Rimado de Palacio [Texto impreso]

Subtítulo del material anejo: Cuaderno 9º, estrofas 1493-1687

Proactive and reactive thermal aware optimization techniques to minimize the environmental impact of data centers

Los Centros de Datos se encuentran actualmente en cualquier sector de la economía mundial. Están compuestos por miles de servidores, dando servicio a los usuarios de forma global, las 24 horas del día y los 365 días del año. Durante los últimos años, las aplicaciones del ámbito de la e-Ciencia, como la e-Salud o las Ciudades Inteligentes han experimentado un desarrollo muy significativo. La necesidad de manejar de forma eficiente las necesidades de cómputo de aplicaciones de nueva generación, junto con la creciente demanda de recursos en aplicaciones tradicionales, han facilitado el rápido crecimiento y la proliferación de los Centros de Datos. El principal inconveniente de este aumento de capacidad ha sido el rápido y dramático incremento del consumo energético de estas infraestructuras. En 2010, la factura eléctrica de los Centros de Datos representaba el 1.3% del consumo eléctrico mundial. Sólo en el año 2012, el consumo de potencia de los Centros de Datos creció un 63%, alcanzando los 38GW. En 2013 se estimó un crecimiento de otro 17%, hasta llegar a los 43GW. Además, los Centros de Datos son responsables de más del 2% del total de emisiones de dióxido de carbono a la atmósfera. Esta tesis doctoral se enfrenta al problema energético proponiendo técnicas proactivas y reactivas conscientes de la temperatura y de la energía, que contribuyen a tener Centros de Datos más eficientes. Este trabajo desarrolla modelos de energía y utiliza el conocimiento sobre la demanda energética de la carga de trabajo a ejecutar y de los recursos de computación y refrigeración del Centro de Datos para optimizar el consumo. Además, los Centros de Datos son considerados como un elemento crucial dentro del marco de la aplicación ejecutada, optimizando no sólo el consumo del Centro de Datos sino el consumo energético global de la aplicación. Los principales componentes del consumo en los Centros de Datos son la potencia de computación utilizada por los equipos de IT, y la refrigeración necesaria para mantener los servidores dentro de un rango de temperatura de trabajo que asegure su correcto funcionamiento. Debido a la relación cúbica entre la velocidad de los ventiladores y el consumo de los mismos, las soluciones basadas en el sobre-aprovisionamiento de aire frío al servidor generalmente tienen como resultado ineficiencias energéticas. Por otro lado, temperaturas más elevadas en el procesador llevan a un consumo de fugas mayor, debido a la relación exponencial del consumo de fugas con la temperatura. Además, las características de la carga de trabajo y las políticas de asignación de recursos tienen un impacto importante en los balances entre corriente de fugas y consumo de refrigeración. La primera gran contribución de este trabajo es el desarrollo de modelos de potencia y temperatura que permiten describes estos balances entre corriente de fugas y refrigeración; así como la propuesta de estrategias para minimizar el consumo del servidor por medio de la asignación conjunta de refrigeración y carga desde una perspectiva multivariable. Cuando escalamos a nivel del Centro de Datos, observamos un comportamiento similar en términos del balance entre corrientes de fugas y refrigeración. Conforme aumenta la temperatura de la sala, mejora la eficiencia de la refrigeración. Sin embargo, este incremente de la temperatura de sala provoca un aumento en la temperatura de la CPU y, por tanto, también del consumo de fugas. Además, la dinámica de la sala tiene un comportamiento muy desigual, no equilibrado, debido a la asignación de carga y a la heterogeneidad en el equipamiento de IT. La segunda contribución de esta tesis es la propuesta de técnicas de asigación conscientes de la temperatura y heterogeneidad que permiten optimizar conjuntamente la asignación de tareas y refrigeración a los servidores. Estas estrategias necesitan estar respaldadas por modelos flexibles, que puedan trabajar en tiempo real, para describir el sistema desde un nivel de abstracción alto. Dentro del ámbito de las aplicaciones de nueva generación, las decisiones tomadas en el nivel de aplicación pueden tener un impacto dramático en el consumo energético de niveles de abstracción menores, como por ejemplo, en el Centro de Datos. Es importante considerar las relaciones entre todos los agentes computacionales implicados en el problema, de forma que puedan cooperar para conseguir el objetivo común de reducir el coste energético global del sistema. La tercera contribución de esta tesis es el desarrollo de optimizaciones energéticas para la aplicación global por medio de la evaluación de los costes de ejecutar parte del procesado necesario en otros niveles de abstracción, que van desde los nodos hasta el Centro de Datos, por medio de técnicas de balanceo de carga. Como resumen, el trabajo presentado en esta tesis lleva a cabo contribuciones en el modelado y optimización consciente del consumo por fugas y la refrigeración de servidores; el modelado de los Centros de Datos y el desarrollo de políticas de asignación conscientes de la heterogeneidad; y desarrolla mecanismos para la optimización energética de aplicaciones de nueva generación desde varios niveles de abstracción. ABSTRACT Data centers are easily found in every sector of the worldwide economy. They consist of tens of thousands of servers, serving millions of users globally and 24-7. In the last years, e-Science applications such e-Health or Smart Cities have experienced a significant development. The need to deal efficiently with the computational needs of next-generation applications together with the increasing demand for higher resources in traditional applications has facilitated the rapid proliferation and growing of data centers. A drawback to this capacity growth has been the rapid increase of the energy consumption of these facilities. In 2010, data center electricity represented 1.3% of all the electricity use in the world. In year 2012 alone, global data center power demand grew 63% to 38GW. A further rise of 17% to 43GW was estimated in 2013. Moreover, data centers are responsible for more than 2% of total carbon dioxide emissions. This PhD Thesis addresses the energy challenge by proposing proactive and reactive thermal and energy-aware optimization techniques that contribute to place data centers on a more scalable curve. This work develops energy models and uses the knowledge about the energy demand of the workload to be executed and the computational and cooling resources available at data center to optimize energy consumption. Moreover, data centers are considered as a crucial element within their application framework, optimizing not only the energy consumption of the facility, but the global energy consumption of the application. The main contributors to the energy consumption in a data center are the computing power drawn by IT equipment and the cooling power needed to keep the servers within a certain temperature range that ensures safe operation. Because of the cubic relation of fan power with fan speed, solutions based on over-provisioning cold air into the server usually lead to inefficiencies. On the other hand, higher chip temperatures lead to higher leakage power because of the exponential dependence of leakage on temperature. Moreover, workload characteristics as well as allocation policies also have an important impact on the leakage-cooling tradeoffs. The first key contribution of this work is the development of power and temperature models that accurately describe the leakage-cooling tradeoffs at the server level, and the proposal of strategies to minimize server energy via joint cooling and workload management from a multivariate perspective. When scaling to the data center level, a similar behavior in terms of leakage-temperature tradeoffs can be observed. As room temperature raises, the efficiency of data room cooling units improves. However, as we increase room temperature, CPU temperature raises and so does leakage power. Moreover, the thermal dynamics of a data room exhibit unbalanced patterns due to both the workload allocation and the heterogeneity of computing equipment. The second main contribution is the proposal of thermal- and heterogeneity-aware workload management techniques that jointly optimize the allocation of computation and cooling to servers. These strategies need to be backed up by flexible room level models, able to work on runtime, that describe the system from a high level perspective. Within the framework of next-generation applications, decisions taken at this scope can have a dramatical impact on the energy consumption of lower abstraction levels, i.e. the data center facility. It is important to consider the relationships between all the computational agents involved in the problem, so that they can cooperate to achieve the common goal of reducing energy in the overall system. The third main contribution is the energy optimization of the overall application by evaluating the energy costs of performing part of the processing in any of the different abstraction layers, from the node to the data center, via workload management and off-loading techniques. In summary, the work presented in this PhD Thesis, makes contributions on leakage and cooling aware server modeling and optimization, data center thermal modeling and heterogeneityaware data center resource allocation, and develops mechanisms for the energy optimization for next-generation applications from a multi-layer perspective.

Arquitecturas en árboles: atenciones contemporáneas, 1990-2010

La tesis abre su mirada hacia uno de los discursos más interesantes, a mi juicio, de la cultura arquitectónica contemporánea: el de la relación establecida entre el ser humano y la naturaleza. Algunos autores creen que esta relación se establece como simbiosis, como un organismo arquitectónico en correlación y analogía con su entorno y emplazamiento. Otros ven una correspodencia en la que la arquitectura se ubica como un artefacto que ”dialoga” y que no imita a la naturaleza. Las arquitecturas en árboles se desarrollan en estos dos sentidos. El panorama de estas arquitecturas está abierto, es incipiente, laberíntico, poliédrico y caleidoscópico. Metodológicamente ha sido necesario acotarlo y el período de estudio elegido ha sido el más fructífero de la historia y cultura de las estructuras en los árboles. En los últimos veinticinco años, éstas han vuelto a generar atracción por el auge de la sensibilización medioambiental. También se ha producido un incremento de las culturas del ocio (con acento en el deseo por encima de la utilidad o la necesidad) y de la introspección (en busca de un retiro espiritual alejado de la cultura de la globalización). Hacia 1990 se producen acontecimientos relevantes que son los precursores de este desarrollo: la aparición en 1988 del libro “Treehouses” de Aikman abre de manera desenfadada esta cultura arquitectónica. Para acotar el final del período de investigación se ha dejado un margen desde 2010 a 2015 por prudencia investigadora. Los objetivos de la tesis se han centrado: Primero, en encuadrar el concepto de “arquitecturas en árboles”; Segundo, en descubrir los motivos, ideas que inspiraron las arquitecturas en árboles anteriores al período de estudio y su posible repercusión en sus descendientes contemporáneas. Principalmente son atenciones ideológicas, culturales, sociales, filosóficas, simbólicas, míticos y funcionales. Tercero, en confeccionar una taxonomía de las intenciones, consideraciones y desencadenantes básicos que pudieran establecerse como claves del proceso imaginario, conceptivo y constructivo de la actuales arquitecturas en árboles (1990-2010). Para ello nos hemos puesto bajo el paraguas metodológico del concepto de atención, defendido por Quaroni, Ferrater, Broadbent y Seguí. Hemos planteado una reflexión sobre el tipo de atenciones y su idoneaidad llegando a distinguir las siguientes atenciones básicas: 1) Las atenciones históricas (del pasado): englobando bajo esta denominación el entramado rizomático de atenciones sociales, culturales, antropológicas, filosóficas, míticas y simbólicas. Estas atenciones permiten al lector posicionarse de manera efectiva en este amplio campo, para entrar con posterioridad en el cuerpo de la investigación. Posteriormente descubriremos que éstas se convierten en atenciones crítico-modales para las arquitecturas contemporáneas. 2) Las atenciones funcionales contemporáneas: en las que estableceremos una conexión multiple con otras atenciones ergonómicas, organizativas, tipológicas y medioambientales básicas que están claramente influenciadas por aquellas. Quedan establecidas en una taxonomía inédita de treinta ocho subcategorías que nos alejan del estereotipo de la casa en el árbol como lugar de defensa y protección, o como espacio lúdico-infantil 3) Las atenciones constructivas contemporáneas: que las relacionaremos con las biológicas, estructurales-portantes, tipológico-constructivas, medioambientales básicas (de los materiales), y que son tenidas en cuenta por los contructores. Asimismo, se revelan los sistemas de construcción de arquitecturas portantes y autoportantes (artificiales-naturales) y las 100% naturales. Además, se decubren los seis mecanismos estructurales de sujeción de habitáculos en árboles más utilizados, así como cuáles son los árboles idóneos para soportar estas estructuras. 4) Las atenciones formales contemporáneas: con sus conexiones hacia las atenciones presenciales, espaciales organizativas y medioambientales básicas. Se establecen taxonomías sistemáticas formales simples y complejas (pragmática, icónica, analógica y canónica). Se estudian con profundidad la analogía con otras realidades y la estructuración geométrica formal (canónica) por considerarlas las más relevantes. Se culmina la investigación con una reflexión sobre el conjunto rizomático de atenciones, disciplinas, nociones y conceptos inherentes al campo de las arquitecturas en árboles, ejemplificándolo con un ideograma. La última vista se fija sobre el arco temporal de estas arquitecturas reflejando las cincuenta más significativas por su mayor coherencia de competencia atencional, total o parcial. ABSTRACT This dissertation looks into one the most interesting discourses in contemporary architectural culture: the relationship between human beings and nature. Some scholars think of this relationship as a symbiosis, as an architectural organism armonically correlated with its environment and location. Others believe that a correspondence exists where architecture stands as an artifact ‘in dialogue’ with, and not as an imitation of, nature. Treehouses develop in both senses. The realm of these architectures is open, embryonic, labyrinthine, polyhedral and kaleidoscopic. It was necessary to methodologically delimit it. We chose for the study the most fruitful period in the history and culture of treehouses. During the last twenty-five years, the latter have exerted great appeal once more due to the rise in environmental awareness. Likewise, leisure cultures (highlighting desire over utility or necessity) and introspection (seeking spiritual retreat far from the culture of globalization) have significantly increased. Around 1990, some relevant events announce this development: the publication of the book Treehouses by Aikman in 1988 inaugurates in an informal fashion such architectural culture. As for the final limit of the period addressed, an open margin between 2010 and 2015 has been established, out of scholarly prudence. The dissertation objectives have focused on: First, framing the concept of “treehouses”. Second, discovering the motifs and ideas that inspired treehouses in previous periods, and their possible influence on their contemporary successors. These consist basically of idelogical, cultural, social, philosophical, symbolic, mythical and functional attentions. Third, elaborate a taxonomy of the different basic intentions, considerations and triggers that might appear as crucial for the imaginary, conceptual and constructive process of current treehouses (1990-2010). To this end, we stood under the methodological umbrella of the notion of attention as defined by Quaroni, Ferrater, Broadbent and Seguí. We have proposed a reflection on the different kind of attentions and their suitability, distinguishing the following basic attentions: 1) Historical attentions (from the past): this denomination comprises the rhizomatic fabric of social, cultural, anthropological, philosophical, mythical and symbolic attentions. These attentions allow the reader to get a foothold on this broad field before being able to go into the main body of research. We will later discover that these become critical modal attentions for contemporary architectures. 2) Contemporary functional attentions. A multiple connection will be established with other basic ergonomic, organisational, typological and environmental attentions clearly influenced by them. They are classified in an unprecedented taxonomy of thirty-eight subcategories that move us away from the stereotype of the tree house as a site of defense and protection, or as a children’s playground. 3) Contemporary constructive attentions. They will be linked with basic biological, structural-carrying, typological-constructive, environmental attentions (of materials) taken into account by constructors. Likewise, the construction systems for carrying and self-carrying (artificial-natural) architectures, as well as for 100% natural ones, are revealed. Besides, we disclose the six structural mechanisms employed to fasten cabins to trees, and which the most suitable trees to support such structures are. 4) Contemporary formal attentions, including their connections with spatial, organizational and basic environmental attentions. Simple and complex formal systematic taxonomies (pragmatic, iconic, analogical and canonical) have been established. Their analogy to other realities and to formal geometrical (canonical) structuring is studied in depth as utterly significant. The research concludes by reflecting on the rhizomatic set of attentions, disciplines, notions and concepts inherent in the field of treehouses through an ideogram. The final view engages with the time span of these architectures by highlighting the fifty most noteworthy on account of the higher consistency of their attentional competence, either total or partial.

Doctrina Christiana, en lengua Arauiga y Castellana [Texto impreso]

Port. con esc. xil. arzobispal

Malaria’s Eve: Evidence of a recent population bottleneck throughout the world populations of Plasmodium falciparum

We have analyzed DNA sequences from world-wide geographic strains of Plasmodium falciparum and found a complete absence of synonymous DNA polymorphism at 10 gene loci. We hypothesize that all extant world populations of the parasite have recently derived (within several thousand years) from a single ancestral strain. The upper limit of the 95% confidence interval for the time when this most recent common ancestor lived is between 24,500 and 57,500 years ago (depending on different estimates of the nucleotide substitution rate); the actual time is likely to be much more recent. The recent origin of the P. falciparum populations could have resulted from either a demographic sweep (P. falciparum has only recently spread throughout the world from a small geographically confined population) or a selective sweep (one strain favored by natural selection has recently replaced all others). The selective sweep hypothesis requires that populations of P. falciparum be effectively clonal, despite the obligate sexual stage of the parasite life cycle. A demographic sweep that started several thousand years ago is consistent with worldwide climatic changes ensuing the last glaciation, increased anthropophilia of the mosquito vectors, and the spread of agriculture. P. falciparum may have rapidly spread from its African tropical origins to the tropical and subtropical regions of the world only within the last 6,000 years. The recent origin of the world-wide P. falciparum populations may account for its virulence, as the most malignant of human malarial parasites.

Plasmodium falciparum antigenic diversity: Evidence of clonal population structure

Plasmodium falciparum, the agent of malignant malaria, is one of mankind’s most severe scourges. Efforts to develop preventive vaccines or remedial drugs are handicapped by the parasite’s rapid evolution of drug resistance and protective antigens. We examine 25 DNA sequences of the gene coding for the highly polymorphic antigenic circumsporozoite protein. We observe total absence of silent nucleotide variation in the two nonrepeated regions of the gene. We propose that this absence reflects a recent origin (within several thousand years) of the world populations of P. falciparum from a single individual; the amino acid polymorphisms observed in these nonrepeat regions would result from strong natural selection. Analysis of these polymorphisms indicates that: (i) the incidence of recombination events does not increase with nucleotide distance; (ii) the strength of linkage disequilibrium between nucleotides is also independent of distance; and (iii) haplotypes in the two nonrepeat regions are correlated with one another, but not with the central repeat region they span. We propose two hypotheses: (i) variation in the highly polymorphic central repeat region arises by mitotic intragenic recombination, and (ii) the population structure of P. falciparum is clonal—a state of affairs that persists in spite of the necessary stage of physiological sexuality that the parasite must sustain in the mosquito vector to complete its life cycle.

DNA variation at the Sod locus of Drosophila melanogaster: An unfolding story of natural selection

Patterns of variation at the Sod locus of Drosophila melanogaster suggest that the protein polymorphism at this locus has very recently arisen. In addition, it appears that a previously rare DNA variant has been recently and rapidly driven to intermediate frequency. From the size of the region (>20 kb) that has been swept along with this rare variant, and patterns of linkage disequilibrium in the region, it is inferred that strength of selection was large (s > 0.01) and that the sweep occurred more than 25,000 generations ago. In addition, there are striking similarities to patterns of variation observed at the Est6 and Est-P loci, which are located approximately 1,000 kb from Sod.

Vagaries of the molecular clock

The hypothesis of the molecular evolutionary clock asserts that informational macromolecules (i.e., proteins and nucleic acids) evolve at rates that are constant through time and for different lineages. The clock hypothesis has been extremely powerful for determining evolutionary events of the remote past for which the fossil and other evidence is lacking or insufficient. I review the evolution of two genes, Gpdh and Sod. In fruit flies, the encoded glycerol-3-phosphate dehydrogenase (GPDH) protein evolves at a rate of 1.1 × 10−10 amino acid replacements per site per year when Drosophila species are compared that diverged within the last 55 million years (My), but a much faster rate of ≈4.5 × 10−10 replacements per site per year when comparisons are made between mammals (≈70 My) or Dipteran families (≈100 My), animal phyla (≈650 My), or multicellular kingdoms (≈1100 My). The rate of superoxide dismutase (SOD) evolution is very fast between Drosophila species (16.2 × 10−10 replacements per site per year) and remains the same between mammals (17.2) or Dipteran families (15.9), but it becomes much slower between animal phyla (5.3) and still slower between the three kingdoms (3.3). If we assume a molecular clock and use the Drosophila rate for estimating the divergence of remote organisms, GPDH yields estimates of 2,500 My for the divergence between the animal phyla (occurred ≈650 My) and 3,990 My for the divergence of the kingdoms (occurred ≈1,100 My). At the other extreme, SOD yields divergence times of 211 My and 224 My for the animal phyla and the kingdoms, respectively. It remains unsettled how often proteins evolve in such erratic fashion as GPDH and SOD.

Population structure and recent evolution of Plasmodium falciparum

Plasmodium falciparum is the agent of malignant malaria, one of mankind's most severe maladies. The parasite exhibits antigenic polymorphisms that have been postulated to be ancient. We have proposed that the extant world populations of P. falciparum have derived from one single parasite, a cenancestor, within the last 5,000–50,000 years. This inference derives from the virtual or complete absence of synonymous nucleotide polymorphisms at genes not involved in immune or drug responses. Seeking to conciliate this claim with extensive antigenic polymorphism, we first note that allele substitutions or polymorphisms can arise very rapidly, even in a single generation, in large populations subject to strong natural selection. Second, new alleles can arise not only by single-nucleotide mutations, but also by duplication/deletion of short simple-repeat DNA sequences, a process several orders of magnitude faster than single-nucleotide mutation. We analyze three antigenic genes known to be extremely polymorphic: Csp, Msp-1, and Msp-2. We identify regions consisting of tandem or proximally repetitive short DNA sequences, including some previously unnoticed. We conclude that the antigenic polymorphisms are consistent with the recent origin of the world populations of P. falciparum inferred from the analysis of nonantigenic genes.

Evidence for clonal propagation in natural isolates of Plasmodium falciparum from Venezuela

We have analyzed 75 isolates of Plasmodium falciparum, collected in Venezuela during both the dry (November) and rainy (May–July) seasons, with a range of genetic markers including antigen genes and 14 random amplified polymorphic DNA (RAPD) primers. Thirteen P. falciparum stocks from Kenya and four other Plasmodium species are included in the analysis for comparison. Cross-hybridization shows that the 14 RAPD primers reveal 14 separate regions of the parasite's genome. The P. falciparum isolates are a monophyletic clade, significantly different from the other Plasmodium species. We identify three RAPD characters that could be useful as “tags” for rapid species identification. The Venezuelan genotypes fall into two discrete genetic subdivisions associated with either the dry or the rainy season; the isolates collected in the rainy season exhibit greater genetic diversity. There is significant linkage disequilibrium in each seasonal subsample and in the full sample. In contrast, no linkage disequilibrium is detected in the African sample. These results support the hypothesis that the population structure of P. falciparum in Venezuela, but not in Africa, is predominantly clonal. However, the impact of genetic recombination on Venezuelan P. falciparum seems higher than in parasitic species with long-term clonal evolution like Trypanosoma cruzi, the agent of Chagas' disease. The genetic structure of the Venezuelan samples is similar to that of Escherichia coli, a bacterium that propagates clonally, with occasional genetic recombination.

Nucleotide sequences provide evidence of genetic exchange among distantly related lineages of Trypanosoma cruzi

Simple phylogenetic tests were applied to a large data set of nucleotide sequences from two nuclear genes and a region of the mitochondrial genome of Trypanosoma cruzi, the agent of Chagas' disease. Incongruent gene genealogies manifest genetic exchange among distantly related lineages of T. cruzi. Two widely distributed isoenzyme types of T. cruzi are hybrids, their genetic composition being the likely result of genetic exchange between two distantly related lineages. The data show that the reference strain for the T. cruzi genome project (CL Brener) is a hybrid. Well-supported gene genealogies show that mitochondrial and nuclear gene sequences from T. cruzi cluster, respectively, in three or four distinct clades that do not fully correspond to the two previously defined major lineages of T. cruzi. There is clear genetic differentiation among the major groups of sequences, but genetic diversity within each major group is low. We estimate that the major extant lineages of T. cruzi have diverged during the Miocene or early Pliocene (3–16 million years ago).

Molecular clock or erratic evolution? A tale of two genes.

We have investigated the evolution of glycerol-3-phosphate dehydrogenase (Gpdh). The rate of amino acid replacements is 1 x 10(-10)/site/year when Drosophila species are compared. The rate is 2.7 times greater when Drosophila and Chymomyza species are compared; and about 5 times greater when any of those species are compared with the medfly Ceratitis capitata. This rate of 5 x 10(-10)/site/year is also the rate observed in comparisons between mammals, or between different animal phyla, or between the three multicellular kingdoms. We have also studied the evolution of Cu,Zn superoxide dismutase (Sod). The rate of amino acid replacements is about 17 x 10(-10)/site/year when comparisons are made between dipterans or between mammals, but only 5 x 10(-10) when animal phyla are compared, and only 3 x 10(-10) when the multicellular kingdoms are compared. The apparent decrease by about a factor of 5 in the rate of SOD evolution as the divergence between species increases can be consistent with the molecular clock hypothesis by assuming the covarion hypothesis (namely, that the number of amino acids that can change is constant, but the set of such amino acids changes from time to time and from lineage to lineage). However, we know of no model consistent with the molecular clock hypothesis that would account for the increase in the rate of GPDH evolution as the divergence between species increases.