@misc{WeiserGoetschel, author = {Weiser, Martin and G{\"o}tschel, Sebastian}, title = {State Trajectory Compression for Optimal Control with Parabolic PDEs}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11676}, number = {10-05}, abstract = {In optimal control problems with nonlinear time-dependent 3D PDEs, full 4D discretizations are usually prohibitive due to the storage requirement. For this reason gradient and quasi-Newton methods working on the reduced functional are often employed. The computation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. The state enters into the adjoint equation, again requiring the storage of a full 4D data set. We propose a lossy compression algorithm using an inexact but cheap predictor for the state data, with additional entropy coding of prediction errors. As the data is used inside a discretized, iterative algorithm, lossy coding maintaining an error bound is sufficient.}, language = {en} } @misc{GoetschelWeiserMaierhoferetal., author = {G{\"o}tschel, Sebastian and Weiser, Martin and Maierhofer, Christiane and Richter, Regina}, title = {Data Enhancement for Active Thermography}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-15243}, abstract = {Pulse thermography is a non-destructive testing method based on infrared imaging of transient thermal patterns. Heating the surface of the structure under test for a short period of time generates a non-stationary temperature distribution and thus a thermal contrast between the defect and the sound material. Due to measurement noise, preprocessing of the experimental data is necessary, before reconstruction algorithms can be applied. We propose a decomposition of the measured temperature into Green's function solutions to eliminate noise.}, language = {en} } @misc{GoetschelWeiserSchiela, author = {G{\"o}tschel, Sebastian and Weiser, Martin and Schiela, Anton}, title = {Solving Optimal Control Problems with the Kaskade 7 Finite Element Toolbox}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-11909}, number = {10-25}, abstract = {This paper presents concepts and implementation of the finite element toolbox Kaskade 7, a flexible C++ code for solving elliptic and parabolic PDE systems. Issues such as problem formulation, assembly and adaptivity are discussed at the example of optimal control problems. Trajectory compression for parabolic optimization problems is considered as a case study.}, language = {en} } @misc{GoetschelvonTycowiczPolthieretal., author = {G{\"o}tschel, Sebastian and von Tycowicz, Christoph and Polthier, Konrad and Weiser, Martin}, title = {Reducing Memory Requirements in Scientific Computing and Optimal Control}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42695}, abstract = {In high accuracy numerical simulations and optimal control of time-dependent processes, often both many time steps and fine spatial discretizations are needed. Adjoint gradient computation, or post-processing of simulation results, requires the storage of the solution trajectories over the whole time, if necessary together with the adaptively refined spatial grids. In this paper we discuss various techniques to reduce the memory requirements, focusing first on the storage of the solution data, which typically are double precision floating point values. We highlight advantages and disadvantages of the different approaches. Moreover, we present an algorithm for the efficient storage of adaptively refined, hierarchic grids, and the integration with the compressed storage of solution data.}, language = {en} } @misc{GoetschelMinion, author = {G{\"o}tschel, Sebastian and Minion, Michael L.}, title = {Parallel-in-Time for Parabolic Optimal Control Problems Using PFASST}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64989}, abstract = {In gradient-based methods for parabolic optimal control problems, it is necessary to solve both the state equation and a backward-in-time adjoint equation in each iteration of the optimization method. In order to facilitate fully parallel gradient-type and nonlinear conjugate gradient methods for the solution of such optimal control problems, we discuss the application of the parallel-in-time method PFASST to adjoint gradient computation. In addition to enabling time parallelism, PFASST provides high flexibility for handling nonlinear equations, as well as potential extra computational savings from reusing previous solutions in the optimization loop. The approach is demonstrated here for a model reaction-diffusion optimal control problem.}, language = {en} } @article{FischerGoetschelWeiser, author = {Fischer, Lisa and G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Lossy data compression reduces communication time in hybrid time-parallel integrators}, series = {Comput. Vis. Sci.}, volume = {19}, journal = {Comput. Vis. Sci.}, number = {1}, doi = {10.1007/s00791-018-0293-2}, pages = {19 -- 30}, abstract = {Parallel in time methods for solving initial value problems are a means to increase the parallelism of numerical simulations. Hybrid parareal schemes interleaving the parallel in time iteration with an iterative solution of the individual time steps are among the most efficient methods for general nonlinear problems. Despite the hiding of communication time behind computation, communication has in certain situations a significant impact on the total runtime. Here we present strict, yet no sharp, error bounds for hybrid parareal methods with inexact communication due to lossy data compression, and derive theoretical estimates of the impact of compression on parallel efficiency of the algorithms. These and some computational experiments suggest that compression is a viable method to make hybrid parareal schemes robust with respect to low bandwidth setups.}, language = {en} } @misc{GoetschelWeiserMaierhoferetal., author = {G{\"o}tschel, Sebastian and Weiser, Martin and Maierhofer, Christiane and Richter, Regina}, title = {Data Enhancement for Active Thermography}, series = {E-book Proceedings, 11th International Conference on Quantitative Infrared Thermography, Naples}, journal = {E-book Proceedings, 11th International Conference on Quantitative Infrared Thermography, Naples}, editor = {Cardone, Gennaro}, abstract = {Pulse thermography is a non-destructive testing method based on infrared imaging of transient thermal patterns. Heating the surface of the structure under test for a short period of time generates a non-stationary temperature distribution and thus a thermal contrast between the defect and the sound material. Due to measurement noise, preprocessing of the experimental data is necessary, before reconstruction algorithms can be applied. We propose a decomposition of the measured temperature into Green's function solutions to eliminate noise.}, language = {en} } @misc{GoetschelWeiserSchiela, author = {G{\"o}tschel, Sebastian and Weiser, Martin and Schiela, Anton}, title = {Solving Optimal Control Problems with the Kaskade 7 Finite Element Toolbox}, series = {Advances in DUNE}, journal = {Advances in DUNE}, editor = {Dedner, A. and Flemisch, B. and Kl{\"o}fkorn, R.}, publisher = {Springer}, pages = {101 -- 112}, abstract = {This paper presents concepts and implementation of the finite element toolbox Kaskade 7, a flexible C++ code for solving elliptic and parabolic PDE systems. Issues such as problem formulation, assembly and adaptivity are discussed at the example of optimal control problems. Trajectory compression for parabolic optimization problems is considered as a case study.}, language = {en} } @article{WeiserGoetschel, author = {Weiser, Martin and G{\"o}tschel, Sebastian}, title = {State Trajectory Compression for Optimal Control with Parabolic PDEs}, series = {SIAM J. Sci. Comput.}, volume = {34}, journal = {SIAM J. Sci. Comput.}, number = {1}, doi = {10.1137/11082172X}, pages = {A161 -- A184}, abstract = {In optimal control problems with nonlinear time-dependent 3D PDEs, full 4D discretizations are usually prohibitive due to the storage requirement. For this reason gradient and quasi-Newton methods working on the reduced functional are often employed. The computation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. The state enters into the adjoint equation, again requiring the storage of a full 4D data set. We propose a lossy compression algorithm using an inexact but cheap predictor for the state data, with additional entropy coding of prediction errors. As the data is used inside a discretized, iterative algorithm, lossy coding maintaining an error bound is sufficient.}, language = {en} } @article{GoetschelWeiser, author = {G{\"o}tschel, Sebastian and Weiser, Martin}, title = {State Trajectory Compression in Optimal Control}, series = {PAMM}, volume = {10}, journal = {PAMM}, number = {1}, doi = {10.1002/pamm.201010282}, pages = {579 -- 580}, abstract = {In optimal control problems with nonlinear time-dependent 3D PDEs, the computation of the reduced gradient by adjoint methods requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. Since the state enters into the adjoint equation, the storage of a 4D discretization is necessary. We propose a lossy compression algorithm using a cheap predictor for the state data, with additional entropy coding of prediction errors. Analytical and numerical results indicate that compression factors around 30 can be obtained without exceeding the FE discretization error.}, language = {en} } @misc{FischerGoetschelWeiser, author = {Fischer, Lisa and G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Lossy data compression reduces communication time in hybrid time-parallel integrators}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63961}, abstract = {Parallel in time methods for solving initial value problems are a means to increase the parallelism of numerical simulations. Hybrid parareal schemes interleaving the parallel in time iteration with an iterative solution of the individual time steps are among the most efficient methods for general nonlinear problems. Despite the hiding of communication time behind computation, communication has in certain situations a significant impact on the total runtime. Here we present strict, yet no sharp, error bounds for hybrid parareal methods with inexact communication due to lossy data compression, and derive theoretical estimates of the impact of compression on parallel efficiency of the algorithms. These and some computational experiments suggest that compression is a viable method to make hybrid parareal schemes robust with respect to low bandwidth setups.}, language = {en} } @inproceedings{MuellerGoetschelWeiseretal., author = {M{\"u}ller, Jan and G{\"o}tschel, Sebastian and Weiser, Martin and Maierhofer, Christiane}, title = {Thermografie mit optimierter Anregung f{\"u}r die quantitative Untersuchung von Delaminationen in kohlenstofffaserverst{\"a}rkten Kunststoffen}, series = {NDT.net Proc. DGZfP 2017}, booktitle = {NDT.net Proc. DGZfP 2017}, abstract = {Da kohlenstofffaserverst{\"a}rkte Kunststoffe (CFK) in anspruchsvollen sicherheitsrelevanten Einsatzgebieten wie im Automobilbau und in der Luftfahrt eingesetzt werden, besteht ein zunehmender Bedarf an zerst{\"o}rungsfreien Pr{\"u}fmethoden. Ziel ist die Gew{\"a}hrleistung der Sicherheit und Zuverl{\"a}ssigkeit der eingesetzten Bauteile. Aktive Thermografieverfahren erm{\"o}glichen die effiziente Pr{\"u}fung großer Fl{\"a}chen mit hoher Aufl{\"o}sung in wenigen Arbeitsschritten. Ein wichtiges Teilgebiet der Pr{\"u}fungen ist die Ortung und Charakterisierung von Delaminationen, die sowohl bereits in der Fertigung als auch w{\"a}hrend der Nutzung eines Bauteils auftreten k{\"o}nnen, und dessen strukturelle Integrit{\"a}t schw{\"a}chen. ;In diesem Beitrag werden CFK-Strukturen mit k{\"u}nstlichen und nat{\"u}rlichen Delaminationen mit Hilfe unterschiedlich zeitlich modulierter Strahlungsquellen experimentell untersucht. Verwendet werden dabei Anregungen mit Blitzlampen und mit frequenzmodulierten Halogenlampen. Mittels Filterfunktionen im Zeit- und Frequenzbereich wird das Kontrast-zu-Rausch-Verh{\"a}ltnis (CNR) der detektierten Fehlstellen optimiert. Verglichen werden anschließend die Nachweisempfindlichkeit, das CNR und die Ortsaufl{\"o}sung der zu charakterisierenden Delaminationen f{\"u}r die unterschiedlichen Anregungs- und Auswertungstechniken. Erg{\"a}nzt werden die Experimente durch numerische Simulationen des dreidimensionalen W{\"a}rmetransportes.}, language = {de} } @misc{GoetschelMinion, author = {G{\"o}tschel, Sebastian and Minion, Michael L.}, title = {Parallel-in-Time for Parabolic Optimal Control Problems Using PFASST}, series = {Domain Decomposition Methods in Science and Engineering XXIV}, journal = {Domain Decomposition Methods in Science and Engineering XXIV}, publisher = {Springer}, address = {Cham}, doi = {10.1007/978-3-319-93873-8_34}, pages = {363 -- 371}, abstract = {In gradient-based methods for parabolic optimal control problems, it is necessary to solve both the state equation and a backward-in-time adjoint equation in each iteration of the optimization method. In order to facilitate fully parallel gradient-type and nonlinear conjugate gradient methods for the solution of such optimal control problems, we discuss the application of the parallel-in-time method PFASST to adjoint gradient computation. In addition to enabling time parallelism, PFASST provides high flexibility for handling nonlinear equations, as well as potential extra computational savings from reusing previous solutions in the optimization loop. The approach is demonstrated here for a model reaction-diffusion optimal control problem.}, language = {en} } @inproceedings{GoetschelHoehneKolkoorietal., author = {G{\"o}tschel, Sebastian and H{\"o}hne, Christian and Kolkoori, Sanjeevareddy and Mitzscherling, Steffen and Prager, Jens and Weiser, Martin}, title = {Ray Tracing Boundary Value Problems: Simulation and SAFT Reconstruction for Ultrasonic Testing}, series = {Proceedings 19th World Conference on Non-Destructive Testing (WCNDT 2016)}, booktitle = {Proceedings 19th World Conference on Non-Destructive Testing (WCNDT 2016)}, language = {en} } @inproceedings{GoetschelMaierhoferMuelleretal., author = {G{\"o}tschel, Sebastian and Maierhofer, Christiane and M{\"u}ller, Jan and Rothbart, Nick and Weiser, Martin}, title = {Quantitative Defect Reconstruction in Active Thermography for Fiber-Reinforced Composites}, series = {Proceedings 19th World Conference on Non-Destructive Testing (WCNDT 2016)}, booktitle = {Proceedings 19th World Conference on Non-Destructive Testing (WCNDT 2016)}, language = {en} } @inproceedings{MuellerGoetschelMaierhoferetal., author = {M{\"u}ller, Jan and G{\"o}tschel, Sebastian and Maierhofer, Christiane and Weiser, Martin}, title = {Determining the material parameters for the reconstruction of defects in carbon fiber reinforced polymers from data measured by flash thermography}, series = {AIP Conference Proceedings}, volume = {1806}, booktitle = {AIP Conference Proceedings}, doi = {10.1063/1.4974671}, language = {en} } @misc{GoetschelNagaiahKunischetal., author = {G{\"o}tschel, Sebastian and Nagaiah, Chamakuri and Kunisch, Karl and Weiser, Martin}, title = {Lossy Compression in Optimal Control of Cardiac Defibrillation}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-18566}, abstract = {This paper presents efficient computational techniques for solving an optimization problem in cardiac defibrillation governed by the monodomain equations. Time-dependent electrical currents injected at different spatial positions act as the control. Inexact Newton-CG methods are used, with reduced gradient computation by adjoint solves. In order to reduce the computational complexity, adaptive mesh refinement for state and adjoint equations is performed. To reduce the high storage and bandwidth demand imposed by adjoint gradient and Hessian-vector evaluations, a lossy compression technique for storing trajectory data is applied. An adaptive choice of quantization tolerance based on error estimates is developed in order to ensure convergence. The efficiency of the proposed approach is demonstrated on numerical examples.}, language = {en} } @misc{GoetschelWeiser, author = {G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Lossy Compression for PDE-constrained Optimization: Adaptive Error Control}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-18575}, abstract = {For the solution of optimal control problems governed by nonlinear parabolic PDEs, methods working on the reduced objective functional are often employed to avoid a full spatio-temporal discretization of the problem. The evaluation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the ad-joint equation. The state enters into the adjoint equation, requiring the storage of a full 4D data set. If Newton-CG methods are used, two additional trajectories have to be stored. To get numerical results which are accurate enough, in many case very fine discretizations in time and space are necessary, which leads to a significant amount of data to be stored and transmitted to mass storage. Lossy compression methods were developed to overcome the storage problem by reducing the accuracy of the stored trajectories. The inexact data induces errors in the reduced gradient and reduced Hessian. In this paper, we analyze the influence of such a lossy trajectory compression method on Newton-CG methods for optimal control of parabolic PDEs and design an adaptive strategy for choosing appropriate quantization tolerances.}, language = {en} } @misc{GoetschelMaierhoferMuelleretal., author = {G{\"o}tschel, Sebastian and Maierhofer, Christiane and M{\"u}ller, Jan P. and Rothbart, Nick and Weiser, Martin}, title = {Quantitative Defect Reconstruction in Active Thermography for Fiber-Reinforced Composites}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58374}, abstract = {Carbon-fiber reinforced composites are becoming more and more important in the production of light-weight structures, e.g., in the automotive and aerospace industry. Thermography is often used for non-destructive testing of these products, especially to detect delaminations between different layers of the composite. In this presentation, we aim at methods for defect reconstruction from thermographic measurements of such carbon-fiber reinforced composites. The reconstruction results shall not only allow to locate defects, but also give a quantitative characterization of the defect properties. We discuss the simulation of the measurement process using finite element methods, as well as the experimental validation on flat bottom holes. Especially in pulse thermography, thin boundary layers with steep temperature gradients occurring at the heated surface need to be resolved. Here we use the combination of a 1D analytical solution combined with numerical solution of the remaining defect equation. We use the simulations to identify material parameters from the measurements. Finally, fast heuristics for reconstructing defect geometries are applied to the acquired data, and compared for their accuracy and utility in detecting different defects like back surface defects or delaminations.}, language = {en} } @misc{GoetschelHoehneKolkoorietal., author = {G{\"o}tschel, Sebastian and H{\"o}hne, Christian and Kolkoori, Sanjeevareddy and Mitzscherling, Steffen and Prager, Jens and Weiser, Martin}, title = {Ray Tracing Boundary Value Problems: Simulation and SAFT Reconstruction for Ultrasonic Testing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-58386}, abstract = {The application of advanced imaging techniques for the ultrasonic inspection of inhomogeneous anisotropic materials like austenitic and dissimilar welds requires information about acoustic wave propagation through the material, in particular travel times between two points in the material. Forward ray tracing is a popular approach to determine traveling paths and arrival times but is ill suited for inverse problems since a large number of rays have to be computed in order to arrive at prescribed end points. In this contribution we discuss boundary value problems for acoustic rays, where the ray path between two given points is determined by solving the eikonal equation. The implementation of such a two point boundary value ray tracer for sound field simulations through an austenitic weld is described and its efficiency as well as the obtained results are compared to those of a forward ray tracer. The results are validated by comparison with experimental results and commercially available UT simulation tools. As an application, we discuss an implementation of the method for SAFT (Synthetic Aperture Focusing Technique) reconstruction. The ray tracer calculates the required travel time through the anisotropic columnar grain structure of the austenitic weld. There, the formulation of ray tracing as a boundary value problem allows a straightforward derivation of the ray path from a given transducer position to any pixel in the reconstruction area and reduces the computational cost considerably.}, language = {en} } @inproceedings{GoetschelTycowiczPolthieretal., author = {G{\"o}tschel, Sebastian and Tycowicz, Christoph von and Polthier, Konrad and Weiser, Martin}, title = {Reducing Memory Requirements in Scientific Computing and Optimal Control}, series = {Multiple Shooting and Time Domain Decomposition Methods}, booktitle = {Multiple Shooting and Time Domain Decomposition Methods}, editor = {Carraro, T. and Geiger, M. and Koerkel, S. and Rannacher, R.}, publisher = {Springer}, pages = {263 -- 287}, language = {en} } @article{GoetschelNagaiahKunischetal., author = {G{\"o}tschel, Sebastian and Nagaiah, Chamakuri and Kunisch, Karl and Weiser, Martin}, title = {Lossy Compression in Optimal Control of Cardiac Defibrillation}, series = {J. Sci. Comput.}, volume = {60}, journal = {J. Sci. Comput.}, number = {1}, doi = {10.1007/s10915-013-9785-x}, pages = {35 -- 59}, abstract = {This paper presents efficient computational techniques for solving an optimization problem in cardiac defibrillation governed by the monodomain equations. Time-dependent electrical currents injected at different spatial positions act as the control. Inexact Newton-CG methods are used, with reduced gradient computation by adjoint solves. In order to reduce the computational complexity, adaptive mesh refinement for state and adjoint equations is performed. To reduce the high storage and bandwidth demand imposed by adjoint gradient and Hessian-vector evaluations, a lossy compression technique for storing trajectory data is applied. An adaptive choice of quantization tolerance based on error estimates is developed in order to ensure convergence. The efficiency of the proposed approach is demonstrated on numerical examples.}, language = {en} } @article{GoetschelWeiser, author = {G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Lossy Compression for PDE-constrained Optimization: Adaptive Error Control}, series = {Comput. Optim. Appl.}, volume = {62}, journal = {Comput. Optim. Appl.}, number = {1}, publisher = {Springer}, pages = {131 -- 155}, abstract = {For the solution of optimal control problems governed by nonlinear parabolic PDEs, methods working on the reduced objective functional are often employed to avoid a full spatio-temporal discretization of the problem. The evaluation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the ad-joint equation. The state enters into the adjoint equation, requiring the storage of a full 4D data set. If Newton-CG methods are used, two additional trajectories have to be stored. To get numerical results which are accurate enough, in many case very fine discretizations in time and space are necessary, which leads to a significant amount of data to be stored and transmitted to mass storage. Lossy compression methods were developed to overcome the storage problem by reducing the accuracy of the stored trajectories. The inexact data induces errors in the reduced gradient and reduced Hessian. In this paper, we analyze the influence of such a lossy trajectory compression method on Newton-CG methods for optimal control of parabolic PDEs and design an adaptive strategy for choosing appropriate quantization tolerances.}, language = {en} } @phdthesis{Goetschel, author = {G{\"o}tschel, Sebastian}, title = {Adaptive Lossy Trajectory Compression for Optimal Control of Parabolic PDEs}, abstract = {Optimal control problems governed by nonlinear, time-dependent PDEs on three-dimensional spatial domains are an important tool in many fields, ranging from engineering applications to medicine. For the solution of such optimization problems, methods working on the reduced objective functional are often employed to avoid a full spatio-temporal discretization of the problem. The evaluation of the reduced gradient requires one solve of the state equation forward in time, and one backward solve of the adjoint equation. The state enters into the adjoint equation, requiring the storage of a full 4D data set. If Newton-CG methods are used, two additional trajectories have to be stored. To get numerical results that are accurate enough, in many cases very fine discretizations in time and space are necessary, leading to a significant amount of data to be stored and transmitted to mass storage. This thesis deals with the development and analysis of methods for lossy compression of such finite element solutions. The algorithms are based on a change of basis to reduce correlations in the data, combined with quantization. This is achieved by transforming the finite element coefficient vector from the nodal to the hierarchical basis, followed by rounding the coefficients to a prescribed precision. Due to the inexact reconstruction, and thus inexact data for the adjoint equation, the error induced in the reduced gradient, and reduced Hessian, has to be controlled, to not impede convergence of the optimization. Accuracy requirements of different optimization methods are analyzed, and computable error estimates for the influence of lossy trajectory storage are derived. These tools are used to adaptively control the accuracy of the compressed data. The efficiency of the algorithms is demonstrated on several numerical examples, ranging from a simple linear, scalar equation to a semi-linear system of reaction-diffusion equations. In all examples considerable reductions in storage space and bandwidth requirements are achieved, without significantly influencing the convergence behavior of the optimization methods. Finally, to go beyond pointwise error control, the hierarchical basis transform can be replaced by more sophisticated wavelet transforms. Numerical experiments indicate that choosing suitable norms for error control allows higher compression factors.}, language = {en} } @article{GoetschelWeiserMaierhoferetal., author = {G{\"o}tschel, Sebastian and Weiser, Martin and Maierhofer, Christiane and Richter, Regina and R{\"o}llig, Mathias}, title = {Fast Defect Shape Reconstruction Based on the Travel Time in Pulse Thermography}, series = {Nondestructive Testing of Materials and Structures}, volume = {6}, journal = {Nondestructive Testing of Materials and Structures}, pages = {83 -- 89}, language = {en} } @article{WeberFischerDamerauetal., author = {Weber, Marie-Christin and Fischer, Lisa and Damerau, Alexandra and Ponomarev, Igor and Pfeiffenberger, Moritz and Gaber, Timo and G{\"o}tschel, Sebastian and Lang, Jens and R{\"o}blitz, Susanna and Buttgereit, Frank and Ehrig, Rainald and Lang, Annemarie}, title = {In vitro and in silico modeling of cellular and matrix-related changes during the early phase of osteoarthritis}, series = {BioRxiv}, journal = {BioRxiv}, doi = {10.1101/725317}, abstract = {Understanding the pathophysiological processes of osteoarthritis (OA) require adequate model systems. Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific parts of the disease. This study aimed to combine in vitro and in silico modeling to describe cellular and matrix-related changes during the early phase of OA. We developed an in vitro OA model based on scaffold-free cartilage-like constructs (SFCCs), which was mathematically modeled using a partial differential equation (PDE) system to resemble the processes during the onset of OA. SFCCs were produced from mesenchymal stromal cells and analyzed weekly by histology and qPCR to characterize the cellular and matrix-related composition. To simulate the early phase of OA, SFCCs were treated with interleukin-1β (IL-1β), tumor necrosis factor α (TNFα) and examined after 3 weeks or cultivated another 3 weeks without inflammatory cytokines to validate the regeneration potential. Mathematical modeling was performed in parallel to the in vitro experiments. SFCCs expressed cartilage-specific markers, and after stimulation an increased expression of inflammatory markers, matrix degrading enzymes, a loss of collagen II (Col-2) and a reduced cell density was observed which could be partially reversed by retraction of stimulation. Based on the PDEs, the distribution processes within the SFCCs, including those of IL-1β, Col-2 degradation and cell number reduction was simulated. By combining in vitro and in silico methods, we aimed to develop a valid, efficient alternative approach to examine and predict disease progression and new therapeutic strategies.}, language = {en} } @article{WeberFischerDamerauetal., author = {Weber, Marie-Christin and Fischer, Lisa and Damerau, Alexandra and Ponomarev, Igor and Pfeiffenberger, Moritz and Gaber, Timo and G{\"o}tschel, Sebastian and Lang, Jens and R{\"o}blitz, Susanna and Buttgereit, Frank and Ehrig, Rainald and Lang, Annemarie}, title = {Macroscale mesenchymal condensation to study cytokine-driven cellular and matrix-related changes during cartilage degradation}, series = {Biofabrication}, volume = {12}, journal = {Biofabrication}, number = {4}, doi = {10.1088/1758-5090/aba08f}, abstract = {Understanding the pathophysiological processes of cartilage degradation requires adequate model systems to develop therapeutic strategies towards osteoarthritis (OA). Although different in vitro or in vivo models have been described, further comprehensive approaches are needed to study specific disease aspects. This study aimed to combine in vitro and in silico modeling based on a tissue-engineering approach using mesenchymal condensation to mimic cytokine-induced cellular and matrix-related changes during cartilage degradation. Thus, scaffold-free cartilage-like constructs (SFCCs) were produced based on self-organization of mesenchymal stromal cells (mesenchymal condensation) and i) characterized regarding their cellular and matrix composition or secondly ii) treated with interleukin-1β (IL-1β) and tumor necrosis factor α (TNFα) for 3 weeks to simulate OA-related matrix degradation. In addition, an existing mathematical model based on partial differential equations was optimized and transferred to the underlying settings to simulate distribution of IL-1β, type II collagen degradation and cell number reduction. By combining in vitro and in silico methods, we aim to develop a valid, efficient alternative approach to examine and predict disease progression and effects of new therapeutics.}, language = {en} } @article{GoetschelMinion, author = {G{\"o}tschel, Sebastian and Minion, Michael L.}, title = {An Efficient Parallel-in-Time Method for Optimization with Parabolic PDEs}, series = {SIAM J. Sci. Comput.}, volume = {41}, journal = {SIAM J. Sci. Comput.}, number = {6}, doi = {10.1137/19M1239313}, pages = {C603 -- C626}, abstract = {To solve optimization problems with parabolic PDE constraints, often methods working on the reduced objective functional are used. They are computationally expensive due to the necessity of solving both the state equation and a backward-in-time adjoint equation to evaluate the reduced gradient in each iteration of the optimization method. In this study, we investigate the use of the parallel-in-time method PFASST in the setting of PDE-constrained optimization. In order to develop an efficient fully time-parallel algorithm, we discuss different options for applying PFASST to adjoint gradient computation, including the possibility of doing PFASST iterations on both the state and the adjoint equations simultaneously. We also explore the additional gains in efficiency from reusing information from previous optimization iterations when solving each equation. Numerical results for both a linear and a nonlinear reaction-diffusion optimal control problem demonstrate the parallel speedup and efficiency of different approaches.}, language = {en} } @misc{GoetschelWeiser, author = {G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Lossy Compression for Large Scale PDE Problems}, issn = {1438-0064}, doi = {10.1101/506378}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-73817}, abstract = {Solvers for partial differential equations (PDE) are one of the cornerstones of computational science. For large problems, they involve huge amounts of data that needs to be stored and transmitted on all levels of the memory hierarchy. Often, bandwidth is the limiting factor due to relatively small arithmetic intensity, and increasingly so due to the growing disparity between computing power and bandwidth. Consequently, data compression techniques have been investigated and tailored towards the specific requirements of PDE solvers during the last decades. This paper surveys data compression challenges and corresponding solution approaches for PDE problems, covering all levels of the memory hierarchy from mass storage up to main memory. Exemplarily, we illustrate concepts at particular methods, and give references to alternatives.}, language = {en} } @article{GoetschelWeiser, author = {G{\"o}tschel, Sebastian and Weiser, Martin}, title = {Compression Challenges in Large Scale Partial Differential Equation Solvers}, series = {Algorithms}, volume = {12}, journal = {Algorithms}, number = {9}, doi = {10.3390/a12090197}, pages = {197}, abstract = {Solvers for partial differential equations (PDEs) are one of the cornerstones of computational science. For large problems, they involve huge amounts of data that need to be stored and transmitted on all levels of the memory hierarchy. Often, bandwidth is the limiting factor due to the relatively small arithmetic intensity, and increasingly due to the growing disparity between computing power and bandwidth. Consequently, data compression techniques have been investigated and tailored towards the specific requirements of PDE solvers over the recent decades. This paper surveys data compression challenges and discusses examples of corresponding solution approaches for PDE problems, covering all levels of the memory hierarchy from mass storage up to the main memory. We illustrate concepts for particular methods, with examples, and give references to alternatives.}, language = {en} } @article{GoetschelSchielaWeiser, author = {G{\"o}tschel, Sebastian and Schiela, Anton and Weiser, Martin}, title = {Kaskade 7 - a Flexible Finite Element Toolbox}, series = {Computers and Mathematics with Applications}, volume = {81}, journal = {Computers and Mathematics with Applications}, doi = {10.1016/j.camwa.2020.02.011}, pages = {444 -- 458}, abstract = {Kaskade 7 is a finite element toolbox for the solution of stationary or transient systems of partial differential equations, aimed at supporting application-oriented research in numerical analysis and scientific computing. The library is written in C++ and is based on the \textsc{Dune} interface. The code is independent of spatial dimension and works with different grid managers. An important feature is the mix-and-match approach to discretizing systems of PDEs with different ansatz and test spaces for all variables. We describe the mathematical concepts behind the library as well as its structure, illustrating its use at several examples on the way.}, language = {en} } @misc{GoetschelSchielaWeiser, author = {G{\"o}tschel, Sebastian and Schiela, Anton and Weiser, Martin}, title = {Kaskade 7 -- a Flexible Finite Element Toolbox}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74616}, abstract = {Kaskade 7 is a finite element toolbox for the solution of stationary or transient systems of partial differential equations, aimed at supporting application-oriented research in numerical analysis and scientific computing. The library is written in C++ and is based on the Dune interface. The code is independent of spatial dimension and works with different grid managers. An important feature is the mix-and-match approach to discretizing systems of PDEs with different ansatz and test spaces for all variables. We describe the mathematical concepts behind the library as well as its structure, illustrating its use at several examples on the way.}, language = {en} } @misc{GoetschelMinion, author = {G{\"o}tschel, Sebastian and Minion, Michael L.}, title = {An Efficient Parallel-in-Time Method for Optimization with Parabolic PDEs}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-71490}, abstract = {To solve optimization problems with parabolic PDE constraints, often methods working on the reduced objective functional are used. They are computationally expensive due to the necessity of solving both the state equation and a backward-in-time adjoint equation to evaluate the reduced gradient in each iteration of the optimization method. In this study, we investigate the use of the parallel-in-time method PFASST in the setting of PDE constrained optimization. In order to develop an efficient fully time-parallel algorithm we discuss different options for applying PFASST to adjoint gradient computation, including the possibility of doing PFASST iterations on both the state and adjoint equations simultaneously. We also explore the additional gains in efficiency from reusing information from previous optimization iterations when solving each equation. Numerical results for both a linear and a non-linear reaction-diffusion optimal control problem demonstrate the parallel speedup and efficiency of different approaches.}, language = {en} }