Parallel Numerical Methods for Model Coupling in Nutrient Cycle Simulations

We present a new approach to ecosystem nutrient cycle simulations. Nutrient conversion and fluxes between ecosystem compartments are driven by highly complex biogeochemical and hydrological processes. Nutrient cycles in soils supply vegetation and crop growth, affect groundwater and surface water eutrophication, and release greenhouse gases into the atmosphere. Simulating nutrient cycles is regarded a grand challenge due to the multi-scale properties and involved multiphysics of the considered ecosystems. Common approaches are restricted on several levels, often suffering from limited temporal and spatial extent, resolution or accuracy, model simplifications, or inability to use high performance computing effectively. In order to cope with their inherent complexity, we consider nutrient cycle simulations as a multiphysics problem by means of a coupling of dedicated biogeochemical and hydrological models. We formulate the model coupling problem in an abstract multiphysics setup to manage the complexity. We propose a new variant of operator splitting schemes for the time propagation of the coupled models. Our scheme employs local model propagators such that accuracy is maintained on the global level. Furthermore, the scheme features an inherent parallelism on the coupling level which is independent of possible parallelizations of the models. We present advances in a software technique which facilitates the model coupling on high performance computing platforms. Our development allows for dynamically changing the parallel configuration of models and their data distribution during runtime. We validate our approach to nutrient cycle simulations by means of numerical experiments using a greenhouse gas emission scenario and a nitrate leaching scenario. The results show the benefits of the proposed scheme in terms of an improved coverage of indirect and local effects. Furthermore, we present performance tests showing the superior parallel efficiency of our methodology over common approaches, which is due to its parallelism with respect to the coupling strategy

CS-FDP: Community-spezifische Forschungsdatenpublikation

Das Kompetenzzentrum Forschungsdaten der Universität Heidelberg, eine gemeinsame Serviceeinrichtung der Universitätsbibliothek und des Universitätsrechenzentrums, unterstützt Wissenschaftler/-innen der Universität Heidelberg beim professionellen Management ihrer Forschungsdaten. Ziel des Projekts „Community-spezifische Forschungsdatenpublikation“ (CS-FDP) ist die Weiterentwicklung des Serviceangebots des Kompetenzzentrums durch den Aufbau eines Pools von generischen Softwarewerkzeugen zur Erstellung dynamischer Publikationsportale für Forschungsdaten, die Entwicklung eines Konzepts zur nachhaltigen Integration der Heidelberger Forschungsdaten in übergreifende Archivierungskonzepte sowie die weitere Professionalisierung des Datenmanagements an der Universität durch die Verankerung des Themas in Forschung und Lehre

Offene Forschungsdaten an der Universität Heidelberg: von generischen institutionellen Repositorien zu fach- und projektspezifischen Diensten

Die Universität Heidelberg hat 2014 das Kompetenzzentrum Forschungsdaten als gemeinsame Serviceeinrichtung der Universitätsbibliothek und des Universitätsrechenzentrums eingerichtet. Der vorliegende Beitrag stellt die Angebote des Kompetenzzentrums zur Publikation von Forschungsdaten vor, fasst bisherige Erfahrungen zusammen und diskutiert auf dieser Grundlage exemplarisch die Rolle von institutionellen Veröffentlichungsplattformen für Open Research Data. Im Einzelnen werden dabei das institutionelle Datenrepositorium heiDATA, die Bild- und Multimediadatenbank heidICON sowie die derzeitige Weiterentwicklung des Dienstleistungsportfolios des Kompetenzzentrums im Rahmen des Projekts „Community-spezifische Forschungsdatenpublikation (CS-FDP)“ vorgestellt. In 2014 Heidelberg University established the Competence Centre for Research Data as a joint facility of the University Library and the university’s Computing Centre. This article describes the Competence Centre’s services for publishing research data and examines on that basis the role of institutional publication platforms for open research data. In particular the paper discusses the institutional research data repository heiDATA, the image and multimedia database heidICON and the current refinement of the Competence Centre’s service portfolio within the project “Community Specific Research Data Publication (CS-FDP)”

Energy-Aware High Performance Computing

High performance computing centres consume substantial amounts of energy to power large-scale supercomputers and the necessary building and cooling infrastructure. Recently, considerable performance gains resulted predominantly from developments in multi-core, many-core and accelerator technology. Computing centres rapidly adopted this hardware to serve the increasing demand for computational power. However, further performance increases in large-scale computing systems are limited by the aggregate energy budget required to operate them. Power consumption has become a major cost factor for computing centres. Furthermore, energy consumption results in carbon dioxide emissions, a hazard for the environment and public health; and heat, which reduces the reliability and lifetime of hardware components. Energy efficiency is therefore crucial in high performance computing

PDE MODELING WITH MODELICA VIA FMI IMPORT OF HIFLOW3 C++ COMPONENTS WITH PARALLEL MULTI-CORE SIMULATIONS

ABSTRACT The Modelica modeling and simulation language is widely used in academia and industry to model complex, coupled dynamic systems which can be described by systems of ordinary differential equations (ODE) or differential algebraic equations (DAE). Recent work by the authors showed a way to enable partial differential equation (PDE) modeling with Modelica via functional mock-up interface (FMI) import of C++ components based on the multi-purpose finite element library HiFlow3. The finite element method (FEM) is largely used in both research and industry as a reliable technique for solving PDE problems. In contrast to methods based on language extensions or automatic semi-discretizations in space, the approach with FMI import of HiFlow3 components into Modelica requires no change to the Modelica language, enables the use of specialized PDE solvers, and it allows for full flexibility in the choice of geometry, model parameters, and space discretization between simulation runs without recompilation. However, the computationally intensive PDE solving part in this approach can form a bottleneck in the simulations. In this work, we enhance the PDE solver by using a distributed memory parallelization based on a domain decomposition. As an example application, we consider a mechanical linear elasticity problem consisting of physical forces applied on a beam. Beams, plates and shells are common elements of solid structures with a sizable quantity of application in engineering design, appearing in fuselage, ship hulls, concrete roof structure, etc. The derivation of elastic stress strain relations is a crucial point for mechanical analysis and validation, as the bending properties of the structure effects greatly the stability properties. In this work the actual beam is modeled and solved in parallel using a C++ HiFlow3 component whereas the physical force acting on the beam is modeled using Modelica. We use the OpenModelica development environment but the same approach can be adapted to other Modelica environments

PDE Modeling with Modelica via FMI import of Hiflow3 C++ Components with Parallel Multi-Core Simulations

The Modelica modeling and simulation language is widely used in academia and industry to model complex, coupled dynamic systems which can be described by systems of ordinary differential equations (ODE) or differential algebraic equations (DAE). Recent work by the authors showed a way to enable partial differential equation (PDE) modeling with Modelica via functional mock-up interface (FMI) import of C++ components based on the multi-purpose finite element library HiFlow3. The finite element method (FEM) is largely used in both research and industry as a reliable technique for solving PDE problems. In contrast to methods based on language extensions or automatic semi-discretizations in space, the approach with FMI import of HiFlow3 components into Modelica requires no change to the Modelica language, enables the use of specialized PDE solvers, and it allows for full flexibility in the choice of geometry, model parameters, and space discretization between simulation runs without recompilation. However, the computationally intensive PDE solving part in this approach can form a bottleneck in the simulations. In this work, we enhance the PDE solver by using a distributed memory parallelization based on a domain decomposition. As an example application, we consider a mechanical linear elasticity problem consisting of physical forces applied on a beam. Beams, plates and shells are common elements of solid structures with a sizable quantity of application in engineering design, appearing in fuselage, ship hulls, concrete roof structure, etc. The derivation of elastic stress strain relations is a crucial point for mechanical analysis and validation, as the bending properties of the structure effects greatly the stability properties. In this work the actual beam is modeled and solved in parallelusing a C++ HiFlow3 component whereas the physical force acting on the beam is modeled using Modelica. We use the OpenModelica development environment but the same approach can be adapted to other Modelica environments

Terrestrial ages of meteorites from the Nullarbor region, Australia, based on 14C and 14C-10Be measurements

We have investigated the terrestrial ages, or residence times, of 78 meteorites (representing 73 discrete falls recovered in Western Australia, and one from South Australia, using both 14C measurements and also 14C⁄ 10Be. The samples studied included two ureilites, one CK and one EL chondrite. We have included 10Be measurements from 30 meteorites, including some meteorites for which the 14C terrestrial age was previously determined. We find that the 14C⁄ 10Be terrestrial ages are more precise than 14C alone, as we can correct for shielding effects. In general, the two different age determinations age by 14C–10Be are precise to 0.5–1 ka and 14C alone within 1–2 ka. However, measurement of the 14C age alone gives good agreement with the 14C–10Be for most samples. The study of the terrestrial ages of meteorites gives us useful information concerning the storage and weathering of meteorites and the study of fall times and terrestrial age. We have compared the terrestrial ages to weathering, degree of oxidation (estimated from Mossbauer studies)and D17O. In this study, we found that weathering is not well correlated with terrestrial age for Nullarbor meteorites. However, there is a good correlation between degree of oxidation and D17O. The implications for the study of terrestrial ages and weathering from other desert environments will be discussed

Inhibition of stimulated meningeal blood flow by a calcitonin gene-related peptide binding mirror-image RNA oligonucleotide

1. Calcitonin gene-related peptide (CGRP) released from trigeminal afferents is known to play an important role in the control of intracranial blood flow. In a rat preparation with exposed cranial dura mater, periods of electrical stimulation induce increases in meningeal blood flow. These responses are due to arterial vasodilatation mediated in part by the release of CGRP. In this preparation, the effect of a CGRP-binding mirror-image oligonucleotide (Spiegelmer NOX-C89) was examined. 2. Spiegelmer NOX-C89 applied topically at concentrations between 10(−7)and 10(−5) M to the exposed dura mater led to a dose-dependent inhibition of the electrically evoked blood flow increases. The highest dose reduced the mean increases in flow to 56% of the respective control levels. A nonfunctional control Spiegelmer (not binding to CGRP) was ineffective in changing blood flow increases. Intravenous injection of NOX-C89 (5 mg kg(−1)) reduced the evoked blood flow increases to an average of 65.5% of the control. The basal blood flow was not changed by any of the applied substances. 3. In addition, an ex vivo preparation of the hemisected rat skull was used to determine CGRP release from the cranial dura mater caused by antidromic activation of meningeal afferents. In this model, 10(−6) M of NOX-C89 reduced the evoked CGRP release by about 50%. 4. We conclude that increases in meningeal blood flow due to afferent activation can be reduced by sequestering the released CGRP and thus preventing it from activating vascular CGRP receptors. Moreover, the Spiegelmer NOX-C89 may inhibit CGRP release from meningeal afferents. Therefore, the approach to interfere with the CGRP/CGRP receptor system by binding the CGRP may open a new opportunity for the therapy of diseases that are linked to excessive CGRP release such as some forms of primary headaches