Efficient Broadcast for Multicast-Capable Interconnection Networks

The broadcast function MPI_Bcast() from the MPI-1.1 standard is one of the most heavily used collective operations for the message passing programming paradigm. This diploma thesis makes use of a feature called "Multicast", which is supported by several network technologies (like Ethernet or InfiniBand), to create an efficient MPI_Bcast() implementation, especially for large communicators and small-sized messages. A preceding analysis of existing real-world applications leads to an algorithm which does not only perform well for synthetical benchmarks but also even better for a wide class of parallel applications. The finally derived broadcast has been implemented for the open source MPI library "Open MPI" using IP multicast. The achieved results prove that the new broadcast is usually always better than existing point-to-point implementations, as soon as the number of MPI processes exceeds the 8 node boundary. The performance gain reaches a factor of 4.9 on 342 nodes, because the new algorithm scales practically independently of the number of involved processes.Die Broadcastfunktion MPI_Bcast() aus dem MPI-1.1 Standard ist eine der meistgenutzten kollektiven Kommunikationsoperationen des nachrichtenbasierten Programmierparadigmas. Diese Diplomarbeit nutzt die Multicastfähigkeit, die von mehreren Netzwerktechnologien (wie Ethernet oder InfiniBand) bereitgestellt wird, um eine effiziente MPI_Bcast() Implementation zu erschaffen, insbesondere für große Kommunikatoren und kleinere Nachrichtengrößen. Eine vorhergehende Analyse von existierenden parallelen Anwendungen führte dazu, dass der neue Algorithmus nicht nur bei synthetischen Benchmarks gut abschneidet, sondern sein Potential bei echten Anwendungen noch besser entfalten kann. Der letztendlich daraus entstandene Broadcast wurde für die Open-Source MPI Bibliothek "Open MPI" entwickelt und basiert auf IP Multicast. Die erreichten Ergebnisse belegen, dass der neue Broadcast üblicherweise immer besser als jegliche Punkt-zu-Punkt Implementierungen ist, sobald die Anzahl von MPI Prozessen die Grenze von 8 Knoten überschreitet. Der Geschwindigkeitszuwachs erreicht einen Faktor von 4,9 bei 342 Knoten, da der neue Algorithmus praktisch unabhängig von der Knotenzahl skaliert

Global dataset of monthly growing areas of 26 irrigated crops : version 1.0

A data set of monthly growing areas of 26 irrigated crops (MGAG-I) and related crop calendars (CC-I) was compiled for 402 spatial entities. The selection of the crops consisted of all major food crops including regionally important ones (wheat, rice, maize, barley, rye, millet, sorghum, soybeans, sunflower, potatoes, cassava, sugar cane, sugar beets, oil palm, rapeseed/canola, groundnuts/peanuts, pulses, citrus, date palm, grapes/vine, cocoa, coffee), major water-consuming crops (cotton), and unspecified other crops (other perennial crops, other annual crops, managed grassland). The data set refers to the time period 1998-2002 and has a spatial resolution of 5 arc minutes by 5 arc minutes which is 8 km by 8 km at the equator. This is the first time that a data set of cell-specific irrigated growing areas of irrigated crops with this spatial resolution was created. The data set is consistent to the irrigated area and water use statistics of the AQUASTAT programme of the Food and Agriculture Organization of the United Nations (FAO) (http://www.fao.org/ag/agl/aglw/aquastat/main/index.stm) and the Global Map of Irrigation Areas (GMIA) (http://www.fao.org/ag/agl/aglw/aquastat/irrigationmap/index.stm). At the cell-level it was tried to maximise consistency to the cropland extent and cropland harvested area from the Department of Geography and Earth System Science Program of the McGill University at Montreal, Quebec, Canada and the Center for Sustainability and the Global Environment (SAGE) of the University of Wisconsin at Madison, USA (http://www.geog.mcgill.ca/~nramankutty/ Datasets/Datasets.html and http://geomatics.geog.mcgill.ca/~navin/pub/Data/175crops2000/). The consistency between the grid product and the input data was quantified. MGAG-I and CC-I are fully consistent to each other on entity level. For input data other than CC-I, the consistency of MGAG-I on cell level was calculated. The consistency of MGAG-I with respect to the area equipped for irrigation (AEI) of GMIA and to the cropland extent of SAGE was characterised by the sum of the cell-specific maximum difference between the MGAG-I monthly total irrigated area and the reference area when the latter was exceeded in the grid cell. The consistency of the harvested area contained in MGAG-I with respect to SAGE harvested area was characterised by the crop-specific sum of the cell-specific difference between MGAG-I harvested area and the SAGE harvested area when the latter was exceeded in the grid cell. In all three cases, the sums are the excess areas that should not have been distributed under the assumption that the input data were correct. Globally, this cell-level excess of MGAG-I as compared to AEI is 331,304 ha or only about 0.12 % of the global AEI of 278.9 Mha found in the original grid. The respective cell-level excess of MGAG-I as compared to the SAGE cropland extent is 32.2 Mha, corresponding to about 2.2 % of the total cropland area. The respective cell-level excess of MGAG-I as compared to the SAGE harvested area is 27 % of the irrigated harvested area, or 11.5 % of the AEI. In a further step that will be published later also rainfed areas were compiled in order to form the Global data set of monthly irrigated and rainfed crop areas around the year 2000 (MIRCA2000). The data set can be used for global and continental-scale studies on food security and water use. In the future, it will be improved, e.g. with a better spatial resolution of crop calendars and an improved crop distribution algorithm. The MIRCA2000 data set, its full documentation together with future updates will be freely available through the following long-term internet site: http://www.geo.uni-frankfurt.de/ipg/ag/dl/forschung/MIRCA/index.html. The research presented here was funded by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) within the framework of the research project entitled "Consistent assessment of global green, blue and virtual water fluxes in the context of food production: regional stresses and worldwide teleconnections". The authors thank Navin Ramankutty and Chad Monfreda for making available the current SAGE datasets on cropland extent (Ramankutty et al., 2008) and harvested area (Monfreda et al., 2008) prior to their publication

The effects of bar-spiral coupling on stellar kinematics in the Galaxy

We investigate models of the Milky Way disc taking into account simultaneously the bar and a two-armed quasi-static spiral pattern. Away from major resonance overlaps, the mean stellar radial motions in the plane are essentially a linear superposition of the isolated effects of the bar and spirals. Thus, provided the bar is strong enough, even in the presence of spiral arms, these mean radial motions are predominantly affected by the Galactic bar for large scale velocity fluctuations. This is evident when comparing the peculiar line-of-sight velocity power spectrum of our coupled models with bar-only models. However, we show how forthcoming spectroscopic surveys could disentangle bar-only non-axisymmetric models of the Galaxy from models in which spiral arms have a significant amplitude. We also point out that overlaps of low-order resonances are sufficient to enhance stellar churning within the disc, even when the spirals amplitude is kept constant. Nevertheless, for churning to be truly non-local, stronger or (more likely) transient amplitudes would be needed: otherwise the disc is actually mostly unaffected by churning in the present models. Finally, regarding vertical breathing modes, the combined effect of the bar and spirals on vertical motions is a clear non-linear superposition of the isolated effects of both components, significantly superseding the linear superposition of modes produced by each perturber separately, thereby providing an additional effect to consider when analysing the observed breathing mode of the Galactic disc in the extended Solar neighbourhood.Comment: 13 pages, 12 figures. MNRAS. Accepted for publication. v2 is the published versio

Applying rare earth elements, Uranium, and 87Sr/86Sr to disentangle structurally forced confluence of regional groundwater resources: The case of the Lower Yarmouk Gorge

The conjoint discussion of tectonic features, correlations of element concentrations, δ18O, δD, and 87Sr/86Sr of groundwater leads to new insight into sources of groundwater, their flow patterns, and salinization in the Yarmouk Basin. The sources of groundwater are precipitation infiltrating into basaltic rock or limestone aquifers. Leaching of relic brines and dissolution of gypsum and calcite from the limestone host rocks generate enhanced salinity in groundwater in different degrees. High U(VI) suggests leaching of U from phosphorite-rich Upper Cretaceous B2 formation. Both very low U(VI) and specific rare earth element including yttrium (REY) distribution patterns indicate interaction with ferric oxyhydroxides formed during weathering of widespread alkali olivine basalts in the catchment area. REY patterns of groundwater generated in basaltic aquifers are modified by interaction with underlying limestones. Repeated sampling over 18 years revealed that the flow paths towards certain wells of groundwater varied as documented by changes in concentrations of dissolved species and REY patterns and U(VI) contents. In the Yarmouk Gorge, groundwater with basaltic REY patterns but high U(VI) and low Sr2+ and intermediate sulfate concentrations mainly ascends in artesian wells tapping a buried flower structure fault system crossing the trend of the gorge

Faulting patterns in the Lower Yarmouk Gorge potentially influence groundwater flow paths

Recent studies investigating groundwater parameters, e.g., heads, chemical composition, and heat transfer, argued that groundwater flow paths in the Lower Yarmouk Gorge (LYG) area are controlled by geological features such as faults or dikes. However, the nature of such features, as well as their exact locations, were so far unknown. In the present paper, we propose a new fault pattern in the LYG area by compiling and revising geological and geophysical data from the study area, including borehole information, geological map cross sections, and seismic data from the southern Golan Heights and northern Ajloun mountains. The presented pattern is composed of strike–slip and thrust faults, which are associated with the Dead Sea transform system and with the Kinnarot pull-apart basin. Compressional and tensional structures developed in different places, forming a series of fault blocks probably causing a non-uniform spatial hydraulic connection between them. This study provides a coarse fault-block model and improved structural constraints that serve as fundamental input for future hydrogeological modeling which is a suggested solution for an enigmatic hydrological situation concerning three riparian states (Syria, Jordan, and Israel) in a water-scarce region. In areas of water scarcity and transboundary water resources, transient 3-D flow simulations of the resource are the most appropriate solution to understand reservoir behavior. This is an important tool for the development of management strategies. However, those models must be based on realistic geometry, including structural features. The study at the LYG is intended to show the importance of such kinds of structural investigations for providing the necessary database in geologically stressed areas without sufficient data. Furthermore, during the hydrogeological investigation, a mismatch with results of pull-apart basin rim fault evolution studies was discovered. We argue that this mismatch may result from the settings at the eastern rim of the basin as the en-echelon changes from pull-apart basins (Dead Sea, Kinnarot, Hula) to a push-up ridge (Hermon)

Bioaktive Kollagenfragmente : Neue strukturbiologische Studien an Kollagen-Integrin-Komplexen belegen Justus Liebigs wegweisende Ideen

In seinem bahnbrechenden Werk „Thierchemie“ von 1843 beschreibt Justus Liebig Ge latine, das Abbauprodukt von Kollagen, als Leim gebendes Gebilde. Bis heute ist in der Human- wie in der Veterinärmedizin umstritten, ob die Verabreichung von Kollagenfragmenten in Form von Nahrungsergänzungsmitteln eine wirksame Strategie darstellt, um einem Gelenkverschleiß vorzubeugen, der sich z.B. in einer Arthrose manifestieren kann. Die Arbeitsgruppe von Prof. Hans-Christian Siebert kombiniert nanotechnologische Analysemethoden mit Bioinformatikalgorithmen, um die submolekularen Mechanismen zu ergründen, die die hochkomplexen Wechselwirkungen bestimmter Rezeptoren in der extra-zellulären Matrix mit unterschiedlichen bioaktiven Kollagenfragmenten ermöglichen

ALS-linked loss of Cyclin-F function affects HSP90

The founding member of the F-box protein family, Cyclin-F, serves as a substrate adaptor for the E3 ligase Skp1-Cul1-F-box (SCF)Cyclin-F which is responsible for ubiquitination of proteins involved in cell cycle progression, DNA damage and mitotic fidelity. Missense mutations in CCNF encoding for Cyclin-F are associated with amyotrophic lateral sclerosis (ALS). However, it remains elusive whether CCNF mutations affect the substrate adaptor function of Cyclin-F and whether altered SCFCyclin-F–mediated ubiquitination contributes to pathogenesis in CCNF mutation carriers. To address these questions, we set out to identify new SCFCyclin-F targets in neuronal and ALS patient–derived cells. Mass spectrometry–based ubiquitinome profiling of CCNF knockout and mutant cell lines as well as Cyclin-F proximity and interaction proteomics converged on the HSP90 chaperone machinery as new substrate candidate. Biochemical analyses provided evidence for a Cyclin-F–dependent association and ubiquitination of HSP90AB1 and implied a regulatory role that could affect the binding of a number of HSP90 clients and co-factors. Together, our results point to a possible Cyclin-F loss-of-function–mediated chaperone dysregulation that might be relevant for ALS

Влияние интенсивной пластической деформации методом кручения под квазигидростатическим давлением на структуру и фазовый состав высокоазотистой аустенитной стали Х20АГ20Ф2

We investigate the microstructure and microhardness of high-nitrogen austenitic steel Fe-20Cr-20Mn-2.6V-0.3C-0.8N (in wt. %) after upset and high-pressure torsion (HPT) (6GPa) for ?, ?, and 1 revolutions at room temperature. As the result of deformation, steel microhardness increases by 1.5 times after HPT. Slip, twinning, formation of localized deformation microbands, and precipitation hardening are the main deformation mechanisms under HPT, and the level of solid solution strengthening of steel remains high after deformation

Transient simulations of large-scale hydrogeological processes causing temperature and salinity anomalies in the Tiberias Basin

Hot and salty waters occur in the surroundings of the Lake Tiberias. Transient numerical simulations of thermally-driven flow without salinity effects show that mixed convection can explain the upsurge of thermal waters through permeable faults and the high temperature gradient in the Lower Yarmouk Gorge (LYG). It turns out that by including salinity effects, the flow patterns differ from those of a purely thermal regime because heavy brines dampen upward buoyant flow and convective cells. Accordingly, the fault permeability had to be increased to restore a good fit with the measured temperatures. This further supports the hypothesis that the high temperature gradient in the LYG is likely due to fractures or faults in that area. The thermohaline simulations also suggest that the derivatives of relic seawater brines are the major source of salinity. Deep brines leaching salt diapirs cannot reach the surface. However, the presence of local shallower salt bodies below the lake can potentially contribute to the salinity of the western spring and well waters, though in very small amount. This is in agreement with geochemical data according to which the major source of the brines of the Tiberias Basin represents seawater evaporation brines. Besides being of importance for understanding the hydrogeological processes that salinize Lake Tiberias, the presented simulations provide a real-case example illustrating large-scale fluid patterns due to only one source of buoyancy (heat) and those that are additionally coupled to salinity