Mesh traversal and sorting for efficient memory usage in scientific codes

Applications that operate on meshes are very popular in High Performance Computing (HPC) environments. In the past, many techniques have been developed in order to optimize the memory accesses for these datasets. Different loop transformations and domain decompositions are com- monly used for structured meshes. However, unstructured grids are more challenging. The memory accesses, based on the mesh connectivity, do not map well to the usual lin- ear memory model. This work presents a method to improve the memory performance which is suitable for HPC codes that operate on meshes. We develop a method to adjust the sequence in which the data are used inside the algorithm, by means of traversing and sorting the mesh. This sorted mesh can be transferred sequentially to the lower memory levels and allows for minimum data transfer requirements. The method also reduces the lower memory requirements dra- matically: up to 63% of the L1 cache misses are removed in a traditional cache system. We have obtained speedups of up to 2.58 on memory operations as measured in a general- purpose CPU. An improvement is also observed with se- quential access memories, where we have observed reduc- tions of up to 99% in the required low-level memory size.

A proposed two-stage two-tether scientific mission at Jupiter

A two-stage mission to place a spacecraft (SC) below the Jovian radiation belts, using a spinning bare tether with plasma contactors at both ends to provide propulsion and power,is proposed. Capture by Lorentz drag on the tether, at the periapsis of a barely hyperbolic equatorial orbit, is followed by a sequence of orbits at near-constant periapsis, drag finally bringing the SC down to a circular orbit below the halo ring. Although increasing both tether heating and bowing, retrograde motion can substantially reduce accumulated dose as compared with prograde motion, at equal tether-to-SC mass ratio. In the second stage,the tether is cut to a segment one order of magnitude smaller, with a single plasma contactor, making the SC to slowly spiral inward over severalmonths while generating large onboard power, which would allow multiple scientific applications, including in situ study of Jovian grains, auroral sounding of upper atmosphere, and space- and time-resolved observations of surface and subsurface.

Common motifs in scientific workflows: An empirical analysis

Workflow technology continues to play an important role as a means for specifying and enacting computational experiments in modern science. Reusing and re-purposing workflows allow scientists to do new experiments faster, since the workflows capture useful expertise from others. As workflow libraries grow, scientists face the challenge of finding workflows appropriate for their task, understanding what each workflow does, and reusing relevant portions of a given workflow.We believe that workflows would be easier to understand and reuse if high-level views (abstractions) of their activities were available in workflow libraries. As a first step towards obtaining these abstractions, we report in this paper on the results of a manual analysis performed over a set of real-world scientific workflows from Taverna, Wings, Galaxy and Vistrails. Our analysis has resulted in a set of scientific workflow motifs that outline (i) the kinds of data-intensive activities that are observed in workflows (Data-Operation motifs), and (ii) the different manners in which activities are implemented within workflows (Workflow-Oriented motifs). These motifs are helpful to identify the functionality of the steps in a given workflow, to develop best practices for workflow design, and to develop approaches for automated generation of workflow abstractions.

Frozen orbits for scientific missions using rotating tethers

We derive a semi-analytic formulation that permits to study the long-term dynamics of fast-rotating inert tethers around planetary satellites. Since space tethers are extensive bodies they generate non-keplerian gravitational forces which depend solely on their mass geometry and attitude, that can be exploited for controlling science orbits. We conclude that rotating tethers modify the geometry of frozen orbits, allowing for lower eccentricity frozen orbits for a wide range of orbital inclination, where the length of the tether becomes a new parameter that the mission analyst may use to shape frozen orbits to tighter operational constraints.

Entrevista a Eugene Garfield, director del Institute for Scientific Information (ISI) de Estados Unidos

El químico norteamericano Eugene Garfield es considerado por muchos investigadores como el "santón" de la documentación científica en el mundo. Bajo el prisma de Garfield y a través de publicaciones tan prestigiosas como "Current Contents" o "Science Citation Index", cualquier investigador puede conocer el índice de impacto que ha alcanzado su trabajo en la comunidad científica.

Vibrations loads in the process of designing scientific spacecraft payloads

Scientific missions constitute fundamental cornerstones of space agencies such as ESA and NASA. Modern astronomy could not be understood without the data provided by these missions. Scientists need to design very carefully onboard instruments. Payloads have to survive the crucial launch moment and later perform well in the really harsh space environ-ment. It is very important that the instrument conceptual idea can be engineered to sustain all those loads

Leveraging Semantics to Improve Reproducibility in Scientific Workflows

Reproducibility of published results is a cornerstone in scientific publishing and progress. Therefore, the scientific community has been encouraging authors and editors to publish their contributions in a verifiable and understandable way. Efforts such as the Reproducibility Initiative [1], or the Reproducibility Projects on Biology [2] and Psychology [3] domains, have been defining standards and patterns to assess whether an experimental result is reproducible.

Electrodynamic tether for scientific mission in low Jovian orbit

An electrodynamic bare tether is shown to allow carrying out scientific observations very close to Jupiter, for exploration of its surface and subsurface, and ionospheric and atmospheric in-situ measurements. Starting at a circular equatorial orbit of radius about 1.3/1.4 times the Jovian radius, continuous propellantless Lorentz drag on a thin-tape tether in the 1-5 km length range would make a spacecraft many times as heavy as the tape slowly spiral in, over a period of many months, while generating power at a load plugged in the tether circuit for powering instruments in science data acquisition and transmission. Lying under the Jovian radiation belts, the tape would avoid the most severe problem facing tethers in Jupiter, which are capable of producing both power and propulsion but, operating slowly, could otherwise accumulate too high a radiation dose . The tether would be made to spin in its orbit to keep taut; how to balance the Lorentz torque is discussed. Constraints on heating and bowing are also discussed, comparing conditions for prograde versus retrograde orbits. The system adapts well to the moderate changes in plasma density and motional electric field through the limited radial range in their steep gradients near Jupiter.

Experimental investigation of radio signal propagation in scientific facilities for telerobotic applications

Understanding the radio signal transmission characteristics in the environment where the telerobotic application is sought is a key part of achieving a reliable wireless communication link between a telerobot and a control station. In this paper, wireless communication requirements and a case study of a typical telerobotic application in an underground facility at CERN are presented. Then, the theoretical and experimental characteristics of radio propagation are investigated with respect to time, distance, location and surrounding objects. Based on analysis of the experimental findings, we show how a commercial wireless system, such as Wi-Fi, can be made suitable for a case study application at CERN.

Task-based telemanipulation for maintenance in large scientific facilities

This thesis presents a task-oriented approach to telemanipulation for maintenance in large scientific facilities, with specific focus on the particle accelerator facilities at European Organization for Nuclear Research (CERN) in Geneva, Switzerland and GSI Helmholtz Centre for Heavy Ion Research (GSI) in Darmstadt, Germany. It examines how telemanipulation can be used in these facilities and reviews how this differs from the representation of telemanipulation tasks within the literature. It provides methods to assess and compare telemanipulation procedures as well a test suite to compare telemanipulators themselves from a dexterity perspective. It presents a formalisation of telemanipulation procedures into a hierarchical model which can be then used as a basis to aid maintenance engineers in assessing tasks for telemanipulation, and as the basis for future research. The model introduces a new concept of Elemental Actions as the building block of telemanipulation movements and incorporates the dependent factors for procedures at a higher level of abstraction. In order to gain insight into realistic tasks performed by telemanipulation systems within both industrial and research environments a survey of teleoperation experts is presented. Analysis of the responses is performed from which it is concluded that there is a need within the robotics community for physical benchmarking tests which are geared towards evaluating the dexterity of telemanipulators for comparison of their dexterous abilities. A three stage test suite is presented which is designed to allow maintenance engineers to assess different telemanipulators for their dexterity. This incorporates general characteristics of the system, a method to compare kinematic reachability of multiple telemanipulators and physical test setups to assess dexterity from a both a qualitative perspective and measurably by using performance metrics. Finally, experimental results are provided for the application of the proposed test suite onto two telemanipulation systems, one from a research setting and the other within CERN. It describes the procedure performed and discusses comparisons between the two systems, as well as providing input from the expert operator of the CERN system.

Rocks are human beings: researching the humanizing metaphor in earth science scientific texts

This paper describes a corpus-based analysis of the humanizing metaphor and supports that constitutive metaphor in science and technology may be highly metaphorical and active. The study, grounded in Lakoff’s Theory of Metaphor and in Langacker’s relational networks, consists of two phases: firstly, Earth Science metaphorical terms were extracted from databases and dictionaries and, then, contextualized by means of the “Wordsmith” tool in a digitalized corpus created to establish their productivity. Secondly, the terms were classified to disclose the main conceptual metaphors underlying them; then, the mappings and the relational networks of the metaphor were described. Results confirm the systematicity and productivity of the metaphor in this field, show evidence that metaphoricity of scientific terms is gradable, and support that Earth Science metaphors are not only created in terms of their concrete salient properties and attributes, but also on abstract human anthropocentric projections.

Rhetorical purpose and the use of definitions as a coherence device in scientific communication

Se analiza la función de las definiciones en los textos científicos como elemento esencial para crear coherencia y dotar de comprensibilidad al texto. Se presentan varios ejemplos en textos de divulgación y en artículos dirigidos a pares.

FragFlow: automated fragment detection in scientific workflows

Scientific workflows provide the means to define, execute and reproduce computational experiments. However, reusing existing workflows still poses challenges for workflow designers. Workflows are often too large and too specific to reuse in their entirety, so reuse is more likely to happen for fragments of workflows. These fragments may be identified manually by users as sub-workflows, or detected automatically. In this paper we present the FragFlow approach, which detects workflow fragments automatically by analyzing existing workflow corpora with graph mining algorithms. FragFlow detects the most common workflow fragments, links them to the original workflows and visualizes them. We evaluate our approach by comparing FragFlow results against user-defined sub-workflows from three different corpora of the LONI Pipeline system. Based on this evaluation, we discuss how automated workflow fragment detection could facilitate workflow reuse.

A semantic-based approach to attain reproducibility of computational environments in scientific workflows: a case study

Reproducible research in scientific workflows is often addressed by tracking the provenance of the produced results. While this approach allows inspecting intermediate and final results, improves understanding, and permits replaying a workflow execution, it does not ensure that the computational environment is available for subsequent executions to reproduce the experiment. In this work, we propose describing the resources involved in the execution of an experiment using a set of semantic vocabularies, so as to conserve the computational environment. We define a process for documenting the workflow application, management system, and their dependencies based on 4 domain ontologies. We then conduct an experimental evaluation using a real workflow application on an academic and a public Cloud platform. Results show that our approach can reproduce an equivalent execution environment of a predefined virtual machine image on both computing platforms.

Mining Abstractions in Scientific Workows

Los flujos de trabajo científicos han sido adoptados durante la última década para representar los métodos computacionales utilizados en experimentos in silico, así como para dar soporte a sus publicaciones asociadas. Dichos flujos de trabajo han demostrado ser útiles para compartir y reproducir experimentos científicos, permitiendo a investigadores visualizar, depurar y ahorrar tiempo a la hora de re-ejecutar un trabajo realizado con anterioridad. Sin embargo, los flujos de trabajo científicos pueden ser en ocasiones difíciles de entender y reutilizar. Esto es debido a impedimentos como el gran número de flujos de trabajo existentes en repositorios, su heterogeneidad o la falta generalizada de documentación y ejemplos de uso. Además, dado que normalmente es posible implementar un mismo método utilizando algoritmos o técnicas distintas, flujos de trabajo aparentemente distintos pueden estar relacionados a un determinado nivel de abstracción, basándose, por ejemplo, en su funcionalidad común. Esta tesis se centra en la reutilización de flujos de trabajo y su abstracción mediante la exploración de relaciones entre los flujos de trabajo de un repositorio y la extracción de abstracciones que podrían ayudar a la hora de reutilizar otros flujos de trabajo existentes. Para ello, se propone un modelo simple de representación de flujos de trabajo y sus ejecuciones, se analizan las abstracciones típicas que se pueden encontrar en los repositorios de flujos de trabajo, se exploran las prácticas habituales de los usuarios a la hora de reutilizar flujos de trabajo existentes y se describe un método para descubrir abstracciones útiles para usuarios, basadas en técnicas existentes de teoría de grafos. Los resultados obtenidos exponen las abstracciones y prácticas comunes de usuarios en términos de reutilización de flujos de trabajo, y muestran cómo las abstracciones que se extraen automáticamente tienen potencial para ser reutilizadas por usuarios que buscan diseñar nuevos flujos de trabajo. Abstract Scientific workflows have been adopted in the last decade to represent the computational methods used in in silico scientific experiments and their associated research products. Scientific workflows have demonstrated to be useful for sharing and reproducing scientific experiments, allowing scientists to visualize, debug and save time when re-executing previous work. However, scientific workflows may be difficult to understand and reuse. The large amount of available workflows in repositories, together with their heterogeneity and lack of documentation and usage examples may become an obstacle for a scientist aiming to reuse the work from other scientists. Furthermore, given that it is often possible to implement a method using different algorithms or techniques, seemingly disparate workflows may be related at a higher level of abstraction, based on their common functionality. In this thesis we address the issue of reusability and abstraction by exploring how workflows relate to one another in a workflow repository, mining abstractions that may be helpful for workflow reuse. In order to do so, we propose a simple model for representing and relating workflows and their executions, we analyze the typical common abstractions that can be found in workflow repositories, we explore the current practices of users regarding workflow reuse and we describe a method for discovering useful abstractions for workflows based on existing graph mining techniques. Our results expose the common abstractions and practices of users in terms of workflow reuse, and show how our proposed abstractions have potential to become useful for users designing new workflows.