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At least 1,423 records · Page 79
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

HPDF Data Catalog and Lakehouse Demo Heuristic Evaluation and Roadshow Feedback Reports

The December 2025 roadshow gathered rapid feedback from community members on the proof of concept AmSC/HPDF data lakehouse and catalog solution 1. This provided the opportunity to demonstrate our current state of progress and gather input on workflows and AI agents. We recognize that the proofs of concept interfaces (OpenMetadata and Goose) are not intended for our end users so we have captured feedback to keep in mind as additional technical and conceptual design work is undertaken.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2013

SDS: A Framework for Scientific Data Services

Large-scale scientific applications typically write their data to parallel file systems with organizations designed to achieve fast write speeds. Analysis tasks frequently read the data in a pattern that is different from the write pattern, and therefore experience poor I/O performance. In this paper, we introduce a prototype framework for bridging the performance gap between write and read stages of data access from parallel file systems. We call this framework Scientific Data Services, or SDS for short. This initial implementation of SDS focuses on reorganizing previously written files into data layouts that benefit read patterns, and transparently directs read calls to the reorganized data. SDS follows a client-server architecture. The SDS Server manages partial or full replicas of reorganized datasets and serves SDS Clients' requests for data. The current version of the SDS client library supports HDF5 programming interface for reading data. The client library intercepts HDF5 calls and transparently redirects them to the reorganized data. The SDS client library also provides a querying interface for reading part of the data based on user-specified selective criteria. We describe the design and implementation of the SDS client-server architecture, and evaluate the response time of the SDS Server and the performance benefits of SDS.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Qthreads Support for MPICH

SAND2024-00944O Qthread Support for MPICH is software that provides additions needed to enable the use of the Qthreads library. The high-performance message passing interface (MPICH) is an open-source implementation of MPI mainly developed and distributed by Argonne National Laboratory. Qthreads is a lightweight, user-level threading library developed and distributed by Sandia National Laboratories. MPICH currently supports Posix threads, Windows threads, and Argobots. This software enables parallel programs built with the MPICH implementation of MPI to use Qthreads user-level threads rather than Posix system-level threads. The software uses existing infrastructure in MPICH to interface to the Qthreads library. The existing interfaces in MPICH allow for creating, destroying, and managing the execution of multiple threads within a process and this software translates these calls to the equivalent Qthreads library functions. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Ciesko, Jan↗
DOE OSTI2024

RadSim: Particle Transport Wrapper

RadSim is being developed to provide the capability to simulate radiation source emissions, interpolate results from radiation transport tools into a common format to prepare incident flux, and model radiation detector response. This software package includes wrapper API code which is utilized in the development of the second (transport) task of the RadSim project. This software package only contains tools to interface RadSim with radiation transport tools (GEANT4 and MCNP) and does not include any part of the transport source code itself. The users will need prior access to the transport tools (GEANT4 and MCNP), and can use this software package to interface with the transport tool of their choice. This software package takes the geometry file for a radiation transport problem and converts it into an input deck for the transport tools (GEANT4 and MCNP). Additionally, it also contains filters that convert the output of the transport tools to a common flux format.

Cheung, Hoi Sing↗
DOE OSTI2018

WebTRAGIS: Transportation Routing Analysis Geographic System User’s Manual

The Web-Based Transportation Routing Analysis Geographic Information System (WebTRAGIS) model is a geographic information system tool for modeling transportation routing. WebTRAGIS is deployed as a browser-based application interface, and the routing engine is located on a server at Oak Ridge National Laboratory (ORNL). WebTRAGIS offers users numerous options for route calculation using uniquely value-added network databases for highway, rail, and waterway infrastructures in the continental United States. The model also provides reporting information on population densities for all transportation segments using the LandScan USA population distribution data model.

42 ENGINEERING↗
DOE OSTI2017

CHISSL: A Human-Machine Collaboration Space for Unsupervised Learning

We developed CHISSL, a human-machine interface that utilizes supervised machine learning in an unsupervised context to help the user group unlabeled instances by her own mental model. The user primarily interacts via correction (moving a misplaced instance into its correct group) or confirmation (accepting that an instance is placed in its correct group). Concurrent with the user's interactions, CHISSL trains a classification model guided by the user's grouping of the data. It then predicts the group of unlabeled instances and arranges some of these alongside the instances manually organized by the user. We hypothesize that this mode of human and machine collaboration is more effective than Active Learning, wherein the machine decides for itself which instances should be labeled by the user. We found supporting evidence for this hypothesis in a pilot study where we applied CHISSL to organize a collection of handwritten digits.

Active Learning↗
DOE OSTI2023

BaseBuddy v1

The software "BaseBuddy" (basebuddy.lbl.gov) is a user-friendly web app designed for codon optimization of heterologous genes. Codon optimization is a widely used technique to enhance the expression levels of non-native genes. Our app is built on the DNA Chisel Python library (Zulkower and Rosser, 2020), which offers highly customizable and transparent gene optimization. Unlike DNA Chisel, which is a command-line interface software with numerous optional functions, our web app simplifies the process for users. Additionally, while DNA Chisel relies on the outdated Kazusa codon usage database, our app introduces the option to utilize the most recent version of the CoCoPUTs database (Athey et al., 2017). By incorporating CoCoPUTs, we also expand the range of target organisms and maintain up-to-date sequencing data for more accurate codon optimization results.

Schmidt, Matthias↗
DOE OSTI2020

A time-domain electromechanical co-simulation framework for power system transient analysis with retainment of user defined models

This paper proposes a time-domain electromechanical co-simulation framework to accomplish concurrent running of multiple simulators in order to preserve user-defined models and allow maximum simulation accuracy for power system transient analysis. Here, a middleware interface is developed to manage the interaction and synchronization of the multiple simulators via boundary model. Consequently, it eliminates the requirement of model conversion of each subsystem and thus ensure the user-defined models in each specific software are retained for entire system situational awareness. Preliminary testing results on 140-bus Northeastern Power Coordinating Council (NPCC) model validate the effectiveness and accuracy of the proposed framework for PSS/E and PSLF co-simulation.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2015

CORE (Common Operating Response Environment) Software Technology Suite

Agencies that oversee complex, multi-stakeholder programs need efficient, secure ways to link people and knowledge within and across organizations. The Common Operating Response Environment (CORE), a software suite developed by PNNL researchers does just that. The CORE tool—which is customizable for a multitude of uses—facilitates situational awareness by integrating diverse data streams without the need to reformat them, summarizing that information, and providing users with the information they need to rapidly understand and appropriately respond to situations. It is mobile device-ready, has a straightforward interface for ease of use across organizations and skill sets, and is incredibly configurable to the needs of each specific user, whether they require data summaries for high-level decision makers or tactical maps, operational data, or weather information for responders in the field. Information can be input into CORE and queried in a variety of ways—using customized forms, reports, visuals, or other organizational templates—according to the needs of each user’s organization, teams, and business processes. CORE data forms, for instance, could be accessed and used in real-time to capture information about vessels being inspected for nuclear material.

42 ENGINEERING↗
DOE OSTI2025

Characterization of Peripheral Neurophotonic Systems for High-Performance Human-Computer Interfaces (CRADA Final Report)

As part of the Cyclotron Road program, Morphosis Inc. sought to investigate a non-invasive neuromuscular sensing approach for use as an intuitive and secure human–computer interface. These highly miniaturized, wearable neural interfaces were completely non-invasive and maintained stable, high-bandwidth, long-term access to a user’s actions, intent, and identity, while offering an exceptionally high signal-to-noise ratio compared to contemporary neural recording technologies. The widespread adoption of neural interfaces had the potential to reshape how people interact with technology, with profound societal impacts. Millions worldwide suffered from movement and/or speech disabilities, and these tools had the potential to democratize access to technology to enhance autonomy and quality of life. More broadly, interfaces capable of accurately conveying intentions and safeguarding identities could serve as a cornerstone for privacy, trust, and personal authenticity in digital environments. The use of thought-driven control of digitally enabled devices and governance of digital identities had the potential to revolutionize relationships with technology, transforming how people learn, communicate, and interact with the world.

42 ENGINEERING↗
DOE OSTI2015

Design & Implementation of MACSio

We are proposing to develop “MACSio” (pronounced “max-ee-oh”), a Multi-purpose, Application-Centric, Scalable I/O proxy application. It is being proposed to fill a long existing void in co-design proxy applications that allow for I/O performance testing and evaluation of tradeoffs in data model interfaces and parallel I/O paradigms for multi-physics, HPC applications. Two key design features of MACSio will set it apart from existing I/O benchmarking tools. The first is the level of abstraction (LOA) at which MACSio is being designed to operate. The second is the degree of flexibility MACSio is being designed to provide in driving an HPC I/O workload through parameterized, user-defined data objects and a variety of parallel I/O paradigms and I/O interfaces. Combined, these features will allow MACSio to closely mimic I/O workloads for a wide variety of real applications and, in particular, multi-physics applications where data object distribution and composition vary dramatically both within and across parallel tasks. These data objects can then be marshaled using one or more I/O interfaces and parallel I/O paradigms, allowing for direct comparisons of software interfaces, parallel I/O paradigms, and filesystem technologies with the same set of customizable data objects.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Phase Segmentation in Atom-Probe Tomography Using Deep Learning-Based Edge Detection

Abstract Atom-probe tomography (APT) facilitates nano- and atomic-scale characterization and analysis of microstructural features. Specifically, APT is well suited to study the interfacial properties of granular or heterophase systems. Traditionally, the identification of the interface between, for precipitate and matrix phases, in APT data has been obtained either by extracting iso-concentration surfaces based on a user-supplied concentration value or by manually perturbing the concentration value until the iso-concentration surface qualitatively matches the interface. These approaches are subjective, not scalable, and may lead to inconsistencies due to local composition inhomogeneities. We introduce a digital image segmentation approach based on deep neural networks that transfer learned knowledge from natural images to automatically segment the data obtained from APT into different phases. This approach not only provides an efficient way to segment the data and extract interfacial properties but does so without the need for expensive interface labeling for training the segmentation model. We consider here a system with a precipitate phase in a matrix and with three different interface modalities—layered, isolated, and interconnected—that are obtained for different relative geometries of the precipitate phase. We demonstrate the accuracy of our segmentation approach through qualitative visualization of the interfaces, as well as through quantitative comparisons with proximity histograms obtained by using more traditional approaches.

47 OTHER INSTRUMENTATION↗
DOE OSTI2017

ESTEEM: A Novel Framework for Qualitatively Evaluating and Visualizing Spatiotemporal Embeddings in Social Media

Analyzing and visualizing large amounts of social media communications and contrasting short-term conversation changes over time and geo-locations is extremely important for commercial and government applications. Earlier approaches for large-scale text stream summarization used dynamic topic models and trending words. Instead, we rely on text embeddings – low-dimensional word representations in a continuous vector space where similar words are embedded nearby each other. This paper presents ESTEEM,1 a novel tool for visualizing and evaluating spatiotemporal embeddings learned from streaming social media texts. Our tool allows users to monitor and analyze query words and their closest neighbors with an interactive interface. We used state-of- the-art techniques to learn embeddings and developed a visualization to represent dynamically changing relations between words in social media over time and other dimensions. This is the first interactive visualization of streaming text representations learned from social media texts that also allows users to contrast differences across multiple dimensions of the data.

social media dynamics↗
DOE OSTI2018

A Magnetoencephalographic/Encephalographic (MEG/EEG) Brain-Computer Interface Driver for Interactive iOS Mobile Videogame Applications Utilizing the Hadoop Ecosystem, MongoDB, and Cassandra NoSQL Databases

In Phase I, we collected data on five subjects yielding over 90% positive performance in Magnetoencephalographic (MEG) mid-and post-movement activity. In addition, a driver was developed that substituted the actions of the Brain Computer Interface (BCI) as mouse button presses for real-time use in visual simulations. The process was interfaced to a flight visualization demonstration utilizing left or right brainwave thought movement, the user experiences, the aircraft turning in the chosen direction, or on iOS Mobile Warfighter Videogame application. The BCI’s data analytics of a subject’s MEG brain waves and flight visualization performance videogame analytics were stored and analyzed using the Hadoop Ecosystem as a quick retrieval data warehouse. In Phase II portion of the project involves the Emotiv Encephalographic (EEG) Wireless Brain–Computer interfaces (BCIs) allow for people to establish a novel communication channel between the human brain and a machine, in this case, an iOS Mobile Application(s). The EEG BCI utilizes advanced and novel machine learning algorithms, as well as the Spark Directed Acyclic Graph (DAG), Cassandra NoSQL database environment, and also the competitor NoSQL MongoDB database for housing BCI analytics of subject’s response and users’ intent illustrated for both MEG/EEG brainwave signal acquisition. The wireless EEG signals that were acquired from the OpenVibe and the Emotiv EPOC headset can be connected via Bluetooth to an iPhone utilizing a thin Client architecture. The use of NoSQL databases were chosen because of its schema-less architecture and Map Reduce computational paradigm algorithm for housing a user’s brain signals from each referencing sensor. Thus, in the near future, if multiple users are playing on an online network connection and an MEG/EEG sensor fails, or if the connection is lost from the smartphone and the webserver due to low battery power or failed data transmission, it will not nullify the NoSQL document-oriented (MongoDB) or column-oriented Cassandra databases. Additionally, NoSQL databases have fast querying and indexing methodologies, which are perfect for online game analytics and technology. In Phase II, we collected data on five MEG subjects, yielding over 90% positive performance on iOS Mobile Applications with Objective-C and C++, however on EEG signals utilized on three subjects with the Emotiv wireless headsets and (n < 10) subjects from the OpenVibe EEG database the Variational Bayesian Factor Analysis Algorithm (VBFA) yielded below 60% performance and we are currently pursuing extending the VBFA algorithm to work in the time-frequency domain referred to as VBFA-TF to enhance EEG performance in the near future. The novel usage of NoSQL databases, Cassandra and MongoDB, were the primary main enhancements of the BCI Phase II MEG/EEG brain signal data acquisition, queries, and rapid analytics, with MapReduce and Spark DAG demonstrating future implications for next generation biometric MEG/EEG NoSQL databases.

McClay, Wilbert↗
DOE OSTI2023

pvlib iotools—Open-source Python functions for seamless access to solar irradiance data

Access to accurate solar resource data is critical for numerous applications, including estimating the yield of solar energy systems, developing radiation models, and validating irradiance datasets. However, lack of standardization in data formats and access interfaces across providers constitutes a major barrier to entry for new users. pvlib python’s iotools subpackage aims to solve this issue by providing standardized Python functions for reading local files and retrieving data from external providers. All functions follow a uniform pattern and return convenient data outputs, allowing users to seamlessly switch between data providers and explore alternative datasets. The pvlib package is community-developed on GitHub: https://github.com/pvlib/pvlib-python. As of pvlib python version 0.9.5, the iotools subpackage supports 12 different datasets, including ground measurement, reanalysis, and satellite-derived irradiance data. The supported ground measurement networks include the Baseline Surface Radiation Network (BSRN), NREL MIDC, SRML, SOLRAD, SURFRAD, and the US Climate Reference Network (CRN). Additionally, satellite-derived and reanalysis irradiance data from the following sources are supported: PVGIS (SARAH & ERA5), NSRDB PSM3, and CAMS Radiation Service (including McClear clear-sky irradiance).

14 SOLAR ENERGY↗
DOE OSTI2013

ModBase, a database of annotated comparative protein structure models and associated resources

ModBase (http://salilab.org/modbase) is a database of annotated comparative protein structure models. The models are calculated by ModPipe, an automated modeling pipeline that relies primarily on Modeller for fold assignment, sequence-structure alignment, model building and model assessment (http://salilab.org/modeller/). ModBase currently contains almost 30 million reliable models for domains in 4.7 million unique protein sequences. ModBase allows users to compute or update comparative models on demand, through an interface to the ModWeb modeling server (http://salilab.org/ modweb). ModBase models are also available through the Protein Model Portal (http://www.prote inmodelportal.org/). Recently developed associated resources include the AllosMod server for modeling ligand-induced protein dynamics (http://salilab.org/ allosmod), the AllosMod-FoXS server for predicting a structural ensemble that fits an SAXS profile (http://salilab.org/allosmod-foxs), the FoXSDock server for protein–protein docking filtered by an SAXS profile (http://salilab.org/foxsdock), the SAXS Merge server for automatic merging of SAXS profiles (http://salilab.org/saxsmerge) and the Pose & Rank server for scoring protein–ligand complexes (http://salilab.org/poseandrank). In this update, we also highlight two applications of ModBase: a PSI:Biology initiative to maximize the structural coverage of the human alpha-helical transmembrane proteome and a determination of structural determinants of human immunodeficiency virus-1 protease specificity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

An Efficient Silent Data Corruption Detection Method with Error-Feedback Control and Even Sampling for HPC Applications

The silent data corruption (SDC) problem is attracting more and more attentions because it is expected to have a great impact on exascale HPC applications. SDC faults are hazardous in that they pass unnoticed by hardware and can lead to wrong computation results. In this work, we formulate SDC detection as a runtime one-step-ahead prediction method, leveraging multiple linear prediction methods in order to improve the detection results. The contributions are twofold: (1) we propose an error feedback control model that can reduce the prediction errors for different linear prediction methods, and (2) we propose a spatial-data-based even-sampling method to minimize the detection overheads (including memory and computation cost). We implement our algorithms in the fault tolerance interface, a fault tolerance library with multiple checkpoint levels, such that users can conveniently protect their HPC applications against both SDC errors and fail-stop errors. We evaluate our approach by using large-scale traces from well-known, large-scale HPC applications, as well as by running those HPC applications on a real cluster environment. Experiments show that our error feedback control model can improve detection sensitivity by 34-189% for bit-flip memory errors injected with the bit positions in the range [20,30], without any degradation on detection accuracy. Furthermore, memory size can be reduced by 33% with our spatial-data even-sampling method, with only a slight and graceful degradation in the detection sensitivity.

Di, Sheng↗
DOE OSTI2018

Paracousti v. 2.0.0

Paracousti simulates 3-D acoustic wave propagation in fixed (non-moving) complex media. It solves the linear acoustic equations of motion using the velocity-pressure system of first order linear differential equations on a finite-difference Cartesian grid using Newton’s law of motion and mass continuity equations. It also has the ability to incorporate acoustic attenuation to simulate non-recoverable energy losses via the velocity-memory-pressure system of linear differential equations. We assume stationary, non-heat conducting, adiabatic media (fluid) where the background sound speed and material density are fixed in time. Capabilities include massively parallel design, optimization for high contrast media interfaces, inclusion of arbitrary pressure and force sources defined by the user, inclusion of arbitrary pressure and velocity receivers defined by the user, acoustic wavefield snapshots in time for visualization, and convolutional perfectly matched layers to minimize artificial grid boundary reflections. Paracousti was built upon the foundational framework of TDAAPS (Time-Domain Atmospheric Acoustic Propagation Suite) by Neill Symons, Dave Aldridge, and Leiph Preston.

Preston, Leiph↗