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At least 271 records · Page 15

The Galley Parallel File System

As the I/O needs of parallel scientific applications increase, file systems for multiprocessors are being designed to provide applications with parallel access to multiple disks. Many parallel file systems present applications with a conventional Unix-like interface that allows the application to access multiple disks transparently. The interface conceals the parallelism within the file system, which increases the ease of programmability, but makes it difficult or impossible for sophisticated programmers and libraries to use knowledge about their I/O needs to exploit that parallelism. Furthermore, most current parallel file systems are optimized for a different workload than they are being asked to support. We introduce Galley, a new parallel file system that is intended to efficiently support realistic parallel workloads. We discuss Galley's file structure and application interface, as well as an application that has been implemented using that interface.

Nieuwejaar, Nils↗

An X-Ray Analysis Database of Photoionization Cross Sections Including Variable Ionization

Results of research efforts in the following areas are discussed: review of the major theoretical and experimental data of subshell photoionization cross sections and ionization edges of atomic ions to assess the accuracy of the data, and to compile the most reliable of these data in our own database; detailed atomic physics calculations to complement the database for all ions of 17 cosmically abundant elements; reconciling the data from various sources and our own calculations; and fitting cross sections with functional approximations and incorporating these functions into a compact computer code.Also, efforts included adapting an ionization equilibrium code, tabulating results, and incorporating them into the overall program and testing the code (both ionization equilibrium and opacity codes) with existing observational data. The background and scientific applications of this work are discussed. Atomic physics cross section models and calculations are described. Calculation results are compared with available experimental data and other theoretical data. The functional approximations used for fitting cross sections are outlined and applications of the database are discussed.

Wang, Ping↗

Parallel supercomputing with commodity components

We have implemented a parallel computer architecture based entirely upon commodity personal computer components. Using 16 Intel Pentium Pro microprocessors and switched fast ethernet as a communication fabric, we have obtained sustained performance on scientific applications in excess of one Gigaflop. During one production astrophysics treecode simulation, we performed 1.2 x 10(sup 15) floating point operations (1.2 Petaflops) over a three week period, with one phase of that simulation running continuously for two weeks without interruption. We report on a variety of disk, memory and network benchmarks. We also present results from the NAS parallel benchmark suite, which indicate that this architecture is competitive with current commercial architectures. In addition, we describe some software written to support efficient message passing, as well as a Linux device driver interface to the Pentium hardware performance monitoring registers.

Performance↗

Preliminary Work in Obtaining Site-Directed Mutants of Hen Egg White Lysozyme

Protein crystal growth studies are recognized as a critical endeavor in the field of molecular biotechnology. The scientific applications of this field include the understanding of how enzymes function and the accumulation of accurate information of atomic structures, a key factor in the process of rational drug design. NASA has committed substantial investment and resources to the field of protein crystal growth and has conducted many microgravity protein crystal growth experiments aboard shuttle flights. Crystals grown in space tend to be larger, denser and have a more perfect habit and geometry. These improved properties gained in the microgravity environment of space result largely from the reduction of solutal convection, and the elimination of sedimentation at the growing crystal surface. Shuttle experiments have yielded many large, high quality crystals that are suitable for high resolution X-ray diffraction analysis. Examples of biologically important macromolecules which have been successfully crystallized during shuttle missions include: lysozyme, isocitrate lyase, gamma-interferon, insulin, human serum albumin and canavalin. Numerous other examples are also available. In addition to obtaining high quality crystals, investigators are also interested in learning the mechanisms by which the growth events take place. Crystallization experiments indicate that for the enzyme HEWL, measured growth rates do not follow mathematical models for 2D nucleation and dislocation-led growth of tetragonal protein crystals. As has been suggested by the laboratory of Marc L. Pusey, a possible explanation for the disagreement between observation and data is that HEWL tetraconal crystals form by aggregated units of lysozyme in supersaturated solutions. Surface measurement data was shown to fit very well with a model using an octamer unit cell as the growth unit. According to this model, the aggregation pathway and subsequent crystal growth is described by: monomer < ------ > dimer < ------- > tetramer < ------ > octamer < ------ > higher order. It is believed that multimer aggregation of lysozyme occurs by interaction at specific binding sites on the surface of the protein crystals. If the presence of discrete binding sites and the aggregation hypothesis is true, then it follows that the alteration of the binding site(s) should have significant effect on the measurements obtained during growth experiments. Site-directed mutagenesis allows the specific alteration of proteins by replacement, deletion or addition of specific amino acid residues. This report outlines the approach for this strategy and the progress made thus far toward that end.

Holmes, Leonard D.↗

Precision Spectroscopy, Diode Lasers, and Optical Frequency Measurement Technology

This compilation is a selected set of reprints from the Optical Frequency Measurement Group of the Time and Frequency Division of the National Institute of Standards and Technology, and consists of work published between 1987 and 1997. The two main programs represented here are (1) development of tunable diode-laser technology for scientific applications and precision measurements, and (2) research toward the goal of realizing optical-frequency measurements and synthesis. The papers are organized chronologically in five, somewhat arbitrarily chosen categories: Diode Laser Technology, Tunable Laser Systems, Laser Spectroscopy, Optical Synthesis and Extended Wavelength Coverage, and Multi-Photon Interactions and Optical Coherences.

DIODE LASERS↗

QuikSCAT Mission

The QuikSCAT Mission of the National Aeronautics and Space Administration (NASA) is planned for launch in Spring 1999, reducing the data gap in ocean-wind vector created by the loss of the NASA Scatterometer (NSCAT) on the Japanese Advanced Earth Observing Satellite (ADEOS) spacecraft. The NSCAT instrument ceased functioning when ADEOS failed on June 30, 1997. The follow-on scatterometer for monitoring ocean winds, called SeaWinds, is scheduled for launch on the Japanese ADEOS-II spacecraft in 2000. The Jet Propulsion Laboratory (JPL) has met the challenge to develop and integrate the instrument, ground system, and launch vehicle in less than a year. QuikSCAT will use pencil-beam-antennas in a conical-scan design which is more compact than the fixed fan-beam design of NSCAT. The antenna will radiate ku-band microwaves at 40 and 46 incident angle and measure the backscatter power across a continuous 1800 km swath. QuikSCAT is capable of providing wind-speed and wind-direction at 25 km resolution over 92 percent of the Earth's ice-free oceans every day, under both clear and cloudy conditions. Standard data products will be delivered to science users within 14-days, and fast data products will be available to operational users within two hours of data acquisition. QuikSCAT will be managed by JPL for the NASA's Office of Earth Science Enterprise. It will be launched from Vandenberg Air Force Base, aboard a Titan II vehicle. The satellite core-systems was built by Ball Aerospace Systems Division, Boulder, CO. The operation of QuikSCAT is expected to overlap with ERS-2 and SeaWinds. Spaceborne scatterometers have demonstrated a broad spectrum of scientific applications, including weather systems, wind-driven ocean circulation, land vegetation, polar ice morphology and dynamics, and Ocean-atmosphere-ice interaction.

Liu, W. Timothy↗

Enhancing the Remote Variable Operations in NPSS/CCDK

Many scientific applications in aerodynamics and solid mechanics are written in Fortran. Refitting these legacy Fortran codes with distributed objects can increase the code reusability. The remote variable scheme provided in NPSS/CCDK helps programmers easily migrate the Fortran codes towards a client-server platform. This scheme gives the client the capability of accessing the variables at the server site. In this paper, we review and enhance the remote variable scheme by using the operator overloading features in C++. The enhancement enables NPSS programmers to use remote variables in much the same way as traditional variables. The remote variable scheme adopts the lazy update approach and the prefetch method. The design strategies and implementation techniques are described in details. Preliminary performance evaluation shows that communication overhead can be greatly reduced.

Sang, Janche↗

Discovering Communicable Scientific Knowledge from Spatio-Temporal Data

This paper describes how we used regression rules to improve upon a result previously published in the Earth science literature. In such a scientific application of machine learning, it is crucially important for the learned models to be understandable and communicable. We recount how we selected a learning algorithm to maximize communicability, and then describe two visualization techniques that we developed to aid in understanding the model by exploiting the spatial nature of the data. We also report how evaluating the learned models across time let us discover an error in the data.

Schwabacher, Mark↗

High Performance Computing at NASA

The speaker will give an overview of high performance computing in the U.S. in general and within NASA in particular, including a description of the recently signed NASA-IBM cooperative agreement. The latest performance figures of various parallel systems on the NAS Parallel Benchmarks will be presented. The speaker was one of the authors of the NAS (National Aerospace Standards) Parallel Benchmarks, which are now widely cited in the industry as a measure of sustained performance on realistic high-end scientific applications. It will be shown that significant progress has been made by the highly parallel supercomputer industry during the past year or so, with several new systems, based on high-performance RISC processors, that now deliver superior performance per dollar compared to conventional supercomputers. Various pitfalls in reporting performance will be discussed. The speaker will then conclude by assessing the general state of the high performance computing field.

Bailey, David H.↗

Performance and the NAS Parallel Benchmarks

This talk will describe the NAS (National Aerospace Standards) Parallel Benchmarks, which are now widely cited in the high performance computing field as a measure of sustained performance on realistic scientific applications. The latest performance results will be included. It will be shown that significant progress has been made by several systems during the past year or so, with sustained performance on a par with the best conventional systems, and with performance per dollar significantly exceeding the conventional systems. This talk will also describe many of the pitfalls of performance reporting, and will give advice on how to avoid such pitfalls. The overall state of the field of high performance computing will also be discussed.

Bailey, David H.↗

Programming Tools: Status, Evaluation, and Comparison

In this tutorial I will first describe the characteristics of scientific applications and their developers, and describe the computing environment in a typical high-performance computing center. I will define the user requirements for tools that support application portability and present the difficulties to satisfy them. These form the basis of the evaluation and comparison of the tools. I will then describe the tools available in the market and the tools available in the public domain. Specifically, I will describe the tools for converting sequential programs, tools for developing portable new programs, tools for debugging and performance tuning, tools for partitioning and mapping, and tools for managing network of resources. I will introduce the main goals and approaches of the tools, and show main features of a few tools in each category. Meanwhile, I will compare tool usability for real-world application development and compare their different technological approaches. Finally, I will indicate the future directions of the tools in each category.

Cheng, Doreen Y.↗

Microcalorimetry: The First Two Decades

Our group at GSFC began experimental and theoretical work on microcalorimetry almost twenty years ago, in August of 1982. Over the next 10 months, we completed the initial demonstration of a Si impurity thermometer-based calorimeter as an X-ray spectrometer. This successful demonstration resulted in the development by many investigators of scientific applications for microcalorimeters, ranging from optical spectroscopy to dark matter detection to particle physics applications. Many new technical approaches for cryogenic detectors were proposed by investigators and have been developed. In this presentation, I will describe the early development of microcalorimeters at GSFC and University of Wisconsin and the subsequent rapid growth of this work around the world The key milestones in the early development were the initial spectroscopy demonstrations and the selection of XRS, our microlcalorimeter-based instrument for the Advanced X-ray Astrophysics Facility (AXAF) and ultimately for ASTRO-E. An additional key event was the development of the direct detection of dark matter experiment and the formation of the Center for Particle Astrophysics. Both of these programs provided long term support for this technology in its precarious early days. A major additional technical step in the development of detectors was the demonstration of devices based on superconducting transition edge sensors (TES). These detectors promised (and have delivered) improved energy resolution and higher event rate capabilities. They couple naturally to SQUIDS, which operate well at the low temperatures where the detectors must operate. The past two decades have taken microcalorimeters from their infancy to applications in real experiments. I will provide an overview of the early development of the devices and review the breadth of the present technology and applications.

Moseley, Harvey↗

Performance of the Wavelet Decomposition on Massively Parallel Architectures

Traditionally, Fourier Transforms have been utilized for performing signal analysis and representation. But although it is straightforward to reconstruct a signal from its Fourier transform, no local description of the signal is included in its Fourier representation. To alleviate this problem, Windowed Fourier transforms and then wavelet transforms have been introduced, and it has been proven that wavelets give a better localization than traditional Fourier transforms, as well as a better division of the time- or space-frequency plane than Windowed Fourier transforms. Because of these properties and after the development of several fast algorithms for computing the wavelet representation of any signal, in particular the Multi-Resolution Analysis (MRA) developed by Mallat, wavelet transforms have increasingly been applied to signal analysis problems, especially real-life problems, in which speed is critical. In this paper we present and compare efficient wavelet decomposition algorithms on different parallel architectures. We report and analyze experimental measurements, using NASA remotely sensed images. Results show that our algorithms achieve significant performance gains on current high performance parallel systems, and meet scientific applications and multimedia requirements. The extensive performance measurements collected over a number of high-performance computer systems have revealed important architectural characteristics of these systems, in relation to the processing demands of the wavelet decomposition of digital images.

El-Ghazawi, Tarek A.↗

Parallel Processing of Adaptive Meshes with Load Balancing

Many scientific applications involve grids that lack a uniform underlying structure. These applications are often also dynamic in nature in that the grid structure significantly changes between successive phases of execution. In parallel computing environments, mesh adaptation of unstructured grids through selective refinement/coarsening has proven to be an effective approach. However, achieving load balance while minimizing interprocessor communication and redistribution costs is a difficult problem. Traditional dynamic load balancers are mostly inadequate because they lack a global view of system loads across processors. In this paper, we propose a novel and general-purpose load balancer that utilizes symmetric broadcast networks (SBN) as the underlying communication topology, and compare its performance with a successful global load balancing environment, called PLUM, specifically created to handle adaptive unstructured applications. Our experimental results on an IBM SP2 demonstrate that the SBN-based load balancer achieves lower redistribution costs than that under PLUM by overlapping processing and data migration.

Das, Sajal K.↗

Dynamic Load Balancing for Adaptive Meshes using Symmetric Broadcast Networks

Many scientific applications involve grids that lack a uniform underlying structure. These applications are often dynamic in the sense that the grid structure significantly changes between successive phases of execution. In parallel computing environments, mesh adaptation of grids through selective refinement/coarsening has proven to be an effective approach. However, achieving load balance while minimizing inter-processor communication and redistribution costs is a difficult problem. Traditional dynamic load balancers are mostly inadequate because they lack a global view across processors. In this paper, we compare a novel load balancer that utilizes symmetric broadcast networks (SBN) to a successful global load balancing environment (PLUM) created to handle adaptive unstructured applications. Our experimental results on the IBM SP2 demonstrate that performance of the proposed SBN load balancer is comparable to results achieved under PLUM.

Das, Sajal K.↗

Safety on Earth From MARSS

ENSCO, Inc., developed the Meteorological and Atmospheric Real-time Safety Support (MARSS) system for real-time assessment of meteorological data displays and toxic material spills. MARSS also provides mock scenarios to guide preparations for emergencies involving meteorological hazards and toxic substances. Developed under a Small Business Innovation Research (SBIR) contract with Kennedy Space Center, MARSS was designed to measure how safe NASA and Air Force range safety personnel are while performing weather sensitive operations around launch pads. The system augments a ground operations safety plan that limits certain work operations to very specific weather conditions. It also provides toxic hazard prediction models to assist safety managers in planning for and reacting to releases of hazardous materials. MARSS can be used in agricultural, industrial, and scientific applications that require weather forecasts and predictions of toxic smoke movement. MARSS is also designed to protect urban areas, seaports, rail facilities, and airports from airborne releases of hazardous chemical substances. The system can integrate with local facility protection units and provide instant threat detection and assessment data that is reportable for local and national distribution.

Source record↗

Scalability of a Low-Cost Multi-Teraflop Linux Cluster for High-End Classical Atomistic and Quantum Mechanical Simulations

Scalability of a low-cost, Intel Xeon-based, multi-Teraflop Linux cluster is tested for two high-end scientific applications: Classical atomistic simulation based on the molecular dynamics method and quantum mechanical calculation based on the density functional theory. These scalable parallel applications use space-time multiresolution algorithms and feature computational-space decomposition, wavelet-based adaptive load balancing, and spacefilling-curve-based data compression for scalable I/O. Comparative performance tests are performed on a 1,024-processor Linux cluster and a conventional higher-end parallel supercomputer, 1,184-processor IBM SP4. The results show that the performance of the Linux cluster is comparable to that of the SP4. We also study various effects, such as the sharing of memory and L2 cache among processors, on the performance.

Kikuchi, Hideaki↗

Discovering Communicable Models from Earth Science Data

This chapter describes how we used regression rules to improve upon results previously published in the Earth science literature. In such a scientific application of machine learning, it is crucially important for the learned models to be understandable and communicable. We recount how we selected a learning algorithm to maximize communicability, and then describe two visualization techniques that we developed to aid in understanding the model by exploiting the spatial nature of the data. We also report how evaluating the learned models across time let us discover an error in the data.

Schwabacher, Mark↗