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Improvements to Bison Validation Base for LWR Fuel

The Bison fuel performance code is being developed by Idaho National Laboratory (INL) to analyze a wide range of fuel forms and operating conditions with the flexibility to conduct simulations in 1D through 3D geometries. Bison plays an important role in the development of advanced fuel with improved accident tolerance for existing light water reactors (LWRs), the improved understanding of mechanisms in fuel designs in a wider range of operating conditions, and the facilitation of future development of fuel for advanced reactor designs. Additionally, industry interest in advanced fuels has also driven Bison development for advanced fuels in the last few years. All of these factors combine to create a potential increase of new Bison users. These new users will potentially be interested in the Bison LWR validation base for examples of Bison's capabilities and how to use Bison. Current users also rely on the Bison validation base as a demonstration of the best practices settings and material behavioral models. Bison, both through direct updates to the Bison source code and to the nearly daily changes and improvements in the underlying MOOSE framework source code, undergoes nearly continuous changes. It is necessary that these source code changes are reflected with updated input files in the Bison validation base. Periodic updates of the validation case input files should also be accompanied by a review and revision of the validation case documentation on which our users rely. Therefore our efforts under this milestone were guided by two objectives: (1) Update the Bison LWR validation input files to use current Bison simulation settings, and (2) Enhance the ease-of-use for Bison through improved documentation These objectives build on the goals identified FY18 CASL milestone reports. During FY18 we addressed issues with the robustness of Bison and identified a need to migrate the assessment suite to the more reliable tensor mechanics module system and set a goal of standardizing the Bison input files. The FY18 CASL milestone report on updates to the Bison documentation system listed continued development of user-focused guides and examples along with revisions to the validation case documentation as future development goals. During FY19 we have separated these two objectives into four different focus areas for our work on this milestone. Our first two focus areas target the existing Bison validation suite: update the existing LWR validation cases and the accompanying documentation. The second two focus areas center on adding new capabilities: a new Bison LWR validation case and expansion of user support documentation. In the following report each of these four focus areas are discussed as a separate section. We conclude the report with a summary of potential future work to build on the efforts of this year.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

A Fault-Oblivious Extreme-Scale Execution Environment (FOX)

IBM Research’s contribution to the Fault Oblivious Extreme-scale Execution Environment (FOX) revolved around three core research deliverables: • collaboration with Boston University around the Kittyhawk cloud infrastructure which both enabled a development and deployment platform for the project team and provided a fault-injection testbed to evaluate prototypes • operating systems research focused on exploring role-based operating system technologies through collaboration with Sandia National Labs on the NIX research operating system and collaboration with the broader IBM Research community around a hybrid operating system model which became known as FusedOS • IBM Research also participated in an advisory capacity with the Boston University SESA project, the core of which was derived from the K42 operating system research project funded in part by DARPA’s HPCS program. Both of these contributions were built on a foundation of previous operating systems research funding by the Department of Energy’s FastOS Program. Through the course of the X-stack funding we were able to develop prototypes, deploy them on production clusters at scale, and make them available to other researchers. As newer hardware, in the form of BlueGene/Q, came online, we were able to port the prototypes to the new hardware and release the source code for the resulting prototypes as open source to the community. In addition to the open source coded for the Kittyhawk and NIX prototypes, we were able to bring the BlueGene/Q Linux patches up to a more recent kernel and contribute them for inclusion by the broader Linux community. The lasting impact of the IBM Research work on FOX can be seen in its effect on the shift of IBM’s approach to HPC operating systems from Linux and Compute Node Kernels to role-based approaches as prototyped by the NIX and FusedOS work. This impact can be seen beyond IBM in follow-on ideas being incorporated into the proposals for the Exasacale Operating Systems/Runtime program.

97 MATHEMATICS AND COMPUTING↗

Preproduction Using Automated Process Design

A new approach to the computer-assisted design (CAD) of machining processes is outlined. Mathematical apparatus for the solution of standard problems is proposed, and the source code for its implementation is developed. The source code for an experimental CAD system is developed. An interactive graphical input is used for dimensional data.

42 ENGINEERING↗

STOMP-W

Fortran 90 source code, example problems, and output conversion scripts for the STOMP-W simulator. STOMP-W is a numerical simulator written in Fortran 90 for solving problems involving fluid flow and solute/species transport in variably saturated geologic media. The zipped file contains five directories: 1) src (the source code), 2) scripts (output conversion scripts written in perl, 3) prb-w-1 (example problem 1), 4) prb-w-2 (example problem 2), and 5) prb-w-3 (example problem 3). After downloading and unzipping the file, the user must create an executable from the files stored in the src directory. Generic instructions for compiling the source code is shown below as a UNIX/Linux command line, with f90 representing the user's Fortran 90 compiler.

White, Mark↗

Palm: Easing the Burden of Analytical Performance Modeling

Analytical (predictive) application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult because they must be both accurate and concise. To ease the burden of performance modeling, we developed Palm, a modeling tool that combines top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. To express insight, Palm defines a source code modeling annotation language. By coordinating models and source code, Palm's models are `first-class' and reproducible. Unlike prior work, Palm formally links models, functions, and measurements. As a result, Palm (a) uses functions to either abstract or express complexity (b) generates hierarchical models (representing an application's static and dynamic structure); and (c) automatically incorporates measurements to focus attention, represent constant behavior, and validate models. We discuss generating models for three different applications.

annotation languages↗

Novel Visual and Analytical Methods in Repurposing Legacy Scientific Code - A Case Study

Scientific computing is dominated by team-authored legacy code that has evolved over decades with the purpose of capturing the evolving understanding of a scientific discipline. Accumulated deprecated code, various optimization techniques, and evolving algorithms lead to convoluted source code that is impractical to reverse engineer using mainstream methods. This prevents codes from being truly repeatable or understandable, which are two of the most essential needs in scientific computing. We refactored a long-standing implementation of a common biosequence alignment algorithm in an effort to reproduce its salient behaviors in usable form. Because of the sheer size and complexity of this code base, we developed custom tools to visualize and manipulate the source code behavior under a variety of conditions. We present a case study of extracting and refactoring the algorithmic core and a novel process of discovery/prototyping/testing using a combination of openly available and custom-built tools. The result is a reduction in code size of over 2 orders of magnitude while reconstructing the key protein alignment function in BLAST

bioinformatics, scientific computing↗

NPTFit: A Code Package for Non-Poissonian Template Fitting

We present NPTFit, an open-source code package, written in Python and Cython, for performing non-Poissonian template fits (NPTFs). The NPTF is a recently developed statistical procedure for characterizing the contribution of unresolved point sources (PSs) to astrophysical data sets. The NPTF was first applied to Fermi gamma-ray data to provide evidence that the excess of ∼GeV gamma-rays observed in the inner regions of the Milky Way likely arises from a population of sub-threshold point sources, and the NPTF has since found additional applications studying sub-threshold extragalactic sources at high Galactic latitudes. The NPTF generalizes traditional astrophysical template fits to allow for the ability to search for populations of unresolved PSs that may follow a given spatial distribution. NPTFit builds upon the framework of the fluctuation analyses developed in X-ray astronomy, thus it likely has applications beyond those demonstrated with gamma-ray data. The NPTFit package utilizes novel computational methods to perform the NPTF efficiently. The code is available at http://github.com/bsafdi/NPTFit and up-to-date and extensive documentation may be found at http://nptfit.readthedocs.io.

79 ASTRONOMY AND ASTROPHYSICS↗

Performing aggressive code optimization with an ability to rollback changes made by the aggressive optimizations

Mechanisms for aggressively optimizing computer code are provided. With these mechanisms, a compiler determines an optimization to apply to a portion of source code and determines if the optimization as applied to the portion of source code will result in unsafe optimized code that introduces a new source of exceptions being generated by the optimized code. In response to a determination that the optimization is an unsafe optimization, the compiler generates an aggressively compiled code version, in which the unsafe optimization is applied, and a conservatively compiled code version in which the unsafe optimization is not applied. The compiler stores both versions and provides them for execution. Mechanisms are provided for switching between these versions during execution in the event of a failure of the aggressively compiled code version. Moreover, predictive mechanisms are provided for predicting whether such a failure is likely.

97 MATHEMATICS AND COMPUTING↗

MatLib-1.2: Nuclear Material Properties Library

The U.S. Nuclear Regulatory Commission (NRC) uses the computer code Fuel Analysis under Steady-state and Transients (FAST) to model steady-state and transient fuel behavior to support regulatory decisions. FAST relies on a material properties library (MatLib) that contains the thermal and mechanical properties of the nuclear materials and coolants of interest to support the US commercial nuclear industry. MatLib contains properties for a variety of nuclear fuels, cladding and other structural materials, gases, and coolants. In this document, material property correlations for the materials contained within MatLib are presented and discussed. When available, comparisons are made between the material property correlations and available data. Additionally, uncertainties are quantified on the material proper- ties, which is then used by the NRC to support uncertainty quantification for best-estimate plus uncertainty safety evaluation reviews. This document describes MatLib-1.2, which was updated from MatLib-1.1 to include cleanup of the code for streamlined calls to MatLib from the main FAST source code, and to enable easier readability of the code by developers that maintain and enhance the FAST code. The results of MatLib did not change between MatLib-1.1 and MatLib-1.2; however, the source code changes warranted incrementing the minor numbering of the software version number. The changes may result in faster execution times of FAST-1.2 as compared to FAST-1.1. This document is one of a series of documents on FAST; the other documents detail the models used by FAST as well as its integral assessment to experiments and commercial data.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

WEC-SIM Phase 1 Validation Testing -- Numerical Modeling of Experiments: Preprint

The Wave Energy Converter Simulator (WEC-Sim) is an open-source code jointly developed by Sandia National Laboratories and the National Renewable Energy Laboratory. It is used to model wave energy converters subjected to operational and extreme waves. In order for the WEC-Sim code to be beneficial to the wave energy community, code verification and physical model validation is necessary. This paper describes numerical modeling of the wave tank testing for the 1:33-scale experimental testing of the floating oscillating surge wave energy converter. The comparison between WEC-Sim and the Phase 1 experimental data set serves as code validation. This paper is a follow-up to the WEC-Sim paper on experimental testing, and describes the WEC-Sim numerical simulations for the floating oscillating surge wave energy converter.

16 TIDAL AND WAVE POWER↗

Modeling and Simulation of Membrane-Based Dehumidification and Energy Recovery Process

This paper introduces a first-order physics-based model that accounts for the fundamental heat and mass transfer between a humid-air vapor stream on feed side to another flow stream on permeate side. The model comprises a few optional submodels for membrane mass transport; and it adopts a segment-by-segment method for discretizing heat and mass transfer governing equations for flow streams on feed and permeate sides. The model is able to simulate both dehumidifiers and energy recovery ventilators in parallel-flow, cross-flow, and counter-flow configurations. The predicted tresults are compared reasonably well with the measurements. The open-source codes are written in C++. The model and open-source codes are expected to become a fundament tool for the analysis of membrane-based dehumidification in the future.

Gao, Zhiming↗

Thermochimica User Manual – v1.0

A new software library called Thermochimica has been developed that determines a unique combination of phases and their compositions at thermochemical equilibrium. The development of Thermochimica in this research is aimed at direct integration in multi-physics codes and to address several concerns with using commercially available software, including: licensing entanglements associated with code distribution, access to the source code, convenient incorporation into other codes with quality assurance considerations, and computational performance. In particular, significant research efforts have been dedicated to enhance computational performance through advanced algorithm development, such as improved estimation techniques and non-linear solvers. The overall goal of this undertaking is to provide an open source computational tool to enhance the predictive capability of multiphysics codes without significantly impeding computational performance. The purpose of this document is to describe the design of Thermochimica and the basic use of the software library. A brief background to computational thermodynamics and the conditions for thermodynamic equilibrium is given in §2, details of the code development is discussed in §3, details of building and compiling Thermochimica is given in §4, specific programming details for each subroutine in the library is given in the Appendix. The open license for Thermochimica is provided with the source code. As is always the case, software quality assurance (SQA) is an extremely important subject in software development. The importance of this warrants an independent document dedicated to SQA, which has been developed in parallel to this document. The subject of thermodynamic model validation is also of extreme importance in scientific computing and must be given careful attention. To be clear, this document is concerned with the development and use of a general thermodynamic solver and the validation of any models should be included in the discussion of the development of a thermodynamic model that is specific to a particular system.

36 MATERIALS SCIENCE↗

A large-scale analysis of bioinformatics code on GitHub

In recent years, the explosion of genomic data and bioinformatic tools has been accompanied by a growing conversation around reproducibility of results and usability of software. However, the actual state of the body of bioinformatics software remains largely unknown. Here, the purpose of this paper is to investigate the state of source code in the bioinformatics community, specifically looking at relationships between code properties, development activity, developer communities, and software impact. To investigate these issues, we curated a list of 1,720 bioinformatics repositories on GitHub through their mention in peer-reviewed bioinformatics articles. Additionally, we included 23 high-profile repositories identified by their popularity in an online bioinformatics forum. We analyzed repository metadata, source code, development activity, and team dynamics using data made available publicly through the GitHub API, as well as article metadata. We found key relationships within our dataset, including: certain scientific topics are associated with more active code development and higher community interest in the repository; most of the code in the main dataset is written in dynamically typed languages, while most of the code in the high-profile set is statically typed; developer team size is associated with community engagement and high-profile repositories have larger teams; the proportion of female contributors decreases for high-profile repositories and with seniority level in author lists; and, multiple measures of project impact are associated with the simple variable of whether the code was modified at all after paper publication. In addition to providing the first large-scale analysis of bioinformatics code to our knowledge, our work will enable future analysis through publicly available data, code, and methods.

97 MATHEMATICS AND COMPUTING↗

System and method for investigating sub-surface features of a rock formation with acoustic sources generating coded signals

A system and a method for investigating rock formations includes generating, by a first acoustic source, a first acoustic signal comprising a first plurality of pulses, each pulse including a first modulated signal at a central frequency; and generating, by a second acoustic source, a second acoustic signal comprising a second plurality of pulses. A receiver arranged within the borehole receives a detected signal including a signal being generated by a non-linear mixing process from the first-and-second acoustic signal in a non-linear mixing zone within the intersection volume. The method also includes-processing the received signal to extract the signal generated by the non-linear mixing process over noise or over signals generated by a linear interaction process, or both.

47 OTHER INSTRUMENTATION↗

Ice Load Project Final Technical Report

As interest and investment in offshore wind projects increase worldwide, some turbines will be installed in locations where ice of significant thickness forms on the water surface. This ice moves under the driving forces of wind, current, and thermal effects and may result in substantial forces on bottom-fixed support structures. The North and Baltic Seas in Europe have begun to see significant wind energy development and the Great Lakes of the United States and Canada may host wind energy development in the near future. Design of the support structures for these projects is best performed through the use of an integrated tool that can calculate the cumulative effects of forces due to turbine operations, wind, waves, and floating ice. The dynamic nature of ice forces requires that these forces be included in the design simulations, rather than added as static forces to simulation results. The International Electrotechnical Commission (IEC) standard[2] for offshore wind turbine design and the International Organization for Standardization (ISO) standard[3] for offshore structures provide requirements and algorithms for the calculation of forces induced by surface ice; however, currently none of the major wind turbine dynamic simulation codes provides the ability to model ice loads. The scope of work of the project described in this report includes the development of a suite of subroutines, collectively named IceFloe, that meet the requirements of the IEC and ISO standards and couples with four of the major wind turbine dynamic simulation codes. The mechanisms by which ice forces impinge on offshore structures generally include the forces required for crushing of the ice against vertical-sided structures and the forces required to fracture the ice as it rides up on conical-sided structures. Within these two broad categories, the dynamic character of the forces with respect to time is also dependent on other factors such as the velocity and thickness of the moving ice and the response of the structure. In some cases, the dynamic effects are random and in other cases they are deterministic, such as the effect of structural resonance and coupling of the ice forces with the defection of the support structure. The initial versions of the IceFloe routines incorporate modules that address these varied force and dynamic phenomena with seven alternative algorithms that can be specified by the user. The IceFloe routines have been linked and tested with four major wind turbine aeroelastic simulation codes: FAST, a tool developed under the management of the National Renewable Energy Laboratory (NREL) and available free of charge from its web site; Bladed[4], a widely-used commercial package available from DNV GL; ADAMS[5], a general purpose multi-body simulation code used in the wind industry and available from MSC Software; and HAWC2[6], a code developed by and available for purchase from Danmarks Tekniske Universitet (DTU). Interface routines have been developed and tested with full wind turbine simulations for each of these codes and the source code and example inputs and outputs are available from the NREL website.

17 WIND ENERGY↗

Systems and methods for binary code analysis

Human-readable (HR) code may be derived from a binary. The HR code may be configured to have statistical properties suitable for machine-learned (ML) translation. The HR code may comprise source code, intermediate code, assembly code, or the like. A machine-learned translator may be configured to translate the HR code into labels comprising semantic information pertaining to respective functions of the binary, such as a function name, role, or the like. Execution of the binary may be blocked in response to translating the HR code to a label associated with malware, such as cryptocurrency mining malware or the like. Conversely, the binary may be permitted to proceed to execution in response to determining that the translation is free from labels indicative of malware.

Anderson, Matthew W.↗

MCNP6 Modification for the Calculation of Rossi and Feynman Distributions

The Rossi distribution is given by the number of captured neutron pairs as a function of the time interval between the two capture events. This distribution contains a random part, which is given by neutron captures caused by neutrons of different fission chains, and a correlated part, which is given by neutron captures caused by neutrons from the same fission chain. The correlated part exponentially vanishes with the {Delta}t time interval following the decay of prompt neutrons. The Rossi distribution peaks when the time interval between two capture events is small since this condition is satisfied for neutrons generated from the same fission chain. In the Poisson probability distribution, the variance is equal to the mean and the next event probability is independent of the elapsed time since the previous event. Neutron captures events do not follow the Poisson probability distribution because they are correlated events via fission chains. Consequently, the Feynman distribution Y is defined as the variance to mean ratio minus one, of the neutron counts array as a function of a fixed time interval. The MCNP6 source code has been modified to allow the calculation of the Rossi and Feynman distributions. The source code modification takes into account the time when a neutron is emitted by the external neutron source and gives a precision in the timestamp lower than a fraction of nanosecond. The modified MCNP6 version has been used to model KUKA facility driven by a californium neutron source. The prompt neutron decay constants obtained by the Rossi and Feynman methods are in agreement.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

SolTrace™ (Optical Analysis Software) [SWR-26-065 and SWR-01-45]

SolTrace™ is a software tool developed at the National Renewable Energy Laboratory (NREL) to model concentrating solar power (CSP) systems and analyze their optical performance. Although ideally suited for solar applications, the code can also be used to model and characterize many general optical systems. The creation of the code evolved out of a need to model more complex solar optical systems than could be modeled with existing tools. SolTrace can be installed either using the official NREL packaged distribution or from source code at the SolTrace open source project website. NREL welcomes contributions from programmers to the simulation engine or to the interface and encourages interested persons to get involved. More information on contributing, compiling the source code, and license requirements is available on the project website.(https://www.nrel.gov/csp/soltrace.html). For details on integration with SAM, see the SAM website. (https://sam.nrel.gov/)

Wendelin, Tim↗