@misc{MelenkNeun1989, author = {Melenk, Herbert and Neun, Winfried}, title = {Implementation of Portable Standard LISP for the SPARC Processor.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4625}, number = {TR-89-06}, year = {1989}, abstract = {The SPARC processor is a RISC (Reduced Instruction Set Computer) microcomputer, built into the SUN4 workstations. Since RISC processors are very well-suited for LISP processing, the implementation of a dialect of LISP (Portable Standard LISP, PSL) boded well for a great speed-up in comparison with other types of microcomputers. A first approach was done at The RAND Corporation in Santa Monica, which was derived from classical processor types like MC68000 or VAX. At the Konrad- Zuse-Zentrum f{\"u}r Informationstechnik Berlin (ZIB) that initial implementation was redesigned in order to adapt PSL to the specific features of the SPARC processor. The present implementation, in some parts, is very close to Cray PSL version also done in ZIB. Some timing informations are given in the appendix.}, language = {en} } @misc{Roitzsch1989, author = {Roitzsch, Rainer}, title = {KASKADE Programmer's Manual.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4617}, number = {TR-89-05}, year = {1989}, abstract = {The Programmers Manual contains the documentation of the C-KASKADE implementation. KASKADE is an adaptive finite element code (see SC ). The interfaces of all modules are described.}, language = {en} } @misc{Roitzsch1989, author = {Roitzsch, Rainer}, title = {KASKADE User's Manual.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4605}, number = {TR-89-04}, year = {1989}, abstract = {The Users Manual contains an introduction to the usage of the C-KASKADE implementation. KASKADE is an adaptive finite element code (see SC ). The manual includes a description of all commands, a simple recipe to define a new problem by changing the KASKADE source and a complete example.}, language = {en} } @misc{Walter1989, author = {Walter, Artur}, title = {Ein Finite-Element-Verfahren zur numerischen L{\"o}sung von Erhaltungsgleichungen.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4597}, number = {TR-89-03}, year = {1989}, abstract = {A new approach for the discretisation of hyperbolic conservation laws via a finite element method is developed and analysed. Appropriate forms of the Eulers equation of gas dynamic are considered to employ the algorithm in a reasonable way for this system of nonlinear equations. Both mathematical and physical stability results are obtained. A main part of the paper is devoted to the convergence proof with energy methods under strong regularity of the solution of a scalar nonlinear conservation law. Some hints on the implementation and numerical results for the calculation of transonic gasflow through a Laval nozzle are given. The necessary amount of numerical work is compared to an established finite difference method and the efficiency of the algorithm is shown. A survey on recent literature about finite element methods for hyperbolic problem is included.}, language = {de} } @misc{Deuflhard1989, author = {Deuflhard, Peter}, title = {Numerik von Anfangswertmethoden f{\"u}r gew{\"o}hnliche Differentialgleichungen.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4580}, number = {TR-89-02}, year = {1989}, abstract = {Das voliegende Skriptum entstand aus einer Vorlesung, die ich im WS 87/88 an der Freien Universit{\"a}t Berlin im Fachbereich Mathematik gehalten habe. Mein urspr{\"u}ngliches Vorlesungsmanuskript wurde von Herrn F. Bornemann in weiten Teilen {\"u}berarbeitet, reorganisiert und substantiell erg{\"a}nzt. Der Inhalt stammt gr{\"o}ßtenteils aus Originalarbeiten j{\"u}ngeren Datums. Dar{\"u}berhinaus finden sich zahlreiche Teile, die aus meiner jahrelangen Besch{\"a}ftigung mit dem Thema entstanden aber unpubliziert geblieben sind. Das Skriptum erhebt nicht den Anspruch, ein Lehrbuch zu sein. Es war zun{\"a}chst als Ausarbeitung f{\"u}r meinen studentischen H{\"o}rerkreis sowie als internes Arbeitspapier f{\"u}r das ZIB bestimmt. Die Kunde von der bloßen Existenz eines solchen Skriptums hat jedoch zu einer derart regen Nachfrage gef{\"u}hrt, daß es hiermit als Technischer Report des ZIB einer breiteren ffentlichkeit zug{\"a}nglich gemacht werden soll. In der vorliegenden Form richtet es sich in erster Linie an Mathematiker; es soll sich jedoch auch f{\"u}r Naturwissenschaftler und Ingenieure eignen, die sich einen Einblick in den theoretischen und algorithmischen Hintergrund der von ihnen verwendeten wissenschaftlichen Software verschaffen wollen.}, language = {de} } @misc{OPUS4-457, title = {CRAY-HANDBUCH. Einf{\"u}hrung in die Benutzung der CRAY X-MP unter UNICOS. (veraltet)}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4574}, number = {TR-89-01}, year = {1989}, language = {de} } @misc{MaierhoeferSkorobohatyj1988, author = {Maierh{\"o}fer, Gerhard and Skorobohatyj, Georg}, title = {Parallel-TRAPEX (Ein paralleler adaptiver Algorithmus zur numerischen Integration; seine Implementierung f{\"u}r SUPRENUM-artige Architekturen mit SUSI).}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4560}, number = {TR-88-05}, year = {1988}, abstract = {This paper describes some ways of transforming a sequential adaptive algorithm for numerical evaluation of an integral (Romberg- Quadrature with polynomial Extrapolation method) to a parallel one, such as have been implementad by the authors. We developed an algorithm which preserves the sequential adaptivity and is capable of running on various architectures, dynamically controlling the number of avtive processors depending on the problem. To study the time behaviour, we used the simulator SUSI(SUprenum SImulatur) which is able to simulate SUPRENUM-like architectures. Results are given in part 3. {\bf Keywords:} Romberg quadrature; numerical integration; parallel adaptive algorithm; SUSI; simulation; SUPRENUM; MIMD-Fortran; computer architecture; granularity; load balacing; master-slave-principle.}, language = {de} } @misc{BuhtzLangendorfPaetsch1988, author = {Buhtz, Danuta Anna and Langendorf, Jens and Paetsch, Olaf}, title = {GRAZIL - 3D. Ein graphisches Anwendungsprogramm zur Darstellung von Kurven- und Funktionsverl{\"a}ufen im r{\"a}umlichen Koordinatensystem.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4556}, number = {TR-88-04}, year = {1988}, abstract = {GRAZIL - 3D ist ein interaktives Programmpaket zur graphischen Darstellung von dreidimensionalen Kurvenverl{\"a}ufen. Das Aussehen der r{\"a}umlichen Ausgabe des Bildes wird durch Angabe des Blickwinkels und der Perspektive festgelegt.}, language = {de} } @misc{MelenkNeun1988, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE Installation Guide for CRAY 1 / X-MP Systems Running UNICOS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4541}, number = {TR-88-03}, year = {1988}, abstract = {This guide describes the CRAY/UNICOS REDUCE distribution tape and the procedures for installing, testing and maintaining REDUCE on a CRAY 1 or CRAY X-MP running UNICOS. This document was derived from the corresponding document for Vax/UNIX prepared by A. C. Hearn and L.R. Seward, The Rand Corporation, Santa Monica, publication CP84.}, language = {en} } @misc{MelenkNeun1988, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE User s Guide for the CRAY 1 / CRAY X-MP Series Running UNICOS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4539}, number = {TR-88-02}, year = {1988}, abstract = {This document describes operating procedures for running REDUCE specific to the CRAY 1 and CRAY X-MP computers running the Operating System UNICOS. The document was derived from the corresponding document for Vax/UNIX prepared by A. C. Hearn and L. R. Seward, The Rand Corporation, Santa Monica, (CP85).}, language = {en} } @misc{BuhtzBuhtz1988, author = {Buhtz, Rainer and Buhtz, Danuta Anna}, title = {TDLG 3.1 - Ein interaktives Programm zur Darstellung dreidimensionaler Modelle auf Rastergraphikger{\"a}ten.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4522}, number = {TR-88-01}, year = {1988}, abstract = {TDLG 3.1 dient zur Darstellung von dreidimensionalen Objekten, die sich aus offenen Linienz{\"u}gen, Dreieck- und Viereckelementen zusammensetzen. Dabei k{\"o}nnen verschiedene Visualisierungstechniken benutzt werden: Drahtmodell, Schattierung mit und ohne Lichtquelle, Hidden Surface Removal. Durch Verwendung von Konvertierungsprogrammen k{\"o}nnen auch IGES- und VDAFS- Dateien dargestellt werden.}, language = {de} } @misc{LangendorfPaetsch1987, author = {Langendorf, Jens and Paetsch, Olaf}, title = {GRAZIL (Graphical ZIB Language).}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4518}, number = {TR-87-07}, year = {1987}, abstract = {GRAZIL ist ein interaktives Programmpaket zur graphischen Darstellung von zwei-dimensionalen Kurvenverl{\"a}ufen. Dem Benutzer stehen zahlreiche Kommandos zum Gestalten des Layouts der Zeichnung zur Verf{\"u}gung. Die Eingabedaten m{\"u}ssen dem ZUGRIFF- Konzept gen{\"u}gen, wodurch die genaue Struktur der Daten erst zur Laufzeit bekannt sein muß und somit eine hohe Flexibilit{\"a}t und eine große Bandbreite der Einsatzm{\"o}glichkeiten erreicht wird. GRAZIL wurde mit der graphischen Grundsoftware BIZEPS2 und GKS entwickelt. Dadurch kann ein breites Rechner- und Ausgabeger{\"a}tespektrum genutzt werden.}, language = {de} } @misc{BuhtzLangendorfPaetschetal.1987, author = {Buhtz, Rainer and Langendorf, Jens and Paetsch, Olaf and Buhtz, Danuta Anna}, title = {ZUGRIFF - Eine vereinheitlichte Datenspezifikation f{\"u}r graphische Darstellungen und ihre graphische Aufbereitung.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4506}, number = {TR-87-06}, year = {1987}, abstract = {ZUGRIFF ist eine Dateischnittstelle f{\"u}r Graphikausgabe speziell numerischer Anwenderprogramme. Dieser Report beschreibt den Leistungsumfang der Spezifikation sowie die interaktive graphische Verarbeitung von ZUGRIFF- Dateien.}, language = {de} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE Users Guide for the CRAY 1 / X-MP Series Running COS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4498}, number = {TR-87-05}, year = {1987}, abstract = {This document describes operating procedures for running REDUCE specific to the CRAY 1 and CRAY X-MP computers running the CRAY Operating System (COS). The document was derived from the corresponding document for Vax/UNIX prepared by A.C. Hearn and L.R. Seward, The Rand Corporation, Santa Monica, (CP85).}, language = {en} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {REDUCE Installation Guide for CRAY 1 / X-MP Systems Running COS. Version 3.3.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4486}, number = {TR-87-04}, year = {1987}, abstract = {This guide describes the CRAY/COS REDUCE distribution tape and the procedures for installing, testing and maintaining REDUCE on a CRAY 1 or CRAY X-MP running COS. This document was derived from the corresponding document for Vax/Unix prepared by A. C. Hearn and L. R. Seward, The Rand Corporation, Santa Monica, publication CP84.}, language = {en} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {Portable Common LISP Subset Implementation for CRAY X+MP Computers.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4479}, number = {TR-87-03}, year = {1987}, abstract = {This document describes the installation procedure and maintenance for the Portable Common LISP Subset (PCLS) developed at the University of Utah.}, language = {en} } @misc{MelenkNeun1987, author = {Melenk, Herbert and Neun, Winfried}, title = {Portable Standard LISP Implementation for CRAY X+MP Computers. Release of PSL 3.4 for COS.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4465}, number = {TR-87-02}, year = {1987}, abstract = {Portable Standard LISP (PSL) is a portable implementation of the programming language LISP constructed at the University of Utah. The version 3.4 of PSL was implemented for CRAY X-MP computers by Konrad Zuse-Zentrum Berlin; this implementation is based to an important part on the earlier implementation of PSL 3.2 at Salt Lake City, Los Alamos and Mendota Heights.}, language = {en} } @misc{BuschPoehleStech1987, author = {Busch, Hubert and P{\"o}hle, Uwe and Stech, Wolfgang}, title = {CRAY-Handbuch. - Einf{\"u}hrung in die Benutzung der CRAY.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4459}, number = {TR-87-01}, year = {1987}, abstract = {Das vorliegende Handbuch wendet sich an alle Benutzer des f{\"u}r den Norddeutschen Vektorrechnerverbund im ZIB installierten Rechners CRAY X-MP/24. Ein großer Teil der Darstellung ist der Optimierung von Programmen gewidmet, die in FORTRAN geschrieben sind. Gerade weil die CRAY einer der schnellsten Rechner der Welt ist, wird jeder Benutzer fr{\"u}her oder sp{\"a}ter selbst auf dieses Thema stoßen, denn die Maschine ist vornehmlich f{\"u}r Probleme bestimmt, die f{\"u}r die meisten anderen Rechner zu komplex sind. Maschinen der CRAY-Leistungsklasse beziehen einen erheblichen Teil ihrer Geschwindigkeit aus der parallelen Arbeit vieler Komponenten. Programme, die die jeweilige Architektur der Maschine ber{\"u}cksichtigen, k{\"o}nnen um Gr{\"o}ßenordnungen schneller (also wirtschaftlicher) sein als Programme, deren Autor beim Schreiben einen sogenannten "klassischen" Rechner vor seinem geistigen Auge hatte. Daher wird auch der technische Aufbau der CRAY X-MP im Handbuch erl{\"a}utert. Weitere Teile des Handbuches besch{\"a}ftigen sich mit den Vorrechnern und dem Rechnernetz.}, language = {de} } @misc{WitzigBeckenbachEifleretal.2016, author = {Witzig, Jakob and Beckenbach, Isabel and Eifler, Leon and Fackeldey, Konstantin and Gleixner, Ambros and Grever, Andreas and Weber, Marcus}, title = {Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes}, issn = {1438-0064}, doi = {10.1137/16M1091162}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60353}, year = {2016}, abstract = {In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst.}, language = {en} } @misc{EhlkeRammLameckeretal.2013, author = {Ehlke, Moritz and Ramm, Heiko and Lamecker, Hans and Hege, Hans-Christian and Zachow, Stefan}, title = {Fast Generation of Virtual X-ray Images from Deformable Tetrahedral Meshes}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41896}, year = {2013}, abstract = {We propose a novel GPU-based approach to render virtual X-ray projections of deformable tetrahedral meshes. These meshes represent the shape and the internal density distribution of a particular anatomical structure and are derived from statistical shape and intensity models (SSIMs). We apply our method to improve the geometric reconstruction of 3D anatomy (e.g.\ pelvic bone) from 2D X-ray images. For that purpose, shape and density of a tetrahedral mesh are varied and virtual X-ray projections are generated within an optimization process until the similarity between the computed virtual X-ray and the respective anatomy depicted in a given clinical X-ray is maximized. The OpenGL implementation presented in this work deforms and projects tetrahedral meshes of high resolution (200.000+ tetrahedra) at interactive rates. It generates virtual X-rays that accurately depict the density distribution of an anatomy of interest. Compared to existing methods that accumulate X-ray attenuation in deformable meshes, our novel approach significantly boosts the deformation/projection performance. The proposed projection algorithm scales better with respect to mesh resolution and complexity of the density distribution, and the combined deformation and projection on the GPU scales better with respect to the number of deformation parameters. The gain in performance allows for a larger number of cycles in the optimization process. Consequently, it reduces the risk of being stuck in a local optimum. We believe that our approach contributes in orthopedic surgery, where 3D anatomy information needs to be extracted from 2D X-rays to support surgeons in better planning joint replacements.}, language = {en} } @misc{WinkelmannSchuettevonKleist2013, author = {Winkelmann, Stefanie and Sch{\"u}tte, Christof and von Kleist, Max}, title = {Markov Control Processes with Rare State Observation: Theory and Application to Treatment Scheduling in HIV-1}, issn = {1438-0064}, doi = {10.4310/CMS.2014.v12.n5.a4}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41955}, year = {2013}, abstract = {Markov Decision Processes (MDP) or Partially Observable MDPs (POMDP) are used for modelling situations in which the evolution of a process is partly random and partly controllable. These MDP theories allow for computing the optimal control policy for processes that can continuously or frequently be observed, even if only partially. However, they cannot be applied if state observation is very costly and therefore rare (in time). We present a novel MDP theory for rare, costly observations and derive the corresponding Bellman equation. In the new theory, state information can be derived for a particular cost after certain, rather long time intervals. The resulting information costs enter into the total cost and thus into the optimization criterion. This approach applies to many real world problems, particularly in the medical context, where the medical condition is examined rather rarely because examination costs are high. At the same time, the approach allows for efficient numerical realization. We demonstrate the usefulness of the novel theory by determining, from the national economic perspective, optimal therapeutic policies for the treatment of the human immunodefficiency virus (HIV) in resource-rich and resource-poor settings. Based on the developed theory and models, we discover that available drugs may not be utilized efficiently in resource-poor settings due to exorbitant diagnostic costs.}, language = {en} } @misc{WendeSteinke2013, author = {Wende, Florian and Steinke, Thomas}, title = {Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU}, issn = {1438-0064}, doi = {10.1145/2503210.2503254}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42187}, year = {2013}, abstract = {Simulations of the critical Ising model by means of local update algorithms suffer from critical slowing down. One way to partially compensate for the influence of this phenomenon on the runtime of simulations is using increasingly faster and parallel computer hardware. Another approach is using algorithms that do not suffer from critical slowing down, such as cluster algorithms. This paper reports on the Swendsen-Wang multi-cluster algorithm on Intel Xeon Phi coprocessor 5110P, Nvidia Tesla M2090 GPU, and x86 multi-core CPU. We present shared memory versions of the said algorithm for the simulation of the two- and three-dimensional Ising model. We use a combination of local cluster search and global label reduction by means of atomic hardware primitives. Further, we describe an MPI version of the algorithm on Xeon Phi and CPU, respectively. Significant performance improvements over known im plementations of the Swendsen-Wang algorithm are demonstrated.}, language = {en} } @misc{LieFackeldeyWeber2013, author = {Lie, Han Cheng and Fackeldey, Konstantin and Weber, Marcus}, title = {A square root approximation of transition rates for a Markov State Model}, issn = {1438-0064}, doi = {10.1137/120899959}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42195}, year = {2013}, abstract = {Trajectory- or mesh-based methods for analyzing the dynamical behavior of large molecules tend to be impractical due to the curse of dimensionality - their computational cost increases exponentially with the size of the molecule. We propose a method to break the curse by a novel square root approximation of transition rates, Monte Carlo quadrature and a discretization approach based on solving linear programs. With randomly sampled points on the molecular energy landscape and randomly generated discretizations of the molecular configuration space as our initial data, we construct a matrix describing the transition rates between adjacent discretization regions. This transition rate matrix yields a Markov State Model of the molecular dynamics. We use Perron cluster analysis and coarse-graining techniques in order to identify metastable sets in configuration space and approximate the transition rates between the metastable sets. Application of our method to a simple energy landscape on a two-dimensional configuration space provides proof of concept and an example for which we compare the performance of different discretizations. We show that the computational cost of our method grows only polynomially with the size of the molecule. However, finding discretizations of higher-dimensional configuration spaces in which metastable sets can be identified remains a challenge.}, language = {en} } @misc{DresslerSteinke2013, author = {Dreßler, Sebastian and Steinke, Thomas}, title = {An Automated Approach for Estimating the Memory Footprint of Non-Linear Data Objects}, issn = {1438-0064}, doi = {10.1007/978-3-642-54420-0_25}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42224}, year = {2013}, abstract = {Current programming models for heterogeneous devices with disjoint physical memory spaces require explicit allocation of device memory and explicit data transfers. While it is quite easy to manually implement these operations for linear data objects like arrays, this task becomes more difficult for non-linear objects, e.g. linked lists or multiple inherited classes. The difficulties arise due to dynamic memory requirements at run-time and the dependencies between data structures. In this paper we present a novel method to build a graph-based static data type description which is used to create code for injectable functions that automatically determine the memory footprint of data objects at run-time. Our approach is extensible to implement automatically generated optimized data transfers across physical memory spaces.}, language = {en} } @misc{RammMorilloVictoriaTodtetal.2013, author = {Ramm, Heiko and Morillo Victoria, Oscar Salvador and Todt, Ingo and Schirmacher, Hartmut and Ernst, Arneborg and Zachow, Stefan and Lamecker, Hans}, title = {Visual Support for Positioning Hearing Implants}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42495}, year = {2013}, abstract = {We present a software planning tool that provides intuitive visual feedback for finding suitable positions of hearing implants in the human temporal bone. After an automatic reconstruction of the temporal bone anatomy the tool pre-positions the implant and allows the user to adjust its position interactively with simple 2D dragging and rotation operations on the bone's surface. During this procedure, visual elements like warning labels on the implant or color encoded bone density information on the bone geometry provide guidance for the determination of a suitable fit.}, language = {en} } @misc{HombergBaumWiebeletal.2013, author = {Homberg, Ulrike and Baum, Daniel and Wiebel, Alexander and Prohaska, Steffen and Hege, Hans-Christian}, title = {Definition, Extraction, and Validation of Pore Structures in Porous Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42510}, year = {2013}, abstract = {An intuitive and sparse representation of the void space of porous materials supports the efficient analysis and visualization of interesting qualitative and quantitative parameters of such materials. We introduce definitions of the elements of this void space, here called pore space, based on its distance function, and present methods to extract these elements using the extremal structures of the distance function. The presented methods are implemented by an image processing pipeline that determines pore centers, pore paths and pore constrictions. These pore space elements build a graph that represents the topology of the pore space in a compact way. The representations we derive from μCT image data of realistic soil specimens enable the computation of many statistical parameters and, thus, provide a basis for further visual analysis and application-specific developments. We introduced parts of our pipeline in previous work. In this chapter, we present additional details and compare our results with the analytic computation of the pore space elements for a sphere packing in order to show the correctness of our graph computation.}, language = {en} } @misc{MeiselRoeblitz2013, author = {Meisel, Kristin and R{\"o}blitz, Susanna}, title = {Mathematische Modellierung der Knochenremodellierung}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42010}, year = {2013}, abstract = {Knochenremodellierung beinhaltet den Auf- und Abbau der Knochenmasse durch die verschiedenen Knochenzellen und findet fast {\"u}berall, auch am Skelett Erwachsener, statt. F{\"u}r die Erneuerung der Knochensubstanz sind die Osteoblasten zust{\"a}ndig. Sie ersetzen exakt die Menge der Knochenmasse, welche zuvor durch Osteoklasten abgebaut wurde. St{\"o}rungen dieses, durch viele Faktoren beeinflussten Prozesses f{\"u}hren zu pathologischen Ver{\"a}nderungen, beispielsweise zu Osteoporose oder Arthritis. Auf der Grundlage analysierter publizierter Modelle wurde ein Modell entwickelt, welches den Einfluss einiger dieser Faktoren realistisch abbildet. Auf diese Weise kann die Wirkung von basalem PTH, des RANKL-OPG-Systems ( RANKL: Receptor activator of nuclear factor kappa-B ligand, OPG: Osteoprotegerin) und des Estradiols auf den Knochenstoffwechsel am vorgestellten System untersucht werden. Außerdem wurde durch Estradiolmangel hervorgerufene Osteoporose und der kurative Effekt von synthetischen Medikamenten wie Estradiol oder intermittierend verabreichtem PTH modelliert. Mit der Parametersch{\"a}tzung anhand des Gauß-Newton-Verfahrens wird des Weiteren eine Methode vorgestellt, die es erm{\"o}glicht, mathematische Modelle bestm{\"o}glich durch Variation der Parameterwerte an experimentelle Daten anzupassen. Das am Zuse-Institut Berlin entwickelte Softwarepaket POEM wendet diesen Algorithmus an und wird ebenfalls erl{\"a}utert.}, language = {de} } @misc{Pyszkalski2013, author = {Pyszkalski, Wolfgang}, title = {{\"U}bersicht {\"u}ber die Datenhaltung im ZIB und die M{\"o}glichkeiten einer Nutzung durch Projekte}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42060}, year = {2013}, abstract = {Dieser Bericht beschreibt in allgemein verst{\"a}ndlicher Form die Struktur der Datenhaltung im Zuse-Institut Berlin (ZIB) und die aktuell verwendeten Strategien im Umgang mit immer st{\"a}rker wachsenden Datenmengen, sowie der Herausforderung der Speicherung unwiederbringlicher Daten {\"u}ber im Grunde unbegrenzte Zeit.}, language = {de} } @misc{BujotzekSchuettNielsenetal.2013, author = {Bujotzek, Alexander and Sch{\"u}tt, Ole and Nielsen, Adam and Fackeldey, Konstantin and Weber, Marcus}, title = {Efficient Conformational Analysis by Partition-of-Unity Coupling}, journal = {Math Chem}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42570}, year = {2013}, abstract = {Obtaining a sufficient sampling of conformational space is a common problem in molecular simulation. We present the implementation of an umbrella-like adaptive sampling approach based on function-based meshless discretization of conformational space that is compatible with state of the art molecular dynamics code and that integrates an eigenvector-based clustering approach for conformational analysis and the computation of inter-conformational transition rates. The approach is applied to three example systems, namely n-pentane, alanine dipeptide, and a small synthetic host-guest system, the latter two including explicitly modeled solvent.}, language = {en} } @misc{GoetschelvonTycowiczPolthieretal.2013, author = {G{\"o}tschel, Sebastian and von Tycowicz, Christoph and Polthier, Konrad and Weiser, Martin}, title = {Reducing Memory Requirements in Scientific Computing and Optimal Control}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42695}, year = {2013}, abstract = {In high accuracy numerical simulations and optimal control of time-dependent processes, often both many time steps and fine spatial discretizations are needed. Adjoint gradient computation, or post-processing of simulation results, requires the storage of the solution trajectories over the whole time, if necessary together with the adaptively refined spatial grids. In this paper we discuss various techniques to reduce the memory requirements, focusing first on the storage of the solution data, which typically are double precision floating point values. We highlight advantages and disadvantages of the different approaches. Moreover, we present an algorithm for the efficient storage of adaptively refined, hierarchic grids, and the integration with the compressed storage of solution data.}, language = {en} } @misc{VincensWittHomberg2014, author = {Vincens, Eric and Witt, Karl Josef and Homberg, Ulrike}, title = {Approaches to Determine the Constriction Size Distribution for Understanding Filtration Phenomena in Granular Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-43960}, year = {2014}, abstract = {Granular filters in hydraulically loaded earth structures constitute the ultimate barrier for the blockage of small particles moving through the structure regularly or along concentrated leaks. If filters are inefficient to block small particles several types of internal erosion may be initiated. A corresponding phenomenon appears during suffusion in a wide graded hydraulically loaded fill, when fine particles, embedded in the pore structure of a soil skeleton, are washed out. The cumulative constriction size distribution (CSD) is physically the key property that qualifies the soils retention capability as like a spatial acting sieve. Constrictions are defined as the narrowest sections of channels between larger volumes (pores) within the pore network of granular material and they are the main obstacles for a small particle to overcome when flowing along pathways. At least three different approaches are available to determine and compute the CSD, i.e. experimental, numerical and analytical methods. The purpose of this review is to present and discuss these methods pointing out their limits, advantages and significance related to internal erosion phenomena.}, language = {en} } @misc{BorndoerferKarbstein2013, author = {Bornd{\"o}rfer, Ralf and Karbstein, Marika}, title = {A Primal-Dual Approximation Algorithm for the Steiner Connectivity Problem}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42430}, year = {2013}, abstract = {We extend the primal-dual approximation technique of Goemans and Williamson to the Steiner connectivity problem, a kind of Steiner tree problem in hypergraphs. This yields a (k+1)-approximation algorithm for the case that k is the minimum of the maximal number of nodes in a hyperedge minus 1 and the maximal number of terminal nodes in a hyperedge. These results require the proof of a degree property for terminal nodes in hypergraphs which generalizes the well-known graph property that the average degree of terminal nodes in Steiner trees is at most 2.}, language = {en} } @misc{GamrathKochMartinetal.2013, author = {Gamrath, Gerald and Koch, Thorsten and Martin, Alexander and Miltenberger, Matthias and Weninger, Dieter}, title = {Progress in Presolving for Mixed Integer Programming}, issn = {1438-0064}, doi = {10.1007/s12532-015-0083-5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42530}, year = {2013}, abstract = {Presolving attempts to eliminate redundant information from the problem formulation and simultaneously tries to strengthen the formulation. It can be very effective and is often essential for solving instances. Especially for mixed integer programming problems, fast and effective presolving algorithms are very important. In this paper, we report on three new presolving techniques. The first method searches for singleton continuous columns and tries to fix the corresponding variables. Then we present a presolving technique which exploits a partial order of the variables to induce fixings. Finally, we show an approach based on connected components in graphs. Our computational results confirm the profitable use of the algorithms in practice.}, language = {en} } @misc{Schuster1986, author = {Schuster, H. J.}, title = {T{\"a}tigkeitsbericht-1985.}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4443}, number = {TR-86-01}, year = {1986}, language = {de} } @misc{KrauseFackeldeyKrause2013, author = {Krause, Dorian and Fackeldey, Konstantin and Krause, Rolf}, title = {A parallel multiscale simulation toolbox for coupling molecular dynamics and finite elements}, issn = {1438-0064}, doi = {10.1007/978-3-319-00786-1_14}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42354}, year = {2013}, abstract = {It is the ultimate goal of concurrent multiscale methods to provide computational tools that allow to simulation physical processes with the accuracy of micro-scale and the computational speed of macro-scale models. As a matter of fact, the efficient and scalable implementation of concurrent multiscale methods on clusters and supercomputers is a complicated endeavor. In this article we present the parallel multiscale simulation tool MACI which has been designed for efficient coupling between molecular dynamics and finite element codes. We propose a specification for a thin yet versatile interface for the coupling of molecular dynamics and finite element codes in a modular fashion. Further we discuss the parallelization strategy pursued in MACI, in particular, focusing on the parallel assembly of transfer operators and their efficient execution.}, language = {en} } @misc{HartmannBanischSarichetal.2013, author = {Hartmann, Carsten and Banisch, Ralf and Sarich, Marco and Badowski, Thomas and Sch{\"u}tte, Christof}, title = {Characterization of Rare Events in Molecular Dynamics}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42410}, year = {2013}, abstract = {A good deal of molecular dynamics simulations aims at predicting and quantifying rare events, such as the folding of a protein or a phase transition. Simulating rare events is often prohibitive, especially if the equations of motion are high-dimensional, as is the case in molecular dynamics. Various algorithms have been proposed for efficiently computing mean first passage times, transition rates or reaction pathways. This article surveys and discusses recent developments in the field of rare event simulation and outlines a new approach that combines ideas from optimal control and statistical mechanics. The optimal control approach described in detail resembles the use of Jarzynski's equality for free energy calculations, but with an optimized protocol that speeds up the sampling, while (theoretically) giving variance-free estimators of the rare events statistics. We illustrate the new approach with two numerical examples and discuss its relation to existing methods.}, language = {en} } @misc{SarichBanischHartmannetal.2013, author = {Sarich, Marco and Banisch, Ralf and Hartmann, Carsten and Sch{\"u}tte, Christof}, title = {Markov State Models for Rare Events in Molecular Dynamics}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42420}, year = {2013}, abstract = {Rare but important transition events between long lived states are a key feature of many molecular systems. In many cases the computation of rare event statistics by direct molecular dynamics (MD) simulations is infeasible even on the most powerful computers because of the immensely long simulation timescales needed. Recently a technique for spatial discretization of the molecular state space designed to help overcome such problems, so-called Markov State Models (MSMs), has attracted a lot of attention. We review the theoretical background and algorithmic realization of MSMs and illustrate their use by some numerical examples. Furthermore we introduce a novel approach to using MSMs for the efficient solution of optimal control problems that appear in applications where one desires to optimize molecular properties by means of external controls.}, language = {en} } @misc{SchuetteNielsenWeber2014, author = {Sch{\"u}tte, Christof and Nielsen, Adam and Weber, Marcus}, title = {Markov State Models and Molecular Alchemy}, issn = {1438-0064}, doi = {10.1080/00268976.2014.944597}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-46718}, year = {2014}, abstract = {In recent years Markov State Models (MSMs) have attracted a consid- erable amount of attention with regard to modelling conformation changes and associated function of biomolecular systems. They have been used successfully, e.g., for peptides including time-resolved spectroscopic ex- periments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multi- valent scenarios. In this article a novel reweighting scheme is introduced that allows to construct an MSM for certain molecular system out of an MSM for a similar system. This permits studying how molecular proper- ties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under con- sideration. The performance of the reweighting scheme is illustrated for simple test cases including one where the main wells of the respective en- ergy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed.}, language = {en} } @misc{ShinanoAchterbergBertholdetal.2013, author = {Shinano, Yuji and Achterberg, Tobias and Berthold, Timo and Heinz, Stefan and Koch, Thorsten and Winkler, Michael}, title = {Solving hard MIPLIB2003 problems with ParaSCIP on Supercomputers: An update}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42888}, year = {2013}, abstract = {Contemporary supercomputers can easily provide years of CPU time per wall-clock hour. One challenge of today's software development is how to harness this wast computing power in order to solve really hard mixed integer programming instances. In 2010, two out of six open MIPLIB2003 instances could be solved by ParaSCIP in more than ten consecutive runs, restarting from checkpointing files. The contribution of this paper is threefold: For the first time, we present computational results of single runs for those two instances. Secondly, we provide new improved upper and lower bounds for all of the remaining four open MIPLIB2003 instances. Finally, we explain which new developments led to these results and discuss the current progress of ParaSCIP. Experiments were conducted on HLRNII, on HLRN III, and on the Titan supercomputer, using up to 35,200 cores.}, language = {en} } @misc{FuegenschuhGroesserVierhaus2013, author = {F{\"u}genschuh, Armin and Gr{\"o}sser, Stefan N. and Vierhaus, Ingmar}, title = {A Global Approach to the Control of an Industry Structure System Dynamics Model}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42932}, year = {2013}, abstract = {We consider a system dynamics model that describes the effect of human activity on natural resources. The central stocks are the accumulated profit, the industry structures, and the water resources. The model can be controlled through two time-dependent parameters. The goal in this paper is to find a parameter setting that leads to a maximization of a performance index, which reflects both environmental and economic aspects. Thus, the goal is to identify the most sustainable stock of industry structures within the model's constraints and assumptions. In order to find a proven global optimal parameter set, we formulate the System Dynamics Optimization model as a mixed-integer nonlinear problem that is accessible for numerical solvers. Due to the dynamic structure of the model, certain steps of the solution process must be handled with greater care, compared to standard non-dynamic problems. We describe our approach of solving the industry structure model and present computational results. In addition, we discuss the limitations of the approach and next steps.}, language = {en} } @misc{BleyD'AndreagiovanniKarch2013, author = {Bley, Andreas and D'Andreagiovanni, Fabio and Karch, Daniel}, title = {Scheduling technology migration in WDM Networks}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42654}, year = {2013}, abstract = {The rapid technological evolution of telecommunication networks demands service providers to regularly update their technology, with the aim of remaining competitive in the marketplace. However, upgrading the technology in a network is not a trivial task. New hardware components need to be installed in the network and during the installation network connectivity may be temporarily compromised. The Wavelength Division Multiplexing (WDM) technology, whose upgrade is considered in here, shares fiber links among several optical connections and tearing down a single link may disrupt several optical connections at once. When the upgrades involve large parts of a network, typically not all links can be upgraded in parallel, which may lead to an unavoidable longer disruption of some connections. A bad scheduling of the overall endeavor, however, can dramatically increase the disconnection time of parts of the networks, causing extended service disruption. In this contribution, we study the problem of finding a schedule of the fiber link upgrades that minimizes the total service disruption time. To the best of our knowledge, this problem has not yet been formalized and investigated. The aim of our work is to close this gap by presenting a mathematical optimization model for the problem and an innovative solution algorithm that tackles the intrinsic difficulties of the problem. Computational experience on realistic instances completes our study. Our original investigations have been driven by real needs of DFN, operator of the German National Research and Education Network and our partner in the BMBF research project ROBUKOM (http://www.robukom.de/).}, language = {en} } @misc{BuesingD'Andreagiovanni2013, author = {B{\"u}sing, Christina and D'Andreagiovanni, Fabio}, title = {A new theoretical framework for Robust Optimization under multi-band uncertainty}, issn = {1438-0064}, doi = {10.1007/978-3-319-00795-3_17}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42644}, year = {2013}, abstract = {We provide an overview of our main results about studying Linear Programming Problems whose coefficient matrix is subject to uncertainty and the uncertainty is modeled through a multi-band set. Such an uncertainty set generalizes the classical one proposed by Bertsimas and Sim and is particularly suitable in the common case of arbitrary non-symmetric distributions of the parameters. Our investigations were inspired by practical needs of our industrial partner in ongoing projects with focus on the design of robust telecommunications networks.}, language = {en} } @misc{BlancoSchlechte2013, author = {Blanco, Marco and Schlechte, Thomas}, title = {Analysis of Micro-Macro Transformations of Railway Networks}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42710}, year = {2013}, abstract = {A common technique in the solution of large or complex optimization problems is the use of micro-macro transformations. In this paper, we carry out a theoretical analysis of such transformations for the track allocation problem in railway networks. We prove that the cumulative rounding technique of Schlechte et al. satisfies two of three natural optimality criteria and that this performance cannot be improved. We also show that under extreme circumstances, this technique can perform inconvieniently by underestimating the global optimal value.}, language = {en} } @misc{ZakrzewskaD'AndreagiovanniRueppetal.2013, author = {Zakrzewska, Anna and D'Andreagiovanni, Fabio and Ruepp, Sarah and Berger, Michael S.}, title = {Biobjective Optimization of Radio Access Technology Selection and Resource Allocation in Heterogeneous Wireless Networks}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42675}, year = {2013}, abstract = {We propose a novel optimization model for resource assignment in heterogeneous wireless network. The model adopts two objective functions maximizing the number of served users and the minimum granted utility at once. A distinctive feature of our new model is to consider two consecutive time slots, in order to include handover as an additional decision dimension. Furthermore, the solution algorithm that we propose refines a heuristic solution approach recently proposed in literature, by considering a real joint optimization of the considered resources. The simulation study shows that the new model leads to a significant reduction in handover frequency, when compared to a traditional scheme based on maximum SNR.}, language = {en} } @misc{BauschertBuesingD'Andreagiovannietal.2013, author = {Bauschert, Thomas and B{\"u}sing, Christina and D'Andreagiovanni, Fabio and Koster, Arie M.C.A. and Kutschka, Manuel and Steglich, Uwe}, title = {Network Planning under Demand Uncertainty with Robust Optimization}, issn = {1438-0064}, doi = {10.1109/MCOM.2014.6736760}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42557}, year = {2013}, abstract = {The planning of a communication network is inevitably depending on the quality of both the planning tool and the demand forecast used. In this article, we show exemplarily how the emerging area of Robust Optimization can advance the network planning by a more accurate mathematical description of the demand uncertainty. After a general introduction of the concept and its application to a basic network design problem, we present two applications: multi-layer and mixed-line-rate network design. We conclude with a discussion of extensions of the robustness concept to increase the accuracy of handling uncertainties.}, language = {en} } @misc{BorndoerferMehrgardtReutheretal.2013, author = {Bornd{\"o}rfer, Ralf and Mehrgardt, Julika and Reuther, Markus and Schlechte, Thomas and Waas, Kerstin}, title = {Re-optimization of Rolling Stock Rotations}, issn = {1438-0064}, doi = {10.1007/978-3-319-07001-8_8}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42569}, year = {2013}, abstract = {The Rolling Stock Rotation Problem is to schedule rail vehicles in order to cover timetabled trips by a cost optimal set of vehicle rotations. The problem integrates several facets of railway optimization, i.e., vehicle composition, maintenance constraints, and regularity aspects. In industrial applications existing schedules often have to be re-optimized to integrate timetable changes or construction sites. We present an integrated modeling and algorithmic approach for this task as well as computational results for industrial problem instances of DB Fernverkehr AG.}, language = {en} } @misc{SagnolHarman2013, author = {Sagnol, Guillaume and Harman, Radoslav}, title = {Computing exact D-optimal designs by mixed integer second order cone programming}, issn = {1438-0064}, doi = {10.1214/15-AOS1339}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-41932}, year = {2013}, abstract = {Let the design of an experiment be represented by an \$s\$-dimensional vector \$\vec{w}\$ of weights with non-negative components. Let the quality of \$\vec{w}\$ for the estimation of the parameters of the statistical model be measured by the criterion of \$D\$-optimality defined as the \$m\$-th root of the determinant of the information matrix \$M(\vec{w})=\sum_{i=1}^s w_iA_iA_i^T\$, where \$A_i\$, \$i=1,...,s\$, are known matrices with \$m\$ rows. In the paper, we show that the criterion of \$D\$-optimality is second-order cone representable. As a result, the method of second order cone programming can be used to compute an approximate \$D\$-optimal design with any system of linear constraints on the vector of weights. More importantly, the proposed characterization allows us to compute an \emph{exact} \$D\$-optimal design, which is possible thanks to high-quality branch-and-cut solvers specialized to solve mixed integer second order cone problems. We prove that some other widely used criteria are also second order cone representable, for instance the criteria of \$A\$-, and \$G\$-optimality, as well as the criteria of \$D_K\$- and \$A_K\$-optimality, which are extensions of \$D\$-, and \$A\$-optimality used in the case when only a specific system of linear combinations of parameters is of interest. We present several numerical examples demonstrating the efficiency and universality of the proposed method. We show that in many cases the mixed integer second order cone programming approach allows us to find a provably optimal exact design, while the standard heuristics systematically miss the optimum.}, language = {en} } @misc{Berthold2013, author = {Berthold, Timo}, title = {Primal MINLP Heuristics in a nutshell}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42170}, year = {2013}, abstract = {Primal heuristics are an important component of state-of-the-art codes for mixed integer nonlinear programming (MINLP). In this article we give a compact overview of primal heuristics for MINLP that have been suggested in the literature of recent years. We sketch the fundamental concepts of different classes of heuristics and discuss specific implementations. A brief computational experiment shows that primal heuristics play a key role in achieving feasibility and finding good primal bounds within a global MINLP solver.}, language = {en} } @misc{ShinanoHeinzVigerskeetal.2013, author = {Shinano, Yuji and Heinz, Stefan and Vigerske, Stefan and Winkler, Michael}, title = {FiberSCIP - A shared memory parallelization of SCIP}, issn = {1438-0064}, doi = {10.1287/ijoc.2017.0762}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42595}, year = {2013}, abstract = {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.}, language = {en} } @misc{Gamrath2013, author = {Gamrath, Gerald}, title = {Improving strong branching by domain propagation}, issn = {1438-0064}, doi = {10.1007/s13675-014-0021-8}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42546}, year = {2013}, abstract = {One of the essential components of a branch-and-bound based mixed-integer linear programming (MIP) solver is the branching rule. Strong branching is a method used by many state-of-the-art branching rules to select the variable to branch on. It precomputes the dual bounds of potential child nodes by solving auxiliary linear programs (LPs) and thereby helps to take good branching decisions that lead to a small search tree. In this paper, we describe how these dual bound predictions can be improved by including domain propagation into strong branching. Domain propagation is a technique usually used at every node of the branch-and-bound tree to tighten the local domains of variables. Computational experiments on standard MIP instances indicate that our improved strong branching method significantly improves the quality of the predictions and causes almost no additional effort. For a full strong branching rule, we are able to obtain substantial reductions of the branch-and-bound tree size as well as the solving time. Moreover, also the state-of-the-art hybrid branching rule can be improved this way. This paper extends previous work by the author published in the proceedings of the CPAIOR 2013.}, language = {en} } @misc{BorndoerferHoangKarbsteinetal.2013, author = {Bornd{\"o}rfer, Ralf and Hoang, Nam-Dung and Karbstein, Marika and Koch, Thorsten and Martin, Alexander}, title = {How Many Steiner Terminals Can You Connect in 20 Years?}, issn = {1438-0064}, doi = {10.1007/978-3-642-38189-8_10}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-42524}, year = {2013}, abstract = {Steiner trees are constructed to connect a set of terminal nodes in a graph. This basic version of the Steiner tree problem is idealized, but it can effectively guide the search for successful approaches to many relevant variants, from both a theoretical and a computational point of view. This article illustrates the theoretical and algorithmic progress on Steiner tree type problems on two examples, the Steiner connectivity and the Steiner tree packing problem.}, language = {en} }