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At least 37 records · Page 2

The MolSSI QCArchive project: An open-source platform to compute, organize, and share quantum chemistry data

The Molecular Sciences Software Institute's (MolSSI) Quantum Chemistry Archive (QCArchive) project is an umbrella name that covers both a central server hosted by MolSSI for community data and the Python-based software infrastructure that powers automated computation and storage of quantum chemistry (QC) results. The MolSSI-hosted central server provides the computational molecular sciences community a location to freely access tens of millions of QC computations for machine learning, methodology assessment, force-field fitting, and more through a Python interface. Facile, user-friendly mining of the centrally archived quantum chemical data also can be achieved through web applications found at the website. The software infrastructure can be used as a standalone platform to compute, structure, and distribute hundreds of millions of QC computations for individuals or groups of researchers at any scale. The QCArchiveInfrastructure is open-source (BSD-3C), code repositories can be found at github, and releases can be downloaded via PyPI and Conda. This article is categorized under: Electronic Structure Theory > Ab Initio Electronic Structure Methods Software > Quantum Chemistry Data Science > Computer Algorithms and Programming

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

High Energy Physics Network Requirements Review: Final Report, July 2024–December 2024

The world-class research infrastructure at the US Department of Energy (DOE) Office of Science (SC) provides the research community with premier observational, experimental, computational, and network capabilities. Each user facility is designed to provide unique capabilities to advance the core DOE mission in science and technology for its SC program to stimulate rich scientific discoveries and enhance its innovation ecosystem. Research communities gather and flourish around each user facility, bringing together new and enhanced perspectives. The continual reinvention of the practice of science — as users and staff forge novel approaches expressed in research workflows — unlocks new discoveries and propels scientific progress. Within this research ecosystem, the high-performance computing (HPC) and networking user facilities stewarded by the SC’s Advanced Scientific Computing Research (ASCR) program play a dynamic cross-cutting role, enabling complex workflows demanding high-performance data, networking, and computing solutions. The ASCR facilities enterprise seeks to understand and meet the needs and requirements across SC and DOE domain science programs and priority efforts, highlighted by the formal requirements review methodology. Between July and December 2024, the Energy Sciences Network (ESnet) and the Office of High Energy Physics (HEP) of the DOE-SC organized an ESnet requirements review of HEP-supported program activities. Preparation for these events included identification of key stakeholders: program and facility management, research groups, and technology providers. Each stakeholder group was asked to prepare formal case study documents about its relationship to the HEP program to build a complete understanding of the current, near-term, and long-term status, expectations, and processes that will support the science going forward.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Transforming Science Through Software: Improving While Delivering 100×

The U.S. Department of Energy (DOE) Exascale Computing Project (ECP) funded the development of new (and the transformation of important existing) applications, libraries, and tools that realized improvement in performance and capabilities of often 100 times or more on emerging exascale computers. This exceptional gain inspired the title of this special issue: Transforming Science through Software: Improving while delivering 100X. The term 100X refers to advancing capabilities in modeling, simulation, and analysis by a factor of 100 or more using some combination of new algorithms, optimization techniques, software libraries, and programming models, coupled with the next generation of hardware for high-performance computing (HPC). The papers in this issue share experiences with the practice and science of scientific software development, with an emphasis on developing a coherent, portable, and sustainable HPC software ecosystem for next-generation computational science. Finally, we hope to foster expanded community efforts related to the fundamental role of sustainable scientific software ecosystems in advancing the computing sciences.

97 MATHEMATICS AND COMPUTING↗

Good practices for documenting AI-based studies on energy and buildings

Artificial intelligence has transformed building science research over the past decade, with applications spanning energy modeling, energy prediction, HVAC optimization and controls, fault detection, and occupancy modeling. However, many studies lack adequate documentation of datasets, algorithms, training procedures, and validation methods. Building science research faces additional challenges including inconsistent evaluation metrics, limited generalizability across building types, climates, and significant gaps between experimental studies and deployed systems. This communication provides practical guidance for good practices in documenting and publishing AI-based research following established standards from the computer science and machine learning communities. By adopting frameworks such as Datasheets for Datasets, Model Cards, and standardized reproducibility checklists, researchers can ensure their work meets the rigorous documentation standards necessary for reproducible, comparable, and impactful building science research.

Hong, Tianzhen [Lawrence Berkeley National Laborat↗

A differentiable approach to the maximum independent set problem using dataless neural networks

The success of machine learning solutions for reasoning about discrete structures has brought attention to its adoption within combinatorial optimization algorithms. Such approaches generally rely on supervised learning by leveraging datasets of the combinatorial structures of interest drawn from some distribution of problem instances. Reinforcement learning has also been employed to find such structures. Here, in this paper, we propose a different approach in that no data is required for training the neural networks that produce the solution. In this sense, what we present is not a machine learning solution, but rather one that is dependent on neural networks and where backpropagation is applied to a loss function defined by the structure of the neural network architecture as opposed to a training dataset. In particular, we reduce the popular combinatorial optimization problem of finding a maximum independent set to a neural network and employ a dataless training scheme to refine the parameters of the network such that those parameters yield the structure of interest. Additionally, we propose a universal graph reduction procedure to handle large-scale graphs. The reduction exploits community detection for graph partitioning and is applicable to any graph type and/or density. Experimental results on both real and synthetic graphs demonstrate that our proposed method performs on par or outperforms state-of-the-art learning-based methods in terms of the size of the found set without requiring any training data.

97 MATHEMATICS AND COMPUTING↗

Community-Driven Methods for Open and Reproducible Software Tools for Analyzing Datasets from Atom Probe Microscopy

Atom probe tomography, and related methods, probe the three-dimensional architecture of a material. The software tools that microscopists use, and how these tools are connected into workflows, makes a substantial contribution to the accuracy and precision of such a material characterization experiment. Typically, we adapt methods from other communities like mathematics, data science, computational geometry, artificial intelligence, or scientific computing. We also realize that improving on research data management is a challenge when it comes to align with the FAIR data stewardship principles. Faced with this global challenge, we are convinced that collaborating is useful. Here, we report the results and challenges with an inter-laboratory call for developing test cases for several types of atom probe software tools. The results support why defining detailed recipes of software workflows and sharing these recipes is necessary and rewarding: Open source tools and (meta)data exchange can help to make our day-to-day data processing tasks become more efficient, the training of new users and knowledge transfer become easier, and assist us with automated quantification of uncertainties to gain access to substantiated results.

36 MATERIALS SCIENCE↗

Robust A-Optimal Experimental Design for Sensor Placement in Bayesian Linear Inverse Problems

Optimal design of experiments for Bayesian inverse problems has recently gained wide popularity and attracted much attention, especially in the computational science and Bayesian inversion communities. An optimal design maximizes a predefined utility function that is formulated in terms of the elements of an inverse problem, an example being optimal sensor placement for parameter identification. The state-of-the-art algorithmic approaches following this simple formulation generally overlook misspecification of the elements of the inverse problem, such as the prior or the measurement uncertainties. This work presents an efficient algorithmic approach for designing optimal experimental design schemes for Bayesian linear inverse problems such that the optimal design is robust to misspecification of elements of the inverse problem. Specifically, we consider a worst-case scenario approach for the uncertain or misspecified parameters, formulate robust objectives, and propose an algorithmic approach for optimizing such objectives. Furthermore, both relaxation and stochastic solution approaches are discussed with detailed analysis and insight into the interpretation of the problem and the proposed algorithmic approach. Extensive numerical experiments to validate and analyze the proposed approach are carried out for sensor placement in a parameter identification problem.

Bayesian inverse problems↗

Network Slicing for Federated Learning in Operational Technology Environment

Industrial Control Systems (ICS) and Supervisory Control and Data Acquisition (SCADA) environments are essential to modern infrastructure, facing challenges in ensuring low-latency, high-throughput communication while mitigating cyber threats. This paper presents a framework integrating Federated Learning (FL) and network slicing with Quality of Service (QoS) to enable real-time monitoring without disrupting OT operations. Leveraging digital twin technology and Network Function Virtualization (NFV), the architecture supports predictive analytics and Industry 4.0 requirements. FL facilitates decentralized model training, preserving data privacy and scalability, though it introduces potential throughput constraints. Network slicing addresses this by creating dedicated virtualized segments optimized for performance and security. Advanced fault tolerance at the container and instance levels enhances system reliability. The proposed architecture ensures high throughput, low latency, and secure orchestration for real-time anomaly detection in OT networks. Performance evaluations validate its efficiency in throughput, deployment, and learning accuracy, providing a robust foundation for future ICS automation and data-driven decision-making.

Delgado, Brian G. Rodiles [University of Texas at ↗

Hands-On Computer Science: The Array of Things Experimental Urban Instrument

Chicago's Array of Things (AoT) project is aptly described as a technology experiment or a "smart city" prototype. The concept of such an extensible "instrument" arose within a larger translational research vision applying computer science and engineering research for the multidimensional benefit of people and communities in cities. The AoT project hypothesized that wireless intelligent sensor networks could enable both quantitative social science and urban monitoring while also stimulating youth interest in science and technology. Successful deployment of such sensor networks could provide open data from urban measurements not only in support of diverse research questions-in environmental dynamics, urban architecture, engineering, and social sciences-but also informing community groups and city planners. Further, the AoT project and its successor SAGE project are a computer science and engineering experiment, but its success is inextricably tied to community engagement and experiential education. Simply put, community acceptance is a prerequisite to installing and testing the instrument.

97 MATHEMATICS AND COMPUTING↗

A Case Study of Multimodal, Multi-institutional Data Management for the Combinatorial Materials Science Community

Although the convergence of high-performance computing, automation, and machine learning has significantly altered the materials design timeline, transformative advances in functional materials and acceleration of their design will require addressing the deficiencies that currently exist in materials informatics, particularly a lack of standardized experimental data management. The challenges associated with experimental data management are especially true for combinatorial materials science, where advancements in automation of experimental workflows have produced datasets that are often too large and too complex for human reasoning. The data management challenge is further compounded by the multimodal and multi-institutional nature of these datasets, as they tend to be distributed across multiple institutions and can vary substantially in format, size, and content. Furthermore, modern materials engineering requires the tuning of not only composition but also of phase and microstructure to elucidate processing–structure–property–performance relationships. To adequately map a materials design space from such datasets, an ideal materials data infrastructure would contain data and metadata describing (i) synthesis and processing conditions, (ii) characterization results, and (iii) property and performance measurements. In this work, we present a case study for the low-barrier development of such a dashboard that enables standardized organization, analysis, and visualization of a large data lake consisting of combinatorial datasets of synthesis and processing conditions, X-ray diffraction patterns, and materials property measurements generated at several different institutions. While this dashboard was developed specifically for data-driven thermoelectric materials discovery, we envision the adaptation of this prototype to other materials applications, and, more ambitiously, future integration into an all-encompassing materials data management infrastructure.

36 MATERIALS SCIENCE↗

US Department of Energy, Office of Science, High-Performance Computing Facility 2024 Operational Assessment Oak Ridge Leadership Computing Facility

The Oak Ridge Leadership Computing Facility (OLCF) was established to accelerate scientific discovery by providing world-leading computational performance and advanced data infrastructure to the US Department of Energy (DOE) computing community. As a DOE Office of Science user facility, the OLCF has managed the successful deployment and operation of a succession of leadership-class resources dedicated to open science. In addition to these resources, the OLCF staff continually strive to develop innovative processes and technologies, improve security, and empower users through effective allocation management and comprehensive user support and training. These efforts support the advancement of science by the OLCF users and benefit high-performance computing (HPC) facilities around the world.

97 MATHEMATICS AND COMPUTING↗

Distinguished honors for LANL ASC program associates: E.O. Lawrence Awards and Laboratory Fellow Appointments

LANL ASC program associates have been honored as recipients of highly competitive scientific achievement awards. Luis Chacon and Dana Dattelbaum received DOE E.O. Lawrence awards in 2021 and 2020, respectively. Tim Germann, Lin Yin, Ricardo Lebensohn and Hui Li were four of nine LANL Laboratory Fellows appointed for membership in 2022. Each of these awardees has been an influential technical leader in computational sciences impacting both the ASC program and international scientific communities.

97 MATHEMATICS AND COMPUTING↗

Fusion Energy Sciences Network Requirements Review: Mild-cycle Update

The US Department of Energy (DOE) Office of Science (SC) world-class research infrastructure provides the research community with premier observational, experimental, computational, and network capabilities. Each user facility is designed to provide unique capabilities to advance core DOE mission science for its sponsor SC program and to stimulate a rich discovery and innovation ecosystem. Research communities gather and flourish around each user facility, bringing together diverse perspectives. The continual reinvention of the practice of science — as users and staff forge novel approaches expressed in research workflows — unlocks new discoveries and propels scientific progress.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

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↗

Co-design for Particle Applications at Exascale

Co-design across the Exascale Computing Project (ECP) has been critical for both enabling science applications and bringing disparate communities together. Developing and porting applications to the various high-performance computing (HPC) architectures on pre-exascale and exascale computers has been quite challenging due to the diversity of hardware features and software stacks. The Co-design Center for Particle Applications (CoPA) has developed and enhanced the Cabana and PROGRESS/BML libraries to facilitate the creation of new particle applications, make existing particle applications exascale capable, and allow teams to explore new capabilities. Particle methods from atomistic, mesoscale, continuum, through cosmological scales have been built with Cabana, along with new possibilities for application coupling. Similarly, the PROGRESS/BML library has enabled quantum particle applications with linear algebra solvers to use advanced hardware. Across these CoPA-developed libraries, the co-design abstraction layer combines performance portability with math library support to facilitate separation of concerns and directly support science runs.

97 MATHEMATICS AND COMPUTING↗

ESnet Requirements Review Program Through the IRI Lens: A Meta-Analysis of Workflow Patterns Across DOE Office of Science Programs (Final Report)

The Department of Energy (DOE) ensures America’s security and prosperity by addressing its energy, environmental, and nuclear challenges through transformative science and technology solutions. The DOE’s Office of Science (SC) delivers groundbreaking scientific discoveries and major scientific tools that transform our understanding of nature and advance the energy, economic, and national security of the United States. The SC’s programs advance DOE mission science across a wide range of disciplines and have developed the research infrastructure needed to remain at the forefront of scientific discovery. The DOE SC’s world-class research infrastructure — exemplified by the 28 SC scientific user facilities — provides the research community with premier observational, experimental, computational, and network capabilities. Each user facility is designed to provide unique capabilities to advance core DOE mission science for its sponsor SC program and to stimulate a rich discovery and innovation ecosystem. Research communities gather and flourish around each user facility, bringing together diverse perspectives. A hallmark of many facilities is the large population of students, postdoctoral researchers, and early-career scientists who contribute as full-fledged users. These facility staff and users collaborate over years to devise new approaches to utilizing the user facility’s core capabilities. The history of the SC user facilities has many examples of wildly inventive researchers challenging operational orthodoxy to pioneer new vistas of discovery; for example, the use of the synchrotron X-ray light sources for study of proteins and other large biological molecules. This continual reinvention of the practice of science — as users and staff forge novel approaches expressed in research workflows — unlocks new discoveries and propels scientific progress. Within this research ecosystem, the high-performance computing (HPC) and networking user facilities stewarded by SC’s Advanced Scientific Computing Research (ASCR) program play a dynamic cross-cutting role, enabling complex workflows demanding high performance data, networking, and computing solutions. The DOE SC’s three HPC user facilities and the Energy Sciences Network (ESnet) high-performance research network serve all of the SC’s programs as well as the global research community. Argonne Leadership Computing Facility (ALCF), the National Energy Research Scientific Computing Center (NERSC), and Oak Ridge Leadership Computing Facility (OLCF) conceive, build, and provide access to a range of supercomputing, advanced computing, and large-scale data-infrastructure platforms, while ESnet interconnects DOE SC research infrastructure and enables seamless exchange of scientific data. All four facilities operate testbeds to expand the frontiers of computing and networking research. Together, the ASCR facilities enterprise seeks to understand and meet the needs and requirements across SC and DOE domain science programs and priority efforts, highlighted by the formal requirements reviews (RRs) methodology. In recent years, the research communities around the SC user facilities have begun experimenting with and demanding solutions integrated with HPC and data infrastructure. This rise of integrated-science approaches is documented in many community and high-level government reports. At the dawn of the era of exascale science and the acceleration of artificial intelligence (AI) innovation, there is a broad need for integrated computational, data, and networking solutions. In response to these drivers, DOE has developed a vision for an Integrated Research Infrastructure (IRI): To empower researchers to meld DOE’s world-class research tools, infrastructure, and user facilities seamlessly and securely in novel ways to radically accelerate discovery and innovation.

42 ENGINEERING↗

US Department of Energy, Office of Science High Performance Computing Facility Operational Assessment 2021: Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory’s (ORNL’s) Leadership Computing Facility (OLCF) continues to surpass its operational target goals of supporting users; delivering fast, reliable computational ecosystems; creating innovative solutions for high-performance computing (HPC) needs; contributing to the community to build the next generation HPC workforce, and managing risks, safety, and security associated with operating some of the most powerful computers in the world. The results can be seen in the cutting-edge science conducted by users and the praise from the research community. Calendar year (CY) 2021 saw continued excellence in research supported by the OLCF’s leadership-class computing resources, including Summit (the nation’s most powerful supercomputer), the global scratch file system Alpine, the Scalable Protected Infrastructure (SPI), the Exploratory Visualization Environment for Research in Science and Technology (EVEREST), and the archival mass-storage resource High-Performance Storage System (HPSS). While maintaining access and exceptional user support for Summit, the OLCF continued to make progress on the installation and deployment of Frontier, which will be the nation’s first exascale system when it comes online at the start of CY 2023. Users have already begun running and optimizing scientific codes on Crusher, the OLCF test and development system equipped with Frontier’s architecture. Throughout the year, the OLCF maintained a strong culture of operational excellence, including risk management, workplace safety, and cybersecurity. The OLCF’s rigorous risk management strategy anticipated and mitigated risks, and at this time there are no high-priority operational risks. Similarly, ORNL and the OLCF were committed to operating under the US Department of Energy’s (DOE’s) safety regulations that ensure a safe workplace. Technical staff tracked and monitored existing threats and vulnerabilities within the OLCF while continually developing tools and practices to enhance operations without increasing the facility’s risk. CY 2021 was filled with outstanding results and accomplishments, including a very high rating from users on overall satisfaction for the eighth consecutive year; a tremendous number of node hours delivered to 1,671 researchers on Summit; and the successful delivery of the allocation split of roughly 60%, 20%, and 20% of core-hours offered for the Innovative and Novel Computational Impact on Theory and Experiment (INCITE), Advanced Scientific Computing Research Leadership Computing Challenge (ALCC), and Director’s Discretionary (DD) programs, respectively (Section 2). COVID-19 research remained a focus in 2021, and the ALCC and DD programs allocated over 1 million Summit hours to the COVID-19 High Performance Computing Consortium. These accomplishments, coupled with the high utilization rates (i.e., overall and capability usage), represent the fulfillment of the promise of leadership class machines: efficient facilitation of leadership-class computational applications.

97 MATHEMATICS AND COMPUTING↗

Experimental and Theoretical Confirmation of Covalent Bonding in α‐Pu

Plutonium's radioactivity provides functionality for nuclear batteries, nuclear reactors, etc., but its complex electronic properties harbor strongly correlated behavior giving rise to a host of interesting phenomena including the presence of a ca. 25% volume collapse between δ-Pu and α-Pu. The complex bonding environments of the ground state allotrope, α-Pu, serve as a unique testing ground for new computational and experimental approaches within the Pu science community. For the first time, a combination of novel ansatzes is used in all-electron density functional theory (DFT) and pair distribution functions (PDF) obtained from high-Q X-ray diffraction to study the bonding behavior in α-Pu. This first experimental and theoretical co-informed description of local bonding behavior for α-Pu reveals covalent bonds, which is a topic that remains of interest in this allotrope. The covalent bonding present at the atomistic level accounts for several of α-Pu's macropscopic properties (e.g., Poisson's ratio) that in turn explains its physical functionalities relative to other allotropic phases like δ-Pu.

36 MATERIALS SCIENCE↗