TY - CHAP A1 - Lößer, Ansgar A1 - Schlecht, Max A1 - Schintke, Florian A1 - Witzke, Joel A1 - Weidlich, Matthias A1 - Scheuermann, Björn T1 - Fast Min-ϵ Segmented Regression using Constant-Time Segment Merging T2 - Proceedings of the 42nd International Conference on Machine Learning Y1 - 2025 UR - https://proceedings.mlr.press/v267/losser25a.html VL - 267 SP - 40312 EP - 40327 ER - TY - JOUR A1 - Agarwal, A. A1 - Greve, Nico A1 - Reinefeld, Alexander A1 - Schintke, Florian A1 - et al., T1 - Performance of the prototype Silicon Tracking System of the CBM experiment tested with heavy-ion beams at SIS18 JF - Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment Y1 - 2025 U6 - https://doi.org/10.1016/j.nima.2025.171059 SN - 0168-9002 N1 - This paper has 343 authors. For the complete list of authors use the DOI, please. VL - 1082 SP - 171059 PB - Elsevier BV ER - TY - CHAP A1 - Clausecker, Robert A1 - Schintke, Florian T1 - A Measure of Quality for IDA* Heuristics T2 - Proceedings of the Fourteenth International Symposium on Combinatorial Search (SoCS 2021) Y1 - 2021 N1 - Best SoCS21 paper award SP - 55 EP - 63 ER - TY - JOUR A1 - Alhaddad, Samer A1 - Förstner, Jens A1 - Groth, Stefan A1 - Grünewald, Daniel A1 - Grynko, Yevgen A1 - Hannig, Frank A1 - Kenter, Tobias A1 - Pfreundt, F.J. A1 - Plessl, Christian A1 - Schotte, Merlind A1 - Steinke, Thomas A1 - Teich, J. A1 - Weiser, Martin A1 - Wende, Florian T1 - The HighPerMeshes Framework for Numerical Algorithms on Unstructured Grids JF - Concurrency and Computation: Practice and Experience N2 - Solving PDEs on unstructured grids is a cornerstone of engineering and scientific computing. Heterogeneous parallel platforms, including CPUs, GPUs, and FPGAs, enable energy-efficient and computationally demanding simulations. In this article, we introduce the HPM C++-embedded DSL that bridges the abstraction gap between the mathematical formulation of mesh-based algorithms for PDE problems on the one hand and an increasing number of heterogeneous platforms with their different programming models on the other hand. Thus, the HPM DSL aims at higher productivity in the code development process for multiple target platforms. We introduce the concepts as well as the basic structure of the HPM DSL, and demonstrate its usage with three examples. The mapping of the abstract algorithmic description onto parallel hardware, including distributed memory compute clusters, is presented. A code generator and a matching back end allow the acceleration of HPM code with GPUs. Finally, the achievable performance and scalability are demonstrated for different example problems. Y1 - 2022 U6 - https://doi.org/10.1002/cpe.6616 VL - 34 IS - 14 ER - TY - CHAP A1 - Kaiser, Benjamin A1 - Clausecker, Robert T1 - CleanMaple T2 - Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions Y1 - 2021 UR - http://hdl.handle.net/10138/333647 SP - 24 ER - TY - CHAP A1 - Kaiser, Benjamin A1 - Clausecker, Robert T1 - CleanMaple_PriPro, CaDiCaL_PriPro and CaDiCaL_PriPro_no_bin T2 - Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions Y1 - 2021 UR - http://hdl.handle.net/10138/333647 N1 - CaDiCaL_PriPro won the Special Innovation Price at the SAT Competition 2021 SP - 25 ER - TY - JOUR A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - Höfling, Felix T1 - Stochastic pH oscillations in a model of the urea–urease reaction confined to lipid vesicles JF - J. Phys. Chem. Lett. N2 - The urea-urease clock reaction is a pH switch from acid to basic that can turn into a pH oscillator if it occurs inside a suitable open reactor. We numerically study the confinement of the reaction to lipid vesicles, which permit the exchange with an external reservoir by differential transport, enabling the recovery of the pH level and yielding a constant supply of urea molecules. For microscopically small vesicles, the discreteness of the number of molecules requires a stochastic treatment of the reaction dynamics. Our analysis shows that intrinsic noise induces a significant statistical variation of the oscillation period, which increases as the vesicles become smaller. The mean period, however, is found to be remarkably robust for vesicle sizes down to approximately 200 nm, but the periodicity of the rhythm is gradually destroyed for smaller vesicles. The observed oscillations are explained as a canard-like limit cycle that differs from the wide class of conventional feedback oscillators. Y1 - 2021 U6 - https://doi.org/10.1021/acs.jpclett.1c03016 VL - 12 SP - 9888 EP - 9893 ER - TY - CHAP A1 - Fürst, Steffen A1 - Rakow, Christian T1 - Parallelization of large-scale agent-based epidemiological simulations T2 - Proceedings of the 34th European Modeling & Simulation Symposium N2 - Agent-based epidemiological models have been applied widely successfully during the SARS-CoV-2 pandemic and assisted policymakers in assessing the effectiveness of intervention strategies. The computational complexity of agent-based models is still challenging, and therefore it is important to utilize modern multi-core systems as good as possible. In this paper, we are presenting our work on parallelizing the epidemiological simulation model MATSim Episim. Episim combines a large-scale person-centric human mobility model with a mechanistic model of infection and a person-centric disease progression model. In general, the parallelization of agent-based models with an inherent sequential structure — in the case of epidemiological models, the temporal order of the individual movements of the agents — is challenging. Especially when the underlying social network is irregular and dynamic, they require frequent communication between the processing elements. In Episim, however, we were able to take advantage of the fact that people are not contagious on the same day they become infected, and therefore immediate health synchronization is not required. By parallelizing some of the most computationally intensive submodels, we are now able to run MATSim Episim simulations up to eight times faster than the serial version. This makes it feasible to increase the number of agents, e.g. to run simulations for the whole of Germany instead of just Berlin as before. Y1 - 2022 U6 - https://doi.org/https://doi.org/10.46354/i3m.2022.emss.008 ER - TY - JOUR A1 - Höfling, Felix A1 - Dietrich, Siegfried T1 - Finite-size corrections for the static structure factor of a liquid slab with open boundaries JF - The Journal of Chemical Physics N2 - The presence of a confining boundary can modify the local structure of a liquid markedly. In addition, small samples of finite size are known to exhibit systematic deviations of thermodynamic quantities relative to their bulk values. Here, we consider the static structure factor of a liquid sample in slab geometry with open boundaries at the surfaces, which can be thought of as virtually cutting out the sample from a macroscopically large, homogeneous fluid. This situation is a relevant limit for the interpretation of grazing-incidence diffraction experiments at liquid interfaces and films. We derive an exact, closed expression for the slab structure factor, with the bulk structure factor as the only input. This shows that such free boundary conditions cause significant differences between the two structure factors, in particular, at small wavenumbers. An asymptotic analysis of this result yields the scaling exponent and an accurate, useful approximation of these finite-size corrections. Furthermore, the open boundaries permit the interpretation of the slab as an open system, supporting particle exchange with a reservoir. We relate the slab structure factor to the particle number fluctuations and discuss conditions under which the subvolume of the slab represents a grand canonical ensemble with chemical potential μ and temperature T. Thus, the open slab serves as a test-bed for the small-system thermodynamics in a μT reservoir. We provide a microscopically justified and exact result for the size dependence of the isothermal compressibility. Our findings are corroborated by simulation data for Lennard-Jones liquids at two representative temperatures. Y1 - 2020 U6 - https://doi.org/10.1063/5.0017923 VL - 153 SP - 054119 ER - TY - JOUR A1 - Ebrahimi Viand, Roya A1 - Höfling, Felix A1 - Klein, Rupert A1 - Delle Site, Luigi T1 - Theory and simulation of open systems out of equilibrium JF - The Journal of Chemical Physics N2 - We consider the theoretical model of Bergmann and Lebowitz for open systems out of equilibrium and translate its principles in the adaptive resolution simulation molecular dynamics technique. We simulate Lennard-Jones fluids with open boundaries in a thermal gradient and find excellent agreement of the stationary responses with the results obtained from the simulation of a larger locally forced closed system. The encouraging results pave the way for a computational treatment of open systems far from equilibrium framed in a well-established theoretical model that avoids possible numerical artifacts and physical misinterpretations. Y1 - 2020 U6 - https://doi.org/10.1063/5.0014065 VL - 153 SP - 101102 ER - TY - CHAP A1 - Gholami, Masoud A1 - Schintke, Florian T1 - Combining XOR and Partner Checkpointing for Resilient Multilevel Checkpoint/Restart T2 - 2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS) Y1 - 2021 U6 - https://doi.org/10.1109/IPDPS49936.2021.00036 SP - 277 EP - 288 ER - TY - CHAP A1 - Thostrup, Lasse A1 - Skrzypczak, Jan A1 - Jasny, Matthias A1 - Ziegler, Tobias A1 - Binnig, Carsten T1 - DFI: The Data Flow Interface for High-Speed Networks T2 - SIGMOD '21: International Conference on Management of Data Y1 - 2021 U6 - https://doi.org/10.1145/3448016.3452816 SP - 1825 EP - 1837 PB - ACM ER - TY - JOUR A1 - Stein, Lewin A1 - Straube, Florian A1 - Weinzierl, Stefan A1 - Lemke, Mathias T1 - Directional sound source modeling using the adjoint Euler equations in a finite-difference time-domain approach JF - Acoustical Society of America N2 - An adjoint-based approach for synthesizing complex sound sources by discrete, grid-based monopoles in finite-difference time-domain simulations is presented. Previously [Stein et al., 2019a, J. Acoust. Soc. Am. 146(3), 1774–1785] demonstrated that the approach allows to consider unsteady and non-uniform ambient conditions such as wind flow and thermal gradient in contrast to standard methods of numerical sound field simulation. In this work, it is proven that not only ideal monopoles but also realistic sound sources with complex directivity characteristics can be synthesized. In detail, an oscillating circular piston and a real 2-way near-field monitor are modeled. The required number of monopoles in terms of the SPL deviation between the directivity of the original and the synthesized source is analyzed. Since the computational effort is independent of the number of monopoles used for the synthesis, also more complex sources can be reproduced by increasing the number of monopoles utilized. In contrast to classical least-square problem solvers, this does not increase the computational effort, which makes the method attractive for predicting the effect of sound reinforcement systems with highly directional sources under difficult acoustic boundary conditions. Y1 - 2020 U6 - https://doi.org/https://doi.org/10.1121/10.0002425 VL - 148 IS - 5 SP - 3075 EP - 3085 PB - The Journal of the Acoustical Society of America ER - TY - CHAP A1 - Lemke, Mathias A1 - Stein, Lewin T1 - Adjoint-Based Identification of Sound Sources for Sound Reinforcement and Source Localization T2 - Notes on Numerical Fluid Mechanics and Multidisciplinary Design N2 - The identification of sound sources is a common problem in acoustics. Different parameters are sought, among these are signal and position of the sources. We present an adjoint-based approach for sound source identification, which employs computational aeroacoustic techniques. Two different applications are presented as a proof-of-concept: optimization of a sound reinforcement setup and the localization of (moving) sound sources. Y1 - 2020 SN - 978-3-030-52429-6 U6 - https://doi.org/https://doi.org/10.1007/978-3-030-52429-6_17 VL - 145 SP - 263 EP - 278 PB - Springer, Cham ER - TY - GEN A1 - Lemke, Mathias A1 - Stein, Lewin A1 - Hölter, Arne A1 - Straube, Florian A1 - Weinzierl, Stefan ED - Peissig, Jürgen T1 - Synthese komplexer Richtcharakteristiken für eine Schallfeldoptimierung im Zeitbereich N2 - Die Bestimmung optimaler Treiberfunktionen von Lautsprechern in beliebiger Anordnung ist ein schlecht gestelltes Optimierungsproblem, da die Anzahl der Quellen immer erheblich kleiner als die Anzahl der Empfänger ist. Typischerweise werden frequenz-basierte Löser eingesetzt. In einem vorangegangenen Beitrag haben die Autoren einen Adjungierten-basierten Ansatz vorgestellt, um optimale Treiberfunktionen im Zeitbereich zu bestimmen. Die Methode erlaubt es, inhomogene Windprofile und Temperaturschichtungen einzubeziehen, die typischerweise bei auf der Wellengleichung beruhenden Lösungen nicht berücksichtigt werden. Daru ̈ber hinaus können komplexe Geometrien und Randbedingungen berücksichtigt werden. Bisher war diese Methode auf Monopolquellen beschränkt. Hier stellen die Autoren eine Erweiterung des Ansatzes in Bezug auf eine Adjungierten-basierte Monopolsynthese vor, die es ermöglicht, auch Quellen mit komplexen Richtcharakteristiken zu betrachten. Das Verfahren wird für typische Quellsignale und ein repräsentatives Lautsprechermodell mit komplexer Richtcharakteristik validiert. Y1 - 2020 SN - 978-3939296171 U6 - https://doi.org/https://doi.org/10.14279/depositonce-9997 PB - Deutsche Gesellschaft für Akustik e.V. ER - TY - CHAP A1 - Christgau, Steffen A1 - Knaust, Marius A1 - Steinke, Thomas T1 - A First Step towards Support for MPI Partitioned Communication on SYCL-programmed FPGAs T2 - IEEE/ACM International Workshop on Heterogeneous High-performance Reconfigurable Computing, H2RC@SC 2022, Dallas, TX, USA, November 13-18, 2022 N2 - Version 4.0 of the Message Passing Interface standard introduced the concept of Partitioned Communication which adds support for multiple contributions to a communication buffer. Although initially targeted at multithreaded MPI applications, Partitioned Communication currently receives attraction in the context of accelerators, especially GPUs. In this publication it is demonstrated that this communication concept can also be implemented for SYCL-programmed FPGAs. This includes a discussion of the design space and the presentation of a prototypical implementation. Experimental results show that a lightweight implementation on top of an existing MPI library is possible. In addition, the presented approach also reveals issues in both the SYCL and the MPI standard which need to be addresses for improved support of the intended communication style. Y1 - 2022 U6 - https://doi.org/10.1109/H2RC56700.2022.00007 SP - 9 EP - 17 PB - IEEE ER - TY - CHAP A1 - Läuter, Matthias A1 - Kramer, Tobias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Determination of the ice composition near the surface of comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - During the apparition of comet 67P/Churyumov-Gerasimenko (67P/C-G) solar irradiation causes varying rates for sublimation of volatile species from the cometary nucleus. Because sublimation processes take place close to the cometary surface, the relative abundance of volatiles in the coma and the ice composition are related to each other. To quantify this relation we assume a model for the expansion of a collisionless gas from the surface into the surrounding space. We use an inverse model approach to relate the in situ measurements of gas densities from the two Rosetta instruments COPS (COmet Pressure Sensor) and DFMS (Double Focusing Mass Spectrometer) at the positions of the spacecraft to the locations of surface gas emissions during the Rosetta mission 2014-2016. We assume the temporally integrated gas emissions to be representative for the ice composition close to the surface. Our analysis shows characteristic differences in the ice compositions between both hemispheres of 67P/C-G. In particular CO2 ice has a reduced abundance on the northern hemisphere. In contrast to the hemispherical differences, the two lobes do not show significant differences in terms of their ice composition. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-826 SP - EPSC2022-826 ER - TY - CHAP A1 - Brook, Glenn A1 - Fuller, Douglas A1 - Swinburne, John A1 - Christgau, Steffen A1 - Läuter, Matthias A1 - Rodrigues Pelá, Ronaldo A1 - Lewin, Stein A1 - Christian, Tuma A1 - Steinke, Thomas T1 - An Early Scalability Study of Omni-Path Express N2 - This work provides a brief description of Omni-Path Express and the current status of its development, stability, and performance. Basic benchmarks that highlight the gains of OPX over PSM2 are provided, and the results of an initial performance and scalability study of several applications are presented. Y1 - 2022 UR - https://www.ixpug.org/events/isc22-ixpug-workshop U6 - https://doi.org/10.13140/RG.2.2.21353.57442 CY - Hamburg ER - TY - GEN A1 - Straube, Arthur A1 - Winkelmann, Stefanie A1 - Höfling, Felix T1 - Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles N2 - Our theoretical study concerns an urea-urease-based pH oscillator confined to giant lipid vesicles. Under suitable conditions, differential transport of urea and hydrogen ion across the unilamellar vesicle membrane periodically resets the pH clock that switches the system from acid to basic, resulting in self-sustained oscillations. We analyse the structure of the limit cycle, which controls the dynamics for giant vesicles and dominates the strongly stochastic oscillations in small vesicles of submicrometer size. To this end, we derive reduced models, amenable to analytic treatments, and show that the accuracy of predictions, including the period of oscillations, is highly sensitive to the choice of the reduction scheme. In particular, we suggest an accurate two-variable model and show its equivalence to a three-variable model that admits an interpretation in terms of a chemical reaction network. The accurate description of a single pH oscillator appears crucial for rationalizing experiments and understanding communication of vesicles and synchronization of rhythms. T3 - ZIB-Report - 22-21 Y1 - 2022 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-88179 SN - 1438-0064 ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - The near nucleus gas and dust environment around comet 67P/Churyumov-Gerasimenko T2 - Europlanet Science Congress N2 - The Rosetta mission to comet 67P/C-G provided a detailed view of the near nucleus environment of an active Jupiter family comet. The continuous monitoring of the gas pressure with the ROSINA experiment at the location of the Rosetta spacecraft in combination with the images of the dust environment acquired by the OSIRIS cameras allows one to test different hypotheses about the origin of the dust and gas emissions. In addition the orbital elements and the rotation axis and spin rate of the nucleus are affected by the gas release. Y1 - 2022 U6 - https://doi.org/10.5194/epsc2022-281 SP - EPSC2022-281 ER -