Bibliothek

Beschreibung: Standard offload programming models for the Xeon Phi, e.g. Intel LEO and OpenMP 4.0, are restricted to a single compute node and hence a limited number of coprocessors. Scaling applications across a Xeon Phi cluster/supercomputer thus requires hybrid programming approaches, usually MPI+X. In this work, we present a framework based on heterogeneous active messages (HAM-Offload) that provides the means to offload work to local and remote (co)processors using a unified offload API. Since HAM-Offload provides similar primitives as current local offload frameworks, existing applications can be easily ported to overcome the single-node limitation while keeping the convenient offload programming model. We demonstrate the effectiveness of the framework by using it to enable a real-world application from the field of molecular dynamics to use multiple local and remote Xeon Phis. The evaluation shows good scaling behavior. Compared with LEO, performance is equal for large offloads and significantly better for small offloads.

Beschreibung: Small-scale computations usually cannot fully utilize the compute capabilities of modern GPGPUs. With the Fermi GPU architecture Nvidia introduced the concurrent kernel execution feature allowing up to 16 GPU kernels to execute simultaneously on a shared GPU device for a better utilization of the respective resources. Insufficient scheduling capabilities in this respect, however, can significantly reduce the theoretical concurrency level. With the Kepler GPU architecture Nvidia addresses this issue by introducing the Hyper-Q feature with 32 hardware managed work queues for concurrent kernel execution. We investigate the Hyper-Q feature within heterogeneous workloads with multiple concurrent host threads or processes offloading computations to the GPU each. By means of a synthetic benchmark kernel and a hybrid parallel CPU-GPU real-world application, we evaluate the performance obtained with Hyper-Q on GPU and compare it against a kernel reordering mechanism introduced by the authors for the Fermi architecture.

Beschreibung: The third generation of the North German Supercomputing Alliance (HLRN) compute and storage facilities comprises a Cray XC30 architecture with exclusively Intel Ivy Bridge compute nodes. In the second phase, scheduled for November 2014, the HLRN-III configuration will undergo a substantial upgrade together with the option of integrating accelerator nodes into the system. To support the decision-making process, a four-node Intel Xeon Phi cluster is integrated into the present HLRN-III infrastructure at ZIB. This integration includes user/project management, file system access and job management via the HLRN-III batch system. For selected workloads, in-depth analysis, migration and optimization work on Xeon Phi is in progress. We will report our experiences and lessons learned within the Xeon Phi installation and integration process. For selected examples, initial results of the application evaluation on the Xeon Phi cluster platform will be discussed.

Beschreibung: Schedule disruptions are commonplace in the airline industry with many flight-delaying events occurring each day. Recently there has been a focus on introducing robustness into airline planning stages to reduce the effect of these disruptions. We propose a recoverable robustness technique as an alternative to robust optimisation to reduce the effect of disruptions and the cost of recovery. We formulate the recoverable robust tail assignment problem (RRTAP) as a stochastic program, solved using column generation in the master and subproblems of the Benders' decomposition. We implement a two-phase algorithm for the Benders' decomposition and identify pareto-optimal cuts. The RRTAP includes costs due to flight delays, cancellation, and passenger rerouting, and the recovery stage includes cancellation, delay, and swapping options. To highlight the benefits of simultaneously solving planning and recovery problems in the RRTAP we compare our tail assignment solution against current approaches from the literature. Using airline data we demonstrate that by developing a better tail assignment plan via the RRTAP framework, one can reduce recovery costs in the event of a disruption.

Beschreibung: Aircraft maintenance planning is of critical importance to the safe and efficient operations of an airline. It is common to solve the aircraft routing and maintenance planning problems many months in advance, with the solution spanning multiple days. An unfortunate consequence of this approach is the possible infeasibility of the maintenance plan due to frequent perturbations occurring in operations. There is an emerging concept that focuses on the generation of aircraft routes for a single day to ensure maintenance coverage that night, alleviating the effects of schedule perturbations from preceding days. In this paper, we present a novel approach to ensure that a sufficient number of aircraft routes are provided each day so maintenance critical aircraft receive maintenance that night. By penalising the under supply of routes terminating at maintenance stations from each overnight airport, we construct a single day routing to provide the best possible maintenance plan. This single day aircraft maintenance routing problem (SDAMRP) is further protected from disruptions by applying the recoverable robustness framework. To efficiently solve the recoverable robust SDAMRP acceleration techniques, such as identifying Pareto-optimal cuts and a trust region approach, have been applied. The SDAMRP is evaluated against a set of flight schedules and the results demonstrate a significantly improved aircraft maintenance plan. Further, the results demonstrate the magnitude of recoverability improvement that is achieved by employing recoverable robustness to the SDAMRP.

Beschreibung: Wir leben im digitalen Informationszeitalter, unsere Welt ist geprägt von Bits und Bytes. Unser Alltag wird zunehmend von technischen Hilfsmitteln bestimmt, das Handy ist zu unserem täglichen Begleiter geworden. Für jeden Bedarf gibt es mittlerweile eine kleine mobile Applikation (App), die uns das Leben erleichtern soll. Der Wandel von analog zu digital beeinflusst auch das Arbeitsumfeld von Bibliotheken und anderen Informationseinrichtungen. Im Zuge der strategischen Allianz, die seit Dezember 2007 zwischen Kooperativem Bibliotheksverbund Berlin-Brandenburg (KOBV) und Bayerischem Bibliotheksverbund (BVB) besteht, werden gemeinsame Entwicklungsprojekte durchgeführt. Die vorliegende Arbeit ist im Rahmen dieser strategischen Allianz entstanden, sie soll einen Überblick zu mobilen Angeboten der deutschsprachigen Bibliothekslandschaft bieten und damit zusammenhängende Mehrwerte für die Institutionen herausarbeiten.

Beschreibung: A mixed-integer linear programming methodutilizing the hierarchical relationship between design and operation variables proposed ot solve the optimal design problem of energy supply systems efficiently is extended ot search K-best solutions: At the upper level, the optimal values ofdesign variables are searched with operation variables relaxed to continuous ones; At the lower level, the values of operation variables are optimized with the values of design variables given tentatively; The obtained solution is used to renew K-best incumbent solutions, and the upper bound for the value of the objective function for K-best solutions is replaced correspondingly. A practical case study is conducted, and the validity and effectiveness of the proposed method are clarified.

Beschreibung: A mixed-integer linear programming (MILP) method utilizing the hierarchical relationship between design and op- eration variables is proposed to solve the optimal design problem of energy supply systems efficiently: At the upper level, the optimal values of design variables are searched by the branch and bound method; At the lower level, the values of operation variables are optimized by the branch and bound method under the values of design variables given tentatively during the search at the upper level; Lower bounds for the optimal value of the objective function are evaluated, and are utilized for the bounding operations at both the levels. This method is implemented into open and commercial MILP solvers. Illustrative and practical case studies on the optimal design of cogeneration systems are conducted, and the validity and effectiveness of the proposed method are clarified.

Beschreibung: 最適化研究におけるアプリケーション駆動研究サイクルを紹介する．アプリケーション駆動研究サイクルは，学術機関での研究と企業における研究成果の利用とのつながりを良くする点では優れている．一方で，ソフトウェア開発・維持に多大な労力を要するため，日本の大学や研究機関における実施には困難さが伴う．ZIBにおいてアプリケーション駆動研究サイクルが，比較的うまく機能している背景を説明する．また，日本においてアプリケーション駆動研究サイクルを活性化するための第一歩として，論文投稿時に，論文中の数値実験に利用した全データ提出の義務化を提案したい．

Beschreibung: 近年，大規模かつ複雑な最適化問題を高速に解く需要はさまざまな産業界や学術分野において急速に高まりつつある．これからの研究においては最先端理論 (Theory)+超大規模実データ (Practice)+最新計算技術(Computation) の三つを有機的に組み合わせることによって，実用に耐えうる解決策の提示と大規模最適化問題を扱う際の先例となることが求められている．本稿では最適化と計算に関する最新の傾向に触れるとともに，最適化の計算の今後についても考えていきたい．

Beschreibung: In the framework of time series analysis with recurrence networks, we introduce SAIMeR, a heuristic self-adapted method that determines the elusive recurrence threshold and identifies metastable states in complex time series. To identify metastable states as well as the transitions between them, we use graph theory concepts and a fuzzy partitioning clustering algorithm. We illustrate SAIMeR by applying it to three real-world time series and show that it is able to identify metastable states in real-world data with noise and missing data points. Finally, we suggest a way to choose the embedding parameters used to construct the state space in which this method is performed, based on the analysis of how the values of these parameters affect two recurrence quantitative measurements: recurrence rate and entropy.

Beschreibung: The rebinding effect is a phenomenon which occurs when observing a ligand-receptor binding process. On the macro scale this process comprises the Markov property. This Makovian view is spoiled when switching to the atomistic scale of a binding process. We therefore suggest a model which accurately describes the rebinding effect on the atomistic scale by allowing ''intermediate'' bound states. This allows us to define an indicator for the magnitude of rebinding and to formulate an optimization problem. The results form our examples show good agreement with data form laboratory.

Beschreibung: Ergopeptides, like ergocornine and a-ergocryptine, exist in an S- and in an R-configuration. Kinetic experiments imply that certain configurations are preferred depending on the solvent. The experimental methods are explained in this article. Furthermore, computational methods are used to understand this configurational preference. Standard quantum chemical methods can predict the favored configurations by using minimum energy calculations on the potential energy landscape. However, the explicit role of the solvent is not revealed by this type of methods. In order to better understand its influence, classical mechanical molecular simulations are applied. It appears from our research that “folding” the ergopeptide molecules into an intermediate state (between the S- and the R-configuration) is mechanically hindered for the preferred configurations.

Beschreibung: In this article a method to improve the precision of the classical molecular dynamics force field by solving an approximation problem with scattered quantum mechanical data is presented. This novel technique is based on two steps. In the first step a partition of unity scheme is used for partitioning the state space by meshfree basis functions. As a consequence the potential can be localized for each basis function. In a second step, for one state in each meshfree basis function, the precise QM-based charges are computed. These local QM-based charges are then used, to optimize the local potential function. The performance of this method is shown for the alanine tripeptide.

Beschreibung: We study the cross-entropy method for diffusions. One of the results is a versatile cross-entropy algorithm that can be used to design efficient importance sampling strategies for rare events or to solve optimal control problems. The approach is based on the minimization of a suitable cross-entropy functional, with a parametric family of exponentially tilted probability distributions. We illustrate the new algorithm with several numerical examples and discuss algorithmic issues and possible extensions of the method.

Beschreibung: Many optimization problems can be modeled as Mixed Integer Programs (MIPs). In general, MIPs cannot be solved efficiently, since solving MIPs is NP-hard, see, e.g., Schrijver, 2003. Common methods for solving NP-hard problems are branch-and-bound and column generation. In the case of column generation, the original problem becomes decomposed or re-formulated into one ore more smaller subproblems, which are easier to solve. Each of these subproblems is solved separately and recurrently, which can be interpreted as solving a sequence of optimization problems. In this thesis, we consider a sequence of MIPs which only differ in the respective objective functions. Furthermore, we assume each of these MIPs get solved with a branch-and-bound algorithm. This thesis aims to figure out whether the solving process of a given sequence of MIPs can be accelerated by reoptimization. As reoptimization we understand starting the solving process of a MIP of this sequence at a given frontier of a search tree corresponding to another MIP of this sequence. At the beginning we introduce an LP-based branch-and-bound algorithm. This algorithm is inspired by the reoptimizing algorithm of Hiller, Klug, and the author of this thesis, 2013. Since most of the state-of-the-art MIP solvers come to decisions based on dual information, which leads to the loss of feasible solutions after changing the objective function, we present a technique to guarantee optimality despite using these information. A decision is based on a dual information if this decision is valid for at least one feasible solution, whereas a decision is based on a primal information if this decision is valid for all feasible solutions. Afterwards, we consider representing the search frontier of the tree by a set of nodes of a given size. We call this the Tree Compression Problem. Moreover, we present a criterion characterizing the similarity of two objective functions. To evaluate our approach of reoptimization we extend the well-known and well-maintained MIP solver SCIP to an LP-based branch-and-bound framework, introduce two heuristics for solving the Tree Compression Problem, and a primal heuristic which is especially fitted to column generation. Finally, we present computational experiments on several problem classes, e.g., the Vertex Coloring and k-Constrained Shortest Path. Our experiments show, that a straightforward reoptimization, i.e., without additional heuristics, provides no benefit in general. However, in combination with the techniques and methods presented in this thesis, we can accelerate the solving of a given sequence up to the factor 14. For this purpose it is essential to take the differences of the objective functions into account and to restart the reoptimization, i.e., solve the subproblem from scratch, if the objective functions are not similar enough. Finally, we discuss the possibility to parallelize the solving process of the search frontier at the beginning of each solving process.

Beschreibung: Recent years have seen an increased interest in non-equilibrium molecular dynamics (NEMD) simulations, especially for molecular systems with periodic forcing by external fields, e.g., in the context of studying effects of electromagnetic radiation on the human body tissue. Lately, an NEMD methods with local thermostating has been proposed that allows for studying non-equilibrium processes in a statistically reliable and thermodynamically consistent way. In this article, we demonstrate how to construct Markov State Models (MSMs) for such NEMD simulations. MSM building has been well-established for systems in equilibrium where MSMs with just a few (macro-)states allow for accurate reproduction of the essential kinetics of the molecular system under consideration. Non-equilibrium MSMs have been lacking so far. The article presents how to construct such MSMs and illustrates their validity and usefulness for the case of conformation dynamics of alanine dipeptide in an external electric field.