arXiv subjects

Dominik Göddeke

Publications and source records attributed to Dominik Göddeke.

11 recordsLinked to original sources

arXiv2026

Thermodynamically consistent phase-field modeling and numerical simulation for reactive two-phase fluid-solid dynamics

We introduce a coupled Cahn-Hilliard Navier-Stokes model that governs the reactive two-phase dynamics of a system that consists of a fluid and a solid phase and prove its thermodynamic consistency. Moreover, we present an associated fully-discrete numerical method that relies on a continuous finite element approach and a semi-implicit time-stepping method. Our main theoretical result establishes that the fully discrete method satisfies an analog of the free energy dissipation inequality, provided that the phase-field variable remains within prescribed bounds. Numerical experiments confirm the theoretical findings and show the applicability of the method for realistic settings. In this context, we provide a preprocessing strategy that enables computing fluid flow in complex geometries given a sharp-interface formulation of the initial phase distribution. Moreover, we briefly introduce different solution strategies for the novel discretization based on the monolithic and partitioned solution paradigms and assess these in a comparative study.

math.NA↗

arXiv2026

Making Mathematical Knowledge Explainable, Accessible and Interoperable Through Large Language Model Integration

Mathematical models are central to formalizing research problems, yet their documentation often falls short of FAIR principles. Knowledge bases such as the Mathematical Model Database (MathModDB) address this gap by providing curated, semantically rich representations of mathematical models. Built on Wikibase, the same open-source infrastructure underlying Wikidata, MathModDB utilizes Semantic Web technologies to support Linked Open Data, collaborative editing, and the storage of semantically enriched metadata, making it a domain-specific knowledge graph within the broader Wikidata ecosystem. However, access to MathModDB currently requires either navigating a complex web interface or proficiency in SPARQL and Wikibase APIs, posing significant barriers for potential users. In addition, the combination of such curated knowledge bases with actual research data stored, e.g., in Dataverse repository instances, remains a challenge. To overcome these limitations, we propose integrating Large Language Models (LLMs) with MathModDB via a Model Context Protocol (MCP) server that exposes a vector-indexed schema retrieval and Steiner-tree-based join planner, combining dialogue-based natural language interaction with curated, epistemically grounded knowledge. Although instantiated on MathModDB, the architecture can be applied to other Wikibase-based systems. We demonstrate that this approach enables epistemically grounded LLM usage, improves model explainability and accessibility beyond what the standard Wikibase interface offers, and simplifies interoperability with external databases and tools, such as Dataverse data repositories. We illustrate the benefits of combining the accessibility of an LLM with the epistemic safety of a curated knowledge base through the adaptability of the MCP protocol by two use cases involving mathematical models in the fields of continuum mechanics and enzyme kinetics.

cs.AI↗

arXiv2026

Solving Approximation Tasks with Greedy Deep Kernel Methods

Kernel methods are versatile tools for function approximation and surrogate modeling. In particular, greedy techniques offer computational efficiency and reliability through inherent sparsity and provable convergence. Inspired by the success of deep neural networks and structured deep kernel networks, we consider deep, multilayer kernels for greedy approximation. This multilayer structure, consisting of linear kernel layers and optimizable kernel activation function layers in an alternating fashion, increases the expressiveness of the kernels and thus of the resulting approximants. Compared to standard kernels, deep kernels are able to adapt kernel intrinsic shape parameters automatically, incorporate transformations of the input space and induce a data-dependent reproducing kernel Hilbert space. For this, deep kernels need to be pretrained using a specifically tailored optimization objective. In this work, we not only introduce deep kernel greedy models, but also present numerical investigations and comparisons with neural networks, which clearly show the advantages in terms of approximation accuracies. As applications we consider the approximation of model problems, the prediction of breakthrough curves for reactive flow through porous media and the approximation of solutions for parameterized ordinary differential equation systems.

math.NA↗

arXiv2025

Towards a Knowledge Graph for Models and Algorithms in Applied Mathematics

Mathematical models and algorithms are an essential part of mathematical research data, as they are epistemically grounding numerical data. In order to represent models and algorithms as well as their relationship semantically to make this research data FAIR, two previously distinct ontologies were merged and extended, becoming a living knowledge graph. The link between the two ontologies is established by introducing computational tasks, as they occur in modeling, corresponding to algorithmic tasks. Moreover, controlled vocabularies are incorporated and a new class, distinguishing base quantities from specific use case quantities, was introduced. Also, both models and algorithms can now be enriched with metadata. Subject-specific metadata is particularly relevant here, such as the symmetry of a matrix or the linearity of a mathematical model. This is the only way to express specific workflows with concrete models and algorithms, as the feasible solution algorithm can only be determined if the mathematical properties of a model are known. We demonstrate this using two examples from different application areas of applied mathematics. In addition, we have already integrated over 250 research assets from applied mathematics into our knowledge graph.

cs.AI↗

arXiv2024

Ontologies for Models and Algorithms in Applied Mathematics and Related Disciplines

In applied mathematics and related disciplines, the modeling-simulation-optimization workflow is a prominent scheme, with mathematical models and numerical algorithms playing a crucial role. For these types of mathematical research data, the Mathematical Research Data Initiative has developed, merged and implemented ontologies and knowledge graphs. This contributes to making mathematical research data FAIR by introducing semantic technology and documenting the mathematical foundations accordingly. Using the concrete example of microfracture analysis of porous media, it is shown how the knowledge of the underlying mathematical model and the corresponding numerical algorithms for its solution can be represented by the ontologies.

cs.AI↗

arXiv2021

Partitioned Coupling vs. Monolithic Block-Preconditioning Approaches for Solving Stokes-Darcy Systems

We consider the time-dependent Stokes-Darcy problem as a model case for the challenges involved in solving coupled systems. Keeping the model, its discretization, and the underlying numerics for the subproblems in the free-flow domain and the porous medium constant, we focus on different solver approaches for the coupled problem. We compare a partitioned coupling approach using the coupling library preCICE with a monolithic block-preconditioned one that is tailored to different formulations of the problem. Both approaches enable the reuse of already available iterative solvers and preconditioners, in our case, from the DuMux framework. Our results indicate that the approaches can yield performance and scalability improvements compared to using direct solvers: Partitioned coupling is able to solve large problems faster if iterative solvers with suitable preconditioners are applied for the subproblems. The monolithic approach shows even stronger requirements on preconditioning, as standard simple solvers fail to converge. Our monolithic block preconditioning yields the fastest runtimes for large systems, but they vary strongly with the preconditioner configuration. Interestingly, using a specialized Uzawa preconditioner for the Stokes subsystem leads to overall increased runtimes compared to block preconditioners utilizing a more general algebraic multigrid. This highlights that optimizing for the non-coupled cases does not always pay off.

math.NA↗

arXiv2020

Bayesian inversion for electromyography using low-rank tensor formats

The reconstruction of the structure of biological tissue using electromyographic data is a non-invasive imaging method with diverse medical applications. Mathematically, this process is an inverse problem. Furthermore, electromyographic data are highly sensitive to changes in the electrical conductivity that describes the structure of the tissue. Modeling the inevitable measurement error as a stochastic quantity leads to a Bayesian approach. Solving the discretized Bayes-inverse problem means drawing samples from the posterior distribution of parameters, e.g., the conductivity, given measurement data. Using, e.g., a Metropolis-Hastings algorithm for this purpose involves solving the forward problem for different parameter combinations which requires a high computational effort. Low-rank tensor formats can reduce this effort by providing a data-sparse representation of all occurring linear systems of equations simultaneously and allow for their efficient solution. The application of Bayes' theorem proves the well-posedness of the Bayes-inverse problem. The derivation and proof of a low-rank representation of the forward problem allow for the precomputation of all solutions of this problem under certain assumptions, resulting in an efficient and theory-based sampling algorithm. Numerical experiments support the theoretical results, but also indicate that a high number of samples is needed to obtain reliable estimates for the parameters. The Metropolis-Hastings sampling algorithm, using the precomputed forward solution in a tensor format, draws this high number of samples and therefore enables solving problems which are infeasible using classical methods.

math.NA↗

arXiv2019

Exa-Dune -- Flexible PDE Solvers, Numerical Methods and Applications

In the Exa-Dune project we have developed, implemented and optimised numerical algorithms and software for the scalable solution of partial differential equations (PDEs) on future exascale systems exhibiting a heterogeneous massively parallel architecture. In order to cope with the increased probability of hardware failures, one aim of the project was to add flexible, application-oriented resilience capabilities into the framework. Continuous improvement of the underlying hardware-oriented numerical methods have included GPU-based sparse approximate inverses, matrix-free sum-factorisation for high-order discontinuous Galerkin discretisations as well as partially matrix-free preconditioners. On top of that, additional scalability is facilitated by exploiting massive coarse grained parallelism offered by multiscale and uncertainty quantification methods where we have focused on the adaptive choice of the coarse/fine scale and the overlap region as well as the combination of local reduced basis multiscale methods and the multilevel Monte-Carlo algorithm. Finally, some of the concepts are applied in a land-surface model including subsurface flow and surface runoff.

cs.MS↗

arXiv2019

Simulation of Nonlinear Signal Propagation in Multimode Fibers on Multi-GPU Systems

Mode-division multiplexing (MDM) is seen as a possible solution to satisfy the rising capacity demands of optical communication networks. To make MDM a success, fibers supporting the propagation of a huge number of modes are of interest. Many of the system aspects occurring during the propagation can be evaluated by using appropriate models. However, fibers are a nonlinear medium and, therefore, numerical simulations are required. For a large number of modes, the simulation of the nonlinear signal propagation leads to new challenges, for example regarding the required memory, which we address with an implementation incorporating multiple GPU-accelerators. Within this paper, we evaluate two different approaches to realize the communication between the GPUs and analyze the performance for simulations involving up to 8 Tesla GPUs. We show results for a MDM transmission system utilizing the extremely large but practically very relevant number of 120 spatial modes as an application example and analyze the impact of the nonlinear effects on the transmitted signals.

physics.comp-ph↗

arXiv2018

A high-level C++ approach to manage local errors, asynchrony and faults in an MPI application

C++ advocates exceptions as the preferred way to handle unexpected behaviour of an implementation in the code. This does not integrate well with the error handling of MPI, which more or less always results in program termination in case of MPI failures. In particular, a local C++ exception can currently lead to a deadlock due to unfinished communication requests on remote hosts. At the same time, future MPI implementations are expected to include an API to continue computations even after a hard fault (node loss), i.e. the worst possible unexpected behaviour. In this paper we present an approach that adds extended exception propagation support to C++ MPI programs. Our technique allows to propagate local exceptions to remote hosts to avoid deadlocks, and to map MPI failures on remote hosts to local exceptions. A use case of particular interest are asynchronous 'local failure local recovery' resilience approaches. Our prototype implementation uses MPI-3.0 features only. In addition we present a dedicated implementation, which integrates seamlessly with MPI-ULFM, i.e. the most prominent proposal for extending MPI towards fault tolerance. Our implementation is available at https://gitlab.dune-project.org/christi/test-mpi-exceptions .

cs.DC↗

arXiv2018

Towards realistic HPC models of the neuromuscular system

Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow for a high flexibility and generality in model development. Flexibility and model development, however, are often a limiting factor for large-scale simulations. Therefore, new models are typically tested and run on small-scale compute facilities. By using a detailed biophysics-based, chemo-electromechanical skeletal muscle model and the international open-source software library OpenCMISS as an example, we present an approach to upgrade an existing muscle simulation framework from a moderately parallel version towards a massively parallel one that scales both in terms of problem size and in terms of the number of parallel processes. For this purpose, we investigate different modeling, algorithmic and implementational aspects. We present improvements addressing both numerical and parallel scalability. In addition, our approach includes a novel visualization environment, which is based on the MegaMol environment capable of handling large amounts of simulated data. It offers a platform for fast visualization prototyping, distributed rendering, and advanced visualization techniques. We present results of a variety of scaling studies at the Tier-1 supercomputer HazelHen at the High Performance Computing Center Stuttgart (HLRS). We improve the overall runtime by a factor of up to 2.6 and achieved good scalability on up to 768 cores, where the previous implementation used only 4 cores.

cs.CE↗