Showing papers by "Argonne National Laboratory published in 1998"

The Grid 2: Blueprint for a New Computing Infrastructure

Abstract: Preface Foreword 1. Grids in Context 2. Computational Grids I Applications 3 Distributed Supercomputing Applications 4 Real-Time Widely Distributed Instrumentation Systems 5 Data-Intensive Computing 6 Teleimmersion II Programming Tools 7 Application-Specific Tools 8 Compilers, Languages, and Libraries 9 Object-Based Approaches 10 High-Performance Commodity Computing III Services 11 The Globus Toolkit 12 High-Performance Schedulers 13 High-Throughput Resource Management 14 Instrumentation and Measurement 15 Performance Analysis and Visualization 16 Security, Accounting, and Assurance IV Infrastructure 17 Computing Platforms 18 Network Protocols 19 Network Quality of Service 20 Operating Systems and Network Interfaces 21 Network Infrastructure 22 Testbed Bridges from Research to Infrastructure Glossary Bibliography Contributor Biographies

A security architecture for computational grids

Abstract: State-of-the-art and emerging scientific applications require fast access to large quantities of data and commensurately fast computational resources. Both resources and data are often distributed in a wide-area network with components administered locally and independently. Computations may involve hundreds of processes that must be able to acquire resources dynamically and communicate efficiently. This paper analyzes the unique security requirements of large-scale distributed (grid) computing and develops a security policy and a corresponding security architecture. An implementation of the architecture within the Globus metacomputing toolkit is discussed.

The complete genome of the hyperthermophilic bacterium Aquifex aeolicus

Abstract: Aquifex aeolicus was one of the earliest diverging, and is one of the most thermophilic, bacteria known. It can grow on hydrogen, oxygen, carbon dioxide, and mineral salts. The complex metabolic machinery needed for A. aeolicus to function as a chemolithoautotroph (an organism which uses an inorganic carbon source for biosynthesis and an inorganic chemical energy source) is encoded within a genome that is only one-third the size of the E. coli genome. Metabolic flexibility seems to be reduced as a result of the limited genome size. The use of oxygen (albeit at very low concentrations) as an electron acceptor is allowed by the presence of a complex respiratory apparatus. Although this organism grows at 95 degrees C, the extreme thermal limit of the Bacteria, only a few specific indications of thermophily are apparent from the genome. Here we describe the complete genome sequence of 1,551,335 base pairs of this evolutionarily and physiologically interesting organism.

Destruction of the Fermi surface in underdoped high- T c superconductors

Abstract: The Fermi surface—the set of points in momentum space describing gapless electronic excitations—is a central concept in the theory of metals. In this context, the normal ‘metallic’ state of the optimally doped high-temperature superconductors is not very unusual: above the superconducting transition temperature, Tc, there is evidence for a large Fermi surface1,2,3, despite the absence of well-defined elementary excitations. In contrast, the normal state of underdoped high-temperature superconductors differs in that there is evidence for a ‘pseudogap’ above Tc (4–7). Here we examine, using angle-resolved photoemission spectroscopy, the temperature dependence of the Fermi surface in underdoped Bi2Sr2CaCu2O8+δ. We find that, on cooling the sample, the pseudogap opens up at different temperatures for different points in momentum space. This leads to an initial breakup of the Fermi surface, at a temperature T*, into disconnected arcs, which then shrink with decreasing temperature before collapsing to the point nodes of the superconducting ground state below Tc. This unusual behaviour, where the Fermi surface does not form a continuous contour in momentum space as in conventional metals, is unprecedented in that it occurs in the absence of long-range order. Moreover, although the superconducting gap below Tc evolves smoothly into the pseudogap above Tc, the pseudogap differs in its unusual temperature-dependent anisotropy, implying an intimate but non-trivial relationship between the pseudogap and the superconducting gap.

A Resource Management Architecture for Metacomputing Systems

Abstract: Metacomputing systems are intended to support remote and/or concurrent use of geographically distributed computational resources. Resource management in such systems is complicated by five concerns that do not typically arise in other situations: site autonomy and heterogeneous substrates at the resources, and application requirements for policy extensibility, co-allocation, and online control. We describe a resource management architecture that addresses these concerns. This architecture distributes the resource management problem among distinct local manager, resource broker, and resource co-allocator components and defines an extensible resource specification language to exchange information about requirements. We describe how these techniques have been implemented in the context of the Globus metacomputing toolkit and used to implement a variety of different resource management strategies. We report on our experiences applying our techniques in a large testbed, GUSTO, incorporating 15 sites, 330 computers, and 3600 processors.

Molecular-wire behaviour in p-phenylenevinylene oligomers

Abstract: Electron transfer from electron-donor to electron-acceptor molecules via a molecular ‘bridge’ is a feature of many biological andchemical systems. The electronic structure of the bridge component in donor–bridge–acceptor (DBA) systems is known to play a critical role in determining the ease of electron transfer1,2. In most DBA systems, the rate at which electron transfer occurs scales exponentially with the donor–acceptor distance — effectively the length of the bridge molecule. But theory predicts that regimes exist wherein the distance dependence may be very weak, the bridge molecules essentially acting as incoherent molecular wires3,4,5,6. Here we show how these regimes can be accessed by molecular design. We have synthesized a series of structurally well-defined DBA molecules that incorporate tetracene as the donor and pyromellitimide as the acceptor, linked by p -phenylenevinylene oligomers of various lengths. Photoinduced electron transfer in this series exhibits very weak distance dependence for donor–acceptor separations as large as 40 A, with rate constants of the order of 1011 s−1. These findings demonstrate the importance of energy matching between the donor and bridge components for achieving molecular-wire behaviour.

The NEOS Server

Abstract: The Network-Enabled Optimization System (NEOS) is an Internet based optimization service. The NEOS Server introduces a novel approach for solving optimization problems. Users of the NEOS Server submit a problem and their choice of optimization solver over the Internet. The NEOS Server computes all information (for example, derivatives and sparsity patterns) required by the solver, links the optimization problem with the solver, and returns a solution.

The Globus project: a status report

Abstract: The Globus project is a multi-institutional research effort that seeks to enable the construction of computational grids providing pervasive, dependable, and consistent access to high-performance computational resources, despite geographical distribution of both resources and users. Computational grid technology is being viewed as a critical element of future high-performance computing environments that will enable entirely new classes of computation-oriented applications, much as the World Wide Web fostered the development of new classes of information-oriented applications. The authors report on the status of the Globus project as of early 1998. They describe the progress that has been achieved to date in the development of the Globus toolkit, a set of core services for constructing grid tools and applications. They also discuss the Globus Ubiquitous Supercomputing Testbed (GUSTO) that they have constructed to enable large-scale evaluation of Globus technologies, and they review early experiences with the development of large-scale grid applications on the GUSTO testbed.

Application of interior-point methods to model predictive control

Abstract: We present a structured interior-point method for the efficient solution of the optimal control problem in model predictive control. The cost of this approach is linear in the horizon length, compared with cubic growth for a naive approach. We use a discrete-time Riccati recursion to solve the linear equations efficiently at each iteration of the interior-point method, and show that this recursion is numerically stable. We demonstrate the effectiveness of the approach by applying it to three process control problems.

Imaging and control of domain structures in ferroelectric thin films via scanning force microscopy

Abstract: ▪ Abstract Scanning force microscopy (SFM) is becoming a powerful technique with great potential both for imaging and for control of domain structures in ferroelectric materials at the nanometer scale. Application of SFM to visualization of domain structures in ferroelectric thin films is described. Imaging methods of ferroelectric domains are based on the detection of surface charges in the noncontact mode of SFM and on the measurement of the piezoelectric response of a ferroelectric film to an external field applied by the tip in the SFM contact mode. This latter mode can be used for nondestructive evaluation of local ferroelectric and piezoelectric properties and for manipulation of domains of less than 50 nm in diameter. The effect of the film thickness and crystallinity on the imaging resolution is discussed. Scanning force microscopy is shown to be a technique well suited for nanoscale investigation of switching processes and electrical degradation effects in ferroelectric thin films.

Contributions of interacting biological mechanisms to soil aggregate stabilization in restored prairie

Abstract: A better understanding of the soil aggregation process is needed to address a variety of concerns, including soil quality and erosion, agricultural sustainability, soil C sequestration, the mobility of hazardous chemicals and remediation of contaminated sites We used data from a chronosequence of tallgrass prairie restorations and a path analysis approach to evaluate how the lengths of two dia size classes of fibrous roots, the length of external mycorrhizal hyphae, microbial biomass C, hot-water soluble carbohydrate C and soil organic C interact to promote the stabilization of soil aggregates The measured binding agents accounted for 88% of the variation in macroaggregates >212 μm diameter and goodness-of-fit indexes indicated a good practical fit of the path model to the data The restoration of macroaggregate structure in this system was apparently driven by the direct and indirect effects of roots and external hyphae, with lesser relative contributions by the three measured C pools Although the two root size classes had similar direct effects on the percentage of macroaggregates, their indirect contributions differed substantially Fine roots (02–1 mm diameter) exerted considerable indirect effects via their strong influences on external hyphae and microbial biomass C Very fine roots (<02 mm dia) made a stronger contribution to soil organic C than fine roots, but their overall indirect contribution to aggregation was minimal In addition, the relative importance of each binding agent varied for different size fractions of macroaggregates and generally supported the hypothesis that the effectiveness of various binding mechanisms depends on the physical dimensions of the binding agents relative to the spatial scales of the aggregate planes of weakness being bridged

Data sieving and collective I/O in ROMIO.

Abstract: The I/O access patterns of parallel programs often consist of accesses to a large number of small, noncontiguous pieces of data. If an application's I/O needs are met by making many small, distinct I/O requests, however, the I/O performance degrades drastically. To avoid this problem, MPI-IO allows users to access a noncontiguous data set with a single I/O function call. This feature provides MPI-IO implementations an opportunity to optimize data access. We describe how our MPI-IO implementation, ROMIO, delivers high performance in the presence of noncontiguous requests. We explain in detail the two key optimizations ROMIO performs: data sieving for noncontiguous requests from one process and collective I/O for noncontiguous requests from multiple processes. We describe how one can implement these optimizations portably on multiple machines and file systems, control their memory requirements, and also achieve high performance. We demonstrate the performance and portability with performance results for three applications--an astrophysics-application template (DIST3D), the NAS BTIO benchmark, and an unstructured code (UNSTRUC)--on five different parallel machines: HP Exemplar, IBM SP, Intel Paragon, NEC SX-4, and SGI Origin2000.

Exchange-spring behavior in epitaxial hard/soft magnetic bilayers

Abstract: We present results on the magnetic reversal process in epitaxial Sm-Co(11\ifmmode\bar\else\textasciimacron\fi{}00)/TM (TM=Fe,Co) bilayer films prepared via magnetron sputtering. The magnetically hard Sm-Co films have 20-T uniaxial anisotropy and coercivities g3 T at room temperature, that double on cooling, as determined by magnetometry. The TM layers are exchange coupled to the Sm-Co layer and exhibit reversible demagnetization curves expected for an exchange-spring magnet. We also present numerical solutions of a one-dimensional model that provide the spin configuration for each atomic layer. Comparison of the experimental results with the model simulations indicates that our exchange-spring behavior can be understood from the intrinsic parameters of the hard and soft layers. The simulations are extended to realistically estimate the ultimate gain in the energy product that potentially can be realized based on the exchange hardening principle.

Height growth rate tradeoffs determine northern and southern range limits for trees

Abstract: Identifying the biological determinants of range limits of trees is an unsolved problem of critical importance for predicting the effects of climate change on forests. Data showing that many boreal trees can grow in temperate climates indicate that southern range limits do not necessarily result from excessive temperature per se. A growth tradeoff could exist between freezing tolerance and height growth rate if adaptations to tolerate cold climates interfered with growth. Analysis of height growth rate versus freezing tolerance for twenty-two North American trees provided evidence for such a tradeoff. Provenance trials of numerous tree species also showed that a tradeoff exists within species, indicating a genetic basis for these traits. The result of this tradeoff is that at their southern range margins most species do not suffer from too much heat but rather face competitors with a faster growth rate. The implication for future climate change is that forests will not suffer catastrophic dieback due to increased temperatures but will rather be replaced gradually by faster growing types, perhaps over hundreds of years.

Predicting Application Run Times Using Historical Information

Abstract: We present a technique for deriving predictions for the run times of parallel applications from the run times of “similar” applications that have executed in the past. The novel aspect of our work is the use of search techniques to determine those application characteristics that yield the best definition of similarity for the purpose of making predictions. We use four workloads recorded from parallel computers at Argonne National Laboratory, the Cornell Theory Center, and the San Diego Supercomputer Center to evaluate the effectiveness of our approach. We show that on these workloads our techniques achieve predictions that are between 14 and 60 percent better than those achieved by other researchers; our approach achieves mean prediction errors that are between 40 and 59 percent of mean application run times.

The HERMES Spectrometer

Abstract: The HERMES experiment is collecting data on inclusive and semi-inclusive deep inelastic scattering of polarised positrons from polarised targets of H, D, and 3 He. These data give information on the spin structure of the nucleon. This paper describes the forward angle spectrometer built for this purpose. The spectrometer includes numerous tracking chambers (micro-strip gas chambers, drift and proportional chambers) in front of and behind a 1.3 T.m magnetic field, as well as an extensive set of detectors for particle identification (a lead-glass calorimeter, a pre-shower detector, a transition radiation detector, and a threshold Cherenkov detector). Two of the main features of the spectrometer are its good acceptance and identification of both positrons and hadrons, in particular pions. These characteristics, together with the purity of the targets, are allowing HERMES to make unique contributions to the understanding of how the spins of the quarks contribute to the spin of the nucleon.

Control of diamond film microstructure by Ar additions to CH4/H2 microwave plasmas

Abstract: The transition from microcrystalline to nanocrystalline diamond films grown from Ar/H2/CH4 microwave plasmas has been investigated. Both the cross-section and plan-view micrographs of scanning electron microscopy reveal that the surface morphology, the grain size, and the growth mechanism of the diamond films depend strongly on the ratio of Ar to H2 in the reactant gases. Microcrystalline grain size and columnar growth have been observed from films produced from Ar/H2/CH4 microwave discharges with low concentrations of Ar in the reactant gases. By contrast, the films grown from Ar/H2/CH4 microwave plasmas with a high concentration of Ar in the reactant gases consist of phase pure nanocrystalline diamond, which has been characterized by transmission electron microscopy, selected area electron diffraction, and electron energy loss spectroscopy. X-ray diffraction and Raman spectroscopy reveal that the width of the diffraction peaks and the Raman bands of the as-grown films depends on the ratio of Ar to H2 in...

A Grid-Enabled MPI: Message Passing in Heterogeneous Distributed Computing Systems

Abstract: Application development for high-performance distributed computing systems, or computational grids as they are sometimes called, requires ``grid-enabled'' tools that hide mundane aspects of the heterogeneous grid environment without compromising performance. As part of an investigation of these issues, we have developed MPICH-G, a grid-enabled implementation of the Message Passing Interface (MPI) that allows a user to run MPI programs across multiple computers at different sites using the same commands that would be used on a parallel computer. This library extends the Argonne MPICH implementation of MPI to use services provided by the Globus grid toolkit. In this paper, we describe the MPICH-G implementation and present preliminary performance results.

Protostellar Cosmic Rays and Extinct Radioactivities in Meteorites

Abstract: Calcium-aluminum-rich inclusions (CAIs) and chondrules of chondritic meteorites may originate with the melting of dustballs launched by a magnetically driven bipolar outflow from the inner edge of the primitive solar nebula. Bombardment by protostellar cosmic rays may make the rock precursors of CAIs and chondrules radioactive, producing radionuclides found in meteorites that are difficult to obtain with other mechanisms. Reasonable scalings from the observed hard X-rays for the cosmic-ray protons released by flares in young stellar objects yield the correct amounts of 41Ca,53Mn, and 138La inferred for meteorites, but proton- and α-induced transformations underproduce 26Al by a factor of about 20. The missing 26Al may be synthesized by 3He nuclei accelerated in impulsive flares reacting primarily with 24Mg, an abundant isotope in the target precursor rocks. The mechanism allows a simple explanation for the very different ratios of 26Al/27Al inferred for normal CAIs, CAIs with fractionated and unidentified nuclear (FUN) anomalies, and chondrules. The overproduction of 41Ca by analogous 3He reactions and the case of 60Fe inferred for eucritic meteorites require special interpretations in this picture.

Observation of the Bc meson in pp¯ collisions at √s = 1.8 TeV

Abstract: We have observed bottom-charm mesons via the decay mode B{sub c}{sup {+-}}{yields}J/{psi}{ell}{sup {+-}}v in 1.8 TeV p{ovr p}collisions using the CDF detector at the Fermilab Tevatron. A fit of background and signal contributions to the J/{psi}{ell} mass distribution yielded 20.4{sub -5.5}{sup +6.2} events from B{sub c} mesons. A fit to the same distribution with background alone was rejected at the level of 4.8 standard deviations. We measured the B{sub c}{sup +} mass to be 6.40{+-}0.39(stat){+-}0.13(syst) GeV/c{sup 2} and the B{sub c}{sup +} lifetime to be 0.46{sub -0.16}{sup +0.18}(stat){+-}0.03(syst) ps. Our measured yield (production cross section times branching ratio) for B{sub c}{sup +}{yields}J/{psi}{ell}{sup +}v relative to that for B{sup +}{yields}J/{psi} K{sup +} is 0.132{sub -0.037}{sup +0.041}(stat){+-}0.031(syst){sub -0.020}{sup +0.032}(lifetime).

Phenomenology of the low-energy spectral function in high-T c superconductors

Abstract: We introduce a simple phenomenological form for the self-energy which allows us to extract important information from angle-resolved photoemission data on the high-${T}_{c}$ superconductor ${\mathrm{Bi}}_{2}{\mathrm{Sr}}_{2}{\mathrm{CaCu}}_{2}{\mathrm{O}}_{8}$ for binding energies of order the spectral gap. First, we find a rapid suppression of the single particle scattering rate below ${T}_{c}$ for all doping levels. Second, we find that in the overdoped materials the gap $\ensuremath{\Delta}$ at all k points on the Fermi surface has significant temperature dependence and vanishes near ${T}_{c}.$ In contrast, in the underdoped samples such behavior is found only at k points close to the diagonal. Near $(\ensuremath{\pi},0)$, $\ensuremath{\Delta}$ is essentially $T$ independent in the underdoped samples. The filling-in of the pseudogap with increasing $T$ is described by a broadening proportional to $T\ensuremath{-}{T}_{c},$ which is naturally explained by pairing correlations above ${T}_{c}.$

Parallel thermodynamic analysis of duplexes on oligodeoxyribonucleotide microchips

Abstract: A microchip method has been developed for massive and parallel thermodynamic analyses of DNA duplexes. Fluorescently labeled oligonucleotides were hybridized with oligonucleotides immobilized in the 100 x 100 x 20 mum gel pads of the microchips. The equilibrium melting curves for all microchip duplexes were measured in real time in parallel for all microchip duplexes. Thermodynamic data for perfect and mismatched duplexes that were obtained using the microchip method directly correlated with data obtained in solution. Fluorescent labels or longer linkers between the gel and the oligonucleotides appeared to have no significant effect on duplex stability. Extending the immobilized oligonucleotides with a four-base mixture from the 3'-end or one or two universal bases (5-nitroindole) from the 3'- and/or 5'-end increased the stabilities of their duplexes. These extensions were applied to increase the stabilities of the duplexes formed with short oligonucleotides in microchips, to significantly lessen the differences in melting curves of the AT- and GC-rich duplexes, and to improve discrimination of perfect duplexes from those containing poorly recognized terminal mismatches. This study explored a way to increase the efficiency of sequencing by hybridization on oligonucleotide microchips.

Features of time-independent Wigner functions

Abstract: The Wigner phase-space distribution function provides the basis for Moyal{close_quote}s deformation quantization alternative to the more conventional Hilbert space and path integral quantizations. The general features of time-independent Wigner functions are explored here, including the functional ({open_quotes}star{close_quotes}) eigenvalue equations they satisfy; their projective orthogonality spectral properties; their Darboux ({open_quotes}supersymmetric{close_quotes}) isospectral potential recursions; and their canonical transformations. These features are illustrated explicitly through simple solvable potentials: the harmonic oscillator, the linear potential, the P{umlt o}schl-Teller potential, and the Liouville potential. {copyright} {ital 1998} {ital The American Physical Society}

Strong Dependence of the Superconducting Gap on Oxygen Doping from Tunneling Measurements on Bi 2 Sr 2 CaCu 2 O 8 − δ

Abstract: Tunneling measurements are reported for break junctions on ${\mathrm{Bi}}_{2}{\mathrm{Sr}}_{2}{\mathrm{CaCu}}_{2}{O}_{8\ensuremath{-}\ensuremath{\delta}}$ single crystals with various oxygen concentrations. Superconducting energy gaps $\ensuremath{\Delta}$ are observed in the underdoped samples which are considerably larger $(\ensuremath{\sim}30%)$ than found in optimal doped crystals. The trend of decreasing $\ensuremath{\Delta}$ and $2\ensuremath{\Delta}{/kT}_{c}$ with increasing hole doping is continued into the overdoped region. Thus the superconducting gap and strong-coupling ratio change monotonically and dramatically over a narrow doping region where ${T}_{c}$ exhibits a maximum.

A fault detection service for wide area distributed computations

Abstract: The potential for faults in distributed computing systems is a significant complicating factor for application developers. While a variety of techniques exist for detecting and correcting faults, the implementation of these techniques in a particular context can be difficult. Hence, we propose a fault detection service designed to be incorporated, in a modular fashion, into distributed computing systems, tools, or applications. This service uses well-known techniques based on unreliable fault detectors to detect and report component failure, while allowing the user to tradeoff timeliness of reporting against false positive rates. We describe the architecture of this service, report on experimental results that quantify its cost and accuracy, and describe its use in two applications, monitoring the status of system components of the GUSTO computational grid testbed and as part of the NetSolve network-enabled numerical solver.

Synthesis of nanocrystalline diamond thin films from an Ar–CH4 microwave plasma

Abstract: Nanocrystalline diamond thin films have been synthesized in an Ar–CH4 microwave discharge, without the addition of molecular hydrogen. X-ray diffraction, transmission electron microscopy, and electron energy loss spectroscopy characterizations show that the films consist of a pure crystalline diamond phase with very small grain sizes ranging from 3 to 20 nm. Atomic force microscopy analysis demonstrates that the surfaces of the nanocrystalline diamond films remain smooth independent of the film thicknesses. Furthermore, the reactant gas pressure, which strongly affects the concentration of C2 dimer in the Ar–CH4 plasma as well as the growth rate of the films, has been found to be a key parameter for the nanocrystalline diamond thin film depositions.

In Situ Synthesis of Polymer−Clay Nanocomposites from Silicate Gels

Abstract: Polymer-containing silicate gels were hydrothermally crystallized to form layered magnesium silicate hectorite clays containing polymers that are incorporated in situ. Gels consist of silica sol, magnesium hydroxide sol, lithium fluoride, and the polymer of choice. Dilute solutions of gel in water are refluxed for various lengths of time and then isolated via centrifugation, washed, and air-dried. Polymer loadings up to 86% were attained by adding more polymer to the solutions after 2-day reaction times, reacting for another 24 h, and continuing this process prior to isolation. Polyaniline (PANI)- and polyacrylonitrile (PACN)-clay samples contain up to 57% and 76% polymer, respectively, after just one sequential addition at high polymer loading. Series of PANI-, PACN-, poly(vinylpyrrolidone) (PVP)-, and hydroxypropylmethylcellulose (HPMC)-clays also were prepared by several sequential additions of lower polymer loading to the silicate gel during crystallization. Final polymer loadings were determined by thermal analysis. Basal spacings between clay interlayers were measured by X-ray powder diffraction for all samples. Increases in polymer loadings and basal spacings were observed for all the neutral polymers studied, until or unless delamination occurred. Delamination was evident for PACN- and PANI-clay nanocomposites. The highest loadings were observed for the PACN-clays, up to 86%. For the cationic polymermore » polydimethyldiallylammonium chloride, however, the loading could not be increased beyond about 20%. This is due to electrostatic interactions that balance the negatively charged sites on the silicate lattice with those on the cationic polymer chain. Beyond charge compensation, there is no driving force for further incorporation. Charge compensation in the case of the neutral polymers is attained by interlayer lithium(I) cations.« less