Gabriel Wittum

Goethe-Universität Frankfurt am Main, Frankfurt, Hesse, Germany

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Publications (154)141.88 Total impact

  • Björn Dick · Andreas Vogel · Dmitry Khabi · Martin Rupp · Uwe Küster · Gabriel Wittum ·
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    ABSTRACT: In order to enable exascale computing, concepts for substantial energy savings are required. Dynamic voltage and frequency scaling (DVFS) is widely known to provide suitable energy saving potentials. However, the customarily utilized DVFS mechanism of the Linux kernel determines clock frequencies solely based on an idle time analysis. In contrast to this, we use an empirical approach based on preparatory measurements of the energy consumption at all available frequencies. From the resulting data we deduce energy-optimal frequencies, which are used in subsequent production runs. The described methodology can be deployed with routine granularity to account for varying code characteristics. For evaluation purposes, the approach is applied to the UG4 numerical simulation software. First results exhibit an average energy saving potential of approximately 10 % while increasing the runtime by about 19 %.
    Computing and Visualization in Science 10/2015; 17(2). DOI:10.1007/s00791-015-0251-1
  • Alfio Grillo · Raphael Prohl · Gabriel Wittum ·
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    ABSTRACT: A computational algorithm for solving anelastic problems in finite deformations is introduced. The presented procedure, termed the Generalised Plasticity Algorithm (GPA) hereafter, takes inspiration from the Return Mapping Algorithm (RMA), which is typically employed to solve the Karush–Kuhn–Tucker (KKT) system arising in finite elastoplasticity, but aims to modify and extend the RMA to the case of more general flow rules and strain energy density functions as well as to non-classical formulations of elastoplasticity, in which the plastic variables are not treated as internal variables. To assess its reliability, the GPA is tested in two different contexts. First, it is used for solving two classical problems (a shear-compression test and the necking of a circular bar). In both cases, the GPA is compared with the RMA in terms of structural set-up, computational effort and flexibility, and its convergence is evaluated by solving several benchmarks. Some restrictions of the classical form of the RMA are pointed out, and it is shown how these can be overcome by adopting the proposed algorithm. Second, the GPA is applied to characterise the mechanical response of a biological tissue that undergoes large deformations and remodelling of its internal structure.
    Mathematics and Mechanics of Solids 09/2015; DOI:10.1177/1081286515598661 · 1.30 Impact Factor
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    ABSTRACT: In this technical report we study the convergence of Parareal for 2D incompressible flow around a cylinder for different viscosities. Two methods are used as fine integrator: backward Euler and a fractional step method. It is found that Parareal converges better for the implicit Euler, likely because it under-resolves the fine-scale dynamics as a result of numerical diffusion.
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    ABSTRACT: We consider the problem of uncertainty quantification for extreme scale parameter dependent problems where an underlying low rank property of the parameter dependency is assumed. For this type of dependency the hierarchical Tucker format offers a suitable framework to approximate a given output function of the solutions of the parameter dependent problem from a number of samples that is linear in the number of parameters. In particular we can a posteriori compute the mean, variance or other interesting statistical quantities of interest. In the extreme scale setting it is already assumed that the underlying fixed-parameter problem is distributed and solved for in parallel. We provide in addition a parallel evaluation scheme for the sampling phase that allows us on the one hand to combine several solves and on the other hand parallelise the sampling.
    Computing and Visualization in Science 08/2015; 17(2):67-78. DOI:10.1007/s00791-015-0247-x
  • Alfio Grillo · Raphael Prohl · Gabriel Wittum ·

    Continuum Mechanics and Thermodynamics 08/2015; DOI:10.1007/s00161-015-0465-y · 1.78 Impact Factor
  • Arne Nägel · Volker Schulz · Martin Siebenborn · Gabriel Wittum ·
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    ABSTRACT: In this work we consider inverse modeling of the shape of cells in the outermost layer of human skin. We propose a novel algorithm that combines mathematical shape optimization with high-performance computing. Our aim is to fit a parabolic model for drug diffusion through the skin to data measurements. The degree of freedom is not the permeability itself, but the shape that distinguishes regions of high and low diffusivity. These are the cells and the space in between. The key part of the method is the computation of shape gradients, which are then applied as deformations to the finite element mesh, in order to minimize a tracking type objective function. Fine structures in the skin require a very high resolution in the computational model. We therefor investigate the scalability of our algorithm up to millions of discretization elements.
    Computing and Visualization in Science 08/2015; 17(2). DOI:10.1007/s00791-015-0248-9
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    Konstantinos Xylouris · Gabriel Wittum ·
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    ABSTRACT: In order to be able to examine the extracellular potential's influence on network activity and to better understand dipole properties of the extracellular potential, we present and analyze a three-dimensional formulation of the cable equation which facilitates numeric simulations. When the neuron's intra- and extracellular space is assumed to be purely resistive (i.e., no free charges), the balance law of electric fluxes leads to the Laplace equation for the distribution of the intra- and extracellular potential. Moreover, the flux across the neuron's membrane is continuous. This observation already delivers the three dimensional cable equation. The coupling of the intra- and extracellular potential over the membrane is not trivial. Here, we present a continuous extension of the extracellular potential to the intracellular space and combine the resulting equation with the intracellular problem. This approach makes the system numerically accessible. On the basis of the assumed pure resistive intra- and extracellular spaces, we conclude that a cell's out-flux balances out completely. As a consequence neurons do not own any current monopoles. We present a rigorous analysis with spherical harmonics for the extracellular potential by approximating the neuron's geometry to a sphere. Furthermore, we show with first numeric simulations on idealized circumstances that the extracellular potential can have a decisive effect on network activity through ephaptic interactions.
    Frontiers in Computational Neuroscience 07/2015; 9:94. DOI:10.3389/fncom.2015.00094 · 2.20 Impact Factor
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    ABSTRACT: In-silico investigations of skin permeation are an important but also computationally demanding problem. To resolve all involved scales in full detail will probably not only require exascale computing capacities but also suitable parallel algorithms. This article investigates the applicability of the time-parallel Parareal algorithm to a brick and mortar setup, a precursory problem to skin permeation. A C++ library implementing Parareal is combined with the UG4 simulation framework, which provides the spatial discretization and parallelization. The combination's performance is studied with respect to convergence and speedup. While limited speedup from the time parallelization is shown to be possible, load balancing is identified as an important issue in the application of Parareal with implicit integrators to complex PDEs.
    Computing and Visualization in Science 02/2015; 17(2). DOI:10.1007/s00791-015-0246-y
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    Zeitschrift für Gastroenterologie 01/2015; 53(01). DOI:10.1055/s-0034-1397244 · 1.05 Impact Factor
  • A. Vogel · A. Calotoiu · A. Strube · S. Reiter · A. Nägel · F. Wolf · G. Wittum ·
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    ABSTRACT: Numerically addressing scientific questions such as simulating drug diffusion through the human stratum corneum is a challenging task requiring complex codes and plenty of computational resources. The UG4 framework is used for such simulations, and though empirical tests have shown good scalability so far, its sheer size precludes analytical modeling of the entire code. We have developed a process which combines the power of our automated performance modeling method and the workflow manager JUBE to create insightful models for entire UG4 simulations. Examining three typical use cases, we identified and resolved a previously unknown latent scalability bottleneck. In collaboration with the code developers, we validated the performance expectations in each of the use cases, creating over 10,000 models in less than a minute, a feat previously impossible without our automation techniques.
  • Michael Hoffer · Christian Poliwoda · Gabriel Wittum ·
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    ABSTRACT: The automated mapping of program functionality to intuitive user interfaces is a highly challenging task. Nevertheless it is a promising way to significantly improve software quality by simplifying the development process. This paper describes a method for a declarative and fully automated creation of graphical user interfaces from Java objects, i.e. the information accessible via the Java Reflection API. For this purpose we created the Visual Reflection Library (VRL). VRL interfaces are able to represent complex workflows and allow for a certain degree of visual programming. We start by describing an application: the development of an interactive user interface for the simulation system UG. By shortly discussing the requirements for such an interface, we will explain the reasons for creating VRL and the benefits we gained from it. After that we give an overview of our methods and show several applications. We end by summarizing our results and giving a future outlook.
    Computing and Visualization in Science 12/2014; 16(4). DOI:10.1007/s00791-014-0230-y
  • Andreas Vogel · Sebastian Reiter · Martin Rupp · Arne Nägel · Gabriel Wittum ·
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    ABSTRACT: In this paper we describe the concept of the renewed software package UG, that is used as a flexible simulation framework for the solution of partial differential equations. A general overview of the concepts of the new implementation is given: The modularization of the software package into several libraries libGrid, libAlgebra, libDiscretization and pcl is described and all major modules are discussed in detail. User backends through scripting and visual editing are briefly considered and examples show the new features of the current implementation.
    Computing and Visualization in Science 12/2014; 16(4). DOI:10.1007/s00791-014-0232-9
  • Arne Nägel · Andreas Vogel · Gabriel Wittum ·
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    ABSTRACT: This study investigates properties of different solvers for density driven flow problems. The focus is on both non-linear and linear solvers. For the non-linear part, we compare fully coupled method using a Newton linearization and iteratively coupled versions of Jacobi and Gauss-Seidel type. Fully coupled methods require effective preconditioners for the Jacobian. To that end we present a transformation eliminating some couplings and present a strategy for employing algebraic multigrid to the transformed system as well. The work covers theoretical aspects, and provides numerical experiments. Although the primary focus is on density driven flow, we believe that the analysis may well be extended beyond to similar equations with coupled phenomena, such as geomechanics.
    Computer Methods in Applied Mechanics and Engineering 12/2014; 292. DOI:10.1016/j.cma.2014.11.041 · 2.96 Impact Factor
  • Rossitza Piperkova · Sebastian Reiter · Martin Rupp · Gabriel Wittum ·
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    ABSTRACT: This research studies what influences various properties of a soundboard may have upon the acoustic feedback to gain a better understanding about the relevance of different properties regarding the sound characteristics. It may also help to improve the quality of simulations. We did a modal analysis of a real soundboard of a harpsichord using a Laser-Doppler-Vibrometer and also simulated several models of the very same soundboard in three space dimensions using the simulation software UG4. The used models of the sound board differed from each other by changing or skipping several properties and components. Then, we compared the simulated vibration patterns with the patterns measured on the real sound board to gain a better understanding about their influences on the vibrations. In particular, we used models with and without soundboard bars and bridge, but also were using different thicknesses for the soundboard itself.
    The Journal of the Acoustical Society of America 10/2014; 136(4):2202-2202. DOI:10.1121/1.4899986 · 1.50 Impact Factor
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    ABSTRACT: The morphology of presynaptic specializations can vary greatly ranging from classical single-release-site boutons in the central nervous system to boutons of various sizes harboring multiple vesicle release sites. Multi-release-site boutons can be found in several neural contexts, for example at the neuromuscular junction (NMJ) of body wall muscles of Drosophila larvae. These NMJs are built by two motor neurons forming two types of glutamatergic multi-release-site boutons with two typical diameters. However, it is unknown why these distinct nerve terminal configurations are used on the same postsynaptic muscle fiber. To systematically dissect the biophysical properties of these boutons we developed a full three-dimensional model of such boutons, their release sites and transmitter-harboring vesicles and analyzed the local vesicle dynamics of various configurations during stimulation. Here we show that the rate of transmission of a bouton is primarily limited by diffusion-based vesicle movements and that the probability of vesicle release and the size of a bouton affect bouton-performance in distinct temporal domains allowing for an optimal transmission of the neural signals at different time scales. A comparison of our in silico simulations with in vivo recordings of the natural motor pattern of both neurons revealed that the bouton properties resemble a well-tuned cooperation of the parameters release probability and bouton size, enabling a reliable transmission of the prevailing firing-pattern at diffusion-limited boutons. Our findings indicate that the prevailing firing-pattern of a neuron may determine the physiological and morphological parameters required for its synaptic terminals.
    Frontiers in Computational Neuroscience 09/2014; 8:101. DOI:10.3389/fncom.2014.00101 · 2.20 Impact Factor
  • Ivo Muha · Bernd Linke · Gabriel Wittum ·
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    ABSTRACT: The focus of this work is the development of a model for the estimation of methane emissions for storage tanks of biogas plants. Those can be estimated depending on (i) hydraulic retention time in the digester, (ii) an arbitrary removal rate of the digestate from the storage tank and (iii) arbitrary temperature conditions in the storage tank. Furthermore, the model is capable of considering an arbitrary mixture of manure and crops in the input material. The model was validated by data from 21 full scale biogas plants in Germany digesting cow manure and crops. A realistic scenario for the removal rate and temperature conditions in the storage tank was then investigated and special emphasis was given to the effect of hydraulic retention time and proportion of crops in the mixture on the input VS methane yield from the digester and the storage tank.
    Bioresource Technology 08/2014; 178. DOI:10.1016/j.biortech.2014.08.060 · 4.49 Impact Factor
  • Sebastian Reiter · Andreas Vogel · Ingo Heppner · Martin Rupp · Gabriel Wittum ·
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    ABSTRACT: A parallel geometric multigrid solver on hierarchically distributed grids is presented. Using a tree-structure for grid distribution onto the processing entities, the multigrid cycle is performed similarly to the serial algorithm, using additional vertical communication during transfer operations. The workload is gathered to fewer processes on coarser levels. Involved parallel structures are described in detail and the multigrid algorithm is formulated, discussing parallelization details. A performance study is presented that shows close to optimal efficiency for weak scaling up to 262k processes in 2 and 3 space dimensions.
    Computing and Visualization in Science 08/2014; 16(4):151-164. DOI:10.1007/s00791-014-0231-x
  • A. Grillo · G. Wittum · A. Tomic · S. Federico ·
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    ABSTRACT: We present a mathematical model of structural reorganisation in a fibre-reinforced composite material in which the fibres are oriented statistically, i.e. obey a probability distribution of orientation. Such a composite material exemplifies a biological tissue (e.g. articular cartilage or a blood vessel) whose soft matrix is reinforced by collagen fibres. The structural reorganisation of the composite takes place as fibres reorient, in response to mechanical stimuli, in order to optimise the stress distribution in the tissue. Our mathematical model is based on the Principle of Virtual Powers and the study of dissipation. Besides incompressibility, our main hypothesis is that the composite is characterised by a probability density distribution that measures the probability of finding a family of fibres aligned along a given direction at a fixed material point. Under this assumption, we describe the reorientation of fibres as the evolution of the most probable direction along which the fibres are aligned. To test our theory, we compare our simulations of a benchmark problem with selected results taken from the literature.
    Mathematics and Mechanics of Solids 01/2014; 20(9). DOI:10.1177/1081286513515265 · 1.30 Impact Factor
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    ABSTRACT: The application of X-radiography in ceramic studies is becoming an increasingly valued method. Using the potential of industrial X-ray computed tomography (CT) for non-destructive testing as an archaeometric or archaeological method in pottery studies, especially regarding aspects such as manufacturing techniques or pottery abrics, requires controlled data-acquisition and post-processing by scientific computing adjusted to archaeological issues. The first results of this evaluation project show that, despite the difficulties inherent in CT technology, considerable information can be extracted for pottery analysis. The application of surface morphology reconstructions and volumetric measurements based on CT data will open a new field in future non-invasive archaeology.
  • S. Reiter · D. Logashenko · S. Stichel · G. Wittum · A. Grillo ·
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    ABSTRACT: We develop a numerical technique for variable-density flow in fractured porous media, in which fractures are (d − 1)-dimensional manifolds, with d being the dimension of the ambient space. The PDEs of variable-density flow are firstly presented in the same form for both the fractures and the enclosing medium. Then, the equations defined in the fractures are averaged along the fracture width and formulated in (d − 1)-dimensions. The resulting PDEs are solved together with those defined in the enclosing medium, which maintain their d-dimensional form. The discretisation of the coupled system of d- and (d − 1)-dimensional PDEs follows a finite-volume method requiring a special construction of the discretisation grid, obtained by the algorithm explained in this paper. The accuracy of our technique is tested by comparing the produced results with those obtained in simulations in which the fractures maintain dimension d. In all simulations the fractured medium is three-dimensional.
    International Journal of Computational Science and Engineering 01/2014; 9(5/6):416-432. DOI:10.1504/IJCSE.2014.064527

Publication Stats

1k Citations
141.88 Total Impact Points


  • 2008-2015
    • Goethe-Universität Frankfurt am Main
      • Goethe Center for Scientific Computing
      Frankfurt, Hesse, Germany
  • 2002-2014
    • Universität Heidelberg
      • • Department of Neurobiology
      • • Bernstein Center for Computational Neuroscience
      • • Interdisciplinary Center for Scientific Computing
      Heidelburg, Baden-Württemberg, Germany
  • 2009
    • University Hospital Frankfurt
      Frankfurt, Hesse, Germany
  • 1996-1999
    • Universität Stuttgart
      Stuttgart, Baden-Württemberg, Germany