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At least 145 records · Page 8
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Wilkins: HPC in situ workflows made easy

In situ approaches can accelerate the pace of scientific discoveries by allowing scientists to perform data analysis at simulation time. Current in situ workflow systems, however, face challenges in handling the growing complexity and diverse computational requirements of scientific tasks. In this work, we present Wilkins, an in situ workflow system that is designed for ease-of-use while providing scalable and efficient execution of workflow tasks. Wilkins provides a flexible workflow description interface, employs a high-performance data transport layer based on HDF5, and supports tasks with disparate data rates by providing a flow control mechanism. Wilkins seamlessly couples scientific tasks that already use HDF5, without requiring task code modifications. We demonstrate the above features using both synthetic benchmarks and two science use cases in materials science and cosmology.

HPC↗
NASA NTRSDate not supplied

High Performance Access to Archival Data Stored in HDF4 and HDF5 on Cloud Object Stores Without Reformatting the Files

Cloud computing offers numerous advantages for users of extensive Earth science data collections. These benefits encompass direct online access to data files and granules from any location, scalable access supporting parallel computing workflows, and flexible computing tools enabling innovative experimentation with processing techniques. However, older archival file formats designed for distinct computing systems hinder efficient access to decade-long time-series data when compared to data stored in modern cloud-optimized formats like Web Object Stores (WOS), exemplified by Amazon Web Services’ Simple Storage Service (S3). We describe DMR++ (Dataset Metadata Response plus plus), a technology facilitating efficient access to HDF5 (Hierarchical Data Format, version 5) and HDF4 files stored on WOS systems without requiring data reformatting. DMR++ achieves performance comparable to technologies like Zarr while preserving the original file structure, a substantial benefit considering the vast quantity of archival files held by organizations such as NASA. Moreover, DMR++ typically outperforms cloud-optimized versions of HDF5. Essentially an XML (Extensible Markup Language) document usually stored alongside the described data, DMR++ can also be generated on-the-fly but is generally created during data staging to the WOS. Archival files that use HDF4/5 often store large arrays of numerical data. The data in these files is often compressed, typically reducing their size by a factor of four or more. To achieve efficient access to portions of those arrays, they are 'chunked' into smaller sub-arrays, each individually compressed. The chunk size is a compromise, where spinning disks can efficiently access data in smaller chunks while S3 favors larger chunks. A simple optimization of aggregating smaller chunks that are stored adjacently, transferring them in a single access and then individually decompressing them will improve performance. NASA data pose an additional challenge: special Application Programmer Interface (API) libraries are often needed to compute some variables. These libraries are incompatible with WOS environments. Our solution involves storing computed values in the DMR++ document or a companion file, making them accessible like other variables and eliminating the need for specialized APIs. We outline specific optimizations for both satellite grid and swath data stored in HDF4-EOS2 (Earth Observing System).

James Gallagher↗
DOE OSTI2024

Improving I/O-aware Workflow Scheduling via Data Flow Characterization and trade-off Analysis

The scientific computing paradigm has transitioned from compute-intensive to I/O-intensive and memory-intensive in the past decade, especially when data-driven science has become common practice. Numerous empirical I/O-aware scheduling optimizations have been developed by incorporating I/O capacity and bandwidth as constraints into scheduling. Unfortunately, there is a lack of data flow (I/O) characterization tool and an understanding of trade-offs between concurrency, locality, and I/O bandwidth. To bridge the gap, this work 1) presents a set of descriptors to characterize, organize, and visualize I/O profiles, including flow size, I/O bandwidth, and operation count, which group data flows by I/O types, tasks, and files; 2) proposes an I/O Roofline model-based trade-off analysis to find the optimal trade-off between flow operational intensity, concurrency, and flow performance. The I/O descriptors generate useful insights into complicated I/O behaviors, suggesting distinct concurrency, storage, and scheduling to be used by types, tasks, and files. The proposed trade-off analysis guides scheduling decisions that generate resource assignment with the best flow parallelism. We evaluate our I/O-aware scheduling methodology on a highly I/O-intensive workflow–1000 Genomes. The experimental results demonstrate speedups of up to 2.4× compared to the state-of-the- art methods.

Guo, Luanzheng [BATTELLE (PACIFIC NW LAB)]↗
DOE OSTI2024

PanDA: Production and Distributed Analysis System

The Production and Distributed Analysis (PanDA) system is a data-driven workload management system engineered to operate at the LHC data processing scale. The PanDA system provides a solution for scientific experiments to fully leverage their distributed heterogeneous resources, showcasing scalability, usability, flexibility, and robustness. The system has successfully proven itself through nearly two decades of steady operation in the ATLAS experiment, addressing the intricate requirements such as diverse resources distributed worldwide at about 200 sites, thousands of scientists analyzing the data remotely, the volume of processed data beyond the exabyte scale, dozens of scientific applications to support, and data processing over several billion hours of computing usage per year. PanDA’s flexibility and scalability make it suitable for the High Energy Physics community and wider science domains at the Exascale. Beyond High Energy Physics, PanDA’s relevance extends to other big data sciences, as evidenced by its adoption in the Vera C. Rubin Observatory and the sPHENIX experiment. As the significance of advanced workflows continues to grow, PanDA has transformed into a comprehensive ecosystem, effectively tackling challenges associated with emerging workflows and evolving computing technologies. The paper discusses PanDA’s prominent role in the scientific landscape, detailing its architecture, functionality, deployment strategies, project management approaches, results, and evolution into an ecosystem.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

The Carbon Storage Technical Viability Approach (CS TVA)

The Carbon Storage Technical Viability Approach (CS TVA) StoryMap provides an in-depth overview of the products created during the CS TVA research effort. In detail, the StoryMap addresses the CS TVA Matrix, Database Version 2.0, Database Catalog, Workflow, and Data Availability Result Database, discussing how each was developed and implemented. Information on how the matrix, database, and database catalog are interconnected, and their usage is also explained. The workflow section provides information on the CS TVA product development from the data-gathering stage to the final data availability results. A section on an expansion of the CS TVA workflow that utilizes Natural Language processing (NLP) section was included. Finally, the Data Availability Results Database is discussed. These results provide data science-informed insights into potential data gaps when assessing the viability of carbon storage in a given area or region.

Carbon Storage↗
DOE OSTI2023

ASC Data Science Infrastructure Project June 2023 [Slides]

Data Science Infrastructure (DSI) Project offers a standardized but flexible way of storing data and associated metadata to support AI/ML and data intensive scientific workflows: Establish requirements via use case interviews; Develop DSI framework to support flexible, secure, and accessible data stores tailored to researcher needs; Augment existing institutional frameworks for code management, performance testing and file indexing via automated DSI interfaces; Deploy DSI framework to support key use cases in collaboration with domain scientists.

97 MATHEMATICS AND COMPUTING↗
NASA NTRS2004

Grid Enabled Geospatial Catalogue Web Service

Geospatial Catalogue Web Service is a vital service for sharing and interoperating volumes of distributed heterogeneous geospatial resources, such as data, services, applications, and their replicas over the web. Based on the Grid technology and the Open Geospatial Consortium (0GC) s Catalogue Service - Web Information Model, this paper proposes a new information model for Geospatial Catalogue Web Service, named as GCWS which can securely provides Grid-based publishing, managing and querying geospatial data and services, and the transparent access to the replica data and related services under the Grid environment. This information model integrates the information model of the Grid Replica Location Service (RLS)/Monitoring & Discovery Service (MDS) with the information model of OGC Catalogue Service (CSW), and refers to the geospatial data metadata standards from IS0 19115, FGDC and NASA EOS Core System and service metadata standards from IS0 191 19 to extend itself for expressing geospatial resources. Using GCWS, any valid geospatial user, who belongs to an authorized Virtual Organization (VO), can securely publish and manage geospatial resources, especially query on-demand data in the virtual community and get back it through the data-related services which provide functions such as subsetting, reformatting, reprojection etc. This work facilitates the geospatial resources sharing and interoperating under the Grid environment, and implements geospatial resources Grid enabled and Grid technologies geospatial enabled. It 2!so makes researcher to focus on science, 2nd not cn issues with computing ability, data locztic~, processir,g and management. GCWS also is a key component for workflow-based virtual geospatial data producing.

Chen, Ai-Jun↗
NASA NTRS2011

Framework for Integrating Science Data Processing Algorithms Into Process Control Systems

A software framework called PCS Task Wrapper is responsible for standardizing the setup, process initiation, execution, and file management tasks surrounding the execution of science data algorithms, which are referred to by NASA as Product Generation Executives (PGEs). PGEs codify a scientific algorithm, some step in the overall scientific process involved in a mission science workflow. The PCS Task Wrapper provides a stable operating environment to the underlying PGE during its execution lifecycle. If the PGE requires a file, or metadata regarding the file, the PCS Task Wrapper is responsible for delivering that information to the PGE in a manner that meets its requirements. If the PGE requires knowledge of upstream or downstream PGEs in a sequence of executions, that information is also made available. Finally, if information regarding disk space, or node information such as CPU availability, etc., is required, the PCS Task Wrapper provides this information to the underlying PGE. After this information is collected, the PGE is executed, and its output Product file and Metadata generation is managed via the PCS Task Wrapper framework. The innovation is responsible for marshalling output Products and Metadata back to a PCS File Management component for use in downstream data processing and pedigree. In support of this, the PCS Task Wrapper leverages the PCS Crawler Framework to ingest (during pipeline processing) the output Product files and Metadata produced by the PGE. The architectural components of the PCS Task Wrapper framework include PGE Task Instance, PGE Config File Builder, Config File Property Adder, Science PGE Config File Writer, and PCS Met file Writer. This innovative framework is really the unifying bridge between the execution of a step in the overall processing pipeline, and the available PCS component services as well as the information that they collectively manage.

Mattmann, Chris A.↗
DOE OSTI2024

Automated Network Services for Exascale Data Movement

The Large Hadron Collider (LHC) experiments distribute data by leveraging a diverse array of National Research and Education Networks (NRENs), where experiment data management systems treat networks as a “blackbox” resource. After the High Luminosity upgrade, the Compact Muon Solenoid (CMS) experiment alone will produce roughly 0.5 exabytes of data per year. NREN Networks are a critical part of the success of CMS and other LHC experiments. However, during data movement, NRENs are unaware of data priorities, importance, or need for quality of service, and this poses a challenge for operators to coordinate the movement of data and have predictable data flows across multi-domain networks. The overarching goal of SENSE (The Software-defined network for End-to-end Networked Science at Exascale) is to enable National Labs and universities to request and provision end-to-end intelligent network services for their application workflows leveraging SDN (Software-Defined Networking) capabilities. This work aims to allow LHC Experiments and Rucio, the data management software used by CMS Experiment, to allocate and prioritize certain data transfers over the wide area network. In this paper, we will present the current progress of the integration of SENSE, Multi-domain end-to-end SDN Orchestration with QoS (Quality of Service) capabilities, with Rucio, the data management software used by CMS Experiment.

Balcas, Justas↗
DOE OSTI2023

Towards physics-informed explainable machine learning and causal models for materials research

From emergent material descriptions to estimation of properties stemming from structures to optimization of process parameters for achieving best performance – all key facets of materials science and related fields have experienced tremendous growth with the introduction of data-driven models. This gradual progression goes at par with developments of machine learning workflows, from purely data-driven shallow models to those that are well-capable in encoding more complex graphs, symbolic representations, invariances, and positional embeddings. Furthermore, this perspective aims at summarizing strategic aspects of such transitions while providing insights into the requirements of bringing in explainable, interpretable predictive models, and causal learning to aid in materials design and discovery. Although the focus remains on a variety of functional materials by providing a handful of case studies, the applications of such integrated methodologies are universal to facilitate fundamental understandings of materials physics while enabling autonomous experiments.

36 MATERIALS SCIENCE↗
NASA NTRS2018

End-to-End Solution for Data Customization with NASA's Earthdata Search

The goal of NASA's Earthdata Search End-to-End Services workflow is to take the pain and headache out of searching for data and getting that data back in a format that is usable with only that data that is relevant for you. For too long scientists have had to jump through endless hoops, use tools that only offer specific data or specific services, and perform any number of other non-science tasks just to get started on their actual project. Earthdata Search leverages the Common Metadata Repository's (CMR) newly implemented Unified Metadata Models for Services and Variables as well as a new service broker to expose and seamlessly integrate a collection's service capabilities and variables into an intuitive user interface. Using the new End-to-End Services workflow, scientists will be able to quickly see what data is available to be customized, what customization options are available, and actually perform those customizations on the data all within Earthdata Search, regardless of who the data provider is. This talk will demonstrate the simple workflow that will be available to end users and also give an overview covering how the workflow is enabled by the metadata stored within the CMR. (https://search.earthdata.nasa.gov/)

Reese, Mark↗
NASA NTRSDate not supplied

TPSAS-NF1676L-33992-DND

The CERES Science Team integrates and fuses observations from 6 CERES instruments aboard the Terra, Aqua, S-NPP, and NOAA-20 missions with data from more than 20 other unique data sources. Following the November 2017 launch of CERES Flight Model 6 (FM6) onboard NOAA20, CERES has now amassed over 80 instrument-years of valuable Earth radiation budget data. The rapidly growing volume of CERES data coupled with the introduction of new data products alongside improvements to existing science algorithms fosters the requirement for faster, more flexible, and scalable data production and orchestration. New virtualized, cloud-centric compute hardware hosted by the NASA Langley Research Center’s (LaRC) Atmospheric Sciences Data Center (ASDC) provides an ideal environment for these ever-increasing data production demands for CERES. This poster discusses updates to the implementation of the CERES Data Management Team’s (DMT) CERES AuTomAted job Loading sYSTem (CATALYST), a custom data processing workflow engine for CERES, to use on-demand computing resources to perform automated CERES data production processing in a Linux-based container environment. Linux containers provide CERES the flexibility to build multiple production environments in containers tailored for specific workloads and allow effortless provisioning of resources based on the CERES Science Team’s data production requirements.

Thomas N. Hillyer↗
DOE OSTI2023

Persistence Control of Engineered Functions in Complex Soil Microbiomes (PerCon SFA), Secure Biosystems Design Project Data Catalog at PNNL DataHub

The Persistence Control of Engineered Functions in Complex Soil Microbiomes Project (PerCon SFA) at Pacific Northwest National Laboratory (PNNL) is a Genomic Sciences Program Biosystems Design, Science Focus Area research project consortium. Collaborating across highly integrated institutions, PerCon SFA scientists are exploring how environmental niches can be sculpted using the mechanisms of genome reduction and metabolic addiction to drive secure rhizosphere community design for robust biomass cropping in challenging environments. The PerCon SFA DataHub project repository contains publication-relevant digital dataset and metadata DOI packages, enabling exploration and download of integrated experimental dataset catalogs publicly available to a global scientific community. and metadata repository allow for exploring and downloading integrated experimental biodesign omics dataset catalogs, including experimental protocols and/or workflows, raw and/or processed data, as required by the repository, and other relevant supporting materials and/or metadata required for research reproducibility and reporting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Extending the Publish/Subscribe Abstraction for High-Performance I/O and Data Management at Extreme Scale

The Adaptable I/O System (ADIOS) represents the culmination of substantial investment in Scientific Data Management, and it has demonstrated success for several important extreme-scale science cases. However, looking towards the exascale and beyond, we see the development of yet more stringent data management requirements that require new abstractions. Therefore, there is an opportunity to attempt to connect the traditional realms of HPC I/O optimization with the Database / Data Management community. As such, in this paper we offer some specific examples from our ongoing work in managing data structures, services, and performance at the extreme scale for scientific computing. Using the publish/subscribe model afforded by ADIOS, we demonstrate a set of services that connect data format, metadata, queries, data reduction, and high-performance delivery. The resulting publish/subscribe framework facilitates connection to on-line workflow systems to enable the dynamic capabilities that will be required for exascale science.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
DOE OSTI2022

OASIS: Open-Source AI Software Infrastructure for Science-SBIR Phase I

OASIS: Open source AI Software Infrastructure for Science is developed for researchers in the scientific domain. OASIS provides a data API to ingest and serve scientific data formats and annotations within AI workflows. It delivers a unique integration of features such as coupling of data to AI models, scalable training, cloud deployment into a cohesive web and command-line interface, and state-of-the-art techniques to debug and enhance AI models.

Chaudhary, Aashish↗
DOE OSTI2024

Massive all-atom analysis of 2D materials with quantum properties (Final report)

Improvements in microscopy have enabled the acquisition of data at a scale that is difficult to process manually, making automated machine learning approaches to analyzing experimental images essential. In this project, we developed and applied machine learning (ML) workflows for atomic resolution scanning transmission electron microscopy (STEM) images. This development included improving both methodology as well as generating user-friendly codes. We developed machine learning architectures which, after training, automatically identify the location and types of defects throughout a material. We used these data to produce class-averaged images of 2D atomic coordinates with up to 0.3 pm precision, uncovering the structure and oscillations of long-range strain fields around point defects in WSe 2-2x Te 2x . We also resolved a long-standing problem in this field in the training of ML models, a lack of labeled experimental data, by developing a cycle-GAN that transformed simulated-generated labeled data into labeled data indistinguishable from experiment and therefore suitable for training. This removed the remaining parts of the ML data processing workflow where human intervention was still critical and therefore a bottleneck to working at scale. Codes have been developed and released for this full machine learning workflow. ML approaches to partially automate STEM acquisition were also developed. Finally we applied ML and other advanced data processing methods to several materials science problems in two-dimensional materials, including studying the evolution of hyperuniformity with defect concentration in WSe2, understanding phase transformations in transition metal dichalcogenides during in-situ heating in the STEM, and exploring how 2D interfaces transform from twisted into aligned structures.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2025

BOSC 2025, the 26th Bioinformatics Open Source Conference

The 26th annual Bioinformatics Open Source Conference (BOSC 2025, open-bio.org/events/bosc-2025) brought its community-driven focus on open-source bioinformatics and open science to the 2025 conference on Intelligent Systems for Molecular Biology and the European Conference on Computational Biology (ISMB/ECCB 2025). Since its launch in 2000, BOSC has been the premier annual meeting covering open-source bioinformatics and open science. Framed by two keynote addresses and a thought-provoking panel discussion, the two-day conference included sessions dedicated to open data, analytic tools and pipelines, workflow platforms, knowledge representation, and the application of AI/ML. The first keynote talk was delivered by Christine Orengo: “Working together to develop, promote and protect our data resources: Lessons learnt developing CATH and TED.” A joint session with the Bio-Ontologies and Knowledge Representation (BOKR) track the second day of BOSC started with a keynote talk by Chris Mungall entitled “Open Knowledge Bases in the Age of Generative AI”. A closing panel on Data Sustainability, moderated by Mónica Muñoz Torres, featured panelists Scott Edmunds, Varsha Khodiyar, Tony Burdett, Nicky Mulder, and Chris Mungall. This year, the CollaborationFest collaborative work event that typically precedes or follows ISMB was incorporated as part of the main conference and organized by BOSC with help from the Function and 3D-SIG tracks.

bioinformatics↗