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At least 145 records · Page 8

Storage media pipelining: Making good use of fine-grained media

This paper proposes a new high-performance paradigm for accessing removable media such as tapes and especially magneto-optical disks. In high-performance computing the striping of data across multiple devices is a common means of improving data transfer rates. Striping has been used very successfully for fixed magnetic disks improving overall system reliability as well as throughput. It has also been proposed as a solution for providing improved bandwidth for tape and magneto-optical subsystems. However, striping of removable media has shortcomings, particularly in the areas of latency to data and restricted system configurations, and is suitable primarily for very large I/Os. We propose that for fine-grained media, an alternative access method, media pipelining, may be used to provide high bandwidth for large requests while retaining the flexibility to support concurrent small requests and different system configurations. Its principal drawback is high buffering requirements in the host computer or file server. This paper discusses the possible organization of such a system including the hardware conditions under which it may be effective, and the flexibility of configuration. Its expected performance is discussed under varying workloads including large single I/O's and numerous smaller ones. Finally, a specific system incorporating a high-transfer-rate magneto-optical disk drive and autochanger is discussed.

Vanmeter, Rodney↗

On the Floating Point Performance of the i860 Microprocessor

The i860 microprocessor is a pipelined processor that can deliver two double precision floating point results every clock. It is being used in the Touchstone project to develop a teraflop computer by the year 2000. With such high computational capabilities it was expected that memory bandwidth would limit performance on many kernels. Measured performance of three kernels showed performance is less than what memory bandwidth limitations would predict. This paper develops a model that explains the discrepancy in terms of memory latencies and points to some problems involved in moving data from memory to the arithmetic pipelines.

Lee, King↗

Methods and Results of a Search for Gravitational Waves Associated with Gamma-Ray Bursts Using the GEO 600, LIGO, and Virgo Detectors

In this paper we report on a search for short-duration gravitational wave bursts in the frequency range 64 Hz-1792 Hz associated with gamma-ray bursts (GRBs), using data from GEO600 and one of the LIGO or Virgo detectors. We introduce the method of a linear search grid to analyze GRB events with large sky localization uncertainties such as the localizations provided by the Fermi Gamma-ray Burst Monitor (GBM). Coherent searches for gravitational waves (GWs) can be computationally intensive when the GRB sky position is not well-localized, due to the corrections required for the difference in arrival time between detectors. Using a linear search grid we are able to reduce the computational cost of the analysis by a factor of O(10) for GBM events. Furthermore, we demonstrate that our analysis pipeline can improve upon the sky localization of GRBs detected by the GBM, if a high-frequency GW signal is observed in coincidence. We use the linear search grid method in a search for GWs associated with 129 GRBs observed satellite-based gamma-ray experiments between 2006 and 2011. The GRBs in our sample had not been previously analyzed for GW counterparts. A fraction of our GRB events are analyzed using data from GEO600 while the detector was using squeezed-light states to improve its sensitivity; this is the first search for GWs using data from a squeezed-light interferometric observatory. We find no evidence for GW signals, either with any individual GRB in this sample or with the population as a whole. For each GRB we place lower bounds on the distance to the progenitor, assuming a fixed GW emission energy of 10(exp -2)Stellar Mass sq c, with a median exclusion distance of 0.8 Mpc for emission at 500 Hz and 0.3 Mpc at 1 kHz. The reduced computational cost associated with a linear search grid will enable rapid searches for GWs associated with Fermi GBM events in the Advanced detector era.

methods↗

Low power signal processing research at Stanford

This paper gives an overview of the research being conducted at Stanford University's Space, Telecommunications, and Radioscience Laboratory in the area of low energy computation. It discusses the work we are doing in large scale digital VLSI neural networks, interleaved processor and pipelined memory architectures, energy estimation and optimization, multichip module packaging, and low voltage digital logic.

Burr, J.↗

Optimization of Particle-in-Cell Codes on RISC Processors

General strategies are developed to optimize particle-cell-codes written in Fortran for RISC processors which are commonly used on massively parallel computers. These strategies include data reorganization to improve cache utilization and code reorganization to improve efficiency of arithmetic pipelines.

particle-cell-codes cache utilization code reorgan↗

Product Operations Status Summary Metrics

The Product Operations Status Summary Metrics (POSSUM) computer program provides a readable view into the state of the Phoenix Operations Product Generation Subsystem (OPGS) data pipeline. POSSUM provides a user interface that can search the data store, collect product metadata, and display the results in an easily-readable layout. It was designed with flexibility in mind for support in future missions. Flexibility over various data store hierarchies is provided through the disk-searching facilities of Marsviewer. This is a proven program that has been in operational use since the first day of the Phoenix mission.

Takagi, Atsuya↗

GeoAI advances in specific landform mapping

Landform mapping (also referred to as geomorphology or geomorphometry) can be divided into two domains: general and specific (Evans 2012). Whereas general landform mapping categorizes all elements of the study area into landform classes, such as ridges, valleys, peaks, and depressions, the mapping of specific landforms requires the delineation (even if fuzzy) of individual landforms. The former is mainly driven by physical properties such as elevation, slope, and curvature. The latter, however, must consider the cognitive (human) reasoning that discriminates individual landforms in addition to these physical properties (Arundel and Sinha 2018). Both mapping forms are important. General geomorphometry is needed to understand geological and ecological processes and as boundary layer input to climate and environmental models. Specific geomorphometry supports such activities as disaster management and recovery, emergency response, transportation, and navigation. In the United States, individual landforms of interest are named in the U.S. Geological Survey (USGS) Geographic Names Information System, a point dataset captured specifically to digitize geographic names from the USGS Historical Topographic Map Collection (HTMC). Named landform extent is represented only by the name placement in the HTMC. Recent work has investigated CNN-based deep learning methods to capture these extents in machine-readable form. These studies first relied on physical properties (Arundel et al. 2020) and then included the HTMC as a band in RGB images in limited testing (Arundel et al. 2023). Results from the HTMC dataset surpassed those using just physical properties and using the HTMC alone performed best due to the hillshading and elevation (contour) data incorporated into the topographic maps. However, results fell short of an operational capacity to map all named landforms in the United States. Thus, our current work expands upon past research by focusing on the HTMC and physical information as inputs and the named landform label extents. Specifically, we propose to leverage pre-trained foundation models for segmentation and optical character recognition (OCR) models to jointly map landforms in the United States. Our approach aims to bridge the disparities among the independent information sources to facilitate informed decision-making. The modeling pipeline performs (1) segmentation using the physical information and (2) information extraction using OCR, in parallel. Then a computer vision approach merges the two branches into a labeled segmentation. References: Arundel, Samantha T., Wenwen Li, and Sizhe Wang. 2020. “GeoNat v1.0: A Dataset for Natural Feature Mapping with Artificial Intelligence and Supervised Learning.” Transactions in GIS 24 (3): 556–72. https://doi.org/10.1111/tgis.12633. Arundel, Samantha T, and Gaurav Sinha. 2018. “Validating GEOBIA Based Terrain Segmentation and Classification for Automated Delineation of Cognitively Salient Landforms BT - Proceedings of Workshops and Posters at the 13th International Conference on Spatial Information Theory (COSIT 2017).” In Proceedings of Workshops and Posters at the 13th International Conference on Spatial Information Theory (COSIT 2017), Lecture Notes in Geoinformation and Cartography, edited by Paolo Fogliaroni, Andrea Ballatore, and Eliseo Clementini, 9–14. Cham: Springer International Publishing. Arundel, Samantha T., Gaurav Sinha, Wenwen Li, David P. Martin, Kevin G. McKeehan, and Philip T. Thiem. 2023. “Historical Maps Inform Landform Cognition in Machine Learning.” Abstracts of the ICA 6 (August): 1–2. https://doi.org/10.5194/ica-abs-6-10-2023. Evans, Ian S. 2012. “Geomorphometry and Landform Mapping: What Is a Landform?” Geomorphology 137 (1): 94–106. https://doi.org/10.1016/j.geomorph.2010.09.029.

machine learning↗

GeoAI Advances in Specific Landform Mapping

Landform mapping (also referred to as geomorphology or geomorphometry) can be divided into two domains: general and specific (Evans 2012). Whereas general landform mapping categorizes all elements of the study area into landform classes, such as ridges, valleys, peaks, and depressions, the mapping of specific landforms requires the delineation (even if fuzzy) of individual landforms. The former is mainly driven by physical properties such as elevation, slope, and curvature. The latter, however, must consider the cognitive (human) reasoning that discriminates individual landforms in addition to these physical properties (Arundel and Sinha 2018). Both mapping forms are important. General geomorphometry is needed to understand geological and ecological processes and as boundary layer input to climate and environmental models. Specific geomorphometry supports such activities as disaster management and recovery, emergency response, transportation, and navigation. In the United States, individual landforms of interest are named in the U.S. Geological Survey (USGS) Geographic Names Information System, a point dataset captured specifically to digitize geographic names from the USGS Historical Topographic Map Collection (HTMC). Named landform extent is represented only by the name placement in the HTMC. Recent work has investigated CNN-based deep learning methods to capture these extents in machine-readable form. These studies first relied on physical properties (Arundel et al. 2020) and then included the HTMC as a band in RGB images in limited testing (Arundel et al. 2023). Results from the HTMC dataset surpassed those using just physical properties and using the HTMC alone performed best due to the hillshading and elevation (contour) data incorporated into the topographic maps. However, results fell short of an operational capacity to map all named landforms in the United States. Thus, our current work expands upon past research by focusing on the HTMC and physical information as inputs and the named landform label extents. Specifically, we propose to leverage pre-trained foundation models for segmentation and optical character recognition (OCR) models to jointly map landforms in the United States. Our approach aims to bridge the disparities among the independent information sources to facilitate informed decision-making. The modeling pipeline performs (1) segmentation using the physical information and (2) information extraction using OCR, in parallel. Then a computer vision approach merges the two branches into a labeled segmentation.

machine learning↗

GL4U: Using Space Biology Omics Data to Provide Bioinformatics Training for Students and Educators

NASA’s GeneLab project provides researchers open access to space-relevant multi-omics data via the Open Science Data Repository (OSDR) that can be mined to understand the effects of spaceflight on biological systems. To maximize the number of scientists who understand and utilize GeneLab data and data processing pipelines, GeneLab created GeneLab for Colleges and Universities (GL4U). GL4U provides space biology-relevant training in bioinformatics to the next generation of scientists through direct (training students) and indirect (training educators) approaches. The GL4U pilot programs were conducted in June 2021 (direct training) and 2022 (indirect training). During the pilots, students and educators at Historically Black Colleges and Universities (HBCUs) and Minority Serving Institutions (MSIs) participated in a week-long (direct training) or two-week-long (indirect training) bootcamp consisting of space biology-specific lectures and hands-on instruction using Jupyter Notebooks to analyze space biology RNA sequencing data from OSDR. During the educator pilot, participants received materials, training, and the necessary compute resources to enable them to run the bootcamp at their home institutions, thereby extending the reach of this initiative. In July 2023, GeneLab is partnering with JPL to expand GL4U to include amplicon sequencing (Amp-Seq) analysis training. During the GL4U Amp-Seq bootcamp, student and educator participants will receive training on how to analyze and interpret Amp-Seq data using the NASA GeneLab data processing pipeline. All bootcamp material, including instructions for requesting compute resources, will be made publicly available on GitHub for educators to teach the GL4U content in subsequent semesters. GL4U provides undergraduate students from underrepresented groups the opportunity to learn about NASA and Space Biology, and to enhance their career prospects by gaining hands-on experience analyzing omics data, a skillset that is highly applicable and marketable in the life sciences. We present results from pre- and post-training surveys completed by all participants of the Amp-Seq bootcamp.

Amanda M Saravia-Butler↗

Circuit for high resolution decoding of multi-anode microchannel array detectors

A circuit for high resolution decoding of multi-anode microchannel array detectors consisting of input registers accepting transient inputs from the anode array; anode encoding logic circuits connected to the input registers; midpoint pipeline registers connected to the anode encoding logic circuits; and pixel decoding logic circuits connected to the midpoint pipeline registers is described. A high resolution algorithm circuit operates in parallel with the pixel decoding logic circuit and computes a high resolution least significant bit to enhance the multianode microchannel array detector's spatial resolution by halving the pixel size and doubling the number of pixels in each axis of the anode array. A multiplexer is connected to the pixel decoding logic circuit and allows a user selectable pixel address output according to the actual multi-anode microchannel array detector anode array size. An output register concatenates the high resolution least significant bit onto the standard ten bit pixel address location to provide an eleven bit pixel address, and also stores the full eleven bit pixel address. A timing and control state machine is connected to the input registers, the anode encoding logic circuits, and the output register for managing the overall operation of the circuit.

Kasle, David B.↗

Recent Mascon Solutions from GRACE

Mascon (mass concentration) solutions computed for entire land area of Earth with several variants from Jul. 2003 through Dec. 2005 Automated scripts developed, "pipeline" now in place. Solutions generally consistent with harmonics for large features but appear able to resolve and localize smaller features more cleanly. Greenland solutions generally consistent with areas of max ice mass loss in South, but mascons seem to clearly identify sub-regions of ice mass growth. May be amplified by mascon sensitivity and ground tracks. Irregular coverage, errors due to tides in Arctic or other leakage from nearby sources? Although mascons are technically 30+ years old, gravity/geodesy community has vastly more experience with harmonics and thus we are still learning the full advantages, limitations, and idiosyncrasies of mascons.

GRACE↗

Probabilistic Structural Analysis Program

NASA/NESSUS 6.2c is a general-purpose, probabilistic analysis program that computes probability of failure and probabilistic sensitivity measures of engineered systems. Because NASA/NESSUS uses highly computationally efficient and accurate analysis techniques, probabilistic solutions can be obtained even for extremely large and complex models. Once the probabilistic response is quantified, the results can be used to support risk-informed decisions regarding reliability for safety-critical and one-of-a-kind systems, as well as for maintaining a level of quality while reducing manufacturing costs for larger-quantity products. NASA/NESSUS has been successfully applied to a diverse range of problems in aerospace, gas turbine engines, biomechanics, pipelines, defense, weaponry, and infrastructure. This program combines state-of-the-art probabilistic algorithms with general-purpose structural analysis and lifting methods to compute the probabilistic response and reliability of engineered structures. Uncertainties in load, material properties, geometry, boundary conditions, and initial conditions can be simulated. The structural analysis methods include non-linear finite-element methods, heat-transfer analysis, polymer/ceramic matrix composite analysis, monolithic (conventional metallic) materials life-prediction methodologies, boundary element methods, and user-written subroutines. Several probabilistic algorithms are available such as the advanced mean value method and the adaptive importance sampling method. NASA/NESSUS 6.2c is structured in a modular format with 15 elements.

Pai, Shantaram S.↗

Kepler Data Validation Time Series File: Description of File Format and Content

The Kepler space mission searches its time series data for periodic, transit-like signatures. The ephemerides of these events, called Threshold Crossing Events (TCEs), are reported in the TCE tables at the NASA Exoplanet Archive (NExScI). Those TCEs are then further evaluated to create planet candidates and populate the Kepler Objects of Interest (KOI) table, also hosted at the Exoplanet Archive. The search, evaluation and export of TCEs is performed by two pipeline modules, TPS (Transit Planet Search) and DV (Data Validation). TPS searches for the strongest, believable signal and then sends that information to DV to fit a transit model, compute various statistics, and remove the transit events so that the light curve can be searched for other TCEs. More on how this search is done and on the creation of the TCE table can be found in Tenenbaum et al. (2012), Seader et al. (2015), Jenkins (2002). For each star with at least one TCE, the pipeline exports a file that contains the light curves used by TPS and DV to find and evaluate the TCE(s). This document describes the content of these DV time series files, and this introduction provides a bit of context for how the data in these files are used by the pipeline.

DV Time Series↗

NavP: Structured and Multithreaded Distributed Parallel Programming

We present Navigational Programming (NavP) -- a distributed parallel programming methodology based on the principles of migrating computations and multithreading. The four major steps of NavP are: (1) Distribute the data using the data communication pattern in a given algorithm; (2) Insert navigational commands for the computation to migrate and follow large-sized distributed data; (3) Cut the sequential migrating thread and construct a mobile pipeline; and (4) Loop back for refinement. NavP is significantly different from the current prevailing Message Passing (MP) approach. The advantages of NavP include: (1) NavP is structured distributed programming and it does not change the code structure of an original algorithm. This is in sharp contrast to MP as MP implementations in general do not resemble the original sequential code; (2) NavP implementations are always competitive with the best MPI implementations in terms of performance. Approaches such as DSM or HPF have failed to deliver satisfying performance as of today in contrast, even if they are relatively easy to use compared to MP; (3) NavP provides incremental parallelization, which is beyond the reach of MP; and (4) NavP is a unifying approach that allows us to exploit both fine- (multithreading on shared memory) and coarse- (pipelined tasks on distributed memory) grained parallelism. This is in contrast to the currently popular hybrid use of MP+OpenMP, which is known to be complex to use. We present experimental results that demonstrate the effectiveness of NavP.

navigational programming (NavP)↗

A software simulation study of a (255,223) Reed-Solomon encoder-decoder

A set of software programs which simulates a (255,223) Reed-Solomon encoder/decoder pair is described. The transform decoder algorithm uses a modified Euclid algorithm, and closely follows the pipeline architecture proposed for the hardware decoder. Uncorrectable error patterns are detected by a simple test, and the inverse transform is computed by a finite field FFT. Numerical examples of the decoder operation are given for some test codewords, with and without errors. The use of the software package is briefly described.

Pollara, F.↗

The Virtual Test Bed Project

This is a report of my activities as a NASA Fellow during the summer of 2002 at the NASA Kennedy Space Center (KSC). The core of these activities is the assigned project: the Virtual Test Bed (VTB) from the Spaceport Engineering and Technology Directorate. The VTB Project has its foundations in the NASA Ames Research Center (ARC) Intelligent Launch & Range Operations program. The objective of the VTB project is to develop a new and unique collaborative computing environment where simulation models can be hosted and integrated in a seamless fashion. This collaborative computing environment will be used to build a Virtual Range as well as a Virtual Spaceport. This project will work as a technology pipeline to research, develop, test and validate R&D efforts against real time operations without interfering with the actual operations or consuming the operational personnel s time. This report will also focus on the systems issues required to conceptualize and provide form to a systems architecture capable of handling the different demands.

Rabelo, Luis C.↗

Development of Computational Environmental Microbiome Workflows for the Laboratory and the International Space Station

Identification of microorganisms in the spaceflight environment is critical for crew health risk assessment on the International Space Station (ISS). Since 2017, nanopore sequencing technology has been used to support thein situ identification of microbial species during spaceflight. Beginning in 2018, a culture-independent, swab-to-sequencer method was implemented onboard the ISS to provide a more thorough insight of the ISS microbiome. Eliminating microbial culture enables identification of difficult-to-culture organisms, reduces risks associated with potentially pathogenic cultures, and could significantly reduce the time from sample-to-answer. However, this molecular-based approach generates large metagenomic datasets that require substantial computational resources for analysis. To process nanopore-generated sequencing data, the JSC Microbiology Laboratory established a bioinformatics workflow on Amazon EC2 under the security guidance of the NASA Science Managed Cloud Environment (SMCE).This resource allows for the development, testing, and accessing of computational tools for processing large and complex datasets. The work described here will address the downlinking of data from the ISS, the automated pipeline developed to identify targeted bacterial and fungal organisms, and the time from sampling onboard to microbial identification. The pipelines have been enhanced to address high and low biomass samples using optimization based on sample source (air, water, or surface) and type of collection (filter, colony, or swab).The resulting microbiome data can be assessed beyond microbial identifications to gain understanding toward population changes over time, potential selective environmental pressures, and evaluating correlations with a wide range of additional data sets. Metagenome analysis pipelines in development could allow for simultaneous identification of microbial species, gene function, and gene pathways present in the environment. Beyond the ground processing, the developed analysis pipeline is currently deployed onboard the ISS to allow for near real-time assessments of the ISS microbiome. This study serves as a critical foundation for exploration missions, where rapid microbiome analyses will be required.

G. Marie Sharp↗

Ramdb: The NASA Raman Spectral Database (version 1.00).

Given that, in most instances, minimal sample preparation is required and due to its contactless instrument design, Raman spectroscopy is one of the most versatile vibrational spectroscopic techniques for the chemical analysis of environmental and biological specimens. The diversity of applications of Raman spectroscopy ranges anywhere from art [1] to planetary science missions [2]. The advancement in the use of Raman spectroscopy in Solar System missions, notably in post-mission sample return analysis, requires a spectral library holding the broad range of specimens that could be found in Solar System sources. For this purpose, we have initiated the development of a Raman spectral database (Ramdb) at NASA Ames Research Center. Currently, the database includes experimental and theoretical Raman spectra of PAHs [3, 4], as well as laboratory Raman spectra of amino acids, carbon allotropes, minerals, and analogs relevance to Earth Sciences [5], Exobiology [6], Planetary [7], and Astrochemistry [8] to name just a few examples. Ramdb can be found on the web at www.astrochemistry.org/ramdb, where raw and processed Raman spectra can be downloaded in CSV format. The laboratory Raman spectra are measured using a laser Raman spectrometer (JASCO NRS-5500-532QRI). The Raman instrument is equipped with three excitation lasers, with wavelengths of 405, 532, and 785 nm. A clean silicon substrate is used as the internal standard for wavenumber calibration. Powdered samples were prepared (microscopic >10 um, grounded microscopic < 10 um) on glass slides. Some raw data exhibited a background signal arising as a combination of laser-induced fluorescence from the sample. To correct this background, we developed a Python pipeline that uses open-source Python libraries. Ramdb provides both raw and processed (using Python pipeline) data, which includes tabulated Raman shift transitions and other measurement details. The theoretical Raman band positions of PAHs (pyrene monomers and tetramer clusters) were computed using density functional theory (DFT) with the help of the Gaussian 16 suite of programs [9]. In the near future, Ramdb will serve as a repository of Raman spectral data from Laboratory Astrophysics and Planetary Science experiments involving the irradiation of organic compounds under simulated space and planetary conditions. In addition, online and offline tools will be developed for utilising the database for comparison to the user’s sample.

N Punnakayathil↗