Parallel architectures and runtime systems co-design for task-based programming models

The increasing parallelism levels in modern computing systems has extolled the need for a holistic vision when designing multiprocessor architectures taking in account the needs of the programming models and applications. Nowadays, system design consists of several layers on top of each other from the architecture up to the application software. Although this design allows to do a separation of concerns where it is possible to independently change layers due to a well-known interface between them, it is hampering future systems design as the Law of Moore reaches to an end. Current performance improvements on computer architecture are driven by the shrinkage of the transistor channel width, allowing faster and more power efficient chips to be made. However, technology is reaching physical limitations were the transistor size will not be able to be reduced furthermore and requires a change of paradigm in systems design. This thesis proposes to break this layered design, and advocates for a system where the architecture and the programming model runtime system are able to exchange information towards a common goal, improve performance and reduce power consumption. By making the architecture aware of runtime information such as a Task Dependency Graph (TDG) in the case of dataflow task-based programming models, it is possible to improve power consumption by exploiting the critical path of the graph. Moreover, the architecture can provide hardware support to create such a graph in order to reduce the runtime overheads and making possible the execution of fine-grained tasks to increase the available parallelism. Finally, the current status of inter-node communication primitives can be exposed to the runtime system in order to perform a more efficient communication scheduling, and also creates new opportunities of computation and communication overlap that were not possible before. An evaluation of the proposals introduced in this thesis is provided and a methodology to simulate and characterize the application behavior is also presented.El aumento del paralelismo proporcionado por los sistemas de cómputo modernos ha provocado la necesidad de una visión holística en el diseño de arquitecturas multiprocesador que tome en cuenta las necesidades de los modelos de programación y las aplicaciones. Hoy en día el diseño de los computadores consiste en diferentes capas de abstracción con una interfaz bien definida entre ellas. Las limitaciones de esta aproximación junto con el fin de la ley de Moore limitan el potencial de los futuros computadores. La mayoría de las mejoras actuales en el diseño de los computadores provienen fundamentalmente de la reducción del tamaño del canal del transistor, lo cual permite chips más rápidos y con un consumo eficiente sin apenas cambios fundamentales en el diseño de la arquitectura. Sin embargo, la tecnología actual está alcanzando limitaciones físicas donde no será posible reducir el tamaño de los transistores motivando así un cambio de paradigma en la construcción de los computadores. Esta tesis propone romper este diseño en capas y abogar por un sistema donde la arquitectura y el sistema de tiempo de ejecución del modelo de programación sean capaces de intercambiar información para alcanzar una meta común: La mejora del rendimiento y la reducción del consumo energético. Haciendo que la arquitectura sea consciente de la información disponible en el modelo de programación, como puede ser el grafo de dependencias entre tareas en los modelos de programación dataflow, es posible reducir el consumo energético explotando el camino critico del grafo. Además, la arquitectura puede proveer de soporte hardware para crear este grafo con el objetivo de reducir el overhead de construir este grado cuando la granularidad de las tareas es demasiado fina. Finalmente, el estado de las comunicaciones entre nodos puede ser expuesto al sistema de tiempo de ejecución para realizar una mejor planificación de las comunicaciones y creando nuevas oportunidades de solapamiento entre cómputo y comunicación que no eran posibles anteriormente. Esta tesis aporta una evaluación de todas estas propuestas, así como una metodología para simular y caracterizar el comportamiento de las aplicacionesPostprint (published version

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

Effect of Vitrification on Epigenetic Modifications and the Meiotic Spindle of Bovine Oocytes

While oocyte vitrification has become a common practice, it still faces some challenges such as the low survival rates after warming, probably related to cryoinjuries and cryoprotectant (CPA) toxicity. Evidence suggests that vitrification might have an effect on the patterns of some epigenetic marks including DNA methylation and histone acetylation. During fertilization and embryogenesis, key events for healthy and adequate embryo development take place, not only governed by the information contained within the DNA sequence, but also by epigenetic mechanisms. This study was aimed at determining the effect of vitrification and CPA exposure, using a combination of ethylene glycol (EG) with either DMSO or glycerol (Gly), on DNA methylation and histone acetylation of bovine oocytes. Additionally, the effect of vitrification and cryoprotective solutions on the meiotic spindle was evaluated. To achieve this goal, three experiments were carried out. The first experiment was intended to evaluate the effect of vitrification on DNA methylation of bovine cumulus-oocyte complexes (COCs) at two different maturation stages, germinal vesicle (GV) and metaphase II (MII). The second was designed to determine the effect of CPA exposure on DNA methylation and histone acetylation. The last experiment assessed the impact of vitrification and CPA exposure on microtubule distribution and chromosome arrangement, and if a subsequent incubation period after vitrification could promote the reorganization of the spindle. Results obtained suggest that vitrification of bovine oocytes at the GV stage does not have an effect on DNA methylation patterns. Similar outcomes were obtained when comparing oocytes in the MII vitrified with DMSO and fresh oocytes. However, oocytes vitrified with Gly showed an abnormality presented in the form of DNA fragmentation. On the other hand, exposure to EG + DMSO increases the levels of DNA methylations in comparison with fresh oocytes. CPA exposure does not have an effect on histone acetylation levels. Finally, results of the third experiment indicate that CPA exposure has no impact on the incidence of abnormal meiotic spindles. In contrast, vitrification using DMSO increases the occurrence of abnormal meiotic spindles and the damage seems to be irreversible. The incubation period following vitrification with EG + Gly promotes the reorganization of microtubules

Construction of higher-order curl-conforming finite elements and its assembly

Different choices are available when constructing vector finite element bases in real coordinates. In this communication, two different designs of higher-order curl-conforming basis functions are introduced and explained, showing the particularities of its assembly. Tetrahedra and hexahedra are used as element shapes to assess the effect of triangular and quadrilateral faces on the two considered constructions of basis functions. A comparison of their robustness in terms of the condition number of the finite element matrices for a number of distortions is includedMinisterio de Ciencia y Tecnología, Grant/Award Numbers: TEC2013- 47753-C3, TEC2016-80386-P; Ministerio de Educación, Cultura y Deporte, Grant/Award Number: FPU14/0374

Adaptive Semi-Structured Mesh Refinement Techniques for the Finite Element Method

The adaptive mesh techniques applied to the Finite Element Method have continuously been an active research line. However, these techniques are usually applied to tetrahedra. Here, we use the triangular prismatic element as the discretization shape for a Finite Element Method code with adaptivity. The adaptive process consists of three steps: error estimation, marking, and refinement. We adapt techniques already applied for other shapes to the triangular prisms, showing the differences here in detail. We use five different marking strategies, comparing the results obtained with different parameters. We adapt these strategies to a conformation process necessary to avoid hanging nodes in the resulting mesh. We have also applied two special rules to ensure the quality of the refined mesh. We show the effect of these rules with the Method of Manufactured Solutions and numerical results to validate the implementation introduced.This work has been financially supported by TEC2016-80386-

Producción y evaluación de un biosurfactante para la biorremediación de suelos contaminados con hidrocarburos

147 páginas. Doctorado en Ciencias e Ingeniería de Materiales.Los crudos pesados están constituidos por diferentes fracciones de asfaltenos, resinas, compuestos aromáticos y saturados, que contribuyen a sus altas viscosidades, por lo que son intrínsecamente difíciles de biodegradar. Por otro lado, los suelos contaminados que contienen rocas calizas son preferiblemente mojables a los aceites, lo que dificulta su remoción. Los biosurfactantes son capaces de modificar la mojabilidad en el sistema roca/aceite/agua y reducir la tensión interfacial, lo que promueve la liberación del aceite, haciéndolo biodisponible. Este trabajo tuvo como objetivo producir y evaluar un biosurfactante biosintetizado por una cepa de Bacillus subtilis para mejorar la biodegradación del crudo pesado impregnado en arena de caliza. Se realizó la producción del biosurfactante en un reactor agitado de 3L. La actividad biosurfactante se determinó a diferentes temperaturas, pH y salinidades para establecer su estabilidad. Se evaluaron la tensión interfacial y el ángulo de contacto para determinar los mecanismos involucrados en la liberación de aceite pesado. Finalmente, se dilucidó el efecto del biosurfactante sobre la liberación del aceite pesado impregnado en arena de caliza, para su posterior biodegradación utilizando una cepa de Rhodococcus sp. Se encontró que la tasa máxima de producción de CO₂, utilizada como indicador de actividad biológica, mejoró en un 32.84% en los sistemas donde se utilizó biosu factante, en comparación con aquellos donde no se usó. Al menos el 67% de la fracción > C₂₀ se degradó en los sistemas con biosurfactante, reduciendo las fracciones aromática y de resinas (12.5% y 2%, respectivamente), mientras que en los sistemas sin biosurfactante solo se eliminó el 37% de la fracción> C₂₀ y la reducción de aromáticos y resinas fue nula. El biosurfactante demostró ser efectivo en la liberación del crudo y mejoró notablemente el proceso de biodegradación.Heavy crude oils are comprised of different fractions of asphaltenes, resins, aromatic and saturated compounds, which contribute to their high viscosities, making them intrinsically difficult to biodegrade. Besides, contaminated soils that contain limestone rocks are preferably oil wet, which makes their removal difficult. Biosurfactants are capable of modifying the wettability of rock/oil/water system and reduce interfacial tension, which promotes the release of oil, making it bioavailable. The objective of this work was to produce and evaluate a biosurfactant biosynthesized by a strain of Bacillus subtilis to improve the biodegradation of a heavy crude oil impregnated in limestone sand. The biosurfactant production was carried out in a 3L stirred reactor. The biosurfactant activity was determined at different temperatures, pH and salinities to establish its stability. Interfacial tension and contact angle were evaluated to determine the mechanisms involved in heavy oil release. Finally, the effect of the biosurfactant on the release of heavy oil impregnated in limestone sand was elucidated, for its subsequent biodegradation using a strain of Rhodococcus sp. It was found that the maximum CO₂ production rate, used as an indicator of biological activity, improved by 32.84% in systems where biosurfactant was used, compared to those where it was not used. At least 67% of the fraction > C₂₀ was degraded in the systems with biosurfactant, reducing the aromatic and resin fractions (12.5% and 2%, respectively), while in systems without biosurfactant only 37% was removed of the fraction > C₂₀ and the reduction of aromatics and resins was null. The biosurfactant proved to be effective in the release of crude oil and significantly improved the biodegradation process.Investigación realizada con el apoyo del Programa Nacional de Posgrados de Calidad del Consejo Nacional de Ciencia y Tecnología (CONACYT)

An interface between an hp-adaptive finite element package and the pre- and post-processor GiD

An interface between GiD, the interactive graphical user interface used for numerical simulations, developed at the International Center for Numerical Methods in Engineering (CIMNE) of the Universidad Politécnica de Cataluña and the Geometrical Modeling Package (GMP) of the fully automatic hp-adaptive finite element (FE) software, developed at the Institute for Computational Engineering and Sciences (ICES) of the University of Texas at Austin, is presented. GiD is used to construct a tessellation of the problem domain into FE-like regions (blocks in GMP terminology), and the interface obtains and transfers all the topological and geometrical information to GMP. Then, GMP automatically constructs a parameterization for each FE-like region of the GMP mesh, which later can be used to generate the actual FE-mesh and support geometry updates during mesh refinements

Método de Elementos Finitos hp con Adaptabilidad Automática Orientada a un Objetivo para Problemas Abiertos en 2D

In this paper, we describe a fully automatic goaloriented hp-adaptive Finite Element strategy, which is applied to open problems (radiation and scattering). The methodology produces exponential convergence rates in terms of an upper bound of an user-prescribed quantity of interest (in our case, the S-parameter, the far radiated field or far scattering field) against the problem size (number of degrees of freedom). We illustrate the efficiency of the method with 2D numerical simulations of open problems (radiation and scattering). Applications include the far scattering (radiated) field by an object (antenna) and the computation of mutual coupling of the antennas (S-parameters). Results show that self-adaptive goal-oriented hp obtains more accuracy in the quantity of interest than self-adaptive energynorm hp with the same number of degrees of freedom

High-accuracy adaptive simulations of a Petri dish exposed to electromagnetic radiation

This paper analyses numerically the electric field distribution of a liquid contained in a Petri dish when exposed to electromagnetic waves excited in a rectangular waveguide. Solutions exhibit high-gradients due to the presence of the dielectric liquid contained in the dish. Furthermore, electromagnetic fields within the dielectric have a dramatically lower value than on the remaining part of the domain, which difficults its simulation. Additionally, various singularities of different intensity appear along the boundary of the Petri dish. To properly reproduce and numerically study those effects, we employ a highly-accurate hp-adaptive finite element method. Results of this study demonstrate that the electric field generated within the circular Petri dish is non-homogeneous, and thus, a better shape, size, or location of the dish is needed to achieve an equally distributed radiation enabling the uniform growth of cell cultives

Architectural support for task dependence management with flexible software scheduling

The growing complexity of multi-core architectures has motivated a wide range of software mechanisms to improve the orchestration of parallel executions. Task parallelism has become a very attractive approach thanks to its programmability, portability and potential for optimizations. However, with the expected increase in core counts, finer-grained tasking will be required to exploit the available parallelism, which will increase the overheads introduced by the runtime system. This work presents Task Dependence Manager (TDM), a hardware/software co-designed mechanism to mitigate runtime system overheads. TDM introduces a hardware unit, denoted Dependence Management Unit (DMU), and minimal ISA extensions that allow the runtime system to offload costly dependence tracking operations to the DMU and to still perform task scheduling in software. With lower hardware cost, TDM outperforms hardware-based solutions and enhances the flexibility, adaptability and composability of the system. Results show that TDM improves performance by 12.3% and reduces EDP by 20.4% on average with respect to a software runtime system. Compared to a runtime system fully implemented in hardware, TDM achieves an average speedup of 4.2% with 7.3x less area requirements and significant EDP reductions. In addition, five different software schedulers are evaluated with TDM, illustrating its flexibility and performance gains.This work has been supported by the RoMoL ERC Advanced Grant (GA 321253), by the European HiPEAC Network of Excellence, by the Spanish Ministry of Science and Innovation (contracts TIN2015-65316-P, TIN2016-76635-C2-2-R and TIN2016-81840-REDT), by the Generalitat de Catalunya (contracts 2014-SGR-1051 and 2014-SGR-1272), and by the European Union’s Horizon 2020 research and innovation programme under grant agreement No 671697 and No. 671610. M. Moretó has been partially supported by the Ministry of Economy and Competitiveness under Juan de la Cierva postdoctoral fellowship number JCI-2012-15047.Peer ReviewedPostprint (author's final draft