proposed problems we provide a "strong sense verification benchmark," consisting of (i) a clear mathematical statement of the problem with sufficient information to run a computer simulation, (ii) an explanation of how the code result and benchmark solution are to be evaluated, and (iii) a description of the acceptance criterion for simulation code results.

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“…By providing an efficient peptide-centric interface into the data, toffee allows algorithm developers to write tests of their implementation down to individual units of work while still retaining the complexity of real world data. This testing approach is fundamental to scientific software development 20 , for example, in high-energy physics, the US National Laboratories have developed the Tri-Lab test suite that pits algorithms against toy problems with analytic solutions 21 .…”

Section: Raw Data Accessmentioning

confidence: 99%

Toffee – a highly efficient, lossless file format for DIA-MS

Tully

2020

Sci Rep

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The closed nature of vendor file formats in mass spectrometry is a significant barrier to progress in developing robust bioinformatics software. In response, the community has developed the open mzML format, implemented in XML and based on controlled vocabularies. Widely adopted, mzML is an important step forward; however, it suffers from two challenges that are particularly apparent as the field moves to high-throughput proteomics: large increase in file size, and a largely sequential I/O access pattern. Described here is 'toffee', an open, random I/O format backed by HDF5, with lossless compression that gives file sizes similar to the original vendor format and can be reconverted back to mzML without penalty. It is shown that mzML and toffee are equivalent when processing data using OpenSWATH algorithms, in additional to novel applications that are enabled by new data access patterns. For instance, a peptide-centric deep-learning pipeline for peptide identification is proposed.

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Verification Test Suite for Physics Simulation Codes

Cited by 5 publications

References 1 publication

Enhanced Verification Test Suite for Physics Simulation Codes

Enhanced Verification Test Suite for Physics Simulation Codes

Enhanced verification test suite for physics simulation codes

Toffee – a highly efficient, lossless file format for DIA-MS

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