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At least 145 records · Page 8

ASCR Workshop on In Situ Data Management

In January 2019, the U.S. Department of Energy, Office of Science program in Advanced Scientific Computing Research, convened a workshop to identify priority research directions for in situ data management (ISDM). The workshop defined ISDM as the practices, capabilities, and procedures to control the organization of data and enable the coordination and communication among heterogeneous tasks, executing simultaneously in a high-performance computing system, cooperating toward a common objective. The workshop revealed two primary, interdependent motivations for processing and managing data in situ. The first motivation is that the in situ methodology enables scientific discovery from a broad range of data sources over a wide scale of computing platforms: leadership-class systems, clusters, clouds, workstations, and embedded devices at the edge. The successful development of ISDM capabilities will benefit real-time decision-making, design optimization, and data-driven scientific discovery. The second motivation is the need to decrease data volumes. ISDM can make critical contributions to managing large data volumes from computations and experiments to minimize data movement, save storage space, and boost resource efficiency, often while simultaneously increasing scientific precision.

96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗

User Scientific Data Systems: Experience Report

This paper presents an abbreviated history of NASA science data management system development over the past ten years by selecting two case studies, each representative of a distinct era of science data management systems.

Scientific Data↗

DataHub: Science Data Management in Support of Interactive Exploratory Analysis

The DataHub addresses four areas of significant need: scientific visualization and analysis; science data management; interactions in a distributed, heterogeneous environment; and knowledge-based assistance for these functions. The fundamental innovation embedded within the DataHub is the integration of three technologies, videlicet knowledge-based expert systems, science visualization, and science data management. With the DataHub concept, science investigators are able to apply a more complete solution to all nodes of a distributed system.

science↗

Cross-facility science with the Superfacility Project at LBNL

As data sets from DOE user science facilities grow in both size and complexity there is an urgent need for new capabilities to transfer, analyze and manage the data underlying scientific discoveries. LBNL's Superfacility project brings together experimental and observational research instruments with computational and network facilities at the National Energy Research Scientific Computing Center (NERSC) and the Energy Sciences Network (ESnet) with the goal of enabling user science. Here, we report on recent innovations in the Superfacility project, including advanced data management, API-based automation, real-Time interactive user interfaces, and supported infrastructure for 'edge' services.

Enders, B↗

Empowering Scientific Discovery Through Computing at the Advanced Photon Source

This paper explores the challenges and solutions for managing and processing the vast amount of data generated by the Advanced Photon Source (APS), a synchrotron light source facility producing ultra-bright x-rays for diverse scientific domains. With 68 experimental beamlines covering materials research, biology, and more, the APS serves a wide user base across academia, government, and industry. The ongoing upgrade of the APS storage ring and installation of new instruments will amplify data generation and processing demands. This paper discusses the approach to address these demands through automated data processing using standardized workflows that produce faster scientific insights. The APS Data Management System coordinates various data related tasks to manage storage, data transfer, metadata cataloging, data processing, and interfaces with tools provided by Globus. Through integration with the Argonne Leadership Computing Facility (ALCF), APS users can efficiently access high-performance computing resources. Standardized workflows have led to reduced computational burdens on scientists and greater accessibility of high performance computing resources. We demonstrate how standardization and collaboration enable scientists to rapidly convert raw data into meaningful scientific results, establishing a streamlined path from data collection to analysis and ultimately to publication.

Parraga, Hannah↗

Simulation of Enhanced Geothermal Systems: A Benchmarking and Code Intercomparison Study

Numerical simulation codes have become critical tools for understanding complex geologic processes, as applied to technology assessment, system design, monitoring, and operational guidance. Recently the need for quantitatively evaluating coupled Thermodynamic, Hydrologic, geoMechanical, and geoChemical (THMC) processes has grown, driven by new applications such as geologic sequestration of greenhouse gases and development of unconventional energy sources. Here we focus on Enhanced Geothermal Systems (EGS), which are man-made geothermal reservoirs created where hot rock exists but there is insufficient natural permeability and/or pore fluids to allow efficient energy extraction. In an EGS, carefully controlled subsurface fluid injection is performed to enhance the permeability of pre-existing fractures, which facilitates fluid circulation and heat transport. EGS technologies are relatively new, and pose significant simulation challenges. To become a trusted analytical tool for EGS, numerical simulation codes must be tested to demonstrate that they adequately represent the coupled THMC processes of concern. This presentation describes the approach and status of a benchmarking and code intercomparison effort currently underway, supported by the U. S. Department of Energy’s Geothermal Technologies Program. This study is being closely coordinated with a parallel international effort sponsored by the International Partnership for Geothermal Technology (IPGT). We have defined an extensive suite of benchmark problems, test cases, and challenge problems, ranging in complexity and difficulty, and a number of modeling teams are applying various simulation tools to these problems. The descriptions of the problems and modeling results are being compiled using the Velo framework, a scientific workflow and data management environment accessible through a simple web-based interface.

benchmark↗

HPC-FAIR: A Framework Managing Data and AI Models for Analyzing and Optimizing Scientific Applications

The increasing reliance on machine learning (ML) to analyze and optimize large-scale scientific applications on supercomputers faces a significant bottleneck: the lack of readily available, high-quality training datasets and the difficulty in reusing existing AI models. This project was motivated by the urgent need to address the “FAIR” principles (Findability, Accessibility, Interoperability, Reusability) for both training datasets and AI models in the high-performance computing (HPC) domain. The project developed HPC-FAIR, a high-performance computing data management framework designed to centralize HPC-related datasets and AI models within a unified hub. To ensure interoperability, the framework established a standardized representation and vocabulary (ontology) for both data and models. HPC-FAIR also implemented automated workflows to streamline data processing, model access, and benchmarking. Additionally, the project focused on optimizing data harnessing efficiency through advanced techniques like deep reuse and compression-based analytics.

97 MATHEMATICS AND COMPUTING↗

University Data Management Pilot Utilizing the Nuclear Research Data System

Background In 2022, the Office of Science and Technology Policy (OSTP) issued a memo that significantly reshaped the landscape of access to federally funded research. The memo mandated that all taxpayer-funded research be made available to the public without delay upon publication, without an embargo period, superseding the 2013 OSTP public access policy. This public access policy promotes transparency and the democratization of knowledge, ensuring that the fruits of scientific endeavors funded by federal agencies could be immediately accessed and built upon by scientists, educators, students, and the public at large. To implement the requirements of the OSTP guidance and DOE Public Access Plan, the Office of Nuclear Energy (NE) has implemented public access plan guidance and has identified several areas where better data management practices would further expand public access to important nuclear energy related scientific data, reports, and other technical products. Significant NE supported efforts are already underway for data management and public access to important nuclear energy related data.1 2 To address gaps in data management practices, and improve retention and accessibility of data, NE is actively exploring enhanced data management options utilizing its high-performance computing resources administered by its Nuclear Scientific User Facility Program. A newly piloted system, the Nuclear Research Data System (NRDS) acts as a portal for data collection and dissemination. Nuclear Energy University Program Research and Development Portfolio According to Web of Science, NEUP has produced 2,345 journal publication that have been cited more than 61,000 times3 and countless conference proceedings. These publications are publicly available through OSTI.gov and in the open literature. Additional scientific and technical products including project milestones that are not publications and NEUP project final reports are vetted through OSTI.gov and released once reviewed and approved by DOE. Since 2009, NEUP has awarded close to 1,000 different R&D projects in technical areas across the NE research programs. As of June 2023, 512 NEUP reports are publicly available on OSTI. The underlying data for projects is still held at universities, and data transfer, co-location, and dissemination has not occurred in a systematic way. NEUP data is currently accessible through myriad university-based data repositories, or through direct requests to PIs. The program identified this patchwork of repositories, or often lack of publicly available data, as a significant barrier to an organized, accessible, and comprehensive solution to sharing data with the larger nuclear energy community. Approach The goal of this pilot project is to establish a pathway to a consolidated long-term repository for NEUP project data. To accomplish this goal, the pilot strives to accomplish the following objectives: Establish data collection standards, including a standard set of required supplementary information to contextualize and support raw data files. Work with the HPC group collect and upload information and to modify the NRDS system, as needed, to support a standardized approach. Resolve potential barriers to successful roll out of an expanded data collection strategy, including modifying data management plan guidelines and establishing a document and data release process that accounts for potential intellectual property and/or export control concerns. Results Overall, the pilot was successful in collecting 8,982 raw and processes data files, 220 reports, 56 calibration files, and 5,931 other supplementary documents. Supplementary documents included experimental plans, methods, journal publications and conference proceedings, milestone reports, and final reports. Figure 2 shows the number of data sets and supplementary project information provided by each project. Projects has significantly different input, depending on experimental data produced and completeness of the datasets provided.

Data collection↗

Canopus: A Paradigm Shift Towards Elastic Extreme-Scale Data Analytics on HPC

Scientific simulations on high performance computing (HPC) platforms generate large quantities of data. To bridge the widening gap between compute and I/O, and enable data to be more efficiently stored and analyzed, simulation outputs need to be refactored, reduced, and appropriately mapped to storage tiers. However, a systematic solution to support these steps has been lacking on the current HPC software ecosystem. To that end, this paper develops Canopus, a progressive JPEGlike data management scheme for storing and analyzing big scientific data. It co-designs the data decimation, compression and data storage, taking the hardware characteristics of each storage tier into considerations. With reasonably low overhead, our approach refactors simulation data into a much smaller, reduced-accuracy base dataset, and a series of deltas that is used to augment the accuracy if needed. The base dataset and deltas are compressed and written to multiple storage tiers. Data saved on different tiers can then be selectively retrieved to restore the level of accuracy that satisfies data analytics. Thus, Canopus provides a paradigm shift towards elastic data analytics and enables end users to make trade-offs between analysis speed and accuracy on-the-fly. We evaluate the impact of Canopus on unstructured triangular meshes, a pervasive data model used by scientific modeling and simulations. In particular, we demonstrate the progressive data exploration of Canopus using the “blob detection” use case on the fusion simulation data.

Lu, Tao↗

SIRIUS: Enabling Progressive Data Exploration for Extreme-Scale Scientific Data

Scientific simulations on high performance computing (HPC) platforms generate large quantities of data. To bridge the widening gap between compute and I/O, and enable data to be more efficiently stored and analyzed, simulation outputs need to be refactored, reduced, and appropriately mapped to storage tiers. However, a systematic solution to support these steps has been lacking in the current HPC software ecosystem. To that end, this paper develops SIRIUS, a progressive JPEG-like data management scheme for storing and analyzing big scientific data. It co-designs data decimation, compression, and data storage, taking the hardware characteristics of each storage tier into considerations. With reasonably low overhead, our approach refactors simulation data, using either topological or uniform decimation, into a much smaller, reduced-accuracy base dataset, and a series of deltas that is used to augment the accuracy if needed. The base dataset and deltas are compressed and written to multiple storage tiers. Data saved on different tiers can then be selectively retrieved to restore the level of accuracy that satisfies data analytics. Thus, SIRIUS provides a paradigm shift towards elastic data analytics and enables end users to make trade-offs between analysis speed and accuracy on-the-fly. This paper further develops algorithms to preserve statistics for data decimation, a common requirement for reducing data. Here, we assess the impact of SIRIUS on unstructured triangular meshes, a pervasive data model used in scientific simulations. In particular, we evaluate two realistic use cases: the blob detection in fusion and high-pressure area extraction in computational fluid dynamics.

97 MATHEMATICS AND COMPUTING↗

Parallel membership queries on very large scientific data sets using bitmap indexes

© 2019 John Wiley & Sons, Ltd. Many scientific applications produce very large amounts of data as advances in hardware fuel computing and experimental facilities. Managing and analyzing massive quantities of scientific data is challenging as data are often stored in specific formatted files, such as HDF5 and NetCDF, which do not offer appropriate search capabilities. In this research, we investigated a special class of search capability, called membership query, to identify whether queried elements of a set are members of an attribute. Attributes that naturally have classification values appear frequently in scientific domains such as category and object type as well as in daily life such as zip code and occupation. Because classification attribute values are discrete and require random data access, performing a membership query on a large scientific data set creates challenges. We applied bitmap indexing and parallelization to membership queries to overcome these challenges. Bitmap indexing provides high performance not only for low cardinality attributes but also for high cardinality attributes, such as floating-point variables, electric charge, or momentum in a particle physics data set, due to compression algorithms such as Word-Aligned Hybrid. We conducted experiments, in a highly parallelized environment, on data obtained from a particle accelerator model and a synthetic data set.

Yildiz, Beytullah↗

Simons Foundation Data Management

The Simons Foundation is a non-profit organization that funds scientific research. Their Autism Research is generating significant amounts of genomic data, which they need to both archive and make available for researchers around the globe. The Foundation already stores data at Fermilab, as per agreement FRA-2015-0006. With this CRADA, the Fermilab Scientific Computing Division has developed a prototype solution for the data management needs of the Foundation, modifying services developed for High Energy Physics. The tools allow researchers to select datasets from a metadata catalogue of Foundation data, transfer selected files or datasets from Fermilab to remote storage, and enable the Foundation to manage access and authorization of the files. The prototypical solutions developed through this CRADA is considered the Phase I of a body of work that can be expanded and transitioned to production quality in a subsequent phase II, to be determined with the Foundation.

97 MATHEMATICS AND COMPUTING↗

TagIt: An Integrated Indexing and Search Service for File Systems

Data services such as search, discovery, and management in scalable distributed environments have traditionally been decoupled from the underlying file systems, and are often deployed using external databases and indexing services. However, modern data production rates, looming data movement costs, and the lack of metadata, entail revisiting the decoupled file system-data services design philosophy.In this paper, we present TagIt, a scalable data management service framework aimed at scientific datasets, which is tightly integrated into a shared-nothing distributed file system. A key feature of TagIt is a scalable, distributed metadata indexing framework, using which we implement a flexible tagging capability to support data discovery. The tags can also be associated with an active operator, for pre-processing, filtering, or automatic metadata extraction, which we seamlessly offload to file servers in a load-aware fashion. Our evaluation shows that TagIt can expedite data search by up to 10X over the extant decoupled approach.

Sim, Hyogi↗

Autonomic and Apoptotic, Aeronautical and Aerospace Systems, and Controlling Scientific Data Generated Therefrom

A self-managing system that uses autonomy and autonomicity is provided with the self-* property of autopoiesis (self-creation). In the event of an agent in the system self-destructing, autopoiesis auto-generates a replacement. A self-esteem reward scheme is also provided and can be used for autonomic agents, based on their performance and trust. Art agent with greater self-esteem may clone at a greater rate compared to the rate of an agent with lower self-esteem. A self-managing system is provided for a high volume of distributed autonomic/self-managing mobile agents, and autonomic adhesion is used to attract similar agents together or to repel dissimilar agents from an event horizon. An apoptotic system is also provided that accords an "expiry date" to data and digital objects, for example, that are available on the internet, which finds usefulness not only in general but also for controlling the loaning and use of space scientific data.

Sterritt, Roy↗

A guide to NASA's Pilot Land Data System (PLDS)

NASA's Pilot Land Data System (PLDS) is a distributed information management system designed to support NASA's land science community. The PLDS provides a wide range of services including management of information about scientific data, access to a library of scientific data, a data ordering capability, communications, connection to data analysis facilities, and electronic mail. The PLDS provides these services by offering the scientist the capability to search for and order data, and to communicate electronically with other scientists and computers. Three functions enable scientists to find what data are available and where they reside. The first two, Find data summaries and Read detailed descriptions give summary and detailed descriptions about data sets or groups of related data sets, science, projects, and institutions which archive land data. The third, gives information about specific pieces of data. This last function has two components, Search systemwide inventory and Search local inventory. The first component enables the user to find data elements (images, geological samples, transects, maps, etc.) that exist anywhere in the PLDS while the second has only information about data at the local site. The first enables the user to find pieces of data from several different data sets with the same temporal and spatial coverage and other elements common to most data sets, while the second allows the user to select a data set based on these descriptors and on those that are unique to a data set. The PLDS provides capabilities that enable electronic file transfers, intercomputer connection, and electronic mail. Both TCP/IP and DECnet protocols are supported via the NASA Science Internet (NIS). Access is also available through Telenet.

Source record↗

Exascale Virtualized and Programmable Distributed Cyber Resource Control: Final Scientific Technical Report

Extreme-science drives the need for distributed exascale processing and communications that are carefully, yet flexibly, managed. Exponential growth of data for scientific simulations, experimental data, collaborative data analyses, remote visualization and GRID computing requirements of scientists in fields as diverse as high energy physics, climate change, genomics, fusion, synchrotron radiation, material science, medicine, and other scientific disciplines cannot be accommodated by simply applying existing transport protocols to faster pipes. Further, scientific challenges today demand diverse research teams, heightening the need for and increasing the complexity of collaboration. To address these issues within the network layer and physical layer, we have performed a number of research activities surrounding effective allocation and management of elastic optical network (EON) resources, particularly focusing on FlexGrid transponders. FlexGrid transponders support the opportunity to build Layer-1 connections at a wide range of bandwidths and to reconfigure them rapidly. The new flexibility supports complex new ways of using the physical layer that must be carefully managed and hidden from the scientist end-users. FlexGrid networks utilize flexible (or elastic) spectral bandwidths for each data link without using fixed wavelength grids. The flexibility in spectrum allocation brings many appealing features to network operations. Current networks are designed for the worst case impairments in transmission performance and the assigned spectrum is over-provisioned. In contrast, the FlexGrid networks can operate with the highest spectral efficiency and minimum bandwidth for the given traffic demand while meeting the minimum quality of transmission (QoT) requirement. Two primary focuses of our research are: (1) resource and spectrum allocation (RSA) for IP traffic over EONs, and (2) RSA for cross-domain optical networks. Previous work concentrates primarily on large file transfers within a single domain. Adding support for IP traffic changes the nature of the RSA problem: instead of choosing to accept or deny each request for network support, IP traffic is inherently elastic and thus lends itself to a bandwidth maximization formulation. We developed a number of algorithms that could be easily deployed within existing and new FlexGrid networks, leading to networks that better support scientific collaboration. Cross-domain RSA research is essential to support large-scale FlexGrid networks, since configuration information is generally not shared or coordinated across domains. The results presented here are in their early stages. They are technically feasible and practical, but still require coordination among organizations and equipment owners and a higher-layer framework for managing network requests.

42 ENGINEERING↗

ISABELA for effective in situ compression of scientific data: ISABELA FOR EFFECTIVE IN-SITU REDUCTION OF SPATIO-TEMPORAL DATA

Exploding dataset sizes from extreme-scale scientific simulations necessitates efficient data management and reduction schemes to mitigate I/O costs. With the discrepancy between I/O bandwidth and computational power, scientists are forced to capture data infrequently, thereby making data collection an inherently lossy process. Although data compression can be an effective solution, the random nature of real-valued scientific datasets renders lossless compression routines ineffective. These techniques also impose significant overhead during decompression, making them unsuitable for data analysis and visualization, which require repeated data access. To address this problem, we propose an effective method for In situ Sort-And-B-spline Error-bounded Lossy Abatement (ISABELA) of scientific data that is widely regarded as effectively incompressible. With ISABELA, we apply a pre-conditioner to seemingly random and noisy data along spatial resolution to achieve an accurate fitting model that guarantees a ≥0.99 correlation with the original data. We further take advantage of temporal patterns in scientific data to compress data b ≈ 85%, while introducing only a negligible overhead on simulations in terms of runtime. ISABELA significantly outperforms existing lossy compression methods, such as wavelet compression, in terms of data reduction and accuracy. We extend upon our previous paper by additionally building a communication-free, scalable parallel storage framework on top of ISABELA-compressed data that is ideally suited for extreme-scale analytical processing. The basis for our storage framework is an inherently local decompression method (it need not decode the entire data), which allows for random access decompression and low-overhead task division that can be exploited over heterogeneous architectures. Furthermore, analytical operations such as correlation and query processing run quickly and accurately over data in the compressed space. Copyright © 2012 John Wiley & Sons, Ltd.

Computer Science↗