@inproceedings{LoesserSchlechtSchintkeetal.2025, author = {L{\"o}ßer, Ansgar and Schlecht, Max and Schintke, Florian and Witzke, Joel and Weidlich, Matthias and Scheuermann, Bj{\"o}rn}, title = {Fast Min-ϵ Segmented Regression using Constant-Time Segment Merging}, volume = {267}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, pages = {40312 -- 40327}, year = {2025}, language = {en} } @article{AgarwalGreveReinefeldetal.2025, author = {Agarwal, A. and Greve, Nico and Reinefeld, Alexander and Schintke, Florian and et al.,}, title = {Performance of the prototype Silicon Tracking System of the CBM experiment tested with heavy-ion beams at SIS18}, volume = {1082}, journal = {Nuclear Instruments and Methods in Physics Research Section A: Accelerators, Spectrometers, Detectors and Associated Equipment}, publisher = {Elsevier BV}, issn = {0168-9002}, arxiv = {http://arxiv.org/abs/2505.20517}, doi = {10.1016/j.nima.2025.171059}, pages = {171059}, year = {2025}, language = {en} } @inproceedings{ClauseckerSchintke2021, author = {Clausecker, Robert and Schintke, Florian}, title = {A Measure of Quality for IDA* Heuristics}, booktitle = {Proceedings of the Fourteenth International Symposium on Combinatorial Search (SoCS 2021)}, pages = {55 -- 63}, year = {2021}, language = {en} } @article{AlhaddadFoerstnerGrothetal.2022, author = {Alhaddad, Samer and F{\"o}rstner, Jens and Groth, Stefan and Gr{\"u}newald, Daniel and Grynko, Yevgen and Hannig, Frank and Kenter, Tobias and Pfreundt, F.J. and Plessl, Christian and Schotte, Merlind and Steinke, Thomas and Teich, J. and Weiser, Martin and Wende, Florian}, title = {The HighPerMeshes Framework for Numerical Algorithms on Unstructured Grids}, volume = {34}, journal = {Concurrency and Computation: Practice and Experience}, number = {14}, doi = {10.1002/cpe.6616}, year = {2022}, abstract = {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.}, language = {en} } @inproceedings{KaiserClausecker2021, author = {Kaiser, Benjamin and Clausecker, Robert}, title = {CleanMaple}, booktitle = {Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions}, pages = {24}, year = {2021}, language = {en} } @inproceedings{KaiserClausecker2021, author = {Kaiser, Benjamin and Clausecker, Robert}, title = {CleanMaple_PriPro, CaDiCaL_PriPro and CaDiCaL_PriPro_no_bin}, booktitle = {Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions}, pages = {25}, year = {2021}, language = {en} } @article{StraubeWinkelmannSchuetteetal.2021, author = {Straube, Arthur and Winkelmann, Stefanie and Sch{\"u}tte, Christof and H{\"o}fling, Felix}, title = {Stochastic pH oscillations in a model of the urea-urease reaction confined to lipid vesicles}, volume = {12}, journal = {J. Phys. Chem. Lett.}, doi = {10.1021/acs.jpclett.1c03016}, pages = {9888 -- 9893}, year = {2021}, abstract = {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.}, language = {en} } @inproceedings{FuerstRakow2022, author = {F{\"u}rst, Steffen and Rakow, Christian}, title = {Parallelization of large-scale agent-based epidemiological simulations}, booktitle = {Proceedings of the 34th European Modeling \& Simulation Symposium}, doi = {https://doi.org/10.46354/i3m.2022.emss.008}, year = {2022}, abstract = {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.}, language = {en} } @article{HoeflingDietrich2020, author = {H{\"o}fling, Felix and Dietrich, Siegfried}, title = {Finite-size corrections for the static structure factor of a liquid slab with open boundaries}, volume = {153}, journal = {The Journal of Chemical Physics}, doi = {10.1063/5.0017923}, pages = {054119}, year = {2020}, abstract = {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.}, language = {en} } @article{EbrahimiViandHoeflingKleinetal.2020, author = {Ebrahimi Viand, Roya and H{\"o}fling, Felix and Klein, Rupert and Delle Site, Luigi}, title = {Theory and simulation of open systems out of equilibrium}, volume = {153}, journal = {The Journal of Chemical Physics}, doi = {10.1063/5.0014065}, pages = {101102}, year = {2020}, abstract = {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.}, language = {en} } @inproceedings{GholamiSchintke2021, author = {Gholami, Masoud and Schintke, Florian}, title = {Combining XOR and Partner Checkpointing for Resilient Multilevel Checkpoint/Restart}, booktitle = {2021 IEEE International Parallel and Distributed Processing Symposium (IPDPS)}, doi = {10.1109/IPDPS49936.2021.00036}, pages = {277 -- 288}, year = {2021}, language = {en} } @inproceedings{ThostrupSkrzypczakJasnyetal.2021, author = {Thostrup, Lasse and Skrzypczak, Jan and Jasny, Matthias and Ziegler, Tobias and Binnig, Carsten}, title = {DFI: The Data Flow Interface for High-Speed Networks}, booktitle = {SIGMOD '21: International Conference on Management of Data}, publisher = {ACM}, doi = {10.1145/3448016.3452816}, pages = {1825 -- 1837}, year = {2021}, language = {en} } @article{SteinStraubeWeinzierletal.2020, author = {Stein, Lewin and Straube, Florian and Weinzierl, Stefan and Lemke, Mathias}, title = {Directional sound source modeling using the adjoint Euler equations in a finite-difference time-domain approach}, volume = {148}, journal = {Acoustical Society of America}, number = {5}, publisher = {The Journal of the Acoustical Society of America}, doi = {https://doi.org/10.1121/10.0002425}, pages = {3075 -- 3085}, year = {2020}, abstract = {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.}, language = {en} } @incollection{LemkeStein2020, author = {Lemke, Mathias and Stein, Lewin}, title = {Adjoint-Based Identification of Sound Sources for Sound Reinforcement and Source Localization}, volume = {145}, booktitle = {Notes on Numerical Fluid Mechanics and Multidisciplinary Design}, publisher = {Springer, Cham}, isbn = {978-3-030-52429-6}, doi = {https://doi.org/10.1007/978-3-030-52429-6_17}, pages = {263 -- 278}, year = {2020}, abstract = {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.}, language = {en} } @misc{LemkeSteinHoelteretal.2020, author = {Lemke, Mathias and Stein, Lewin and H{\"o}lter, Arne and Straube, Florian and Weinzierl, Stefan}, title = {Synthese komplexer Richtcharakteristiken f{\"u}r eine Schallfeldoptimierung im Zeitbereich}, editor = {Peissig, J{\"u}rgen}, publisher = {Deutsche Gesellschaft f{\"u}r Akustik e.V.}, isbn = {978-3939296171}, doi = {https://doi.org/10.14279/depositonce-9997}, year = {2020}, abstract = {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 Empf{\"a}nger ist. Typischerweise werden frequenz-basierte L{\"o}ser 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 L{\"o}sungen nicht ber{\"u}cksichtigt werden. Daru ̈ber hinaus k{\"o}nnen komplexe Geometrien und Randbedingungen ber{\"u}cksichtigt werden. Bisher war diese Methode auf Monopolquellen beschr{\"a}nkt. Hier stellen die Autoren eine Erweiterung des Ansatzes in Bezug auf eine Adjungierten-basierte Monopolsynthese vor, die es erm{\"o}glicht, auch Quellen mit komplexen Richtcharakteristiken zu betrachten. Das Verfahren wird f{\"u}r typische Quellsignale und ein repr{\"a}sentatives Lautsprechermodell mit komplexer Richtcharakteristik validiert.}, language = {de} } @inproceedings{ChristgauKnaustSteinke2022, author = {Christgau, Steffen and Knaust, Marius and Steinke, Thomas}, title = {A First Step towards Support for MPI Partitioned Communication on SYCL-programmed FPGAs}, booktitle = {IEEE/ACM International Workshop on Heterogeneous High-performance Reconfigurable Computing, H2RC@SC 2022, Dallas, TX, USA, November 13-18, 2022}, publisher = {IEEE}, doi = {10.1109/H2RC56700.2022.00007}, pages = {9 -- 17}, year = {2022}, abstract = {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.}, language = {en} } @inproceedings{LaeuterKramerRubinetal.2022, author = {L{\"a}uter, Matthias and Kramer, Tobias and Rubin, Martin and Altwegg, Kathrin}, title = {Determination of the ice composition near the surface of comet 67P/Churyumov-Gerasimenko}, booktitle = {Europlanet Science Congress}, doi = {10.5194/epsc2022-826}, pages = {EPSC2022-826}, year = {2022}, abstract = {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.}, language = {en} } @inproceedings{BrookFullerSwinburneetal.2022, author = {Brook, Glenn and Fuller, Douglas and Swinburne, John and Christgau, Steffen and L{\"a}uter, Matthias and Rodrigues Pel{\´a}, Ronaldo and Lewin, Stein and Christian, Tuma and Steinke, Thomas}, title = {An Early Scalability Study of Omni-Path Express}, address = {Hamburg}, organization = {ISC 2022 IXPUG}, doi = {10.13140/RG.2.2.21353.57442}, pages = {8}, year = {2022}, abstract = {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.}, language = {en} } @misc{StraubeWinkelmannHoefling2022, author = {Straube, Arthur and Winkelmann, Stefanie and H{\"o}fling, Felix}, title = {Accurate reduced models for the pH oscillations in the urea-urease reaction confined to giant lipid vesicles}, issn = {1438-0064}, doi = {10.12752/8817}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-88179}, year = {2022}, abstract = {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.}, language = {en} } @inproceedings{KramerLaeuter2022, author = {Kramer, Tobias and L{\"a}uter, Matthias}, title = {The near nucleus gas and dust environment around comet 67P/Churyumov-Gerasimenko}, booktitle = {Europlanet Science Congress}, doi = {10.5194/epsc2022-281}, pages = {EPSC2022-281}, year = {2022}, abstract = {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.}, language = {en} }