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DOE OSTI2016

High Performance Computing Facility Operational Assessment 2015: Oak Ridge Leadership Computing Facility

Oak Ridge National Laboratory’s (ORNL’s) Leadership Computing Facility (OLCF) continues to surpass its operational target goals: supporting users; delivering fast, reliable systems; creating innovative solutions for high-performance computing (HPC) needs; and managing risks, safety, and security aspects associated with operating one of the most powerful computers in the world. The results can be seen in the cutting-edge science delivered by users and the praise from the research community. Calendar year (CY) 2015 was filled with outstanding operational results and accomplishments: a very high rating from users on overall satisfaction that ties the highest-ever mark set in CY 2014; the greatest number of core-hours delivered to research projects; the largest percentage of capability usage since the OLCF began tracking the metric in 2009; and success in delivering on the allocation of 60, 30, and 10% of core hours offered for the INCITE (Innovative and Novel Computational Impact on Theory and Experiment), ALCC (Advanced Scientific Computing Research Leadership Computing Challenge), and Director’s Discretionary programs, respectively. These accomplishments, coupled with the extremely high utilization rate, represent the fulfillment of the promise of Titan: maximum use by maximum-size simulations. The impact of all of these successes and more is reflected in the accomplishments of OLCF users, with publications this year in notable journals Nature, Nature Materials, Nature Chemistry, Nature Physics, Nature Climate Change, ACS Nano, Journal of the American Chemical Society, and Physical Review Letters, as well as many others. The achievements included in the 2015 OLCF Operational Assessment Report reflect first-ever or largest simulations in their communities; for example Titan enabled engineers in Los Angeles and the surrounding region to design and begin building improved critical infrastructure by enabling the highest-resolution Cybershake map for Southern California to date. The Titan system provides the largest extant heterogeneous architecture for computing and computational science. Usage is high, delivering on the promise of a system well-suited for capability simulations for science. This success is due in part to innovations in tracking and reporting the activity on the compute nodes, and using this information to further enable and optimize applications, extending and balancing workload across the entire node. The OLCF continues to invest in innovative processes, tools, and resources necessary to meet continuing user demand. The facility’s leadership in data analysis and workflows was featured at the Department of Energy (DOE) booth at SC15, for the second year in a row, highlighting work with researchers from the National Library of Medicine coupled with unique computational and data resources serving experimental and observational data across facilities. Effective operations of the OLCF play a key role in the scientific missions and accomplishments of its users. Building on the exemplary year of 2014, as shown by the 2014 Operational Assessment Report (OAR) review committee response in Appendix A, this OAR delineates the policies, procedures, and innovations implemented by the OLCF to continue delivering a multi-petaflop resource for cutting-edge research. This report covers CY 2015, which, unless otherwise specified, denotes January 1, 2015, through December 31, 2015.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2017

High Performance Computing Facility Operational Assessment 2016 - Oak Ridge Leadership Computing Facility

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2022

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↗

DOE OSTI2025

Bottom-up carbon dots: purification, single-particle dynamics, and electronic structure

For carbon dots, careful purification and electronic structure calculations facilitate learning about the origin of optical properties.

Bian, Zhengyi [Department of Chemistry, University↗

DOE OSTI2024

FacultyHack Events: Faculty-Focused Hackathons for High-Performance Computing Curriculum Development

Broadening participation initiatives are important for engaging underrepresented groups in science, technology, engineering, and math (STEM). Such initiatives help foster supportive and inclusive work environments that promote creativity and productivity. While there are initiatives that aim to engage students and faculty, opportunities remain to improve faculty support. Hackathons have proved to be a useful approach for student engagement. There are, however, limited insights into whether and how such events would also work for faculty aiming to develop curricula. This paper discusses the design of a faculty-focused hackathon event, FacultyHack, for curriculum development. We outline the logistics and structure for two past FacultyHack events, detail changes between events, and describe potential improvements and lessons learned.

Holmen, John [ORNL] (ORCID:0000000259342641)↗

DOE OSTI2024

Computational and Systems Biology Advances to Enable Bioagent Agnostic Signatures

Enumerated threat agent lists have long driven biodefense priorities. The global SARS-CoV-2 pandemic demonstrated the limitations of searching for known threat agents as compared to a more agnostic approach. Recent technological advances are enabling agent-agnostic biodefense, especially through the integration of multi-modal observations of host-pathogen interactions directed by a human immunological model. Although well-developed technical assays exist for many aspects of human-pathogen interaction, the analytic methods and pipelines to combine and holistically interpret the results of such assays are immature and require further investments to exploit new technologies. In this manuscript, we discuss potential immunologically based bioagent-agnostic approaches and the computational tool gaps the community should prioritize filling.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Exploring solvation structure and transport behavior for rational design of advanced electrolytes for next generation of lithium batteries

The efficacy of electrolytes significantly affects battery performance, leading to the development of several strategies to enhance them. Despite this, the understanding of solvation structure remains inadequate. It is imperative to understand the structure–property–performance relationship of electrolytes using diverse techniques. Here, this review explores the recent advancements in electrolyte design strategies for high capacity, high-voltage, wide-temperature, fast-charging, and safe applications. To begin, the current state-of-the-art electrolyte design directions are comprehensively reviewed. Subsequently, advanced techniques and computational methods used to understand the solvation structure are discussed. Additionally, the importance of high-throughput screening and advanced computation of electrolytes with the help of machine learning is emphasized. Finally, future horizons for studying electrolytes are proposed, aimed at improving battery performance and promoting their application in various fields by enhancing the microscopic understanding of electrolytes.

25 ENERGY STORAGE↗

DOE OSTI2018

Oncentra brachytherapy planning system

In modern cancer management, treatment planning has progressed as a contemporary tool with all the advances in computing power in recent years. One of the advanced planning tools uses 3-dimensional (3D) data sets for accurate dose distributions in patient prescription. Among these planning processes, brachytherapy has been a very important part of a successful cancer management program, offering clinical benefits with specific or combined treatments with external beam therapy. In this chapter, we mainly discussed the Elekta Oncentra planning system, which is the main treatment planning tool for high-dose rate (HDR) modality in our facility and in many other facilities in the United States. HDR is a technically advanced form of brachytherapy; a high-intensity radiation source (3.6 mm in length) is delivered with step motor in submillimeter precision under computer guidance directly into the tumor areas while minimizing injury to surrounding normal healthy tissue. Oncentra planning is the key component to generate a deliverable brachytherapy procedure, which is executed on the microSelectron V3 remote afterloader treatment system. Creating a highly conformal plan can be a time-consuming task. The development of Oncentra software (version 4.5.3) offers a variety of useful tools that facilitate many of the clinical challenging tasks for planning, such as contouring and image reconstruction, as well as rapid planning calculations with dose and dose volume histogram analysis. Oncentra Brachy module creates workflow and optimizes the planning accuracy for wide varieties of clinical HDR treatments, such as skin, gynecologic (GYN), breast, prostate, and many other applications. The treatment file can also be transferred to the afterloader control station for speedy delivery. The design concept, calculation algorithms, and optimization modules presented some key characteristics to plan and treat the patients effectively and accurately. The dose distribution and accuracy of several clinical sample cases were discussed to illustrate the effectiveness and clinical efficacy. The American Association of Physicists in Medicine brachytherapy reports of TG-43 and TG-186 were also described and compared in evaluations of fundamental calculation methodologies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2024

Towards interpretable Cryo-EM: disentangling latent spaces of molecular conformations

Molecules are essential building blocks of life and their different conformations (i.e., shapes) crucially determine the functional role that they play in living organisms. Cryogenic Electron Microscopy (cryo-EM) allows for acquisition of large image datasets of individual molecules. Recent advances in computational cryo-EM have made it possible to learn latent variable models of conformation landscapes. However, interpreting these latent spaces remains a challenge as their individual dimensions are often arbitrary. The key message of our work is that this interpretation challenge can be viewed as an Independent Component Analysis (ICA) problem where we seek models that have the property of identifiability. That means, they have an essentially unique solution, representing a conformational latent space that separates the different degrees of freedom a molecule is equipped with in nature. Thus, we aim to advance the computational field of cryo-EM beyond visualizations as we connect it with the theoretical framework of (nonlinear) ICA and discuss the need for identifiable models, improved metrics, and benchmarks. Moving forward, we propose future directions for enhancing the disentanglement of latent spaces in cryo-EM, refining evaluation metrics and exploring techniques that leverage physics-based decoders of biomolecular systems. Moreover, we discuss how future technological developments in time-resolved single particle imaging may enable the application of nonlinear ICA models that can discover the true conformation changes of molecules in nature. The pursuit of interpretable conformational latent spaces will empower researchers to unravel complex biological processes and facilitate targeted interventions. This has significant implications for drug discovery and structural biology more broadly. More generally, latent variable models are deployed widely across many scientific disciplines. Thus, the argument we present in this work has much broader applications in AI for science if we want to move from impressive nonlinear neural network models to mathematically grounded methods that can help us learn something new about nature.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2019

Leveraging latest computer science tools to advance nuclear cardiology

Nuclear cardiology has unique advantages compared to other modalities, since the image analysis is already much more automated compared to what is currently clinically performed for CT, MR, or echocardiography imaging. The diverse image and clinical data available to assess coronary disease function, perfusion, flow, and associated CT data provide new opportunities, but logistically these additional assessments increase the overall complexity of SPECT/PET reporting, necessitating additional expertise and time. The advances in artificial intelligence software can be leveraged to obtain comprehensive risk predictions and diagnoses from all available data. They will allow nuclear cardiology to retain competitive edge compared to other modalities and improve its overall clinical utility. These tools will enhance diagnosis and risk prediction beyond what is possible by subjective visual analysis and mental integration of data by physicians.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

DOE OSTI2021

Enhancing Resilience of Urban Systems Against Climate-Induced Floods Using Advanced Data-Driven and Computing Techniques: A Driver-Pressure-State-Impact-Response (DPSIR) Framework

Focal Area: This white paper proposes advanced data-driven and computing techniques to improve the predictability of extreme climate events (precipitation) and focuses on comprehending their impact dynamics to enhance resilience of urban systems. Science Challenge: In urban systems, climate change has presented significant challenges related to accurate spatiotemporal prediction of extreme climate events (heavy precipitation) and their impacts, i.e. flooding. The occurrence of extreme climate events and their compounding repercussions on the built environment make urban systems increasingly more vulnerable. The interactions between extreme climate events, urban systems, and the corresponding impacts are irregular, non-linear, and dynamic, making it difficult to standardize resilience. As it stands, the management of complex urban systems is affected by uncertainties related to the nature of short- and long-term consequences caused by extreme events.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2024

Modern chemical graph theory

Abstract Graph theory has a long history in chemistry. Yet as the breadth and variety of chemical data is rapidly changing, so too do graph encoding methods and analyses that yield qualitative and quantitative insights. Using illustrative cases within a basic mathematical framework, we showcase modern chemical graph theory's utility in Chemists' analysis and model development toolkit. The encoding of both experimental and simulation data is discussed at various levels of granularity of information. This is followed by a discussion of the two major classes of graph theoretical analyses: identifying connectivity patterns and partitioning methods. Measures, metrics, descriptors, and topological indices are then introduced with an emphasis upon enhancing interpretability and incorporation into physical models. Challenging data cases are described that include strategies for studying time dependence. Throughout, we incorporate recent advancements in computer science and applied mathematics that are propelling chemical graph theory into new domains of chemical study. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Structure and Mechanism > Computational Materials Science Structure and Mechanism > Molecular Structures

Leite, Leonardo S. G.↗

DOE OSTI2015

Lawrence Livermore National Laboratories Perspective on Code Development and High Performance Computing Resources in Support of the National HED/ICF Effort

Through its Advanced Scientific Computing (ASC) and Inertial Confinement Fusion (ICF) code development efforts, Lawrence Livermore National Laboratory (LLNL) provides a world leading numerical simulation capability for the National HED/ICF program in support of the Stockpile Stewardship Program (SSP). In addition the ASC effort provides high performance computing platform capabilities upon which these codes are run. LLNL remains committed to, and will work with, the national HED/ICF program community to help insure numerical simulation needs are met and to make those capabilities available, consistent with programmatic priorities and available resources.

42 ENGINEERING↗

DOE OSTI2016

Modality-Driven Classification and Visualization of Ensemble Variance

Paper for the IEEE Visualization Conference Advances in computational power now enable domain scientists to address conceptual and parametric uncertainty by running simulations multiple times in order to sufficiently sample the uncertain input space.

Bensema, Kevin↗

DOE OSTI2012

Open-source MFIX-DEM software for gas-solids flows: Part II — Validation studies

With rapid advancements in computer hardware and numerical algorithms, computational fluid dynamics (CFD) has been increasingly employed as a useful tool for investigating the complex hydrodynamics inherent in multiphase flows. An important step during the development of a CFD model and prior to its application is conducting careful and comprehensive verification and validation studies. Accordingly, efforts to verify and validate the open-source MFIX-DEM software, which can be used for simulating the gas–solids flow using an Eulerian reference frame for the continuum fluid and a Lagrangian discrete framework (Discrete Element Method) for the particles, have been made at the National Energy Technology Laboratory (NETL). In part I of this paper, extensive verification studies were presented and in this part, detailed validation studies of MFIX-DEM are presented. A series of test cases covering a range of gas–solids flow applications were conducted. In particular the numerical results for the random packing of a binary particle mixture, the repose angle of a sandpile formed during a side charge process, velocity, granular temperature, and voidage profiles from a bounded granular shear flow, lateral voidage and velocity profiles from a monodisperse bubbling fluidized bed, lateral velocity profiles from a spouted bed, and the dynamics of segregation of a binary mixture in a bubbling bed were compared with available experimental data, and in some instances with empirical correlations. In addition, sensitivity studies were conducted for various parameters to quantify the error in the numerical simulation.

42 ENGINEERING↗

DOE OSTI2021

Critical Experiment Design Phase 2 Report for Integral Request 304

This report documents the second phase of the critical experiment design process (CED-2) conducted as part of integral experiment request (IER) 304. The purpose of IER-304 is to develop a temperature-dependent critical experiment capability at the Sandia National Laboratories critical experiment facility using low-enriched uranium oxide fuel. Only a few benchmark quality critical experiments are currently available to validate criticality safety computational methods at temperatures other than room temperature. Recent advancements in computational techniques such as implementation of on-the-fly Doppler broadening techniques and advanced treatment of thermal scattering data necessitate the development of additional experimental capabilities in this area. The work described in this report developed representative configurations using 7uPCX and BUCCX fuels, analyzed the physics exercised by the different arrays, and analyzed the estimated experimental uncertainties. This report also scopes the information necessary for performing modifications to the reactor to accommodate operation at elevated and reduced temperatures.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

DOE OSTI2016

Advanced SAPHIRE 8 Modeling Methods for Probabilistic Risk Assessment via the Systems Analysis Program for Hands-On Integrated Reliability Evaluations (SAPHIRE) Software P-202

1.1. Overview of the Advanced SAPHIRE Material The Advanced SAPHIRE course material is intended to both (1) provide guidance for learning advanced SAPHIRE features during the class and (2) become a stand-alone reference document after finishing the class. Thus, the format for the class material is a combination of the traditional “overhead-type” of presentation information with a structured, reference-type document. Major topics that are covered in the Advanced SAPHIRE class include: Advanced data base concepts such as Model Type (e.g., random, seismic, fire, flood). Definition of house events and how they are used on a sequence-by-sequence basis to manipulate individual fault tree logic using sequence flag sets or fault tree flag sets. ? Basic event templates, compound basic event equation editors, and human error worksheets. A rule-based event tree top event substitution feature (called the Link Event Tree Rule Editor) which allows for top event substitutions. A rule-based cut set post-processing feature (called the Recovery Rules) which allows cut set manipulation. Cut set analysis based upon rule-based end state categories (called End State Analysis). Cut set generation options for both fault trees and event tree sequences. The large event tree methodology and how SAPHIRE can be used to generate sequence cut sets for this method. The transfer of data between SAPHIRE data bases and between other PRA codes (MAR-D).

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Implications of stop-and-go traffic on training learning-based car-following control

Learning-based car-following control (LCC) of connected and autonomous vehicles (CAVs) is gaining significant attention with the advancement of computing power and data accessibility. While the flexibility and large model capacity of model-free architecture enable LCC to potentially outperform the model-based car-following (CF) model in improving traffic efficiency and mitigating congestion, the generalizability of LCC for traffic conditions different from the training environment/dataset is not well-understood. Herein, this study seeks to explore the impact of stop-and-go traffic in the training dataset on the generalizability of LCC. It uses the characteristics of lead vehicle trajectories to describe stop-and-go traffic, and links the theory of identifiability (i.e., obtaining a unique parameter estimation result using sensor measurements) to the generalizability of behavior cloning (BC) and policy-based deep reinforcement learning (DRL). Correspondingly, the study shows theoretically that: (i) stop-and-go traffic can enable the property of identifiability and enhance the control performance of BC-based LCC in different traffic conditions; (ii) stop-and-go traffic is not necessary for DRL-based LCC to generalize to different traffic conditions; (iii) DRL-based LCC trained with only constant-speed lead vehicle trajectories (not sufficient to ensure identifiability) can be generalized to different traffic conditions; and (iv) stop-and-go traffic increases variance in the training dataset, which improves the convergence of parameter estimation while negatively impacting the convergence of DRL to the optimal control policy. Numerical experiments validate the above findings, illustrating that BC-based LCC entails comprehensive training datasets for generalizing to different traffic conditions, while DRL-based LCC can achieve generalization with simple free-flow traffic training environments. This further suggests DRL as a more promising and cost-effective LCC approach to reduce operational costs, mitigate traffic congestion, and enhance safety and mobility, which can accelerate the deployment and acceptance of CAVs.

33 ADVANCED PROPULSION SYSTEMS↗