Mesh traversal and sorting for efficient memory usage in scientific codes

Applications that operate on meshes are very popular in High Performance Computing (HPC) environments. In the past, many techniques have been developed in order to optimize the memory accesses for these datasets. Different loop transformations and domain decompositions are com- monly used for structured meshes. However, unstructured grids are more challenging. The memory accesses, based on the mesh connectivity, do not map well to the usual lin- ear memory model. This work presents a method to improve the memory performance which is suitable for HPC codes that operate on meshes. We develop a method to adjust the sequence in which the data are used inside the algorithm, by means of traversing and sorting the mesh. This sorted mesh can be transferred sequentially to the lower memory levels and allows for minimum data transfer requirements. The method also reduces the lower memory requirements dra- matically: up to 63% of the L1 cache misses are removed in a traditional cache system. We have obtained speedups of up to 2.58 on memory operations as measured in a general- purpose CPU. An improvement is also observed with se- quential access memories, where we have observed reduc- tions of up to 99% in the required low-level memory size.

Unravelling past flash flood activity in a forested mountain catchment of the Spanish Central System

Flash floods represent one of the most common natural hazards in mountain catchments, and are frequent in Mediterranean environments. As a result of the widespread lack of reliable data on past events, the understanding of their spatio-temporal occurrence and their climatic triggers remains rather limited. Here, we present a dendrogeomorphic reconstruction of past flash flood activity in the Arroyo de los Puentes stream (Sierra de Guadarrama, Spanish Central System). We analyze a total of 287 increment cores from 178 disturbed Scots pine trees (Pinus sylvestris L.) which yielded indications on 212 growth disturbances related to past flash flood impact. In combination with local archives, meteorological data, annual forest management records and highly-resolved terrestrial data (i.e., LiDAR data and aerial imagery), the dendrogeomorphic time series allowed dating 25 flash floods over the last three centuries, with a major event leaving an intense geomorphic footprint throughout the catchment in 1936. The analysis of meteorological records suggests that the rainfall thresholds of flash floods vary with the seasonality of events. Dated flash floods in the 20th century were primarily related with synoptic troughs owing to the arrival of air masses from north and west on the Iberian Peninsula during negative indices of the North Atlantic Oscillation. The results of this study contribute considerably to a better understanding of hazards related with hydrogeomorphic processes in central Spain in general and in the Sierra de Guadarrama National Park in particular.

Changes in Petrophysical Properties of the Stone Surface due to Past Conservation Treatments in Archaeological Sites of Merida (Spain)

Petrophysical properties, such as porosity, permeability, density or anisotropy de-termine the alterability of stone surfaces from archaeological sites, and therefore, the future preservation of the material. Others, like superficial roughness or color, may point out changes due to alteration processes, natural or man-induced, for ex-ample, by conservation treatments. The application of conservation treatments may vary some of these properties forcing the stone surface to a re-adaptation to the new conditions, which could generate new processes of deterioration. In this study changes resulting from the application of consolidating and hydrophobic treatments on stone materials from the Roman Theatre (marble and granite) and the Mitreo’s House (mural painting and mosaics), both archaeological sites from Merida (Spain), are analyzed. The use of portable field devices allows us to perform analyses both on site and in la-boratory, comparing treated and untreated samples. Treatments consisted of syn-thetic resins, consolidating (such as tetraethoxysilane TEOS) and hydrophobic products. Results confirm that undesirable changes may occur, with consequences ranging from purely aesthetic variations to physical, chemical and mechanical damages. This also permits us to check limitations in the use of these techniques for the evaluation of conservation treatments.

Analysis of air flow past and through the 2415-3S airfoil for an unmanned aerial vehicle with internal propulsion system

This paper deals with the prediction of velocity fields on the 2415-3S airfoil which will be used for an unmanned aerial vehicle with internal propulsion system and in this way analyze the air flow through an internal duct of the airfoil using computational fluid dynamics. The main objective is to evaluate the effect of the internal air flow past the airfoil and how this affects the aerodynamic performance by means of lift and drag forces. For this purpose, three different designs of the internal duct were studied; starting from the base 2415-3S airfoil developed in previous investigation, basing on the hypothesis of decreasing the flow separation produced when the propulsive airflow merges the external flow, and in this way obtaining the best configuration. For that purpose, an exhaustive study of the mesh sensitivity was performed. It was used a non-structured mesh since the computational domain is three-dimensional and complex. The selected mesh contains approximately 12.5 million elements. Both the computational domain and the numerical solution were made with commercial CAD and CFD software, respectively. Air, incompressible and steady was analyzed. The boundary conditions are in concordance with experimental setup in the AF 6109 wind tunnel. The k-e model is utilized to describe the turbulent flow process as followed in references. Results allowed obtaining velocity contours as well as lift and drag coefficients and also the location of separation and reattachment regions in some cases for zero degrees of angle of attack on the internal and external surfaces of the airfoil. Finally, the selection of the configuration with the best aerodynamic performance was made, selecting the option without curved baffles.

Numerical analysis of air flow past the 2415-3S airfoil for an unmanned aerial vehicle with internal propulsion system

This paper deals with the prediction of pressure and velocity fields on the 2415-3S airfoil which will be used for and unmanned aerial vehicle with internal propulsion system and in this way analyze the air flow through an internal duct of the airfoil using computational fluid dynamics. The main objective is to evaluate the effect of the internal air flow past the airfoil and how this affects the aerodynamic performance by means of lift and drag forces. For this purpose, three different designs of the internal duct were studied; starting from the base 2415-3S airfoil developed in previous investigation, basing on the hypothesis of decreasing the flow separation produced when the propulsive airflow merges the external flow, and in this way obtaining the best configuration. For that purpose, an exhaustive study of the mesh sensitivity was performed. It was used a non-structured mesh since the computational domain is tridimensional and complex. The selected mesh contains approximately 12.5 million elements. Both the computational domain and the numerical solution were made with commercial CAD and CFD software respectively. Air, incompressible and steady was analyzed. The boundary conditions are in concordance with experimental setup in the AF 6109 wind tunnel. The k-ε model is utilized to describe the turbulent flow process as followed in references. Results allowed obtaining pressure and velocity contours as well as lift and drag coefficients and also the location of separation and reattachment regions in some cases for zero degrees of angle of attack on the internal and external surfaces of the airfoil. Finally, the selection of the configuration with the best aerodynamic performance was made, selecting the option without curved baffles.

Is the present the key to the past? : A global characterization of modern sedimentary basins

Date of Acceptance: 06/05/2015 We thank the FORCE Consortium for funding this research, Rob Butler and Walter Wheeler for quality control on the global basin classification, and David MacDonald for reviewing an earlier draft of this manuscript. We also thank Gary Weissmann, Andrew Miall, Raymond Ingersoll, John Holbrook, Stephen Flint, and editor Ellen Thomas for their constructive reviews.

Stream biodiversity: The ghost of land use past

The influence of past land use on the present-day diversity of stream invertebrates and fish was investigated by comparing watersheds with different land-use history. Whole watershed land use in the 1950s was the best predictor of present-day diversity, whereas riparian land use and watershed land use in the 1990s were comparatively poor indicators. Our findings indicate that past land-use activity, particularly agriculture, may result in long-term modifications to and reductions in aquatic diversity, regardless of reforestation of riparian zones. Preservation of habitat fragments may not be sufficient to maintain natural diversity in streams, and maintenance of such biodiversity may require conservation of much or all of the watershed.

Lessons from the past: Evolutionary impacts of mass extinctions

Mass extinctions have played many evolutionary roles, involving differential survivorship or selectivity of taxa and traits, the disruption or preservation of evolutionary trends and ecosystem organization, and the promotion of taxonomic and morphological diversifications—often along unexpected trajectories—after the destruction or marginalization of once-dominant clades. The fossil record suggests that survivorship during mass extinctions is not strictly random, but it often fails to coincide with factors promoting survival during times of low extinction intensity. Although of very serious concern, present-day extinctions have not yet achieved the intensities seen in the Big Five mass extinctions of the geologic past, which each removed ≥50% of the subset of relatively abundant marine invertebrate genera. The best comparisons for predictive purposes therefore will involve factors such as differential extinction intensities among regions, clades, and functional groups, rules governing postextinction biotic interchanges and evolutionary dynamics, and analyses of the factors that cause taxa and evolutionary trends to continue unabated, to suffer setbacks but resume along the same trajectory, to survive only to fall into a marginal role or disappear (“dead clade walking”), or to undergo a burst of diversification. These issues need to be addressed in a spatially explicit framework, because the fossil record suggests regional differences in postextinction diversification dynamics and biotic interchanges. Postextinction diversifications lag far behind the initial taxonomic and morphological impoverishment and homogenization; they do not simply reoccupy vacated adaptive peaks, but explore opportunities as opened and constrained by intrinsic biotic factors and the ecological and evolutionary context of the radiation.

Lessons from the past: Biotic recoveries from mass extinctions

Although mass extinctions probably account for the disappearance of less than 5% of all extinct species, the evolutionary opportunities they have created have had a disproportionate effect on the history of life. Theoretical considerations and simulations have suggested that the empty niches created by a mass extinction should refill rapidly after extinction ameliorates. Under logistic models, this biotic rebound should be exponential, slowing as the environmental carrying capacity is approached. Empirical studies reveal a more complex dynamic, including positive feedback and an exponential growth phase during recoveries. Far from a model of refilling ecospace, mass extinctions appear to cause a collapse of ecospace, which must be rebuilt during recovery. Other generalities include the absence of a clear correlation between the magnitude of extinction and the pace of recovery or the resulting ecological and evolutionary disruption the presence of a survival interval, with few originations, immediately after an extinction and preceding the recovery phase, and the presence of many lineages that persist through an extinction event only to disappear during the subsequent recovery. Several recoveries include numerous missing lineages, groups that are found before the extinction, then latter in the recovery, but are missing during the initial survival–recovery phase. The limited biogeographic studies of recoveries suggest considerable variability between regions.

Peopling the past: New perspectives on the ancient Maya

The new direction in Maya archaeology is toward achieving a greater understanding of people and their roles and their relations in the past. To answer emerging humanistic questions about ancient people's lives Mayanists are increasingly making use of new and existing scientific methods from archaeology and other disciplines. Maya archaeology is bridging the divide between the humanities and sciences to answer questions about ancient people previously considered beyond the realm of archaeological knowledge.

The past and the future fate of the universe and the formation of structure in it

The history and the ultimate future fate of the universe as a whole depend on how much the expansion of the universe is decelerated by its own mass. In particular, whether the expansion of the universe will ever come to a halt can be determined from the past expansion. However, the mass density in the universe does not only govern the expansion history and the curvature of space, but in parallel also regulates the growth of hierarchical structure, including the collapse of material into the dense, virialized regions that we identify with galaxies. Hence, the formation of galaxies and their clustered distribution in space depend not only on the detailed physics of how stars are formed but also on the overall structure of the universe. Recent observational efforts, fueled by new large, ground-based telescopes and the Hubble Space Telescope, combined with theoretical progress, have brought us to the verge of determining the expansion history of the universe and space curvature from direct observation and to linking this to the formation history of galaxies.

Characteristics of the deep ocean carbon system during the past 150,000 years: ΣCO2 distributions, deep water flow patterns, and abrupt climate change

Studies of carbon isotopes and cadmium in bottom-dwelling foraminifera from ocean sediment cores have advanced our knowledge of ocean chemical distributions during the late Pleistocene. Last Glacial Maximum data are consistent with a persistent high-ΣCO2 state for eastern Pacific deep water. Both tracers indicate that the mid-depth North and tropical Atlantic Ocean almost always has lower ΣCO2 levels than those in the Pacific. Upper waters of the Last Glacial Maximum Atlantic are more ΣCO2-depleted and deep waters are ΣCO2-enriched compared with the waters of the present. In the northern Indian Ocean, δ13C and Cd data are consistent with upper water ΣCO2 depletion relative to the present. There is no evident proximate source of this ΣCO2-depleted water, so I suggest that ΣCO2-depleted North Atlantic intermediate/deep water turns northward around the southern tip of Africa and moves toward the equator as a western boundary current. At long periods (>15,000 years), Milankovitch cycle variability is evident in paleochemical time series. But rapid millennial-scale variability can be seen in cores from high accumulation rate series. Atlantic deep water chemical properties are seen to change in as little as a few hundred years or less. An extraordinary new 52.7-m-long core from the Bermuda Rise contains a faithful record of climate variability with century-scale resolution. Sediment composition can be linked in detail with the isotope stage 3 interstadials recorded in Greenland ice cores. This new record shows at least 12 major climate fluctuations within marine isotope stage 5 (about 70,000–130,000 years before the present).