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DOE OSTI2017

Empirical Comparison of Visualization Tools for Larger-Scale Network Analysis

Gene expression, signal transduction, protein/chemical interactions, biomedical literature cooccurrences, and other concepts are often captured in biological network representations where nodes represent a certain bioentity and edges the connections between them. While many tools to manipulate, visualize, and interactively explore such networks already exist, only few of them can scale up and follow today’s indisputable information growth. In this review, we shortly list a catalog of available network visualization tools and, from a user-experience point of view, we identify four candidate tools suitable for larger-scale network analysis, visualization, and exploration. Lastly, we comment on their strengths and their weaknesses and empirically discuss their scalability, user friendliness, and postvisualization capabilities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Queue wait time prediction in high performance computing (HPC) systems

High Performance Computing (HPC) systems are critical enablers for groundbreaking scientific research across various domains. Efficient resource allocation, facilitated by job scheduling, is paramount for maximizing the utilization of HPC systems. However, the variability in wait times for queued jobs poses challenges for users, necessitating accurate job wait time estimation. This paper explores the influence of job characteristics, including job size (the number of nodes requested and walltime), the queue to which the job is submitted and other resource requirements, on job wait times in leadership-class HPC systems. Focusing on the Theta Cray XC40 and Polaris machines at Argonne National Laboratory, the study evaluates the performance of different supervised learning algorithms in predicting job wait times. It also evaluates the impact of data preprocessing, including outlier detection, Principal Component Analysis (PCA), and feature selection, on the performance of wait time prediction models. The findings reveal insights into the relationship between job characteristics and wait times, offering a foundation for optimizing resource allocation and enhancing user experience. The methodologies and tools developed in this study are adaptable to other leadership-class HPC systems, providing a valuable contribution to the broader HPC community aiming to improve job scheduling efficiency and user satisfaction.

Okafor, Nwamaka↗

DOE OSTI2023

Meshing, Language Server Protocol, and other User-Oriented MOOSE Framework Improvements to Enhance Reactor Analysis Capabilities and Workflows

The open-source Multiphysics Object-Oriented Simulation Environment (MOOSE) framework underpins most of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) physics applications and coupling methods. Users interact with MOOSE in multiple ways to enable the construction of complex multiphysics models, including but not limited to compilation, input creation and syntax validation, meshing, solving the physics problem via MOOSE-based solvers and coupling, and output inspection. In FY23, numerous enhancements have been made to MOOSE to enhance the user experience. Reactor-oriented meshing capabilities in MOOSE have been expanded, an online tutorial was created and hosted on the MOOSE site, and a hands-on workshop was held for more than 100 users. The Language Server Protocol (LSP) capability has been implemented in MOOSE to better communicate correct syntax to the NEAMS Workbench user interface which is commonly used to validate input and submit jobs by users. Finally, several other user-facing improvements were made including the implementation of improved screen output and logging control, enhancements to the initial condition system, and enhancements of the MultiApp system commonly used for coupling. Collectively, these enhancements were driven by user needs and directly improve user ability to construct complex multiphysics models for nuclear reactors.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

PyARC Status Report: New Integrations and Upgrades to the Fast Reactor Analysis Workflow Management Tool

PyARC was initially developed as an open source tool to support fast reactor analyses using the Argonne Reactor Computation (ARC) code suite as a part of the Nuclear Energy Advanced Modeling and Simulation (NEAMS) Workbench initiative in FY17. The goal of this initiative is to provide a common user interface for model generation, real-time validation, execution, output processing, and visualization for all integrated codes. This is accomplished through the reliance on tools available in the Workbench framework and runtime environment. While initially developed to support the ARC codes, PyARC was extended in FY22 to wrap other NEAMS and non-ARC codes, including Griffin and OpenMC, in the supported other neutronics workflows, and support users in the adoption of NEAMS-supported high fidelity analysis codes. Most recently, NUBOW-3D, a recently adopted ARC code, was integrated to support reactor bowing calculations as well. Integration of these codes into the NEAMS Workbench directly benefits the advanced reactor modeling community by: • Providing a set of controlled, maintained, documented and validated scripts to generate inputs, which promotes best practices, reduces the learning curve, and facilitates project collaboration. • Improving the user experience: the Workbench interface provides assistance for building an input through auto-completion, real-time validation, document navigation, and geometry and results visualization. • Automating complex calculations and workflows for reactor analysis. • Helping users transition to using high-fidelity NEAMS codes along-side the ARC codes. In FY22, a progress report was published that described the state of each of the tools integrated into PyARC. Since then, there have been many enhancements and upgrades to the existing integrations as well as entirely new code integrations as well. This report details all new integrations and major developments in PyARC since the version 2.0.0 release highlighted in the FY22 report.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2021

A VR-based volumetric medical image segmentation and visualization system with natural human interaction

Volume rendering produces informative two-dimensional (2D) images from a 3-dimensional (3D) volume. It highlights the region of interest and facilitates a good comprehension of the entire data set. However, volume rendering faces a few challenges. First, a high-dimensional transfer function is usually required to differentiate the target from its neighboring objects with subtle variance. Unfortunately, designing such a transfer function is a strenuously trial-and-error process. Second, manipulating/visualizing a 3D volume with a traditional 2D input/output device suffers dimensional limitations. To address all the challenges, we design NUI-VR 2 , a natural user interface-enabled volume rendering system in the virtual reality space. NUI-VR 2 marries volume rendering and interactive image segmentation. It transforms the original volume into a probability map with image segmentation. A simple linear transfer function will highlight the target well in the probability map. More importantly, we set the entire image segmentation and volume rendering pipeline in an immersive virtual reality environment with a natural user interface. NUI-VR 2 eliminates the dimensional limitations in manipulating and perceiving 3D volumes and dramatically improves the user experience.

42 ENGINEERING↗

DOE OSTI2023

Usage Pattern Analysis for the Summit Login Nodes

High performance computing (HPC) users interact with Summit through dedicated gateways, also known as login nodes. The performance and stability of these login nodes can have a significant impact on the user experience. In this study, the performance and stability of Summit’s five login nodes are evaluated by analyzing the log data from 2020 and 2021. The analysis focuses on the computing capability (CPU average load, users and tasks) and the storage performance, along with the associated job scheduler activity. The outcome of this study can serve as the foundation of a predictive modeling framework that enables the system admin of an HPC system to preemptively deploy countermeasures before the onset of a system failure.

Eiffert, Brett↗

DOE OSTI2024

Summary of October 2023 ARM User Executive Committee Meeting

The User Executive Committee (UEC) provides objective, timely feedback to the leadership of the Atmospheric Radiation Measurement (ARM) user facility with respect to the user experience. The UEC held a hybrid meeting at the ARM Southern Great Plains Observatory in October 2023. Four goals were identified for this meeting: (1) to take an in-depth look at the ARM user facility, (2) to provide actionable items to ARM within the context of the UEC subgroups, (3) to develop new user engagement strategies, and (4) to see an ARM facility in operation, providing valuable context for future UEC discussions. The outcomes of the successful meeting are highlighted in this report. The UEC is grateful to ARM for facilitating this in-person meeting and to our gracious hosts at SGP.

54 ENVIRONMENTAL SCIENCES↗

NASA NTRS1990

US development and commercialization of a North American mobile satellite service

U.S. policies promoting applications and commercialization of space technology for the 'benefit of mankind,' and emphasis on international competitiveness, formed the basis of NASA's Mobile Satellite (MSAT) R&D and user experiments program to develop a commercial U.S. Mobile Satellite Service. Exemplifying this philosophy, the MSAT program targets the reduction of technical, regulatory, market, and financial risks that inhibit commercialization. The program strategy includes industry and user involvement in developing and demonstrating advanced technologies, regulatory advocacy, and financial incentives to industry. Approximately two decades of NASA's satellite communications development and demonstrations have contributed to the emergence of a new multi-billion dollar industry for land, aeronautical, and maritime mobile communications via satellite. NASA's R&D efforts are now evolving from the development of 'enabling' ground technologies for VHF, UHF, and L-Band mobile terminals, to Ka-Band terminals offering additional mobility and user convenience.

Arnold, Ray J.↗

NASA NTRS1993

The computer integrated documentation project: A merge of hypermedia and AI techniques

To generate intelligent indexing that allows context-sensitive information retrieval, a system must be able to acquire knowledge directly through interaction with users. In this paper, we present the architecture for CID (Computer Integrated Documentation). CID is a system that enables integration of various technical documents in a hypertext framework and includes an intelligent browsing system that incorporates indexing in context. CID's knowledge-based indexing mechanism allows case based knowledge acquisition by experimentation. It utilizes on-line user information requirements and suggestions either to reinforce current indexing in case of success or to generate new knowledge in case of failure. This allows CID's intelligent interface system to provide helpful responses, based on previous experience (user feedback). We describe CID's current capabilities and provide an overview of our plans for extending the system.

Mathe, Nathalie↗

DOE OSTI2020

Heavy ion beam physics at Facility for Rare Isotope Beams

The Facility for Rare Isotope Beams (FRIB) will be the world's premier rare-isotope beam facility. Experiments with the majority (~80%) of the isotope predicted to exist will become available. The FRIB facility is based on a superconducting (SC) heavy ion linac with output energy above 200 MeV/u for any ions at beam power of 400 kW. FRIB includes a target facility for in-flight production of rare isotopes. A three-stage fragment separator will be used to prepare fast rare isotope beams with high-purity for nuclear physics experiments. The installation work of the accelerator and experimental systems is approaching completion and multi-stage beam commissioning activities started in summer 2017 with expected project completion in early 2022. In conclusion, the commencement of operation for users' experiments is planned immediately following the project completion.

43 PARTICLE ACCELERATORS↗

DOE OSTI2013

Low Background Materials and Assay: A Supplement to the Cosmic Frontier CF1 Summary.

Executive Summary The next generation of direct detection dark matter experiments will require stringent radiopurity in their target materials, internal instrumentation, and shielding components. A survey of major material assay facilities worldwide and of anticipated assay needs of generation 2 (G2) experiments indicate the current assay capability is marginally adequate in sensitivity and inadequate in throughput. High purity germanium (HPGe) gamma-ray assay has been the workhorse for material screening. It appears hundreds of samples will require screening at the limits of current achievable HPGe sensitivity. Mass spectroscopy methods and neutron activation analysis have demonstrated superior assay sensitivity in some specific cases. However, they are also currently throughput limited. In addition, both alpha/beta screening and radon emanation analysis at or beyond the current achievable sensitivity levels will be needed for dozens of samples. Experiments that follow G2 will have even more stringent material radiopurity specifications, exceeding current assay capabilities in both sensitivity and throughput. These screening needs must precede the commissioning of experiments by 3-5 years to inform design and quality control of components. Achieving the radiopurity goals of the next decade’s experiments will require investment in new techniques and tools to improve material assay sensitivity and throughput. Engineered low-background materials are a significant R&D expenditure, requiring developmental lead-time, and should benefit many end-user experiments. Reserving underground real estate for assay methods affected by cosmic rays (e.g. HPGe) and engineered radiopure materials activated by cosmic rays (e.g. electroformed copper) is judicious forward planning. In many cases, these spaces will require radon-suppressed sample preparation and material storage space. The above-mentioned survey of material assay facilities indicated very little development is taking place to improve sensitivity or throughput capability. In order to create the necessary infrastructure, it may help to form a consortium of low-background assay centers in the U.S that is managed by a scientific board with representatives from the community. This would provide for common use of existing screening facilities and a unified plan for new infrastructure and site development (see the Facilities White Paper). Such a loose organization already exists as AARM (Assay and Acquisition of Radiopure Materials), which is currently populating a community-wide materials database with published assay information. A more formal organization such as a Consortium is being actively investigated with DOE and NSF. Eventually, results of all screening performed in Consortium assay centers could be input directly to the open-access database, reducing duplication and providing for more efficient vendor selection.

Cooley-Sekula, Jodi↗

DOE OSTI2021

The 23rd National School on Neutron & X-Ray Scattering 2021—Virtual School with Remote Experiments

The National School on Neutron and X-ray Scattering (NXS) has been a yearly “institution” for North American graduate students interested in neutron and X-ray scattering since its inception 23 years ago. For the second year in a row, it was forced to go virtual. Nevertheless, the aim was to include user experiments and maximize interactions in this second virtual iteration rather than simply repeat the lecture series of the first virtual iteration. In this paper, we share our newly adopted methods and experiences.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Community Requirements Meta-Analysis: Characterizing Needs and Opportunities for HPDF

This High Performance Data Facility (HPDF) Project is creating a new scientific user facility to provide advanced infrastructure for data-intensive science, supporting the DOE’s Office of Science (SC) community. HPDF’s mission is to enable and accelerate scientific discovery by delivering state-of-the-art data management infrastructure, capabilities, and tools. This meta-analysis examines the needs of the breadth of the SC community, captured in publicly available community reports or mission documents. The meta-analysis identifies and provides initial characterization of fifteen core requirements for the HPDF Project team to consider during the conceptual design phase. The fifteen requirements illustrate how scientific work among SC communities requires modern, seamless user experiences across the ASCR Ecosystem to advance the use of large volumes of heterogeneous data. The scientific community requires support for the missing middle of compute between local and HPC to interactively and collaboratively use growing datasets. Data producers and end users will benefit from enhanced data catalogs and portals that improve data access through advanced search of well curated data. The fifteen requirements are examined here organized across five themes for discussion. Examples in each theme illustrate the array of scientific needs that convey the important role that the fully realized and operational High Performance Data Facility will be able to play as an integral part of the evolving ASCR Ecosystem. Our amalgamated data tables from ESnet reports demonstrate ranges to the volumes of data HPDF must be concerned with, but limitations are inherent to this meta-analysis (see Key Challenges & Limitations). Feedback and validation of these requirements along with additional details and emergent community requirements will be gathered through user research and design activities.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2018

System Applications Software Development and Testing for the Spaceport Command and Control System

Known as "America's Spaceport," one of Kennedy Space Center's (KSC) primary responsibilities is the successful preparation for and launch of rockets into space. KSC's Engineering Software Branch has been tasked with creating a new command and control system that will provide check-out and launch control for future rockets and spacecraft. While work on the software began several years ago, development is ongoing and the operators who use the software on a daily basis have requested several features to improve their user experience. My internship in the fall of 2018 involved developing the source code and unit tests for two of these requested features: "Display Data with Persistence" (DDP) and "Save Events Button" (SEB). DDP's primary goal is to aid with ergonomics. Currently, users must press-and-hold on the mouse button to display information about points on a data plot. Once DDP is integrated, users will have the ability to double-click on a data plot to display that same information with persistence. Independent from DDP, the SEB provides users the ability to take information about different events that occur in the control system and save that data into a simple Comma Separated File (.csv) file format for easier analysis at a future time.

Niemoeller, Samantha↗

DOE OSTI2019

SAM User's Guide

The System Analysis Module (SAM) is a modern system analysis tool being developed at Argonne National Laboratory for advanced non-LWR safety analysis. It aims to provide fast-running, whole-plant transient analyses capability with improved-fidelity for Sodium-cooled Fast Reactors (SFR), Lead-cooled Fast Reactors (LFR), and Molten Salt Reactors (MSR) or Fluoride-cooled High-temperature Reactors (FHR). SAM takes advantage of advances in physical modeling, numerical methods, and software engineering to enhance its user experience and usability. It utilizes an object-oriented application framework (MOOSE), and its underlying meshing and finite-element library (libMesh) and linear and non-linear solvers (PETSc), to leverage the modern advanced software environments and numerical methods. This document provides a user’s guide, which will help users understand the input description and core capabilities of the SAM code. A brief overview of the code is presented, as well as how to obtain and run it. The input syntax for various parts of the code is provided. Additionally, a number of example problems, starting with simple unit component problems to problems with increasing complexity, are provided. Because the code is still under active development, this SAM User’s Guide will evolve with periodic updates.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗

DOE OSTI2021

SAM User’s Guide

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2025

SAM User's Guide

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

DOE OSTI2024

Digital Twin for Chemical Science (DTCS) v0.01

Directly visualizing the trajectories of chemistry can unravel novel insights into the behavior of catalysts, gas phase reactions, photo-induced dynamics, and building blocks for quantum information processing. The ability of explicitly identifying, tracking, and tagging the exchange of matter, hence the annihilation and creation of new chemical species, can be best realized through a close coupling of theory and experiment. While the synchrotron-based characterization facilities propelled rapidly in its hardware, providing higher brightness, better resolution, and more precision, the software infrastructure is lagging. We developed DTCS (Digital Twin for Chemical Science) v.01, a central platform that faithfully mimics advanced instrumentations in Scientific User Facilities, by solving a variety of technical challenges in data acquisition, analysis, and model-driven interpretation. Rooted in physics and accelerated by AI, we validated this concept by direct comparison with precise experimental X-ray Photoelectron Spectroscopy (XPS) observations using a ubiquitous metal-water interfacial scenario, i.e., Ag/H2O as our main narrative. The DTCS v.01 input mirrors how the bench chemists work, with the output directly linked to the end station computer, thereby providing a user-friendly, knowledge-driven, and accessible user experience with mechanistic insights standardized in a way that are ready to be published, versioned, and transferred flexibly.

Qian, Jin↗