FLASH is a publicly available high performance application code which has evolved into a modular, extensible software system from a collection of unconnected legacy codes. FLASH has been successful because its capabilities have been driven by the needs of scientific applications, without compromising maintainability, performance, and usability. In its newest incarnation, FLASH3 consists of inter-operable modules that can be combined to generate different applications. The FLASH architecture allows arbitrarily many alternative implementations of its components to co-exist and interchange with each other, resulting in greater flexibility. Further, a simple and elegant mechanism exists for customization of code functionality without the need to modify the core implementation of the source. A built-in unit test framework providing verifiability, combined with a rigorous software maintenance process, allow the code to operate simultaneously in the * Corresponding author dual mode of production and development. In this paper we describe the FLASH3 architecture, with emphasis on solutions to the more challenging conflicts arising from solver complexity, portable performance requirements, and legacy codes. We also include results from user surveys conducted in 2005 and 2007, which highlight the success of the code.
We uscil molecular sequence data from the tuiclear ribosonial inlernal Iranscribed spacers and from the inlron and spacer of the (niL'trnV chloroplast region to study phylogenelic relationships within the large (ca. 2(KKJ species), wideranging, and taxonomically difficult tribe Justici(\ie (Acanthaceae). The partition homogeneity test indicated tlial the data sets for the two loci were congnient, and sejiarate analyses of the two gave similar results. Analysis of the combined data set [)rovitles a highly resolved hypothesis of relationships, much of it strongly sup[)()rted. Justicieae are strongly supported as monopliyletic; within the tribe, five lineages and one parajjli)letic grade are related as follows: \Pseuderanthemum lineage (Isoglossinae [Teiramcrium lineage [multijih* clades of Old World "justicioids" (Dichpterinae + New World "justicioids")]})]. Many aspects of this phvlogenetic hypothesis are supported by data from morphology and cytology, and some conform to earlier classifications of the grou[). There are, however, a number of novel aspects. Notably, the large genus Juslicia (ca, 700 species) is not monophylctic; the Old World members form a grade and the New World members are monophylctic only if a number of odier genera are included. The very strongly supported sister-group rehitionship between Dichpterinae and the New World "justicioid" lineage is novel, and we cannot identify non-molecular synapornorphies to confirm this relali(niship. Rliindcanllius. a "juslicioid'' {Justuia and mor])hol(>gica]ly similar genera) by all but ph}logenclic criteria, is strongly supported as a basal member of Diclipterinae, and cytological evidence confirms this placement. The Pscuderanlheriiufii lineage is only modestly supported as monophylctic and may, in fact, represent a series of basal bneages. These plants an^ marked by having four staminal elements (four stamens or two stamens plus two staminod**s). a plesiomor[)hic condition for all Acanthaceae. Additional evidence (bolli laxa and characters) will be necessary' to resolve this uncertainty, as well as to determine die phylogenetic status of Old World "justlcioitls." Our analysis does provide considerable resolutujn of relationships within mono|)liyletic lineages, and these relationships are discussed in the context of non-molecular evidcnice and previous classifications.
Recent Chandra and XMM-Newton observations of galaxy cluster cooling flows have revealed X-ray emission voids of up to 30 kpc in size that have been identified with buoyant, magnetized bubbles. Motivated by these observations, we have investigated the behavior of rising bubbles in stratified atmospheres using the Flash adaptive-mesh simulation code. We present results from 2-D simulations with and without the effects of magnetic fields, and with varying bubble sizes and background stratifications. We find purely hydrodynamic bubbles to be unstable; a dynamically important magnetic field is required to maintain a bubble's integrity. This suggests that, even absent thermal conduction, for bubbles to be persistent enough to be regularly observed, they must be supported in large part by magnetic fields. Thermal conduction unmitigated by magnetic fields can dissipate the bubbles even faster. We also observe that the bubbles leave a tail as they rise; the structure of these tails can indicate the history of the dynamics of the rising bubble.
We look in detail at the process of mapping an astrophysical initial model from a stellar evolution code onto the computational grid of an explicit, Godunov type code while maintaining hydrostatic equilibrium. This mapping process is common in astrophysical simulations, when it is necessary to follow short-timescale dynamics after a period of long timescale buildup. We look at the effects of spatial resolution, boundary conditions, the treatment of the gravitational source terms in the hydrodynamics solver, and the initialization process itself. We conclude with a summary detailing the mapping process that yields the lowest ambient velocities in the mapped model.Comment: 59 pages, 21 figures, accepted to ApJS. Some figures are degraded for size constraint
Developing and tuning computational science applications to run on extreme scale systems are increasingly complicated processes. Challenges such as managing memory access and tuning message-passing behavior are made easier by tools designed specifically to aid in these processes. Tools that can help users better understand the behavior of their application with respect to I/O have not yet reached the level of utility necessary to play a central role in application development and tuning. This deficiency in the tool set means that we have a poor understanding of how specific applications interact with storage. Worse, the community has little knowledge of what sorts of access patterns are common in today's applications, leading to confusion in the storage research community as to the pressing needs of the computational science community. This paper describes the Darshan I/O characterization tool. Darshan is designed to capture an accurate picture of application I/O behavior, including properties such as patterns of access within files, with the minimum possible overhead. This characterization can shed important light on the I/O behavior of applications at extreme scale. Darshan also can enable researchers to gain greater insight into the overall patterns of access exhibited by such applications, helping the storage community to understand how to best serve current computational science applications and better predict the needs of future applications. In this work we demonstrate Darshan's ability to characterize the I/O behavior of four scientific applications and show that it induces negligible overhead for I/O intensive jobs with as many as 65,536 processes.
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