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The case for free and open source software in research and scholarship

Free and open source software (FOSS) is any computer program released under a licence that grants users rights to run the program for any purpose, to study it, to modify it, and to redistribute it in original or modified form. Here, our aim is to explore the intersection between FOSS and computational reproducibility. We begin by situating FOSS in relation to other ‘open’ initiatives, and specifically open science, open research, and open scholarship. In this context, we argue that anyone who actively contributes to the research process today is a computational researcher, in that they use computers to manage and store information. We then provide a primer to FOSS suitable for anyone concerned with research quality and sustainability—including researchers in any field, as well as support staff, administrators, publishers, funders, and so on. Next, we illustrate how the notions introduced in the primer apply to resources for scientific computing, with reference to the GNU Scientific Library as a case study. We conclude by discussing why the common interpretation of ‘open source’ as ‘open code’ is misplaced, and we use this example to articulate the role of FOSS in research and scholarship today.

97 MATHEMATICS AND COMPUTING↗

A simulation‐based integrated virtual testbed for dynamic optimization in smart manufacturing systems

Abstract In a manufacturing system, production control‐related decision‐making activities occur at different levels. At the process level, one of the main control activities is to tune the parameters of individual manufacturing equipment. At the system level, the main activity is to coordinate production resources and to route parts to appropriate workstations based on their processing requirement, priority indices, and control policy. At the factory level, the goal is to plan and schedule the processing of parts at different operations for the entire system in order to optimize certain objectives. Note that the results of such activities at different levels are closely coupled and affect the overall performance of the manufacturing system as a whole. Therefore, it is important to systematically integrate these control and optimization activities into one unified platform to ensure the goal of each individual activity is aligned with the overall performance of the system. In this paper, we develop a simulation‐based virtual testbed that implements dynamic optimization, automatic information exchange, and decision‐making from the process‐level, system‐level, and factory‐level of a manufacturing system into an integrated computation environment. This is demonstrated by connecting a Python‐based numerical computation program, discrete‐event simulation software (Simul8), and an optimization solver (CPLEX) via a third‐party master program. The application of this simulation‐based virtual testbed is illustrated by a case study in a machining shop.

Sun, Yuting↗

Extending C++ for Heterogeneous Quantum-Classical Computing

In this report we present qcor - a language extension to C++ and compiler implementation that enables heterogeneous quantum-classical programming, compilation, and execution in a single-source context. Our work provides a first-of-its-kind C++ compiler enabling high-level quantum kernel (function) expression in a quantum-language agnostic manner, as well as a hardware-agnostic, retargetable compiler workflow targeting a number of physical and virtual quantum computing backends. qcor leverages novel Clang plugin interfaces and builds upon the XACC system-level quantum programming framework to provide a state-of-the-art integration mechanism for quantum-classical compilation that leverages the best from the community at-large. qcor translates quantum kernels ultimately to the XACC intermediate representation, and provides user-extensible hooks for quantum compilation routines like circuit optimization, analysis, and placement. This work details the overall architecture and compiler workflow for qcor, and provides a number of illuminating programming examples demonstrating its utility for near-term variational tasks, quantum algorithm expression, and feed-forward error correction schemes.

97 MATHEMATICS AND COMPUTING↗

S4PST: Sustainability for Programming Systems and Tools: May Workshop Report

The US Department of Energy (DOE) Exascale Computing Project (ECP) has fostered and strengthened the use of modern software engineering practices for developing applications and libraries, and this effort has resulted in the coordinated and interoperable E4S1 and xSDK2 ecosystems. Although this approach is cost-effective, it relies on robust programming systems and tools (PST) as the underlying foundation for our HPC software. At present, our primary PST stack consists of traditional high-performance computing (HPC) languages, namely Fortran, C, C++, and the popular Python language for data analysis and AI workflows. These languages support various programming frameworks and run-time abstractions that enable parallelism and concurrency across multiple node architectures and thousands of nodes through a variety of interconnect systems. However, to accommodate users’ diverse needs, certain aspects of the HPC ecosystem are delegated to vendor-specific or third-party implementations that extend beyond a particular scientific domain. This broader scope results in a multitude of specifications and variations, which leads to a complex orchestration of many-ecosystems. Unfortunately, this complexity in the ecosystem imposes additional overhead costs on consumers during the latter stages of the development cycle. In addition to the software ecosystem challenge, the upcoming conclusion of the ECP by December 2023 has raised significant concerns within the HPC programming systems community, from both the economic and social perspectives. The ECP has implemented a management structure for software development and funding decisions across all ECP participants by following a conventional hierarchical and centralized approach. However, this structure has prompted certain considerations within the community, particularly in anticipation of the Software Sustainability initiative by the DOE’s Advanced Scientific Computing Research Program (ASCR). For the success of this new initiative, it is of utmost importance to secure consistent funding and foster close engagement with researchers and core developers of existing programming-system products. This collaboration is vital to maintaining the critical capabilities of the current software during the transition phase while proactively adapting to future technology and workforce trends. The community recognizes the significance of adapting to emerging trends and is aware of the inherent fragility of the HPC software ecosystem, particularly in relation to programming systems that cater to all users. The ability to adapt and evolve is essential to staying relevant and effectively addressing these technical, economic, and social challenges. The S4PST team, which represents one of the six ASCR Software Sustainability seedling projects, is dedicated to tackling these challenges through community-based approaches that go beyond the scope of the DOE. This involves collaboration between national laboratories with academia, non-DOE institutions, hardware and system vendors, and international partners. By fostering these partnerships, we aim to create a robust and sustainable HPC software ecosystem that can effectively meet the needs of the community. This new community effort, driven by the eight DOE labs, will take on the responsibility of guiding funding decisions for programming-systems development and maintenance with transparency and consistency across all decisions. Additionally, the team will offer common technical services to the programming systems community, irrespective of their funding situations, and facilitate community-wide incubation to proactively nurture the software ecosystem. By actively engaging with stakeholders and employing a collaborative approach, we can collectively shape the future of programming systems and ensure a robust and thriving HPC software landscape. On May 11–12, 2023, the S4PST team conducted its inaugural kick-off workshop at the Innovative Computing Laboratory (ICL) in the University of Tennessee, Knoxville, hosted by Hartwig Anzt. The workshop encompassed various sessions dedicated to presentations and discussions, with the aim of comprehending the team members’ perspectives on the vision of software sustainability. Additionally, the workshop aimed to identify the technical, economic, and social requirements for sustaining the programming-systems community in the field of HPC. This report provides a summary of the S4PST effort by highlighting five major thrust areas discussed during the workshop: (i) community, (ii) technical support, (iii) training and diversity, (iv) verification, validation and correctness, and (v) emerging technologies. It also encompasses an overview of the presentations and discussions held throughout the event, our views and potential synergies with other seedling efforts, along with the outcomes and key takeaways from our initial discussions.

97 MATHEMATICS AND COMPUTING↗

Virtual Engineering Software Framework for Integrated Biomass Conversion Modeling

This presentation covers the design and implementation of a software tool to systematically connect computational models of unit operations to simulate an integrated process of low-temperature conversion of biomass to fuel. This virtual engineering (VE) software was designed with the overarching goal of connecting unit models written in various programming languages and requiring different computational resources within a single, flexible framework. The models and features currently considered for the VE library include mechanistic models for pretreatment, enzymatic hydrolysis, and aerobic bioreaction; high-fidelity computational fluid dynamics (CFD) simulations for enzymatic hydrolysis and aerobic bioreaction; and the capability to perform techno-economic analyses (TEA) using Aspen Plus, a commercial software package. The CFD models require access to high-performance computing (HPC) resources, so in addition to handling multiple programming languages and interfaces, the VE software must also be capable of interacting with an HPC scheduler to submit, run, and post-process jobs. Using the Python programming language, a new VE software package has been developed that contains functionality to manage the input-output communication between various unit models, schedule simulations to run on NREL's HPC and analyze those results, and interface with existing TEA software workflows. A Jupyter-notebook GUI was also created to solicit user input and provide documentation. In cases where multiple models for a particular unit-operation exist, selection between models is accomplished through a simple checkbox, with the appropriate inputs and outputs being parsed and converted seamlessly in the background. Each operation makes use of a different programming language, but the flow of information from pretreatment to enzymatic hydrolysis to bioreaction is managed with an intuitive, centralized file-communication strategy. In this talk, the programming approach and implementation details of the notebook are presented for multiple possibilities of the conversion process, including a demonstration of the ability to manage HPC resources. Additionally, an example of a sensitivity study of treatment parameters governing the overall conversion outcome is shown which highlights the ease of defining new problems using the VE Notebook workflow and leads into a discussion of ongoing work to enable outer-loop optimization studies.

biofuel↗

Advanced Simulation and Computing: ASC FY24 Implementation Plan

The DOE National Nuclear Security Administration (NNSA) Stockpile Stewardship Program (SSP) is an integrated technical program for maintaining the safety, security, and reliability of the U.S. nuclear stockpile. The SSP incorporates nuclear test data, computational modeling and simulation, and experimental facilities to advance understanding of nuclear weapons. The suite of data analyzed comes from activities including previous nuclear tests, stockpile surveillance, experimental research, and development and engineering programs. This integrated national program requires the continued use of experimental facilities and the computational capabilities to support the SSP missions. These component parts, in addition to an appropriately scaled production capability, enable NNSA to support stockpile requirements. The ultimate goal of the SSP, and thus of the Advanced Simulation and Computing (ASC) program, is to ensure that the U.S. maintains a safe, secure, and effective strategic deterrent. The ASC program is a cornerstone of the SSP, providing simulation capabilities and computational resources to support the annual stockpile assessment and certification process, study advanced nuclear weapons design and manufacturing processes, analyze accident scenarios and weapons aging, and provide the tools to enable stockpile Life Extension Programs (LEPs) and the resolution of Significant Finding Investigations (SFIs). This work requires a balance of resources, including technical staff, hardware, simulation software, and computer science solutions. The ASC program focuses on increasing the predictive capabilities in a three-dimensional (3D) simulation environment while maintaining support to the SSP. The Program continues to improve its unique tools for understanding and solving progressively more difficult stockpile problems (sufficient resolution, dimensionality, and scientific details), and quantifying critical margins and uncertainties. Resolving each issue requires increasingly difficult analyses because the aging process has progressively moved the stockpile further from the original test base. While the focus remains on the U.S. nuclear weapons program, where possible, the Program also enables the use of high-performance computing (HPC) and simulation tools to address broader national security needs, such as foreign nuclear weapon assessments and nuclear counterterrorism. The 2022 Nuclear Posture Review (NPR) calls for NNSA to “deliver a modern, adaptive nuclear security enterprise based on an integrated strategy for risk management, production-based resilience, science and technology innovation, and workforce initiatives.” Furthermore, “NNSA will establish a Science and Technology Innovation Initiative to accelerate the integration of science and technology (S&T) throughout its activities.” Executing this strategy necessitates the continued emphasis on developing and sustaining high-quality scientific and engineering staff, as well as supporting computational and experimental capabilities. These components constitute the foundation of the nuclear weapons program. The continued success of the SSP and LEPs is predicated upon the ability to credibly certify the stockpile, without a return to underground nuclear tests (UGTs). Shortly after the nuclear test moratorium entered into force in 1992, the Accelerated Strategic Computing Initiative (ASCI) was established to provide an extensive simulation capability to underpin stockpile certification. While computing and simulation have always been essential to the success of the nuclear weapons program, the program goal of ASCI was to execute NNSA’s vision of using these tools in support of the stockpile stewardship mission. The ASCI program was essential to the successful demonstration of the SSP, providing critical nuclear weapons simulation and modeling capabilities. ASCI officially evolved into the ASC program in fiscal year (FY) 2005, but the mission remains essentially the same: provide the simulation and computational capabilities that underpin the ability to maintain a safe, secure, effective nuclear weapon stockpile, without returning to underground nuclear testing. The capabilities that the ASC program provides at the national laboratories play a vital role in the nuclear security enterprise and are necessary for fulfilling the stockpile stewardship and life extension requirements outlined for NNSA. The Program develops modern simulation tools that provide insights into stockpile aging issues, provide the computational and simulation tools that enable designers and analysts to certify the current stockpile and life-extended nuclear weapons, and inform the decision-making process when any modifications in nuclear warheads or the associated manufacturing processes are deemed necessary. Furthermore, ASC is enhancing the predictive simulation capabilities that are essential to evaluate weapons effects, design experiments, and ensure test readiness. The ASC program continues to improve its unique tools to solve stockpile problems— with a focus on sufficient resolution, dimensionality, and scientific detail—to enable Quantification of Margins and Uncertainties (QMU) and to resolve the increasingly difficult analyses needed for stockpile stewardship. The needs of the Stockpile Management and Production Modernization programs (formerly Directed Stockpile Work) also drive the requirements for simulation and computational resources. These requirements include planned LEPs, stockpile support activities, and mitigation efforts against the potential for technical surprise. All of the weapons within the current stockpile are in some stage of the life extension process. The simulation and computational capabilities are crucial for successful execution of these life extensions and for ensuring NNSA can certify these life-extended weapons without conducting a UGT.

97 MATHEMATICS AND COMPUTING↗

Reducing the small-heart effect in pediatric gated myocardial perfusion single-photon emission computed tomography

Background: We compared two reconstruction algorisms and two cardiac functional evaluation software programs in terms of their accuracy for estimating ejection fraction (EF) of small hearts (SH). Methods: The study group consisted of 66 pediatric patients. Data were reconstructed using a filtered back projection (FBP) method without the resolution correction (RC) and an iterative method based on an ordered subset expectation maximization (OSEM) algorithm with the RC. EF was evaluated using two software programs of quantitative gated single-photon emission computed tomography (SPECT) (QGS) and cardioREPO. We compared the EF of gated myocardial perfusion SPECT to echocardiographic measurement (Echo). Results: Forty-eight of 66 patients had an end-systolic volume < 20 mL which was used as the criterion for being included in the SH group, and the SH effect led to an overestimation of EF. While significant differences were observed between Echo (66.9 ± 5.0%) and QGS-FBP without RC (76.9 ± 8.4%, P < .0001), QGS-OSEM with RC (76.6 ± 8.6%, P < .0001), and cardioREPO-FBP without RC (72.1 ± 10.0%, P = .0011), no significant difference was observed between Echo and cardioREPO-OSEM with RC (67.4 ± 6.1%) in SH group. Conclusions: In pediatric gated myocardial perfusion SPECT, the SH effect can be significantly reduced when an OSEM algorithm is used with RC in combination with the specific cardioREPO algorithm.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

LLNL Response to the DOE ASCR RFI, "Stewardship of Software for Scientific and High-Performance Computing"

For decades, Lawrence Livermore National Laboratory (LLNL) has been engaged in significant research, development, and support for software to enable scientific computing and, particularly, the use of high performance computing (HPC) in the NNSA mission space. In particular, the move in the mid-1990’s to simulation as a leading component of stockpile stewardship through the ASCI and the successor ASC programs, as well as the need for reliable data acquisition and control software for the National Ignition Facility, have been important drivers in building expertise in production-quality software development at LLNL. LLNL has also been a leader in the DOE SciDAC FASTMath Institute and the DOE Exascale Computing Project (ECP), both of which have striven to make scientific computing software – in particular, the enabling technologies underpinning simulation capabilities – more widely adopted and sustainable. As such, we believe that our experience can inform the broader goal of software stewardship for scientific and high-performance computing. LLNL strongly supports the formation of a new DOE ASCR program element in software stewardship and sustainment. Historically, DOE ASCR has funded applied mathematics and computer science research that has led to the development of important new capabilities and algorithms that are expressed as artifacts in research software. Such frameworks, libraries, and tools have seldom been directly funded to address the important issues of code maintenance, documentation, robustness, and community building. Software engineering and support have typically been done on the side in support of the ASCR-driven research products. DOE funding priorities have been slow to recognize that good software engineering, the kind that ensures research investments have more adoption and longevity, requires significant resources. Based upon our experiences, we have prepared this response to highlight the concerns and issues we believe to be important as DOE ASCR considers its role in scientific software stewardship. We believe that role is important and will require a significant investment of new funding to legitimately support the technologies past and future DOE ASCR investments have and will produce to facilitate their uptake and adoption in the broader scientific computing community. Following a summary of our involvement in scientific software development, the remainder our response is organized around the nine topics specifically identified in the RFI.

97 MATHEMATICS AND COMPUTING↗

Job Management with mpi_jm

About this book: This book constitutes the refereed post-conference proceedings of 13 workshops held at the 33rd International ISC High Performance 2018 Conference, in Frankfurt, Germany, in June 2018: HPC I/O in the Data Center, HPC-IODC 2018; Workshop on Performance and Scalability of Storage Systems, WOPSSS 2018; 13th Workshop on Virtualization in High­-Performance Cloud Computing, VHPC 2018; Third International Workshop on In Situ Visualization, WOIV 2018; 4th International Workshop on Communication Architectures for HPC, Big Data, Deep Learning and Clouds at Extreme Scale, ExaComm 2018; International Workshop on OpenPOWER for HPC, IWOPH 2018; IXPUG Workshop: Many-Core Computing on Intel Processors; Workshop on Sustainable Ultrascale Computing Systems; Approximate and Transprecision Computing on Emerging Technologies, ATCET 2018; First Workshop on the Convergence of Large-Scale Simulation and Artificial Intelligence; Third Workshop for Open Source Supercomputing, OpenSuCo 2018; First Workshop on Interactive High-Performance Computing; Workshop on Performance Portable Programming Models for Accelerators, P^3MA 2018. The 53 full papers included in this volume were carefully reviewed and selected from 80 submissions. They cover all aspects of research, development, and application of large-scale, high performance experimental and commercial systems. Topics include HPC computer architecture and hardware; programming models, system software, and applications; solutions for heterogeneity, reliability, power efficiency of systems; virtualization and containerized environments; big data and cloud computing; and artificial intelligence.

Berkowitz, Evan↗

Position Papers for the 2024 ASCR Workshop on Energy-Efficient Computing for Science

On behalf of the Advanced Scientific Computing Research (ASCR) program in the US Department of Energy (DOE) Office of Science, we are organizing a Workshop on Energy-Efficient Computing for Science (EECS). Energy efficiency involves coordination across all the interoperating components of a computing system—in particular, applications, algorithms, system software, programming models, data management, and the hardware on which they run. Looking 10-15 years into the future, the goal is to dramatically lower the energy costs of the computational platforms (from the data center to the edge) serving DOE science while expanding the capabilities of these systems, broadening their applicability to science challenges of interest to DOE and the nation.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

XPRESS: eXascale PRogramming Environment and System Software

The XPRESS Project is one of four major projects of the DOE Office of Science Advanced Scientific Computing Research X-stack Program initiated in September, 2012. The purpose of XPRESS is to devise an innovative system software stack to enable practical and useful exascale computing around the end of the decade with near-term contributions to efficient and scalable operation of trans-Petaflops performance systems in the next two to three years; both for DOE mission-critical applications. To this end, XPRESS directly addresses critical challenges in computing of efficiency, scalability, and programmability through introspective methods of dynamic adaptive resource management and task scheduling.

97 MATHEMATICS AND COMPUTING↗

Connecting Minds: AI Use Cases to Bridge Power Systems and Large Language Models for Practical Applications

Recent advances in artificial intelligence (AI) and development of large language models (LLMs) present the opportunity to develop a new generation of power systems applications. In contrast with early power system AI applications based on structured numerical data, LLMs offer unique capabilities to perform logical reasoning using text documents, unstructured data, and application programming interface (API) calls to computational software. This paper seeks to bridge the knowledge gap between power systems engineers and LLM developers through a crosscutting explanation of use cases, characteristics, requirements, practical considerations from the perspectives of both LLM capabilities and industry needs. Specific focus is given to applications that can be realistically deployed by electric utilities. After introducing the architecture of LLMs and unique challenges of the power systems domain, this paper proposes twenty representative LLM applications grouped into categories of 1) power system operations, 2) asset management, 3) system planning and analytics, and 4) energy management and protection systems. Five use cases are presented within each category with descriptions of the motivation, objectives, approaches, example inputs / outputs, and benefits of each use case.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Providing a Flexible and Comprehensive Software Stack Via Spack, an Extreme-Scale Scientific Software Stack, and Software Development Kits

To manage the complex demands of modern high-performance computing (HPC), software applications increasingly depend on software developed by other teams, often at other institutions. An HPC software ecosystem approach is required to support dependencies on third-party scientific software. An ecosystem approach provides layers of activity above the individual software product level that promote interoperability, quality improvement, porting, testing, and deployment. The U.S. Exascale Computing Project (ECP) developed its HPC software ecosystem using a three-pronged approach. First, the ECP adopted and invested in Spack, a package manager designed to handle complex HPC package dependencies. Second, the ECP created the Extreme Scale Scientific Software Stack, an effort that supports developing, deploying, and running scientific applications on HPC platforms. Third, the ECP supported software product communities, or software development kits, to develop and promote best practices, improve software interoperability, and other collaborative efforts. This article describes ECP contributions to HPC software ecosystem challenges.

97 MATHEMATICS AND COMPUTING↗

Architecture for Quantum Time-dependent Circuits (ArQTIC) v1.0

ArQTiC is a domain-specific full-stack software package built for the dynamic simulations of materials on quantum computers. Its main contributions include providing a software library for high-level programming of such simulations on quantum computers, and providing post-processing capabilities that allow users to more efficiently analyze results from the quantum computer. Paired with the power to optimize and execute quantum circuits, ArQTiC opens the field of dynamic materials simulations on quantum computers to a broader community of scientists from a wider range of domain sciences, paving the way for accelerated progress towards physical quantum supremacy.

Bassman, Lindsay↗

Theoretical Multinary Perovskite Oxides Dataset

Perovskite oxides (ternary chemical formula ABO3) are a diverse class of materials with applications including heterogeneous catalysis, solid-oxide fuel cells, thermochemical conversion, and oxygen transport membranes. However, their multicomponent chemical space is underexplored due to the immense number of possible compositions. To expand the number of computed compounds we report a dataset of 66,516 theoretical multinary oxides, 59,708 of which are perovskites. First, the AA'BB'O6 compositions were generated in the a-b+a- Glazer tilting mode using the computationally-inexpensive Structure Prediction and Diagnostic Software (SPuDS) program. Next, we optimized these structures with DFT using parameters compatible with the Materials Project (MP) database. Our dataset contains these optimized structures and their formation (ΔHf) and decomposition enthalpies (ΔHd) computed relative to MP tabulated elemental references and competing phases, respectively. This dataset can be mined, used to train machine learning models, and rapidly and systematically expanded by optimizing more SPuDS-generated AA'BB'O6 perovskite structures using MP-compatible DFT calculations

Bare, Zachary↗

Dataset of theoretical multinary perovskite oxides

Perovskite oxides (ternary chemical formula ABO 3 ) are a diverse class of materials with applications including heterogeneous catalysis, solid-oxide fuel cells, thermochemical conversion, and oxygen transport membranes. However, their multicomponent (chemical formula $A_xA^{'}_{1-x}B_yB^{'}_{1-y}O_3$) chemical space is underexplored due to the immense number of possible compositions. To expand the number of computed $A_xA^{'}_{1-x}B_yB^{'}_{1-y}O_3$ compounds we report a dataset of 66,516 theoretical multinary oxides, 59,708 of which are perovskites. First, 69,407 $A_{0.5}A^{'}_{0.5}B_{0.5}B^{'}_{0.5}O_3$ compositions were generated in the a - b + a - Glazer tilting mode using the computationally-inexpensive Structure Prediction and Diagnostic Software (SPuDS) program. Next, we optimized these structures with density functional theory (DFT) using parameters compatible with the Materials Project (MP) database. Our dataset contains these optimized structures and their formation (ΔH f ) and decomposition enthalpies (ΔH d ) computed relative to MP tabulated elemental references and competing phases, respectively. This dataset can be mined, used to train machine learning models, and rapidly and systematically expanded by optimizing more SPuDS-generated $A_{0.5}A^{'}_{0.5}B_{0.5}B^{'}_{0.5}O_3$ perovskite structures using MP-compatible DFT calculations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗