17,927 research outputs found
The LifeV library: engineering mathematics beyond the proof of concept
LifeV is a library for the finite element (FE) solution of partial
differential equations in one, two, and three dimensions. It is written in C++
and designed to run on diverse parallel architectures, including cloud and high
performance computing facilities. In spite of its academic research nature,
meaning a library for the development and testing of new methods, one
distinguishing feature of LifeV is its use on real world problems and it is
intended to provide a tool for many engineering applications. It has been
actually used in computational hemodynamics, including cardiac mechanics and
fluid-structure interaction problems, in porous media, ice sheets dynamics for
both forward and inverse problems. In this paper we give a short overview of
the features of LifeV and its coding paradigms on simple problems. The main
focus is on the parallel environment which is mainly driven by domain
decomposition methods and based on external libraries such as MPI, the Trilinos
project, HDF5 and ParMetis.
Dedicated to the memory of Fausto Saleri.Comment: Review of the LifeV Finite Element librar
AiiDA: Automated Interactive Infrastructure and Database for Computational Science
Computational science has seen in the last decades a spectacular rise in the
scope, breadth, and depth of its efforts. Notwithstanding this prevalence and
impact, it is often still performed using the renaissance model of individual
artisans gathered in a workshop, under the guidance of an established
practitioner. Great benefits could follow instead from adopting concepts and
tools coming from computer science to manage, preserve, and share these
computational efforts. We illustrate here our paradigm sustaining such vision,
based around the four pillars of Automation, Data, Environment, and Sharing. We
then discuss its implementation in the open-source AiiDA platform
(http://www.aiida.net), that has been tuned first to the demands of
computational materials science. AiiDA's design is based on directed acyclic
graphs to track the provenance of data and calculations, and ensure
preservation and searchability. Remote computational resources are managed
transparently, and automation is coupled with data storage to ensure
reproducibility. Last, complex sequences of calculations can be encoded into
scientific workflows. We believe that AiiDA's design and its sharing
capabilities will encourage the creation of social ecosystems to disseminate
codes, data, and scientific workflows.Comment: 30 pages, 7 figure
REST API to Access and Manage Geospatial Pipeline Integrity Data
Today’s economy and infrastructure is dependent on raw natural resources, like crude oil and natural gases, that are optimally transported through a net- work of hundreds of thousands of miles of pipelines throughout America[28]. A damaged pipe can negatively a↵ect thousands of homes and businesses so it is vital that they are monitored and quickly repaired[1]. Ideally, pipeline operators are able to detect damages before they occur, but ensuring the in- tegrity of the vast amount of pipes is unrealistic and would take an impractical amount of time and manpower[1].
Natural disasters, like earthquakes, as well as construction are just two of the events that could potentially threaten the integrity of pipelines. Due to the diverse collection of data sources, the necessary geospatial data is scat- tered across di↵erent physical locations, stored in di↵erent formats, and owned by di↵erent organizations. Pipeline companies do not have the resources to manually gather all input factors to make a meaningful analysis of the land surrounding a pipe.
Our solution to this problem involves creating a single, centralized system that can be queried to get all necessary geospatial data and related informa- tion in a standardized and desirable format. The service simplifies client-side computation time by allowing our system to find, ingest, parse, and store the data from potentially hundreds of repositories in varying formats. An online web service fulfills all of the requirements and allows for easy remote access to do critical analysis of the data through computer based decision support systems (DSS).
Our system, REST API for Pipeline Integrity Data (RAPID), is a multi- tenant REST API that utilizes HTTP protocol to provide a online and intuitive set of functions for DSS. RAPID’s API allows DSS to access and manage data stored in a geospatial database with a supported Django web framework. Full documentation of the design and implementation of RAPID’s API are detailed in this thesis document, supplemented with some background and validation of the completed system
The Topology ToolKit
This system paper presents the Topology ToolKit (TTK), a software platform
designed for topological data analysis in scientific visualization. TTK
provides a unified, generic, efficient, and robust implementation of key
algorithms for the topological analysis of scalar data, including: critical
points, integral lines, persistence diagrams, persistence curves, merge trees,
contour trees, Morse-Smale complexes, fiber surfaces, continuous scatterplots,
Jacobi sets, Reeb spaces, and more. TTK is easily accessible to end users due
to a tight integration with ParaView. It is also easily accessible to
developers through a variety of bindings (Python, VTK/C++) for fast prototyping
or through direct, dependence-free, C++, to ease integration into pre-existing
complex systems. While developing TTK, we faced several algorithmic and
software engineering challenges, which we document in this paper. In
particular, we present an algorithm for the construction of a discrete gradient
that complies to the critical points extracted in the piecewise-linear setting.
This algorithm guarantees a combinatorial consistency across the topological
abstractions supported by TTK, and importantly, a unified implementation of
topological data simplification for multi-scale exploration and analysis. We
also present a cached triangulation data structure, that supports time
efficient and generic traversals, which self-adjusts its memory usage on demand
for input simplicial meshes and which implicitly emulates a triangulation for
regular grids with no memory overhead. Finally, we describe an original
software architecture, which guarantees memory efficient and direct accesses to
TTK features, while still allowing for researchers powerful and easy bindings
and extensions. TTK is open source (BSD license) and its code, online
documentation and video tutorials are available on TTK's website
DAMEWARE - Data Mining & Exploration Web Application Resource
Astronomy is undergoing through a methodological revolution triggered by an
unprecedented wealth of complex and accurate data. DAMEWARE (DAta Mining &
Exploration Web Application and REsource) is a general purpose, Web-based,
Virtual Observatory compliant, distributed data mining framework specialized in
massive data sets exploration with machine learning methods. We present the
DAMEWARE (DAta Mining & Exploration Web Application REsource) which allows the
scientific community to perform data mining and exploratory experiments on
massive data sets, by using a simple web browser. DAMEWARE offers several tools
which can be seen as working environments where to choose data analysis
functionalities such as clustering, classification, regression, feature
extraction etc., together with models and algorithms.Comment: User Manual of the DAMEWARE Web Application, 51 page
The space physics environment data analysis system (SPEDAS)
With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform (www.spedas.org), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have “crib-sheets,” user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer’s Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its “modes of use” with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans.Published versio
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