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

Stability of three-dimensional relativistic jets: implications for jet collimation

The stable propagation of jets in FRII sources is remarkable if one takes into account that large-scale jets are subjected to potentially highly disruptive three-dimensional (3D) Kelvin-Helmholtz instabilities. Numerical simulations can address this problem and help clarify the causes of this remarkable stability. Following previous studies of the stability of relativistic flows in two dimensions (2D), it is our aim to test and extend the conclusions of such works to three dimensions. We present numerical simulations for the study of the stability properties of 3D, sheared, relativistic flows. This work uses a fully parallelized code Ratpenat that solves equations of relativistic hydrodynamics in 3D. The results of the present simulations confirm those in 2D. We conclude that the growth of resonant modes in sheared relativistic flows could be important in explaining the long-term collimation of extragalactic jets.Comment: Accepted for publication in A&

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

Overview on agent-based social modelling and the use of formal languages

Transdisciplinary Models and Applications investigates a variety of programming languages used in validating and verifying models in order to assist in their eventual implementation. This book will explore different methods of evaluating and formalizing simulation models, enabling computer and industrial engineers, mathematicians, and students working with computer simulations to thoroughly understand the progression from simulation to product, improving the overall effectiveness of modeling systems.Postprint (author's final draft

Toward an automatic full-wave inversion: Synthetic study cases

Full-waveform inversion (FWI) in seismic scenarios continues to be a complex procedure for subsurface imaging that might require extensive human interaction in terms of model setup, constraints, and data preconditioning. The underlying reason is the strong nonlinearity of the problem that forces the addition of a priori knowledge (or bias) in order to obtain geologically sound results. In particular, when the use of a long-offset receiver is not possible or may not favor the reconstruction of the fine structure of the model, one needs to rely on reflection data. As a consequence, the inversion process is more prone to becoming stuck in local minima. Nevertheless, misfit functionals can be devised that can either cope with missing long-wavenumber features of initial models (e.g., cross-correlation-based misfit) or invert reflection-dominated data whenever the models are sufficiently good (e.g., normalized offset-limited least-squares misfit). By combining both, high-frequency data content with poor initial models can be successfully inverted. If one can figure out simple parameterizations for such functionals, the amount of uncertainty and manual work related to tuning FWI would be substantially reduced. Thus, FWI might become a semiautomatized imaging tool.We want to thank Repsol for funding this research by means of the Aurora project. This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 644202. Additionally, 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. We acknowledge Chevron for the dataset that was used in our second example.Peer ReviewedPostprint (author's final draft

Microdroplet fabrication of silver–agarose nanocomposite beads for SERS optical accumulation

Microdroplets have been used as reactors for the fabrication of agarose beads with high uniformity in shape and size, and densely loaded with silver ions, which were subsequently reduced into nanoparticles using hydrazine. The resulting nanocomposite beads not only display a high plasmonic activity, but can also trap/concentrate analytes, which can be identified by means of surface-enhanced Raman scattering (SERS) spectroscopy. The size of the beads is such that it allows the detection of a single bead under a conventional optical microscope, which is very useful to reduce the amount of material required for SERS detectio

ETeach3D: Designing a 3D virtual environment for evaluating the digital competence of preservice teachers

The acquisition of teacher digital competence is a key aspect in the initial training of teachers. However, most existing evaluation instruments do not provide sufficient evidence of this teaching competence. In this study, we describe the design and development process of a three-dimensional (3D) virtual environment for evaluating the teacher digital competence of future teachers, through a performance-based, collaborative and contextual evaluation. This environment, named ETeach3D, has been constructed using the educational design research approach. It is based on successive iterative cycles and is in accordance with the criteria of usefulness, validity, and effectiveness. In addition to the research team responsible for the project, participating in this study were 187 Spanish undergraduate students of Education and 22 experts in the field of educational technology. Results show that these environments, in addition to other characteristics, should (a) function smoothly and have simple interfaces, realistic scenes, and interactive activities and (b) follow a systematic evaluation procedure that integrates several strategies and levels of complexity. This research helps to improve the initial training of preservice teachers and contributes to the growing number of educational design research studies that focus in the field of evaluation of the curriculum domain.This research is funded by the Ministry of Economy and Competitiveness of Spain, SIMUL@B (ref: EDU2013-42223-P), and supported by the Secretary of Universities and Research, Department of Economy and Knowledge, Government of Catalonia. The project is coordinated by the ARGET research group (ref: 2014SGR1399)

Radiation-Induced Error Criticality in Modern HPC Parallel Accelerators

In this paper, we evaluate the error criticality of radiation-induced errors on modern High-Performance Computing (HPC) accelerators (Intel Xeon Phi and NVIDIA K40) through a dedicated set of metrics. We show that, as long as imprecise computing is concerned, the simple mismatch detection is not sufficient to evaluate and compare the radiation sensitivity of HPC devices and algorithms. Our analysis quantifies and qualifies radiation effects on applications’ output correlating the number of corrupted elements with their spatial locality. Also, we provide the mean relative error (dataset-wise) to evaluate radiation-induced error magnitude. We apply the selected metrics to experimental results obtained in various radiation test campaigns for a total of more than 400 hours of beam time per device. The amount of data we gathered allows us to evaluate the error criticality of a representative set of algorithms from HPC suites. Additionally, based on the characteristics of the tested algorithms, we draw generic reliability conclusions for broader classes of codes. We show that arithmetic operations are less critical for the K40, while Xeon Phi is more reliable when executing particles interactions solved through Finite Difference Methods. Finally, iterative stencil operations seem the most reliable on both architectures.This work was supported by the STIC-AmSud/CAPES scientific cooperation program under the EnergySFE research project grant 99999.007556/2015-02, EU H2020 Programme, and MCTI/RNP-Brazil under the HPC4E Project, grant agreement n° 689772. Tested K40 boards were donated thanks to Steve Keckler, Timothy Tsai, and Siva Hari from NVIDIA.Postprint (author's final draft