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At least 1,225 records · Page 68
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

PaperBLAST: Text Mining Papers for Information about Homologs

With the recent explosion of genome sequencing data, there are now millions of uncharacterized proteins. If a scientist becomes interested in one of these proteins, it can be very difficult to find information as to its likely function. Often a protein whose sequence is similar, and which is likely to have a similar function, has been studied already, but this information is not available in any database. To help find articles about similar proteins, PaperBLAST searches the full text of scientific articles for protein identifiers or gene identifiers, and it links these articles to protein sequences. Then, given a protein of interest, it can quickly find similar proteins in its database by using standard software (BLAST), and it can show snippets of text from relevant papers. We hope that PaperBLAST will make it easier for biologists to predict proteins’ functions.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

pnnl/psl

software library of structured linear maps that can be used as drop in replacements for Pytorch linear layers. These maps can be used to enforce physically realistic outcomes to data-driven machine learning scientific modeling problems.

Tuor, Aaron↗
DOE OSTI2012

Thermochimica User Manual – v1.0

A new software library called Thermochimica has been developed that determines a unique combination of phases and their compositions at thermochemical equilibrium. The development of Thermochimica in this research is aimed at direct integration in multi-physics codes and to address several concerns with using commercially available software, including: licensing entanglements associated with code distribution, access to the source code, convenient incorporation into other codes with quality assurance considerations, and computational performance. In particular, significant research efforts have been dedicated to enhance computational performance through advanced algorithm development, such as improved estimation techniques and non-linear solvers. The overall goal of this undertaking is to provide an open source computational tool to enhance the predictive capability of multiphysics codes without significantly impeding computational performance. The purpose of this document is to describe the design of Thermochimica and the basic use of the software library. A brief background to computational thermodynamics and the conditions for thermodynamic equilibrium is given in §2, details of the code development is discussed in §3, details of building and compiling Thermochimica is given in §4, specific programming details for each subroutine in the library is given in the Appendix. The open license for Thermochimica is provided with the source code. As is always the case, software quality assurance (SQA) is an extremely important subject in software development. The importance of this warrants an independent document dedicated to SQA, which has been developed in parallel to this document. The subject of thermodynamic model validation is also of extreme importance in scientific computing and must be given careful attention. To be clear, this document is concerned with the development and use of a general thermodynamic solver and the validation of any models should be included in the discussion of the development of a thermodynamic model that is specific to a particular system.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Report on local data recovery approaches suitable for weather and climate prediction (Deliverable 1.3) (V.1.0)

Numerical weather and climate prediction rates as one of the scientific applications whose accuracy improvements greatly depend on the growth of the available computing power. As the number of cores in top computing facilities pushes into the millions, increasing average frequency of hardware and software failures forces users to review their algorithms and systems in order to protect simulations from breakdown. This report surveys approaches for fault-tolerance in numerical algorithms and system resilience in parallel simulations from the perspective of numerical weather and climate prediction systems. A selection of existing strategies is analyzed, featuring interpolation-restart and compressed checkpointing for the numerics, in-memory checkpointing, user-level failure mitigation-based and backup-based methods for the systems. Numerical examples showcase the performance of the techniques in addressing faults, with particular emphasis on iterative solvers for linear systems, a staple of atmospheric fluid flow solvers. The potential impact of these strategies is discussed in relation to current development of numerical weather prediction algorithms and systems towards the exascale. Trade-offs between performance, efficiency and effectiveness of resiliency strategies are analyzed and some recommendations outlined for future developments.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Triton: Environmental Monitoring Technology Development, Collision Risk Data Collection (Final Report)

In this project, we assembled a sensor suite that combines a scientific echosounder (sonar) system with video and acoustic cameras (secondary sensors). The sensor suite generates data that is amenable to automated target detection algorithms and can provide inputs to animal encounter models. We developed software (archiving software) to collect data simultaneously from all sensors in the suite, analyze the sonar data automatically in near real-time to identify time periods when targets of interest were present, and automatically archive data from the secondary sensors for these time periods. The product of the archiving software is a data set for the secondary sensors, containing data only for the times when targets of interest were determined to be present by the sonar. We performed controlled field testing to verify the operation of the sensor suite and the archiving software.

47 OTHER INSTRUMENTATION↗
DOE OSTI2023

The Eighteenth Data Release of the Sloan Digital Sky Surveys: Targeting and First Spectra from SDSS-V

The eighteenth data release (DR18) of the Sloan Digital Sky Survey (SDSS) is the first one for SDSS-V, the fifth generation of the survey. SDSS-V comprises three primary scientific programs or “Mappers”: the Milky Way Mapper (MWM), the Black Hole Mapper (BHM), and the Local Volume Mapper. This data release contains extensive targeting information for the two multiobject spectroscopy programs (MWM and BHM), including input catalogs and selection functions for their numerous scientific objectives. We describe the production of the targeting databases and their calibration and scientifically focused components. DR18 also includes ~25,000 new SDSS spectra and supplemental information for X-ray sources identified by eROSITA in its eFEDS field. We present updates to some of the SDSS software pipelines and preview changes anticipated for DR19. We also describe three value-added catalogs (VACs) based on SDSS-IV data that have been published since DR17, and one VAC based on the SDSS-V data in the eFEDS field.

79 ASTRONOMY AND ASTROPHYSICS↗
NASA NTRS1980

A ranking algorithm for spacelab crew and experiment scheduling

The problem of obtaining an optimal or near optimal schedule for scientific experiments to be performed on Spacelab missions is addressed. The current capabilities in this regard are examined and a method of ranking experiments in order of difficulty is developed to support the existing software. Experimental data is obtained from applying this method to the sets of experiments corresponding to Spacelab mission 1, 2, and 3. Finally, suggestions are made concerning desirable modifications and features of second generation software being developed for this problem.

Grone, R. D.↗
NASA NTRS1993

VPU(tm) demonstration mission vicinity processor unit(tm) overview

Evolving Technologies Corporation is designing a new type of computer called a Vicinity Processor Unit (VPU). The VPU is designed to monitor and control payloads using an operating system, control process and software environment that specifically takes into account the time delay associated with remotely controlling and monitoring a group of payloads in real time. This is a fundamentally different way of computing which has vast scientific implications for the design and implementation of data processing systems for future space flight missions. As a demonstration mission, the VPU is expected to be flown aboard the Space Shuttle (Payload Identification No. G-700) as a part of NASA's Small Self-Contained Payloads (SSCP) Program. We believe this mission can greatly facilitate the development and validation of technology which may prove to be mission critical for many future space flight missions.

Abdulezer, Loren↗
NASA NTRS2003

Development of a High Accuracy Angular Measurement System for Langley Research Center Hypersonic Wind Tunnel Facilities

Modern experimental and test activities demand innovative and adaptable procedures to maximize data content and quality while working within severely constrained budgetary and facility resource environments. This report describes development of a high accuracy angular measurement capability for NASA Langley Research Center hypersonic wind tunnel facilities to overcome these deficiencies. Specifically, utilization of micro-electro-mechanical sensors including accelerometers and gyros, coupled with software driven data acquisition hardware, integrated within a prototype measurement system, is considered. Development methodology addresses basic design requirements formulated from wind tunnel facility constraints and current operating procedures, as well as engineering and scientific test objectives. Description of the analytical framework governing relationships between time dependent multi-axis acceleration and angular rate sensor data and the desired three dimensional Eulerian angular state of the test model is given. Calibration procedures for identifying and estimating critical parameters in the sensor hardware is also addressed.

Newman, Brett↗
NASA NTRS2012

A Look at the Impact of High-End Computing Technologies on NASA Missions

From its bold start nearly 30 years ago and continuing today, the NASA Advanced Supercomputing (NAS) facility at Ames Research Center has enabled remarkable breakthroughs in the space agency s science and engineering missions. Throughout this time, NAS experts have influenced the state-of-the-art in high-performance computing (HPC) and related technologies such as scientific visualization, system benchmarking, batch scheduling, and grid environments. We highlight the pioneering achievements and innovations originating from and made possible by NAS resources and know-how, from early supercomputing environment design and software development, to long-term simulation and analyses critical to design safe Space Shuttle operations and associated spinoff technologies, to the highly successful Kepler Mission s discovery of new planets now capturing the world s imagination.

Biswas, Rupak↗
NASA NTRS1995

File-System Workload on a Scientific Multiprocessor

Many scientific applications have intense computational and I/O requirements. Although multiprocessors have permitted astounding increases in computational performance, the formidable I/O needs of these applications cannot be met by current multiprocessors a their I/O subsystems. To prevent I/O subsystems from forever bottlenecking multiprocessors and limiting the range of feasible applications, new I/O subsystems must be designed. The successful design of computer systems (both hardware and software) depends on a thorough understanding of their intended use. A system designer optimizes the policies and mechanisms for the cases expected to most common in the user's workload. In the case of multiprocessor file systems, however, designers have been forced to build file systems based only on speculation about how they would be used, extrapolating from file-system characterizations of general-purpose workloads on uniprocessor and distributed systems or scientific workloads on vector supercomputers (see sidebar on related work). To help these system designers, in June 1993 we began the Charisma Project, so named because the project sought to characterize 1/0 in scientific multiprocessor applications from a variety of production parallel computing platforms and sites. The Charisma project is unique in recording individual read and write requests-in live, multiprogramming, parallel workloads (rather than from selected or nonparallel applications). In this article, we present the first results from the project: a characterization of the file-system workload an iPSC/860 multiprocessor running production, parallel scientific applications at NASA's Ames Research Center.

Kotz, David↗
NASA NTRS2004

SOHO Ultraviolet Coronagraph Spectrometer (UVCS) Mission Operations and Data Analysis

The scientific goal of UVCS is to obtain detailed empirical descriptions of the extended solar corona as it evolves over the solar cycle and to use these descriptions to identify and understand the physical processes responsible for coronal heating, solar wind acceleration, coronal mass ejections (CMEs), and the phenomena that establish the plasma properties of the solar wind as measured by "in situ" solar wind instruments. This report covers the period from 15 February 2003 to 14 April 2004. During that time, UVCS observations have consisted of three types: 1) standard synoptic observations comprising, primarily, the H I Lyalpha line profile and the 0 VI 103.2 and 103.7 nm intensity over a range of heights from 1.5 to about 3.0 solar radii and covering 360 degrees about the Sun, 2) sit and stare observations for major flare watches, and 3) special observations designed by the UVCS Lead Observer of the Week for a specific scientific purpose. The special observations are often coordinated with those of other space-based and ground-based instruments and they often are part of SOHO joint observation programs and campaigns. Lead observers have included UVCS Co-Investigators, scientists from the solar physics community and several graduate and undergraduate level students. UVCS has continued to achieve its purpose of using powerful spectroscopic diagnostic techniques to obtain a much more detailed description of coronal structures and dynamic phenomena than existed before the SOHO mission. The new descriptions of coronal mass ejections (CMEs) and coronal structures from UVCS have inspired a large number of theoretical studies aimed at identifying the physical processes responsible for CMEs and solar wind acceleration in coronal holes and streamers. UVCS has proven to be a very stable instrument. Stellar observations have demonstrated its radiometric stability. UVCS has not required any flight software modifications and all mechanisms are operational. The UVCS 0 VI Channel with its redundant optical path for wavelengths near H I Lyalpha is capable of observing the entire UVCS wavelength range. The regions of the detector currently being used require different grating angles for direct OVI observations and redundant path H I Lyalpha observations, and so those can no longer be observed simultaneously. Since December 1998, the 0 VI Channel has been used for all UVCS observations. Although the H I Lyalpha Channel and detector are still operational, increases in the dark count up to about 5x10(exp 4) counts/sec/pixel and an increase in high voltage current to within a factor of two of the maximum used in the laboratory before flight led to the decision to not use that detector after 1998. The visible light channel functioned nominally during the reporting period. UVCS data, data analysis software, calibration files and the mission log are available from the SOHO archive and SAO. All UVCS data are now available within three months of the observations to scientists and the general public via the SOHO Data Archive and SAO. UVCS has resulted in 33 scientific papers in 2003. There were numerous presentations at scientific meetings. UVCS Education and Public Outreach activities involved nine members of the UVCS team. During the reporting period, there were over a dozen events directed at students and teachers, museum audiences, and public audiences via the mass media, internet and educational literature.

Gurman, Joseph↗
DOE OSTI2026

Predictive Chemical Kinetic Modeling: Where We Succeed, Where We Struggle, and What Comes Next

Chemical kinetic modeling plays a foundational role in fields ranging from energy to environmental science, pharmaceuticals, and advanced materials. The past two decades have seen remarkable progress, particularly in modeling gas-phase reactions for thermochemical processes, leading to impactful industrial applications such as steam cracking and air quality management. However, new challenges are emerging. The successful development of systematic methodologies for the description of gas-phase kinetics opens the possibility to apply the same approach to the study of more challenging systems. Here, we review recent advances, including ab initio transition state theory-based master equation estimation of elementary rates, automated mechanism generation, machine-learning-assisted kinetics, and uncertainty quantification, and discuss the advances needed to apply the same methodological approach in areas such as heterogeneous catalysis, electrochemistry, liquid-phase and solid-state reactivity, and multiscale model integration. We advocate for the development of targeted tools, especially methods that go beyond empirical tuning toward first-principles-based predictions. We highlight the need for accessible software and AIaugmented workflows to democratize modeling for industry and academia alike. In this perspective, we call attention to not only what has worked but also what remains unsolved, advocating to avoid overemphasizing successes in scientific works at the expense of realism. The next decade should focus on predictive capability, physical accuracy, and community infrastructure (e.g., databases and services) to enable innovation across diverse fields. We argue that kinetic modeling, properly equipped, can accelerate discovery far beyond its traditional domains.

ab initio calculations↗
DOE OSTI2019

Profiling the Usage of an Extreme-Scale Archival Storage System

Profiling the archival storage system in scientific computing environments has received much less attention compared to the parallel file system, but is equally important since it stores the final data products safely, for a long duration. In this paper, we analyze eight years worth of data transfer logs for accessing the archival file system (HPSS) in the Oak Ridge Leadership Computing Facility (OLCF), which has been hosting the world's largest supercomputers and file systems. Our analysis encompasses about 135 million data transfer activities to the 80 PB High Performance Storage System (HPSS), between 2010 and 2017. We analyze the logs from several dimensions, including studying the workload characteristics (e.g., access patterns, frequency of accesses and temporal behavior), file system characteristics (e.g., directory depth, file system scaling trends, file types), and scientific user behavior (e.g., domain-specific usage and organization). Based on the analysis, we derive insights into the future evolution of the archive in terms of provisioning, desired features and functionality from the archive software, role and right sizing of the archive tiers, quota management, and the importance of smart and efficient metadata and storage management. We believe our study will prove useful for both operating current archival storage and better provisioning future systems.

Sim, Hyogi↗
DOE OSTI2017

A Pattern Language for High-Performance Computing Resilience

High-performance computing systems (HPC) provide powerful capabilities for modeling, simulation, and data analytics for a broad class of computational problems. They enable extreme performance of the order of quadrillion floating-point arithmetic calculations per second by aggregating the power of millions of compute, memory, networking and storage components. With the rapidly growing scale and complexity of HPC systems for achieving even greater performance, ensuring their reliable operation in the face of system degradations and failures is a critical challenge. System fault events often lead the scientific applications to produce incorrect results, or may even cause their untimely termination. The sheer number of components in modern extreme-scale HPC systems and the complex interactions and dependencies among the hardware and software components, the applications, and the physical environment makes the design of practical solutions that support fault resilience a complex undertaking. To manage this complexity, we developed a methodology for designing HPC resilience solutions using design patterns. We codified the well-known techniques for handling faults, errors and failures that have been devised, applied and improved upon over the past three decades in the form of design patterns. In this paper, we present a pattern language to enable a structured approach to the development of HPC resilience solutions. The pattern language reveals the relations among the resilience patterns and provides the means to explore alternative techniques for handling a specific fault model that may have different efficiency and complexity characteristics. Using the pattern language enables the design and implementation of comprehensive resilience solutions as a set of interconnected resilience patterns that can be instantiated across layers of the system stack.

Hukerikar, Saurabh↗
DOE OSTI2012

MyEMSL

MyEMSL provides the following features: user-assisted upload of data from scientific instruments to an archive, tracking data though the upload process, providing metadata for recovery of uploaded data, providing users with access to the data. These features are supplied by a mixture of open source software and internally developed software. MyESML also provides a notification system that allows the system to communicate with users and other parts of the MyEMSL system. This allows the system to support automated workflows and user interaction. Reprocessing of already ingested data is also supported.

Glass, Kevin↗
DOE OSTI2013

Heterogeneous scalable framework for multiphase flows

Two categories of challenges confront the developer of computational spray models: those related to the computation and those related to the physics. Regarding the computation, the trend towards heterogeneous, multi- and many-core platforms will require considerable re-engineering of codes written for the current supercomputing platforms. Regarding the physics, accurate methods for transferring mass, momentum and energy from the dispersed phase onto the carrier fluid grid have so far eluded modelers. Significant challenges also lie at the intersection between these two categories. To be competitive, any physics model must be expressible in a parallel algorithm that performs well on evolving computer platforms. This work created an application based on a software architecture where the physics and software concerns are separated in a way that adds flexibility to both. The develop spray-tracking package includes an application programming interface (API) that abstracts away the platform-dependent parallelization concerns, enabling the scientific programmer to write serial code that the API resolves into parallel processes and threads of execution. The project also developed the infrastructure required to provide similar API s to other application. The API allow object-oriented Fortran applications direct interaction with Trilinos to support memory management of distributed objects in central processing units (CPU) and graphic processing units (GPU) nodes for applications using C++.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2021

The LSST DESC DC2 Simulated Sky Survey

Here, we describe the simulated sky survey underlying the second data challenge (DC2) carried out in preparation for analysis of the Vera C. Rubin Observatory Legacy Survey of Space and Time (LSST) by the LSST Dark Energy Science Collaboration (LSST DESC). Significant connections across multiple science domains will be a hallmark of LSST; the DC2 program represents a unique modeling effort that stresses this interconnectivity in a way that has not been attempted before. This effort encompasses a full end-to-end approach: starting from a large N-body simulation, through setting up LSST-like observations including realistic cadences, through image simulations, and finally processing with Rubin's LSST Science Pipelines. This last step ensures that we generate data products resembling those to be delivered by the Rubin Observatory as closely as is currently possible. The simulated DC2 sky survey covers six optical bands in a wide-fast-deep area of approximately 300 deg 2 , as well as a deep drilling field of approximately 1 deg 2 . We simulate 5 yr of the planned 10 yr survey. The DC2 sky survey has multiple purposes. First, the LSST DESC working groups can use the data set to develop a range of DESC analysis pipelines to prepare for the advent of actual data. Second, it serves as a realistic test bed for the image processing software under development for LSST by the Rubin Observatory. In particular, simulated data provide a controlled way to investigate certain image-level systematic effects. Finally, the DC2 sky survey enables the exploration of new scientific ideas in both static and time domain cosmology.

79 ASTRONOMY AND ASTROPHYSICS↗