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DOE OSTI2019

Proactive Data Containers for Scientific Storage (Final Report)

Emerging HPC systems are expected to be deployed with an unprecedented level of complexity, due to a deep system memory/storage hierarchy and heterogeneity of the storage hardware. This hierarchy is expected to range from CPU cache through several levels of volatile memory to nonvolatile memory, traditional hard disks, and tape. Simple and efficient methods of data management and movement through this hierarchy is critical for scientific applications using exascale systems. Existing storage system and I/O (SSIO) technologies face severe challenges in dealing with these requirements. POSIX and MPI I/O standards that are the basis for existing I/O libraries and parallel file systems present fundamental challenges in the areas of scalable metadata operations, semantics-based data movement performance tuning, asynchronous operation, and support for scalable consistency of distributed operations. Moving toward new paradigms for SSIO in the extreme-scale era, we have proposed to investigate novel object-based data abstractions and storage mechanisms that take advantage of the deep storage hierarchy and enable proactive automated performance tuning. In order to achieve these overarching goals, we initiated an effort to develop a fundamental new data abstraction, called Proactive Data Containers (PDC). A PDC is a container within a locus of storage (memory, NVRAM, disk, etc.) that stores science data in an object-centric manner. Managing data as objects enables powerful optimization opportunities for data movement and transformations. The R&D focus of this project are: 1) formulation of object-oriented PDCs and their mapping in different levels of the exascale storage hierarchy; 2) efficient strategies for moving data in deep storage hierarchies using PDCs; 3) techniques for transforming and reorganizing data based on application requirements; and 4) novel analysis paradigms for enabling data transformations and user-defined analysis on data in PDCs. Toward achieving these overarching goals, we designed an object-centric application programing interface (API) for HPC, scalable metadata management for object-centric storage systems, and data movement optimizations such as Data Elevator for moving data between two levels of storage devices and TAPIOCA for efficient aggregation of data on compute nodes. We then implemented several components of the PDC system. They include metadata management, data placement services, remote procedure calls, data aggregation, etc. We have put them together into the overall PDC framework.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS1999

A Summary of the Quasi-Steady Acceleration Environment on-Board STS-94 (MSL-1)

The continuous free-fall state of a low Earth orbit experienced by NASA's Orbiters results in a unique reduced gravity environment. While microgravity science experiments are conducted in this reduced gravity environment, various accelerometer systems measure and record the microgravity acceleration environment for real-time and post-flight correlation with microgravity science data. This overall microgravity acceleration environment is comprised of quasi-steady, oscillatory, and transient contributions. The First Microgravity Science Laboratory (MSL-1) payload was dedicated to experiments studying various microgravity science disciplines, including combustion, fluid physics, and materials processing. In support of the MSL-1 payload, two systems capable of measuring the quasi-steady acceleration environment were flown: the Orbital Acceleration Research Experiment (OARE) and the Microgravity Measurement Assembly (MMA) system's Accelerometre Spatiale Triaxiale most evident in the quasi-steady acceleration regime. Utilizing such quasi-steady events, a comparison and summary of the quasi-steady acceleration environment for STS-94 will be presented

McPherson, Kevin M.↗

NASA NTRS2018

GRACE-Assimilated Drought Indicators for the U.S. Drought Monitor

The Gravity Recovery and Climate Experiment (GRACE) mission detects changes in Earth's gravity field by precisely monitoring the changes in distance between two satellites orbiting the Earth in tandem. Scientists at NASA's Goddard Space Flight Center generate GRACE-assimilated groundwater and soil moisture drought indicators each week, for drought monitor-related studies and applications. The GRACE-assimilated Drought Indicator Version 2.0 data product (GRACE-DA-DM V2.0) is archived at, and distributed by, the NASA GES DISC (Goddard Earth Sciences Data and Information Services Center). More information about the data and data access is available on the data product landing page at https://disc.gsfc.nasa.gov/datasets /GRACEDADM_CLSM0125US_7D_2.0/summary. The GRACE-DA-DM V2.0 data product contains three drought indicators: Groundwater Percentile, Root Zone Soil Moisture Percentile, and Surface Soil Moisture Percentile. The drought indicators are of wet or dry conditions, expressed as a percentile, indicating the probability of occurrence within the period of record from 1948 to 2012. These GRACE-assimilated drought indicators, with improved spatial and temporal resolutions, should provide a more comprehensive and objective identification of drought conditions. This presentation describes the basic characteristics of the data and data services at NASA GES DISC and collaborative organizations, and uses a few examples to demonstrate the simple ways to explore the GRACE-assimilated drought indicator data.

hydrology↗

NASA NTRS2018

Initial Operations Experience and Results from the Juno Gravity Experiment

Radio communications between the Juno spacecraft, in orbit around Jupiter, and the Earth-based observing stations of NASA’s Deep Space Network enable measurements of the Doppler shift induced on the radio signals by Juno’s motion in the Jovian environment. This measurement of the Doppler shift improves the knowledge of Jupiter’s gravitational field. As a radio science instrument, Juno’s gravity science instrument utilizes a ground component at the Deep Space Network’s DSS-25 antenna, equipped with simultaneous dual X- and Ka-band transmitters and receivers, and a spacecraft component, which includes X- and Ka-band transponders to relay the transmitted signal back to Earth. Originally planned to be in 14-day orbits around Jupiter, a risk identified in the propulsion system led to the decision to stay in the 53-day orbit period. Rapid turnaround of observation planning led to successful near-term perijove passes. Although maintaining a 53-day orbit period provides a scientific benefit to the gravity science investigation, the longer orbit period further increases the large dynamic range in Doppler shift and pointing angles induced by the geometry of each perijove. Between entering orbit at Jupiter on July 5, 2016 and September 2017, the Juno spacecraft has executed eight closest approach periods every 53 days where science data was collected. The first five perijove passes were conducted in different telecom configurations, each presenting unique challenges in data collection and processing. Perijoves PJ-01, PJ-02, PJ-03, and PJ-06 utilized the high-gain antenna and various configurations of the X- and Ka-bands. Perijoves PJ-04 and PJ-05 utilized the medium-gain antenna at X-band only while the spacecraft was off-Earth point. Additional perijoves are planned every 53-days, with an additional five by March 2018. Lessons learned from operating and collecting data at each perijove are documented and will be utilized in future perijoves. Analysis of the first two gravity science perijoves has improved the precision of Jupiter’s gravity field by a factor of five, providing crucial constraints on the interior structure of Jupiter.

Buccino, Dustin↗

NASA NTRS2018

THz Technology for Space Communications

As space instruments become ubiquitous along with advancing capabilities, one of the central challenge is to provide more efficient communication links, between the control center and the instrument or between a cluster of satellites or instruments. Similarly, high-data rate communications between a mother ship and a lander is highly desirable not only for navigation but for science data as well. THz communications systems present a number of advantages in implementing efficient data-links between various scenarios for space applications. This review article will discuss some of the recent advances in solid-state coherent sources that has now made it possible to design and implement THz communication systems specifically for space applications. An example architecture at 240 GHz has been suggested as it is now possible to achieve >100 mW of output power at 240 GHz. With highly sensitive and linear heterodyne mixers, such a system could potentially provide higher data rate capability than in use today.

Jornet, Josep M.↗

NASA NTRS2018

THz technology for space communications

Jornet, Josep M.↗

NASA NTRSDate not supplied

Multidimensional Data Aggregation in the Cloud with Application to Geostationary Satellite-based Air Quality Monitoring

Scientists use satellite data for studying Earth's systems, and the remote sensing data that these satellites collect are typically separated into files of a size small enough for efficient network transfer and storage. However, researchers usually prefer to analyze the data based on real-world dimensions like time, space, or elevation. To help with this, NASA's Atmospheric Science Data Center (ASDC) developed a new cloud-based tool that combines these smaller data chunks into larger, more useful datasets. The tool works on Network Common Data Form (netCDF4) and some HDF5 formatted files, and it is available as a service in NASA's Earthdata Cloud. In this presentation, we showcase this service using data from the Tropospheric Emissions: Monitoring of Pollution (TEMPO) instrument. By combining TEMPO's continuous observations over time, we create longer and more informative analysis-ready time series to facilitate the study of air quality patterns. Insights gained will provide a more comprehensive understanding of pollution sources, transport patterns, and their effects on the environment and human health.

Daniel Kaufman↗

NASA NTRS1999

Work on Planetary Atmospheres and Planetary Atmosphere Probes

A major objective of the grant was to complete the fabrication, test, and evaluation of the atmosphere structure experiment on the Galileo Probe, and to receive, analyze, and interpret data received from the spacecraft. The grantee was competitively selected to be Principal Investigator of Jupiter's atmosphere structure on the Galileo Probe. His primary motivation was to learn as much as possible about Jupiter's atmosphere by means of a successful atmosphere structure experiment, and to support the needs and schedule of the Galileo Project. After a number of launch delays, the Flight instrument was shipped to Kennedy Space Center 2 years after the start of this collaboration, on April 14, 1989, at which time it was determined from System level tests of the ASI on the Probe that the instrument was in good working order and ready for flight. The spacecraft was launched on October 18, 1989. Data analysis of test and calibration data taken over a period of years of instrument testing was continued in preparation for the encounter. The initial instrument checkout in space was performed on October 26, 1989. The data set received by telemetry was thoroughly analyzed, and a report of the findings was transmitted to the Probe Operations Office on Feb. 28, 1990. Key findings reported were that the accelerometer biases had shifted by less than 1 mg through launch and since calibration at Bell Aerospace in 1983; accelerometer scale factors, evaluated by means of calibration currents, fell on lines of variation with temperature established in laboratory calibrations; pressure sensor offsets, correlated as a function of temperature, fell generally within the limits of several years of ground test data; atmospheric and engineering temperature sensor data were internally consistent within a few tenths of a degree; and the instrument electronics performed all expected functions without any observable fault. Altogether, this checkout was highly encouraging of the prospects of instrument performance, although performed greater than 5 years prior to Jupiter encounter. Capability of decoding the science data from the Experiment Data Record to be provided at encounter was developed and exercised using the tape recording of the first Cruise Checkout data. A team effort was organized to program the selection and combination of data words defining pressure, temperature, acceleration, turbulence, and engineering quantities; to apply decalibration algorithms to convert readings from digital numbers to physical quantities; and to organize the data into a suitable printout. A paper on the Galileo Atmosphere Structure Instrument was written and submitted for publication in a special issue of Space Science Reviews. At the Journal editor's request, the grantee reviewed other Probe instrument papers submitted for this special issue. Calibration data were carefully taken for all experiment sensors and accumulated over a period of 10 years. The data were analyzed, fitted with algorithms, and summarized in a calibration report for use in analyzing and interpreting data returned from Jupiter's atmosphere. The sensors included were the primary science pressure, temperature, and acceleration sensors, and the supporting engineering temperature sensors. This report was distributed to experiment coinvestigators and the Probe Project Office.

Seiff, Alvin↗

DOE OSTI2017

EpiK: A Knowledge Base for Epidemiological Modeling and Analytics of Infectious Diseases

Computational epidemiology seeks to develop computational methods to study the distribution and determinants of health-related states or events (including disease), and the application of this study to the control of diseases and other health problems. Recent advances in computing and data sciences have led to the development of innovative modeling environments to support this important goal. The datasets used to drive the dynamic models as well as the data produced by these models presents unique challenges owing to their size, heterogeneity and diversity. These datasets form the basis of effective and easy to use decision support and analytical environments. As a result, it is important to develop scalable data management systems to store, manage and integrate these datasets. In this paper, we develop EpiK —a knowledge base that facilitates the development of decision support and analytical environments to support epidemic science. An important goal is to develop a framework that links the input as well as output datasets to facilitate effective spatio-temporal and social reasoning that is critical in planning and intervention analysis before and during an epidemic. The data management framework links modeling workflow data and its metadata using a controlled vocabulary. The metadata captures information about storage, the mapping between the linked model and the physical layout, and relationships to support services. EpiK is designed to support agent-based modeling and analytics frameworks—aggregate models can be seen as special cases and are thus supported. We use semantic web technologies to create a representation of the datasets that encapsulates both the location and the schema heterogeneity. The choice of RDF as a representation language is motivated by the diversity and growth of the datasets that need to be integrated. A query bank is developed—the queries capture a broad range of questions that can be posed and answered during a typical case study pertaining to disease outbreaks. The queries are constructed using SPARQL Protocol and RDF Query Language (SPARQL) over the EpiK. EpiK can hide schema and location heterogeneity while efficiently supporting queries that span the computational epidemiology modeling pipeline: from model construction to simulation output. As a result, we show that the performance of benchmark queries varies significantly with respect to the choice of hardware underlying the database and resource description framework (RDF) engine.

60 APPLIED LIFE SCIENCES↗

NASA NTRS1992

Data and information system requirements for Global Change Research

Efforts to develop local information systems for supporting interdisciplinary Global Change Research are described. A prototype system, the Interdisciplinary Science Data and Information System (IDS-DIS), designed to interface the larger archives centers of EOS-DIS is presented. Particular attention is given to a data query information management system (IMS), which has been used to tabulate information of Landsat data worldwide. The use of these data in a modeling analysis of deforestation and carbon dioxide emissions is demonstrated. The development of distributed local information systems is considered to be complementary to the development of central data archives. Global Change Research under the EOS program is likely to result in proliferation of data centers. It is concluded that a distributed system is a feasible and natural way to manage data and information for global change research.

Skole, David L.↗

DOE OSTI2019

Data Mining Scientific Literature Demonstrates Use of Biological and Medical Data Across Scientific Disciplines

The Protein Data Bank (PDB) was established as the 1st open access digital data resource in biology and medicine. Today, the PDB archive contains over 140,000 atomic‐level biomolecular structures determined by crystallography, NMR spectroscopy, and 3D electron microscopy. About 20 new structures are deposited daily. PDB data is used in basic and applied research, patent applications, discovery of lifesaving drugs, product innovation, and education. About 80% of all PDB structures deposited have a “primary citation,” which is the first paper to describe the molecule and its structure and function. In turn, these primary citations have contributed to more than 1 million publications. An initial study by Clarivate Analytics on the Nucleic Acids Research publication demonstrated that PDB data drive high‐impact research in diverse scientific fields. To build on this study, we used Python programming to perform several data mining studies to understand the impact of these structures in fundamental biology, biomedicine, and energy in the scientific literature. The scientific literature database, Web of Science, tracks scientific article metrics such as the number of times cited, subject category, year published, funding source, and keywords. Web of Science data for PDB primary citations was compiled as used as the data set. Two main investigations were performed. In the first, we examined the number of citations per article (data overall and by individual subject categories) to develop “top 10 cited structures” lists and analyzed for trends. In the second investigation, we extended our data mining analysis to consider for each main subject category, the papers with the most citations and the structures they cite, and the most frequently occuring keywords. We have observed different aspects of biological data utility in various subject areas, at times in ways unanticipated from the structures' primary citation. This research demonstrates the value of biological data from the PDB by showing the diverse ways in which the data are being used. Support or Funding Information RCSB PDB is funded by a grant (DBI‐1338415) from the National Science Foundation, the National Institutes of Health, and the US Department of Energy. This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Verdiguel, Natalie↗

NASA NTRS2012

Global Long-Term SeaWiFS Deep Blue Aerosol Products available at NASA GES DISC

Long-term climate data records about aerosols are needed in order to improve understanding of air quality, radiative forcing, and for many other applications. The Sea-viewing Wide Field-of-view Sensor (SeaWiFS) provides a global well-calibrated 13- year (1997-2010) record of top-of-atmosphere radiance, suitable for use in retrieval of atmospheric aerosol optical depth (AOD). Recently, global aerosol products derived from SeaWiFS with Deep Blue algorithm (SWDB) have become available for the entire mission, as part of the NASA Making Earth Science data records for Use in Research for Earth Science (MEaSUREs) program. The latest Deep Blue algorithm retrieves aerosol properties not only over bright desert surfaces, but also vegetated surfaces, oceans, and inland water bodies. Comparisons with AERONET observations have shown that the data are suitable for quantitative scientific use [1],[2]. The resolution of Level 2 pixels is 13.5x13.5 km2 at the center of the swath. Level 3 daily and monthly data are composed by using best quality level 2 pixels at resolution of both 0.5ox0.5o and 1.0ox1.0o. Focusing on the southwest Asia region, this presentation shows seasonal variations of AOD, and the result of comparisons of 5-years (2003- 2007) of AOD from SWDB (Version 3) and MODIS Aqua (Version 5.1) for Dark Target (MYD-DT) and Deep Blue (MYD-DB) algorithms.

Shen, Suhung↗

DOE OSTI2023

In-depth analysis on parallel processing patterns for high-performance Dataframes

The Data Science domain has expanded monumentally in both research and industry communities during the past decade, predominantly owing to the Big Data revolution. Artificial Intelligence (AI) and Machine Learning (ML) are bringing more complexities to data engineering applications, which are now integrated into data processing pipelines to process terabytes of data. Typically, a significant amount of time is spent on data preprocessing in these pipelines, and hence improving its efficiency directly impacts the overall pipeline performance. The community has recently embraced the concept of Dataframes as the de-facto data structure for data representation and manipulation. However, the most widely used serial Dataframes today (R, pandas) experience performance limitations while working on even moderately large data sets. We believe that there is plenty of room for improvement by taking a look at this problem from a high-performance computing point of view. In a prior publication, we presented a set of parallel processing patterns for distributed dataframe operators and the reference runtime implementation, Cylon. In this paper, we are expanding on the initial concept by introducing a cost model for evaluating the said patterns. Furthermore, we evaluate the performance of Cylon on the ORNL Summit supercomputer.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2020

Exascale applications: skin in the game

As noted in Wikipedia, skin in the game refers to having ‘incurred risk by being involved in achieving a goal’, where ‘ skin is a synecdoche for the person involved, and game is the metaphor for actions on the field of play under discussion’. For exascale applications under development in the US Department of Energy Exascale Computing Project, nothing could be more apt, with the skin being exascale applications and the game being delivering comprehensive science-based computational applications that effectively exploit exascale high-performance computing technologies to provide breakthrough modelling and simulation and data science solutions. These solutions will yield high-confidence insights and answers to the most critical problems and challenges for the USA in scientific discovery, national security, energy assurance, economic competitiveness and advanced healthcare. This article is part of a discussion meeting issue ‘Numerical algorithms for high-performance computational science’.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2024

Curating Carbon Storage Data for Reuse: Enabling Research and Modeling from Earth’s Surface to Subsurface

The volume of public geologic carbon storage (GCS) data resources has continued to increase in recent years as the result of an increase in funding from government, industry, and academia towards national, basin, regional and field scale studies to ensure carbon capture and storage becomes a commercially viable operation. Despite the increasing volume of data, GCS data applied towards analyses such as geologic, cost, and risk modeling continues to be multi-sourced and often disparate in nature, published across government agencies, websites, data repositories and buried in derivative reports and documents. Much of the time preparing for an analysis and derivative product development is spent collecting, aggregating, transforming and preparing input data. There have been significant efforts within the DOE National Energy Technology Laboratory’s Carbon Storage Program to optimize multi-source, multi-scale subsurface geologic data curation and aggregation to support data discovery, interoperability, and reuse. Methods include the use of artificial intelligence, machine learning, and data science techniques. This talk will discuss the workflows, best practices, and processes developed to support the aggregation and curation of data through the whole system – surface to subsurface data - that support multi-scale, multi-purpose analysis for carbon storage research.

Morkner, Paige↗

DOE OSTI2024

Optimizing Batch Crystallization with Model-based Design of Experiments

Adaptive and self-optimizing intelligent systems such as digital twins are increasingly important in science and engineering. Digital twins utilize mathematical models to provide added precision to decision-making. However, physics-informed models are challenging to build, calibrate, and validate with existing data science methods. Model-based design of experiments (MBDoE) is a popular framework for optimizing data collection to maximize parameter precision in mathematical models and digital twins. In this work, we apply MBDoE, facilitated by the open-source package Pyomo.DoE, to train and validate mathematical models for batch crystallization. We quantitatively examined the estimability of the model parameters for experiments with different cooling rates. This analysis provides a quantitative explanation for the heuristic of using multiple experiments at different cooling rates.

Lynch, Hailey↗

NASA NTRS1993

MAC to VAX Connectivity: Heartrate Spectral Analysis System

The heart rate Spectral Analysis System (SAS) acquires and analyzes, in real-time, the Space Shuttle onboard electrocardiograph (EKG) experiment signals, calculates the heartrate, and applies a Fast Fourier Transformation (FFT) to the heart rate. The system also calculates other statistical parameters such as the 'mean heart rate' over specific time period and heart rate histogram. This SAS is used by NASA Principal Investigators as a research tool to determine the effects of weightlessness on the human cardiovascular system. This is also used to determine if Lower Body Negative Pressure (LBNP) is an effective countermeasure to the orthostatic intolerance experienced by astronauts upon return to normal gravity. In microgravity, astronauts perform the LBNP experiment in the mid deck of the Space Shuttle. The experiment data are downlinked by the orbiter telemetry system, then processed and analyzed in real-time by the integrated Life Sciences Data Acquisition (LSDS) - Spectral Analysis System. The data system is integrated within the framework of two different computer systems, VAX and Macintosh (Mac), using the networking infrastructure to assist the investigators in further understanding the most complex machine on Earth--the human body.

Rahman, Hasan H.↗

NASA NTRS2006

Experiences in managing the Prometheus Project

Congress authorized NASA?s Prometheus Project in February 2003, with the first Prometheus mission slated to explore the icy moons of Jupiter. The Project had two major objectives: (1) to develop a nuclear reactor that would provide unprecedented levels of power and show that it could be processed safely and operated reliably in space for long-duration, deep-space exploration and (2) to explore the three icy moons of Jupiter - Callisto, Ganymede, and Europa - and return science data that would meet the scientific goals as set forth in the Decadal Survey Report of the National Academy of Sciences. Early in Project planning, it was determined that the development of the Prometheus nuclear powered Spaceship would be complex and require the intellectual knowledge residing at numerous organizations across the country. In addition, because of the complex nature of the Project and the multiple partners, approaches beyond those successfully used to manage a typical JPL project would be needed. This paper1 will describe the key experiences in managing Prometheus that should prove useful for future projects of similar scope and magnitude

nuclear↗