TY - GEN A1 - Gamrath, Gerald A1 - Fischer, Tobias A1 - Gally, Tristan A1 - Gleixner, Ambros A1 - Hendel, Gregor A1 - Koch, Thorsten A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Puchert, Christian A1 - Rehfeldt, Daniel A1 - Schenker, Sebastian A1 - Schwarz, Robert A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Vigerske, Stefan A1 - Weninger, Dieter A1 - Winkler, Michael A1 - Witt, Jonas T. A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 3.2 N2 - The SCIP Optimization Suite is a software toolbox for generating and solving various classes of mathematical optimization problems. Its major components are the modeling language ZIMPL, the linear programming solver SoPlex, the constraint integer programming framework and mixed-integer linear and nonlinear programming solver SCIP, the UG framework for parallelization of branch-and-bound-based solvers, and the generic branch-cut-and-price solver GCG. It has been used in many applications from both academia and industry and is one of the leading non-commercial solvers. This paper highlights the new features of version 3.2 of the SCIP Optimization Suite. Version 3.2 was released in July 2015. This release comes with new presolving steps, primal heuristics, and branching rules within SCIP. In addition, version 3.2 includes a reoptimization feature and improved handling of quadratic constraints and special ordered sets. SoPlex can now solve LPs exactly over the rational number and performance improvements have been achieved by exploiting sparsity in more situations. UG has been tested successfully on 80,000 cores. A major new feature of UG is the functionality to parallelize a customized SCIP solver. GCG has been enhanced with a new separator, new primal heuristics, and improved column management. Finally, new and improved extensions of SCIP are presented, namely solvers for multi-criteria optimization, Steiner tree problems, and mixed-integer semidefinite programs. T3 - ZIB-Report - 15-60 KW - mixed-integer linear and nonlinear programming KW - MIP solver KW - MINLP solver KW - linear programming KW - LP solver KW - simplex method KW - modeling KW - parallel branch-and-bound KW - branch-cut-and-price framework KW - generic column generation KW - Steiner tree solver KW - multi-criteria optimization KW - mixed-integer semidefinite programming Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57675 SN - 1438-0064 ER - TY - GEN A1 - Gottwald, Robert Lion A1 - Maher, Stephen J. A1 - Shinano, Yuji T1 - Distributed domain propagation N2 - Portfolio parallelization is an approach that runs several solver instances in parallel and terminates when one of them succeeds in solving the problem. Despite it's simplicity portfolio parallelization has been shown to perform well for modern mixed-integer programming (MIP) and boolean satisfiability problem (SAT) solvers. Domain propagation has also been shown to be a simple technique in modern MIP and SAT solvers that effectively finds additional domain reductions after a variables domain has been reduced. This paper investigates the impact of distributed domain propagation in modern MIP solvers that employ portfolio parallelization. Computational experiments were conducted for two implementations of this parallelization approach. While both share global variable bounds and solutions they communicate differently. In one implementation the communication is performed only at designated points in the solving process and in the other it is performed completely asynchronously. Computational experiments show a positive performance impact of communicating global variable bounds and provide valuable insights in communication strategies for parallel solvers. T3 - ZIB-Report - 16-71 KW - mixed integer programming KW - parallelization KW - domain propagation KW - portfolio solvers Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61380 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 - CHAP A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Pedroso, João Pedro A1 - Rehfeldt, Daniel A1 - Schwarz, Robert A1 - Serrano, Felipe T1 - PySCIPOpt: Mathematical Programming in Python with the SCIP Optimization Suite T2 - Mathematical Software – ICMS 2016 N2 - SCIP is a solver for a wide variety of mathematical optimization problems. It is written in C and extendable due to its plug-in based design. However, dealing with all C specifics when extending SCIP can be detrimental to development and testing of new ideas. This paper attempts to provide a remedy by introducing PySCIPOpt, a Python interface to SCIP that enables users to write new SCIP code entirely in Python. We demonstrate how to intuitively model mixed-integer linear and quadratic optimization problems and moreover provide examples on how new Python plug-ins can be added to SCIP. Y1 - 2016 U6 - https://doi.org/10.1007/978-3-319-42432-3_37 VL - 9725 SP - 301 EP - 307 PB - Springer ER - TY - GEN A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Pedroso, João Pedro A1 - Rehfeldt, Daniel A1 - Schwarz, Robert A1 - Serrano, Felipe T1 - PySCIPOpt: Mathematical Programming in Python with the SCIP Optimization Suite N2 - SCIP is a solver for a wide variety of mathematical optimization problems. It is written in C and extendable due to its plug-in based design. However, dealing with all C specifics when extending SCIP can be detrimental to development and testing of new ideas. This paper attempts to provide a remedy by introducing PySCIPOpt, a Python interface to SCIP that enables users to write new SCIP code entirely in Python. We demonstrate how to intuitively model mixed-integer linear and quadratic optimization problems and moreover provide examples on how new Python plug-ins can be added to SCIP. T3 - ZIB-Report - 16-64 KW - SCIP, Mathematical optimization, Python, Modeling Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-61348 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 - JOUR A1 - Maher, Stephen J. A1 - Murray, John M. T1 - The unrooted set covering connected subgraph problem differentiating between HIV envelope sequences JF - European Journal of Operational Research N2 - This paper presents a novel application of operations research techniques to the analysis of HIV Env gene sequences, aiming to identify key features that are possible vaccine targets. These targets are identified as being critical to the transmission of HIV by being present in early transmitted (founder) sequences and absent in later chronic sequences. Identifying the key features of Env involves two steps: first, calculating the covariance of amino acid combinations and positions to form a network of related and compensatory mutations; and second, developing an integer program to identify the smallest connected subgraph of the constructed covariance network that exhibits a set covering property. The integer program developed for this analysis, labelled the unrooted set covering connected subgraph problem (USCCSP), integrates a set covering problem and connectivity evaluation, the latter formulated as a network flow problem. The resulting integer program is very large and complex, requiring the use of Benders' decomposition to develop an efficient solution approach. The results will demonstrate the necessity of applying acceleration techniques to the Benders' decomposition solution approach and the effectiveness of these techniques and heuristic approaches for solving the USCCSP. Y1 - 2016 U6 - https://doi.org/doi:10.1016/j.ejor.2015.07.011 VL - 248 IS - 2 SP - 668 EP - 680 ER -