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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 55 records · Page 3
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

CFM-ID 4.0 – a web server for accurate MS-based metabolite identification

The CFM-ID 4.0 web server (https://cfmid.wishartlab.com) is an online tool for predicting, annotating and interpreting tandem mass (MS/MS) spectra of small molecules. It is specifically designed to assist researchers pursuing studies in metabolomics, exposomics and analytical chemistry. More specifically, CFM-ID 4.0 supports the: 1) prediction of electrospray ionization quadrupole time-of-flight tandem mass spectra (ESI-QTOF-MS/MS) for small molecules over multiple collision energies (10 eV, 20 eV, and 40 eV); 2) annotation of ESI-QTOF-MS/MS spectra given the structure of the compound; and 3) identification of a small molecule that generated a given ESI-QTOF-MS/MS spectrum at one or more collision energies. The CFM-ID 4.0 web server makes use of a substantially improved MS fragmentation algorithm, a much larger database of experimental and in silico predicted MS/MS spectra and improved scoring methods to offer more accurate MS/MS spectral prediction and MS/MS-based compound identification. Compared to earlier versions of CFM-ID, this new version has an MS/MS spectral prediction performance that is ~22% better and a compound identification accuracy that is ~35% better on a standard (CASMI 2016) testing dataset. CFM-ID 4.0 also features a neutral loss function that allows users to identify similar or substituent compounds where no match can be found using CFM-ID’s regular MS/MS-to-compound identification utility. Finally, the CFM-ID 4.0 web server now offers a much more refined user interface that is easier to use, supports molecular formula identification (from MS/MS data), provides more interactively viewable data (including proposed fragment ion structures) and displays MS mirror plots for comparing predicted with observed MS/MS spectra. These improvements should make CFM-ID 4.0 much more useful to the community and should make small molecule identification much easier, faster, and more accurate.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

Catalytic site identification—a web server to identify catalytic site structural matches throughout PDB

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein structure or model to identify structural matches to a library of catalytic sites. Finally, the server provides a database of pre-calculated matches between all Protein Data Bank proteins and the library of catalytic sites. The database has been used to derive a set of hypothesized novel enzymatic function annotations. In all cases, matches and putative binding sites (protein structure and surfaces) can be visualized interactively online. The website can be accessed at http://catsid.llnl. gov.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

New developments including X-ray standing waves in the dynamical Bragg diffraction program of X-ray Server

X-ray Server (https://x-server.gmca.aps.anl.gov) is a collection of programs for online modelling of X-ray diffraction and scattering. Additionally, the dynamical diffraction program is the second most popular Server program, contributing 34% of total Server usage. It models dynamical X-ray diffraction from strained crystals and multilayers for any Bragg-case geometry including grazing incidence and exit. This paper reports on a revision of equations used by the program, which yields ten times faster calculations in most use cases, on implementing calculations of X-ray standing waves and on adding new options for modelling diffraction from monolayers.

36 MATERIALS SCIENCE↗
DOE OSTI2012

Workload Characterization and Performance Implications of Large-Scale Blog Servers

With the ever-increasing popularity of social network services (SNSs), an understanding of the characteristics of these services and their effects on the behavior of their host servers is critical. However, there has been a lack of research on the workload characterization of servers running SNS applications such as blog services. To fill this void, we empirically characterized real-world web server logs collected from one of the largest South Korean blog hosting sites for 12 consecutive days. The logs consist of more than 96 million HTTP requests and 4.7 TB of network traffic. Our analysis reveals the followings: (i) The transfer size of non-multimedia files and blog articles can be modeled using a truncated Pareto distribution and a log-normal distribution, respectively; (ii) User access for blog articles does not show temporal locality, but is strongly biased towards those posted with image or audio files. We additionally discuss the potential performance improvement through clustering of small files on a blog page into contiguous disk blocks, which benefits from the observed file access patterns. Trace-driven simulations show that, on average, the suggested approach achieves 60.6% better system throughput and reduces the processing time for file access by 30.8% compared to the best performance of the Ext4 file system.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
NASA NTRS1993

Interfacing a high performance disk array file server to a Gigabit LAN

Our previous prototype, RAID-1, identified several bottlenecks in typical file server architectures. The most important bottleneck was the lack of a high-bandwidth path between disk, memory, and the network. Workstation servers, such as the Sun-4/280, have very slow access to peripherals on busses far from the CPU. For the RAID-2 system, we addressed this problem by designing a crossbar interconnect, Xbus board, that provides a 40MB/s path between disk, memory, and the network interfaces. However, this interconnect does not provide the system CPU with low latency access to control the various interfaces. To provide a high data rate to clients on the network, we were forced to carefully and efficiently design the network software. A block diagram of the system hardware architecture is given. In the following subsections, we describe pieces of the RAID-2 file server hardware that had a significant impact on the design of the network interface.

Seshan, Srinivasan↗
NASA NTRS1992

A distributed clients/distributed servers model for STARCAT

STARCAT, the Space Telescope ARchive and CATalogue user interface has been along for a number of years already. During this time it has been enhanced and augmented in a number of different fields. This time, we would like to dwell on a new capability allowing geographically distributed user interfaces to connect to geographically distributed data servers. This new concept permits users anywhere on the internet running STARCAT on their local hardware to access e.g., whichever of the 3 existing HST archive sites is available, or get information on the CFHT archive through a transparent connection to the CADC in BC or to get the La Silla weather by connecting to the ESO database in Munich during the same session. Similarly PreView (or quick look) images and spectra will also flow directly to the user from wherever it is available. Moving towards an 'X'-based STARCAT is another goal being pursued: a graphic/image server and a help/doc server are currently being added to it. They should further enhance the user independence and access transparency.

Pirenne, B.↗
NASA NTRS1994

MO/DSD online information server and global information repository access

Often in the past, standards and new technology information have been available only in hardcopy form, with reproduction and mailing costs proving rather significant. In light of NASA's current budget constraints and in the interest of efficient communications, the Mission Operations and Data Systems Directorate (MO&DSD) New Technology and Data Standards Office recognizes the need for an online information server (OLIS). This server would allow: (1) dissemination of standards and new technology information throughout the Directorate more quickly and economically; (2) online browsing and retrieval of documents that have been published for and by MO&DSD; and (3) searching for current and past study activities on related topics within NASA before issuing a task. This paper explores a variety of available information servers and searching tools, their current capabilities and limitations, and the application of these tools to MO&DSD. Most importantly, the discussion focuses on the way this concept could be easily applied toward improving dissemination of standards and new technologies and improving documentation processes.

Nguyen, Diem↗
NASA NTRS2016

Advancing the Power and Utility of Server-Side Aggregation

During the upcoming Summer 2016 meeting of the ESIP Federation (July 19-22), OpenDAP will hold a Developers and Users Workshop. While a broad set of topics will be covered, a key focus is capitalizing on recent EOSDIS-sponsored advances in Hyrax, OPeNDAPs own software for server-side realization of the DAP2 and DAP4 protocols. These Hyrax advances are as important to data users as to data providers, and the workshop will include hands-on experiences of value to both. Specifically, a balanced set of presentations and hands-on tutorials will address advances in1.server installation,2.server configuration,3.Hyrax aggregation capabilities,4.support for data-access from clients that are HTTP-based, JSON-based or OGC-compliant (especially WCS and WMS),5.support for DAP4,6.use and extension of server-side computational capabilities, and7.several performance-affecting matters.Topics 2 through 7 will be relevant to data consumers, data providers andnotably, due to the open-source nature of all OPeNDAP softwareto developers wishing to extend Hyrax, to build compatible clients and servers, andor to employ Hyrax as middleware that enables interoperability across a variety of end-user and source-data contexts. A session for contributed talks will elaborate the topics listed above and embrace additional ones.

aggregation↗
NASA NTRS2016

A Satellite Data-Driven, Client-Server Decision Support Application for Agricultural Water Resources Management

Water cycle extremes such as droughts and floods present a challenge for water managers and for policy makers responsible for the administration of water supplies in agricultural regions. In addition to the inherent uncertainties associated with forecasting extreme weather events, water planners need to anticipate water demands and water user behavior in a typical circumstances. This requires the use decision support systems capable of simulating agricultural water demand with the latest available data. Unfortunately, managers from local and regional agencies often use different datasets of variable quality, which complicates coordinated action. In previous work we have demonstrated novel methodologies to use satellite-based observational technologies, in conjunction with hydro-economic models and state of the art data assimilation methods, to enable robust regional assessment and prediction of drought impacts on agricultural production, water resources, and land allocation. These methods create an opportunity for new, cost-effective analysis tools to support policy and decision-making over large spatial extents. The methods can be driven with information from existing satellite-derived operational products, such as the Satellite Irrigation Management Support system (SIMS) operational over California, the Cropland Data Layer (CDL), and using a modified light-use efficiency algorithm to retrieve crop yield from the synergistic use of MODIS and Landsat imagery. Here we present an integration of this modeling framework in a client-server architecture based on the Hydra platform. Assimilation and processing of resource intensive remote sensing data, as well as hydrologic and other ancillary information occur on the server side. This information is processed and summarized as attributes in water demand nodes that are part of a vector description of the water distribution network. With this architecture, our decision support system becomes a light weight 'app' that connects to the server to retrieve the latest information regarding water demands, land use, yields and hydrologic information required to run different management scenarios. Furthermore, this architecture ensures all agencies and teams involved in water management use the same, up-to-date information in their simulations.

Agricultural↗
DOE OSTI2012

Fact Sheet: Improving Energy Efficiency for Server Rooms and Closets

Is there a ghost in your IT closet? If your building has one or more IT rooms or closets containing between 5 and 50 servers, chances are that they account for a significant share of the building’s energy use (in some cases, over half!). Servers, data storage arrays, networking equipment, and the cooling and power conditioning that support them tend to draw large amounts of energy 24/7, in many cases using more energy annually than traditional building loads such as HVAC and lighting. The good news is that there are many cost-effective actions, ranging from simple to advanced, that can dramatically reduce that energy use, helping you to save money and reduce pollution.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2016

Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Optimizing High-Throughput Inference on Graph Neural Networks at Shared Computing Facilities with the NVIDIA Triton Inference Server

Abstract With machine learning applications now spanning a variety of computational tasks, multi-user shared computing facilities are devoting a rapidly increasing proportion of their resources to such algorithms. Graph neural networks (GNNs), for example, have provided astounding improvements in extracting complex signatures from data and are now widely used in a variety of applications, such as particle jet classification in high energy physics (HEP). However, GNNs also come with an enormous computational penalty that requires the use of GPUs to maintain reasonable throughput. At shared computing facilities, such as those used by physicists at Fermi National Accelerator Laboratory (Fermilab), methodical resource allocation and high throughput at the many-user scale are key to ensuring that resources are being used as efficiently as possible. These facilities, however, primarily provide CPU-only nodes, which proves detrimental to time-to-insight and computational throughput for workflows that include machine learning inference. In this work, we describe how a shared computing facility can use the NVIDIA Triton Inference Server to optimize its resource allocation and computing structure, recovering high throughput while scaling out to multiple users by massively parallelizing their machine learning inference. To demonstrate the effectiveness of this system in a realistic multi-user environment, we use the Fermilab Elastic Analysis Facility augmented with the Triton Inference Server to provide scalable and high-throughput access to a HEP-specific GNN and report on the outcome.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2017

SeqTU: A web server for identification of bacterial transcription units

A transcription unit (TU) consists of K ≥ 1 consecutive genes on the same strand of a bacterial genome that are transcribed into a single mRNA molecule under certain conditions. Their identification is an essential step in elucidation of transcriptional regulatory networks. We have recently developed a machine-learning method to accurately identify TUs from RNA-seq data, based on two features of the assembled RNA reads: the continuity and stability of RNA-seq coverage across a genomic region. While good performance was achieved by the method on Escherichia coli and Clostridium thermocellum , substantial work is needed to make the program generally applicable to all bacteria, knowing that the program requires organism specific information. A web server, named SeqTU , was developed to automatically identify TUs with given RNA-seq data of any bacterium using a machine-learning approach. The server consists of a number of utility tools, in addition to TU identification, such as data preparation, data quality check and RNA-read mapping. SeqTU provides a user-friendly interface and automated prediction of TUs from given RNA-seq data. Furthermore, the predicted TUs are displayed intuitively using HTML format along with a graphic visualization of the prediction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Embedded EPICS server for PowerPMAC motion controllers

An embedded server layer of Experimental Physics and Industrial Control System (EPICS) for PowerPMAC motion controllers has been developed and deployed at two undulator beamlines of the National Institute of General Medical Sciences and the National Cancer Institute (GM/CA) Structural Biology Facility at the Advanced Photon Source (APS). This compact, open source solution makes the power and versatility of PowerPMAC motion controls directly accessible to distributed EPICS clients. At GM/CA the system controls about 200 servo and stepper motors — both encoded and unencoded — and multiple digital and analog I/O accessories. The server stack comprises two sublayers: a lower-level driver and database that communicates directly with PowerPMAC, and a facility-specific soft sublayer built on top. The paper describes installing EPICS on PowerPMAC, the implementation of both layers and client examples, including on-the-fly scanning.

EPICS↗
DOE OSTI2010

RosettaBackrub--a web server for flexible backbone protein structure modeling and design

The Rosetta-Backrub server (http://kortemmelab .ucsf.edu/backrub) implements the Backrub method, derived from observations of alternative conformations in high-resolution protein crystal structures, for flexible backbone protein modeling. Backrub modeling is applied to three related applications using the Rosetta program for structure prediction and design: (I) modeling of structures of point mutations, (II) generating protein conformational ensembles and designing sequences consistent with these conformations and (III) predicting tolerated sequences at protein–protein interfaces. The three protocols have been validated on experimental data. Starting from a user-provided single input protein structure in PDB format, the server generates near-native conformational ensembles. The predicted conformations and sequences can be used for different applications, such as to guide mutagenesis experiments, for ensemble-docking approaches or to generate sequence libraries for protein design.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

SIFTER search: a web server for accurate phylogeny-based protein function prediction

We are awash in proteins discovered through high-throughput sequencing projects. As only a minuscule fraction of these have been experimentally characterized, computational methods are widely used for automated annotation. Here, we introduce a user-friendly web interface for accurate protein function prediction using the SIFTER algorithm. SIFTER is a state-of-the-art sequence-based gene molecular function prediction algorithm that uses a statistical model of function evolution to incorporate annotations throughout the phylogenetic tree. Due to the resources needed by the SIFTER algorithm, running SIFTER locally is not trivial for most users, especially for large-scale problems. The SIFTER web server thus provides access to precomputed predictions on 16 863 537 proteins from 232 403 species. Users can explore SIFTER predictions with queries for proteins, species, functions, and homologs of sequences not in the precomputed prediction set. Lastly, the SIFTER web server is accessible at http://sifter.berkeley.edu/ and the source code can be downloaded.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

MAPA: Multi-Accelerator Pattern Allocation Policy for Multi-Tenant GPU Servers

Multi-accelerator servers are increasingly being deployed in shared multi-tenant environments (such as in cloud data centers) in order to meet the demands of large-scale compute-intensive workloads. In addition, these accelerators are increasingly being inter-connected in complex topologies and workloads are exhibiting a wider variety of inter-accelerator communication patterns. However, existing al-location policies are ill-suited for these emerging use-cases. Specifically, this work identifies that multi-accelerator workloads are commonly fragmented leading to reduced bandwidth and increased latency for inter-accelerator communication. We propose Multi-Accelerator Pattern Allocation (MAPA), a graph pattern mining approach towards providing generalized allocation support for allocating multi-accelerator workloads on multi-accelerator servers. We demonstrate that MAPA is able to improve the execution time of multi-accelerator workloads and that MAPA is able to provide generalized benefits across various accelerator topologies. Finally, we demonstrate a speedup of 12.4% for75th percentile of jobs with the worst case execution time reduced by up to 35% against baseline policy using MAPA.

Ranganath, Kiran↗
DOE OSTI2015

Sirocco Storage Server v. pre-alpha 0.1

Sirocco is a parallel storage system under development, designed for write-intensive workloads on large-scale HPC platforms. It implements a keyvalue object store on top of a set of loosely federated storage servers that cooperate to ensure data integrity and performance. It includes support for a range of different types of storage transactions. This software release constitutes a conformant storage server, along with the client-side libraries to access the storage over a network.

Curry, MatthewL.↗