VTK-m: ECP Data Management Data Analytics and Visualization Overview.
Abstract not provided.
Moreland, Kenneth D.↗
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Graph Databases for Large-Scale Healthcare Systems: A Framework for Efficient Data Management and Data Services
Designing a database system for both efficient data management and data services has been one of the enduring challenges in the healthcare domain. In many healthcare systems, data services and data management are often viewed as two orthogonal tasks; data services refer to retrieval and analytic queries such as search, joins, statistical data extraction, and simple data mining algorithms, while data management refers to building error-tolerant and non-redundant database systems. The gap between service and management has resulted in rigid database systems and schemas that do not support effective analytics. We compose a rich graph structure from an abstracted healthcare RDBMS to illustrate how we can fill this gap in practice. We show how a healthcare graph can be automatically constructed from a normalized relational database using the proposed 3NF Equivalent Graph (3EG) transformation.We discuss a set of real world graph queries such as finding self-referrals, shared providers, and collaborative filtering, and evaluate their performance over a relational database and its 3EG-transformed graph. Experimental results show that the graph representation serves as multiple de-normalized tables, thus reducing complexity in a database and enhancing data accessibility of users. Based on this finding, we propose an ensemble framework of databases for healthcare applications.
Park, Yubin↗
ATDM Data Management FY2015: Data Warehouse Progress Report
The Advanced Technology Development and Mitigation (ATDM) program at Sandia National Laboratories is a new effort to build next-generation simulation codes that will map well to upcoming exascale computing platforms. Rather than follow traditional single- program, multiple data (SPMD) programming techniques, ATDM is developing applications in an asynchronous many task (AMT) form that describes work as a graph of tasks that have data dependencies. The data management team is focused on developing a data warehouse for ATDM that will enable tasks to store and exchange data objects efficiently. This report summarizes the data management teams efforts during FY15, and documents: (1) an initial API and implementation for the data warehouses key/value store, (2) API requirements for use with ATDMs runtime, (3) initial requirements for storing ATDM-specific data, and (4) the current organization of software components that will be used by the data warehouse.
97 MATHEMATICS AND COMPUTING↗
Project Management, Including Data Management Best Practices Framework (Best Management Practice; Work Product 12.3.b)
The Project Management documentation includes: (1) background on the RCSP Initiative and its best practices development process; (2) a historical perspective of best practices for project management; (3) a comparison of the roles of project managers, functional managers, and operations managers; (4) an overview of project management practices for field activities; and discussions of (5) managing change, (6) managing data, and (7) managing knowledge and information.
01 COAL, LIGNITE, AND PEAT↗
Editorial: Sorption processes in nuclear waste management: data knowledge management and new methodologies for data acquisition/prediction
A fundamental approach to Nuclear Waste Repository research involves the collection of experimental data in a laboratory setting, development of empirical and/or mechanistic numerical models representing those observations, and application of these models (or Reduced Order Models) into reactive transport and performance assessment models as predictive tools for informing society of impacts and risks associated with nuclear waste repository scenarios (Stevens et al., 2020). Therefore, the assimilation and interpretation of experimental data must take advantage of both new data and the rich historical data available in the literature and apply novel modeling approaches to improve predictive tools, particularly from the standpoint of uncertainty quantification, for nuclear waste repository performance assessment (Zavarin et al., 2022).
sorption↗
Global‐view coefficients: a data management solution for parallel quantum Monte Carlo applications
Summary Quantum Monte Carlo (QMC) applications perform simulation with respect to an initial state of the quantum mechanical system, which is often captured by using a cubic B‐spline basis. This representation is stored as a read‐only table of coefficients and accesses to the table are generated at random as part of the Monte Carlo simulation. Current QMC applications, such as QWalk and QMCPACK, replicate this table at every process or node, which limits scalability because increasing the number of processors does not enable larger systems to be run. We present a partitioned global address space approach to transparently managing this data using Global Arrays in a manner that allows the memory of multiple nodes to be aggregated. We develop an automated data management system that significantly reduces communication overheads, enabling new capabilities for QMC codes. Experimental results with QWalk and QMCPACK demonstrate the effectiveness of the data management system. Copyright © 2016 John Wiley & Sons, Ltd.
Niu, Qingpeng↗
Open Data Environment Enabling Mission Data Management and Data Sciences.
Abstract not provided.
Moleres, Richard↗
MaDaTS: Managing Data on Tiered Storage for Scientific Workflows
Scientific workflows are processing large amounts of data through complex simulation and analysis tasks. Meanwhile, the need to minimize I/O costs on next generation systems and the evolution of new technologies (NVRAMs, SSDs etc.) is resulting in deeper storage hierarchies on High Performance Computing (HPC) systems. A multi-tiered storage hierarchy introduces complexities in workflow and data management. There is need for simple and flexible data abstractions that can allow users to seamlessly manage workflow data and tasks on HPC systems with multiple storage tiers. MaDaTS (Managing Data on Tiered Storage for Scientific Workflows) provides an API and a command-line tool that allows users to manage their workflows and data on tiered storage (Ghoshal & Ramakrishnan (2017)).
97 MATHEMATICS AND COMPUTING↗
PANSOPHY, a JLAB SRF engineering data management system, supporting data collection, retrieval and analysis utilized by LCLS-II
Pansophy is an Engineering Data Management System that provides a comprehensive solution for managing information in the production and testing of cryomodules. It is especially suited to supporting the Data & Quality Management Systems for large projects like LCLS-II. With extensive amounts of data collected for an individual project, data retrieval to facilitate feedback and enhancement of production and processing activities is a high priority. The priority shares importance with the needs of managing the project, including production status, NCR, and Quality Management reports. Recent Pansophy enhancements have been to Data and Quality management reports and statistical analysis. Such enhancements include a database driven menu system, extended MSWord macro and preprocessing of travelers, and an extensive reporting system. The reporting system allows managers and group leaders to quickly respond to the needs of the project in areas of cavity and cryomodule production, data collection, NCR, Quality Management and schedule. Extensions include integration with the SRF inventory system PRIMeS, allowing traceability from receiving of manufactured parts to final cryomodule product.
Bookwalter, Valerie D.↗
An Approach to Data Management Planning for Protected Data Projects
This report describes what is required in a data management plan for data that needs to be protected in some fashion. Here we provide an overview of what a data manager should consider, including the data ingestion and various extract-transform-load processes, metadata considerations and documentation, to what might need to be accounted for in the event of data loss. In addition, this report includes two appendices: forms that, when filled out, make the user compliant with DOE data management requirements as well as additional requirements for handling protected data at ORNL.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Managing Data on Tiered Storage for Scientific Workflows (MaDaTS) v1.1.2
MaDaTS provides an integrated data management and workflow execution framework on multi-tiered storage systems. Users of MaDaTS can execute a workflow by either specifying the workflow stages in a YAML description file, or use the API to manage the workflow through a Virtual Data Space (VDS) abstraction.
Ramakrishnan, Lavanya↗
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↗
A Vision for Coupling Operation of US Fusion Facilities with HPC Systems and the Implications for Workflows and Data Management
The operation of large US Department of Energy (DOE) research facilities, like the DIII-D National Fusion Facility, results in the collection of complex multi-dimensional scientific datasets, both experimental and model-generated. In the future, it is envisioned that integrated data analysis coupled with large-scale high performance computing (HPC) simulations will be used to improve experimental planning and operation. Practically, massive data sets from these simulations provide the physics basis for generation of both reduced semi-analytic and machine-learning-based models. Storage of both HPC simulation datasets (generated from US DOE leadership computing facilities) and experimental datasets presents significant challenges. In this paper, we present a vision for a DOE-wide data management workflow that integrates US DOE fusion facilities with leadership computing facilities. Data persistence and long-term availability beyond the length of allocated projects is essential, particularly for verification and recalibration of artificial intelligence and machine learning (AI/ML) models. Because these data sets are often generated and shared among hundreds of users across multiple leadership computing facility centers, they would benefit from cross-platform accessibility, persistent identifiers (e.g. DOI, or digital object identifier), and provenance tracking. Here, the ability to handle different data access patterns suggests that a combination of low cost, high latency (e.g. for storing ML training sets) and high cost, low latency systems (e.g. for real-time, integrated machine control feedback) may be needed.
70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
Priority research directions for in situ data management: Enabling scientific discovery from diverse data sources
In January 2019, the US Department of Energy, Office of Science program in Advanced Scientific Computing Research, convened a workshop to identify priority research directions (PRDs) for in situ data management (ISDM). A fundamental finding of this workshop is that the methodologies used to manage data among a variety of tasks in situ can be used to facilitate scientific discovery from many different data sources—simulation, experiment, and sensors, for example—and that being able to do so at numerous computing scales will benefit real-time decision-making, design optimization, and data-driven scientific discovery. This article describes six PRDs identified by the workshop, which highlight the components and capabilities needed for ISDM to be successful for a wide variety of applications—making ISDM capabilities more pervasive, controllable, composable, and transparent, with a focus on greater coordination with the software stack and a diversity of fundamentally new data algorithms.
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↗
EDX Spatial: Leveraging cloud and hybrid data management resources for spatial data
In the last few years, the National Energy Technology Laboratory has started leveraging cloud-hosted services for hosting spatial data collections published on the Energy Data eXchange (EDX). Using cloud-hosted storage and compute options offers multiple benefits for visualization and tool development through utilization of spatial data resources. The transition from on-premises services to cloud-hosted services has enabled a few key features: increased accessibility of large derivative datasets, dynamic integration of external authoritative data resources directly from outside entities through representational state transfer application programming interfaces (REST API), and the ability to produce complex mapping applications, dashboards, and online maps. As a result of the shift, NETL has launched EDX Spatial, a platform that leverages on-premises resources combined with cloud compute capabilities to enable enhanced online mapping interfaces and optimize data access. In addition, a unified workflow for handling the public release of spatial data products through EDX has been developed, including standardization of data hosting practices, metadata, symbology, and application elements. This poster reviews the opportunity of leveraging cloud-hosted and hybrid data management solutions for spatial data, and discusses the benefits and lessons learned while leveraging these services through the data repository EDX.
Morkner, Paige↗
Efficient Data Management in Neutron Scattering Data Reduction Workflows at ORNL
Oak Ridge National Laboratory (ORNL) experimental neutron science facilities produce 1.2 TB a day of raw event-based data that is stored using the standard metadata-rich NeXus schema built on top of the HDF5 file format. Performance of several data reduction workflows is largely determined by the amount of time spent on the loading and processing algorithms in Mantid, an open-source data analysis framework used across several neutron sciences facilities around the world. The present work introduces new data management algorithms to address identified input output (I/O) bottlenecks on Mantid. First, we introduce an in-memory binary-tree metadata index that resemble NeXus data access patterns to provide a scalable search and extraction mechanism. Second, data encapsulation in Mantid algorithms is optimally redesigned to reduce the total compute and memory runtime footprint associated with metadata I/O reconstruction tasks. Results from this work show speed ups in wall-clock time on ORNL data reduction workflows, ranging from 11% to 30% depending on the complexity of the targeted instrument-specific data. Nevertheless, we highlight the need for more research to address reduction challenges as experimental data volumes increase.
Godoy, William↗