Library

Description: We prove the Fréchet differentiability with respect to the drift of Perron–Frobenius and Koopman operators associated to time-inhomogeneous ordinary stochastic differential equations. This result relies on a similar differentiability result for pathwise expectations of path functionals of the solution of the stochastic differential equation, which we establish using Girsanov's formula. We demonstrate the significance of our result in the context of dynamical systems and operator theory, by proving continuously differentiable drift dependence of the simple eigen- and singular values and the corresponding eigen- and singular functions of the stochastic Perron–Frobenius and Koopman operators.

Description: General solutions of state machine replication have to ensure that all replicas apply the same commands in the same order, even in the presence of failures. Such strict ordering incurs high synchronization costs caused by distributed consensus or by the use of a leader. This paper presents a protocol for linearizable state machine replication of conflict-free replicated data types (CRDTs) that neither requires consensus nor a leader. By leveraging the properties of state-based CRDTs - in particular the monotonic growth of a join semilattice - synchronization overhead is greatly reduced. In addition, updates just need a single round trip and modify the state `in-place' without the need for a log. Furthermore, the message size overhead for coordination consists of a single counter per message. While reads in the presence of concurrent updates are not wait-free without a coordinator, we show that more than 97% of reads can be handled in one or two round trips under highly concurrent accesses. Our protocol achieves high throughput without auxiliary processes like command log management or leader election. It is well suited for all practical scenarios that need linearizable access on CRDT data on a fine-granular scale.

Description: Achieving efficient many-to-many communication on a given network topology is a challenging task when many data streams from different sources have to be scattered concurrently to many destinations with low variance in arrival times. In such scenarios, it is critical to saturate but not to congest the bisectional bandwidth of the network topology in order to achieve a good aggregate throughput. When there are many concurrent point-to-point connections, the communication pattern needs to be dynamically scheduled in a fine-grained manner to avoid network congestion (links, switches), overload in the node’s incoming links, and receive buffer overflow. Motivated by the use case of the Compressed Baryonic Matter experiment (CBM), we study the performance and variance of such communication patterns on a Cray XC40 with different routing schemes and scheduling approaches. We present a distributed Data Flow Scheduler (DFS) that reduces the variance of arrival times from all sources at least 30 times and increases the achieved aggregate bandwidth by up to 50%.

Description: Programs that process linearly indexed fields with structured element types in a data-parallel way usually suffer from the fact that compilers fail to generate efficient code if the selected data layout appears inappropriate for the chosen target architecture. If their internal heuristics cannot proof a performance gain from a data-parallel execution, compilers may fall back to scalar code generation. Data access through proxy types together with a customized container is one means to assist the compiler in generating efficient machine code in these cases without changing the user code. We present an automated proxy-type generator (using Clang’s LibTooling) and a configurable C++ container that supports different data layouts in a transparent way.

Description: The growing discrepancy between CPU computing power and memory bandwidth drives more and more numerical algorithms into a bandwidth- bound regime. One example is the overlapping Schwarz smoother, a highly effective building block for iterative multigrid solution of elliptic equations with higher order finite elements. Two options of reducing the required memory bandwidth are sparsity exploiting storage layouts and representing matrix entries with reduced precision in floating point or fixed point format. We investigate the impact of several options on storage demand and contraction rate, both analytically in the context of subspace correction methods and numerically at an example of solid mechanics. Both perspectives agree on the favourite scheme: fixed point representation of Cholesky factors in nested dissection storage.

Description: Das deutsche Projekt DeepGreen (https://deepgreen.kobv.de/de/deepgreen/) arbeitet an einer automatisierten Lösung, um Artikeldaten (Volltexte und Metadaten) von wissenschaftlichen Verlagen abzuholen und an Repositorien zu liefern, die diese Artikel wiederum Open Access veröffentlichen können. Ausgangspunkt für das Projekt sind die überregional geförderten deutschen Allianz-Lizenzen. Diese enthalten eine Open-Access-Komponente, die es Autor*innen oder deren Institution erlaubt, ihre Artikel nach einer verkürzten Embargofrist in einem Repositorium ihrer Wahl Open Access zugänglich zu machen. DeepGreen wird seit 2016 von der Deutschen Forschungsgemeinschaft gefördert (1. Förderphase: 01.2016–12.2017; 2. Förderphase: 08.2018–07.2020) und besteht aus einem Konsortium aus 6 Institutionen: Kooperativer Bibliotheksverbund Berlin-Brandenburg (KOBV), Bayerische Staatsbibliothek (BSB), Bibliotheksverbund Bayern (BVB), Universitätsbibliothek der Friedrich-Alexander-Universität Erlangen-Nürnberg (FAU), Helmholtz Open Science Koordinationsbüro am Deutschen GeoForschungsZentrum Potsdam (GFZ), Universitätsbibliothek der Technischen Universität Berlin (TUBB).

Description: The concept of reduction has frequently distinguished itself as a pivotal ingredient of exact solving approaches for the Steiner tree problem in graphs. In this paper we broaden the focus and consider reduction techniques for three Steiner problem variants that have been extensively discussed in the literature and entail various practical applications: The prize-collecting Steiner tree problem, the rooted prize-collecting Steiner tree problem and the maximum-weight connected subgraph problem. By introducing and subsequently deploying numerous new reduction methods, we are able to drastically decrease the size of a large number of benchmark instances, already solving more than 90 percent of them to optimality. Furthermore, we demonstrate the impact of these techniques on exact solving, using the example of the state-of-the-art Steiner problem solver SCIP-Jack.

Description: Empirical studies are fundamental in assessing the effectiveness of implementations of branch-and-bound algorithms. The complexity of such implementations makes empirical study difficult for a wide variety of reasons. Various attempts have been made to develop and codify a set of standard techniques for the assessment of optimization algorithms and their software implementations; however, most previous work has been focused on classical sequential algorithms. Since parallel computation has become increasingly mainstream, it is necessary to re-examine and modernize these practices. In this paper, we propose a framework for assessment based on the notion that resource consumption is at the heart of what we generally refer to as the “effectiveness” of an implementation. The proposed framework carefully distinguishes between an implementation’s baseline efficiency, the efficacy with which it utilizes a fixed allocation of resources, and its scalability, a measure of how the efficiency changes as resources (typically additional computing cores) are added or removed. Efficiency is typically applied to sequential implementations, whereas scalability is applied to parallel implementations. Efficiency and scalability are both important contributors in determining the overall effectiveness of a given parallel implementation, but the goal of improved efficiency is often at odds with the goal of improved scalability. Within the proposed framework, we review the challenges to effective evaluation and discuss the strengths and weaknesses of existing methods of assessment.

Description: Mit dem DFG-geförderten Projekt DeepGreen soll eine automatisierte, rechtssichere Lösung entwickelt werden, um Artikeldaten von wissenschaftlichen Verlagen abzuholen und anschließend, nach Ablauf etwaiger lizenzrechtlicher Embargofristen, an berechtigte Repositorien zu verteilen und somit in den Open Access zu überführen. Dabei liegt der Fokus auf den DFG-geförderten und überregional verhandelten Allianz-Lizenzen, mit spezieller Open-Access-Komponente. Die vorliegende Handreichung richtet sich speziell an die Betreiber institutioneller Repositorien und stellt Empfehlungen und einen Workflow bereit, um eine erfolgreiche Veröffentlichung, der durch die DeepGreen-Datendrehscheibe zugeordneten Artikel, zu ermöglichen. Die Handreichung basiert auf den bisherigen Erfahrungen der DeepGreen-Projektbeteiligten.

Description: To assess the influence of the alkali-silica reaction (ASR) on pavement concrete 3D-CT imaging has been applied to concrete samples. Prior to imaging these samples have been drilled out of a concrete beam pre-damaged by fatigue loading. The resulting high resolution 3D-CT images consist of several gigabytes of voxels. Current desktop computers can visualize such big datasets without problems but a visual inspection or manual segmentation of features such as cracks by experts can only be carried out on a few slices. A quantitative analysis of cracks requires a segmentation of the whole specimen which could only be done by an automatic feature detection. This arises the question of the reliability of an automatic crack detection algorithm, its certainty and limitations. Does the algorithm find all cracks? Does it find too many cracks? Can parameters of that algorithm, once identified as good, be applied to other samples as well? Can ensemble computing with many crack parameters overcome the difficulties with parameter finding? By means of a crack detection algorithm based on shape recognition (template matching) these questions will be discussed. Since the author has no access to reliable ground truth data of cracks the assessment of the certainty of the automatic crack is restricted to visual inspection by experts. Therefore, an artificial dataset based on a combination of manually segmented cracks processed together with simple image processing algorithms is used to quantify the accuracy of the crack detection algorithm. Part of the evaluation of cracks in concrete samples is the knowledge of the surrounding material. The surrounding material can be used to assess the detected cracks, e.g. micro-cracks within the aggregate-matrix interface may be starting points for cracks on a macro scale. Furthermore, the knowledge of the surrounding material can help to find better parameter sets for the crack detection itself because crack characteristics may vary depending on their surrounding material. Therefore, in addition to a crack detection a complete segmentation of the sample into the components of concrete, such as aggregates, cement matrix and pores is needed. Since such a segmentation task cannot be done manually due to the amount of data, an approach utilizing convolutional neuronal networks stemming from a medical application has been applied. The learning phase requires a ground truth i.e. a segmentation of the components. This has to be created manually in a time-consuming task. However, this segmentation can be used for a quantitative evaluation of the automatic segmentation afterwards. Even though that work has been performed as a short term subtask of a bigger project funded by the German Research Foundation (DFG) this paper discusses problems which may arise in similar projects, too. [1.2MB | id=23664 ] iCT 2019 Session: Short talks Thu 13:50 Auditorium2019-03 Möglichkeiten und Grenzen automatischer Merkmalserkennung am Beispiel von Risserkennungen in 3D-CT-Aufnahmen von Betonproben O. Paetsch11 Visualisation and Data Analysis; Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany Abstract [1MB | id=23104 ] DE DGZfP 2018 Session: Bauwesen2018-09 Quantitative Rissanalyse im Fahrbahndeckenbeton mit der 3D-Computertomographie D. Meinel125, K. Ehrig128, F. Weise16, O. Paetsch211 1Division 8.5; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany 2Visualisation and Data Analysis; Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany concrete, ROI tomography, in-situ-CT, 3D-CT, Beton, AKR, Feuchtetransport, automatic crack detection Abstract [0.7MB | id=18980 ] DE DGZfP 2015 Session: CT Algorithmen2016-04 3D Corrosion Detection in Time-dependent CT Images of Concrete O. Paetsch111, D. Baum15, S. Prohaska17, K. Ehrig228, D. Meinel225, G. Ebell24 1Visualisation and Data Analysis; Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division 8.5; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany CT, multi-angle radiography, defect detection, Feature Extraction, image processing, concrete, corrosion Abstract [0.5MB | id=18043 ] DIR 2015 Session: Quantitative imaging and image processing2015-08 Korrosionsverfolgung in 3D-computertomographischen Aufnahmen von Stahlbetonproben O. Paetsch111, D. Baum15, G. Ebell24, K. Ehrig228, A. Heyn2, D. Meinel225, S. Prohaska17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany Computertomographie [0.4MB | id=17375 ] DE DGZfP 2014 Session: Bauwesen2015-03 Examination of Damage Processes in Concrete with CT D. Meinel125, K. Ehrig128, V. L’Hostis2, B. Muzeau2, O. Paetsch311 1BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany 2Laboratoire d’Etude du Comportement des Bétons et des Argiles; Commissariat Energie Atomique (CEA)287, Gif-Sur-Yvette, France 3Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany X-ray computed tomography, concrete, corrosion, crack detection, 3D visualization Abstract [4.9MB | id=15692 ] iCT 2014 Session: Non-destructive Testing and 3D Materials Characterisation of...2014-06 3-D-Visualisierung und statistische Analyse von Rissen in mit Computer-Tomographie untersuchten Betonproben O. Paetsch111, D. Baum15, D. Breßler1, K. Ehrig228, D. Meinel225, S. Prohaska1,17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany Radiographic Testing (RT), statistical analysis, 3D Computed Tomography, visualization, concrete structural damage, automated crack detection [1MB | id=15343 ] DE DGZfP 2013 Session: Computertomographie2014-03 Vergleich automatischer 3D-Risserkennungsmethoden für die quantitative Analyse der Schadensentwicklung in Betonproben mit Computertomographie O. Paetsch111, K. Ehrig228, D. Meinel225, D. Baum15, S. Prohaska1,1,17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany Radiographic Testing (RT), visualization, crack detection, Visualisierung, computer tomography, template matching, Hessian eigenvalues, ZIBAmira, automated crack detection, percolation [0.9MB | id=14269 ] DE DGZfP 2012 Session: Computertomographie2013-05 Automated 3D Crack Detection for Analyzing Damage Processes in Concrete with Computed Tomography O. Paetsch111, D. Baum15, K. Ehrig228, D. Meinel225, S. Prohaska1,1,17 1Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 2Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany computed tomography, template matching, Hessian eigenvalues, crack statistics, visualization, crack surface, ZIBAmira [0.6MB | id=13736 ] iCT 2012 Session: Poster - Analysis and Algorithms2012-12 3-D-Visualisierung von Radar- und Ultraschallecho-Daten mit ZIBAmira D. Streicher112, O. Paetsch211, R. Seiler2, S. Prohaska27, M. Krause360 [Profile of Krause] , C. Boller178 1Saarland University74, Saarbrücken, Germany 2Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany 3BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany [0.4MB | id=12284 ] DE DGZfP 2011 Session: Bauwesen2012-05 Comparison of Crack Detection Methods for Analyzing Damage Processes in Concrete with Computed Tomography K. Ehrig128, J. Goebbels153, D. Meinel125, O. Paetsch211, S. Prohaska27, V. Zobel2 1Division VIII.3; BAM Federal Institute for Materials Research and Testing1277, Berlin, Germany 2Konrad-Zuse-Institut Berlin (ZIB)18, Berlin, Germany [0.7MB | id=11150 ] DIR 2011 Session: Poster2011-11 Actual Cooperations 10th International Workshop NDT in Progress 2019 2019 Oct 7-9 11th International Symposium on NDT in Aerospace 2019 2019 Nov 13-15 3rd Singapore International NDT Conference & Exhibition, SINCE 2019 2019 Dec 4-5 10th Conference on Industrial Computed Tomography (iCT) 2020 2020 Feb 4-7 34th European Conference on Acoustic Emission Testing (EWGAE 2020) 2020 Sep 9-11 Contribute Papers and Proceedings to NDT.net Share... Home Exhibition Archive Forum Jobs Members Events Directory NDT A-Z Advertise Privacy Policy Contact About © NDT.net - Where expertise comes together. The Largest Open Access Portal of Nondestructive Testing (NDT)- since 1996

Description: We propose a partially functional autoregressive model with exogenous variables (pFAR) to describe the dynamic evolution of the serially correlated functional data. It provides a unit� ed framework to model both the temporal dependence on multiple lagged functional covariates and the causal relation with ultrahigh-dimensional exogenous scalar covariates. Estimation is conducted under a two-layer sparsity assumption, where only a few groups and elements are supposed to be active, yet without knowing their number and location in advance. We establish asymptotic properties of the estimator and investigate its unite sample performance along with simulation studies. We demonstrate the application of pFAR with the high-resolution natural gas flows in Germany, where the pFAR model provides insightful interpretation as well as good out-of-sample forecast accuracy.

Description: Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of en- ergy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been pro- posed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accor- dance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies.

Description: For the purpose of making a decision in the optimal design of an energy supply system, it is important to investigate not only the optimal solution but also suboptimal ones which follow the optimal one without any omissions, what are called K-best solutions. In this paper, a mixed-integer linear programming method utilizing the hierarchical relationship between design and operation variables proposed previ- ously is extended to search the K-best solutions very efficiently. In addition, methods for updating the incumbents are incorporated into the extended method for three options for the criterion set newly in deriving the K-best solutions. This extended method is implemented into open and commercial MILP solvers, and is applied to illustrative and practical case studies, respectively, on the optimal design of cogeneration systems. Through the studies, it turns out that the proposed method is much superior in terms of solution optimality and computation efficiency to a conventional method, and that the computation efficiency to derive one of the K-best solutions by the proposed method increases with the number of K-best solutions. In addition, features of the K-best solutions in the value of objective function are clarified.

Description: Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accordance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies.

Description: To realize the best performance in energy supply, it is an important task to determine types, capacities, and numbers of energy conversion equipment appropriately. It is also necessary to take account of seasonal and hourly variations in energy demands and corresponding operational strategies of equipment. The mixed-integer linear programming (MILP) method has been utilized widely to derive the optimal solution for such a design problem. From the design viewpoint, it is important to generate not only the optimal solution but also suboptimal ones which follow the optimal one without omission, what are called K-best solutions. In this paper, an MILP method utilizing the hierarchical relationship between design and operation variables is applied along with some strategies to efficiently drive K-best solutions of a multiobjective optimal design problem of a gas turbine cogeneration system for district energy supply. The annual total cost and primary energy consumption are adopted as the objective functions to be minimized. A case study is conducted, and K-best solutions with an allowable increase in the value of the combined objective function are derived for each value of the weight for the annual total cost. Through the study, it is clarified how the weight affects the computation time, the number of the K-best solutions, and the design specifications and the values of the objective functions for the K-best solutions.

Description: Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, a method of clustering periods has been proposed based on the optimal operational strategies of the systems to avoid a large decrease in the lower bound for the optimal value of the objective function by model reduction. This method has been realized only by solving the relaxed optimal design problem at the upper level in advance. The method can decrease the number of operation variables and constraints at the upper level, and thus can decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the proposed clustering method is effective to enhance the computation efficiency in comparison with the conventional one which clusters periods regularly in time series.

Description: Due to the ubiquity of OpenMP and the rise of FPGA-based accelerators in the HPC world, several research groups have attempted to bring the two together by building OpenMP-to-FPGA compilers. This paper is a survey of the current state of the art (with a focus on the OpenMP target pragma). It first introduces and explains a design space for the compilers. Design space dimensions include how FPGA infrastructure is generated, how work is distributed, and where/how target outlining is done. A table concisely condenses the available information on the surveyed projects which are also summarized and compared. The paper concludes with possible future research directions.

Description: The simulation of gas transportation networks becomes increasingly more important as its use-cases broaden to more complex applications. Classically, the purpose of the gas network was the transportation of predominantly natural gas from a supplier to the consumer for long-term scheduled volumes. With the rise of renewable energy sources, gas-fired power plants are often chosen to compensate for the fluctuating nature of the renewables, due to their on-demand power generation capability. Such an only short-term plannable supply and demand setting requires sophisticated simulations of the gas network prior to the dispatch to ensure the supply of all customers for a range of possible scenarios and to prevent damages to the gas network. In this work we describe the modeling of gas networks and present benchmark systems to test implementations and compare new or extended models.

Description: Field-programmable gate arrays (FPGAs) are of great interest for future high-performance computing and data analytics systems, since they are capable of efficient, highly-parallel data processing. Even though high-level synthesis became more popular in the last years, the effort of porting existing scientific software onto FPGAs is still considerable. We propose to use OpenMP target offloading as a solution, which we implement in a first prototype, making use of the preexisting OpenCL SDK of the FPGA vendor. Early results demonstrate the feasibility of this approach and also reveal that further optimizations will be necessary such that code can be written in an FPGA-agnostic way.

Description: To attain the highest performance of energy supply systems, it is necessary to determine design specifications optimally in consideration of operational strategies corresponding to seasonal and hourly variations in energy demands. Mixed-integer linear programming (MILP) methods have been applied widely to such multi-period optimal design problems. A hierarchical MILP method has been proposed to solve the problems very efficiently. In addition, by utilizing features of the hierarchical MILP method, a method of reducing model by clustering periods has also been proposed to search design solution candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, by utilizing features of the hierarchical MILP method, a method of clustering periods is proposed based on the optimal operational strategies of energy supply systems obtained by solving the relaxed optimal design problem. As a case study, the method is applied to the optimal design of a gas turbine cogeneration system, and it is clarified that the method is effective to enhance the computation efficiency in comparison with a conventional method of clustering periods regularly.

Description: Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, three clustering methods are applied to time aggregation and compared with one another in terms of the computation efficiency. Especially, the k-medoids method is applied newly in addition to the time-series and operation-based methods applied previously. A case study is conducted on the optimal design of a gas turbine cogeneration system for district energy supply. Through the study, it turns out the k-medoids method is effective to shorten the computation time as compared with the time-series method, although it is necessary to set the number of clusters artifically in both the methods. It also turns out that the operation-based method is more effective than the k-medoids method in terms of the computation efficiency even with the number of clusters set automatically.

Description: A robust optimal design method of energy supply systems under uncertain energy demands has been proposed using a mixed- integer linear model for constituent equipment. A robust optimal design problem has been formulated as a three-level min-max- min optimization one by expressing uncertain energy demands by intervals, evaluating the robustness in a performance criterion based on the minimax regret criterion, and considering hierarchical relationships among design variables, uncertain energy demands, and operation variables. However, this method takes a long computation time, and thus it can be applied only to small-scale problems. In this paper, mixed-integer linear programming method in consideration of the hierarchical relationship between design and operation variables is applied to parts of the robust optimal design method which take long computation times to solve problems efficiently. In a case study, this revised method is applied to the robust optimal design of a cogeneration system with a simple configuration, and the validity and effectiveness of the method are ascertained.

Description: 本稿では，線形計画問題を解くソフトウェアである線形計画ソルバの標準的な利用方法と，原稿執筆時点で利用可能なソルバを可能な限り紹介する．筆者らはソルバ開発コミュニティの中で仕事をしているので，この機会に現在のソルバ開発現場の様子も紹介するとともに，各ソルバの特徴として何を紹介するべきかは，できる限り開発者，または，開発者に近い研究者に問い合わせて記述した．本稿は，多くの線形計画ソルバの選択肢がある中で，読者がもつ問題を解くのに最も適当なソルバを選択するための指針を与えることを主たる目的としている．

Description: Optimization models often feature disjunctions of polytopes as submodels. Such a disjunctive set is initially at best) relaxed to its convex hull, which is then refined by branching. To measure the error of the convex relaxation, the (relative) difference between the volume of the convex hull and the volume of the disjunctive set may be used. This requires a method to compute the volume of the disjunctive set. We propose a revised variant of an old algorithm by Bieri and Nef (1983) for this purpose. The algorithm uses a sweep-plane to incrementally calculate the volume of the disjunctive set as a function of the offset parameter of the sweep-plane.

Description: Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.

Description: Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.

Description: Compressor stations are the heart of every high-pressure gas transport network. Located at intersection areas of the network they are contained in huge complex plants, where they are in combination with valves and regulators responsible for routing and pushing the gas through the network. Due to their complexity and lack of data compressor stations are usually dealt with in the scientific literature in a highly simplified and idealized manner. As part of an ongoing project with one of Germany's largest Transmission System Operators to develop a decision support system for their dispatching center, we investigated how to automatize control of compressor stations. Each station has to be in a particular configuration, leading in combination with the other nearby elements to a discrete set of up to 2000 possible feasible operation modes in the intersection area. Since the desired performance of the station changes over time, the configuration of the station has to adapt. Our goal is to minimize the necessary changes in the overall operation modes and related elements over time, while fulfilling a preset performance envelope or demand scenario. This article describes the chosen model and the implemented mixed integer programming based algorithms to tackle this challenge. By presenting extensive computational results on real world data we demonstrate the performance of our approach.

Description: Various feature selection algorithms have been proposed to identify cancer prognostic biomarkers. In recent years, however, their reproducibility is criticized. The performance of feature selection algorithms is shown to be affected by the datasets, underlying networks and evaluation metrics. One of the causes is the curse of dimensionality, which makes it hard to select the features that generalize well on independent data. Even the integration of biological networks does not mitigate this issue because the networks are large and many of their components are not relevant for the phenotype of interest. With the availability of multi-omics data, integrative approaches are being developed to build more robust predictive models. In this scenario, the higher data dimensions create greater challenges. We proposed a phenotype relevant network-based feature selection (PRNFS) framework and demonstrated its advantages in lung cancer prognosis prediction. We constructed cancer prognosis relevant networks based on epithelial mesenchymal transition (EMT) and integrated them with different types of omics data for feature selection. With less than 2.5% of the total dimensionality, we obtained EMT prognostic signatures that achieved remarkable prediction performance (average AUC values above 0.8), very significant sample stratifications, and meaningful biological interpretations. In addition to finding EMT signatures from different omics data levels, we combined these single-omics signatures into multi-omics signatures, which improved sample stratifications significantly. Both single- and multi-omics EMT signatures were tested on independent multi-omics lung cancer datasets and significant sample stratifications were obtained.

Description: We develop a data-driven method to learn chemical reaction networks from trajectory data. Modeling the reaction system as a continuous-time Markov chain and assuming the system is fully observed,our method learns the propensity functions of the system with predetermined basis functions by maximizing the likelihood function of the trajectory data under l^1 sparse regularization. We demonstrate our method with numerical examples using synthetic data and carry out an asymptotic analysis of the proposed learning procedure in the infinite-data limit.

Description: In this thesis, I want to analyze how neural networks trained to resemble a given function based on particular values react to additional knowledge about the function in terms of a differential equation that the function satisfies. In the first chapter, I will recall the definition of initial value problems and discuss the existence and uniqueness of their solutions, as well as touch on a method to numerically approximate them. Furthermore, I will give a mathematical introduction to neural networks. Then, I will consider a system of two first-order differential equations and test how their solution will be approximated by a neural net. In the next step, I want to see how added noise to the training data and the influence of the differential equation on the loss functional of the neural net will affect the error of the predicted solution against the exact data. Furthermore, I will test if this influence can help reduce the amount of necessary data points in order to reach similar degrees of accuracy.

Description: Model-based optimal designs of experiments (M-bODE) for nonlinear models are typically hard to compute. The literature on the computation of M-bODE for nonlinear models when the covariates are categorical variables, i.e. factorial experiments, is scarce. We propose second order cone programming (SOCP) and Mixed Integer Second Order Programming (MISOCP) formulations to find, respectively, approximate and exact A- and D-optimal designs for 2𝑘 factorial experiments for Generalized Linear Models (GLMs). First, locally optimal (approximate and exact) designs for GLMs are addressed using the formulation of Sagnol (J Stat Plan Inference 141(5):1684–1708, 2011). Next, we consider the scenario where the parameters are uncertain, and new formulations are proposed to find Bayesian optimal designs using the A- and log det D-optimality criteria. A quasi Monte-Carlo sampling procedure based on the Hammersley sequence is used for computing the expectation in the parametric region of interest. We demonstrate the application of the algorithm with the logistic, probit and complementary log–log models and consider full and fractional factorial designs.

Description: The dynamical response of molecular systems, when the potential energy function is perturbed at a microscopic level, is difficult to predict without a numerical or laboratory experiment. This is due to the non-linearity and high-dimensionality of molecular systems. An efficient investigation of such a behaviour is necessary to better understand the nature of molecules and to improve the predictability of Molecular Dynamics simulations. In this thesis we propose a reweighting scheme for Markov State Models (MSMs), based on the Girsanov theorem, that permits to reduce the computational cost of the analysis when the potential energy function of a molecule is perturbed. The method has been successfully extended and implemented with metadynamics, in order to build the MSM of a molecular system in a significantly shorter computational time compared to a standard unbiased MD simulation. We also propose a new method to discretize the infinitesimal generator into a rate matrix, that could be used to efficiently study Hamiltonian perturbations as well.

Description: Molecular simulations are often used to analyse the stability of protein–ligand complexes. The stability can be characterised by exit rates or using the exit time approach, i.e. by computing the expected holding time of the complex before its dissociation. However determining exit rates by straightforward molecular dynamics methods can be challenging for stochastic processes in which the exit event occurs very rarely. Finding a low variance procedure for collecting rare event statistics is still an open problem. In this work we discuss a novel method for computing exit rates which uses results of Robust Perron Cluster Analysis (PCCA+). This clustering method gives the possibility to define a fuzzy set by a membership function, which provides additional information of the kind ‘the process is being about to leave the set’. Thus, the derived approach is not based on the exit event occurrence and, therefore, is also applicable in case of rare events. The novel method can be used to analyse the temperature effect of protein–ligand systems through the differences in exit rates, and, thus, open up new drug design strategies and therapeutic applications.

Description: This paper gives an overview of the modeling framework that is being developed within the Horizon2020 project plan4res. In the context of energy transition, integration of high shares of renewable energies will play a vital role for achieving the proposed climate targets. This brings new challenges to modeling tools, including data construction, implementation and solution techniques. In order to address these challenges, plan4res aims to create a well-structured and highly modular framework that will provide insights into the needs of future energy systems. An overview of the central modeling aspects is given in this paper. Finally, three case studies are presented that show the adequacy and relevance of the proposed optimization framework.

Description: In this work new approaches for global optimization are developed. We move from theoretical connections in complexity theory to very practical results in protein-ligand docking. In regard to the efficiency of the suggested optimizer, continuity methods are motivated, that yield an improved optimization method.

Description: Der KOBV-Jahresbericht informiert rückblickend im 2-Jahres-Rhythmus über die bibliothekarisch-fachlichen Entwicklungen im Verbund und die Projekte des Kooperativen Bibliotheksverbunds Berlin-Brandenburg (KOBV).

Description: A key task in the field of modeling and analyzing nonlinear dynamical systems is the recovery of unknown governing equations from measurement data only. There is a wide range of application areas for this important instance of system identification, ranging from industrial engineering and acoustic signal processing to stock market models. In order to find appropriate representations of underlying dynamical systems, various data-driven methods have been proposed by different communities. However, if the given data sets are high-dimensional, then these methods typically suffer from the curse of dimensionality. To significantly reduce the computational costs and storage consumption, we propose the method multidimensional approximation of nonlinear dynamical systems (MANDy) which combines data-driven methods with tensor network decompositions. The efficiency of the introduced approach will be illustrated with the aid of several high-dimensional nonlinear dynamical systems.

Description: Markov state models are to date the gold standard for modeling molecular kinetics since they enable the identification and analysis of metastable states and related kinetics in a very instructive manner. The state-of-the-art Markov state modeling methods and tools are very well developed for the modeling of reversible processes in closed equilibrium systems. On the contrary, they are largely not well suited to deal with nonreversible or even nonautonomous processes of nonequilibrium systems. Thus, we generalized the common Robust Perron Cluster Cluster Analysis (PCCA+) method to enable straightforward modeling of nonequilibrium systems as well. The resulting Generalized PCCA (G-PCCA) method readily handles equilibrium as well as nonequilibrium data by utilizing real Schur vectors instead of eigenvectors. This is implemented in the G-PCCA algorithm that enables the semiautomatic coarse graining of molecular kinetics. G-PCCA is not limited to the detection of metastable states but also enables the identification and modeling of cyclic processes. This is demonstrated by three typical examples of nonreversible systems.

Description: In this article, we show that these well-established spectral algorithms (like PCCA+, Perron Cluster Cluster Analysis) also identify coherent sets of non-autonomous dynamical systems. For the identification of coherent sets, one has to compute a discretization (a matrix T) of the transfer operator of the process using a space-time-discretization scheme. The article gives an overview about different time-discretization schemes and shows their applicability in two different fields of application.

Description: In this paper, we study Jarzynski's equality and fluctuation theorems for diffusion processes. While some of the results considered in the current work are known in the (mainly physics) literature, we review and generalize these nonequilibrium theorems using mathematical arguments, therefore enabling further investigations in the mathematical community. On the numerical side, variance reduction approaches such as importance sampling method are studied in order to compute free energy differences based on Jarzynski's equality.

Description: About 20% of the German energy demand is supplied by natural gas. Ad- ditionally, for about twice the amount Germany serves as a transit country. Thereby, the German network represents a central hub in the European natural gas transport network. The transport infrastructure is operated by so-called transmissions system operators or TSOs. The number one priority of the TSOs is to ensure security of supply. However, the TSOs have no knowledge of the intentions and planned actions of the shippers (traders). Open Grid Europe (OGE), one of Germany’s largest TSO, operates a high- pressure transport network of about 12.000 km length. Since flexibility and security of supply is of utmost importance to the German Energy Transition (“Energiewende”) especially with the introduction of peak-load gas power stations, being able to predict in- and out-flow of the network is of great importance. In this paper we introduce a new hybrid forecast method applied to gas flows at the boundary nodes of a transport network. The new method employs optimized feature minimization and selection. We use a combination of an FAR, LSTM DNN and mathematical programming to achieve robust high quality forecasts on real world data for different types of network nodes. Keywords: Gas Forecast, Time series, Hybrid Method, FAR, LSTM, Mathematical Optimisation

Description: Mixed integer nonlinear programs (MINLPs) are arguably among the hardest optimization problems, with a wide range of applications. MINLP solvers that are based on linear relaxations and spatial branching work similar as mixed integer programming (MIP) solvers in the sense that they are based on a branch-and-cut algorithm, enhanced by various heuristics, domain propagation, and presolving techniques. However, the analysis of infeasible subproblems, which is an important component of most major MIP solvers, has been hardly studied in the context of MINLPs. There are two main approaches for infeasibility analysis in MIP solvers: conflict graph analysis, which originates from artificial intelligence and constraint programming, and dual ray analysis. The main contribution of this short paper is twofold. Firstly, we present the first computational study regarding the impact of dual ray analysis on convex and nonconvex MINLPs. In that context, we introduce a modified generation of infeasibility proofs that incorporates linearization cuts that are only locally valid. Secondly, we describe an extension of conflict analysis that works directly with the nonlinear relaxation of convex MINLPs instead of considering a linear relaxation. This is work-in-progress, and this short paper is meant to present first theoretical considerations without a computational study for that part.

Description: Conflict learning algorithms are an important component of modern MIP and CP solvers. But strong conflict information is typically gained by depth-first search. While this is the natural mode for CP solving, it is not for MIP solving. Rapid Learning is a hybrid CP/MIP approach where CP search is applied at the root to learn information to support the remaining MIP solve. This has been demonstrated to be beneficial for binary programs. In this paper, we extend the idea of Rapid Learning to integer programs, where not all variables are restricted to the domain {0, 1}, and rather than just running a rapid CP search at the root, we will apply it repeatedly at local search nodes within the MIP search tree. To do so efficiently, we present six heuristic criteria to predict the chance for local Rapid Learning to be successful. Our computational experiments indicate that our extended Rapid Learning algorithm significantly speeds up MIP search and is particularly beneficial on highly dual degenerate problems.

Description: Conflict learning plays an important role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. A major step for MIP conflict learning is to aggregate the LP relaxation of an infeasible subproblem to a single globally valid constraint, the dual proof, that proves infeasibility within the local bounds. Among others, one way of learning is to add these constraints to the problem formulation for the remainder of the search. We suggest to not restrict this procedure to infeasible subproblems, but to also use global proof constraints from subproblems that are not (yet) infeasible, but can be expected to be pruned soon. As a special case, we also consider learning from integer feasible LP solutions. First experiments of this conflict-free learning strategy show promising results on the MIPLIB2017 benchmark set.

Description: The analysis of infeasible subproblems plays an important role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. There are two fundamentally different concepts to generate valid global constraints from infeasible subproblems. The first is to analyze the sequence of implications, obtained by domain propagation, that led to infeasibility. The result of this analysis is one or more sets of contradicting variable bounds from which so-called conflict constraints can be generated. This concept is called conflict graph analysis and has its origin in solving satisfiability problems and is similarly used in constraint programming. The second concept is to analyze infeasible linear programming (LP) relaxations. Every ray of the dual LP provides a set of multipliers that can be used to generate a single new globally valid linear constraint. This method is called dual proof analysis. The main contribution of this paper is twofold. Firstly, we present three enhancements of dual proof analysis: presolving via variable cancellation, strengthening by applying mixed integer rounding functions, and a filtering mechanism. Further, we provide an intense computational study evaluating the impact of every presented component regarding dual proof analysis. Secondly, this paper presents the first integrated approach to use both conflict graph and dual proof analysis simultaneously within a single MIP solution process. All experiments are carried out on general MIP instances from the standard public test set MIPLIB 2017; the presented algorithms have been implemented within the non-commercial MIP solver SCIP and the commercial MIP solver FICO Xpress.

Description: Two essential ingredients of modern mixed-integer programming (MIP) solvers are diving heuristics that simulate a partial depth-first search in a branch-and-bound search tree and conflict analysis of infeasible subproblems to learn valid constraints. So far, these techniques have mostly been studied independently: primal heuristics under the aspect of finding high-quality feasible solutions early during the solving process and conflict analysis for fathoming nodes of the search tree and improving the dual bound. Here, we combine both concepts in two different ways. First, we develop a diving heuristic that targets the generation of valid conflict constraints from the Farkas dual. We show that in the primal this is equivalent to the optimistic strategy of diving towards the best bound with respect to the objective function. Secondly, we use information derived from conflict analysis to enhance the search of a diving heuristic akin to classical coefficient diving. The computational performance of both methods is evaluated using an implementation in the source-open MIP solver SCIP. Experiments are carried out on publicly available test sets including Miplib 2010 and Cor@l.

Description: Within a wide view to stimulate intermodal transport, this paper is devoted to the examination of the intrinsically related problems of designing freight carrying services and determining their associated prices as observed by the shipper firms. A path-based multicommodity formulation is developed for a medium-term planning horizon, from the perspective of an intermodal operator. In the quest of incorporating nonprice attributes, two approaches are proposed to depict a realistic assessment of the service quality. First, frequency delay constraints are added to the upper level problem. Second, based on a random utility model, behavioural concepts are integrated in the expression of the lower level as a logistics costs minimization problem. Exact tests are invoked on real-world instances, demonstrating the capability of the presented approaches of reaching reasonable results within acceptable computation times and optimality gaps. The broader level-of-service perspective imposes additional costs on the service providers, although to a lesser extent on long-distance freight corridors, as indicated by the computed market share and net profit. Further experiments are conducted to test the impact of certain transport management instruments (e.g. subsidies and service capacities) on the modal split, as well as to assess the intermodality’s future based on a scenario analysis methodology.

Description: 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.

Description: We introduce a concurrent solver for the periodic event scheduling problem (PESP). It combines mixed integer programming techniques, the modulo network simplex method, satisfiability approaches, and a new heuristic based on maximum cuts. Running these components in parallel speeds up the overall solution process. This enables us to significantly improve the current upper and lower bounds for all benchmark instances of the library PESPlib.

Description: This article answers two kinds of questions regarding the Bundesliga which is Germany's primary football (soccer) competition having the highest average stadium attendance worldwide. First "At any point of the season, what final rank will a certain team definitely reach?" and second "At any point of the season, what final rank can a certain team at most reach?". Although we focus especially on the Bundesliga, the models that we use to answer the two questions can easily be adopted to league systems that are similar to that of the Bundesliga.

Description: 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.

Description: We examine a frictional effect on the linear stability of an interface of discontinuity in tangential velocity. The fluid is moving with uniform velocity U in a region but is at rest in the other, and the bottom surface is assumed to exert drag force, quadratic in velocity, on the thin fluid layer. In the absence of the drag, the instability of the Kelvin-Helmholtz type is suppressed for U〉√8 c, with c being the propagating speed of the gravity wave. We find by asymptotic analyses for both small and large values of the drag strength that the drag, regardless of its strength, makes the flow unstable for the whole range of the Froude number U/c.

Description: We examine an effect of side walls on the linear stability of an interface of tangential-velocity discontinuity in shallow-water flow. The flow is pure horizontal in the plane xy, and the fluid is bounded in a finite width 2d in the y− direction. In region 0 〈 y 〈 d, the fluid is moving with uniform velocity U but is at rest for −d 〈 y 〈 0. Without side walls, the flow is unstable for a velocity difference U〈√8c U 〈 √8 c, with c being the velocity of gravity waves. In this work, we show that if the velocity difference U is smaller than 2c, the interface is always destabilized, also known as the flow is unstable. The unstable region of an infinite width model is shrunken by the effects of side walls in the case of narrow width, while there is no range for the Froude number for stabilization in the case of large width. These results play an important role in predicting the wave propagations and have a wide application in the fields of industry. As a result of the interaction of waves and the mean flow boundary, the flow is unstable, which is caused by a decrease in the kinetic energy of disturbance.

Description: Solving mixed-integer nonlinear programs (MINLPs) to global optimality efficiently requires fast solvers for continuous sub-problems. These appear in, e.g., primal heuristics, convex relaxations, and bound tightening methods. Two of the best performing algorithms for these sub-problems are Sequential Quadratic Programming (SQP) and Interior Point Methods. In this paper we study the impact of different SQP and Interior Point implementations on important MINLP solver components that solve a sequence of similar NLPs. We use the constraint integer programming framework SCIP for our computational studies.

Description: 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.

Description: We investigate new convex relaxations for the pooling problem, a classic nonconvex production planning problem in which input materials are mixed in intermediate pools, with the outputs of these pools further mixed to make output products meeting given attribute percentage requirements. Our relaxations are derived by considering a set which arises from the formulation by considering a single product, a single attibute, and a single pool. The convex hull of the resulting nonconvex set is not polyhedral. We derive valid linear and convex nonlinear inequalities for the convex hull, and demonstrate that different subsets of these inequalities define the convex hull of the nonconvex set in three cases determined by the parameters of the set. Computational results on literature instances and newly created larger test instances demonstrate that the inequalities can significantly strengthen the convex relaxation of the pq-formulation of the pooling problem, which is the relaxation known to have the strongest bound.

Description: Computers, servers and supercomputers with more than one GPU become more and more common. To fully utilize such systems the application needs to be aware of the additional GPUs. E.g., computational workload needs to be distributed across the GPUs. Along with that goes data movement as well as communication. Recently, NVIDIA introduced new features, Unified Memory and Cooperative Groups, that enable programmers to extend their applications with multi-GPU capabilities. In this thesis the aforementioned features are presented in detail and evaluated in the context of the GPU molecular dynamics simulation HAL's MD package on the latest NVIDIA GPU architecture Pascal. A hotspot analysis with the NVIDIA Visual Profiler identified the radix sort as a major hotspot within HAL's MD package. This thesis presents an approach towards a multi-GPU implementation of radix sort. The individual kernels are analysed and an implementation is discussed. Then, the radix sort is transformed into a multi-GPU implementation kernel per kernel. For each step the individual runtime measurements and bottlenecks are presented to analyse the approach. A general sequence diagram of the implementation shows how the individual parts interact with each other. The outlook discusses the further development of HAL's MD package, especially the force computation for multi-GPU which has not been covered in this thesis.

Description: Computer, Server und Supercomputer mit mehr als einer GPU sind immer häufiger zu finden. Um solche Systeme komplett ausnutzen zu können, müssen Anwendung für die Verwendung mehrerer GPUs angepasst werden. Z.B. müssen die Berechnungen zwischen den GPUs verteilt werden. Damit einher gehen die Kommunikation zwischen den GPUs sowie der Austausch der Daten. Mit Unified Memory und Cooperative Groups hat NVIDIA zwei neue Funktionen vorgestellt, damit Programmierer ihre Anwendungen einfach an Multi-GPU Systeme anpassen können. Im Rahmen dieser Arbeit werden die oben genannten Funktionen im Detail vorgestellt und anhand der Molekulardynamiksimulation HAL's MD package auf der neuesten NVIDIA GPU Architektur Pascal evaluiert. Eine Hotspot Analyse von HAL's MD package mit dem NVIDIA Visual Profiler hat den Radix Sort als einen großen Hotspot identifiziert. Daher stellt diese Arbeit eine Multi-GPU Implementierung für Radix Sort vor. Dabei werden die einzelnen Kernel Schritt für Schritt vorgestellt und ihre Implementierung, insbesondere Laufzeiten und Probleme bei der Umsetzung, im Detail diskutiert. Ein Sequenzdiagramm der einzelnen Teile von Radix Sort zeigt dabei, wie die einzelnen Teile in der Multi-GPU Implementierung zusammenarbeiten. Abschließend wird, ausgehend von den Ergebnissen, die zukünftige Entwicklung von HAL's MD package unter besonderen Berücksichtigung einer vollständigen Multi-GPU Molekulardynamiksimulation betrachtet.

Description: Small-molecule oxoanions are often imprinted noncovalently as carboxylates into molecularly imprinted polymers (MIPs), requiring the use of an organic counterion. Popular species are either pentamethylpiperidine (PMP) as a protonatable cation or tetraalkylammonium (TXA) ions as permanent cations. The present work explores the influence of the TXA as a function of their alkyl chain length, from methyl to octyl, using UV/vis absorption, fluorescence titrations, and HPLC as well as MD simulations. Protected phenylalanines (Z-L/D-Phe) served as templates/analytes. While the influence of the counterion on the complex stability constants and anion-induced spectral changes shows a monotonous trend with increasing alkyl chain length at the prepolymerization stage, the cross-imprinting/rebinding studies showed a unique pattern that suggested the presence of adaptive cavities in the MIP matrix, related to the concept of induced fit of enzyme–substrate interaction. Larger cavities formed in the presence of larger counterions can take up pairs of Z-x-Phe and smaller TXA, eventually escaping spectroscopic detection. Correlation of the experimental data with the MD simulations revealed that counterion mobility, the relative distances between the three partners, and the hydrogen bond lifetimes are more decisive for the response features observed than actual distances between interacting atoms in a complex or the orientation of binding moieties. TBA has been found to yield the highest imprinting factor, also showing a unique dual behavior regarding the interaction with template and fluorescent monomer. Finally, interesting differences between both enantiomers have been observed in both theory and experiment, suggesting true control of enantioselectivity. The contribution concludes with suggestions for translating the findings into actual MIP development.

Description: Computing the Hierarchical Equations of Motion (HEOM) is by itself a challenging problem, and so is writing portable production code that runs efficiently on a variety of architectures while scaling from PCs to supercomputers. We combined both challenges to push the boundaries of simulating quantum systems, and to evaluate and improve methodologies for scientific software engineering. Our contributions are threefold: We present the first distributed memory implementation of the HEOM method (DM-HEOM), we describe an interdisciplinary development workflow, and we provide guidelines and experiences for designing distributed, performance-portable HPC applications with MPI-3, OpenCL and other state-of-the-art programming models. We evaluated the resulting code on multi- and many-core CPUs as well as GPUs, and demonstrate scalability on a Cray XC40 supercomputer for the PS I molecular light harvesting complex.

Description: We study the problem of finding subpaths with high demand in a given network that is traversed by several users. The demand of a subpath is the number of users who completely cover this subpath during their trip. Especially with large instances, an efficient algorithm for computing all subpaths' demands is necessary. We introduce a path-graph to prevent multiple generations of the same subpath and give a recursive approach to compute the demands of all subpaths. Our runtime analysis shows, that the presented approach compares very well against the theoretical minimum runtime.

Description: The problem of allocating operating rooms (OR) to surgical cases is a challenging task, involving both combinatorial aspects and uncertainty handling. We formulate this problem as a parallel machines scheduling problem, in which job durations follow a lognormal distribution, and a fixed assignment of jobs to machines must be computed. We propose a cutting-plane approach to solve the robust counterpart of this optimization problem. To this end, we develop an algorithm based on fixed-point iterations that identifies worst-case scenarios and generates cut inequalities. The main result of this article uses Hilbert's projective geometry to prove the convergence of this procedure under mild conditions. We also propose two exact solution methods for a similar problem, but with a polyhedral uncertainty set, for which only approximation approaches were known. Our model can be extended to balance the load over several planning periods in a rolling horizon. We present extensive numerical experiments for instances based on real data from a major hospital in Berlin. In particular, we find that: (i) our approach performs well compared to a previous model that ignored the distribution of case durations; (ii) compared to an alternative stochastic programming approach, robust optimization yields solutions that are more robust against uncertainty, at a small price in terms of average cost; (iii) the \emph{longest expected processing time first} (LEPT) heuristic performs well and efficiently protects against extreme scenarios, but only if a good prediction model for the durations is available. Finally, we draw a number of managerial implications from these observations.

Description: We consider the Cumulative Scheduling Problem (CuSP) in which a set of $n$ jobs must be scheduled according to release dates, due dates and cumulative resource constraints. In constraint programming, the CuSP is modeled as the cumulative constraint. Among the most common propagation algorithms for the CuSP there is energetic reasoning (Baptiste et al., 1999) with a complexity of O(n^3) and edge-finding (Vilim, 2009) with O(kn log n) where k 〈= n is the number of different resource demands. We consider the complete versions of the propagators that perform all deductions in one call of the algorithm. In this paper, we introduce the energetic edge-finding rule that is a generalization of both energetic reasoning and edge-finding. Our main result is a complete energetic edge-finding algorithm with a complexity of O(n^2 log n) which improves upon the complexity of energetic reasoning. Moreover, we show that a relaxation of energetic edge-finding with a complexity of O(n^2) subsumes edge-finding while performing stronger propagations from energetic reasoning. A further result shows that energetic edge-finding reaches its fixpoint in strongly polynomial time. Our main insight is that energetic schedules can be interpreted as a single machine scheduling problem from which we deduce a monotonicity property that is exploited in the algorithms. Hence, our algorithms improve upon the strength and the complexity of energetic reasoning and edge-finding whose complexity status seemed widely untouchable for the last decades.

Description: Wir beschreiben die Optimierung des Nahverkehrsnetzes der Stadt Karlsruhe im Zusammmenhang mit den Baumaßnahmen der sogenannten Kombilösung.

Description: We investigate the relation between Hall’s theorem and Kőnig’s theorem in graphs and hypergraphs. In particular, we characterize the graphs satisfying a deficiency version of Hall’s theorem, thereby showing that this class strictly contains all Kőnig–Egerváry graphs. Furthermore, we give a generalization of Hall’s theorem to normal hypergraphs.

Description: Dieses Dokument fasst den Stand der mathematischen Modellierung von Preissystemen des öV mittels eines am ZIB entwickelten Tarifgraphenmodells zusammen. Damit sind sehr einfache und konzise Beschreibungen von Tarifstrukturen möglich, die sich algorithmisch behandeln lassen: Durch das zeitgleiche Tracken eines Pfades im Routinggraphen im Tarifgraphen kann schon während einer Routenberechnung der Preis bestimmt werden. Wir beschreiben zunächst das Konzept. Die konkrete Realisierung wird im Folgenden beispielhaft an den Tarifsystemen der Verkehrsverbünde Warnow, MDV, Vogtland, Bremen/Niedersachsen, Berlin/Brandenburg und Mittelsachsen erläutert. Anschließend folgen Überlegungen zur konkreten Implementierung von Kurzstrecken-Tarifen und zur Behandlung des Verbundübergriffs.

Description: Gene Regulatory Networks are powerful models for describing the mechanisms and dynamics inside a cell. These networks are generally large in dimension and seldom yield analytical formulations. It was shown that studying the conditional expectations between dimensions (vertices or species) of a network could lead to drastic dimension reduction. These conditional expectations were classically given by solving equations of motions derived from the Chemical Master Equation. In this paper we deviate from this convention and take an Algebraic approach instead. That is, we explore the consequences of conditional expectations being described by a polynomial function. There are two main results in this work. Firstly: if the conditional expectation can be described by a polynomial function, then coefficients of this polynomial function can be reconstructed using the classical moments. And secondly: there are dimensions in Gene Regulatory Networks which inherently have conditional expectations with algebraic forms. We demonstrate through examples, that the theory derived in this work can be used to develop new and effective numerical schemes for forward simulation and parameter inference. The algebraic line of investigation of conditional expectations has considerable scope to be applied to many different aspects of Gene Regulatory Networks; this paper serves as a preliminary commentary in this direction.

Description: The paper investigates the efficient use of a linearly implicit stiff integrator for the numerical solution of density driven flow problems. Upon choosing a one-step method of extrapolation type (code LIMEX), the use of full Jacobians and reduced approximations are discussed. Numerical experiments include nonlinear density flow problems such as diffusion from a salt dome (2D), a (modified) Elder problem (3D), the saltpool benchmark (3D) and a real life salt dome problem (2D). The arising linear equations are solved using either a multigrid preconditioner from the software package UG4 or the sparse matrix solver SuperLU.

Description: The perfect matching polytope, i.e. the convex hull of (incidence vectors of) perfect matchings of a graph is used in many combinatorial algorithms. Kotzig, Lovász and Plummer developed a decomposition theory for graphs with perfect matchings and their corresponding polytopes known as the tight cut decomposition which breaks down every graph into a number of indecomposable graphs, so called bricks. For many properties that are of interest on graphs with perfect matchings, including the description of the perfect matching polytope, it suffices to consider these bricks. A key result by Lovász on the tight cut decomposition is that the list of bricks obtained is the same independent of the choice of tight cuts made during the tight cut decomposition procedure. This implies that finding a tight cut decomposition is polynomial time equivalent to finding a single tight cut. We generalise the notions of a tight cut, a tight cut contraction and a tight cut decomposition to hypergraphs. By providing an example, we show that the outcome of the tight cut decomposition on general hypergraphs is no longer unique. However, we are able to prove that the uniqueness of the tight cut decomposition is preserved on a slight generalisation of uniform hypergraphs. Moreover, we show how the tight cut decomposition leads to a decomposition of the perfect matching polytope of uniformable hypergraphs and that the recognition problem for tight cuts in uniformable hypergraphs is polynomial time solvable.

Description: In commodity transport networks such as natural gas, hydrogen and water networks, flows arise from nonlinear potential differences between the nodes, which can be represented by so-called "potential-driven" network models. When operators of these networks face increasing demand or the need to handle more diverse transport situations, they regularly seek to expand the capacity of their network by building new pipelines parallel to existing ones ("looping"). The paper introduces a new mixed-integer non-linear programming (MINLP) model and a new non-linear programming (NLP) model and compares these with existing models for the looping problem and related problems in the literature, both theoretically and experimentally. On this basis, we give recommendations about the circumstances under which a certain model should be used. In particular, it turns out that one of our novel models outperforms the existing models. Moreover, the paper is the first to include the practically relevant option that a particular pipeline may be looped several times.

Description: The Ubiquity Generator (UG) is a general framework for the external parallelization of mixed integer programming (MIP) solvers. In this paper, we present ParaXpress, a distributed memory parallelization of the powerful commercial MIP solver FICO Xpress. Besides sheer performance, an important feature of Xpress is that it provides an internal parallelization for shared memory systems. When aiming for a best possible performance of ParaXpress on a supercomputer, the question arises how to balance the internal Xpress parallelization and the external parallelization by UG against each other. We provide computational experiments to address this question and we show computational results for running ParaXpress on a Top500 supercomputer, using up to 43,344 cores in parallel.

Description: Mathematical models for bioregulatory networks can be based on different formalisms, depending on the quality of available data and the research question to be answered. Discrete boolean models can be constructed based on qualitative data, which are frequently available. On the other hand, continuous models in terms of ordinary differential equations (ODEs) can incorporate time-series data and give more detailed insight into the dynamics of the underlying system. A few years ago, a method based on multivariate polynomial interpolation and Hill functions has been developed for an automatic conversion of boolean models to systems of ordinary differential equations. This method is frequently used by modellers in systems biology today, but there are only a few results available about the conservation of mathematical structures and properties across the formalisms. Here, we consider subsets of the phase space where some components stay fixed, called trap spaces, and demonstrate how boolean trap spaces can be linked to invariant sets in the continuous state space. This knowledge is of practical relevance since finding trap spaces in the boolean setting, which is relatively easy, allows for the construction of reduced ODE models.

Description: Let $G$ be a directed acyclic graph with $n$ arcs, a source $s$ and a sink $t$. We introduce the cone $K$ of flow matrices, which is a polyhedral cone generated by the matrices $1_P 1_P^T \in R^{n\times n}$, where $1_P\in R^n$ is the incidence vector of the $(s,t)$-path $P$. Several combinatorial problems reduce to a linear optimization problem over $K$. This cone is intractable, but we provide two convergent approximation hierarchies, one of them based on a completely positive representation of $K$. We illustrate this approach by computing bounds for a maximum flow problem with pairwise arc-capacities.

Description: Quadratic optimization problems (QPs) are ubiquitous, and solution algorithms have matured to a reliable technology. However, the precision of solutions is usually limited due to the underlying floating-point operations. This may cause inconveniences when solutions are used for rigorous reasoning. We contribute on three levels to overcome this issue. First, we present a novel refinement algorithm to solve QPs to arbitrary precision. It iteratively solves refined QPs, assuming a floating-point QP solver oracle. We prove linear convergence of residuals and primal errors. Second, we provide an efficient implementation, based on SoPlex and qpOASES that is publicly available in source code. Third, we give precise reference solutions for the Maros and Mészáros benchmark library.

Description: Mixed integer programming is a versatile and valuable optimization tool. However, solving specific problem instances can be computationally demanding even for cutting-edge solvers. Such long running times are often significantly reduced by an appropriate change of the solver's parameters. In this paper we investigate "algorithm selection", the task of choosing among a set of algorithms the ones that are likely to perform best for a particular instance. In our case, we treat different parameter settings of the MIP solver SCIP as different algorithms to choose from. Two peculiarities of the MIP solving process have our special attention. We address the well-known problem of performance variability by using multiple random seeds. Besides solving time, primal dual integrals are recorded as a second performance measure in order to distinguish solvers that timed out. We collected feature and performance data for a large set of publicly available MIP instances. The algorithm selection problem is addressed by several popular, feature-based methods, which have been partly extended for our purpose. Finally, an analysis of the feature space and performance results of the selected algorithms are presented.

Description: Estimation of time of death based on a single measurement of body core temperature is a standard procedure in forensic medicine. Mechanistic models using simulation of heat transport promise higher accuracy than established phenomenological models in particular in nonstandard situations, but involve many not exactly known physical parameters. Identifying both time of death and physical parameters from multiple temperature measurements is one possibility to reduce the uncertainty significantly. In this paper, we consider the inverse problem in a Bayesian setting and perform both local and sampling-based uncertainty quantification, where proper orthogonal decomposition is used as model reduction for fast solution of the forward model. Based on the local uncertainty quantification, optimal design of experiments is performed in order to minimize the uncertainty in the time of death estimate for a given number of measurements. For reasons of practicability, temperature acquisition points are selected from a set of candidates in different spatial and temporal locations. Applied to a real corpse model, a significant accuracy improvement is obtained already with a small number of measurements.

Description: Time- and frequency resolved optical signals provide insights into the properties of light harvesting molecular complexes, including excitation energies, dipole strengths and orientations, as well as in the exciton energy flow through the complex. The hierarchical equations of motion (HEOM) provide a unifying theory, which allows one to study the combined effects of system-environment dissipation and non-Markovian memory without making restrictive assumptions about weak or strong couplings or separability of vibrational and electronic degrees of freedom. With increasing system size the exact solution of the open quantum system dynamics requires memory and compute resources beyond a single compute node. To overcome this barrier, we developed a scalable variant of HEOM. Our distributed memory HEOM, DM-HEOM, is a universal tool for open quantum system dynamics. It is used to accurately compute all experimentally accessible time- and frequency resolved processes in light harvesting molecular complexes with arbitrary system-environment couplings for a wide range of temperatures and complex sizes.

Description: Human mobility always had a great influence on the spreading of cultural, social and technological ideas. Developing realistic models that allow for a better understanding, prediction and control of such coupled processes has gained a lot of attention in recent years. However, the modeling of spreading processes that happened in ancient times faces the additional challenge that available knowledge and data is often limited and sparse. In this paper, we present a new agent-based model for the spreading of innovations in the ancient world that is governed by human movements. Our model considers the diffusion of innovations on a spatial network that is changing in time, as the agents are changing their positions. Additionally, we propose a novel stochastic simulation approach to produce spatio-temporal realizations of the spreading process that are instructive for studying its dynamical properties and exploring how different influences affect its speed and spatial evolution.

Description: The reproductive cycle of mono-ovulatory species such as cows or humans is known to show two or more waves of follicular growth and decline between two successive ovulations. Within each wave, there is one dominant follicle escorted by subordinate follicles of varying number. Under the surge of the luteinizing hormone a growing dominant follicle ovulates. Rarely the number of ovulating follicles exceeds one. In the biological literature, the change of hormonal concentrations and individually varying numbers of follicular receptors are made responsible for the selection of exactly one dominant follicle, yet a clear cause has not been identified. In this paper, we suggest a synergistic explanation based on competition, formulated by a parsimoniously defined system of ordinary differential equations (ODEs) that quantifies the time evolution of multiple follicles and their competitive interaction during one wave. Not discriminating between follicles, growth and decline are given by fixed rates. Competition is introduced via a growth-suppressing term, equally supported by all follicles. We prove that the number of dominant follicles is determined exclusively by the ratio of follicular growth and competition. This number turns out to be independent of the number of subordinate follicles. The asymptotic behavior of the corresponding dynamical system is investigated rigorously, where we demonstrate that the ω-limit set only contains fixed points. When also including follicular decline, our ODEs perfectly resemble ultrasound data of bovine follicles. Implications for the involved but not explicitly modeled hormones are discussed.

Description: “Interior point algorithms are a good choice for solving pure LPs or QPs, but when you solve MIPs, all you need is a dual simplex” This is the common conception which disregards that an interior point solution provides some unique structural insight into the problem at hand. In this paper, we will discuss some of the benefits that an interior point solver brings to the solution of difficult MIPs within FICO Xpress. This includes many different components of the MIP solver such as branching variable selection, primal heuristics, preprocessing, and of course the solution of the LP relaxation.

Description: This book promotes the use of mathematical optimization and operations research methods in rail transportation. The editors assembled thirteen contributions from leading scholars to present a unified voice, standardize terminology, and assess the state-of-the-art. There are three main clusters of articles, corresponding to the classical stages of the planning process: strategic, tactical, and operational. These three clusters are further subdivided into five parts which correspond to the main phases of the railway network planning process: network assessment, capacity planning, timetabling, resource planning, and operational planning. Individual chapters cover: Simulation Capacity Assessment Network Design Train Routing Robust Timetabling Event Scheduling Track Allocation Blocking Shunting Rolling Stock Crew Scheduling Dispatching Delay Propagation