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All sources NASA NTRS DOE OSTI

DOE OSTI2017

On the arithmetic intensity of high-order finite-volume discretizations for hyperbolic systems of conservation laws

It has been conjectured that higher-order discretizations for partial differential equations will have advantages over the lower-order counterparts commonly used today. The reasoning is that the increase in arithmetic operations will be more than offset by the reduction in data transfers and the increase in concurrent floating-point units. To evaluate this conjecture, the arithmetic intensity of a class of high-order finite-volume discretizations for hyperbolic systems of conservation laws is theoretically analyzed for spatial discretizations from orders three through eight in arbitrary dimensions. Additionally, three cache models are considered: the limiting cases of no cache and infinite cache as well as a finite-sized cache model. Models are validated experimentally by measuring floating-point operations and data transfers on an IBM Blue Gene/Q node. Theory and experiments demonstrate that high-order finite-volume methods will be able to provide increases in arithmetic intensity that will be necessary to make better utilization of on-node floating-point capability.

97 MATHEMATICS AND COMPUTING↗

NASA NTRS2014

Veggie Hardware Validation Test Preliminary Results and Lessons Learned

The Veggie hardware validation test, VEG-01, was conducted on the International Space Station during Expeditions 39 and 40 from May through June of 2014. The Veggie hardware and the VEG-01 experiment payload were launched to station aboard the SpaceX-3 resupply mission in April, 2014. Veggie was installed in an Expedite-the-Processing-of-Experiments-to-Space-Station (ExPRESS) rack in the Columbus module, and the VEG-01 validation test was initiated. Veggie installation was successful, and power was supplied to the unit. The hardware was programmed and the root mat reservoir and plant pillows were installed without issue. As expected, a small amount of growth media was observed in the sealed bags which enclosed the plant pillows when they were destowed. Astronaut Steve Swanson used the wet/dry vacuum to clean up the escaped particles. Water insertion or priming the first plant pillow was unsuccessful as an issue prevented water movement through the quick disconnect. All subsequent pillows were successfully primed, and the initial pillow was replaced with a backup pillow and successfully primed. Six pillows were primed, but only five pillows had plants which germinated. After about a week and a half it was observed that plants were not growing well and that pillow wicks were dry. This indicated that the reservoir was not supplying sufficient water to the pillows via wicking, and so the team reverted to an operational fix which added water directly to the plant pillows. Direct watering of the pillows led to a recovery in several of the stressed plants; a couple of which did not recover. An important lesson learned involved Veggie's bellows. The bellows tended to float and interfere with operations when opened, so Steve secured them to the baseplate during plant tending operations. Due to the perceived intensity of the LED lights, the crew found it challenging to both work under the lights and read crew procedures on their computer. Although the lights are not a safety hazard, for visual comfort crewmembers were advised to wear sunglasses when working with the plants and then they can lift glasses to read procedures. Steve Swanson had already trail-blazed this procedure when he initiated VEG-01. The temperature and humidity data logger was relocated mid-experiment to provide measurements on both sides of the unit. Images of the plants were downlinked weekly, and videos of installation and harvest were recorded. This imaging frequency was not sufficient to monitor and respond to changes in plant growth. Plants, samples, and data loggers will be returned on SpaceX-4, scheduled to return the fall of 2014. Lessons learned will be translated into hardware and operational modifications for future Veggie payloads.

International Space Station↗

NASA NTRS2019

PIV and Rotational Raman-Based Temperature Measurements for CFD Validation of a Perforated Plate Cooling Flow: Part I

Film cooling is used in a wide variety of engineering applications for protection of surfaces from hot or combusting gases. The design of more efficient film cooling geometries/configurations could be facilitated by an ability to accurately model and predict the effectiveness of current designs using computational fluid dynamics (CFD) code predictions. Hence, a benchmark set of flow field property data were obtained for use in assessing current CFD capabilities and for development of better modeling approaches for these turbulent flow fields where accurate calculation of turbulent heat flux is important. Both Particle Image Velocimetry (PIV) and spontaneous rotational Raman scattering (SRS) spectroscopy were used to acquire high quality, spatially-resolved measurements of the mean velocity, turbulence intensity as well as the mean temperature and root mean square (rms) temperatures in a film cooling flow field. In addition to off-body flow field measurements, infrared thermography (IR) and thermocouple measurements on the plate surface enabled estimates of the film effectiveness. Raman spectra in air were obtained across a matrix of axial locations downstream from a 68.07 mm square nozzle blowing heated air over a range of temperatures (up to TR = 2.7) and Mach numbers (up to M0.9), across a 30.48 cm long plate equipped with three patches of 45 small (~1 mm) diameter cooling holes arranged in a staggered configuration. In addition, both centerline streamwise 2-component PIV and cross-stream 3-component Stereo PIV data at 14 axial stations were collected in the same flows. Only a subset of the data collected in the test program is included in this Part I report and are available from the NASA STI office. The final portion of the data will be published in a future report, Part II, along with CFD predictions of the complex cooling film flow.

IR camera Measurments↗

NASA NTRS2019

PIV and Rotational Raman-Based Temperature Measurements for CFD Validation of a Perforated Plate Cooling Flow: Part 1

Raman Scattering↗

DOE OSTI2018

Investigating power capping toward energy-efficient scientific applications: Investigating Power Capping toward Energy-Efficient Scientific Applications

The emergence of power efficiency as a primary constraint in processor and system design poses new challenges concerning power and energy awareness for numerical libraries and scientific applications. Power consumption also plays a major role in the design of data centers, which may house petascale or exascale-level computing systems. At these extreme scales, understanding and improving the energy efficiency of numerical libraries and their related applications becomes a crucial part of the successful implementation and operation of the computing system. In this paper, we study and investigate the practice of controlling a compute system's power usage, and we explore how different power caps affect the performance of numerical algorithms with different computational intensities. Further, we determine the impact, in terms of performance and energy usage, that these caps have on a system running scientific applications. This analysis will enable us to characterize the types of algorithms that benefit most from these power management schemes. Our experiments are performed using a set of representative kernels and several popular scientific benchmarks. Lastly, we quantify a number of power and performance measurements and draw observations and conclusions that can be viewed as a roadmap to achieving energy efficiency in the design and execution of scientific algorithms.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2016

MultispeQ Beta: a tool for large-scale plant phenotyping connected to the open PhotosynQ network

Large-scale high-throughput plant phenotyping (sometimes called phenomics) is becoming increasingly important in plant biology and agriculture and is essential to cutting-edge plant breeding and management approaches needed to meet the food and fuel needs for the next century. Currently, the application of these approaches is severely limited by the availability of appropriate instrumentation and by the ability to communicate experimental protocols, results and analyses. To address these issues, we have developed a low-cost, yet sophisticated open-source scientific instrument designed to enable communities of researchers, plant breeders, educators, farmers and citizen scientists to collect high-quality field data on a large scale. The MultispeQ provides measurements in the field or laboratory of both, environmental conditions (light intensity and quality, temperature, humidity, CO 2 levels, time and location) and useful plant phenotypes, including photosynthetic parameters—photosystem II quantum yield (Φ II ), non-photochemical exciton quenching (NPQ), photosystem II photoinhibition, light-driven proton translocation and thylakoid proton motive force, regulation of the chloroplast ATP synthase and potentially many others—and leaf chlorophyll and other pigments. Plant phenotype data are transmitted from the MultispeQ to mobile devices, laptops or desktop computers together with key metadata that gets saved to the PhotosynQ platform (https://photosynq.org) and provides a suite of web-based tools for sharing, visualization, filtering, dissemination and analyses. We present validation experiments, comparing MultispeQ results with established platforms, and show that it can be usefully deployed in both laboratory and field settings. We present evidence that MultispeQ can be used by communities of researchers to rapidly measure, store and analyse multiple environmental and plant properties, allowing for deeper understanding of the complex interactions between plants and their environment.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Strangers in a foreign land: ‘Yeastizing’ plant enzymes

Abstract Expressing plant metabolic pathways in microbial platforms is an efficient, cost‐effective solution for producing many desired plant compounds. As eukaryotic organisms, yeasts are often the preferred platform. However, expression of plant enzymes in a yeast frequently leads to failure because the enzymes are poorly adapted to the foreign yeast cellular environment. Here, we first summarize the current engineering approaches for optimizing performance of plant enzymes in yeast. A critical limitation of these approaches is that they are labour‐intensive and must be customized for each individual enzyme, which significantly hinders the establishment of plant pathways in cellular factories. In response to this challenge, we propose the development of a cost‐effective computational pipeline to redesign plant enzymes for better adaptation to the yeast cellular milieu. This proposition is underpinned by compelling evidence that plant and yeast enzymes exhibit distinct sequence features that are generalizable across enzyme families. Consequently, we introduce a data‐driven machine learning framework designed to extract ‘yeastizing’ rules from natural protein sequence variations, which can be broadly applied to all enzymes. Additionally, we discuss the potential to integrate the machine learning model into a full design‐build‐test cycle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

MaDaTS: Managing Data on Tiered Storage for Scientific Workflows

Scientific workflows are increasingly used in High Performance Computing (HPC) environments to manage complex simulation and analyses, often consuming and generating large amounts of data. However, workflow tools have limited support for managing the input, output and intermediate data. The data elements of a workflow are often managed by the user through scripts or other ad-hoc mechanisms. Technology advances for future HPC systems is redefining the memory and storage subsystem by introducing additional tiers to improve the I/O performance of data-intensive applications. These architectural changes introduce additional complexities to managing data for scientific workflows. Thus, we need to manage the scientific workflow data across the tiered storage system on HPC machines. In this paper, we present the design and implementation of MaDaTS (Managing Data on Tiered Storage for Scientific Workflows), a software architecture that manages data for scientific workflows. We introduce Virtual Data Space (VDS), an abstraction of the data in a workflow that hides the complexities of the underlying storage system while allowing users to control data management strategies. We evaluate the data management strategies with real scientific and synthetic workflows, and demonstrate the capabilities of MaDaTS. Our experiments demonstrate the flexibility, performance and scalability gains of MaDaTS as compared to the traditional approach of managing data in scientific workflows.

Ghoshal, Devarshi↗

DOE OSTI2016

Draco,Version 6.x.x

Draco is an object-oriented component library geared towards numerically intensive, radiation (particle) transport applications built for parallel computing hardware. It consists of semi-independent packages and a robust build system. The packages in Draco provide a set of components that can be used by multiple clients to build transport codes. The build system can also be extracted for use in clients. Software includes smart pointers, Design-by-Contract assertions, unit test framework, wrapped MPI functions, a file parser, unstructured mesh data structures, a random number generator, root finders and an angular quadrature component.

Thompson, Kelly↗

DOE OSTI2023

FrESCO

The National Cancer Institute (NCI) monitors population level cancer trends as part of its Surveillance, Epidemiology, and End Results (SEER) program. This program consists of state or regional level cancer registries which collect, analyze, and annotate cancer pathology reports. From these annotated pathology reports, each individual registry aggregates cancer phenotype information and summary statistics about cancer prevalence to facilitate population level monitoring of cancer incidence. Extracting cancer phenotype from these reports is a labor intensive task, requiring specialized knowledge about the reports and cancer. Automating this information extraction process from cancer pathology reports has the potential to improve not only the quality of the data by extracting information in a consistent manner across registries, but to improve the quality of patient outcomes by reducing the time to assimilate new data and enabling time-sensitive applications such as precision medicine. Here we present FrESCO: Framework for Exploring Scalable Computational Oncology, a modular deep-learning natural language processing (NLP) library for extracting pathology information from clinical text documents.

Spannaus, Adam [Oak Ridge National Lab. (ORNL), Oa↗

DOE OSTI2016

PHYSICS OF ECLIPSING BINARIES. II. TOWARD THE INCREASED MODEL FIDELITY

The precision of photometric and spectroscopic observations has been systematically improved in the last decade, mostly thanks to space-borne photometric missions and ground-based spectrographs dedicated to finding exoplanets. The field of eclipsing binary stars strongly benefited from this development. Eclipsing binaries serve as critical tools for determining fundamental stellar properties (masses, radii, temperatures, and luminosities), yet the models are not capable of reproducing observed data well, either because of the missing physics or because of insufficient precision. This led to a predicament where radiative and dynamical effects, insofar buried in noise, started showing up routinely in the data, but were not accounted for in the models. PHOEBE (PHysics Of Eclipsing BinariEs; http://phoebe-project.org) is an open source modeling code for computing theoretical light and radial velocity curves that addresses both problems by incorporating missing physics and by increasing the computational fidelity. In particular, we discuss triangulation as a superior surface discretization algorithm, meshing of rotating single stars, light travel time effects, advanced phase computation, volume conservation in eccentric orbits, and improved computation of local intensity across the stellar surfaces that includes the photon-weighted mode, the enhanced limb darkening treatment, the better reflection treatment, and Doppler boosting. Here we present the concepts on which PHOEBE is built and proofs of concept that demonstrate the increased model fidelity.

79 ASTRONOMY AND ASTROPHYSICS↗

NASA NTRS1977

Prelaunch testing of the laser geodynamic satellite (LAGEOS)

The LAGEOS was extensively tested optically prior to launch. The measurement techniques used are described and resulting data is presented. Principal emphasis was placed on pulse spreading characteristics, range correction for center of mass tracking, and pulse distortion due to coherent effects. A mode-locked freqeuncy doubled Nd:YAG laser with a pulse width of about 60 ps was used as the ranging transmitter and a crossfield photo-multiplier was used in the receiver. High speed sampling electronics were employed to increase receiver bandwidth. LAGEOS reflected pulses typically had a width of 250 ps with a variability in the range correction of less than 2 mm rms. Pulse distortion due to coherent effects was inferred from average waveforms and appears to introduce less than + or - 50 ps jitter in the location of the pulse peak. Analytic results on this effect based on computer simulations are also presented. Theoretical and experimental data on the lidar cross section were developed in order to predict the strength of lidar echoes from the satellite. Cross section was measured using a large aperture laser collimating system to illuminate the LAGEOS. Reflected radiation far-field patterns were measured using the collimator in an autocollimating mode. Data were collected with an optical data digitzer and displayed as a three-dimensional plot of intensity versus the two far-field coordinates. Measurements were made at several wavelengths, for several types of polarizations, and as a function of satellite orientation.

Fitzmaurice, M. W.↗

NASA NTRS1977

A model for microwave intensity propagation in an inhomogeneous medium

A combined analytic and phenomenological approach, utilizing Maxwell's equations in the Born approximation with radiative transfer theory, is used to describe the propagation of microwave intensity in a scattering medium characterized by three-dimensional random fluctuations in refractive index, as well as nonrandom variations in permittivity, temperature, and loss. This approach yields microwave intensities as a function of polarization, direction, and position. Numerical techniques are presented to solve the transport equations, which include cases of spatially varying coefficients, and highly peaked phase functions. Some computed results illustrating the behavior of microwave intensity in various media are presented. Included are the angular and frequency spectra of thermal emission from semi-infinite media, and the diffuse transmission and reflection response of a scattering layer. The effects of scatterer geometry and scale sizes; correlation function; and gradients in temperature, loss, and scattering parameters are also demonstrated. This model should be particularly useful in interpreting active and passive remote sensing data.

Fisher, A. D.↗

NASA NTRS1990

Intensity dependent spread processor and workstation

The Intensity Dependent Spread (IDS) is an adaptive algorithm which is modified according to the local intensity in the scene. (This results in a nonlinear process which cannot take advantage of rather nice linear transform methods.) The computation is similar to a neural net whereby intensity information is moving from each input pixel to a set of surrounding output pixels in a manner described by Cornsweet and Yellott. A prototype of a very large scale integration IDS processor is being developed and implemented in a workstation environment. The workstation consists of a SUN 3/260 and a DATACUBE pipeline processor. The IDS prototype is a board set which operates in the DATA CUBE processor. The SUN 3/260 performs control, background processing, IDS simulation and image display functions.

Westrom, George↗

NASA NTRS1995

Analyzing rocket plume spectral data with neural networks

The Optical Plume Anomaly Detection (OPAD) system is under development to provide early-warning failure detection in support of ground-level testing of the Space Shuttle Main Engine (SSME). Failure detection is to be achieved through the acquisition of spectrally resolved plume emissions and subsequent identification of abnormal levels indicative of engine corrosion or component failure. Two computer codes (one linear and the other non-linear) are used by the OPAD system to iteratively determine specific element concentrations in the SSME plume, given emission intensity and wavelength information. Since this analysis is extremely labor intensive, a study was initiated to develop neural networks that would model the 'inverse' of these computer codes. Optimally connected feed-forward networks with imperceptible prediction error have been developed for each element modeled by the linear code, SPECTRA4. Radial basis function networks were developed for the non-linear code, SPECTRA5, and predict combustion temperature in addition to element concentrations.

Whitaker, Kevin W.↗

DOE OSTI2016

Draco,Version 6.x.x

Thompson, Kelly↗

DOE OSTI2025

Flexible and Effective Object Tiering for Heterogeneous Memory Systems

Computing platforms that package multiple types of memory, each with their own performance characteristics, are quickly becoming mainstream. To operate efficiently, heterogeneous memory architectures require new data management solutions that are able to match the needs of each application with an appropriate type of memory. As the primary generators of memory usage, applications create a great deal of information that can be useful for guiding memory management, but the community still lacks tools to collect, organize, and leverage this information effectively. To address this gap, this work introduces a novel software framework that collects and analyzes object-level information to guide memory tiering. The framework includes tools to monitor the capacity and usage of individual data objects, routines that aggregate and convert this information into tier recommendations for the host platform, and mechanisms to enforce these recommendations according to user-selected policies. Moreover, the developed tools and techniques are fully automatic, work on standard Linux systems, and do not require modification or recompilation of existing software. Using this framework, this study evaluates and compares the impact of a variety of design choices for memory tiering, including different policies for prioritizing objects for the fast memory tier as well as the frequency and timing of migration events. In conclusion, the results, collected on a modern Intel platform with conventional DDR4 SDRAM as well as Intel Optane NVRAM, show that guiding data tiering with object-level information can enable significant performance and efficiency benefits compared with standard hardware- and software-directed data-tiering strategies for a diverse set of memory-intensive workloads.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2015

A new development on measurement and control software of SANS BATAN spectrometer (SMARTer) in Serpong, Indonesia

In 2005, the main computer for data acquisition and control system of Small-angle Neutron Scattering (SANS) BATAN Spectrometer (SMARTer) was replaced since it halted to operate the spectrometer. According to this replacement, the new software for data acquisition and control system has been developed in-house. Visual Basic programming language is used in developing the software. In the last two years, many developments have been made both in the hardware and also the software to conduct the experiment is more effective and efficient. Lately, the previous motor controller card (ISA Card) was replaced with the programmable motor controller card (PCI Card) for driving one motor of position sensitive detector (PSD), eight motors of four collimators, and six motors of six pinhole discs. This new control system software makes all motors can be moved simultaneously, then it reduces significantly the consuming time of setting up the instrument before running the experiment. Along with that development, the new data acquisition software under MS Windows operating system is also developed to drive a beam stopper in X-Y directions as well as to read the equipment status such as position of the collimators and PSD, to acquire neutron counts on monitor and PSD detectors, and also to manage 12 samples position automatically. A timer object which is set in one second to read the equipment status via serial port of the computer (RS232C), and general purpose interface board (GPIB) for reading the total counts of each pixel of the PSD from histogram memory was used in this new software. The experiment result displayed in real time on the main window, and the data is saved in the special format for further data reduction and analysis. The new software has been implemented and performed for experiment using a preset count or preset time mode for absolute scattering intensity method.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗