A review of High Performance Computing foundations for scientists

The increase of existing computational capabilities has made simulation emerge as a third discipline of Science, lying midway between experimental and purely theoretical branches [1, 2]. Simulation enables the evaluation of quantities which otherwise would not be accessible, helps to improve experiments and provides new insights on systems which are analysed [3-6]. Knowing the fundamentals of computation can be very useful for scientists, for it can help them to improve the performance of their theoretical models and simulations. This review includes some technical essentials that can be useful to this end, and it is devised as a complement for researchers whose education is focused on scientific issues and not on technological respects. In this document we attempt to discuss the fundamentals of High Performance Computing (HPC) [7] in a way which is easy to understand without much previous background. We sketch the way standard computers and supercomputers work, as well as discuss distributed computing and discuss essential aspects to take into account when running scientific calculations in computers.Comment: 33 page

Why Philosophers Should Care About Computational Complexity

One might think that, once we know something is computable, how efficiently it can be computed is a practical question with little further philosophical importance. In this essay, I offer a detailed case that one would be wrong. In particular, I argue that computational complexity theory---the field that studies the resources (such as time, space, and randomness) needed to solve computational problems---leads to new perspectives on the nature of mathematical knowledge, the strong AI debate, computationalism, the problem of logical omniscience, Hume's problem of induction, Goodman's grue riddle, the foundations of quantum mechanics, economic rationality, closed timelike curves, and several other topics of philosophical interest. I end by discussing aspects of complexity theory itself that could benefit from philosophical analysis.Comment: 58 pages, to appear in "Computability: G\"odel, Turing, Church, and beyond," MIT Press, 2012. Some minor clarifications and corrections; new references adde

A Survey of Green Networking Research

Reduction of unnecessary energy consumption is becoming a major concern in wired networking, because of the potential economical benefits and of its expected environmental impact. These issues, usually referred to as "green networking", relate to embedding energy-awareness in the design, in the devices and in the protocols of networks. In this work, we first formulate a more precise definition of the "green" attribute. We furthermore identify a few paradigms that are the key enablers of energy-aware networking research. We then overview the current state of the art and provide a taxonomy of the relevant work, with a special focus on wired networking. At a high level, we identify four branches of green networking research that stem from different observations on the root causes of energy waste, namely (i) Adaptive Link Rate, (ii) Interface proxying, (iii) Energy-aware infrastructures and (iv) Energy-aware applications. In this work, we do not only explore specific proposals pertaining to each of the above branches, but also offer a perspective for research.Comment: Index Terms: Green Networking; Wired Networks; Adaptive Link Rate; Interface Proxying; Energy-aware Infrastructures; Energy-aware Applications. 18 pages, 6 figures, 2 table

Theoretical Engineering and Satellite Comlink of a PTVD-SHAM System

This paper focuses on super helical memory system's design, 'Engineering, Architectural and Satellite Communications' as a theoretical approach of an invention-model to 'store time-data'. The current release entails three concepts: 1- an in-depth theoretical physics engineering of the chip including its, 2- architectural concept based on VLSI methods, and 3- the time-data versus data-time algorithm. The 'Parallel Time Varying & Data Super-helical Access Memory' (PTVD-SHAM), possesses a waterfall effect in its architecture dealing with the process of voltage output-switch into diverse logic and quantum states described as 'Boolean logic & image-logic', respectively. Quantum dot computational methods are explained by utilizing coiled carbon nanotubes (CCNTs) and CNT field effect transistors (CNFETs) in the chip's architecture. Quantum confinement, categorized quantum well substrate, and B-field flux involvements are discussed in theory. Multi-access of coherent sequences of 'qubit addressing' in any magnitude, gained as pre-defined, here e.g., the 'big O notation' asymptotically confined into singularity while possessing a magnitude of 'infinity' for the orientation of array displacement. Gaussian curvature of k(k<0) is debated in aim of specifying the 2D electron gas characteristics, data storage system for defining short and long time cycles for different CCNT diameters where space-time continuum is folded by chance for the particle. Precise pre/post data timing for, e.g., seismic waves before earthquake mantle-reach event occurrence, including time varying self-clocking devices in diverse geographic locations for radar systems is illustrated in the Subsections of the paper. The theoretical fabrication process, electromigration between chip's components is discussed as well.Comment: 50 pages, 10 figures (3 multi-figures), 2 tables. v.1: 1 postulate entailing hypothetical ideas, design and model on future technological advances of PTVD-SHAM. The results of the previous paper [arXiv:0707.1151v6], are extended in order to prove some introductory conjectures in theoretical engineering advanced to architectural analysi

Parallel Lagrangian particle transport : application to respiratory system airways

This thesis is focused on particle transport in the context of high computing performance (HPC) in its widest range, from the numerical modeling to the physics involved, including its parallelization and post-process. The main goal is to obtain a general framework that enables understanding all the requirements and characteristics of particle transport using the Lagrangian frame of reference. Although the idea is to provide a suitable model for any engineering application that involves particle transport simulation, this thesis uses the respiratory system framework. This means that all the simulations are focused on this topic, including the benchmarks for testing, verifying and optimizing the results. Other applications, such as combustion, ocean residuals, or automotive, have also been simulated by other researchers using the same numerical model proposed here. However, they have not been included here in the interest of allowing the project to advance in a specific direction, and facilitate the structure and comprehension of this work. Human airways and respiratory system simulations are of special interest for medical purposes. Indeed, human airways can be significantly different in every individual. This complicates the study of drug delivery efficiency, deposition of polluted particles, etc., using classic in-vivo or in-vitro techniques. In other words, flow and deposition results may vary depending on the geometry of the patient and simulations allow customized studies using specific geometries. With the help of the new computational techniques, in the near future it may be possible to optimize nasal drugs delivery, surgery or other medical studies for each individual patient though a more personalized medicine. In summary, this thesis prioritizes numerical modeling, wide usability, performance, parallelization, and the study of the physics that affects particle transport. In addition, the simulation of the respiratory system should carry out interesting biological and medical results. However, the interpretation of these results will be only done from a pure numerical point of view.Aquesta tesi se centra en el transport de partícules dins el context de la computació d'alt rendiment (HPC), en el seu ventall més ampli; des del model numèric fins a la física involucrada, incloent-hi la part de paral·lelització del codi i de post-procés. L'objectiu principal és obtenir un esquema general que permeti entendre tant els requeriments com les característiques del transport de partícules fent servir el marc de referència Lagrangià. Encara que la idea sigui definir un model capaç¸ de simular qualsevol aplicació en el camp de l'enginyeria que involucri el transport de partícules, aquesta tesi utilitza el sistema respiratori com a temàtica de referència. Això significa que totes les simulacions estan emmarcades en aquest camp d'estudi, incloent-hi els tests de referència, verificacions i optimitzacions de resultats. L'estudi d'altres aplicacions, com ara la combustió, els residus oceànics, l'automoció o l'aeronàutica també han estat dutes a terme per altres investigadors utilitzant el mateix model numèric proposat aquí. Tot i així, aquests resultats no han estat inclosos en aquesta tesi per simplificar-la i avançar en una sola direcció; facilitant així l'estructura i millor comprensió d'aquest treball. Pel que fa al sistema respiratori humà i les seves simulacions, tenen especial interès per a propòsits mèdics. Particularment, la geometria dels conductes respiratoris pot variar de manera considerable en cada persona. Això complica l'estudi en aspectes com el subministrament de medicaments o la deposició de partícules contaminants, per exemple, utilitzant les tècniques clàssiques de laboratori (in-vivo o in-vitro). En altres paraules, tant el flux com la deposició poden canviar en funció de la geometria del pacient i aquí és on les simulacions permeten estudis adaptats a geometries concretes. Gràcies a les noves tècniques de computació, en un futur proper és probable que puguem optimitzar el subministrament de medicaments per via nasal, la cirurgia o altres estudis mèdics per a cada pacient mitjançant una medicina més personalitzada. En resum, aquesta tesi prioritza el model numèric, l'amplitud d'usos, el rendiment, la paral·lelització i l'estudi de la física que afecta directament a les partícules. A més, el fet de basar les nostres simulacions en el sistema respiratori dota aquesta tesi d'un interès biològic i mèdic pel que fa als resultats