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Software Management Plan developed in HPO-Navi
No full textThis publication comprises the Software Management Plan (SMP) developed in the HPO-Navi project.
The project was funded in the Literature and Information System (LIS) track of the DFG with the aim of increasing the maturity level of scientific software under development, developing improved measures for the quality assurance of this software and for long-term availability.
The Ubiquity Generator Framework (UG) software developed in the project provides a software infrastructure to make existing sequential implementations HPC-capable. The UG framework is of interest to developers of specialized optimization algorithms and can be used directly to solve specific problem classes in the field of scientific computing.
Due to the naturally high software technology hurdles on HPC systems, UG was initially a highly specialized tool and could only be used to a limited extent without the involvement of the main developer. The central challenge of the project was to create a mechanism for the sustainable development and permanent provision and archiving of the research software.
The aim was for UG to achieve the status of a "software product" with implementation of the following project content:
- Documentation of the software: a description of the API and the simple connection of further basic solvers, installation instructions for various target platforms and a description of the structure and documentation of the source code as a basis for the distributed sustainable development of UG.
- Development of missing user functions of UG: increased platform independence for shared memory parallelization and better logging function for the analysis and verification of results.
- Development of a sample data management plan for future research projects that want to use UG and document their research results according to DFG standards for good scientific practice.
- Quality assurance: by defining code guidelines, uniform concepts and criteria for the qualitative evaluation of new functions and implementing standards for code review and processes for continuous integration.
A complementary goal was to improve the provision, accessibility and long-term reusability of the research software.
- Use of an open Git server as a distributed development platform, provision of a download server for releases and sustainable storage of the software code and the associated meta-information.
- Improved presentation and visibility through publication in publicly accessible repositories. This includes the prototypical extension of the OPUS 4 repository software widely used in Germany as a means of publishing software with a landing page that can be resolved via a DOI, and improved linking and presentation of UG in swMATH.
- Digital long-term archiving: experimental inclusion of software code in an OAIS-compliant digital archiving system and evaluation of the approach in the areas of digital archiving and research data management
Finding Rules and Patterns in Egyptological Research Objects using Boolean Polynomial Rings
No full textTargeted multiobjective Dijkstra Algorithm
No full textWe introduce the Targeted Multiobjective Dijkstra Algorithm (T-MDA), a label setting algorithm for the One-to-One Multiobjective Shortest Path (MOSP) Problem. It is based on the recently published Multiobjective Dijkstra Algorithm (MDA) and equips it with A*-like techniques. For any explored subpath, a label setting MOSP algorithm decides whether the subpath can be discarded or must be stored as part of the output. A major design choice is how to store subpaths from the moment they are first explored until the mentioned final decision can be made. The T-MDA combines the polynomially bounded size of the priority queue used in the MDA and alazy management of paths that are not in the queue. The running time bounds from the MDA remain valid. In practice, the T-MDA outperforms known algorithms from the literature and the increased memory consumption is negligible. In this paper, we benchmark the T-MDA against an improved version of the state of the art NAMOA∗drOne-to-One MOSP algorithm from the literature on a standard testbed
Model Based Exploration of Hypokalemia in Dairy Cows
No full textHypokalemia, characterized by too low serum potassium levels, is a severe mineral disorder which can be life threatening. It is increasingly diagnosed in veterinarian healthcare and a topic of ongoing research. In this paper, we explore the different originating conditions of hypokalemia: reduced potassium intake, increased excretion, acid-base disturbances, or increased insulin, by using a dynamic mathematical model for potassium balance in non-lactating and lactating cows.
Simulations are compared with literature. The results give insights into the network dynamics and point to scenarios on which experimental effort should be focused. Application of mathematical models can assist in experimental planning as well as the reduction, refinement and replacement of animal experiments
Effect of depth discontinuity on interfacial stability of tangential-velocity discontinuity in shallow-water flow
No full textIt is well known as the Kelvin-Helmholtz instability (KHI) that an interface of tangential velocity discontinuity is necessarily unstable, regardless of the velocity difference's strength. However, the KHI is suppressed for shallow water flows if the Froude number, defined by the ratio of the velocity difference to the gravity wave's speed, is sufficiently large. In this investigation, we examine the effect of the depth difference of two fluid layers on the KHI. The depth difference enhances instability. Given the Froude number in the instability range, the growth rate sensitively depends on the depth ratio and increases monotonically with the depth ratio difference from unity. The critical value of the Froude number for stabilization varies with the depth ratio and attains the minimum value √8 for equal depth. This behavior is verified by asymptotic analysis
A probabilistic framework for particle-based reaction–diffusion dynamics using classical Fock space representations
No full textA Safe Computational Framework for Integer Programming applied to Chvátal's Conjecture
No full textWe describe a general and safe computational framework that provides integer programming results with the degree of certainty that is required for machine-assisted proofs of mathematical theorems. At its core, the framework relies on a rational branch-and-bound certificate produced by an exact integer programming solver, SCIP, in order to circumvent floating-point roundoff errors present in most state-of-the-art solvers for mixed-integer programs.The resulting certificates are self-contained and checker software exists that can verify their correctness independently of the integer programming solver used to produce the certificate. This acts as a safeguard against programming errors that may be present in complex solver software. The viability of this approach is tested by applying it to finite cases of Chvátal's conjecture, a long-standing open question in extremal combinatorics. We take particular care to verify also the correctness of the input for this specific problem, using the Coq formal proof assistant. As a result we are able to provide a first machine-assisted proof that
Chvátal's conjecture holds for all downsets whose union of sets contains seven elements or less
On generalized surrogate duality in mixed-integer nonlinear programming
No full textThe most important ingredient for solving mixed-integer nonlinear programs (MINLPs) to global ϵ-optimality with spatial branch and bound is a tight, computationally tractable relaxation. Due to both theoretical and practical considerations, relaxations of MINLPs are usually required to be convex. Nonetheless, current optimization solvers can often successfully handle a moderate presence of nonconvexities, which opens the door for the use of potentially tighter nonconvex relaxations. In this work, we exploit this fact and make use of a nonconvex relaxation obtained via aggregation of constraints: a surrogate relaxation. These relaxations were actively studied for linear integer programs in the 70s and 80s, but they have been scarcely considered since. We revisit these relaxations in an MINLP setting and show the computational benefits and challenges they can have. Additionally, we study a generalization of such relaxation that allows for multiple aggregations simultaneously and present the first algorithm that is capable of computing the best set of aggregations. We propose a multitude of computational enhancements for improving its practical performance and evaluate the algorithm’s ability to generate strong dual bounds through extensive computational experiments