## D. Software

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Mixed-integer programming (MIP) problem is arguably among the hardest classes of optimization problems. This paper describes how we solved 21 previously unsolved MIP instances from the MIPLIB benchmark sets. To achieve these results we used an enhanced version of ParaSCIP, setting a new record for the largest scale MIP computation: up to 80,000 cores in parallel on the Titan supercomputer. In this paper, we describe the basic parallelization mechanism of ParaSCIP, improvements of the dynamic load balancing and novel techniques to exploit the power of parallelization for MIP solving. We give a detailed overview of computing times and statistics for solving open MIPLIB instances.

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.

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.

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.

Mixed integer programming has become a very powerful tool for modeling and
solving real-world planning and scheduling problems, with the breadth of
applications appearing to be almost unlimited. A critical component in
the solution of these mixed-integer programs is a set of routines commonly
referred to as presolve. Presolve can be viewed as a collection of
preprocessing techniques that reduce the size of and, more importantly,
improve the ``strength'' of the given model formulation, that is, the degree
to which the constraints of the formulation accurately describe the
underlying polyhedron of integer-feasible solutions. As our computational
results will show, presolve is a key factor in the speed with which we can
solve mixed-integer programs, and is often the difference between a model
being intractable and solvable, in some cases easily solvable. In this
paper we describe the presolve functionality in the Gurobi commercial
mixed-integer programming code.
This includes an overview, or taxonomy of the different methods that are
employed, as well as more-detailed descriptions of several of the techniques,
with some of them appearing, to our knowledge, for the first time in the
literature.

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.

Spawned by practical applications, numerous variations of the classical Steiner tree problem in graphs have been studied during the last decades. Despite the strong relationship between the different variants, solution approaches employed so far have been prevalently problem-specific.
In contrast, we pursue a general-purpose strategy resulting in a solver able to solve both the classical Steiner tree problem and ten of its variants without modification. These variants include well-known problems such as the prize-collecting Steiner tree problem, the maximum-weight connected subgraph problem or the rectilinear minimum Steiner tree problem. Bolstered by a variety of new methods, most notably reduction techniques, our solver is not only of unprecedented versatility, but furthermore competitive or even superior to specialized state-of-the-art programs for several Steiner problem variants.

This paper describes how we solved 12 previously unsolved mixed-integer program-
ming (MIP) instances from the MIPLIB benchmark sets. To achieve these results we
used an enhanced version of ParaSCIP, setting a new record for the largest scale MIP
computation: up to 80,000 cores in parallel on the Titan supercomputer. In this paper
we describe the basic parallelization mechanism of ParaSCIP, improvements of the
dynamic load balancing and novel techniques to exploit the power of parallelization
for MIP solving. We give a detailed overview of computing times and statistics for
solving open MIPLIB instances.

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.

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.