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1,053 records · Page 59

SpF: Enabling Petascale Performance for Pseudospectral Dynamo Models

Pseudospectral (PS) methods possess a number of characteristics (e.g., efficiency, accuracy, natural boundary conditions) that are extremely desirable for dynamo models. Unfortunately, dynamo models based upon PS methods face a number of daunting challenges, which include exposing additional parallelism, leveraging hardware accelerators, exploiting hybrid parallelism, and improving the scalability of global memory transposes. Although these issues are a concern for most models, solutions for PS methods tend to require far more pervasive changes to underlying data and control structures. Further, improvements in performance in one model are difficult to transfer to other models, resulting in significant duplication of effort across the research community.We have developed an extensible software framework for pseudospectral methods called SpF that is intended to enable extreme scalability and optimal performance. High-level abstractions provided by SpF unburden applications of the responsibility of managing domain decomposition and load balance while reducing the changes in code required to adapt to new computing architectures. The key design concept in SpF is that each phase of the numerical calculation is partitioned into disjoint numerical kernels that can be performed entirely in-processor. The granularity of domain-decomposition provided by SpF is only constrained by the data-locality requirements of these kernels. SpF builds on top of optimized vendor libraries for common numerical operations such as transforms, matrix solvers, etc., but can also be configured to use open source alternatives for portability. SpF includes several alternative schemes for global data redistribution and is expected to serve as an ideal testbed for further research into optimal approaches for different network architectures.In this presentation, we will describe the basic architecture of SpF as well as preliminary performance data and experience with adapting legacy dynamo codes. We will conclude with a discussion of planned extensions to SpF that will provide pseudospectral applications with additional flexibility with regard to time integration, linear solvers, and discretization in the radial direction.

Pseudospectral (PS)↗

Effect of track structure and radioprotectors on the induction of oncogenic transformation in murine fibroblasts by heavy ions

The oncogenic potential of high-energy 56Fe particles (1 GeV/nucleon) accelerated with the Alternating Gradient Synchrotron at the Brookhaven National Laboratory was examined utilizing the mouse C3H 10T1/2 cell model. The dose-averaged LET for high-energy 56Fe is estimated to be 143 keV/micrometer with the exposure conditions used in this study. For 56Fe ions, the maximum relative biological effectiveness (RBEmax) values for cell survival and oncogenic transformation were 7.71 and 16.5 respectively. Compared to 150 keV/micrometer 4He nuclei, high-energy 56Fe nuclei were significantly less effective in cell killing and oncogenic induction. The prostaglandin E1 analog misoprostol, an effective oncoprotector of C3H 10T1/2 cells exposed to X rays, was evaluated for its potential as a radioprotector of oncogenic transformation with high-energy 56Fe. Exposure of cells to misoprostol did not alter 56Fe cytotoxicity or the rate of 56Fe-induced oncogenic transformation.

NASA Discipline Radiation Health↗

Dynamics and control of coherent structures in the turbulent wall layer: An overview

We expand the velocity field in the vicinity of the wall in empirical eigenfunctions obtained from experiment. Truncating our system and using Galerkin projection, we obtain a closed set of non-linear ordinary differential equations with ten degrees of freedom. We find a rich dynamical behavior, including in particular a heteroclinic attracting orbit giving rise to intermittency. The intermittent jump from one attracting point to the other resembles in many respects the bursts observed in experiments. Specifically, the time between jumps and the duration of the jumps, is approximately that observed in a burst; the jump begins with the formation of a narrowed and intensified updraft, like the ejection phase of a burst, and is followed by a gentle, diffuse downdraft like the sweep phase of a burst. The magnitude of the Reynolds stress spike produced during a burst is limited by our truncation. The behavior is quite robust, much of it being due to the symmetries present (Aubry's group has examined dimensions up to 128 with persistence of the global behavior). We have examined eigenvalues and coefficients obtained from experiment, and from exact simulation, which differ in magnitude. Similar behavior is obtained in both cases; in the latter case, the heteroclinic orbits connect limit cycles instead of fixed points, corresponding to cross-stream waving of the streamwise rolls. The bifurcation diagram remains structurally similar, but somewhat distorted. The role of the pressure term is made clear - it triggers the intermittent jumps, which otherwise would occur at longer and longer intervals, as the system trajectory is attracted closer and closer to the heteroclinic cycle. The pressure term results in the jumps occurring at essentially random times, and the magnitude of the signal determines the average timing. Stretching of the wall region shows that the model is consistent with observations of polymer drag reduction. Change of the third order coefficients, corresponding to acceleration or deceleration of the mean flow, changes the heteroclinic cycles from attracting to repelling, increasing or decreasing the stability, in agreement with observations. The existence of fixed points is an artifact introduced by the projection; however, a decoupled model still displays the rich dynamics. Numerous assumptions made in Aubry et al. (1988) can now be proved exactly. Feeding back eigenfuncitons with the proper phase can delay the bursting, (the heteroclinic jump to the other fixed point), decreasing the drag. It is also possible to speed up the bursting, increasing mixing to control separation. Our approach is optimal for short time tracking in control.

Berkooz, Gal↗

Scheduling Operations for Massive Heterogeneous Clusters

High-performance computing (HPC) programming has become increasingly difficult with the advent of hybrid supercomputers consisting of multicore CPUs and accelerator boards such as the GPU. Manual tuning of software to achieve high performance on this type of machine has been performed by programmers. This is needlessly difficult and prone to being invalidated by new hardware, new software, or changes in the underlying code. A system was developed for task-based representation of programs, which when coupled with a scheduler and runtime system, allows for many benefits, including higher performance and utilization of computational resources, easier programming and porting, and adaptations of code during runtime. The system consists of a method of representing computer algorithms as a series of data-dependent tasks. The series forms a graph, which can be scheduled for execution on many nodes of a supercomputer efficiently by a computer algorithm. The schedule is executed by a dispatch component, which is tailored to understand all of the hardware types that may be available within the system. The scheduler is informed by a cluster mapping tool, which generates a topology of available resources and their strengths and communication costs. Software is decoupled from its hardware, which aids in porting to future architectures. A computer algorithm schedules all operations, which for systems of high complexity (i.e., most NASA codes), cannot be performed optimally by a human. The system aids in reducing repetitive code, such as communication code, and aids in the reduction of redundant code across projects. It adds new features to code automatically, such as recovering from a lost node or the ability to modify the code while running. In this project, the innovators at the time of this reporting intend to develop two distinct technologies that build upon each other and both of which serve as building blocks for more efficient HPC usage. First is the scheduling and dynamic execution framework, and the second is scalable linear algebra libraries that are built directly on the former.

Humphrey, John↗

Induction of genomic instability in TK6 human lymphoblasts exposed to 137Cs gamma radiation: comparison to the induction by exposure to accelerated 56Fe particles

The induction of genomic instability in TK6 human lymphoblasts by exposure to (137)Cs gamma radiation was investigated by measuring the frequency and characteristics of unstable clones isolated approximately 36 generations after exposure. Clones surviving irradiation and control clones were analyzed for 17 characteristics including chromosomal aberrations, growth defects, alterations in response to a second irradiation, and mutant frequencies at the thymidine kinase and Na(+)/K(+) ATPase loci. Putative unstable clones were defined as those that exhibited a significant alteration in one or more characteristics compared to the controls. The frequency and characteristics of the unstable clones were compared in clones exposed to (137)Cs gamma rays or (56)Fe particles. The majority of the unstable clones isolated after exposure to either gamma rays or (56)Fe particles exhibited chromosomal instability. Alterations in growth characteristics, radiation response and mutant frequencies occurred much less often than cytogenetic alterations in these unstable clones. The frequency and complexity of the unstable clones were greater after exposure to (56)Fe particles than to gamma rays. Unstable clones that survived 36 generations after exposure to gamma rays exhibited increases in the incidence of dicentric chromosomes but not of chromatid breaks, whereas unstable clones that survived 36 generations after exposure to (56)Fe particles exhibited increases in both chromatid and chromosome aberrations.

Non-NASA Center↗

Interplanetary Fast Shocks and Associated Drivers Observed through the Twenty-Third Solar Minimum by WIND Over its First 2.5 Years

A list of the interplanetary (IP) shocks observed by WIND from its launch (in November 1994) to May 1997 is presented. Forty two shocks were identified. The magnetohydrodynamic nature of the shocks is investigated, and the associated shock parameters and their uncertainties are accurately computed using a practical scheme which combines two techniques. These techniques are a combination of the "pre-averaged" magnetic-coplanarity, velocity-coplanarity, and the Abraham-Schrauner-mixed methods, on the one hand, and the Vinas and Scudder [1986] technique for solving the non-linear least-squares Rankine-Hugoniot shock equations, on the other. Within acceptable limits these two techniques generally gave the same results, with some exceptions. The reasons for the exceptions are discussed. It is found that the mean strength and rate of occurrence of the shocks appears to correlated with the solar cycle. Both showed a decrease in 1996 coincident with the time of the lowest ultraviolet solar radiance, indicative of solar minimum and start of solar cycle 23, which began around June 1996. Eighteen shocks appeared to be associated with corotating interaction regions (CIRs). The distribution of their shock normals showed a mean direction peaking in the ecliptic plane and with a longitude (phi(sub n)) in that plane between perpendicular to the Parker spiral and radial from the Sun. When grouped according to the sense of the direction of propagation of the shocks the mean azimuthal (longitude) angle in GSE coordinates was approximately 194 deg for the fast-forward and approximately 20 deg for the fast-reverse shocks. Another 16 shocks were determined to be driven by solar transients, including magnetic clouds. These shocks had a broader distribution of normal directions than those of the CIR cases with a mean direction close to the Sun-Earth line. Eight shocks of unknown origin had normal orientation well off the ecliptic plane. No shock propagated with longitude phi(sub n) >= 220 +/- 10 deg, this would suggest strong hindrance to the propagation of shocks contra a rather tightly winding Parker spiral. Examination of the obliquity angle theta(sub Bn) (that between the shock normal and the upstream interplanetary magnetic field) for the full set of shocks revealed that about 58% was quasi-perpendicular, and some were very nearly perpendicular. About 32% of the shocks were oblique, and the rest (only 10%) were quasi-parallel, with one on Dec. 9, 1996 that showed field pulsations. Small uncertainty in the estimated angle theta(sub Bn) was obtained for about 10 shocks with magnetosonic Mach numbers between 1 and 2, hopefully significantly contributing to studies researching particle acceleration mechanisms at IP shocks, and to investigations where accurate values of theta(sub Bn) are crucial.

Mariani, F.↗

Single track effects, Biostack and risk assessment

The scientific career of Prof. Bucker has spanned a very exciting period in the fledgling science of Space Radiation Biology. The capability for placing biological objects in space was developed, and the methods for properly packaging, retrieving and analyzing them were worked out. Meaningful results on the effects of radiation were obtained for the first time. In fact, many of the successful techniques and methodologies for handling biological samples were developed in Prof. Bucker's laboratories, as attested by the extensive Biostack program. He was the first to suggest and successfully carry out experiments in space directly aimed at measuring effects of single tracks of high-energy heavy galactic cosmic rays by specifically identifying whether or not the object had been hit by a heavy particle track. Because the "hit" frequencies of heavy galactic cosmic rays to cell nuclei in the bodies of space travelers will be low, it is expected that any effects to humans on the cellular level will be dominated by single-track cell traversals. This includes the most important generally recognized late effect of space radiation exposure: radiation-induced cancer. This paper addresses the single-track nature of the space radiation environment, and points out the importance of single "hits" in the evaluation of radiation risk for long-term missions occurring outside the earth's magnetic field. A short review is made of biological objects found to show increased effects when "hit" by a single heavy charged-particle in space. A brief discussion is given of the most provocative results from the bacterial spore Bacillus subtilis: experimental evidence that tracks can affect biological systems at much larger distances from the trajectory than previously suspected, and that the resultant inactivation cross section in space calculated for this system is very large. When taken at face value, the implication of these results, when compared to those from experiments performed at ground-based accelerators with beams at low energies in the same LET range, is that high-energy particles can exert their influence a surprising distance from their trajectory and the inactivation cross sections are some 20 times larger than expected. Clearly, beams from high-energy heavy-ion accelerators should be used to confirm these results. For those end points that can also be caused by low-LET beams such as high-energy protons, it is important to measure their action cross sections as well. The ratio of the cross sections for a high-LET beam to that of a low-LET beam is an interesting experimental ratio and, we suggest, of more intrinsic interest than the RBE (Relative Biological Effectiveness). It is a measure of the "biological" importance of one particle type relative to another particle type. This ratio will be introduced and given the name RPPE (Relative Per Particle Effectiveness). Values of RPPE have appeared in the literature and will be discussed. A rather well-known value of this quantity (13,520) has been suggested for the RPPE of high-energy iron ions to high-energy protons. This value was suggested by Letaw et al. Nature 330, 709-710 (1987)] we will call it the Letaw limit. It will be discussed in terms of the importance of the heavy-ion component vs light-ion component of the galactic cosmic rays. It is also pointed out, however, that there may be unique effects from single tracks of heavy ions that do not occur from light-ion tracks. For such effects, the concepts of both RBE and RPPE lose their meaning.

NASA Discipline Radiation Health↗

Gravitational Effects on Flow Instability and Transition in Low Density Jets

Recent experiments have shown that low-density gas jets injected into a high-density ambient gas undergo an instability mode, leading to highly-periodic oscillations in the flow-field for certain conditions. The transition from laminar to turbulent flow in these jets is abrupt, without the gradual change in scales. Even the fine scale turbulent structure repeats itself with extreme regularity from cycle to cycle. Similar observations were obtained in buoyancy-dominated and momentum-dominated jets characterized by the Richardson numbers, Ri = [gD(rho(sub a)-rho(sub j))/rho(sub j)U(sub j)(exp 2) ] where g is the gravitational acceleration, D is the jet diameter, rho(sub a) and rho(sub a) are, respectively, the free-stream and jet densities, and U(sub j) is the mean jet exit velocity. At high Richardson numbers, the instability is presumably caused by buoyancy since the flow-oscillation frequency (f) or the Strouhal number, St = [fD/U(sub j)] scales with Ri. In momentum-dominated jets, however, the Strouhal number of the oscillating flow is relatively independent of the Ri. In this case, a local absolute instability is predicted in the potential core of low-density jets with S [= rho(sub j)/rho(sub a)] < 0.7, which agrees qualitatively with experiments. Although the instability in gas jets of high Richardson numbers is attributed to buoyancy, direct physical evidence has not been acquired in experiments. If the instability is indeed caused by buoyancy, the near-field flow structure of the jet will change significantly when the buoyancy is removed, for example, in the microgravity environment. Thus, quantitative data on the spatial and temporal evolutions of the instability, length and time scale of the oscillating mode and its effects on the mean flow and breakdown of the potential core are needed in normal and microgravity to delineate gravitational effects in buoyant jets. In momentum dominated low-density jets, the instability is speculated to originate in the potential core. However, experiments have not succeeded in identifying the direct physical cause of the instability. For example, the theory predicts an oscillating mode for S<0.62 in the limit of zero momentum thickness, which contradicts with the experimental findings of Kyle and Sreenivasan. The analyses of momentum-dominated jets neglect buoyancy effects because of the small Richardson number. Although this assumption is appropriate in the potential core, the gravitational effects are important in the annular region surrounding the jet, where the density and velocity gradients are large. This reasoning provides basis for the hypothesis that the instability in low Richardosn number jets studied by Kyle and Sreenivasan and Monkewitz et al. is caused by buoyancy. The striking similarity in characteristics of the instability and virtually the identical conclusions reached by Subbarao and Cantwell in buoyant (Ri>0.5) helium jets on one hand and by Kyle and Sreenivasan in momentum-dominated (Ri<1x10(exp -3)) helium jets on the other support this hypothesis. However, quantitative experiments in normal and microgravity are necessary to obtain direct physical evidence of buoyancy effects on the flow instability and structure of momentum-dominated low-density jets. The primary objective of this new research project is to quantify how buoyancy affects the flow instability and structure in the near field of low-density jets. The flow will be described by the spatial and temporal evolutions of the instability, length and time scales of the oscillating mode, and the mean and fluctuating concentration fields. To meet this objective, concentration measurements will be obtained across the whole field using quantitative Rainbow Schlieren Deflectometry, providing spatial resolution of 0.1mm and temporal resolution of 0.017s to 1ms. The experimental effort will be supplemented with linear stability analysis of low-density jets by considering buoyancy. The first objective of this research is to investigate the effects of gravity on the flow instability and structure of low-density jets. The flow instability in these jets has been attributed to buoyancy. By removing buoyancy in our experiments, we seek to obtain the direct physical evidence of the instability mechanism. In the absence of the instability, the flow structure will undergo a significant change. We seek to quantify these changes by mapping the flow field (in terms of the concentration profiles) of these jets at non-buoyant conditions. Such information is presently lacking in the existing literature. The second objective of this research is to determine if the instability in momentum-driven, low-density jets is caused by buoyancy. At these conditions, the buoyancy effects are commonly ignored because of the small Richardson based on global parameters. By eliminating buoyancy in our experiments, globally as well as locally, we seek to examine the possibility that the instability mechanism in self-excited, buoyant or momentum-driven jets is the same. To meet this objective, we would quantify the jet flow in normal and microgravity, while systematically decreasing the Richardson number from buoyancy-driven to momentum driven flow regime. The third objective of this research is to perform a linear stability analysis of low-density gas jets by including the gravitational effects. The flow oscillations in these jets are attributed to an absolute instability, whereby the disturbance grows exponentially at the site to ultimately contaminate the entire flow field. We seek to study the characteristics of both convective and absolute instabilities and demarcate the boundary between them.

Agrawal A. K.↗

Rapid adaptation to Coriolis force perturbations of arm trajectory

1. Forward reaching movements made during body rotation generate tangential Coriolis forces that are proportional to the cross product of the angular velocity of rotation and the linear velocity of the arm. Coriolis forces are inertial forces that do not involve mechanical contact. Virtually no constant centrifugal forces will be present in the background when motion of the arm generates transient Coriolis forces if the radius of body rotation is small. 2. We measured the trajectories of arm movements made in darkness to a visual target that was extinguished as movement began. The reaching movements were made prerotation, during rotation at 10 rpm in a fully enclosed rotating room, and postrotation. During testing the subject was seated at the center of the room and pointed radially. Neither visual nor tactile feedback about movement accuracy was present. 3. In experiment 1, subjects reached at a fast or slow rate and their hands made contact with a horizontal surface at the end of the reach. Their initial perrotary movements were highly significantly deviated relative to prerotation in both trajectories and end-points in the direction of the transient Coriolis forces that had been generated during the reaches. Despite the absence of visual and tactile feedback about reaching accuracy, all subjects rapidly regained straight movement trajectories and accurate endpoints. Postrotation, transient errors of opposite sign were present for both trajectories and endpoints. 4. In a second experiment the conditions were identical except that subjects pointed just above the location of the extinguished target so that no surface contact was involved. All subjects showed significant initial perrotation deviations of trajectories and endpoints in the direction of the transient Coriolis forces. With repeated reaches the trajectories, as viewed from above, again became straight, but there was only partial restoration of endpoint accuracy, so that subjects reached in a straight line to the wrong place. Aftereffects of opposite sign were transiently present in the postrotary movements. 5. These observations fail to support current equilibrium point models, both alpha and lambda, of movement control. Such theories would not predict endpoint errors under our experimental conditions, in which the Coriolis force is absent at the beginning and end of a movement. Our results indicate that detailed aspects of movement trajectory are being continuously monitored on the basis of proprioceptive feedback in relation to motor commands. Adaptive compensations can be initiated after one perturbation despite the absence of either visual or tactile feedback about movement trajectory and endpoint error. Moreover, movement trajectory and end-point can be remapped independently.(ABSTRACT TRUNCATED AT 400 WORDS).

Non-NASA Center↗