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Software reengineering

Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. JSC created a significant set of tools to develop and maintain FORTRAN and C code during development of the Space Shuttle. This tool set forms the basis for an integrated environment to re-engineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. A beta vision of the environment was released in Mar. 1991. The commercial potential for such re-engineering tools is very great. CASE TRENDS magazine reported it to be the primary concern of over four hundred of the top MIS executives.

Fridge, Ernest M., III↗

FLORIS v3.5 Wake Modeling and Wind Farm Controls Software [SWR-17-43 and SWR-14-20]

FLORIS is a controls-focused wind farm simulation software incorporating steady-state engineering wake models into a performance-focused Python framework. It has been in active development at NREL since 2013 and the latest release is FLORIS v3.5.Online documentation is available at https://nrel.github.io/floris. The software is in active development and engagement with the development team is highly encouraged. If you are interested in using FLORIS to conduct studies of a wind farm or extending FLORIS to include your own wake model, please join the conversation in GitHub Discussions! https://www.nrel.gov/wind/floris.html

Fleming, Paul↗

2014-2018 Summary of NCAR activities in the Earth Energy Exascale System Model (E3SM) project

NCAR participation in E3SM activities as part of this funded collaborative project has been successful in leveraging the existing atmosphere model development experience from CESM scientists and applying it to initial v1 atmosphere model (EAM) development and analysis. NCAR partners collectively had many decades of experience in parameterization development, running and tuning coupled models and building the required software infrastructure to support ongoing model developments. Furthermore, collaboration between E3SM and CESM developers was of mutual benefit to both modeling endeavors. In the earlier periods of the project, participation in E3SM both complemented core critical path DOE activities and advanced individual parameterization development; including orographic drag, convection parameterization, convective gustiness and cloud and microphysical processes. Significant progress has been made implementing model capabilities for separating out the physics and dynamics grids, and providing the infrastructure for including orographic elevation class communication between the land and atmosphere models. Our activities working with the E3SM workflow and software engineering teams have established efficient protocols and infrastructure for the sharing of CESM and E3SM model codes of interest to both modeling groups, a large component of which is the mutual communication of common code bugs. As well as these specific project tasks all NCAR project members have been regular participants in atmosphere and coupled group telecons, as well as PI meetings. We have been fully engaged with and contributed to decisions regarding v1 atmosphere model developments, coupled model simulations, model tunings, and software engineering infrastructure. NCAR’s contribution to more recent E3SM development activities has centered on analysis of v1 release and pre-release simulations in order to address outstanding systematic biases and communicate climate improvements. Of particularly note is the work in understanding clouds and cloud feedbacks, shortcomings in ENSO and sub-seasonal variability; in particular the Madden Julian Oscillation (MJO). Contributions have been made to a number of papers that are currently published or in preparation detailing model performance in CMIP6-protocal experiments. They outline the simulations of mean climate, clouds and convection processes, convective gustiness, atmospheric blocking coupled climates. The contributions of NCAR’s funded activities to the E3SM atmosphere in the initial years of the project have had a positive impact on many aspects of the model simulations described in these papers.

58 GEOSCIENCES↗

Generic, Extensible, Configurable Push-Pull Framework for Large-Scale Science Missions

The push-pull framework was developed in hopes that an infrastructure would be created that could literally connect to any given remote site, and (given a set of restrictions) download files from that remote site based on those restrictions. The Cataloging and Archiving Service (CAS) has recently been re-architected and re-factored in its canonical services, including file management, workflow management, and resource management. Additionally, a generic CAS Crawling Framework was built based on motivation from Apache s open-source search engine project called Nutch. Nutch is an Apache effort to provide search engine services (akin to Google), including crawling, parsing, content analysis, and indexing. It has produced several stable software releases, and is currently used in production services at companies such as Yahoo, and at NASA's Planetary Data System. The CAS Crawling Framework supports many of the Nutch Crawler's generic services, including metadata extraction, crawling, and ingestion. However, one service that was not ported over from Nutch is a generic protocol layer service that allows the Nutch crawler to obtain content using protocol plug-ins that download content using implementations of remote protocols, such as HTTP, FTP, WinNT file system, HTTPS, etc. Such a generic protocol layer would greatly aid in the CAS Crawling Framework, as the layer would allow the framework to generically obtain content (i.e., data products) from remote sites using protocols such as FTP and others. Augmented with this capability, the Orbiting Carbon Observatory (OCO) and NPP (NPOESS Preparatory Project) Sounder PEATE (Product Evaluation and Analysis Tools Elements) would be provided with an infrastructure to support generic FTP-based pull access to remote data products, obviating the need for any specialized software outside of the context of their existing process control systems. This extensible configurable framework was created in Java, and allows the use of different underlying communication middleware (at present, both XMLRPC, and RMI). In addition, the framework is entirely suitable in a multi-mission environment and is supporting both NPP Sounder PEATE and the OCO Mission. Both systems involve tasks such as high-throughput job processing, terabyte-scale data management, and science computing facilities. NPP Sounder PEATE is already using the push-pull framework to accept hundreds of gigabytes of IASI (infrared atmospheric sounding interferometer) data, and is in preparation to accept CRIMS (Cross-track Infrared Microwave Sounding Suite) data. OCO will leverage the framework to download MODIS, CloudSat, and other ancillary data products for use in the high-performance Level 2 Science Algorithm. The National Cancer Institute is also evaluating the framework for use in sharing and disseminating cancer research data through its Early Detection Research Network (EDRN).

Foster, Brian M.↗

An Innovative High Throughput Genome Releaser for Rapid and Efficient PCR Screening

High-throughput PCR screening is vital in synthetic biology and metabolic engineering as it allows researchers to rapidly analyze and detect numerous targeted genetic mutation in the genome. Current challenges for high-throughput PCR screening in synthetic biology include efficiently preparing genomic DNA, optimizing protocols for diverse sample types, managing contamination risks, and effectively analyzing the large volumes of data generated while ensuring consistent and accurate results. In this study, we present the development of a High Throughput Genome Releaser (HTGR), an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed based on a squash method for rapid, cost-effective, and efficient DNA release, optimized for subsequent PCR reactions. After experimenting with various synthetic materials, we selected a plastic that closely replicates the smooth surface and compression properties of microscope slides, ensuring reliable performance. We engineered a device featuring a 96-Well Plate and a shear applicator, operable both manually and automatically, and compatible with standard liquid-handling robot platform. This compatibility enhances ease of use in high-throughput PCR workflows. Additionally, we developed software to support its automatic functions. Our results demonstrated that the specially engineered 96-Well Plate and HTGR can effectively squash fungal spores , which release enough genome DNA for PCR screening. The genome releaser facilitates the preparation of PCR-amplifiable genomic DNA substrate from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells, which could significantly advance biomanufacturing processes.

Yuan, Guoliang [BATTELLE (PACIFIC NW LAB)]↗

Overview of integrated programs for aerospace-vehicle design (IPAD)

An overview of a joint industry/government project, denoted Integrated Programs for Aerospace-Vehicle Design (IPAD), which focuses on development of technology and associated software for integrated company-wide management of engineering information is presented. Results to date are summarized and include an in-depth documentation of a representative design process for a large engineering project, the definition and design of computer-aided design software needed to support that process, and the release of prototype software to integrated selected design functions.

Fulton, R. E.↗

E-Area Low-Level Waste Facility GoldSim System Model

This report documents the development of the E-Area Low-Level Waste Facility (ELLWF) trench system model. The GoldSim® Monte Carlo simulation software is utilized to model the release and transport of radiological inventory disposed (both currently and in the future) within Engineered and Slit Trenches. This model is in support of the sensitivity and uncertainty analysis for the ELLWF Performance Assessment. The ELLWF system model utilizes a hybrid-approach to accurately describe the disposal system. The Hydrologic Evaluation of Landfill Performance model provides the infiltration data to both PORFLOW and GoldSim. PORFLOW is used to calibrate the GoldSim model to ensure confidence in the stochastic results. Finally, the concentrations from GoldSim transport simulations are fed into the SRNL Dose Toolkit to calculate dose impacts and assess plume interaction

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Advanced Modeling of Contaminant Fate and Transport in Soil and Groundwater from F-Canyon and the Central Laboratory Facility

F-Canyon (221-F) was constructed in the early 1950's and, together with FB Line, began operations in 1954 as the main processing facilities in FArea of SRS. The primary operations conducted in F-Canyon and FB Line included the separation and recovery of Pu-239 and U-238 from irradiated materials and the stabilization of plutonium residues. The F/H Laboratory Complex consists of buildings 772-F, 772-1F, and 772-4F which began operations in 1954, 1987, and 1993, respectively. The primary mission of the F/H Laboratory Complex for the last 45 years has been to support the chemical separations processing activities at Building 221-F and H-Canyon. The objective of this study is to determine the radionuclide and hazardous material holdup in F-Canyon and its support facilities, and to evaluate In-Situ Disposal (ISD) alternatives for deactivation and decommissioning (D and D) of these facilities to ensure groundwater protection and environmental compliance with the South Carolina Department of Health and Environmental Services (SCDHES) and the United States Environmental Protection Agency (USEPA). GoldSim is a dynamic probabilistic simulation software that allows modeling of chemical mass transport through engineered and environmental systems For this study, it will model the potential future release of radiological contamination through the vadose zone, Upper Three Runs (UTR) Aquifer and the Upper Three Runs Creek. Using a GoldSim model developed for building 235-F D and D, contaminant inventories as well as building geometry were updated to create the basis of the new F-Canyon model. The inventories from F-Canyon, FB Line, and the 800 Series Tanks (Tanks 804, 808, and 809) as well as F/H labs (including buildings 772-F, 772-1F, and 772- 4F) were used to make a total of four sources. The concentrations of total uranium and beta-gamma are within compliance for the study, while radium and alpha concentrations exceed their MCL's around 30,000 years and total effective water dose exceeds its MCL around 1,200 years. This suggests that some level of action will be needed to meet SCDHES and USEPA requirements. This evaluation was conducted only for the no-action alternative. Consideration and modeling of other alternatives will be required in the future to determine the best ISD alternative for D and D of F-Canyon and F/H labs with regard to groundwater protection, worker safety, and financial cost.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Software engineering

Today's software systems generally use obsolete technology, are not integrated properly with other software systems, and are difficult and costly to maintain. The discipline of reverse engineering is becoming prominent as organizations try to move their systems up to more modern and maintainable technology in a cost effective manner. The Johnson Space Center (JSC) created a significant set of tools to develop and maintain FORTRAN and C code during development of the space shuttle. This tool set forms the basis for an integrated environment to reengineer existing code into modern software engineering structures which are then easier and less costly to maintain and which allow a fairly straightforward translation into other target languages. The environment will support these structures and practices even in areas where the language definition and compilers do not enforce good software engineering. The knowledge and data captured using the reverse engineering tools is passed to standard forward engineering tools to redesign or perform major upgrades to software systems in a much more cost effective manner than using older technologies. The latest release of the environment was in Feb. 1992.

Fridge, Ernest M., III↗

High Throughput Genome Releaser

In this study, we present the development of a High Throughput Genome Releaser, an innovative device addressing common challenges in screening PCR. This genome DNA releaser is designed for rapid, cost-effective, and efficient DNA extraction, optimized for subsequent PCR reactions. Our experimentation with various synthetic materials led us to select a particular type of plastic that mirrors the properties of glass cover slides, providing a smooth surface and effective compression capabilities. We engineered a 96-well device equipped with a 96-well plate and a top rod, operable both manually and automatically, which is compatible with widely used liquid-handling robot decks. This compatibility enhances ease of use in high-throughput PCR setups. Additionally, we developed software to support its automatic functions. The genome releaser facilitates the extraction of PCR-amplifiable genomic DNA from 96 samples within minutes, eliminates the need for extraction buffers, and is adaptable to a wide range of microorganisms and cells. This versatility could significantly advance biomanufacturing processes.

42 ENGINEERING↗

Spiking Markov Reward Process v.0.1

SAND2024-11150O The Spiking Markov Reward Process software is a spiking neural network that streams binary arithmetic and computes the state value function of a Markov reward process. The software will be released to the SpiNNcloud group for development of neuromorphic acceleration. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Wang, Felix↗

The Core Flight System (cFS): NASA Quality Flight Software to Power Science and Exploration Available to the World

The presentation is planned to be a continuation of two previous discussions completed at the FSW Workshop regarding the cFS Test Framework (CTF) and Engineering Data Sheets (EDS). The presentation will also cover the latest advancements in cFS, including: 1. Quick into to cFS 2. An overview of our software release process + Git repo 3. Release of EDS files for the cFE + open-source apps 4. Overview of how to independently verify EDS files using CTF + what they can be used for. 5. Future plans for cFS. This presentation complements the talk on configuration management of distributed cFS repos, to be presented by Tam Ngo from Johnson Space Center.

Dan Knutsen↗

The DeepLynx Data Warehouse

Digital Engineering and the development of digital twins necessitate the use of highly sophisticated tools and software. These methodologies and systems bring many benefits but rely on accomplishing challenging goals such as disparate data and systems integration into a single cohesive and holistic system. Idaho National Laboratory has recently released an open-source data warehouse – DeepLynx – to help in the planning, creation, execution, and management of projects in the digital engineering space, with an emphasis on supporting digital twins in an operational space.

97 MATHEMATICS AND COMPUTING↗

STPPHAWKES

SAND2024-08541O STTPHAWKES software solution is a Bayesian estimation approach to a Hawkes process model that treats missing data as a latent variable in the estimation. The open-source software will be released to the R CRAN repository and Sandia National Labs’ Github. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Rowe, Stephen↗

The Kokkos Ecosystem [Brief]

In 2016/2017, the field of High-Performance Computing (HPC) entered a new era driven by fundamental physics challenges to produce ever more energy and cost-efficient processors. Since the convergence on the Message-Passing Interface (MPI) standard in the mid-1990s, application developers enjoyed a seemingly static view of the underlying machine — that of a distributed collection of homogeneous nodes executing in collaboration. However, after almost two decades of dominance, the sole use of MPI to derive parallelism acted as a limiter to improved future performance. While MPI is widely expected to continue to function as the basic mechanism for communication between compute nodes for the immediate future, additional parallelism is required on the computing node itself if high performance and efficiency goals are to be realized. When reviewing the architectures of the top HPC systems today, the change in paradigm is clear: the compute nodes of the leading machines in the world are either powered by many-core chips with a few dozen cores each, or use heterogeneous designs, where traditional CPUs marshal work to massively parallel compute accelerators which has as many as 200,000 processing threads in flight simultaneously. Complicating matters further for application developers, each processor vendor has its own preferred way of writing code for their architecture.The Kokkos EcoSystem was released by Sandia in 2017 to address this new era in HPC system design by providing a vendor independent performance portable programming system for scientific, engineering, and mathematical software applications written in the C++ programming language. Using Kokkos, application developers can be more productive because they will not have to create and maintain separate versions of their software for each architecture, nor will they have to be experts in each architecture's peculiar requirements. Instead, they will have a single method of programming for the diverse set of modern HPC architectures. While Kokkos started in 2011 as a programming model only, it soon became clear that complex applications needed more. It is also critical to have a portable mathematical functions and developers need tools to debug their applications, gain insight into the performance characteristics of their codes and tune algorithm performance parameters through automated processes. The Kokkos EcoSystem addresses those needs through its three main components: the Kokkos Core programming model, the Kokkos Kernels math library, and the Kokkos Tools project.

97 MATHEMATICS AND COMPUTING↗

Online NASA Software Estimating Tools (ONSET): A Suite of Web-Based Cost Analysis Tools

This paper provides an overview of ONSET theOnline NASA Software Estimating Tools suite of web-basedcosts analysis tools. ONSET is comprised of the AnalogySoftware Cost Tool (ASCoT) [1], and the CubeSat Or MicrosatProbabilistic and Analogies Cost Tool (COMPACT) [2]. TheOnline NASA Space Estimation Tool (ONSET) has beendeveloped to provide a standardized platform for hosting webbasedNASA cost estimation tools on NASA ONCE (OneNASA Cost Engineering). It evolved from the BETA version ofASCoT (The NASA Analogy Software Cost Tool) which wasreleased in 2017 and was presented at the 2017 IEEEAerospace Conference. This first release of ONSET contains anew version of ASCoT as well as the first official release ofCOMPACT (CubeSat Or Microsat Probabilistic + AnalogiesCost Tool). In this paper we will provide an overview ofONSET, all its features and a high-level summary of bothASCoT and COMPACT. The heart of both tools arealgorithms for analogy-based estimation based on system levelinputs.

Johnson, James↗

SNL ATDM Visualization (ECP ST Capability Assessment Report)

The SNL ATDM Data and Visualization work consolidates existing ATDM activities in scalable data management and visualization. Part of the responsibilities of the SNL ATDM Data and Visualization Project is the maintenance and development of visualization resources for ATDM applications on Exascale platforms. The ATDM Scalable Visualization project provides visualization and analysis required to satisfy the needs of the ASC/ATDM applications on next-generation, many-core platforms. This involves many activities including the re-engineering of visualization algorithms, services, and tools that enable ASC customers to carry out data analysis on ASC systems and ACES platforms. Current tools include scalable data analysis software released open source through ParaView, VTK, and Catalyst. We are also both leveraging and contributing to VTK-m, a many-core visualization library, to satisfy our visualization needs on advanced architectures. The scope of the Scalable Visualization under ATDM at SNL is R&D for the programming model and implementation of visualization code for ASC/ATDM projects and ASC/ATDM application support.

97 MATHEMATICS AND COMPUTING↗

Let your fingers do the walking: The projects most invaluable tool

The barrage of information pertaining to the software being developed for a project can be overwhelming. Current status information, as well as the statistics and history of software releases, should be 'at the fingertips' of project management and key technical personnel. This paper discusses the development, configuration, capabilities, and operation of a relational database, the System Engineering Database (SEDB) which was designed to assist management in monitoring of the tasks performed by the Network Control Center (NCC) Project. This database has proven to be an invaluable project tool and is utilized daily to support all project personnel.

Zirk, Deborah A.↗