Parallel implementations of streamline simulators

We discuss various strategies for parallelizing streamline simulators and present a single-phase shared memory implementation. The choice of a shared memory programming model is motivated by its suitability for streamline simulation, as well as the rapid advance of multicore processors, which are readily available at low-cost. We show that streamline-based methods are easily parallelizable on shared memory architectures through their decomposition of the multidimensional transport equations into a large set of independent 1D transport solves. We tested both a specialized explicit load balancing algorithm that optimizes the streamline load distribution across threads to minimize the time that any of the threads are idle, and the dynamic load balancing algorithms provided by OpenMP on the shared memory machines. Our results clearly indicate that built-in schedulers are competitive with specialized load balancing strategies as long as the number of streamlines per thread is sufficiently high, which is the case in field applications. The average workload per thread is nominally insensitive to workload variations between individual streamlines, and any load balancing advantage offered by explicit strategies is not sufficient to overcome associated computational and parallel overhead. In terms of the allocation of streamlines or streamline segments to threads, we investigated both the distributed approach, in which threads are assigned streamline segments, and the owner approach, in which threads own complete streamlines. We found that the owner approach is most suitable. The slight advantage that the distributed approach has in terms of load balancing is not enough to compensate for the additional overheads. Moreover, the owner approach allows straightforward re-use of existing sequential codes, which is not the case for the distributed approach in case of implicit or adaptive implicit solution strategies. The tracing and mapping stages in streamline simulation have low parallel efficiency. However, in real-field models, the computational burden of the streamline solves is significantly heavier than that of the tracing and mapping stages, and therefore, the impact of these stages is limited. We tested the parallelization on three shared memory systems: a 24 dual-core processor Sun SPARC server; an eight-way Sun Opteron server, representative of the state-of-the-art shared memory systems in use in the industry; and the very recently released Sun Niagara II multicore machine that has eight floating point compute units on the chip. We test a single-phase flow problem on three heterogeneous reservoirs with varying well placements (this system gives the worst case scenario as the tracing and mapping costs are not negligible compared to the transport costs). For the SPARC and Opteron system, we find parallel efficiencies ranging between 60 and 75 for the tracer flow problems. The sublinear speedup is mostly due to communication overheads in the tracing and mapping stages. In applications with more complex physics, the relative contributions of these stages will decrease significantly, and we predict the parallel performance to be nearly linear. On the Niagara II, we obtain almost perfect linear scalability even for the single-phase flow problem thanks to the lowered communication costs on these architectures that have a shared cache. This result is all the more satisfactory considering that future server designs will be akin to this system.     

Effect on marine sediment nitrogen fluxes caused by organic matter enrichment with varying organic carbon structure and nitrogen content

Enrichments with five types of organic carbon, differing in nitrogen content and type of organic carbon, were made to a marine sediment in order to study effects on nitrogen fluxes. The enrichments used were Ulva lactuca, Ascophyllum nodosum, Zostera marina, Ceratium spp., lignin, and mixtures of U. lactuca and A. nodosum. Fluxes of ammonium, nitrate, and phosphate were measured in short-term (48 h) microcosm experiments, using a carbon enrichment loading similar to that at the sampling site. Changes in microbial community growth and structure due to three types enrichments were also detected using molecular methods in a microcosm experiment run for 4 days to allow for detection at DNA-level.Ammonium fluxes changed from an efflux in the control to an influx for all enrichments apart from U. lactuca. The change was significantly related to the added material's C:N ratio when Ceratium spp. was excluded. All enrichments induced an influx of nitrate suggesting the formation of anoxic micro zones, but there was no relationship with C:N ratio. Instead, the magnitude of the nitrate influx is suggested to be related to the structure of the organic carbon, where enrichments containing a large pool of cellulose and lignin (Z. marina and lignin) gave rise to a lower influx, compared to algal material with more easily degraded organic matter like lipids and starch, which induced the highest influx of nitrate (Ceratium spp., U. lactuca, and A. nodosum). The occurrence of an ammonium influx together with increased nitrate influx and a lower efflux of phosphate in the enrichments suggests a growth of heterotrophic bacteria. This was also confirmed using molecular methods (PCR-DGGE) where the relative abundance of bacterial species in the enrichments increased.The sum of ammonium and nitrate fluxes showed that total nitrogen removal was enhanced in all enrichments compared to the nonenriched control sediment, but in different ways. Ceratium spp. induced the highest removal followed by A. nodosum, U. lactuca, Z. marina, and lastly, by lignin. The same pattern was observed also in a second experiment. These results indicate that easily degradable organic carbon, together with a lower C:N ratio of the added material, will remove nitrogen from the water phase, making the recycling of nitrogen to the overlying water mass smaller.     

Skill assessment of three earth system models with common marine biogeochemistry

We have assessed the ability of a common ocean biogeochemical model, PISCES, to match relevant modern data fields across a range of ocean circulation fields from three distinct Earth system models: IPSL-CM4-LOOP, IPSL-CM5A-LR and CNRM-CM5.1. The first of these Earth system models has contributed to the IPCC 4th assessment report, while the latter two are contributing to the ongoing IPCC 5th assessment report. These models differ with respect to their atmospheric component, ocean subgrid-scale physics and resolution. The simulated vertical distribution of biogeochemical tracers suffer from biases in ocean circulation and a poor representation of the sinking fluxes of matter. Nevertheless, differences between upper and deep ocean model skills significantly point to changes in the underlying model representations of ocean circulation. IPSL-CM5A-LR and CNRM-CM5.1 poorly represent deep-ocean circulation compared to IPSL-CM4-LOOP degrading the vertical distribution of biogeochemical tracers. However, their representations of surface wind, wind stress, mixed-layer depth and geostrophic circulations (e.g., Antarctic Circumpolar Current) have been improved compared to IPSL-CM4-LOOP. These improvements result in a better representation of large-scale structure of biogeochemical fields in the upper ocean. In particular, a deepening of 20–40 m of the summer mixed-layer depth allows to capture the 0–0.5 μgChl L^?1 concentrations class of surface chlorophyll in the Southern Ocean. Further improvements in the representation of the ocean mixed-layer and deep-ocean ventilation are needed for the next generations of models development to better simulate marine biogeochemistry. In order to better constrain ocean dynamics, we suggest that biogeochemical or passive tracer modules should be used routinely for both model development and model intercomparisons.     

我国沙尘暴的时空分布规律及其源地和移动路径

利用1971-1996年的地面气象记录月报和地面天气图资料，系统分析了我国沙尘暴的年际变化趋势及其时空分布规律，研究了沙尘暴的移动路径和源地，结果表明：1971-1996年，除青海、内蒙古的部分地区及北京等地外，我国各地沙尘暴发生的总次数呈现明显的下降趋势；根据沙尘暴的起源，可将发生在我国的沙尘暴天气过程分为外源型和内源型沙尘暴2类；外源型沙尘暴的移动路径主要包括北路和西路2条，其中北路沙尘暴侵我国的范围在西起新疆东部的哈密，东至内蒙古锡林郭勒盟的中蒙边境，西部沙尘暴入侵我国的范围在南疆和北疆的部分地区；我国沙尘暴源地主要集中在南疆和北疆的沙漠及其周边地区，甘肃河西走廓和内蒙古干燥沙漠及青海柴达木盆地等地。     

Sea urchin overgrazing of seagrasses: A review of current knowledge on causes, consequences, and management

Sea urchins are one of the most common seagrass macro-grazers in contemporary seagrass systems. Occasionally their grazing rates exceed seagrass growth rates, a phenomenon sometimes referred to as overgrazing. Because of a reported increasing frequency of overgrazing events, concomitant with loss of seagrass-associated ecosystem services, it has been suggested that overgrazing is one of the key threats to tropical and subtropical seagrasses. In light of this, we review the current knowledge on causes, consequences, and management of sea urchin overgrazing of seagrasses. Initially we argue that the definition of overgrazing must include scale and impairment of ecosystem services, since this is the de facto definition used in the literature, and will highlight the potential societal costs of seagrass overgrazing. A review of 16 identified cases suggests that urchin overgrazing is a global phenomenon, ranging from temperate to tropical coastal waters and involving at least 11 seagrass and 7 urchin species. Even though most overgrazing events seem to affect areas of <0.5 km², and recovery often occurs within a few years, overgrazing can have a range of large, long-term indirect effects such as loss of associated fauna and decreased sediment stabilization. A range of drivers behind overgrazing have been suggested, including bottom-up (nutrient enrichment), top-down (reduced predation control due to e.g. overfishing), “side-in” mechanisms (e.g. changes in water temperature) and natural population fluctuations. Based on recent studies, there seems to be fairly strong support for the top-down and bottom-up hypotheses. However, many potential drivers often co-occur and interact, especially in areas with high anthropogenic pressure, suggesting that multiple disturbances—by simultaneously reducing predation control, increasing urchin recruitment and reducing the resistance of seagrasses—could pave the way for overgrazing. In management, the most common response to overgrazing has been to remove urchins, but limited knowledge of direct and indirect effects makes it difficult to assess the applicability and sustainability of this method. Based on the wide knowledge gaps, which severely limits management, we suggest that future research should focus on (1) identification and quantification of ecosystem and societal scale effects of overgrazing; (2) assessment of the relative importance and interactions of different drivers; and (3) development of a holistic proactive and reactive long-term management agenda.     

Meiofaunal and bacterial community response to diesel additions in a microcosm study

Effects of low PAH-containing diesel were studied in a 60-day microcosm experiment at PAH concentrations 130, 1300 and 13,000μg/kg sediment. Nutrient fluxes, potential nitrification and meiofaunal community composition were analysed at three time points. Changed ∑NOx-fluxes indicated reduced sediment nitrification in Medium and High with time, in agreement with lowered potential nitrification rates in all treatments. Reduction in silicate and phosphate fluxes over time suggested severe effects on activity of meiofauna. Reduced activity increased the anoxic sediment layer, which could have contributed to the changed ∑NOx-fluxes. There were significant differences in meiofaunal community composition after 30 and 60days in Medium and High. Changes were due to increasing numbers of harpacticoids and the foraminiferan group Rotaliina, as well as decreasing numbers of Nematodes and the foraminiferan group Reophax. In spite of the low PAH-level, small additions of this diesel can still have pronounced effects on meiofaunal and bacterial communities.     

侏罗纪末至白垩纪非海相介形类生物地层学:回顾与展望

以非海相介形类为依据而建立的侏罗纪末至白垩纪的生物地层学,尤其是欧洲所谓"Purbeck-Wealden层段"(提塘阶顶部至巴列姆阶/阿普特阶底部)和全球同期沉积层的生物地层学建立已久,但这一生物地层学存有很多问题与局限性。本文对中生代晚期(聚焦于早白垩世)的非海相介形类生物地层学的基本原理、历史、目前进展、存在问题和前景进行了综述。因为介形类的繁殖、扩散与成种机制已有比较成熟的研究,所以介形类的生物地层学的应用潜力被认识已久。然而,全球不同地区中生代晚期的非海相介形类众多的研究积累已构成了一个丰富但常常混乱和矛盾的文献库。这些问题不仅存在于介形类的分类鉴定中,也见于关于古环境和系统发育的解释中。虽然地区性的盆地内的介形类生物地层学研究已产生了好结果,并可能能够用于局部地区的高精度对比。但是在进行地区间(盆地间至全球)的对比时,其实用性广遭怀疑。在过去的二十年间,许多学者采用了将今论古的古生物学研究方法,努力修订和更新中生代晚期的非海相介形类的生物地层学与古环境意义,从而促进了地区间生物地层学研究和对比的发展。古生物学家认识到,对于许多非海相介形类动物来讲,它们的分布和扩散不仅仅局限于单个的水系或较小的地理区域,而是和现生的非海相介形类一样,晚侏罗世至白垩纪的非海相介形类动物和它们的卵可被较大的动物或风长距离搬运,跨越迁移的屏障,进行扩散。鉴于以上事实,地区间的对比必须涉及两大内容:分类学的应用与古环境背景。缺乏适用于地区—全球的稳定和一致的分类学系统是进行正确对比的重要障碍。由于大量地方性分类命名、地方性特有动物的假设、与壳体特征相关的分类和生态型认识的混乱,以及对种内变异尺度的统一认识的缺乏,导致了对生物分异度的过高或过低的估量。非海相白垩纪介形类的地层记录受到诸多因素的影响:分类单元的演化与灭绝、扩散事件、当地的环境变化和地区性至全球的气候变迁。在生物地层学的应用中,我们可以通过不同手段去把握同时代的Cytheroidea,特别是Cypridoidea中具重要地层意义的Cypridea属及其亲近者(即CypridoideaMartin,1940)的分类单元的形态变异度。解释种内变异时需要格外谨慎。区分生物自生(内因)导致的变异(遗传的和形态的变异)和环境(外因)导致的变异(生态表型)是一大难题。比较保守的分类学观念(分类单元很少,但变异极大(分类单元中包含了多种生态表型))有助于不同古环境间的(生物地层)对比。另一方法是运用随着时间的古环境变化及其对介形类组合的组成的影响来进行(生物地层)对比。古生物工作者已在利用受环境控制的周期性介形类组合变化建立对比关系方面进行了大量有意义的尝试,但这些工作仍处在争议中。建立全球生物地层学方法,建立统一而持久的分类概念这一目标可以达到,但不可能在短期内实现。用现代的思想(概念)理解和研究非海相介形类的古生物学和古生物地理学及新资料将有助于修订工作的进展。尽管我们对中生代的非海相介形类的演化和分布的认识还很不全面,但目前我们已取得了可喜的进展。盆地间至大陆间的对比是否可行,早已不是问题。目前和未来的指导原则无疑是发展以介形类为基础,并与其他的年代地层学和地质年代学资料及方案相结合的从地区至全球范围的地层对比系统。因为我们正在迈向一个非海相晚中生代介形类生物地层学的重新解释和应用的新时代,我们必须承认我们还有许多东西需要学习。     

Towards a Validation of Scintillometer Measurements: The LITFASS-2009 Experiment

Scintillometry has been increasingly used over the last decade for the experimental determination of area-averaged turbulent fluxes at a horizontal scale of a few kilometres. Nevertheless, a number of assumptions in the scintillometer data processing and interpretation still call for a thorough evaluation, in particular over heterogeneous terrain. Moreover, a validation of the path-averaged structure parameters derived from scintillometer data (and forming the basis for the flux calculations) by independent measurements is still missing. To achieve this, the LITFASS-2009 field campaign has been performed around the Meteorological Observatory Lindenberg ?C Richard-A?mann-Observatory of the German Meteorological Service (DWD) in July 2009. The experiment combined tower-based in-situ turbulence measurements, field-scale laser scintillometers, long-range optical (large-aperture) and microwave scintillometers, and airborne turbulence measurements using an automatically operating unmanned aircraft. The paper describes the project design and strategy, and discusses first results. Daytime near-surface values of the temperature structure parameter, ${C_{T}^{2}}$ , over different types of farmland differ by more than one order of magnitude in their dependence on the type and status of the vegetation. Considerable spatial variability in ${C_{T}^{2}}$ was also found along the flight legs at heights between 50 and 100?m. However, it appeared difficult to separate the effects of heterogeneity from the temporal variability of the turbulence fields. Aircraft measurements and scintillometer data agreed in magnitude with respect to the temporal variation of the path-averaged ${C_{T}^{2}}$ values during the diurnal cycle. The decrease of ${C_{T}^{2}}$ with height found from the scintillometer measurements close to the surface and at 43?m under daytime convective conditions corresponds to free-convection scaling, whereas the aircraft measurements at 54 and 83?m suggest a different behaviour.     

利用全球电离层地图分析芦山地震电离层异常变化

利用全球电离层地图（ g lobalionos p herema p,gim） 提 供 的 垂 直 电 子 含 量（ verticaltotalelectroncon-tent,vtec） 观测值,采用滑动四分位距法分析了芦山地震前后的电离层异常。为了探讨异常现象与地震之间的相关性,进一步确定了震中附近上空 vtec 东 向 及 北 向 梯 度 变 化,并 比 较 分 析 了2008～2012 年 相 同 时间段的 vtec 变化。结果表明,2013年4月18～20日的负异常现象很可能与地震相关。通过分析震中附近电离层赤道异常的变化,发现赤道异常峰值在震前5d内明显减 小,且 峰 值 的 位 置 向 磁 赤 道 方 向 移 动。结 合电离层负异常现象及赤道异常的变化,本 文 认 为 芦 山 地 震 孕 震 区 内 异 常 电 场 可 能 是 引 起 电 离 层 异 常 的 主 要原因之一。