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At least 253 records · Page 14

Potential of minicomputer/array-processor system for nonlinear finite-element analysis

The potential of using a minicomputer/array-processor system for the efficient solution of large-scale, nonlinear, finite-element problems is studied. A Prime 750 is used as the host computer, and a software simulator residing on the Prime is employed to assess the performance of the Floating Point Systems AP-120B array processor. Major hardware characteristics of the system such as virtual memory and parallel and pipeline processing are reviewed, and the interplay between various hardware components is examined. Effective use of the minicomputer/array-processor system for nonlinear analysis requires the following: (1) proper selection of the computational procedure and the capability to vectorize the numerical algorithms; (2) reduction of input-output operations; and (3) overlapping host and array-processor operations. A detailed discussion is given of techniques to accomplish each of these tasks. Two benchmark problems with 1715 and 3230 degrees of freedom, respectively, are selected to measure the anticipated gain in speed obtained by using the proposed algorithms on the array processor.

Strohkorb, G. A.↗

The Hopkins Ultraviolet Telescope: The Final Archive

The Hopkins Ultraviolet Telescope (HUT) was a 0.9 m telescope and moderate-resolution (Delta)lambda equals 3 A) far-ultraviolet (820-1850 Å) spectrograph that flew twice on the space shuttle, in 1990 December (Astro-1, STS-35) and 1995 March (Astro-2, STS-67). The resulting spectra were originally archived in a nonstandard format that lacked important descriptive metadata. To increase their utility, we have modified the original datareduction software to produce a new and more user-friendly data product, a time-tagged photon list similar in format to the Intermediate Data Files (IDFs) produced by the Far Ultraviolet Spectroscopic Explorer calibration pipeline. We have transferred all relevant pointing and instrument-status information from locally-archived science and engineering databases into new FITS header keywords for each data set. Using this new pipeline, we have reprocessed the entire HUT archive from both missions, producing a new set of calibrated spectral products in a modern FITS format that is fully compliant with Virtual Observatory requirements. For each exposure, we have generated quicklook plots of the fully-calibrated spectrum and associated pointing history information. Finally, we have retrieved from our archives HUT TV guider images, which provide information on aperture positioning relative to guide stars, and converted them into FITS-format image files. All of these new data products are available in the new HUT section of the Mikulski Archive for Space Telescopes (MAST), along with historical and reference documents from both missions. In this article, we document the improved data-processing steps applied to the data and show examples of the new data products.

Hopkins↗

Enabling Highly Efficient Capsule Networks Processing Through A PIM-Based Architecture Design

In recent years, the CNNs have achieved great successes in the image processing tasks, e.g., image recognition and object detection. Unfortunately, traditional CNN's classication is found to be easily misled by increasingly complex image features due to the usage of pooling operations, hence unable to preserve accurate position and pose information of the objects. To address this challenge, a novel neural network structure called Capsule Network has been proposed, which introduces equivariance through capsules to signicantly enhance the learning ability for image segmentation and object detection. Due to its requirement of performing a high volume of matrix operations, CapsNets have been generally accelerated on modern GPU platforms that provide highly optimized software library for common deep learning tasks. However, based on our performance characterization on modern GPUs, CapsNets exhibit low effciency due to the special program and execution features of their routing procedure, including massive unshareable intermediate variables and intensive syn- chronizations, which are very dicult to optimize at software level. To address these challenges, we propose a hybrid computing architecture design named PIM-CapsNet. It preserves GPU's on-chip computing capability for accelerating CNN types of layers in CapsNet, while pipelining with an off-chip in-memory acceleration solution that effectively tackles routing procedure's ineffciency by leveraging the processing-in-memory capability of today's 3D stacked memory. Using routing procedure's inherent parallellization feature, our design enables hierarchical improvements on CapsNet inference effciency through minimizing data movement and maximizing parallel processing in memory. Evaluation results demonstrate that our proposed design can achieve substantial improvement on both performance and energy savings for CapsNet inference, with almost zero accuracy loss. The results also suggest good performance scalability in optimizing the routing procedure with increasing network size.

Zhang, Xingyao↗

Digital Twin for Optimizing Real-time Economy of the Integrated Energy Systems

Economic and safe operation of integrated energy systems (IES) requires real-time optimization (RTO) of the control and actions conducted on each system component. In this regard, digital twins (DTs), which consist of a physical system, a virtual system, and the data communication that occurs between the two, are essential for effective RTO. Through the data warehouse, the virtual system is constantly updated with real-time data from the physical system, and functions as the model in the optimization framework. The reduced-order model of the dynamic process model in the virtual system is used in the optimization framework. The optimization results are then returned, via the data warehouse, as control actions to the physical system. This work demonstrates the software capabilities of DT assets for an IES in the context of preparing a DT for an experimental system comprised of Idaho National Laboratory (INL)’s Thermal Energy Delivery System and battery system. For the virtual demonstration, the DTs encompass (1) a physical system, including the Modelica models of the Thermal Energy Delivery System and the battery system; (2) virtual optimization via the Optimization of Real-Time Capacity Allocation (ORCA) platform; and (3) the open-source data warehouse software DeepLynx. This work assesses the performance of ORCA, which utilizes a reduced-order model built using the Risk Analysis Virtual Environment (RAVEN) and trained on the Modelica models and real-time data pipeline through the graph database hosted in DeepLynx. The proposed optimization workflow will be an RTO model based on DTs and the data they generate.

25 ENERGY STORAGE↗

A laboratory breadboard system for dual-arm teleoperation

The computing architecture of a novel dual-arm teleoperation system is described. The novelty of this system is that: (1) the master arm is not a replica of the slave arm; it is unspecific to any manipulator and can be used for the control of various robot arms with software modifications; and (2) the force feedback to the general purpose master arm is derived from force-torque sensor data originating from the slave hand. The computing architecture of this breadboard system is a fully synchronized pipeline with unique methods for data handling, communication and mathematical transformations. The computing system is modular, thus inherently extendable. The local control loops at both sites operate at 100 Hz rate, and the end-to-end bilateral (force-reflecting) control loop operates at 200 Hz rate, each loop without interpolation. This provides high-fidelity control. This end-to-end system elevates teleoperation to a new level of capabilities via the use of sensors, microprocessors, novel electronics, and real-time graphics displays. A description is given of a graphic simulation system connected to the dual-arm teleoperation breadboard system. High-fidelity graphic simulation of a telerobot (called Phantom Robot) is used for preview and predictive displays for planning and for real-time control under several seconds communication time delay conditions. High fidelity graphic simulation is obtained by using appropriate calibration techniques.

Bejczy, A. K.↗

Anomalous Cases of Astronaut Helmet Detection

An astronaut's helmet is an invariant, rigid image element that is well suited for identification and tracking using current machine vision technology. Future space exploration will benefit from the development of astronaut detection software for search and rescue missions based on EVA helmet identification. However, helmets are solid white, except for metal brackets to attach accessories such as supplementary lights. We compared the performance of a widely used machine vision pipeline on a standard-issue NASA helmet with and without affixed experimental feature-rich patterns. Performance on the patterned helmet was far more robust. We found that four different feature-rich patterns are sufficient to identify a helmet and determine orientation as it is rotated about the yaw, pitch, and roll axes. During helmet rotation the field of view changes to frames containing parts of two or more feature-rich patterns. We took reference images in these locations to fill in detection gaps. These multiple feature-rich patterns references added substantial benefit to detection, however, they generated the majority of the anomalous cases. In these few instances, our algorithm keys in on one feature-rich pattern of the multiple feature-rich pattern reference and makes an incorrect prediction of the location of the other feature-rich patterns. We describe and make recommendations on ways to mitigate anomalous cases in which detection of one or more feature-rich patterns fails. While the number of cases is only a small percentage of the tested helmet orientations, they illustrate important design considerations for future spacesuits. In addition to our four successful feature-rich patterns, we present unsuccessful patterns and discuss the cause of their poor performance from a machine vision perspective. Future helmets designed with these considerations will enable automated astronaut detection and thereby enhance mission operations and extraterrestrial search and rescue.

Dolph, Chester↗

Guiding the choice of informatics software and tools for lipidomics research applications

Progress in mass spectrometry lipidomics has led to a rapid proliferation of studies across biology and biomedicine. These generate extremely large raw datasets requiring sophisticated solutions to support automated data processing. To address this, numerous software tools have been developed and tailored for specific tasks. However, for researchers, deciding which approach best suits their application relies on ad hoc testing, which is inefficient and time consuming. Here we first review the data processing pipeline, summarizing the scope of available tools. Next, to support researchers, LIPID MAPS provides an interactive online portal listing open-access tools with a graphical user interface. This guides users towards appropriate solutions within major areas in data processing, including (1) lipid-oriented databases, (2) mass spectrometry data repositories, (3) analysis of targeted lipidomics datasets, (4) lipid identification and (5) quantification from untargeted lipidomics datasets, (6) statistical analysis and visualization, and (7) data integration solutions. Detailed descriptions of functions and requirements are provided to guide customized data analysis workflows.

59 BASIC BIOLOGICAL SCIENCES↗

Coronal Thermal Structure and Abundance of Super-Metal-Rich Late-Type Stars

This observation is for grating spectroscopy of 30 Ari, a late-type star with very high metallicity. The goal is to use extreme cases to help understand how abundances change from the photosphere to the corona. The only progress is to report to date is preparation for the analysis of the data. The SAO team has produced spectral model predictions for comparison with the observed spectra. The target was obtained by X-ray Multimirror Mission (XMM)-Newton on 2001 January 16 for 28000 sec. Pipeline processing is difficult and the data have not yet been available. Furthermore, we have been cautioned that the data cannot be correctly processed until at least September of this year, as there are problems with the RGS software to extract the spectrum. We have attended two workshops this summer in which results from XMM on late-type stellar coronae were presented including SMM results from GT team members. We noted that only members of the instrument teams are in a position to analyze XMM data.

Brickhouse, N.↗

Validating automated resonance evaluation with synthetic data

The integrity and precision of nuclear data are crucial for a broad spectrum of applications, from national security and nuclear reactor design to medical diagnostics, where the associated uncertainties can significantly impact outcomes. A substantial portion of uncertainty in nuclear data originates from the subjective biases in the evaluation process, a crucial phase in the nuclear data production pipeline. Recent advancements indicate that automation of certain routines can mitigate these biases, thereby standardizing the evaluation process and enhancing reproducibility. This research aims to provide a methodology, framework, and metrics for the validation of automated nuclear data evaluation software leveraging high-quality synthetic data that closely mimic real experimental observables. An introduced error metric provides a scale and intuitive measure of the evaluation quality by quantifying the estimate’s accuracy and performance across the specified energy range. Synthetic data provides access to experimental observables and underlying resonance parameters, enabling comparison of different evaluations. The methodology is demonstrated using Ta-181 isotope data in the resolved resonance region. The Automated Resonance Identification Subroutine (ARIS), which operates without prior resonance information, was used to test and showcase the framework’s capabilities utilizing the proposed error metrics. The results demonstrate the effectiveness of the proposed approach and framework for optimizing software parameters and testing hypotheses through “what-if” controlled experiments, such as modifying assumptions about experimental conditions or average resonance parameters.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

Adapting DESGW Single Epoch Image Differencing to the LSST Software Stack

As gravitational wave detections become an ever-increasing part of cosmological research, the Gravitational Waves Group of the Dark Energy Survey (DESGW) seeks to match and interpret optical observations for these short-lived, transient events.[1]To provide timely analysis for each follow up, DESGW has developed a custom Single Epoch Differencing Pipeline for processing optical data obtained from the Dark Energy Camera (DECam).[2]While effective, the pipeline is a custom design and thus requires extra maintenance and specialized knowledge to operate and modify at a time when new projects are taking precedence.

79 ASTRONOMY AND ASTROPHYSICS↗

Pipeline for Integrated Projects in Energy Systems (PIPES): A Tool for Integrated System Planning [Slides]

The Pipeline for Integrated Projects in Energy Systems (PIPES) is a comprehensive project, data, and workflow management tool designed for integrated modeling teams. PIPES facilitates the management of data requirements, tasks, and progress tracking, serving as a higher-level integration layer that works across various data and modeling software. This tool integrates models, data, and tools to perform large-scale, integrated analysis work at scale. PIPES is designed to streamline integrated modeling projects, enhance collaboration, and ensure the quality and efficiency of data management and workflow processes. This presentation introduces PIPES a multi-model tool for integrated system planning; it describes the underlying architecture, deep dives into common user workflows, and outlines the upcoming development roadmap beyond its current alpha state.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

MAPPRAISER: A massively parallel map-making framework for multi-kilo pixel CMB experiments

Forthcoming cosmic microwave background (CMB) polarized anisotropy experiments have the potential to revolutionize our understanding of the Universe and fundamental physics. The sought-after, tale-telling signatures will be however distributed over voluminous data sets which these experiments will collect. These data sets will need to be efficiently processed and unwanted contributions due to astrophysical, environmental, and instrumental effects characterized and efficiently mitigated in order to uncover the signatures. This poses a significant challenge to data analysis methods, techniques, and software tools which will not only have to be able to cope with huge volumes of data but to do so with unprecedented precision driven by the demanding science goals posed for the new experiments. A keystone of efficient CMB data analysis is solvers of very large linear systems of equations. Such systems appear in very diverse contexts throughout CMB data analysis pipelines, however they typically display similar algebraic structures and can therefore be solved using similar numerical techniques. Linear systems arising in the so-called map-making problem are one of the most prominent and common ones. In this work we present a massively parallel, flexible and extensible framework, comprised of a numerical library, MIDAPACK, and a high level code, MAPPRAISER, which provide tools for solving efficiently such systems. Here, the framework implements iterative solvers based on conjugate gradient techniques: enlarged and preconditioned using different preconditioners. We demonstrate the framework on simulated examples reflecting basic characteristics of the forthcoming data sets issued by ground-based and satellite-borne instruments, executing it on as many as 16,384 compute cores. The software is developed as an open source project freely available to the community at: https://github.com/B3Dcmb/midapack.

79 ASTRONOMY AND ASTROPHYSICS↗

ULTRA-effective labeling of tandem repeats in genomic sequence

In the age of long read sequencing, genomics researchers now have access to accurate repetitive DNA sequence (including satellites) that, due to the limitations of short read-sequencing, could previously be observed only as unmappable fragments. Tools that annotate repetitive sequence are now more important than ever, so that we can better understand newly uncovered repetitive sequences, and also so that we can mitigate errors in bioinformatic software caused by those repetitive sequences. To that end, we introduce the 1.0 release of our tool for identifying and annotating locally repetitive sequence, ULTRA Locates Tandemly Repetitive Areas (ULTRA). ULTRA is fast enough to use as part of an efficient annotation pipeline, produces state-of-the-art reliable coverage of repetitive regions containing many mutations, and provides interpretable statistics and labels for repetitive regions.

59 BASIC BIOLOGICAL SCIENCES↗

Outline of a fast hardware implementation of Winograd's DFT algorithm

The main characteristics of the discrete Fourier transform (DFT) algorithm considered by Winograd (1976) is a significant reduction in the number of multiplications. Its primary disadvantage is a higher structural complexity. It is, therefore, difficult to translate the reduced number of multiplications into faster execution of the DFT by means of a software implementation of the algorithm. For this reason, a hardware implementation is considered in the current study, taking into account a design based on the algorithm prescription discussed by Zohar (1979). The hardware implementation of a FORTRAN subroutine is proposed, giving attention to a pipelining scheme in which 5 consecutive data batches are being operated on simultaneously, each batch undergoing one of 5 processing phases.

Zohar, S.↗

Implementation of an ICS Ransomware Testbed: Scenarios, Variants, and Evaluation Methods

Ransomware attacks on Industrial Control Systems (ICS) have emerged as a formidable threat to the United States’ critical infrastructure, eliciting grave concerns regarding national security. In March 2023, the FBI Internet Crime Complaint Center (IC3) unveiled its 2022 Internet Crime Report, highlighting a concerning 870 complaints related to ransomware impacting U.S. critical infrastructure. Of the country's 16 critical infrastructure sectors, 14 encountered at least one ransomware attack. Notably, while the Healthcare and Public Health sector suffered the most, reporting 210 attacks, sectors pivotal to ICS networks and governmental organizations were also targeted: the Defense Industrial Base reported 1 attack, Water and Wastewater Systems 3, Chemical 19, Energy 15, Government Facilities 115, and Critical Manufacturing 157. For instance, a ransomware attack on a major chemical company could jeopardize not only its production but also pose environmental risks should systems controlling hazardous materials be compromised. In 2022, three ransomware variants predominantly targeted U.S. critical infrastructure: HIVE, with 87 attacks; ALPHV/BlackCat, with 114; and LOCKBIT, with 149. Several cyber-attacks, such as the MOVEit data breach in May 2023 and the Colonial Pipeline ransomware attack in May 2021, have been so impactful that they commanded national attention. The DarkSide hacking group's assault on the Colonial Pipeline, initiated on May 6th, 2021, stands as one of the most substantial and publicly acknowledged cyber-attacks against U.S. critical infrastructure. The group exploited an exposed Virtual Private Network (VPN) password, paving the way for initial intrusion and subsequent data theft. A mere day later, DarkSide unleashed a ransomware attack that compromised vital accounting and billing systems, prompting an immediate shutdown of the pipeline to mitigate further ransomware proliferation across its network. This crisis spurred a robust response from the U.S. president and regulators, culminating in a national emergency declaration related to the pipeline shutdown on May 9th, 2021. This incident mirrors the 2017 NotPetya ransomware attack that significantly impacted the shipping giant Maersk, highlighting an urgent need for fortified cybersecurity across various industries. Future incidents, akin to the Colonial Pipeline attack, could potentially be mitigated—or entirely averted—should government agencies and private entities scrutinize system vulnerabilities, exploring various ransomware types and entry points. Proactive measures, such as conducting experiments on VPN accounts or auditing passwords to pinpoint duplicate usage across diverse systems and software, might illuminate feasible entry points and vulnerability zones within an organization's systems.

22 GENERAL STUDIES OF NUCLEAR REACTORS↗

A Simple Standard for Sharing Ontological Mappings (SSSOM)

Abstract Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec. Database URL: http://w3id.org/sssom/spec

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

Addressing the dynamic nature of reference data: a new nucleotide database for robust metagenomic classification

Accurate metagenomic classification relies on comprehensive, up-to-date, and validated reference databases. While the NCBI BLAST Nucleotide (nt) database, encompassing a vast collection of sequences from all domains of life, represents an invaluable resource, its massive size—currently exceeding 10 12 nucleotides—and exponential growth pose significant challenges for researchers seeking to maintain current nt-based indices for metagenomic classification. Recognizing that no current nt-based indices exist for the widely used Centrifuge classifier, and the last public version currently available was released in 2018, we addressed this critical gap by leveraging advanced high-performance computing resources. We present new Centrifuge-compatible nt databases, meticulously constructed using a novel pipeline incorporating different quality control measures, including reference decontamination and filtering. These measures demonstrably reduce spurious classifications, as shown through our reanalysis of published metagenomic data where Plasmodium annotations were dramatically reduced using our decontaminated database, highlighting how database quality can significantly impact research conclusions. Through temporal comparisons, we also reveal how our approach minimizes inconsistencies in taxonomic assignments stemming from asynchronous updates between public sequence and taxonomy databases. These discrepancies are particularly evident in taxa such as Listeria monocytogenes and Naegleria fowleri, where classification accuracy varied significantly across database versions. These new databases, made available as pre-built Centrifuge indexes, respond to the need for an open, robust, nt-based pipeline for taxonomic classification in metagenomics. Applications such as environmental metagenomics, forensics, and clinical metagenomics, which require comprehensive taxonomic coverage, will benefit from this resource. Our work highlights the importance of treating reference databases as dynamic entities, subject to ongoing quality control and validation akin to software development best practices. This approach is crucial for ensuring accuracy and reliability of metagenomic analysis, especially as databases continue to expand in size and complexity.

59 BASIC BIOLOGICAL SCIENCES↗