TY - GEN A1 - Dercksen, Vincent J. A1 - Hege, Hans-Christian A1 - Oberlaender, Marcel T1 - The Filament Editor: An Interactive Software Environment for Visualization, Proof-Editing and Analysis of 3D Neuron Morphology N2 - Neuroanatomical analysis, such as classification of cell types, depends on reliable reconstruction of large numbers of complete 3D dendrite and axon morphologies. At present, the majority of neuron reconstructions are obtained from preparations in a single tissue slice in vitro, thus suffering from cut off dendrites and, more dramatically, cut off axons. In general, axons can innervate volumes of several cubic millimeters and may reach path lengths of tens of centimeters. Thus, their complete reconstruction requires in vivo labeling, histological sectioning and imaging of large fields of view. Unfortunately, anisotropic background conditions across such large tissue volumes, as well as faintly labeled thin neurites, result in incomplete or erroneous automated tracings and even lead experts to make annotation errors during manual reconstructions. Consequently, tracing reliability renders the major bottleneck for reconstructing complete 3D neuron morphologies. Here, we present a novel set of tools, integrated into a software environment named ‘Filament Editor’, for creating reliable neuron tracings from sparsely labeled in vivo datasets. The Filament Editor allows for simultaneous visualization of complex neuronal tracings and image data in a 3D viewer, proof-editing of neuronal tracings, alignment and interconnection across sections, and morphometric analysis in relation to 3D anatomical reference structures. We illustrate the functionality of the Filament Editor on the example of in vivo labeled axons and demonstrate that for the exemplary dataset the final tracing results after proof-editing are independent of the expertise of the human operator. T3 - ZIB-Report - 13-75 Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-43157 SN - 1438-0064 ER - TY - GEN A1 - Shinano, Yuji T1 - The Ubiquity Generator Framework: 7 Years of Progress in Parallelizing Branch-and-Bound N2 - Mixed integer linear programming (MIP) is a general form to model combinatorial optimization problems and has many industrial applications. The performance of MIP solvers has improved tremendously in the last two decades and these solvers have been used to solve many real-word problems. However, against the backdrop of modern computer technology, parallelization is of pivotal importance. In this way, ParaSCIP is the most successful parallel MIP solver in terms of solving previously unsolvable instances from the well-known benchmark instance set MIPLIB by using supercomputers. It solved two instances from MIPLIB2003 and 12 from MIPLIB2010 for the first time to optimality by using up to 80,000 cores on supercomputers. ParaSCIP has been developed by using the Ubiquity Generator (UG) framework, which is a general software package to parallelize any state-of-the-art branch-and-bound based solver. This paper discusses 7 years of progress in parallelizing branch-and-bound solvers with UG. T3 - ZIB-Report - 17-60 KW - Parallelization, Branch-and-bound, Mixed Integer Programming, UG, ParaSCIP, FiberSCIP, ParaXpress, FiberXpress, SCIP-Jack Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-65545 SN - 1438-0064 ER - TY - GEN A1 - Breuer, Thomas A1 - Bussieck, Michael A1 - Cao, Karl-Kien A1 - Cebulla, Felix A1 - Fiand, Frederik A1 - Gils, Hans Christian A1 - Gleixner, Ambros A1 - Khabi, Dmitry A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Wetzel, Manuel T1 - Optimizing Large-Scale Linear Energy System Problems with Block Diagonal Structure by Using Parallel Interior-Point Methods N2 - Current linear energy system models (ESM) acquiring to provide sufficient detail and reliability frequently bring along problems of both high intricacy and increasing scale. Unfortunately, the size and complexity of these problems often prove to be intractable even for commercial state-of-the-art linear programming solvers. This article describes an interdisciplinary approach to exploit the intrinsic structure of these large-scale linear problems to be able to solve them on massively parallel high-performance computers. A key aspect are extensions to the parallel interior-point solver PIPS-IPM originally developed for stochastic optimization problems. Furthermore, a newly developed GAMS interface to the solver as well as some GAMS language extensions to model block-structured problems will be described. T3 - ZIB-Report - 17-75 KW - energy system models KW - interior-point methods KW - high-performance computing Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66183 SN - 1438-0064 ER - TY - GEN A1 - Sagnol, Guillaume T1 - Picos Documentation. Release 0.1.1. N2 - PICOS is a user friendly interface to several conic and integer programming solvers, very much like YALMIP under MATLAB. The main motivation for PICOS is to have the possibility to enter an optimization problem as a high level model, and to be able to solve it with several different solvers. Multidimensional and matrix variables are handled in a natural fashion, which makes it painless to formulate a SDP or a SOCP. This is very useful for educational purposes, and to quickly implement some models and test their validity on simple examples. Furthermore, with PICOS you can take advantage of the python programming language to read and write data, construct a list of constraints by using python list comprehensions, take slices of multidimensional variables, etc. T3 - ZIB-Report - 12-48 KW - mathematical programming KW - SDP KW - SOCP KW - python Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-17396 SN - 1438-0064 ER - TY - GEN A1 - Gamrath, Gerald A1 - Koch, Thorsten A1 - Maher, Stephen J. A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - SCIP-Jack – A solver for STP and variants with parallelization extensions N2 - The Steiner tree problem in graphs is a classical problem that commonly arises in practical applications as one of many variants. While often a strong relationship between different Steiner tree problem variants can be observed, solution approaches employed so far have been prevalently problem-specific. In contrast, this paper introduces a general-purpose solver that can be used to solve both the classical Steiner tree problem and many of its variants without modification. This versatility is achieved by transforming various problem variants into a general form and solving them by using a state-of-the-art MIP-framework. The result is a high-performance solver that can be employed in massively parallel environments and is capable of solving previously unsolved instances. T3 - ZIB-Report - 16-41 KW - Steiner tree problem KW - SCIP-Jack KW - Steiner tree variants KW - maximum-weight connected subgraph KW - prize-collecting Steiner tree Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60170 SN - 1438-0064 ER - TY - GEN A1 - Rehfeldt, Daniel A1 - Koch, Thorsten A1 - Maher, Stephen J. T1 - Reduction Techniques for the Prize-Collecting Steiner Tree Problem and the Maximum-Weight Connected Subgraph Problem N2 - 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. T3 - ZIB-Report - 16-47 KW - Steiner tree problems KW - reduction techniques KW - prize-collecting Steiner tree problem KW - maximum-weight connected subgraph problem Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60420 SN - 1438-0064 ER - TY - GEN A1 - Tateiwa, Nariaki A1 - Shinano, Yuji A1 - Yasuda, Masaya A1 - Kaji, Shizuo A1 - Yamamura, Keiichiro A1 - Fujisawa, Katsuki T1 - Massively parallel sharing lattice basis reduction N2 - For cryptanalysis in lattice-based schemes, the performance evaluation of lattice basis reduction using high-performance computers is becoming increasingly important for the determination of the security level. We propose a distributed and asynchronous parallel reduction algorithm based on randomization and DeepBKZ, which is an improved variant of the block Korkine-Zolotarev (BKZ) reduction algorithm. Randomized copies of a lattice basis are distributed to up to 103,680 cores and independently reduced in parallel, while some basis vectors are shared asynchronously among all processes via MPI. There is a trade-off between randomization and information sharing; if a substantial amount of information is shared, all processes will work on the same problem, thereby diminishing the benefit of parallelization. To monitor this balance between randomness and sharing, we propose a metric to quantify the variety of lattice bases. We empirically find an optimal parameter of sharing for high-dimensional lattices. We demonstrate the efficacy of our proposed parallel algorithm and implementation with respect to both performance and scalability through our experiments. T3 - ZIB-Report - 21-38 KW - Discrete optimization KW - Lattice problem KW - Lattice-based cryptography KW - Shortest vector problem KW - Parallel algorithms KW - Ubiquity Generator Framework Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-85209 SN - 1438-0064 N1 - under review ER -