Using Java for distributed computing in the Gaia satellite data processing

In recent years Java has matured to a stable easy-to-use language with the flexibility of an interpreter (for reflection etc.) but the performance and type checking of a compiled language. When we started using Java for astronomical applications around 1999 they were the first of their kind in astronomy. Now a great deal of astronomy software is written in Java as are many business applications. We discuss the current environment and trends concerning the language and present an actual example of scientific use of Java for high-performance distributed computing: ESA’s mission Gaia. The Gaia scanning satellite will perform a galactic census of about 1,000 million objects in our galaxy. The Gaia community has chosen to write its processing software in Java. We explore the manifold reasons for choosing Java for this large science collaboration. Gaia processing is numerically complex but highly distributable, some parts being embarrassingly parallel. We describe the Gaia processing architecture and its realisation in Java. We delve into the astrometric solution which is the most advanced and most complex part of the processing. The Gaia simulator is also written in Java and is the most mature code in the system. This has been successfully running since about 2005 on the supercomputer “Marenostrum” in Barcelona. We relate experiences of using Java on a large shared machine. Finally we discuss Java, including some of its problems, for scientific computing.     

Evidence for long‐term site fidelity of snapper (Pagrus auratus) within a marine reserve

Increases in the density of exploited species on unfished reefs logically implies that some individuals are at least temporarily resident, or show fidelity to a particular area. We tagged snapper (Pagrus auratus (Bloch & Schneider 1801)) in the Leigh Marine Reserve, New Zealand using visible implant fluorescent elastomer tags, recoverable by diver visual sightings without the need to recapture the fish. Batch tagging of snapper (n = 907) was done during an angling survey in June and December 1996, and individually coded tags were implanted by divers (n = 117) in January 1999. Snapper tagged during both programmes were recovered on irregular intervals from 1997 to 2000. There were 71 recoveries of batch tags within 500 m of their tagging sites, and these recoveries were still being made >3 years after tagging: Of individually coded fish, 49 (42%) were seen, sometimes repeatedly over several months, close to their respective tagging sites. These observations included snapper as small as 23 cm fork length, contradicting the commonly held impression that only large snapper take up long‐term residency on reefs. This preliminary evidence suggests that some snapper exhibit site fidelity to areas only a few hundred metres wide, and in the absence of fishing may occupy the same area for years.     

The influence of habitat availability on juvenile fish abundance in a northeastern New Zealand estuary

Management of fish populations is often focused on the exploitation of adult fish. Maintaining the habitat requirements of all life stages may also be an important consideration. We investigated the value of structured habitat to juvenile fishes within a northeastern New Zealand harbour using artificial seagrass units (ASUs). Specifically, we deployed ASUs across treatments with high vs. low habitat manipulations. We hypothesised that if the abundance of recruiting juvenile fishes was greater on the high habitat availability treatments this would suggest that the availability of habitat was limiting juvenile fish abundance. Our analyses were focused on the four most abundant fishes that settled on our ASUs: snapper (Pagrus auratus); spotty (Notolabrus celidotus); trevally (Pseudocaranx dentex); and an assemblage of pipefish species. For snapper, spotty and pipefish, abundance was greater on the high habitat availability treatments. This result would be unlikely to occur if the availability of juvenile fishes was limiting, suggesting that juvenile fish abundance is more likely to be limited by habitat. In terms of spatial gradients, spotty abundance and size increased with distance into the harbour. The spatial gradient present for spotty indicates the importance of placing the habitat dependency of juvenile fish into a landscape context. Overall, these results demonstrate that maintaining structured habitats may be an important consideration for some valuable inshore fish populations in northeastern New Zealand.     

Snapper (Chrysophrys auratus): a review of life history and key vulnerabilities in New Zealand

Snapper (Chrysophrys auratus) is an important coastal fish species in New Zealand for a variety of reasons, but the large amount of research conducted on snapper has not been reviewed. Here, we review life history information and potential threats for snapper in New Zealand. We present information on snapper life history, defining stages (eggs and larvae, juvenile and adult), and assess potential threats and knowledge gaps. Overall we identify six key points: 1. post-settlement snapper are highly associated with certain estuarine habitats that are under threat from land-based stressors. This may serve as a bottleneck for snapper populations; 2. the largest knowledge gaps relate to the eggs and larvae. Additional knowledge may help to anticipate the effects of climate change, which will likely have the greatest influence on these early life stages; 3. ocean acidification, from land-based sources and from climate change, may be an important threat to larval snapper; 4. a greater understanding of population connectivity would improve certainty around the sustainability of fishery exploitation; 5. the collateral effects of fishing are likely to be relevant to fishery productivity, ecosystem integrity and enduser value; 6. our understanding of the interrelationships between snapper and other ecosystem components is still deficient.     

METHODOLOGY: A SIMPLE RAINFALL SIMULATOR AND TRICKLE SYSTEM FOR HYDRO-GEOMORPHOLOGICAL EXPERIMENTS

A simple rainfall simulator is described which consists of stand-alone sprinkling units with cone jet nozzles that spray downward. With a fall height of 4.57 m and water pressure of 67 kPa, the median drop size of the simulated rainfall is 2.40 mm. Rainfall from two units irrigating a 2 by 2.5 m plot has a total kinetic energy of 0.57 J/m²/s which is approximately 90% of the equivalent energy of natural rainfall at the simulation intensity of 72.4 mm/h. To simulate overland flow, perforated trickle pipes were designed that permit overland flow rates to be readily adjusted and closely controlled by simply varying the input water pressure. In field experiments in southern Arizona, rates between 572 to 1400 cm³/s were generated from a 19-mm pipe. Given their low cost, simplicity, and portability, the rainfall simulator and trickle system should be attractive to researchers working in a wide variety of geomorphic environments.     

Direct characterization of airborne particles associated with arsenic-rich mine tailings: Particle size,mineralogy and texture

Windblown and vehicle-raised dust from unvegetated mine tailings can be a human health risk. Airborne particles from As-rich abandoned Au mine tailings from Nova Scotia, Canada have been characterized in terms of particle size, As concentration, As oxidation state, mineral species and texture. Samples were collected in seven aerodynamically fractionated size ranges (0.5–16 μm) using a cascade impactor deployed at three tailings fields. All three sites are used for recreational activities and off-road vehicles were racing on the tailings at two mines during sample collection. Total concentrations of As in the <8 μm fraction varied from 65 to 1040 ng/m³ of air as measured by proton-induced X-ray emission (PIXE) analysis. The same samples were analysed by synchrotron-based microfocused X-ray absorption near-edge spectroscopy (μXANES) and X-ray diffraction (μXRD) and found to contain multiple As-bearing mineral species, including Fe–As weathering products. The As species present in the dust were similar to those observed in the near-surface tailings. The action of vehicles on the tailings surface may disaggregate material cemented with Fe arsenate and contribute additional fine-grained As-rich particles to airborne dust. Results from this study can be used to help assess the potential human health risks associated with exposure to airborne particles from mine tailings.     

An experimental study of discharge partitioning and flow structure at symmetrical bifurcations

Recent research has examined the factors controlling the geometrical configuration of bifurcations, determined the range of stability conditions for a number of bifurcation types and assessed the impact of perturbations on bifurcation evolution. However, the flow division process and the parameters that influence flow and sediment partitioning are still poorly characterized. To identify and isolate these parameters, three‐dimensional velocities were measured at 11 cross‐sections in a fixed‐walled experimental bifurcation. Water surface gradients were controlled, and systematically varied, using a weir in each distributary. As may be expected, the steepest distributary conveyed the most discharge (was dominant) while the mildest distributary conveyed the least discharge (was subordinate). A zone of water surface super‐elevation was co‐located with the bifurcation in symmetric cases or displaced into the subordinate branch in asymmetric cases. Downstream of a relatively acute‐angled bifurcation, primary velocity cores were near to the water surface and against the inner banks, with near‐bed zones of lower primary velocity at the outer banks. Downstream of an obtuse‐angled bifurcation, velocity cores were initially at the outer banks, with near‐bed zones of lower velocities at the inner banks, but patterns soon reverted to match the acute‐angled case. A single secondary flow cell was generated in each distributary, with water flowing inwards at the water surface and outwards at the bed. Circulation was relatively enhanced within the subordinate branch, which may help explain why subordinate distributaries remain open, may play a role in determining the size of commonly‐observed topographic features, and may thus exert some control on the stability of asymmetric bifurcations. Further, because larger values of circulation result from larger gradient disadvantages, the length of confluence–diffluence units in braided rivers or between diffluences within delta distributary networks may vary depending upon flow structures inherited from upstream and whether, and how, they are fed by dominant or subordinate distributaries. Copyright © 2011 John Wiley & Sons, Ltd.     

Competing Perceptions of the Rural Idyll: responses to threats from coal seam gas development in Gloucester,NSW, Australia

Threats to rural livelihoods and rural landscapes have increased over time as developed nations in particular look for cheaper and more locally based alternatives to traditional energy sources to drive national economies. In New South Wales, through the expansion of coal mines and coal seam gas (CSG), small towns such as Gloucester on the edge of the Upper Hunter are faced with competing visions which seek to redefine their future. Powerful and competing discourses over land use threaten not only the sustainability of the region but the integrity of its sense of place, centred on community, rurality, agricultural production and confrontation of risk from mining. The different discourses of local groups such as ‘tree-changers’, established residents and farmers conflict with those of external organisations such as the State government and mining/CSG companies which envisage Gloucester as a ‘balanced’ space of co-existence and position it as a new node in the carbon supply chain.     

Eight-phase alkali feldspars: low-temperature cryptoperthite, peristerite and multiple replacement reactions in the Klokken intrusion

Eight feldspar phases have been distinguished within individual alkali feldspar primocrysts in laminated syenite members of the layered syenite series of the Klokken intrusion. The processes leading to the formation of the first four phases have been described previously. The feldspars crystallized as homogeneous sodian sanidine and exsolved by spinodal decomposition, between 750 and 600 °C, depending on bulk composition, to give fully coherent, strain-controlled braid cryptoperthites with sub-μm periodicities. Below ~500 °C, in the microcline field, these underwent a process of partial mutual replacement in a deuteric fluid, producing coarse (up to mm scale), turbid, incoherent patch perthites. We here describe exsolution and replacement processes that occurred after patch perthite formation. Both Or- and Ab-rich patches underwent a new phase of coherent exsolution by volume diffusion. Or-rich patches began to exsolve albite lamellae by coherent nucleation in the range 460–340 °C, depending on patch composition, leading to film perthite with ≤1 μm periodicities. Below ~300 °C, misfit dislocation loops formed, which were subsequently enlarged to nanotunnels. Ab-rich patches (bulk composition ~Ab₉₁Or₁An₈), in one sample, exsolved giving peristerite, with one strong modulation with a periodicity of ~17 nm and a pervasive tweed microtexture. The Ab-rich patches formed with metastable disorder below the peristerite solvus and intersected the peristerite conditional spinodal at ~450 °C. This is the first time peristerite has been imaged using TEM within any perthite, and the first time peristerite has been found in a relatively rapidly cooled geological environment. The lamellar periodicities of film perthite and peristerite are consistent with experimentally determined diffusion coefficients and a calculated cooling history of the intrusion. All the preceding textures were in places affected by a phase of replacement correlating with regions of extreme optical turbidity. We term this material ultra porous late feldspar (UPLF). It is composed predominantly of regions of microporous very Or-rich feldspar (mean Ab_2.5Or_97.4An_0.1) associated with very pure porous albite (Ab_97.0Or_1.6An_1.4) implying replacement below 170–90 °C, depending on degree of order. In TEM, UPLF has complex, irregular diffraction contrast similar to that previously associated with low-temperature albitization and diagenetic overgrowths. Replacement by UPLF seems to have been piecemeal in character. Ghost-like textural pseudomorphs of both braid and film parents occur. Formation of patch perthite, film perthite and peristerite occurred 10⁴–10⁵ year after emplacement, but there are no microtextural constraints on the age of UPLF formation.     

Do agonistic behaviours bias baited remote underwater video surveys of fish?

Marine environments require monitoring to determine the effects of impacts such as climate change, coastal development and pollution and also to assess the effectiveness of conservation measures. Marine protected areas (MPAs) are being established globally and require periodic monitoring to determine whether their objectives are being met. Baited underwater video systems are becoming a popular method for monitoring change within protected fish populations, because they are less damaging to habitats than bottom trawling and allow for more statistical powerful comparisons to determine spatial and temporal patterns in the relative abundances, lengths and biomass of demersal and pelagic fishes. However, much remains uncertain about how interactions between the fish and bait and between the fish themselves affect the results obtained. Agonistic behaviours are frequently observed around the bait of the camera and potentially bias fish density estimates by altering the number and size classes seen at cameras. Here we counted the number of agonistic behaviours between pink snappers (Pagrus auratus), the size of fish involved and whether the fish left the field of view following such behaviours. The study consisted of 20 baited underwater video deployments inside a New Zealand marine reserve and 20 in adjacent open areas. We observed a significant relationship between the peak number of fish observed at the camera and the total number of agonistic behaviours, as well as the number of both aggressor and subordinate fish leaving the camera field of view following interactions. The slope of the latter relationship and thus the absolute numbers of fish leaving were higher for subordinate fish. As subordinates were significantly smaller than aggressors, the apparent size frequency distribution is likely skewed away from smaller size classes. The staying time of the fish and thus the maximum number of fish present at the camera will be reduced by agonistic behaviours and the absolute magnitude of this effect appears to be greater at high fish densities. Our results suggest that an overall effect of these phenomena is to underestimate the differences in abundance between MPAs and open areas, but also to overestimate differences in average size.