@article{OltmannsHaslerPetersKottigetal.2019, author = {Oltmanns, Elias and Hasler, Tim and Peters-Kottig, Wolfgang and Kuper, Heinz-G{\"u}nter}, title = {Different Preservation Levels: The Case of Scholarly Digital Editions}, volume = {18}, journal = {Data Science Journal}, number = {1(51)}, doi = {10.5334/dsj-2019-051}, pages = {9}, year = {2019}, abstract = {Ensuring the long-term availability of research data forms an integral part of data management services. Where OAIS compliant digital preservation has been established in recent years, in almost all cases the services aim at the preservation of file-based objects. In the Digital Humanities, research data is often represented in highly structured aggregations, such as Scholarly Digital Editions. Naturally, scholars would like their editions to remain functionally complete as long as possible. Besides standard components like webservers, the presentation typically relies on project specific code interacting with client software like webbrowsers. Especially the latter being subject to rapid change over time invariably makes such environments awkward to maintain once funding has ended. Pragmatic approaches have to be found in order to balance the curation effort and the maintainability of access to research data over time. A sketch of four potential service levels aiming at the long-term availability of research data in the humanities is outlined: (1) Continuous Maintenance, (2) Application Conservation, (3) Application Data Preservation, and (4) Bitstream Preservation. The first being too costly and the last hardly satisfactory in general, we suggest that the implementation of services by an infrastructure provider should concentrate on service levels 2 and 3. We explain their strengths and limitations considering the example of two Scholarly Digital Editions.}, language = {en} } @article{AnztBachDruskatetal.2020, author = {Anzt, H. and Bach, F. and Druskat, S. and L{\"o}ffler, F. and Loewe, A. and Renard, B. Y. and Seemann, G. and Struck, A. and Achhammer, E. and Appell, F. and Bader, M. and Brusch, L. and Busse, C. and Chourdakis, G. and Dabrowski, P. W. and Ebert, P. and Flemisch, B. and Friedl, S. and Fritzsch, B. and Funk, M. D. and Gast, V. and Goth, F. and Grad, J.-N. and Hermann, Sibylle and Hohmann, F. and Janosch, S. and Kutra, D. and Linxweiler, J. and Muth, T. and Peters-Kottig, Wolfgang and Rack, F. and Raters, F. H. C. and Rave, S. and Reina, G. and Reißig, M. and Ropinski, T. and Schaarschmidt, J. and Seibold, H. and Thiele, J. P. and Uekermann, B. and Unger, S. and Weeber, R.}, title = {An environment for sustainable research software in Germany and beyond: current state, open challenges, and call for action [version 1; peer review: 1 approved, 1 approved with reservations]}, journal = {F1000Research}, number = {9:295}, doi = {10.12688/f1000research.23224.1}, pages = {28}, year = {2020}, abstract = {Research software has become a central asset in academic research. It optimizes existing and enables new research methods, implements and embeds research knowledge, and constitutes an essential research product in itself. Research software must be sustainable in order to understand, replicate, reproduce, and build upon existing research or conduct new research effectively. In other words, software must be available, discoverable, usable, and adaptable to new needs, both now and in the future. Research software therefore requires an environment that supports sustainability. Hence, a change is needed in the way research software development and maintenance are currently motivated, incentivized, funded, structurally and infrastructurally supported, and legally treated. Failing to do so will threaten the quality and validity of research. In this paper, we identify challenges for research software sustainability in Germany and beyond, in terms of motivation, selection, research software engineering personnel, funding, infrastructure, and legal aspects. Besides researchers, we specifically address political and academic decision-makers to increase awareness of the importance and needs of sustainable research software practices. In particular, we recommend strategies and measures to create an environment for sustainable research software, with the ultimate goal to ensure that software-driven research is valid, reproducible and sustainable, and that software is recognized as a first class citizen in research. This paper is the outcome of two workshops run in Germany in 2019, at deRSE19 - the first International Conference of Research Software Engineers in Germany - and a dedicated DFG-supported follow-up workshop in Berlin.}, language = {en} } @misc{TateiwaShinanoYasudaetal.2021, author = {Tateiwa, Nariaki and Shinano, Yuji and Yasuda, Masaya and Kaji, Shizuo and Yamamura, Keiichiro and Fujisawa, Katsuki}, title = {Massively parallel sharing lattice basis reduction}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-85209}, year = {2021}, abstract = {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.}, language = {en} } @misc{BertholdWitzig2020, author = {Berthold, Timo and Witzig, Jakob}, title = {Conflict Analysis for MINLP}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-78964}, year = {2020}, abstract = {The generalization of MIP techniques to deal with nonlinear, potentially non-convex, constraints have been a fruitful direction of research for computational MINLP in the last decade. In this paper, we follow that path in order to extend another essential subroutine of modern MIP solvers towards the case of nonlinear optimization: the analysis of infeasible subproblems for learning additional valid constraints. To this end, we derive two different strategies, geared towards two different solution approaches. These are using local dual proofs of infeasibility for LP-based branch-and-bound and the creation of nonlinear dual proofs for NLP-based branch-and-bound, respectively. We discuss implementation details of both approaches and present an extensive computational study, showing that both techniques can significantly enhance performance when solving MINLPs to global optimality.}, language = {en} } @misc{HosodaMaherShinanoetal.2023, author = {Hosoda, Junko and Maher, Stephen J. and Shinano, Yuji and Villumsen, Jonas Christoffer}, title = {A parallel branch-and-bound heuristic for the integrated long-haul and local vehicle routing problem on an adaptive transportation network}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-89700}, year = {2023}, abstract = {Consolidation of commodities and coordination of vehicle routes are fundamental features of supply chain management problems. While locations for consolidation and coordination are typically known a priori, in adaptive transportation networks this is not the case. The identification of such consolidation locations forms part of the decision making process. Supply chain management problems integrating the designation of consolidation locations with the coordination of long haul and local vehicle routing is not only challenging to solve, but also very difficult to formulate mathematically. In this paper, the first mathematical model integrating location clustering with long haul and local vehicle routing is proposed. This mathematical formulation is used to develop algorithms to find high quality solutions. A novel parallel framework is developed that combines exact and heuristic methods to improve the search for high quality solutions and provide valid bounds. The results demonstrate that using exact methods to guide heuristic search is an effective approach to find high quality solutions for difficult supply chain management problems.}, language = {en} } @misc{FujiiItoKimetal.2021, author = {Fujii, Koichi and Ito, Naoki and Kim, Sunyoung and Kojima, Masakazu and Shinano, Yuji and Toh, Kim-Chuan}, title = {Solving Challenging Large Scale QAPs}, issn = {1438-0064}, doi = {10.12752/8130}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81303}, year = {2021}, abstract = {We report our progress on the project for solving larger scale quadratic assignment problems (QAPs). Our main approach to solve large scale NP-hard combinatorial optimization problems such as QAPs is a parallel branch-and-bound method efficiently implemented on a powerful computer system using the Ubiquity Generator(UG) framework that can utilize more than 100,000 cores. Lower bounding procedures incorporated in the branch-and-bound method play a crucial role in solving the problems. For a strong lower bounding procedure, we employ the Lagrangian doubly nonnegative (DNN) relaxation and the Newton-bracketing method developed by the authors' group. In this report, we describe some basic tools used in the project including the lower bounding procedure and branching rules, and present some preliminary numerical results. Our next target problem is QAPs with dimension at least 50, as we have succeeded to solve tai30a and sko42 from QAPLIB for the first time.}, language = {en} } @misc{FujiiKimKojimaetal.2023, author = {Fujii, Koichi and Kim, Sunyoung and Kojima, Masakazu and Mittelmann, Hans D. and Shinano, Yuji}, title = {An Exceptionally Difficult Binary Quadratic Optimization Problem with Symmetry: a Challenge for The Largest Unsolved QAP Instance Tai256c}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-93072}, year = {2023}, abstract = {Tai256c is the largest unsolved quadratic assignment problem (QAP) instance in QAPLIB. It is known that QAP tai256c can be converted into a 256 dimensional binary quadratic optimization problem (BQOP) with a single cardinality constraint which requires the sum of the binary variables to be 92. As the BQOP is much simpler than the original QAP, the conversion increases the possibility to solve the QAP. Solving exactly the BQOP, however, is still very difficult. Indeed, a 1.48\% gap remains between the best known upper bound (UB) and lower bound (LB) of the unknown optimal value. This paper shows that the BQOP admits a nontrivial symmetry, a property that makes the BQOP very hard to solve. The symmetry induces equivalent subproblems in branch and bound (BB) methods. To effectively improve the LB, we propose an efficient BB method that incorporates a doubly nonnegative relaxation, the standard orbit branching and a technique to prune equivalent subproblems. With this BB method, a new LB with 1.25\% gap is successfully obtained, and computing an LB with 1.0\% gap is shown to be still quite difficult.}, language = {en} } @misc{FujiiItoKimetal.2022, author = {Fujii, Koichi and Ito, Naoki and Kim, Sunyoung and Kojima, Masakazu and Shinano, Yuji and Toh, Kim-Chuan}, title = {大規模二次割当問題への挑戦}, journal = {統計数理研究所共同研究リポート 453 最適化:モデリングとアルゴリズム33 2022年3月 「大規模二次割当問題への挑戦」 p.84-p.92}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-86779}, year = {2022}, abstract = {二次割当問題は線形緩和が弱いことが知られ,強化のため多様な緩和手法が考案されているが,その一つである二重非負値計画緩和( DNN 緩和)及びその解法として近年研究が進んでいるニュートン・ブラケット法を紹介し,それらに基づく分枝限定法の実装及び数値実験結果について報告する.}, language = {ja} } @misc{WitzigBerthold2019, author = {Witzig, Jakob and Berthold, Timo}, title = {Conflict-Free Learning for Mixed Integer Programming}, issn = {1438-0064}, doi = {10.1007/978-3-030-58942-4_34}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-75338}, year = {2019}, abstract = {Conflict learning plays an important role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. A major step for MIP conflict learning is to aggregate the LP relaxation of an infeasible subproblem to a single globally valid constraint, the dual proof, that proves infeasibility within the local bounds. Among others, one way of learning is to add these constraints to the problem formulation for the remainder of the search. We suggest to not restrict this procedure to infeasible subproblems, but to also use global proof constraints from subproblems that are not (yet) infeasible, but can be expected to be pruned soon. As a special case, we also consider learning from integer feasible LP solutions. First experiments of this conflict-free learning strategy show promising results on the MIPLIB2017 benchmark set.}, language = {en} } @misc{Shinano2021, author = {Shinano, Yuji}, title = {UG - Ubiquity Generator Framework v1.0.0beta}, doi = {10.12752/8521}, year = {2021}, abstract = {UG is a generic framework to parallelize branch-and-bound based solvers (e.g., MIP, MINLP, ExactIP) in a distributed or shared memory computing environment. It exploits the powerful performance of state-of-the-art "base solvers", such as SCIP, CPLEX, etc. without the need for base solver parallelization. UG framework, ParaSCIP(ug[SCIP,MPI]) and FiberSCIP (ug[SCIP,Pthreads]) are available as a beta version. v1.0.0: new documentation and cmake, generalization of ug framework, implementation of selfsplitrampup for fiber- and parascip, better memory and time limit handling.}, language = {en} } @inproceedings{WitzigBerthold2020, author = {Witzig, Jakob and Berthold, Timo}, title = {Conflict-Free Learning for Mixed Integer Programming}, booktitle = {Integration of AI and OR Techniques in Constraint Programming. CPAIOR 2020}, number = {12296}, publisher = {Springer, Cham.}, doi = {10.1007/978-3-030-58942-4_34}, pages = {521 -- 530}, year = {2020}, abstract = {Conflict learning plays an important role in solving mixed integer programs (MIPs) and is implemented in most major MIP solvers. A major step for MIP conflict learning is to aggregate the LP relaxation of an infeasible subproblem to a single globally valid constraint, the dual proof, that proves infeasibility within the local bounds. Among others, one way of learning is to add these constraints to the problem formulation for the remainder of the search. We suggest to not restrict this procedure to infeasible subproblems, but to also use global proof constraints from subproblems that are not (yet) infeasible, but can be expected to be pruned soon. As a special case, we also consider learning from integer feasible LP solutions. First experiments of this conflict-free learning strategy show promising results on the MIPLIB2017 benchmark set.}, language = {en} } @misc{HosodaMaherShinano2024, author = {Hosoda, Junko and Maher, Stephen J. and Shinano, Yuji}, title = {Combining Benders' decomposition and parallelisation to solve large-scale adaptive network supply chain management problems}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-98744}, year = {2024}, abstract = {Integrated supply chain network design—combining warehouse clustering with inter- and intra-cluster vehicle routing—is a fundamental feature of supply chain management problems. In this paper, a Benders' decomposition-based parallel heuristic approach for the integrated long-haul and local vehicle routing problem is proposed. The proposed algorithm comprises lower- and upper-bound search algorithms running in parallel to find high-quality solutions for challenging supply chain management problems. A novel Benders' decomposition approach is proposed to aid the improvement in the lower bound for large-scale problems. The results demonstrate that the Benders' decomposition approach is effective in finding strong lower bounds and is beneficial for obtaining high-quality solutions.}, language = {en} } @misc{FujiiKimKojimaetal.2022, author = {Fujii, Koichi and Kim, Sunyoung and Kojima, Masakazu and Mittelmann, Hans D. and Shinano, Yuji}, title = {The Largest Unsolved QAP Instance Tai256c Can Be Converted into A 256-dimensional Simple BQOP with A Single Cardinality Constraint}, issn = {1438-0064}, doi = {10.12752/8808}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-88086}, year = {2022}, abstract = {Tai256c is the largest unsolved quadratic assignment problem (QAP) instance in QAPLIB; a 1.48\% gap remains between the best known feasible objective value and lower bound of the unknown optimal value. This paper shows that the instance can be converted into a 256 dimensional binary quadratic optimization problem (BQOP) with a single cardinality constraint which requires the sum of the binary variables to be 92.The converted BQOP is much simpler than the original QAP tai256c and it also inherits some of the symmetry properties. However, it is still very difficult to solve. We present an efficient branch and bound method for improving the lower bound effectively. A new lower bound with 1.36\% gap is also provided.}, language = {en} } @misc{Khorsandi2021, author = {Khorsandi, Ramin}, title = {Gitram 1.0.0}, doi = {10.12752/8527}, year = {2021}, abstract = {Gitram is a software that processes various metadata and data content from GIT and exports them in the format of an XML file. The software is specifically designed for the HPO-navi project. It is also compatible with Opus4 and any other software that can receive data through the sword interface. Gitram process the metadata and the repository content and sends it to Opus4 via the sword interface. The data is taken from a zip file that is stored in the "dataBackup" folder. Users also have an option of saving the data as a document file on Opus. Metadata can also be received from GitLab via a webhook. The entire project is programmed in Python 3.8+ and can be installed on Ubuntu 16 or above. It is open-source and its functionality can be modified to the users needs.}, language = {en} } @misc{Shinano2020, author = {Shinano, Yuji}, title = {UG - Ubiquity Generator Framework v0.9.1}, doi = {10.12752/8508}, year = {2020}, abstract = {UG is a generic framework to parallelize branch-and-bound based solvers (e.g., MIP, MINLP, ExactIP) in a distributed or shared memory computing environment. It exploits the powerful performance of state-of-the-art "base solvers", such as SCIP, CPLEX, etc. without the need for base solver parallelization. UG framework, ParaSCIP(ug[SCIP,MPI]) and FiberSCIP (ug[SCIP,Pthreads]) are available as a beta version. For MIP solving, ParaSCIP and FiberSCIP are well debugged and should be stable. For MINLP solving, they are relatively stable, but not as thoroughly debugged. This release version should handle branch-and-cut approaches where subproblems are defined by variable bounds and also by constrains for ug[SCIP,*] ParaSCIP and FiberSCIP). Therefore, problem classes other than MIP or MINLP can be handled, but they have not been tested yet. v0.9.1: Update orbitope cip files.}, language = {en} } @misc{HaslerPetersKottigSchloesser2023, author = {Hasler, Tim and Peters-Kottig, Wolfgang and Schl{\"o}sser, Franziska}, title = {Software Management Plan developed in HPO-Navi}, doi = {10.12752/9250}, year = {2023}, abstract = {This 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.}, language = {en} } @misc{BestuzhevaBesanconChenetal.2021, author = {Bestuzheva, Ksenia and Besan{\c{c}}on, Mathieu and Chen, Wei-Kun and Chmiela, Antonia and Donkiewicz, Tim and van Doornmalen, Jasper and Eifler, Leon and Gaul, Oliver and Gamrath, Gerald and Gleixner, Ambros and Gottwald, Leona and Graczyk, Christoph and Halbig, Katrin and Hoen, Alexander and Hojny, Christopher and van der Hulst, Rolf and Koch, Thorsten and L{\"u}bbecke, Marco and Maher, Stephen J. and Matter, Frederic and M{\"u}hmer, Erik and M{\"u}ller, Benjamin and Pfetsch, Marc E. and Rehfeldt, Daniel and Schlein, Steffan and Schl{\"o}sser, Franziska and Serrano, Felipe and Shinano, Yuji and Sofranac, Boro and Turner, Mark and Vigerske, Stefan and Wegscheider, Fabian and Wellner, Philipp and Weninger, Dieter and Witzig, Jakob}, title = {The SCIP Optimization Suite 8.0}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-85309}, year = {2021}, abstract = {The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 8.0 of the SCIP Optimization Suite. Major updates in SCIP include improvements in symmetry handling and decomposition algorithms, new cutting planes, a new plugin type for cut selection, and a complete rework of the way nonlinear constraints are handled. Additionally, SCIP 8.0 now supports interfaces for Julia as well as Matlab. Further, UG now includes a unified framework to parallelize all solvers, a utility to analyze computational experiments has been added to GCG, dual solutions can be postsolved by PaPILO, new heuristics and presolving methods were added to SCIP-SDP, and additional problem classes and major performance improvements are available in SCIP-Jack.}, language = {en} } @misc{BolusaniBesanconBestuzhevaetal.2024, author = {Bolusani, Suresh and Besan{\c{c}}on, Mathieu and Bestuzheva, Ksenia and Chmiela, Antonia and Dion{\´i}sio, Jo{\~a}o and Donkiewicz, Tim and van Doornmalen, Jasper and Eifler, Leon and Ghannam, Mohammed and Gleixner, Ambros and Graczyk, Christoph and Halbig, Katrin and Hedtke, Ivo and Hoen, Alexander and Hojny, Christopher and van der Hulst, Rolf and Kamp, Dominik and Koch, Thorsten and Kofler, Kevin and Lentz, Jurgen and Manns, Julian and Mexi, Gioni and M{\"u}hmer, Erik and E. Pfetsch, Marc and Schl{\"o}sser, Franziska and Serrano, Felipe and Shinano, Yuji and Turner, Mark and Vigerske, Stefan and Weninger, Dieter and Xu, Liding}, title = {The SCIP Optimization Suite 9.0}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-95528}, year = {2024}, abstract = {The SCIP Optimization Suite provides a collection of software packages for mathematical optimization, centered around the constraint integer programming framework SCIP. This report discusses the enhancements and extensions included in the SCIP Optimization Suite 9.0. The updates in SCIP 9.0 include improved symmetry handling, additions and improvements of nonlinear handlers and primal heuristics, a new cut generator and two new cut selection schemes, a new branching rule, a new LP interface, and several bug fixes. The SCIP Optimization Suite 9.0 also features new Rust and C++ interfaces for SCIP, new Python interface for SoPlex, along with enhancements to existing interfaces. The SCIP Optimization Suite 9.0 also includes new and improved features in the LP solver SoPlex, the presolving library PaPILO, the parallel framework UG, the decomposition framework GCG, and the SCIP extension SCIP-SDP. These additions and enhancements have resulted in an overall performance improvement of SCIP in terms of solving time, number of nodes in the branch-and-bound tree, as well as the reliability of the solver.}, language = {en} }