Software Quality Engineering: Paving the path towards research reproducibility.
Abstract not provided.
Turgeon, Jennifer↗
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For the Public Good: Connecting, Retaining, and Recognizing Current and Future RSEs at U.S. National Research Laboratories and Agencies
U.S. national research laboratories and agencies play an integral role in advancing science and technology for the public good. The authors of this article, as research software engineers (RSEs) and allies from eight unique national R&D organizations, came together to explore RSE needs from the perspective of national institutions. We identified three key areas of improvement for future RSEs to pursue science in the national interest: community establishment, hiring and retention, and recognition. In conclusion, to retain and cultivate this essential talent, U.S. national institutions must evolve to support appropriate career pathways for RSEs, and to recognize and reward RSEs’ work.
42 ENGINEERING↗
Using Eye-Tracking to Quantify Reverse Engineering Expertise
Software reverse engineering (RE) requires analysts to closely read and make decisions about code. Little is known about what makes an analyst successful, making it difficult to train new analysts or design tools to augment existing ones. The goal of this project was to quantify the eye movement behaviors supporting RE and code comprehension more generally. We applied eye-tracking methods from the language comprehension literature to understand where analysts direct their attention over time when completing tasks (e.g., function identification, bug detection). Across three studies, we manipulated aspects of code hypothesized to impact comprehension (e.g., variable name meaningfulness, code complexity) and presentation methods (e.g., line-by-line, free viewing, gaze-contingent moving window) to understand effects on accuracy and gaze patterns. Results showed clear benefits of meaningful variable names, and effects of expertise on global and line-specific viewing patterns. Findings could inspire empirically-supported tool or analytic adaptations that help to reduce analyst workload.
97 MATHEMATICS AND COMPUTING↗
The challenges of theory-software translation
Background: Software is now ubiquitous within research. In addition to the general challenges common to all software development projects, research software must also represent, manipulate, and provide data for complex theoretical constructs. Ensuring this process of theory-software translation is robust is essential to maintaining the integrity of the science resulting from it, and yet there has been little formal recognition or exploration of the challenges associated with it. Methods: We thematically analyse the outputs of the discussion sessions at the Theory-Software Translation Workshop 2019, where academic researchers and research software engineers from a variety of domains, and with particular expertise in high performance computing, explored the process of translating between scientific theory and software. Results: We identify a wide range of challenges to implementing scientific theory in research software and using the resulting data and models for the advancement of knowledge. We categorise these within the emergent themes of design, infrastructure, and culture, and map them to associated research questions. Conclusions: Systematically investigating how software is constructed and its outputs used within science has the potential to improve the robustness of research software and accelerate progress in its development. We propose that this issue be examined within a new research area of theory-software translation, which would aim to significantly advance both knowledge and scientific practice.
97 MATHEMATICS AND COMPUTING↗
Engineering Computational Practices (Rev. 1)
This manual will attempt to motivate the use of an automated build system for the purposes of computational science and engineering. As part of this motivation, the surrounding computational practices of version control, documen tation, compute environment management, and regression testing will also be addressed as applied to the practice of computational engineering. Specifically, this manual intends to motivate the adoption of these traditional software engineering practices for use in research and production engineering simulation projects. This manual is not the first such effort in the greater scientific computing community. In fact, the authors relied heavily on the lesson plans of the Software Carpentry, established to teach computing skills to researchers in 1998. As the intention for this manual is to lay out fundamental practices of engineering computing, it will not attempt to fully teach the underlying concepts and will instead reference the well designed lesson plans of the Software Carpentry. Where possible, this manual will explain to general computing practices and concepts and limit discussion of specific software implementations to examples or vehicles for practice in concrete application. The specific software taught by the Software Carpentry curriculum is an excellent starting point to learn the core concepts of computational engi neering. However, the authors have found that applications to engineering simulation and analysis require translation of these software development concepts into the language and workflows of computational engineers. Adopting these computational tools may require engineers to re-imagine their workflows in some combination of traditional engineer ing and software concepts. It has also been necessary to extend existing software build systems for engineering practices beyond the simple wrap ping of engineering software execution. Where necessary, examples of specific software and their method of extension to engineering simulations will be given, with reference to the User Manual for recommended practical use. Where this manual relies on specific implementation examples, it should be understood that the practicing engineer may find that different software is more amenable to their specific work. It is always the overall collection of computational practices is more important than any specific software implementation. The ability to recognize which concepts are implemented by a software package will make a practicing engineer agile to changing project needs, computing resources, numeric solvers, programming languages, and even available funding.
42 ENGINEERING↗
Cyber-Informed Engineering Principles: What’s in it for me?
CIE is an emerging method to integrate cybersecurity considerations into the conception, design, development, and operation of any physical system that has digital connectivity, monitoring, or control. CIE complements—but does not replace—the application of cybersecurity standards or practices currently in place within an organization. Rather, it expands cybersecurity decisions into the engineering space, not by asking engineers to become cyber experts, but by calling on engineers to apply engineering tools and make engineering decisions that improve cybersecurity outcomes. CIE examines the engineering consequences that a sophisticated cyber attacker could achieve, and drives engineering changes that may provide deterministic mitigations to limit or eliminate those consequences. Engineers and technicians that design critical energy infrastructure installations can integrate the 12 principles of CIE into each phase of the engineering lifecycle, from concept to retirement. These principles are aimed at system or design engineers, operators, and technicians, rather than software engineers or operational cybersecurity practitioners, because the engineers who design, build, operate, and maintain the physical infrastructure are best positioned to leverage a system’s engineering design to diminish the severity of cyber attacks or digital technology failures. This approach creates new opportunities for engineering teams—and not just cybersecurity teams—to secure the system using the physics and mechanics of engineering controls—not just digital monitoring and controls.
99 GENERAL AND MISCELLANEOUS↗
Better together: Elements of successful scientific software development in a distributed collaborative community
Many scientific disciplines rely on computational methods for data analysis, model generation, and prediction. Implementing these methods is often accomplished by researchers with domain expertise but without formal training in software engineering or computer science. This arrangement has led to underappreciation of sustainability and maintainability of scientific software tools developed in academic environments. Some software tools have avoided this fate, including the scientific library Rosetta. We use this software and its community as a case study to show how modern software development can be accomplished successfully, irrespective of subject area. Rosetta is one of the largest software suites for macromolecular modeling, with 3.1 million lines of code and many state-of-the-art applications. Since the mid 1990s, the software has been developed collaboratively by the RosettaCommons, a community of academics from over 60 institutions worldwide with diverse backgrounds including chemistry, biology, physiology, physics, engineering, mathematics, and computer science. Developing this software suite has provided us with more than two decades of experience in how to effectively develop advanced scientific software in a global community with hundreds of contributors. Here we illustrate the functioning of this development community by addressing technical aspects (like version control, testing, and maintenance), community-building strategies, diversity efforts, software dissemination, and user support. We demonstrate how modern computational research can thrive in a distributed collaborative community. The practices described here are independent of subject area and can be readily adopted by other software development communities
97 MATHEMATICS AND COMPUTING↗
Near Real-time Data Analysis of Core-collapse Supernova Simulations with Bellerophon
We present an overview of a software system, Bellerophon, built to support a production-level HPC application called CHIMERA, which simulates core-collapse supernova events at the petascale. Developed over the last four years, Bellerophon enables CHIMERA's geographically dispersed team of collaborators to perform data analysis in near real-time. Its n-tier architecture provides an encapsulated, end-to-end software solution that enables the CHIMERA team to quickly and easily access highly customizable animated and static views of results from anywhere in the world via a web- deliverable, cross-platform desktop application. In addition, Bellerophon addresses software engineering tasks for the CHIMERA team by providing an automated mechanism for performing regression testing on a variety of supercomputing platforms. Elements of the team's workflow management needs are met with software tools that dynamically generate code repository statistics, access important online resources, and monitor the current status of several supercomputing resources.
97 MATHEMATICS AND COMPUTING↗
UQpy v4.1: Uncertainty quantification with Python
This paper presents the latest improvements introduced in Version 4 of the UQpy, Uncertainty Quantification with Python, library. In the latest version, the code was restructured to conform with the latest Python coding conventions, refactored to simplify previous tightly coupled features, and improve its extensibility and modularity. To improve the robustness of UQpy, software engineering best practices were adopted. A new software development workflow significantly improved collaboration between team members, and continuous integration and automated testing ensured the robustness and reliability of software performance. Continuous deployment of UQpy allowed its automated packaging and distribution in system agnostic format via multiple channels, while a Docker image enables the use of the toolbox regardless of operating system limitations.
97 MATHEMATICS AND COMPUTING↗
A Survey of Open Source Software Repositories in the U.S. Department of Energy’s National Laboratories
There are 17 national laboratory systems in the United States operating under the auspices of the U.S. Department of Energy (DOE). These government labs employ tens of thousands of people engaging in research software engineering activities across a variety of missions. To support this work, many open source projects are maintained. Further, many of these projects have broad utility to the computing community at large and domain scientists in a variety of fields. However, the complexity and decentralized nature of the laboratory system has resulted in a situation where no one entity even knows about all the open source software projects in this ecosystem, let alone crude metrics of their health. In this article, we do the first external inventory of open source software repositories with a nexus to DOE labs. We posit that a project’s need for sustainability support can be determined by comparing measures of active use to measures of active maintenance.
97 MATHEMATICS AND COMPUTING↗
FEARCE Development - Institutional Computing Report for 2019
This report details the development, uses ,and methods of FEARCE (Fast, Easy, Accurate, and Robust Continuum Engineering) software.
42 ENGINEERING↗
Impacts of software and its engineering on the carbon footprint of ICT
The energy consumption of information and communication technology (ICT) is still increasing. Even though several solutions regarding the hardware side of Green IT exist, the software contribution to Green IT is not well investigated. The carbon footprint is one way to rate the environmental impacts of ICT. In order to get an impression of the induced CO{sub 2} emissions of software, we will present a calculation method for the carbon footprint of a software product over its life cycle. We also offer an approach on how to integrate some aspects of carbon footprint calculation into software development processes and discuss impacts and tools regarding this calculation method. We thus show the relevance of energy measurements and the attention to impacts on the carbon footprint by software within Green Software Engineering.
54 ENVIRONMENTAL SCIENCES↗
Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|SpeedShop
In this project we created a community tool infrastructure for program development tools targeting Petascale class machines and beyond. This includes tools for performance analysis, debugging, and correctness tools, as well as tuning and optimization frameworks. The developed infrastructure provides a comprehensive and extensible set of individual tool building components. We started with the basic elements necessary across all tools in such an infrastructure followed by a set of generic core modules that allow a comprehensive performance analysis at scale. Further, we developed a methodology and workflow that allows others to add or replace modules, to integrate parts into their own tools, or to customize existing solutions. In order to form the core modules, we built on the existing Open|SpeedShop infrastructure and decomposed it into individual modules that match the necessary tool components. At the same time, we addressed the challenges found in performance tools for petascale systems in each module. When assembled, this instantiation of community tool infrastructure provides an enhanced version of Open|SpeedShop, which, while completely different in its architecture, provides scalable performance analysis for petascale applications through a familiar interface. This project also built upon and enhances capabilities and reusability of project partner components as specified in the original project proposal. The overall project team’s work over the project funding cycle was focused on several areas of research, which are described in the following sections. The reminder of this report also highlights related work as well as preliminary work that supported the project. In addition to the project partners funded by the Office of Science under this grant, the project team included several collaborators who contribute to the overall design of the envisioned tool infrastructure. In particular, the project team worked closely with the other two DOE NNSA laboratories Los Alamos and Sandia leveraging co-funding for Krell by ASC’s Common Computing Environment (CCE) program as laid out in the original proposal. The ASC CCE co-funding, coordinated through LLNL, was for 50% of the total project funding, with the ASC CCE portion of the funding going entirely to Krell, while the ASCR funding itself was split between Krell and the funded partners. This report covers the entire project from both funding sources. Additionally, the team leveraged the expertise of software engineering researchers from Carnegie Mellon University, who specialize in software framework design, in order to achieve a broadly acceptable component framework. The Component Based Tool Framework (CBTF) software has been released to the community. Information related to the project and the released software can be found on the CBTF wiki page at: http://sourceforge.net/p/cbtf/wiki/Home.
97 MATHEMATICS AND COMPUTING↗
Shadow of the Future: Developing Trust and Software within the Exascale Computing Project
Collaboration and team science are emerging areas of interest in software production. Historically, multi-institutional research collaborations are difficult to initiate and maintain, negatively impacting communication, negotiation, and dialogue between industry, government, and academic researchers. The Exascale Computing Project (ECP), a massive, multi-team, high-stakes initiative, facilitated broader research collaboration under a shared funding structure and extended timeline to support scientific discovery. Here, we conducted interviews with ECP teams, representing a variety of domain specialties, research institutions, and programming backgrounds. Using thematic analysis, we assessed how ECP’s structure created an environment of increased trust among projects and how software shared between teams facilitated sustained collaboration. We found that the expectation of future collaboration, i.e., the shadow of the future, greatly enhanced trust among teams and the quality of scientific software produced. Based on our findings within ECP projects, we connect to the existing literature on trust in software engineering and share recommendations for sustainable multi-institutional collaboration and shared best software practices.
Exascale computing project↗
Kokkos v.4.0
SAND2023-07883O Kokkos software implements C++ performance portability programming models, tools and math libraries, which enables science and engineering software developers to use single-source codes for a wide range of computer architectures. Kokkos also provides implementations of existing and proposed C++ standard features that support programming model and math libraries that are used for implementing performance-portable scientific and engineering applications. The Kokkos libraries provide algorithms, data structures, and tools to enable high-performance computing developers to write performance-portable code. Capabilities fall into three broad categories: Kokkos Core, Kokkos Kernels, and Kokkos Tools. 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.
SciDAC↗
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
We previously reported MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 is open source software and available at https://bitbucket.org/berkeleylab/metabat .
Kang, Dongwan↗
MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies
We previously reported on MetaBAT, an automated metagenome binning software tool to reconstruct single genomes from microbial communities for subsequent analyses of uncultivated microbial species. MetaBAT has become one of the most popular binning tools largely due to its computational efficiency and ease of use, especially in binning experiments with a large number of samples and a large assembly. MetaBAT requires users to choose parameters to fine-tune its sensitivity and specificity. If those parameters are not chosen properly, binning accuracy can suffer, especially on assemblies of poor quality. Here, we developed MetaBAT 2 to overcome this problem. MetaBAT 2 uses a new adaptive binning algorithm to eliminate manual parameter tuning. We also performed extensive software engineering optimization to increase both computational and memory efficiency. Comparing MetaBAT 2 to alternative software tools on over 100 real world metagenome assemblies shows superior accuracy and computing speed. Binning a typical metagenome assembly takes only a few minutes on a single commodity workstation. We therefore recommend the community adopts MetaBAT 2 for their metagenome binning experiments. MetaBAT 2 is open source software and available at https://bitbucket.org/berkeleylab/metabat .
59 BASIC BIOLOGICAL SCIENCES↗
An Approach to Automate tools for the Risk Assessment of Digital Instrumentation and Control Systems
Reliable digital instrumentation and control systems (DI&C) are integral for sustaining the continued operation of nuclear power plants. These systems ensure that nuclear reactors operate safely, efficiently, and within regulatory requirements. Yet, the cost of designing and licensing new nuclear DI&C can be prohibitively expensive. Under the U.S. Department of Energy Light Water Reactor Sustainability Program, Idaho National Laboratory has developed a framework for supporting the risk-informed design of DI&C systems by offering methods to support the identification, quantification, and evaluation of risks for various DI&C design architectures. The framework indicates potential software failure modes and provides pathways for quantifying the potential for these software failures, including common cause failures. Using the framework’s systematic approach, challenges for assessing risks within new and existing nuclear DI&C systems can be reduced. Nevertheless, the current framework can be further improved using the convenience of automation. This paper introduces the development of Software for the Hazard Identification and Evaluation of Digital Systems (SHIELDS). SHIELDS is an engineering software package that enables the identification, elimination, and mitigation of potential risks and reduces the burden of deploying reliable DI&C systems. This work introduces plans and techniques to digitize and improve the manual risk assessment modules of the framework. These improvements will save time and increase the repeatability and usability of the framework, making it more accessible to a wider range of users. Ultimately, this introduces SHIELDS and how its modules support efficient development of safe and reliable DI&C systems.
46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗