TY - THES A1 - Keidel, Stefan T1 - Snapshots in Scalaris N2 - Eines der größten Hindernisse beim praktischen Einsatz von Scalaris, einer skalierbaren Implementierung einer verteilten Hashtabelle mit Unterstützung für Transaktionen, ist das Fehlen eines Verfahrens zur Aufnahme eines konsistenten Zustandes des gesamten Systems. Wir stellen in dieser Arbeit ein einfaches Protokoll vor, dass diese Aufgabe erfüllt und sich, auf Grund der von uns gewählten Herangehensweise, leicht implementieren lässt. Als Ausgangspunkt dafür wählen wir aus einer Reihe von „klassischen“ Snapshot-Algorithmen ein 1993 von Mattern entworfenes Verfahren, welches auf dem Algorithmus von Lai und Yang basiert, aus. Diese Entscheidung basiert auf einer gründlichen Analyse der Protokolle unter Berücksichtigung der Architektur der existierenden Software. Im nächsten Arbeitsschritt benutzen wir unser vollständiges Wissen über die Interna des Transaktionssystems von Scalaris und vereinfachen damit das Verfahren hinsichtlich Benutzbarkeit und Implementierungskomplexität, ohne die Anforderungen an den aufgenommenen Zustand aufzuweichen. Statt einer losen Anhäufung lokaler Zustände der einzelnen Teilnehmerknoten können wir am Ende eine große Schlüssel-Wert-Tabelle als Ergebnis erzeugen, die konsistent ist, sich leicht weiterverarbeiten lässt und die einem Zustand entspricht, in dem sich das System einmal befunden haben könnte. Nachdem wir das Verfahren dann in Software umgesetzt haben, werten wir die Ergebnisse hinsichtlich des Einflusses auf die Performanz des Gesamtsystems aus und diskutieren mögliche Weiterentwicklungen. KW - scalaris KW - dht KW - algorithm Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42282 ER - TY - GEN A1 - Ito, Satoshi A1 - Shinano, Yuji T1 - Calculation of clinch and elimination numbers for sports leagues with multiple tiebreaking criteria N2 - The clinch (elimination) number is a minimal number of future wins (losses) needed to clinch (to be eliminated from) a specified place in a sports league. Several optimization models and computational results are shown in this paper for calculating clinch and elimination numbers in the presence of predefined multiple tiebreaking criteria. The main subject of this paper is to provide a general algorithmic framework based on integer programming with utilizing possibly multilayered upper and lower bounds. T3 - ZIB-Report - 18-51 KW - Sports league KW - Round-robin tournament KW - Tiebreaking criteria KW - Clinch number KW - Elimination number KW - Combinatorial optimization KW - Integer programming Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70591 SN - 1438-0064 ER - TY - GEN A1 - Costa, Marta A1 - Manton, James D. A1 - Ostrovsky, Aaron D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases N2 - Neural circuit mapping is generating datasets of 10,000s of labeled neurons. New computational tools are needed to search and organize these data. We present NBLAST, a sensitive and rapid algorithm, for measuring pairwise neuronal similarity. NBLAST considers both position and local geometry, decomposing neurons into short segments; matched segments are scored using a probabilistic scoring matrix defined by statistics of matches and non-matches. We validated NBLAST on a published dataset of 16,129 single Drosophila neurons. NBLAST can distinguish neuronal types down to the finest level (single identified neurons) without a priori information. Cluster analysis of extensively studied neuronal classes identified new types and unreported topographical features. Fully automated clustering organized the validation dataset into 1052 clusters, many of which map onto previously described neuronal types. NBLAST supports additional query types including searching neurons against transgene expression patterns. Finally we show that NBLAST is effective with data from other invertebrates and zebrafish. T3 - ZIB-Report - 16-34 KW - neuroinformatics KW - NBLAST KW - neuron similarity KW - cell type KW - clustering Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-59672 SN - 1438-0064 ER - TY - GEN A1 - Wiebel, Alexander A1 - Vos, Frans M. A1 - Hege, Hans-Christian T1 - Perception-Oriented Picking of Structures in Direct Volumetric Renderings N2 - Radiologists from all application areas are trained to read slice-based visualizations of 3D medical image data. Despite the numerous examples of sophisticated three-dimensional renderings, especially all variants of direct volume rendering, such methods are often considered not very useful by radiologists who prefer slice-based visualization. Just recently there have been attempts to bridge this gap between 2D and 3D renderings. These attempts include specialized techniques for volume picking that result in repositioning slices. In this paper, we present a new volume picking technique that, in contrast to previous work, does not require pre-segmented data or metadata. The positions picked by our method are solely based on the data itself, the transfer function and, most importantly, on the way the volumetric rendering is perceived by viewers. To demonstrate the usefulness of the proposed method we apply it for automatically repositioning slices in an abdominal MRI scan, a data set from a flow simulation and a number of other volumetric scalar fields. Furthermore we discuss how the method can be implemented in combination with various different volumetric rendering techniques. T3 - ZIB-Report - 11-45 KW - DVR KW - picking KW - pointing KW - direct volume rendering Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14343 SN - 1438-0064 ER - TY - GEN A1 - Clasen, Malte A1 - Paar, Philip A1 - Prohaska, Steffen T1 - Level of Detail for Trees Using Clustered Ellipsoids N2 - We present a level of detail method for trees based on ellipsoids and lines. We leverage the Expectation Maximization algorithm with a Gaussian Mixture Model to create a hierarchy of high-quality leaf clusterings, while the branches are simplified using agglomerative bottom-up clustering to preserve the connectivity. The simplification runs in a preprocessing step and requires no human interaction. For a fly by over and through a scene of 10k trees, our method renders on average at 40 ms/frame, up to 6 times faster than billboard clouds with comparable artifacts. T3 - ZIB-Report - 11-41 KW - level of detail KW - rendering KW - natural scene KW - Gaussian mixture model Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-14251 SN - 1438-0064 ER - TY - GEN A1 - Shinano, Yuji A1 - Heinz, Stefan A1 - Vigerske, Stefan A1 - Winkler, Michael T1 - FiberSCIP - A shared memory parallelization of SCIP N2 - Recently, parallel computing environments have become significantly popular. In order to obtain the benefit of using parallel computing environments, we have to deploy our programs for these effectively. This paper focuses on a parallelization of SCIP (Solving Constraint Integer Programs), which is a MIP solver and constraint integer programming framework available in source code. There is a parallel extension of SCIP named ParaSCIP, which parallelizes SCIP on massively parallel distributed memory computing environments. This paper describes FiberSCIP, which is yet another parallel extension of SCIP to utilize multi-threaded parallel computation on shared memory computing environments, and has the following contributions: First, the basic concept of having two parallel extensions and the relationship between them and the parallelization framework provided by UG (Ubiquity Generator) is presented, including an implementation of deterministic parallelization. Second, the difficulties to achieve a good performance that utilizes all resources on an actual computing environment and the difficulties of performance evaluation of the parallel solvers are discussed. Third, a way to evaluate the performance of new algorithms and parameter settings of the parallel extensions is presented. Finally, current performance of FiberSCIP for solving mixed-integer linear programs (MIPs) and mixed-integer non-linear programs (MINLPs) in parallel is demonstrated. T3 - ZIB-Report - 13-55 KW - parallel KW - branch-and-bound KW - deterministic parallelism KW - constraint integer programming KW - mixed integer programming KW - mixed integer nonlinear programming KW - SCIP KW - MIP KW - MINLP Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-42595 SN - 1438-0064 ER - TY - GEN A1 - Shinano, Yuji A1 - Achterberg, Tobias A1 - Berthold, Timo A1 - Heinz, Stefan A1 - Koch, Thorsten A1 - Winkler, Michael T1 - Solving Previously Unsolved MIP Instances with ParaSCIP on Supercomputers by using up to 80,000 Cores N2 - Mixed-integer programming (MIP) problem is arguably among the hardest classes of optimization problems. This paper describes how we solved 21 previously unsolved MIP instances from the MIPLIB benchmark sets. To achieve these results we used an enhanced version of ParaSCIP, setting a new record for the largest scale MIP computation: up to 80,000 cores in parallel on the Titan supercomputer. In this paper, we describe the basic parallelization mechanism of ParaSCIP, improvements of the dynamic load balancing and novel techniques to exploit the power of parallelization for MIP solving. We give a detailed overview of computing times and statistics for solving open MIPLIB instances. T3 - ZIB-Report - 20-16 KW - Mixed Integer Programming, Parallel processing, Node merging, Racing, ParaSCIP, Ubiquity Generator Framework, MIPLIB Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78393 SN - 1438-0064 ER - TY - GEN A1 - Hiller, Benjamin A1 - Vredeveld, Tjark T1 - Probabilistic alternatives for competitive analysis N2 - In the last 20 years competitive analysis has become the main tool for analyzing the quality of online algorithms. Despite of this, competitive analysis has also been criticized: It sometimes cannot discriminate between algorithms that exhibit significantly different empirical behavior, or it even favors an algorithm that is worse from an empirical point of view. Therefore, there have been several approaches to circumvent these drawbacks. In this survey, we discuss probabilistic alternatives for competitive analysis. T3 - ZIB-Report - 11-55 KW - online algorithms KW - probabilistic analysis KW - competitive analysis KW - survey Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-15131 SN - 1438-0064 ER - TY - GEN A1 - Kaplan, Bernhard A1 - Laufer, Jan A1 - Prohaska, Steffen A1 - Buchmann, Jens T1 - Monte-Carlo-based inversion scheme for 3D quantitative photoacoustic tomography N2 - The goal of quantitative photoacoustic tomography (qPAT) is to recover maps of the chromophore distributions from multiwavelength images of the initial pressure. Model-based inversions that incorporate the physical processes underlying the photoacoustic (PA) signal generation represent a promising approach. Monte-Carlo models of the light transport are computationally expensive, but provide accurate fluence distributions predictions, especially in the ballistic and quasi-ballistic regimes. Here, we focus on the inverse problem of 3D qPAT of blood oxygenation and investigate the application of the Monte-Carlo method in a model-based inversion scheme. A forward model of the light transport based on the MCX simulator and acoustic propagation modeled by the k-Wave toolbox was used to generate a PA image data set acquired in a tissue phantom over a planar detection geometry. The combination of the optical and acoustic models is shown to account for limited-view artifacts. In addition, the errors in the fluence due to, for example, partial volume artifacts and absorbers immediately adjacent to the region of interest are investigated. To accomplish large-scale inversions in 3D, the number of degrees of freedom is reduced by applying image segmentation to the initial pressure distribution to extract a limited number of regions with homogeneous optical parameters. The absorber concentration in the tissue phantom was estimated using a coordinate descent parameter search based on the comparison between measured and modeled PA spectra. The estimated relative concentrations using this approach lie within 5 % compared to the known concentrations. Finally, we discuss the feasibility of this approach to recover the blood oxygenation from experimental data. T3 - ZIB-Report - 17-04 KW - quantitative photoacoustic tomography KW - model-based inversion KW - oxygen saturation KW - chromophore concentration KW - photoacoustic imaging KW - Monte Carlo methods for light transport KW - boundary conditions KW - coordinate search Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62318 SN - 1438-0064 ER - TY - GEN A1 - Quer, Jannes A1 - Donati, Luca A1 - Keller, Bettina A1 - Weber, Marcus T1 - An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates N2 - In this article we propose an adaptive importance sampling scheme for dynamical quantities of high dimensional complex systems which are metastable. The main idea of this article is to combine a method coming from Molecular Dynamics Simulation, Metadynamics, with a theorem from stochastic analysis, Girsanov's theorem. The proposed algorithm has two advantages compared to a standard estimator of dynamic quantities: firstly, it is possible to produce estimators with a lower variance and, secondly, we can speed up the sampling. One of the main problems for building importance sampling schemes for metastable systems is to find the metastable region in order to manipulate the potential accordingly. Our method circumvents this problem by using an assimilated version of the Metadynamics algorithm and thus creates a non-equilibrium dynamics which is used to sample the equilibrium quantities. T3 - ZIB-Report - 17-09 KW - Adaptive Importance Sampling KW - Molecular Dynamics KW - Metastability KW - Variance Reduction KW - Non Equilibrium Sampling KW - Metadynamics KW - Girsanov Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-62075 SN - 1438-0064 ER -