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At least 55 records · Page 3

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.↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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↗

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.↗

EPICS Channel Access Server for LabVIEW

It can be challenging to interface National Instruments LabVIEW (http://www.ni.com/labview/) with EPICS (http://www.aps.anl.gov/epics/). Such interface is required when an instrument control program was developed in LabVIEW but it also has to be part of global control system. This is frequently useful in big accelerator facilities. The Channel Access Server is written in LabVIEW, so it works on any hardware/software platform where LabVIEW is available. It provides full server functionality, so any EPICS client can communicate with it.

Zhukov, AlexanderP.↗

OpenStudio® Server [SWR-07-40]

OpenStudio® Server is a web application and distributed computing tool, which is the backbone of the OpenStudio Analysis Framework (OSAF). It is intended to make parametric analysis of building energy models accessible to architects, engineers, and designers via the OpenStudio PAT GUI or the OpenStudio Analysis Gem. OpenStudio Server analyses are defined by PAT projects or OSA's. Each analysis may include many OpenStudio simulations, as determined by project configuration.

Long, Nicholas↗

EnergyPlus Model Context Protocol Server (EnergyPlus-MCP) v0.1

EnergyPlus-MCP is the first open-source Model Context Protocol server specifically designed for EnergyPlus building energy simulation. This innovative software enables AI assistants and other applications to interact programmatically with EnergyPlus through a standardized, secure interface, eliminating traditional technical barriers in building energy modeling. The software provides specialized tools across five functional domains: server management, model configuration and loading, comprehensive building component inspection, systematic model modification, and simulation execution with results visualization. Key features include automated HVAC system discovery and topology mapping, advanced schedule analysis, intelligent model validation, and interactive visualization capabilities. EnergyPlus-MCP's layered architecture ensures robust separation between protocol communication and domain expertise, enabling scalable deployment across organizations, educational institutions, and research teams. Unlike direct LLM approaches that suffer from inconsistent results and security gaps, EnergyPlus-MCP provides validated, reliable interactions while maintaining scientific rigor. This democratizes sophisticated building energy analysis, making EnergyPlus accessible to broader audiences through conversational interfaces and streamlined workflows.

Li, Han [Lawrence Berkeley National Laboratory (LB↗

Protein Sequence Annotation Tool (PSAT): a centralized web-based meta-server for high-throughput sequence annotations

Abstract Background Here we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. Results In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resulting functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Conclusions PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/ . PSAT stands apart from other sequence-based genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.

59 BASIC BIOLOGICAL SCIENCES↗

Using NVMe Gen3 PCIe SSD Cards in High-density Servers for High-performance Big Data Transfer Over Multiple Network Channels

This Technical Note describes how the Zettar team came up with a data transfer cluster design that convincingly proved the feasibility of using high-density servers for high-performance Big Data transfers. It then outlines the tests, operations, and observations that address a potential over-heating concern regarding the use of Non-Volatile Memory Host Controller Interface Specification (NVMHCI aka NVM Express or NVMe) Gen 3 PCIe SSD cards in high-density servers. Finally, it points out the possibility of developing a new generation of high-performance Science DMZ data transfer system for the data-intensive research community and commercial enterprises.

97 MATHEMATICS AND COMPUTING↗

Innovation Incubator: LiquidCool Solutions Technical Evaluation. Laboratory Study and Demonstration Results of a Directed-Flow, Liquid Submerged Server for High-Efficiency Data Centers

LiquidCool Solutions (LCS) has developed liquid submerged server (LSS) technology that changes the way computer electronics are cooled. The technology provides an option to cool electronics by the direct contact flow of dielectric fluid (coolant) into a sealed enclosure housing all the electronics of a single server. The intimate dielectric fluid contact with electronics improves the effectiveness of heat removal from the electronics.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DUNE Rucio Server Scalabiilty Studies

The DUNE collaboration has an ongoing production effort to simulate the full detectors and to analyze the various prototypes that are currently running. Rucio is used to manage the 40PB of files made to date. When 500 or more jobs were sending output to Rucio simultaneously via Rucio upload, we observed timeouts, unhandled exceptions, and Rucio server restarts due to slow performance. In collaboration with the core Rucio team we did a full review of the Rucio upload code and identified several optimizations that can be made. We also have deployed the Ingress load balancer in front of our Rucio servers and added a database connection pooling utility. These changes led to significant improvement both in reliability and scalability, yet we anticipate even better performance will eventually be required. We describe in this paper the initial state of the system, the various debugging processes that were used, and our plans to further improve scalability.

Calcutt, J. [Brookhaven Natl. Lab.]↗