Distributed graph-based state space generation

LTSMIN provides a framework in which state space generation can be distributed easily over many cores on a single compute node, as well as over multiple compute nodes. The tool works on the basis of a vector representation of the states; the individual cores are assigned the task of computing all successors of states that are sent to them. In this paper we show how this framework can be applied in the case where states are essentially graphs interpreted up to isomorphism, such as the ones we have been studying for GROOVE. This involves developing a suitable vector representation for a canonical form of those graphs. The canonical forms are computed using a third tool called BLISS. We combined the three tools to form a system for distributed state space generation based on graph grammars. We show that the time performance of the resulting system scales well (i.e., close to linear) with the number of cores. We also report surprising statistics on the memory\ud consumption, which imply that the vector representation used to store graphs in LTSMIN is more compact than the representation used in GROOVE

Improving edge finite element assembly for geophysical electromagnetic modelling on shared-memory architectures

This work presents a set of node-level optimizations to perform the assembly of edge finite element matrices that arise in 3D geophysical electromagnetic modelling on shared-memory architectures. Firstly, we describe the traditional and sequential assembly approach. Secondly, we depict our vectorized and shared-memory strategy which does not require any low level instructions because it is based on an interpreted programming language, namely, Python. As a result, we obtained a simple parallel-vectorized algorithm whose runtime performance is considerably better than sequential version. The set of optimizations have been included to the work-flow of the Parallel Edge-based Tool for Geophysical Electromagnetic Modelling (PETGEM) which is developed as open-source at the Barcelona Supercomputing Center. Finally, we present numerical results for a set of tests in order to illustrate the performance of our strategy.This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 644202. The research leading to these results has received funding from the European Union's Horizon 2020 Programme (2014-2020) and from Brazilian Ministry of Science, Technology and Innovation through Rede Nacional de Pesquisa (RNP) under the HPC4E Project (www.hpc4e.eu), grant agreement No. 689772. Authors gratefully acknowledge the support from the Mexican National Council for Science and Technology (CONACYT). All numerical tests were performed on the MareNostrum supercomputer of the Barcelona Supercomputing Center - Centro Nacional de Supercomputación (www.bsc.es).Peer ReviewedPostprint (author's final draft

Extension of information geometry for modelling non-statistical systems

In this dissertation, an abstract formalism extending information geometry is introduced. This framework encompasses a broad range of modelling problems, including possible applications in machine learning and in the information theoretical foundations of quantum theory. Its purely geometrical foundations make no use of probability theory and very little assumptions about the data or the models are made. Starting only from a divergence function, a Riemannian geometrical structure consisting of a metric tensor and an affine connection is constructed and its properties are investigated. Also the relation to information geometry and in particular the geometry of exponential families of probability distributions is elucidated. It turns out this geometrical framework offers a straightforward way to determine whether or not a parametrised family of distributions can be written in exponential form. Apart from the main theoretical chapter, the dissertation also contains a chapter of examples illustrating the application of the formalism and its geometric properties, a brief introduction to differential geometry and a historical overview of the development of information geometry.Comment: PhD thesis, University of Antwerp, Advisors: Prof. dr. Jan Naudts and Prof. dr. Jacques Tempere, December 2014, 108 page

Adaptive BDDC in Three Dimensions

The adaptive BDDC method is extended to the selection of face constraints in three dimensions. A new implementation of the BDDC method is presented based on a global formulation without an explicit coarse problem, with massive parallelism provided by a multifrontal solver. Constraints are implemented by a projection and sparsity of the projected operator is preserved by a generalized change of variables. The effectiveness of the method is illustrated on several engineering problems.Comment: 28 pages, 9 figures, 9 table

Are there new models of computation? Reply to Wegner and Eberbach

Wegner and Eberbach[Weg04b] have argued that there are fundamental limitations to Turing Machines as a foundation of computability and that these can be overcome by so-called superTuring models such as interaction machines, the [pi]calculus and the $-calculus. In this paper we contest Weger and Eberbach claims

Parallel 3-D marine controlled-source electromagnetic modelling using high-order tetrahedral Nédélec elements

We present a parallel and high-order Nédélec finite element solution for the marine controlled-source electromagnetic (CSEM) forward problem in 3-D media with isotropic conductivity. Our parallel Python code is implemented on unstructured tetrahedral meshes, which support multiple-scale structures and bathymetry for general marine 3-D CSEM modelling applications. Based on a primary/secondary field approach, we solve the diffusive form of Maxwell’s equations in the low-frequency domain. We investigate the accuracy and performance advantages of our new high-order algorithm against a low-order implementation proposed in our previous work. The numerical precision of our high-order method has been successfully verified by comparisons against previously published results that are relevant in terms of scale and geological properties. A convergence study confirms that high-order polynomials offer a better trade-off between accuracy and computation time. However, the optimum choice of the polynomial order depends on both the input model and the required accuracy as revealed by our tests. Also, we extend our adaptive-meshing strategy to high-order tetrahedral elements. Using adapted meshes to both physical parameters and high-order schemes, we are able to achieve a significant reduction in computational cost without sacrificing accuracy in the modelling. Furthermore, we demonstrate the excellent performance and quasi-linear scaling of our implementation in a state-of-the-art high-performance computing architecture.This project has received funding from the European Union's Horizon 2020 programme under the Marie Sklodowska-Curie grant agreement No. 777778. Furthermore, the research leading to these results has received funding from the European Union's Horizon 2020 programme under the ChEESE Project (https://cheese-coe.eu/ ), grant agreement No. 823844. In addition, the authors would also like to thank the support of the Ministerio de Educación y Ciencia (Spain) under Projects TEC2016-80386-P and TIN2016-80957-P. The authors would like to thank the Editors-in-Chief and to both reviewers, Dr. Martin Cuma and Dr. Raphael Rochlitz, for their valuable comments and suggestions which helped to improve the quality of the manuscript. This work benefited from the valuable suggestions, comments, and proofreading of Dr. Otilio Rojas (BSC). Last but not least, Octavio Castillo-Reyes thanks Natalia Gutierrez (BSC) for her support in CSEM modeling with BSIT.Peer ReviewedPostprint (author's final draft