Privacy and the National Information Infrastructure.

ERIC Educational Resources Information Center

Rotenberg, Marc

1994-01-01

Explains the work of Computer Professionals for Social Responsibility regarding privacy issues in the use of electronic networks; recommends principles that should be adopted for a National Information Infrastructure privacy code; discusses the need for public education; and suggests pertinent legislative proposals. (LRW)

Effecting IT infrastructure culture change: management by processes and metrics

NASA Technical Reports Server (NTRS)

Miller, R. L.

2001-01-01

This talk describes the processes and metrics used by Jet Propulsion Laboratory to bring about the required IT infrastructure culture change to update and certify, as Y2K compliant, thousands of computers and millions of lines of code.

Computational Infrastructure for Geodynamics (CIG)

NASA Astrophysics Data System (ADS)

Gurnis, M.; Kellogg, L. H.; Bloxham, J.; Hager, B. H.; Spiegelman, M.; Willett, S.; Wysession, M. E.; Aivazis, M.

2004-12-01

Solid earth geophysicists have a long tradition of writing scientific software to address a wide range of problems. In particular, computer simulations came into wide use in geophysics during the decade after the plate tectonic revolution. Solution schemes and numerical algorithms that developed in other areas of science, most notably engineering, fluid mechanics, and physics, were adapted with considerable success to geophysics. This software has largely been the product of individual efforts and although this approach has proven successful, its strength for solving problems of interest is now starting to show its limitations as we try to share codes and algorithms or when we want to recombine codes in novel ways to produce new science. With funding from the NSF, the US community has embarked on a Computational Infrastructure for Geodynamics (CIG) that will develop, support, and disseminate community-accessible software for the greater geodynamics community from model developers to end-users. The software is being developed for problems involving mantle and core dynamics, crustal and earthquake dynamics, magma migration, seismology, and other related topics. With a high level of community participation, CIG is leveraging state-of-the-art scientific computing into a suite of open-source tools and codes. The infrastructure that we are now starting to develop will consist of: (a) a coordinated effort to develop reusable, well-documented and open-source geodynamics software; (b) the basic building blocks - an infrastructure layer - of software by which state-of-the-art modeling codes can be quickly assembled; (c) extension of existing software frameworks to interlink multiple codes and data through a superstructure layer; (d) strategic partnerships with the larger world of computational science and geoinformatics; and (e) specialized training and workshops for both the geodynamics and broader Earth science communities. The CIG initiative has already started to leverage and develop long-term strategic partnerships with open source development efforts within the larger thrusts of scientific computing and geoinformatics. These strategic partnerships are essential as the frontier has moved into multi-scale and multi-physics problems in which many investigators now want to use simulation software for data interpretation, data assimilation, and hypothesis testing.

Testing of SWMM Model’s LID Modules

EPA Science Inventory

EPA’s Storm Water Management Model (SWMM) is a computational code heavily relied upon by industry for the simulation of wastewater and stormwater infrastructure performance to . design and build multi-billion-dollar, multi-decade infrastructure upgrades. Since the 1970’s, EPA a...

Computer codes developed and under development at Lewis

NASA Technical Reports Server (NTRS)

Chamis, Christos C.

1992-01-01

The objective of this summary is to provide a brief description of: (1) codes developed or under development at LeRC; and (2) the development status of IPACS with some typical early results. The computer codes that have been developed and/or are under development at LeRC are listed in the accompanying charts. This list includes: (1) the code acronym; (2) select physics descriptors; (3) current enhancements; and (4) present (9/91) code status with respect to its availability and documentation. The computer codes list is grouped by related functions such as: (1) composite mechanics; (2) composite structures; (3) integrated and 3-D analysis; (4) structural tailoring; and (5) probabilistic structural analysis. These codes provide a broad computational simulation infrastructure (technology base-readiness) for assessing the structural integrity/durability/reliability of propulsion systems. These codes serve two other very important functions: they provide an effective means of technology transfer; and they constitute a depository of corporate memory.

AlgoRun: a Docker-based packaging system for platform-agnostic implemented algorithms.

PubMed

Hosny, Abdelrahman; Vera-Licona, Paola; Laubenbacher, Reinhard; Favre, Thibauld

2016-08-01

There is a growing need in bioinformatics for easy-to-use software implementations of algorithms that are usable across platforms. At the same time, reproducibility of computational results is critical and often a challenge due to source code changes over time and dependencies. The approach introduced in this paper addresses both of these needs with AlgoRun, a dedicated packaging system for implemented algorithms, using Docker technology. Implemented algorithms, packaged with AlgoRun, can be executed through a user-friendly interface directly from a web browser or via a standardized RESTful web API to allow easy integration into more complex workflows. The packaged algorithm includes the entire software execution environment, thereby eliminating the common problem of software dependencies and the irreproducibility of computations over time. AlgoRun-packaged algorithms can be published on http://algorun.org, a centralized searchable directory to find existing AlgoRun-packaged algorithms. AlgoRun is available at http://algorun.org and the source code under GPL license is available at https://github.com/algorun laubenbacher@uchc.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Automatically generated code for relativistic inhomogeneous cosmologies

NASA Astrophysics Data System (ADS)

Bentivegna, Eloisa

2017-02-01

The applications of numerical relativity to cosmology are on the rise, contributing insight into such cosmological problems as structure formation, primordial phase transitions, gravitational-wave generation, and inflation. In this paper, I present the infrastructure for the computation of inhomogeneous dust cosmologies which was used recently to measure the effect of nonlinear inhomogeneity on the cosmic expansion rate. I illustrate the code's architecture, provide evidence for its correctness in a number of familiar cosmological settings, and evaluate its parallel performance for grids of up to several billion points. The code, which is available as free software, is based on the Einstein Toolkit infrastructure, and in particular leverages the automated code generation capabilities provided by its component Kranc.

Sharing the Code.

ERIC Educational Resources Information Center

Olsen, Florence

2003-01-01

Colleges and universities are beginning to consider collaborating on open-source-code projects as a way to meet critical software and computing needs. Points out the attractive features of noncommercial open-source software and describes some examples in use now, especially for the creation of Web infrastructure. (SLD)

Resilient workflows for computational mechanics platforms

NASA Astrophysics Data System (ADS)

Nguyên, Toàn; Trifan, Laurentiu; Désidéri, Jean-Antoine

2010-06-01

Workflow management systems have recently been the focus of much interest and many research and deployment for scientific applications worldwide [26, 27]. Their ability to abstract the applications by wrapping application codes have also stressed the usefulness of such systems for multidiscipline applications [23, 24]. When complex applications need to provide seamless interfaces hiding the technicalities of the computing infrastructures, their high-level modeling, monitoring and execution functionalities help giving production teams seamless and effective facilities [25, 31, 33]. Software integration infrastructures based on programming paradigms such as Python, Mathlab and Scilab have also provided evidence of the usefulness of such approaches for the tight coupling of multidisciplne application codes [22, 24]. Also high-performance computing based on multi-core multi-cluster infrastructures open new opportunities for more accurate, more extensive and effective robust multi-discipline simulations for the decades to come [28]. This supports the goal of full flight dynamics simulation for 3D aircraft models within the next decade, opening the way to virtual flight-tests and certification of aircraft in the future [23, 24, 29].

Alternative Fuels Data Center: Codes and Standards Resources

Science.gov Websites

codes and standards. Biodiesel Vehicle and Infrastructure Codes and Standards Chart Electric Vehicle and Infrastructure Codes and Standards Chart Ethanol Vehicle and Infrastructure Codes and Standards Chart Natural Gas Vehicle and Infrastructure Codes and Standards Chart Propane Vehicle and Infrastructure Codes and

A Clinician-Centered Evaluation of the Usability of AHLTA and Automated Clinical Practice Guidelines at TAMC

DTIC Science & Technology

2011-03-31

evidence based medicine into clinical practice. It will decrease costs and enable multiple stakeholders to work in an open content/source environment to exchange clinical content, develop and test technology and explore processes in applied CDS. Design: Comparative study between the KMR infrastructure and capabilities developed as an open source, vendor agnostic solution for aCPG execution within AHLTA and the current DoD/MHS standard evaluating: H1: An open source, open standard KMR and Clinical Decision Support Engine can enable organizations to share domain

Computationally-Predicted AOPs and Systems Toxicology

EPA Science Inventory

The Adverse Outcome Pathway has emerged as an internationally harmonized mechanism for organizing biological information in a chemical agnostic manner. This construct is valuable for interpreting the results from high-throughput toxicity (HTT) assessment by providing a mechanisti...

Optimization and parallelization of the thermal–hydraulic subchannel code CTF for high-fidelity multi-physics applications

DOE PAGES

Salko, Robert K.; Schmidt, Rodney C.; Avramova, Maria N.

2014-11-23

This study describes major improvements to the computational infrastructure of the CTF subchannel code so that full-core, pincell-resolved (i.e., one computational subchannel per real bundle flow channel) simulations can now be performed in much shorter run-times, either in stand-alone mode or as part of coupled-code multi-physics calculations. These improvements support the goals of the Department Of Energy Consortium for Advanced Simulation of Light Water Reactors (CASL) Energy Innovation Hub to develop high fidelity multi-physics simulation tools for nuclear energy design and analysis.

The Jupyter/IPython architecture: a unified view of computational research, from interactive exploration to communication and publication.

NASA Astrophysics Data System (ADS)

Ragan-Kelley, M.; Perez, F.; Granger, B.; Kluyver, T.; Ivanov, P.; Frederic, J.; Bussonnier, M.

2014-12-01

IPython has provided terminal-based tools for interactive computing in Python since 2001. The notebook document format and multi-process architecture introduced in 2011 have expanded the applicable scope of IPython into teaching, presenting, and sharing computational work, in addition to interactive exploration. The new architecture also allows users to work in any language, with implementations in Python, R, Julia, Haskell, and several other languages. The language agnostic parts of IPython have been renamed to Jupyter, to better capture the notion that a cross-language design can encapsulate commonalities present in computational research regardless of the programming language being used. This architecture offers components like the web-based Notebook interface, that supports rich documents that combine code and computational results with text narratives, mathematics, images, video and any media that a modern browser can display. This interface can be used not only in research, but also for publication and education, as notebooks can be converted to a variety of output formats, including HTML and PDF. Recent developments in the Jupyter project include a multi-user environment for hosting notebooks for a class or research group, a live collaboration notebook via Google Docs, and better support for languages other than Python.

UNH Data Cooperative: A Cyber Infrastructure for Earth System Studies

NASA Astrophysics Data System (ADS)

Braswell, B. H.; Fekete, B. M.; Prusevich, A.; Gliden, S.; Magill, A.; Vorosmarty, C. J.

2007-12-01

Earth system scientists and managers have a continuously growing demand for a wide array of earth observations derived from various data sources including (a) modern satellite retrievals, (b) "in-situ" records, (c) various simulation outputs, and (d) assimilated data products combining model results with observational records. The sheer quantity of data, and formatting inconsistencies make it difficult for users to take full advantage of this important information resource. Thus the system could benefit from a thorough retooling of our current data processing procedures and infrastructure. Emerging technologies, like OPeNDAP and OGC map services, open standard data formats (NetCDF, HDF) data cataloging systems (NASA-Echo, Global Change Master Directory, etc.) are providing the basis for a new approach in data management and processing, where web- services are increasingly designed to serve computer-to-computer communications without human interactions and complex analysis can be carried out over distributed computer resources interconnected via cyber infrastructure. The UNH Earth System Data Collaborative is designed to utilize the aforementioned emerging web technologies to offer new means of access to earth system data. While the UNH Data Collaborative serves a wide array of data ranging from weather station data (Climate Portal) to ocean buoy records and ship tracks (Portsmouth Harbor Initiative) to land cover characteristics, etc. the underlaying data architecture shares common components for data mining and data dissemination via web-services. Perhaps the most unique element of the UNH Data Cooperative's IT infrastructure is its prototype modeling environment for regional ecosystem surveillance over the Northeast corridor, which allows the integration of complex earth system model components with the Cooperative's data services. While the complexity of the IT infrastructure to perform complex computations is continuously increasing, scientists are often forced to spend considerable amount of time to solve basic data management and preprocessing tasks and deal with low level computational design problems like parallelization of model codes. Our modeling infrastructure is designed to take care the bulk of the common tasks found in complex earth system models like I/O handling, computational domain and time management, parallel execution of the modeling tasks, etc. The modeling infrastructure allows scientists to focus on the numerical implementation of the physical processes on a single computational objects(typically grid cells) while the framework takes care of the preprocessing of input data, establishing of the data exchange between computation objects and the execution of the science code. In our presentation, we will discuss the key concepts of our modeling infrastructure. We will demonstrate integration of our modeling framework with data services offered by the UNH Earth System Data Collaborative via web interfaces. We will layout the road map to turn our prototype modeling environment into a truly community framework for wide range of earth system scientists and environmental managers.

New algorithm for tensor contractions on multi-core CPUs, GPUs, and accelerators enables CCSD and EOM-CCSD calculations with over 1000 basis functions on a single compute node.

PubMed

Kaliman, Ilya A; Krylov, Anna I

2017-04-30

A new hardware-agnostic contraction algorithm for tensors of arbitrary symmetry and sparsity is presented. The algorithm is implemented as a stand-alone open-source code libxm. This code is also integrated with general tensor library libtensor and with the Q-Chem quantum-chemistry package. An overview of the algorithm, its implementation, and benchmarks are presented. Similarly to other tensor software, the algorithm exploits efficient matrix multiplication libraries and assumes that tensors are stored in a block-tensor form. The distinguishing features of the algorithm are: (i) efficient repackaging of the individual blocks into large matrices and back, which affords efficient graphics processing unit (GPU)-enabled calculations without modifications of higher-level codes; (ii) fully asynchronous data transfer between disk storage and fast memory. The algorithm enables canonical all-electron coupled-cluster and equation-of-motion coupled-cluster calculations with single and double substitutions (CCSD and EOM-CCSD) with over 1000 basis functions on a single quad-GPU machine. We show that the algorithm exhibits predicted theoretical scaling for canonical CCSD calculations, O(N 6 ), irrespective of the data size on disk. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

A Framework for Debugging Geoscience Projects in a High Performance Computing Environment

NASA Astrophysics Data System (ADS)

Baxter, C.; Matott, L.

2012-12-01

High performance computing (HPC) infrastructure has become ubiquitous in today's world with the emergence of commercial cloud computing and academic supercomputing centers. Teams of geoscientists, hydrologists and engineers can take advantage of this infrastructure to undertake large research projects - for example, linking one or more site-specific environmental models with soft computing algorithms, such as heuristic global search procedures, to perform parameter estimation and predictive uncertainty analysis, and/or design least-cost remediation systems. However, the size, complexity and distributed nature of these projects can make identifying failures in the associated numerical experiments using conventional ad-hoc approaches both time- consuming and ineffective. To address these problems a multi-tiered debugging framework has been developed. The framework allows for quickly isolating and remedying a number of potential experimental failures, including: failures in the HPC scheduler; bugs in the soft computing code; bugs in the modeling code; and permissions and access control errors. The utility of the framework is demonstrated via application to a series of over 200,000 numerical experiments involving a suite of 5 heuristic global search algorithms and 15 mathematical test functions serving as cheap analogues for the simulation-based optimization of pump-and-treat subsurface remediation systems.

SWMM LID Module Validation Study

EPA Science Inventory

EPA’s Storm Water Management Model (SWMM) is a computational code heavily relied upon by industry for the simulation of wastewater and stormwater infrastructure performance. Many municipalities are relying on SWMM results to design multi-billion-dollar, multi-decade infrastructu...

Fermion-to-qubit mappings with varying resource requirements for quantum simulation

NASA Astrophysics Data System (ADS)

Steudtner, Mark; Wehner, Stephanie

2018-06-01

The mapping of fermionic states onto qubit states, as well as the mapping of fermionic Hamiltonian into quantum gates enables us to simulate electronic systems with a quantum computer. Benefiting the understanding of many-body systems in chemistry and physics, quantum simulation is one of the great promises of the coming age of quantum computers. Interestingly, the minimal requirement of qubits for simulating Fermions seems to be agnostic of the actual number of particles as well as other symmetries. This leads to qubit requirements that are well above the minimal requirements as suggested by combinatorial considerations. In this work, we develop methods that allow us to trade-off qubit requirements against the complexity of the resulting quantum circuit. We first show that any classical code used to map the state of a fermionic Fock space to qubits gives rise to a mapping of fermionic models to quantum gates. As an illustrative example, we present a mapping based on a nonlinear classical error correcting code, which leads to significant qubit savings albeit at the expense of additional quantum gates. We proceed to use this framework to present a number of simpler mappings that lead to qubit savings with a more modest increase in gate difficulty. We discuss the role of symmetries such as particle conservation, and savings that could be obtained if an experimental platform could easily realize multi-controlled gates.

Automated and Assistive Tools for Accelerated Code migration of Scientific Computing on to Heterogeneous MultiCore Systems

DTIC Science & Technology

2017-04-13

modelling code, a parallel benchmark , and a communication avoiding version of the QR algorithm. Further, several improvements to the OmpSs model were...movement; and a port of the dynamic load balancing library to OmpSs. Finally, several updates to the tools infrastructure were accomplished, including: an...OmpSs: a basic algorithm on image processing applications, a mini application representative of an ocean modelling code, a parallel benchmark , and a

Verification and Validation: High Charge and Energy (HZE) Transport Codes and Future Development

NASA Technical Reports Server (NTRS)

Wilson, John W.; Tripathi, Ram K.; Mertens, Christopher J.; Blattnig, Steve R.; Clowdsley, Martha S.; Cucinotta, Francis A.; Tweed, John; Heinbockel, John H.; Walker, Steven A.; Nealy, John E.

2005-01-01

In the present paper, we give the formalism for further developing a fully three-dimensional HZETRN code using marching procedures but also development of a new Green's function code is discussed. The final Green's function code is capable of not only validation in the space environment but also in ground based laboratories with directed beams of ions of specific energy and characterized with detailed diagnostic particle spectrometer devices. Special emphasis is given to verification of the computational procedures and validation of the resultant computational model using laboratory and spaceflight measurements. Due to historical requirements, two parallel development paths for computational model implementation using marching procedures and Green s function techniques are followed. A new version of the HZETRN code capable of simulating HZE ions with either laboratory or space boundary conditions is under development. Validation of computational models at this time is particularly important for President Bush s Initiative to develop infrastructure for human exploration with first target demonstration of the Crew Exploration Vehicle (CEV) in low Earth orbit in 2008.

Parallel Processing of Images in Mobile Devices using BOINC

NASA Astrophysics Data System (ADS)

Curiel, Mariela; Calle, David F.; Santamaría, Alfredo S.; Suarez, David F.; Flórez, Leonardo

2018-04-01

Medical image processing helps health professionals make decisions for the diagnosis and treatment of patients. Since some algorithms for processing images require substantial amounts of resources, one could take advantage of distributed or parallel computing. A mobile grid can be an adequate computing infrastructure for this problem. A mobile grid is a grid that includes mobile devices as resource providers. In a previous step of this research, we selected BOINC as the infrastructure to build our mobile grid. However, parallel processing of images in mobile devices poses at least two important challenges: the execution of standard libraries for processing images and obtaining adequate performance when compared to desktop computers grids. By the time we started our research, the use of BOINC in mobile devices also involved two issues: a) the execution of programs in mobile devices required to modify the code to insert calls to the BOINC API, and b) the division of the image among the mobile devices as well as its merging required additional code in some BOINC components. This article presents answers to these four challenges.

Managing Scientific Software Complexity with Bocca and CCA

DOE PAGES

Allan, Benjamin A.; Norris, Boyana; Elwasif, Wael R.; ...

2008-01-01

In high-performance scientific software development, the emphasis is often on short time to first solution. Even when the development of new components mostly reuses existing components or libraries and only small amounts of new code must be created, dealing with the component glue code and software build processes to obtain complete applications is still tedious and error-prone. Component-based software meant to reduce complexity at the application level increases complexity to the extent that the user must learn and remember the interfaces and conventions of the component model itself. To address these needs, we introduce Bocca, the first tool to enablemore » application developers to perform rapid component prototyping while maintaining robust software-engineering practices suitable to HPC environments. Bocca provides project management and a comprehensive build environment for creating and managing applications composed of Common Component Architecture components. Of critical importance for high-performance computing (HPC) applications, Bocca is designed to operate in a language-agnostic way, simultaneously handling components written in any of the languages commonly used in scientific applications: C, C++, Fortran, Python and Java. Bocca automates the tasks related to the component glue code, freeing the user to focus on the scientific aspects of the application. Bocca embraces the philosophy pioneered by Ruby on Rails for web applications: start with something that works, and evolve it to the user's purpose.« less

Expanding capacity and promoting inclusion in introductory computer science: a focus on near-peer mentor preparation and code review

NASA Astrophysics Data System (ADS)

Pon-Barry, Heather; Packard, Becky Wai-Ling; St. John, Audrey

2017-01-01

A dilemma within computer science departments is developing sustainable ways to expand capacity within introductory computer science courses while remaining committed to inclusive practices. Training near-peer mentors for peer code review is one solution. This paper describes the preparation of near-peer mentors for their role, with a focus on regular, consistent feedback via peer code review and inclusive pedagogy. Introductory computer science students provided consistently high ratings of the peer mentors' knowledge, approachability, and flexibility, and credited peer mentor meetings for their strengthened self-efficacy and understanding. Peer mentors noted the value of videotaped simulations with reflection, discussions of inclusion, and the cohort's weekly practicum for improving practice. Adaptations of peer mentoring for different types of institutions are discussed. Computer science educators, with hopes of improving the recruitment and retention of underrepresented groups, can benefit from expanding their peer support infrastructure and improving the quality of peer mentor preparation.

New Features in the Computational Infrastructure for Nuclear Astrophysics

NASA Astrophysics Data System (ADS)

Smith, M. S.; Lingerfelt, E. J.; Scott, J. P.; Hix, W. R.; Nesaraja, C. D.; Koura, H.; Roberts, L. F.

2006-04-01

The Computational Infrastructure for Nuclear Astrophysics is a suite of computer codes online at nucastrodata.org that streamlines the incorporation of recent nuclear physics results into astrophysical simulations. The freely-available, cross- platform suite enables users to upload cross sections and s-factors, convert them into reaction rates, parameterize the rates, store the rates in customizable libraries, setup and run custom post-processing element synthesis calculations, and visualize the results. New features include the ability for users to comment on rates or libraries using an email-type interface, a nuclear mass model evaluator, enhanced techniques for rate parameterization, better treatment of rate inverses, and creation and exporting of custom animations of simulation results. We also have online animations of r- process, rp-process, and neutrino-p process element synthesis occurring in stellar explosions.

Waggle: A Framework for Intelligent Attentive Sensing and Actuation

NASA Astrophysics Data System (ADS)

Sankaran, R.; Jacob, R. L.; Beckman, P. H.; Catlett, C. E.; Keahey, K.

2014-12-01

Advances in sensor-driven computation and computationally steered sensing will greatly enable future research in fields including environmental and atmospheric sciences. We will present "Waggle," an open-source hardware and software infrastructure developed with two goals: (1) reducing the separation and latency between sensing and computing and (2) improving the reliability and longevity of sensing-actuation platforms in challenging and costly deployments. Inspired by "deep-space probe" systems, the Waggle platform design includes features that can support longitudinal studies, deployments with varying communication links, and remote management capabilities. Waggle lowers the barrier for scientists to incorporate real-time data from their sensors into their computations and to manipulate the sensors or provide feedback through actuators. A standardized software and hardware design allows quick addition of new sensors/actuators and associated software in the nodes and enables them to be coupled with computational codes both insitu and on external compute infrastructure. The Waggle framework currently drives the deployment of two observational systems - a portable and self-sufficient weather platform for study of small-scale effects in Chicago's urban core and an open-ended distributed instrument in Chicago that aims to support several research pursuits across a broad range of disciplines including urban planning, microbiology and computer science. Built around open-source software, hardware, and Linux OS, the Waggle system comprises two components - the Waggle field-node and Waggle cloud-computing infrastructure. Waggle field-node affords a modular, scalable, fault-tolerant, secure, and extensible platform for hosting sensors and actuators in the field. It supports insitu computation and data storage, and integration with cloud-computing infrastructure. The Waggle cloud infrastructure is designed with the goal of scaling to several hundreds of thousands of Waggle nodes. It supports aggregating data from sensors hosted by the nodes, staging computation, relaying feedback to the nodes and serving data to end-users. We will discuss the Waggle design principles and their applicability to various observational research pursuits, and demonstrate its capabilities.

Design Aspects of the Rayleigh Convection Code

NASA Astrophysics Data System (ADS)

Featherstone, N. A.

2017-12-01

Understanding the long-term generation of planetary or stellar magnetic field requires complementary knowledge of the large-scale fluid dynamics pervading large fractions of the object's interior. Such large-scale motions are sensitive to the system's geometry which, in planets and stars, is spherical to a good approximation. As a result, computational models designed to study such systems often solve the MHD equations in spherical geometry, frequently employing a spectral approach involving spherical harmonics. We present computational and user-interface design aspects of one such modeling tool, the Rayleigh convection code, which is suitable for deployment on desktop and petascale-hpc architectures alike. In this poster, we will present an overview of this code's parallel design and its built-in diagnostics-output package. Rayleigh has been developed with NSF support through the Computational Infrastructure for Geodynamics and is expected to be released as open-source software in winter 2017/2018.

Integration of a neuroimaging processing pipeline into a pan-canadian computing grid

NASA Astrophysics Data System (ADS)

Lavoie-Courchesne, S.; Rioux, P.; Chouinard-Decorte, F.; Sherif, T.; Rousseau, M.-E.; Das, S.; Adalat, R.; Doyon, J.; Craddock, C.; Margulies, D.; Chu, C.; Lyttelton, O.; Evans, A. C.; Bellec, P.

2012-02-01

The ethos of the neuroimaging field is quickly moving towards the open sharing of resources, including both imaging databases and processing tools. As a neuroimaging database represents a large volume of datasets and as neuroimaging processing pipelines are composed of heterogeneous, computationally intensive tools, such open sharing raises specific computational challenges. This motivates the design of novel dedicated computing infrastructures. This paper describes an interface between PSOM, a code-oriented pipeline development framework, and CBRAIN, a web-oriented platform for grid computing. This interface was used to integrate a PSOM-compliant pipeline for preprocessing of structural and functional magnetic resonance imaging into CBRAIN. We further tested the capacity of our infrastructure to handle a real large-scale project. A neuroimaging database including close to 1000 subjects was preprocessed using our interface and publicly released to help the participants of the ADHD-200 international competition. This successful experiment demonstrated that our integrated grid-computing platform is a powerful solution for high-throughput pipeline analysis in the field of neuroimaging.

A Smart City Lighting Case Study on an OpenStack-Powered Infrastructure.

PubMed

Merlino, Giovanni; Bruneo, Dario; Distefano, Salvatore; Longo, Francesco; Puliafito, Antonio; Al-Anbuky, Adnan

2015-07-06

The adoption of embedded systems, mobile devices and other smart devices keeps rising globally, and the scope of their involvement broadens, for instance, in smart city-like scenarios. In light of this, a pressing need emerges to tame such complexity and reuse as much tooling as possible without resorting to vertical ad hoc solutions, while at the same time taking into account valid options with regard to infrastructure management and other more advanced functionalities. Existing solutions mainly focus on core mechanisms and do not allow one to scale by leveraging infrastructure or adapt to a variety of scenarios, especially if actuators are involved in the loop. A new, more flexible, cloud-based approach, able to provide device-focused workflows, is required. In this sense, a widely-used and competitive framework for infrastructure as a service, such as OpenStack, with its breadth in terms of feature coverage and expanded scope, looks to fit the bill, replacing current application-specific approaches with an innovative application-agnostic one. This work thus describes the rationale, efforts and results so far achieved for an integration of IoT paradigms and resource ecosystems with such a kind of cloud-oriented device-centric environment, by focusing on a smart city scenario, namely a park smart lighting example, and featuring data collection, data visualization, event detection and coordinated reaction, as example use cases of such integration.

A Smart City Lighting Case Study on an OpenStack-Powered Infrastructure

PubMed Central

Merlino, Giovanni; Bruneo, Dario; Distefano, Salvatore; Longo, Francesco; Puliafito, Antonio; Al-Anbuky, Adnan

2015-01-01

The adoption of embedded systems, mobile devices and other smart devices keeps rising globally, and the scope of their involvement broadens, for instance, in smart city-like scenarios. In light of this, a pressing need emerges to tame such complexity and reuse as much tooling as possible without resorting to vertical ad hoc solutions, while at the same time taking into account valid options with regard to infrastructure management and other more advanced functionalities. Existing solutions mainly focus on core mechanisms and do not allow one to scale by leveraging infrastructure or adapt to a variety of scenarios, especially if actuators are involved in the loop. A new, more flexible, cloud-based approach, able to provide device-focused workflows, is required. In this sense, a widely-used and competitive framework for infrastructure as a service, such as OpenStack, with its breadth in terms of feature coverage and expanded scope, looks to fit the bill, replacing current application-specific approaches with an innovative application-agnostic one. This work thus describes the rationale, efforts and results so far achieved for an integration of IoT paradigms and resource ecosystems with such a kind of cloud-oriented device-centric environment, by focusing on a smart city scenario, namely a park smart lighting example, and featuring data collection, data visualization, event detection and coordinated reaction, as example use cases of such integration. PMID:26153775

Software Attribution for Geoscience Applications in the Computational Infrastructure for Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, L.; Dumit, J.; Fish, A.; Soito, L.; Kellogg, L. H.; Smith, M.

2015-12-01

Scientific software is largely developed by individual scientists and represents a significant intellectual contribution to the field. As the scientific culture and funding agencies move towards an expectation that software be open-source, there is a corresponding need for mechanisms to cite software, both to provide credit and recognition to developers, and to aid in discoverability of software and scientific reproducibility. We assess the geodynamic modeling community's current citation practices by examining more than 300 predominantly self-reported publications utilizing scientific software in the past 5 years that is available through the Computational Infrastructure for Geodynamics (CIG). Preliminary results indicate that authors cite and attribute software either through citing (in rank order) peer-reviewed scientific publications, a user's manual, and/or a paper describing the software code. Attributions maybe found directly in the text, in acknowledgements, in figure captions, or in footnotes. What is considered citable varies widely. Citations predominantly lack software version numbers or persistent identifiers to find the software package. Versioning may be implied through reference to a versioned user manual. Authors sometimes report code features used and whether they have modified the code. As an open-source community, CIG requests that researchers contribute their modifications to the repository. However, such modifications may not be contributed back to a repository code branch, decreasing the chances of discoverability and reproducibility. Survey results through CIG's Software Attribution for Geoscience Applications (SAGA) project suggest that lack of knowledge, tools, and workflows to cite codes are barriers to effectively implement the emerging citation norms. Generated on-demand attributions on software landing pages and a prototype extensible plug-in to automatically generate attributions in codes are the first steps towards reproducibility.

iTools: a framework for classification, categorization and integration of computational biology resources.

PubMed

Dinov, Ivo D; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H V; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D Stott; Toga, Arthur W

2008-05-28

The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.

iTools: A Framework for Classification, Categorization and Integration of Computational Biology Resources

PubMed Central

Dinov, Ivo D.; Rubin, Daniel; Lorensen, William; Dugan, Jonathan; Ma, Jeff; Murphy, Shawn; Kirschner, Beth; Bug, William; Sherman, Michael; Floratos, Aris; Kennedy, David; Jagadish, H. V.; Schmidt, Jeanette; Athey, Brian; Califano, Andrea; Musen, Mark; Altman, Russ; Kikinis, Ron; Kohane, Isaac; Delp, Scott; Parker, D. Stott; Toga, Arthur W.

2008-01-01

The advancement of the computational biology field hinges on progress in three fundamental directions – the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources–data, software tools and web-services. The iTools design, implementation and resource meta - data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu. PMID:18509477

Infrastructure for Multiphysics Software Integration in High Performance Computing-Aided Science and Engineering

DOE Office of Scientific and Technical Information (OSTI.GOV)

Campbell, Michael T.; Safdari, Masoud; Kress, Jessica E.

The project described in this report constructed and exercised an innovative multiphysics coupling toolkit called the Illinois Rocstar MultiPhysics Application Coupling Toolkit (IMPACT). IMPACT is an open source, flexible, natively parallel infrastructure for coupling multiple uniphysics simulation codes into multiphysics computational systems. IMPACT works with codes written in several high-performance-computing (HPC) programming languages, and is designed from the beginning for HPC multiphysics code development. It is designed to be minimally invasive to the individual physics codes being integrated, and has few requirements on those physics codes for integration. The goal of IMPACT is to provide the support needed to enablemore » coupling existing tools together in unique and innovative ways to produce powerful new multiphysics technologies without extensive modification and rewrite of the physics packages being integrated. There are three major outcomes from this project: 1) construction, testing, application, and open-source release of the IMPACT infrastructure, 2) production of example open-source multiphysics tools using IMPACT, and 3) identification and engagement of interested organizations in the tools and applications resulting from the project. This last outcome represents the incipient development of a user community and application echosystem being built using IMPACT. Multiphysics coupling standardization can only come from organizations working together to define needs and processes that span the space of necessary multiphysics outcomes, which Illinois Rocstar plans to continue driving toward. The IMPACT system, including source code, documentation, and test problems are all now available through the public gitHUB.org system to anyone interested in multiphysics code coupling. Many of the basic documents explaining use and architecture of IMPACT are also attached as appendices to this document. Online HTML documentation is available through the gitHUB site. There are over 100 unit tests provided that run through the Illinois Rocstar Application Development (IRAD) lightweight testing infrastructure that is also supplied along with IMPACT. The package as a whole provides an excellent base for developing high-quality multiphysics applications using modern software development practices. To facilitate understanding how to utilize IMPACT effectively, two multiphysics systems have been developed and are available open-source through gitHUB. The simpler of the two systems, named ElmerFoamFSI in the repository, is a multiphysics, fluid-structure-interaction (FSI) coupling of the solid mechanics package Elmer with a fluid dynamics module from OpenFOAM. This coupling illustrates how to combine software packages that are unrelated by either author or architecture and combine them into a robust, parallel multiphysics system. A more complex multiphysics tool is the Illinois Rocstar Rocstar Multiphysics code that was rebuilt during the project around IMPACT. Rocstar Multiphysics was already an HPC multiphysics tool, but now that it has been rearchitected around IMPACT, it can be readily expanded to capture new and different physics in the future. In fact, during this project, the Elmer and OpenFOAM tools were also coupled into Rocstar Multiphysics and demonstrated. The full Rocstar Multiphysics codebase is also available on gitHUB, and licensed for any organization to use as they wish. Finally, the new IMPACT product is already being used in several multiphysics code coupling projects for the Air Force, NASA and the Missile Defense Agency, and initial work on expansion of the IMPACT-enabled Rocstar Multiphysics has begun in support of a commercial company. These initiatives promise to expand the interest and reach of IMPACT and Rocstar Multiphysics, ultimately leading to the envisioned standardization and consortium of users that was one of the goals of this project.« less

ROSE Version 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quinlan, D.; Yi, Q.; Buduc, R.

2005-02-17

ROSE is an object-oriented software infrastructure for source-to-source translation that provides an interface for programmers to write their own specialized translators for optimizing scientific applications. ROSE is a part of current research on telescoping languages, which provides optimizations of the use of libraries in scientific applications. ROSE defines approaches to extend the optimization techniques, common in well defined languages, to the optimization of scientific applications using well defined libraries. ROSE includes a rich set of tools for generating customized transformations to support optimization of applications codes. We currently support full C and C++ (including template instantiation etc.), with Fortran 90more » support under development as part of a collaboration and contract with Rice to use their version of the open source Open64 F90 front-end. ROSE represents an attempt to define an open compiler infrastructure to handle the full complexity of full scale DOE applications codes using the languages common to scientific computing within DOE. We expect that such an infrastructure will also be useful for the development of numerous tools that may then realistically expect to work on DOE full scale applications.« less

Searching for Physics Beyond the Standard Model: Strongly-Coupled Field Theories at the Intensity and Energy Frontiers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Brower, Richard C.

This proposal is to develop the software and algorithmic infrastructure needed for the numerical study of quantum chromodynamics (QCD), and of theories that have been proposed to describe physics beyond the Standard Model (BSM) of high energy physics, on current and future computers. This infrastructure will enable users (1) to improve the accuracy of QCD calculations to the point where they no longer limit what can be learned from high-precision experiments that seek to test the Standard Model, and (2) to determine the predictions of BSM theories in order to understand which of them are consistent with the data thatmore » will soon be available from the LHC. Work will include the extension and optimizations of community codes for the next generation of leadership class computers, the IBM Blue Gene/Q and the Cray XE/XK, and for the dedicated hardware funded for our field by the Department of Energy. Members of our collaboration at Brookhaven National Laboratory and Columbia University worked on the design of the Blue Gene/Q, and have begun to develop software for it. Under this grant we will build upon their experience to produce high-efficiency production codes for this machine. Cray XE/XK computers with many thousands of GPU accelerators will soon be available, and the dedicated commodity clusters we obtain with DOE funding include growing numbers of GPUs. We will work with our partners in NVIDIA's Emerging Technology group to scale our existing software to thousands of GPUs, and to produce highly efficient production codes for these machines. Work under this grant will also include the development of new algorithms for the effective use of heterogeneous computers, and their integration into our codes. It will include improvements of Krylov solvers and the development of new multigrid methods in collaboration with members of the FASTMath SciDAC Institute, using their HYPRE framework, as well as work on improved symplectic integrators.« less

Investigation into Cloud Computing for More Robust Automated Bulk Image Geoprocessing

NASA Technical Reports Server (NTRS)

Brown, Richard B.; Smoot, James C.; Underwood, Lauren; Armstrong, C. Duane

2012-01-01

Geospatial resource assessments frequently require timely geospatial data processing that involves large multivariate remote sensing data sets. In particular, for disasters, response requires rapid access to large data volumes, substantial storage space and high performance processing capability. The processing and distribution of this data into usable information products requires a processing pipeline that can efficiently manage the required storage, computing utilities, and data handling requirements. In recent years, with the availability of cloud computing technology, cloud processing platforms have made available a powerful new computing infrastructure resource that can meet this need. To assess the utility of this resource, this project investigates cloud computing platforms for bulk, automated geoprocessing capabilities with respect to data handling and application development requirements. This presentation is of work being conducted by Applied Sciences Program Office at NASA-Stennis Space Center. A prototypical set of image manipulation and transformation processes that incorporate sample Unmanned Airborne System data were developed to create value-added products and tested for implementation on the "cloud". This project outlines the steps involved in creating and testing of open source software developed process code on a local prototype platform, and then transitioning this code with associated environment requirements into an analogous, but memory and processor enhanced cloud platform. A data processing cloud was used to store both standard digital camera panchromatic and multi-band image data, which were subsequently subjected to standard image processing functions such as NDVI (Normalized Difference Vegetation Index), NDMI (Normalized Difference Moisture Index), band stacking, reprojection, and other similar type data processes. Cloud infrastructure service providers were evaluated by taking these locally tested processing functions, and then applying them to a given cloud-enabled infrastructure to assesses and compare environment setup options and enabled technologies. This project reviews findings that were observed when cloud platforms were evaluated for bulk geoprocessing capabilities based on data handling and application development requirements.

FELIX: a PCIe based high-throughput approach for interfacing front-end and trigger electronics in the ATLAS Upgrade framework

NASA Astrophysics Data System (ADS)

Anderson, J.; Bauer, K.; Borga, A.; Boterenbrood, H.; Chen, H.; Chen, K.; Drake, G.; Dönszelmann, M.; Francis, D.; Guest, D.; Gorini, B.; Joos, M.; Lanni, F.; Lehmann Miotto, G.; Levinson, L.; Narevicius, J.; Panduro Vazquez, W.; Roich, A.; Ryu, S.; Schreuder, F.; Schumacher, J.; Vandelli, W.; Vermeulen, J.; Whiteson, D.; Wu, W.; Zhang, J.

2016-12-01

The ATLAS Phase-I upgrade (2019) requires a Trigger and Data Acquisition (TDAQ) system able to trigger and record data from up to three times the nominal LHC instantaneous luminosity. The Front-End LInk eXchange (FELIX) system provides an infrastructure to achieve this in a scalable, detector agnostic and easily upgradeable way. It is a PC-based gateway, interfacing custom radiation tolerant optical links from front-end electronics, via PCIe Gen3 cards, to a commodity switched Ethernet or InfiniBand network. FELIX enables reducing custom electronics in favour of software running on commercial servers. The FELIX system, the design of the PCIe prototype card and the integration test results are presented in this paper.

Phenomenology tools on cloud infrastructures using OpenStack

NASA Astrophysics Data System (ADS)

Campos, I.; Fernández-del-Castillo, E.; Heinemeyer, S.; Lopez-Garcia, A.; Pahlen, F.; Borges, G.

2013-04-01

We present a new environment for computations in particle physics phenomenology employing recent developments in cloud computing. On this environment users can create and manage "virtual" machines on which the phenomenology codes/tools can be deployed easily in an automated way. We analyze the performance of this environment based on "virtual" machines versus the utilization of physical hardware. In this way we provide a qualitative result for the influence of the host operating system on the performance of a representative set of applications for phenomenology calculations.

clearScience: Infrastructure for Communicating Data-Intensive Science.

PubMed

Bot, Brian M; Burdick, David; Kellen, Michael; Huang, Erich S

2013-01-01

Progress in biomedical research requires effective scientific communication to one's peers and to the public. Current research routinely encompasses large datasets and complex analytic processes, and the constraints of traditional journal formats limit useful transmission of these elements. We are constructing a framework through which authors can not only provide the narrative of what was done, but the primary and derivative data, the source code, the compute environment, and web-accessible virtual machines. This infrastructure allows authors to "hand their machine"- prepopulated with libraries, data, and code-to those interested in reviewing or building off of their work. This project, "clearScience," seeks to provide an integrated system that accommodates the ad hoc nature of discovery in the data-intensive sciences and seamless transitions from working to reporting. We demonstrate that rather than merely describing the science being reported, one can deliver the science itself.

JACOB: an enterprise framework for computational chemistry.

PubMed

Waller, Mark P; Dresselhaus, Thomas; Yang, Jack

2013-06-15

Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code. Paradigms from enterprise software engineering were rigorously applied to create a scalable, testable, secure, and robust framework. A centralized web application is used to configure and control the operation of the framework. The application-programming interface provides a set of generic tools for processing large-scale noninteractive jobs (e.g., systematic studies), or for coordinating systems integration (e.g., complex workflows). The code for the JACOB framework is open sourced and is available at: www.wallerlab.org/jacob. Copyright © 2013 Wiley Periodicals, Inc.

Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers.

PubMed

Jordan, Jakob; Ippen, Tammo; Helias, Moritz; Kitayama, Itaru; Sato, Mitsuhisa; Igarashi, Jun; Diesmann, Markus; Kunkel, Susanne

2018-01-01

State-of-the-art software tools for neuronal network simulations scale to the largest computing systems available today and enable investigations of large-scale networks of up to 10 % of the human cortex at a resolution of individual neurons and synapses. Due to an upper limit on the number of incoming connections of a single neuron, network connectivity becomes extremely sparse at this scale. To manage computational costs, simulation software ultimately targeting the brain scale needs to fully exploit this sparsity. Here we present a two-tier connection infrastructure and a framework for directed communication among compute nodes accounting for the sparsity of brain-scale networks. We demonstrate the feasibility of this approach by implementing the technology in the NEST simulation code and we investigate its performance in different scaling scenarios of typical network simulations. Our results show that the new data structures and communication scheme prepare the simulation kernel for post-petascale high-performance computing facilities without sacrificing performance in smaller systems.

Extremely Scalable Spiking Neuronal Network Simulation Code: From Laptops to Exascale Computers

PubMed Central

Jordan, Jakob; Ippen, Tammo; Helias, Moritz; Kitayama, Itaru; Sato, Mitsuhisa; Igarashi, Jun; Diesmann, Markus; Kunkel, Susanne

2018-01-01

State-of-the-art software tools for neuronal network simulations scale to the largest computing systems available today and enable investigations of large-scale networks of up to 10 % of the human cortex at a resolution of individual neurons and synapses. Due to an upper limit on the number of incoming connections of a single neuron, network connectivity becomes extremely sparse at this scale. To manage computational costs, simulation software ultimately targeting the brain scale needs to fully exploit this sparsity. Here we present a two-tier connection infrastructure and a framework for directed communication among compute nodes accounting for the sparsity of brain-scale networks. We demonstrate the feasibility of this approach by implementing the technology in the NEST simulation code and we investigate its performance in different scaling scenarios of typical network simulations. Our results show that the new data structures and communication scheme prepare the simulation kernel for post-petascale high-performance computing facilities without sacrificing performance in smaller systems. PMID:29503613

Sustaining Open Source Communities through Hackathons - An Example from the ASPECT Community

NASA Astrophysics Data System (ADS)

Heister, T.; Hwang, L.; Bangerth, W.; Kellogg, L. H.

2016-12-01

The ecosystem surrounding a successful scientific open source software package combines both social and technical aspects. Much thought has been given to the technology side of writing sustainable software for large infrastructure projects and software libraries, but less about building the human capacity to perpetuate scientific software used in computational modeling. One effective format for building capacity is regular multi-day hackathons. Scientific hackathons bring together a group of science domain users and scientific software contributors to make progress on a specific software package. Innovation comes through the chance to work with established and new collaborations. Especially in the domain sciences with small communities, hackathons give geographically distributed scientists an opportunity to connect face-to-face. They foster lively discussions amongst scientists with different expertise, promote new collaborations, and increase transparency in both the technical and scientific aspects of code development. ASPECT is an open source, parallel, extensible finite element code to simulate thermal convection, that began development in 2011 under the Computational Infrastructure for Geodynamics. ASPECT hackathons for the past 3 years have grown the number of authors to >50, training new code maintainers in the process. Hackathons begin with leaders establishing project-specific conventions for development, demonstrating the workflow for code contributions, and reviewing relevant technical skills. Each hackathon expands the developer community. Over 20 scientists add >6,000 lines of code during the >1 week event. Participants grow comfortable contributing to the repository and over half continue to contribute afterwards. A high return rate of participants ensures continuity and stability of the group as well as mentoring for novice members. We hope to build other software communities on this model, but anticipate each to bring their own unique challenges.

A Detailed Comparison of Multidimensional Boltzmann Neutrino Transport Methods in Core-collapse Supernovae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richers, Sherwood; Nagakura, Hiroki; Ott, Christian D.

The mechanism driving core-collapse supernovae is sensitive to the interplay between matter and neutrino radiation. However, neutrino radiation transport is very difficult to simulate, and several radiation transport methods of varying levels of approximation are available. We carefully compare for the first time in multiple spatial dimensions the discrete ordinates (DO) code of Nagakura, Yamada, and Sumiyoshi and the Monte Carlo (MC) code Sedonu, under the assumptions of a static fluid background, flat spacetime, elastic scattering, and full special relativity. We find remarkably good agreement in all spectral, angular, and fluid interaction quantities, lending confidence to both methods. The DOmore » method excels in determining the heating and cooling rates in the optically thick region. The MC method predicts sharper angular features due to the effectively infinite angular resolution, but struggles to drive down noise in quantities where subtractive cancellation is prevalent, such as the net gain in the protoneutron star and off-diagonal components of the Eddington tensor. We also find that errors in the angular moments of the distribution functions induced by neglecting velocity dependence are subdominant to those from limited momentum-space resolution. We briefly compare directly computed second angular moments to those predicted by popular algebraic two-moment closures, and we find that the errors from the approximate closures are comparable to the difference between the DO and MC methods. Included in this work is an improved Sedonu code, which now implements a fully special relativistic, time-independent version of the grid-agnostic MC random walk approximation.« less

A Detailed Comparison of Multidimensional Boltzmann Neutrino Transport Methods in Core-collapse Supernovae

DOE PAGES

Richers, Sherwood; Nagakura, Hiroki; Ott, Christian D.; ...

2017-10-03

The mechanism driving core-collapse supernovae is sensitive to the interplay between matter and neutrino radiation. However, neutrino radiation transport is very difficult to simulate, and several radiation transport methods of varying levels of approximation are available. In this paper, we carefully compare for the first time in multiple spatial dimensions the discrete ordinates (DO) code of Nagakura, Yamada, and Sumiyoshi and the Monte Carlo (MC) code Sedonu, under the assumptions of a static fluid background, flat spacetime, elastic scattering, and full special relativity. We find remarkably good agreement in all spectral, angular, and fluid interaction quantities, lending confidence to bothmore » methods. The DO method excels in determining the heating and cooling rates in the optically thick region. The MC method predicts sharper angular features due to the effectively infinite angular resolution, but struggles to drive down noise in quantities where subtractive cancellation is prevalent, such as the net gain in the protoneutron star and off-diagonal components of the Eddington tensor. We also find that errors in the angular moments of the distribution functions induced by neglecting velocity dependence are subdominant to those from limited momentum-space resolution. We briefly compare directly computed second angular moments to those predicted by popular algebraic two-moment closures, and we find that the errors from the approximate closures are comparable to the difference between the DO and MC methods. Finally, included in this work is an improved Sedonu code, which now implements a fully special relativistic, time-independent version of the grid-agnostic MC random walk approximation.« less

A Detailed Comparison of Multidimensional Boltzmann Neutrino Transport Methods in Core-collapse Supernovae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Richers, Sherwood; Nagakura, Hiroki; Ott, Christian D.

The mechanism driving core-collapse supernovae is sensitive to the interplay between matter and neutrino radiation. However, neutrino radiation transport is very difficult to simulate, and several radiation transport methods of varying levels of approximation are available. In this paper, we carefully compare for the first time in multiple spatial dimensions the discrete ordinates (DO) code of Nagakura, Yamada, and Sumiyoshi and the Monte Carlo (MC) code Sedonu, under the assumptions of a static fluid background, flat spacetime, elastic scattering, and full special relativity. We find remarkably good agreement in all spectral, angular, and fluid interaction quantities, lending confidence to bothmore » methods. The DO method excels in determining the heating and cooling rates in the optically thick region. The MC method predicts sharper angular features due to the effectively infinite angular resolution, but struggles to drive down noise in quantities where subtractive cancellation is prevalent, such as the net gain in the protoneutron star and off-diagonal components of the Eddington tensor. We also find that errors in the angular moments of the distribution functions induced by neglecting velocity dependence are subdominant to those from limited momentum-space resolution. We briefly compare directly computed second angular moments to those predicted by popular algebraic two-moment closures, and we find that the errors from the approximate closures are comparable to the difference between the DO and MC methods. Finally, included in this work is an improved Sedonu code, which now implements a fully special relativistic, time-independent version of the grid-agnostic MC random walk approximation.« less

A Detailed Comparison of Multidimensional Boltzmann Neutrino Transport Methods in Core-collapse Supernovae

NASA Astrophysics Data System (ADS)

Richers, Sherwood; Nagakura, Hiroki; Ott, Christian D.; Dolence, Joshua; Sumiyoshi, Kohsuke; Yamada, Shoichi

2017-10-01

The mechanism driving core-collapse supernovae is sensitive to the interplay between matter and neutrino radiation. However, neutrino radiation transport is very difficult to simulate, and several radiation transport methods of varying levels of approximation are available. We carefully compare for the first time in multiple spatial dimensions the discrete ordinates (DO) code of Nagakura, Yamada, and Sumiyoshi and the Monte Carlo (MC) code Sedonu, under the assumptions of a static fluid background, flat spacetime, elastic scattering, and full special relativity. We find remarkably good agreement in all spectral, angular, and fluid interaction quantities, lending confidence to both methods. The DO method excels in determining the heating and cooling rates in the optically thick region. The MC method predicts sharper angular features due to the effectively infinite angular resolution, but struggles to drive down noise in quantities where subtractive cancellation is prevalent, such as the net gain in the protoneutron star and off-diagonal components of the Eddington tensor. We also find that errors in the angular moments of the distribution functions induced by neglecting velocity dependence are subdominant to those from limited momentum-space resolution. We briefly compare directly computed second angular moments to those predicted by popular algebraic two-moment closures, and we find that the errors from the approximate closures are comparable to the difference between the DO and MC methods. Included in this work is an improved Sedonu code, which now implements a fully special relativistic, time-independent version of the grid-agnostic MC random walk approximation.

Report on the Program and Contract Infrastructure Technical Requirements Development for the Guam Realignment Program

DTIC Science & Technology

2012-02-08

Office GRN Guam Road Network GWA Guam Waterworks Authority ICG Interagency Coordination Group JFY Japanese Fiscal Year JRM Joint...PAC) (Pacific) NCTS Naval Computer and Telecommunications Station NEPA National Environmental Policy Act NPDES National Pollutant Discharge...Elimination System OPNAV Operational Navy UFC Unified Facilities Criteria U.S. United States USC United States Code USDA United States

Parallel Higher-order Finite Element Method for Accurate Field Computations in Wakefield and PIC Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Candel, A.; Kabel, A.; Lee, L.

Over the past years, SLAC's Advanced Computations Department (ACD), under SciDAC sponsorship, has developed a suite of 3D (2D) parallel higher-order finite element (FE) codes, T3P (T2P) and Pic3P (Pic2P), aimed at accurate, large-scale simulation of wakefields and particle-field interactions in radio-frequency (RF) cavities of complex shape. The codes are built on the FE infrastructure that supports SLAC's frequency domain codes, Omega3P and S3P, to utilize conformal tetrahedral (triangular)meshes, higher-order basis functions and quadratic geometry approximation. For time integration, they adopt an unconditionally stable implicit scheme. Pic3P (Pic2P) extends T3P (T2P) to treat charged-particle dynamics self-consistently using the PIC (particle-in-cell)more » approach, the first such implementation on a conformal, unstructured grid using Whitney basis functions. Examples from applications to the International Linear Collider (ILC), Positron Electron Project-II (PEP-II), Linac Coherent Light Source (LCLS) and other accelerators will be presented to compare the accuracy and computational efficiency of these codes versus their counterparts using structured grids.« less

Final Report Scalable Analysis Methods and In Situ Infrastructure for Extreme Scale Knowledge Discovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Leary, Patrick

The primary challenge motivating this project is the widening gap between the ability to compute information and to store it for subsequent analysis. This gap adversely impacts science code teams, who can perform analysis only on a small fraction of the data they calculate, resulting in the substantial likelihood of lost or missed science, when results are computed but not analyzed. Our approach is to perform as much analysis or visualization processing on data while it is still resident in memory, which is known as in situ processing. The idea in situ processing was not new at the time ofmore » the start of this effort in 2014, but efforts in that space were largely ad hoc, and there was no concerted effort within the research community that aimed to foster production-quality software tools suitable for use by Department of Energy (DOE) science projects. Our objective was to produce and enable the use of production-quality in situ methods and infrastructure, at scale, on DOE high-performance computing (HPC) facilities, though we expected to have an impact beyond DOE due to the widespread nature of the challenges, which affect virtually all large-scale computational science efforts. To achieve this objective, we engaged in software technology research and development (R&D), in close partnerships with DOE science code teams, to produce software technologies that were shown to run efficiently at scale on DOE HPC platforms.« less

Identification and Analysis of Critical Gaps in Nuclear Fuel Cycle Codes Required by the SINEMA Program

DOE Office of Scientific and Technical Information (OSTI.GOV)

Adrian Miron; Joshua Valentine; John Christenson

2009-10-01

The current state of the art in nuclear fuel cycle (NFC) modeling is an eclectic mixture of codes with various levels of applicability, flexibility, and availability. In support of the advanced fuel cycle systems analyses, especially those by the Advanced Fuel Cycle Initiative (AFCI), Unviery of Cincinnati in collaboration with Idaho State University carried out a detailed review of the existing codes describing various aspects of the nuclear fuel cycle and identified the research and development needs required for a comprehensive model of the global nuclear energy infrastructure and the associated nuclear fuel cycles. Relevant information obtained on the NFCmore » codes was compiled into a relational database that allows easy access to various codes' properties. Additionally, the research analyzed the gaps in the NFC computer codes with respect to their potential integration into programs that perform comprehensive NFC analysis.« less

The Computational Infrastructure for Geodynamics as a Community of Practice

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2016-12-01

Computational Infrastructure for Geodynamics (CIG), geodynamics.org, originated in 2005 out of community recognition that the efforts of individual or small groups of researchers to develop scientifically-sound software is impossible to sustain, duplicates effort, and makes it difficult for scientists to adopt state-of-the art computational methods that promote new discovery. As a community of practice, participants in CIG share an interest in computational modeling in geodynamics and work together on open source software to build the capacity to support complex, extensible, scalable, interoperable, reliable, and reusable software in an effort to increase the return on investment in scientific software development and increase the quality of the resulting software. The group interacts regularly to learn from each other and better their practices formally through webinar series, workshops, and tutorials and informally through listservs and hackathons. Over the past decade, we have learned that successful scientific software development requires at a minimum: collaboration between domain-expert researchers, software developers and computational scientists; clearly identified and committed lead developer(s); well-defined scientific and computational goals that are regularly evaluated and updated; well-defined benchmarks and testing throughout development; attention throughout development to usability and extensibility; understanding and evaluation of the complexity of dependent libraries; and managed user expectations through education, training, and support. CIG's code donation standards provide the basis for recently formalized best practices in software development (geodynamics.org/cig/dev/best-practices/). Best practices include use of version control; widely used, open source software libraries; extensive test suites; portable configuration and build systems; extensive documentation internal and external to the code; and structured, human readable input formats.

Individualized grid-enabled mammographic training system

NASA Astrophysics Data System (ADS)

Yap, M. H.; Gale, A. G.

2009-02-01

The PERFORMS self-assessment scheme measures individuals skills in identifying key mammographic features on sets of known cases. One aspect of this is that it allows radiologists' skills to be trained, based on their data from this scheme. Consequently, a new strategy is introduced to provide revision training based on mammographic features that the radiologist has had difficulty with in these sets. To do this requires a lot of random cases to provide dynamic, unique, and up-to-date training modules for each individual. We propose GIMI (Generic Infrastructure in Medical Informatics) middleware as the solution to harvest cases from distributed grid servers. The GIMI middleware enables existing and legacy data to support healthcare delivery, research, and training. It is technology-agnostic, data-agnostic, and has a security policy. The trainee examines each case, indicating the location of regions of interest, and completes an evaluation form, to determine mammographic feature labelling, diagnosis, and decisions. For feedback, the trainee can choose to have immediate feedback after examining each case or batch feedback after examining a number of cases. All the trainees' result are recorded in a database which also contains their trainee profile. A full report can be prepared for the trainee after they have completed their training. This project demonstrates the practicality of a grid-based individualised training strategy and the efficacy in generating dynamic training modules within the coverage/outreach of the GIMI middleware. The advantages and limitations of the approach are discussed together with future plans.

ClearTK 2.0: Design Patterns for Machine Learning in UIMA

PubMed Central

Bethard, Steven; Ogren, Philip; Becker, Lee

2014-01-01

ClearTK adds machine learning functionality to the UIMA framework, providing wrappers to popular machine learning libraries, a rich feature extraction library that works across different classifiers, and utilities for applying and evaluating machine learning models. Since its inception in 2008, ClearTK has evolved in response to feedback from developers and the community. This evolution has followed a number of important design principles including: conceptually simple annotator interfaces, readable pipeline descriptions, minimal collection readers, type system agnostic code, modules organized for ease of import, and assisting user comprehension of the complex UIMA framework. PMID:29104966

ClearTK 2.0: Design Patterns for Machine Learning in UIMA.

PubMed

Bethard, Steven; Ogren, Philip; Becker, Lee

2014-05-01

ClearTK adds machine learning functionality to the UIMA framework, providing wrappers to popular machine learning libraries, a rich feature extraction library that works across different classifiers, and utilities for applying and evaluating machine learning models. Since its inception in 2008, ClearTK has evolved in response to feedback from developers and the community. This evolution has followed a number of important design principles including: conceptually simple annotator interfaces, readable pipeline descriptions, minimal collection readers, type system agnostic code, modules organized for ease of import, and assisting user comprehension of the complex UIMA framework.

FELIX: a PCIe based high-throughput approach for interfacing front-end and trigger electronics in the ATLAS Upgrade framework

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, J.; Bauer, K.; Borga, A.

The ATLAS Phase-I upgrade (2019) requires a Trigger and Data Acquisition (TDAQ) system able to trigger and record data from up to three times the nominal LHC instantaneous luminosity. Furthermore, the Front-End LInk eXchange (FELIX) system provides an infrastructure to achieve this in a scalable, detector agnostic and easily upgradeable way. It is a PC-based gateway, interfacing custom radiation tolerant optical links from front-end electronics, via PCIe Gen3 cards, to a commodity switched Ethernet or InfiniBand network. FELIX enables reducing custom electronics in favour of software running on commercial servers. Here, the FELIX system, the design of the PCIe prototypemore » card and the integration test results are presented.« less

FELIX: a PCIe based high-throughput approach for interfacing front-end and trigger electronics in the ATLAS Upgrade framework

DOE PAGES

Anderson, J.; Bauer, K.; Borga, A.; ...

2016-12-13

The ATLAS Phase-I upgrade (2019) requires a Trigger and Data Acquisition (TDAQ) system able to trigger and record data from up to three times the nominal LHC instantaneous luminosity. Furthermore, the Front-End LInk eXchange (FELIX) system provides an infrastructure to achieve this in a scalable, detector agnostic and easily upgradeable way. It is a PC-based gateway, interfacing custom radiation tolerant optical links from front-end electronics, via PCIe Gen3 cards, to a commodity switched Ethernet or InfiniBand network. FELIX enables reducing custom electronics in favour of software running on commercial servers. Here, the FELIX system, the design of the PCIe prototypemore » card and the integration test results are presented.« less

A Platform-Independent Plugin for Navigating Online Radiology Cases.

PubMed

Balkman, Jason D; Awan, Omer A

2016-06-01

Software methods that enable navigation of radiology cases on various digital platforms differ between handheld devices and desktop computers. This has resulted in poor compatibility of online radiology teaching files across mobile smartphones, tablets, and desktop computers. A standardized, platform-independent, or "agnostic" approach for presenting online radiology content was produced in this work by leveraging modern hypertext markup language (HTML) and JavaScript web software technology. We describe the design and evaluation of this software, demonstrate its use across multiple viewing platforms, and make it publicly available as a model for future development efforts.

Running SW4 On New Commodity Technology Systems (CTS-1) Platform

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodgers, Arthur J.; Petersson, N. Anders; Pitarka, Arben

We have recently been running earthquake ground motion simulations with SW4 on the new capacity computing systems, called the Commodity Technology Systems - 1 (CTS-1) at Lawrence Livermore National Laboratory (LLNL). SW4 is a fourth order time domain finite difference code developed by LLNL and distributed by the Computational Infrastructure for Geodynamics (CIG). SW4 simulates seismic wave propagation in complex three-dimensional Earth models including anelasticity and surface topography. We are modeling near-fault earthquake strong ground motions for the purposes of evaluating the response of engineered structures, such as nuclear power plants and other critical infrastructure. Engineering analysis of structures requiresmore » the inclusion of high frequencies which can cause damage, but are often difficult to include in simulations because of the need for large memory to model fine grid spacing on large domains.« less

Identification of significantly mutated regions across cancer types highlights a rich landscape of functional molecular alterations

PubMed Central

Araya, Carlos L.; Cenik, Can; Reuter, Jason A.; Kiss, Gert; Pande, Vijay S.; Snyder, Michael P.; Greenleaf, William J.

2015-01-01

Cancer sequencing studies have primarily identified cancer-driver genes by the accumulation of protein-altering mutations. An improved method would be annotation-independent, sensitive to unknown distributions of functions within proteins, and inclusive of non-coding drivers. We employed density-based clustering methods in 21 tumor types to detect variably-sized significantly mutated regions (SMRs). SMRs reveal recurrent alterations across a spectrum of coding and non-coding elements, including transcription factor binding sites and untranslated regions mutated in up to ∼15% of specific tumor types. SMRs reveal spatial clustering of mutations at molecular domains and interfaces, often with associated changes in signaling. Mutation frequencies in SMRs demonstrate that distinct protein regions are differentially mutated among tumor types, as exemplified by a linker region of PIK3CA in which biophysical simulations suggest mutations affect regulatory interactions. The functional diversity of SMRs underscores both the varied mechanisms of oncogenic misregulation and the advantage of functionally-agnostic driver identification. PMID:26691984

Scalable Analysis Methods and In Situ Infrastructure for Extreme Scale Knowledge Discovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bethel, Wes

2016-07-24

The primary challenge motivating this team’s work is the widening gap between the ability to compute information and to store it for subsequent analysis. This gap adversely impacts science code teams, who are able to perform analysis only on a small fraction of the data they compute, resulting in the very real likelihood of lost or missed science, when results are computed but not analyzed. Our approach is to perform as much analysis or visualization processing on data while it is still resident in memory, an approach that is known as in situ processing. The idea in situ processing wasmore » not new at the time of the start of this effort in 2014, but efforts in that space were largely ad hoc, and there was no concerted effort within the research community that aimed to foster production-quality software tools suitable for use by DOE science projects. In large, our objective was produce and enable use of production-quality in situ methods and infrastructure, at scale, on DOE HPC facilities, though we expected to have impact beyond DOE due to the widespread nature of the challenges, which affect virtually all large-scale computational science efforts. To achieve that objective, we assembled a unique team of researchers consisting of representatives from DOE national laboratories, academia, and industry, and engaged in software technology R&D, as well as engaged in close partnerships with DOE science code teams, to produce software technologies that were shown to run effectively at scale on DOE HPC platforms.« less

Toward an automated parallel computing environment for geosciences

NASA Astrophysics Data System (ADS)

Zhang, Huai; Liu, Mian; Shi, Yaolin; Yuen, David A.; Yan, Zhenzhen; Liang, Guoping

2007-08-01

Software for geodynamic modeling has not kept up with the fast growing computing hardware and network resources. In the past decade supercomputing power has become available to most researchers in the form of affordable Beowulf clusters and other parallel computer platforms. However, to take full advantage of such computing power requires developing parallel algorithms and associated software, a task that is often too daunting for geoscience modelers whose main expertise is in geosciences. We introduce here an automated parallel computing environment built on open-source algorithms and libraries. Users interact with this computing environment by specifying the partial differential equations, solvers, and model-specific properties using an English-like modeling language in the input files. The system then automatically generates the finite element codes that can be run on distributed or shared memory parallel machines. This system is dynamic and flexible, allowing users to address different problems in geosciences. It is capable of providing web-based services, enabling users to generate source codes online. This unique feature will facilitate high-performance computing to be integrated with distributed data grids in the emerging cyber-infrastructures for geosciences. In this paper we discuss the principles of this automated modeling environment and provide examples to demonstrate its versatility.

SU-D-BRD-03: A Gateway for GPU Computing in Cancer Radiotherapy Research

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jia, X; Folkerts, M; Shi, F

Purpose: Graphics Processing Unit (GPU) has become increasingly important in radiotherapy. However, it is still difficult for general clinical researchers to access GPU codes developed by other researchers, and for developers to objectively benchmark their codes. Moreover, it is quite often to see repeated efforts spent on developing low-quality GPU codes. The goal of this project is to establish an infrastructure for testing GPU codes, cross comparing them, and facilitating code distributions in radiotherapy community. Methods: We developed a system called Gateway for GPU Computing in Cancer Radiotherapy Research (GCR2). A number of GPU codes developed by our group andmore » other developers can be accessed via a web interface. To use the services, researchers first upload their test data or use the standard data provided by our system. Then they can select the GPU device on which the code will be executed. Our system offers all mainstream GPU hardware for code benchmarking purpose. After the code running is complete, the system automatically summarizes and displays the computing results. We also released a SDK to allow the developers to build their own algorithm implementation and submit their binary codes to the system. The submitted code is then systematically benchmarked using a variety of GPU hardware and representative data provided by our system. The developers can also compare their codes with others and generate benchmarking reports. Results: It is found that the developed system is fully functioning. Through a user-friendly web interface, researchers are able to test various GPU codes. Developers also benefit from this platform by comprehensively benchmarking their codes on various GPU platforms and representative clinical data sets. Conclusion: We have developed an open platform allowing the clinical researchers and developers to access the GPUs and GPU codes. This development will facilitate the utilization of GPU in radiation therapy field.« less

Coupled Physics Environment (CouPE) library - Design, Implementation, and Release

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahadevan, Vijay S.

Over several years, high fidelity, validated mono-­physics solvers with proven scalability on peta-­scale architectures have been developed independently. Based on a unified component-­based architecture, these existing codes can be coupled with a unified mesh-­data backplane and a flexible coupling-­strategy-­based driver suite to produce a viable tool for analysts. In this report, we present details on the design decisions and developments on CouPE, an acronym that stands for Coupled Physics Environment that orchestrates a coupled physics solver through the interfaces exposed by MOAB array-­based unstructured mesh, both of which are part of SIGMA (Scalable Interfaces for Geometry and Mesh-­Based Applications) toolkit.more » The SIGMA toolkit contains libraries that enable scalable geometry and unstructured mesh creation and handling in a memory and computationally efficient implementation. The CouPE version being prepared for a full open-­source release along with updated documentation will contain several useful examples that will enable users to start developing their applications natively using the native MOAB mesh and couple their models to existing physics applications to analyze and solve real world problems of interest. An integrated multi-­physics simulation capability for the design and analysis of current and future nuclear reactor models is also being investigated as part of the NEAMS RPL, to tightly couple neutron transport, thermal-­hydraulics and structural mechanics physics under the SHARP framework. This report summarizes the efforts that have been invested in CouPE to bring together several existing physics applications namely PROTEUS (neutron transport code), Nek5000 (computational fluid-dynamics code) and Diablo (structural mechanics code). The goal of the SHARP framework is to perform fully resolved coupled physics analysis of a reactor on heterogeneous geometry, in order to reduce the overall numerical uncertainty while leveraging available computational resources. The design of CouPE along with motivations that led to implementation choices are also discussed. The first release of the library will be different from the current version of the code that integrates the components in SHARP and explanation on the need for forking the source base will also be provided. Enhancements in the functionality and improved user guides will be available as part of the release. CouPE v0.1 is scheduled for an open-­source release in December 2014 along with SIGMA v1.1 components that provide support for language-agnostic mesh loading, traversal and query interfaces along with scalable solution transfer of fields between different physics codes. The coupling methodology and software interfaces of the library are presented, along with verification studies on two representative fast sodium-­cooled reactor demonstration problems to prove the usability of the CouPE library.« less

Pilot-in-the-Loop CFD Method Development

DTIC Science & Technology

2017-04-20

the methods on the NAVAIR Manned Flight Simulator. Activities this period During this report period, we implemented the CRAFT CFD code on the...Penn State VLRCROE Flight simulator and performed the first Pilot-in-the-Loop PILCFD tests at Penn State using the COCOA5 clusters. The initial tests...integration of the flight simulator and Penn State computing infrastructure. Initial tests showed slower performance than real-time (3x slower than real

ACTS: from ATLAS software towards a common track reconstruction software

NASA Astrophysics Data System (ADS)

Gumpert, C.; Salzburger, A.; Kiehn, M.; Hrdinka, J.; Calace, N.; ATLAS Collaboration

2017-10-01

Reconstruction of charged particles’ trajectories is a crucial task for most particle physics experiments. The high instantaneous luminosity achieved at the LHC leads to a high number of proton-proton collisions per bunch crossing, which has put the track reconstruction software of the LHC experiments through a thorough test. Preserving track reconstruction performance under increasingly difficult experimental conditions, while keeping the usage of computational resources at a reasonable level, is an inherent problem for many HEP experiments. Exploiting concurrent algorithms and using multivariate techniques for track identification are the primary strategies to achieve that goal. Starting from current ATLAS software, the ACTS project aims to encapsulate track reconstruction software into a generic, framework- and experiment-independent software package. It provides a set of high-level algorithms and data structures for performing track reconstruction tasks as well as fast track simulation. The software is developed with special emphasis on thread-safety to support parallel execution of the code and data structures are optimised for vectorisation to speed up linear algebra operations. The implementation is agnostic to the details of the detection technologies and magnetic field configuration which makes it applicable to many different experiments.

Large-Scale Exploratory Analysis, Cleaning, and Modeling for Event Detection in Real-World Power Systems Data

DTIC Science & Technology

2013-11-01

big data with R is relatively new. RHadoop is a mature product from Revolution Analytics that uses R with Hadoop Streaming [15] and provides...agnostic all- data summaries or computations, in which case we use MapReduce directly. 2.3 D&R Software Environment In this work, we use the Hadoop ...job scheduling and tracking, data distribu- tion, system architecture, heterogeneity, and fault-tolerance. Hadoop also provides a distributed key-value

Programmable multi-node quantum network design and simulation

NASA Astrophysics Data System (ADS)

Dasari, Venkat R.; Sadlier, Ronald J.; Prout, Ryan; Williams, Brian P.; Humble, Travis S.

2016-05-01

Software-defined networking offers a device-agnostic programmable framework to encode new network functions. Externally centralized control plane intelligence allows programmers to write network applications and to build functional network designs. OpenFlow is a key protocol widely adopted to build programmable networks because of its programmability, flexibility and ability to interconnect heterogeneous network devices. We simulate the functional topology of a multi-node quantum network that uses programmable network principles to manage quantum metadata for protocols such as teleportation, superdense coding, and quantum key distribution. We first show how the OpenFlow protocol can manage the quantum metadata needed to control the quantum channel. We then use numerical simulation to demonstrate robust programmability of a quantum switch via the OpenFlow network controller while executing an application of superdense coding. We describe the software framework implemented to carry out these simulations and we discuss near-term efforts to realize these applications.

Mapping to Irregular Torus Topologies and Other Techniques for Petascale Biomolecular Simulation

PubMed Central

Phillips, James C.; Sun, Yanhua; Jain, Nikhil; Bohm, Eric J.; Kalé, Laxmikant V.

2014-01-01

Currently deployed petascale supercomputers typically use toroidal network topologies in three or more dimensions. While these networks perform well for topology-agnostic codes on a few thousand nodes, leadership machines with 20,000 nodes require topology awareness to avoid network contention for communication-intensive codes. Topology adaptation is complicated by irregular node allocation shapes and holes due to dedicated input/output nodes or hardware failure. In the context of the popular molecular dynamics program NAMD, we present methods for mapping a periodic 3-D grid of fixed-size spatial decomposition domains to 3-D Cray Gemini and 5-D IBM Blue Gene/Q toroidal networks to enable hundred-million atom full machine simulations, and to similarly partition node allocations into compact domains for smaller simulations using multiple-copy algorithms. Additional enabling techniques are discussed and performance is reported for NCSA Blue Waters, ORNL Titan, ANL Mira, TACC Stampede, and NERSC Edison. PMID:25594075

Parallel Infrastructure Modeling and Inversion Module for E4D

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-10-09

Electrical resistivity tomography ERT is a method of imaging the electrical conductivity of the subsurface. Electrical conductivity is a useful metric for understanding the subsurface because it is governed by geomechanical and geochemical properties that drive subsurface systems. ERT works by injecting current into the subsurface across a pair of electrodes, and measuring the corresponding electrical potential response across another pair of electrodes. Many such measurements are strategically taken across an array of electrodes to produce an ERT data set. These data are then processed through a computationally demanding process known as inversion to produce an image of the subsurfacemore » conductivity structure that gave rise to the measurements. Data can be inverted to provide 2D images, 3D images, or in the case of time-lapse 3D imaging, 4D images. ERT is generally not well suited for environments with buried electrically conductive infrastructure such as pipes, tanks, or well casings, because these features tend to dominate and degrade ERT images. This reduces or eliminates the utility of ERT imaging where it would otherwise be highly useful for, for example, imaging fluid migration from leaking pipes, imaging soil contamination beneath leaking subusurface tanks, and monitoring contaminant migration in locations with dense network of metal cased monitoring wells. The location and dimension of buried metallic infrastructure is often known. If so, then the effects of the infrastructure can be explicitly modeled within the ERT imaging algorithm, and thereby removed from the corresponding ERT image. However,there are a number of obstacles limiting this application. 1) Metallic infrastructure cannot be accurately modeled with standard codes because of the large contrast in conductivity between the metal and host material. 2) Modeling infrastructure in true dimension requires the computational mesh to be highly refined near the metal inclusions, which increases computational demands. 3) The ERT imaging algorithm requires specialized modifications to accomodate high conductivty inclusions within the computational mesh. The solution to each of these challenges was implemented within E4D (formerly FERM3D), which is a parallel ERT imaging code developed at PNNL (IPID #30249). The infrastructure modeling module implement in E4D uses a method of decoupling the model at the metallic interface(s) boundaries, into several well posed sub-problems (one for each distinct metallicinclusion) that are subsequently solved and recombined to form the global solution. The approach is based on the immersed interface method, with has been applied for similar problems in other fields (e.g. semiconductor industry). Comparisons to analytic solutions have shown the results to be very accurate, addressing item 1 above. The solution is implemented about an unstructured mesh, which enables arbitrary shapes to be efficiently modelled, thereby addressing item 2 above. In addition, the algorithm is written in parallel and shows excellent scalability, which also addresses equation 2 above. Finally, because only the boundaries of metallic inclusions are modeled, there are no high conductivity cells within the modeling mesh, and the problem described by item 3 above is no longer applicable.« less

Operationalization of the Religious Support Team Concept Utilizing a Collaborative Leadership Model

DTIC Science & Technology

2013-02-14

19 APPENDIX D50 CHAPLAIN 2005 2012 +/- % ENLISTED 2005 2012 +/- % DENOMINATION DENOMINATION Agnostic Agnostic 1 2 +100 Buddhism ... Buddhism 2 1 -50 Christian 593 465 -21.5 Christian 278 221 -20.5 Christian No Pref 94 106 +12.7 Hindu Hindu 1 0 Jewish 11 7 -36.3 Jewish 3

The SCEC Community Modeling Environment(SCEC/CME): A Collaboratory for Seismic Hazard Analysis

NASA Astrophysics Data System (ADS)

Maechling, P. J.; Jordan, T. H.; Minster, J. B.; Moore, R.; Kesselman, C.

2005-12-01

The SCEC Community Modeling Environment (SCEC/CME) Project is an NSF-supported Geosciences/IT partnership that is actively developing an advanced information infrastructure for system-level earthquake science in Southern California. This partnership includes SCEC, USC's Information Sciences Institute (ISI), the San Diego Supercomputer Center (SDSC), the Incorporated Institutions for Research in Seismology (IRIS), and the U.S. Geological Survey. The goal of the SCEC/CME is to develop seismological applications and information technology (IT) infrastructure to support the development of Seismic Hazard Analysis (SHA) programs and other geophysical simulations. The SHA application programs developed on the Project include a Probabilistic Seismic Hazard Analysis system called OpenSHA. OpenSHA computational elements that are currently available include a collection of attenuation relationships, and several Earthquake Rupture Forecasts (ERFs). Geophysicists in the collaboration have also developed Anelastic Wave Models (AWMs) using both finite-difference and finite-element approaches. Earthquake simulations using these codes have been run for a variety of earthquake sources. Rupture Dynamic Model (RDM) codes have also been developed that simulate friction-based fault slip. The SCEC/CME collaboration has also developed IT software and hardware infrastructure to support the development, execution, and analysis of these SHA programs. To support computationally expensive simulations, we have constructed a grid-based scientific workflow system. Using the SCEC grid, project collaborators can submit computations from the SCEC/CME servers to High Performance Computers at USC and TeraGrid High Performance Computing Centers. Data generated and archived by the SCEC/CME is stored in a digital library system, the Storage Resource Broker (SRB). This system provides a robust and secure system for maintaining the association between the data seta and their metadata. To provide an easy-to-use system for constructing SHA computations, a browser-based workflow assembly web portal has been developed. Users can compose complex SHA calculations, specifying SCEC/CME data sets as inputs to calculations, and calling SCEC/CME computational programs to process the data and the output. Knowledge-based software tools have been implemented that utilize ontological descriptions of SHA software and data can validate workflows created with this pathway assembly tool. Data visualization software developed by the collaboration supports analysis and validation of data sets. Several programs have been developed to visualize SCEC/CME data including GMT-based map making software for PSHA codes, 4D wavefield propagation visualization software based on OpenGL, and 3D Geowall-based visualization of earthquakes, faults, and seismic wave propagation. The SCEC/CME Project also helps to sponsor the SCEC UseIT Intern program. The UseIT Intern Program provides research opportunities in both Geosciences and Information Technology to undergraduate students in a variety of fields. The UseIT group has developed a 3D data visualization tool, called SCEC-VDO, as a part of this undergraduate research program.

Data Mining as a Service (DMaaS)

NASA Astrophysics Data System (ADS)

Tejedor, E.; Piparo, D.; Mascetti, L.; Moscicki, J.; Lamanna, M.; Mato, P.

2016-10-01

Data Mining as a Service (DMaaS) is a software and computing infrastructure that allows interactive mining of scientific data in the cloud. It allows users to run advanced data analyses by leveraging the widely adopted Jupyter notebook interface. Furthermore, the system makes it easier to share results and scientific code, access scientific software, produce tutorials and demonstrations as well as preserve the analyses of scientists. This paper describes how a first pilot of the DMaaS service is being deployed at CERN, starting from the notebook interface that has been fully integrated with the ROOT analysis framework, in order to provide all the tools for scientists to run their analyses. Additionally, we characterise the service backend, which combines a set of IT services such as user authentication, virtual computing infrastructure, mass storage, file synchronisation, development portals or batch systems. The added value acquired by the combination of the aforementioned categories of services is discussed, focusing on the opportunities offered by the CERNBox synchronisation service and its massive storage backend, EOS.

Moving code - Sharing geoprocessing logic on the Web

NASA Astrophysics Data System (ADS)

Müller, Matthias; Bernard, Lars; Kadner, Daniel

2013-09-01

Efficient data processing is a long-standing challenge in remote sensing. Effective and efficient algorithms are required for product generation in ground processing systems, event-based or on-demand analysis, environmental monitoring, and data mining. Furthermore, the increasing number of survey missions and the exponentially growing data volume in recent years have created demand for better software reuse as well as an efficient use of scalable processing infrastructures. Solutions that address both demands simultaneously have begun to slowly appear, but they seldom consider the possibility to coordinate development and maintenance efforts across different institutions, community projects, and software vendors. This paper presents a new approach to share, reuse, and possibly standardise geoprocessing logic in the field of remote sensing. Drawing from the principles of service-oriented design and distributed processing, this paper introduces moving-code packages as self-describing software components that contain algorithmic code and machine-readable descriptions of the provided functionality, platform, and infrastructure, as well as basic information about exploitation rights. Furthermore, the paper presents a lean publishing mechanism by which to distribute these packages on the Web and to integrate them in different processing environments ranging from monolithic workstations to elastic computational environments or "clouds". The paper concludes with an outlook toward community repositories for reusable geoprocessing logic and their possible impact on data-driven science in general.

Sierra Toolkit Manual Version 4.48.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sierra Toolkit Team

This report provides documentation for the SIERRA Toolkit (STK) modules. STK modules are intended to provide infrastructure that assists the development of computational engineering soft- ware such as finite-element analysis applications. STK includes modules for unstructured-mesh data structures, reading/writing mesh files, geometric proximity search, and various utilities. This document contains a chapter for each module, and each chapter contains overview descriptions and usage examples. Usage examples are primarily code listings which are generated from working test programs that are included in the STK code-base. A goal of this approach is to ensure that the usage examples will not fall outmore » of date. This page intentionally left blank.« less

mGrid: A load-balanced distributed computing environment for the remote execution of the user-defined Matlab code

PubMed Central

Karpievitch, Yuliya V; Almeida, Jonas S

2006-01-01

Background Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. Results mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Conclusion Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet. PMID:16539707

mGrid: a load-balanced distributed computing environment for the remote execution of the user-defined Matlab code.

PubMed

Karpievitch, Yuliya V; Almeida, Jonas S

2006-03-15

Matlab, a powerful and productive language that allows for rapid prototyping, modeling and simulation, is widely used in computational biology. Modeling and simulation of large biological systems often require more computational resources then are available on a single computer. Existing distributed computing environments like the Distributed Computing Toolbox, MatlabMPI, Matlab*G and others allow for the remote (and possibly parallel) execution of Matlab commands with varying support for features like an easy-to-use application programming interface, load-balanced utilization of resources, extensibility over the wide area network, and minimal system administration skill requirements. However, all of these environments require some level of access to participating machines to manually distribute the user-defined libraries that the remote call may invoke. mGrid augments the usual process distribution seen in other similar distributed systems by adding facilities for user code distribution. mGrid's client-side interface is an easy-to-use native Matlab toolbox that transparently executes user-defined code on remote machines (i.e. the user is unaware that the code is executing somewhere else). Run-time variables are automatically packed and distributed with the user-defined code and automated load-balancing of remote resources enables smooth concurrent execution. mGrid is an open source environment. Apart from the programming language itself, all other components are also open source, freely available tools: light-weight PHP scripts and the Apache web server. Transparent, load-balanced distribution of user-defined Matlab toolboxes and rapid prototyping of many simple parallel applications can now be done with a single easy-to-use Matlab command. Because mGrid utilizes only Matlab, light-weight PHP scripts and the Apache web server, installation and configuration are very simple. Moreover, the web-based infrastructure of mGrid allows for it to be easily extensible over the Internet.

Virtual Geophysics Laboratory: Exploiting the Cloud and Empowering Geophysicsts

NASA Astrophysics Data System (ADS)

Fraser, Ryan; Vote, Josh; Goh, Richard; Cox, Simon

2013-04-01

Over the last five decades geoscientists from Australian state and federal agencies have collected and assembled around 3 Petabytes of geoscience data sets under public funding. As a consequence of technological progress, data is now being acquired at exponential rates and in higher resolution than ever before. Effective use of these big data sets challenges the storage and computational infrastructure of most organizations. The Virtual Geophysics Laboratory (VGL) is a scientific workflow portal addresses some of the resulting issues by providing Australian geophysicists with access to a Web 2.0 or Rich Internet Application (RIA) based integrated environment that exploits eResearch tools and Cloud computing technology, and promotes collaboration between the user community. VGL simplifies and automates large portions of what were previously manually intensive scientific workflow processes, allowing scientists to focus on the natural science problems, rather than computer science and IT. A number of geophysical processing codes are incorporated to support multiple workflows. For example a gravity inversion can be performed by combining the Escript/Finley codes (from the University of Queensland) with the gravity data registered in VGL. Likewise, tectonic processes can also be modeled by combining the Underworld code (from Monash University) with one of the various 3D models available to VGL. Cloud services provide scalable and cost effective compute resources. VGL is built on top of mature standards-compliant information services, many deployed using the Spatial Information Services Stack (SISS), which provides direct access to geophysical data. A large number of data sets from Geoscience Australia assist users in data discovery. GeoNetwork provides a metadata catalog to store workflow results for future use, discovery and provenance tracking. VGL has been developed in collaboration with the research community using incremental software development practices and open source tools. While developed to provide the geophysics research community with a sustainable platform and scalable infrastructure; VGL has also developed a number of concepts, patterns and generic components of which have been reused for cases beyond geophysics, including natural hazards, satellite processing and other areas requiring spatial data discovery and processing. Future plans for VGL include a number of improvements in both functional and non-functional areas in response to its user community needs and advancement in information technologies. In particular, research is underway in the following areas (a) distributed and parallel workflow processing in the cloud, (b) seamless integration with various cloud providers, and (c) integration with virtual laboratories representing other science domains. Acknowledgements: VGL was developed by CSIRO in collaboration with Geoscience Australia, National Computational Infrastructure, Australia National University, Monash University and University of Queensland, and has been supported by the Australian Government's Education Investment Funds through NeCTAR.

The "Ins" and "Outs" of Rural Teachers: Who Are Atheists, Agnostics, and Freethinkers

ERIC Educational Resources Information Center

Howley, Aimee; Howley, Craig; Dudek, Marged

2016-01-01

Perhaps the most maligned group of people in the United States, atheists and other nonbelievers (e.g., agnostics and freethinkers) reside everywhere and are employed in every field. Disclosure of nonbelief generally imposes costs, such as alienation from family and associates or even loss of employment. As a result, nonbelievers often disguise…

Teach Astronomy: An Educational Resource for Formal and Informal Learners

NASA Astrophysics Data System (ADS)

Impey, Chris David

2018-01-01

Teach Astronomy is an educational resource, available in the form of a user-friendly, platform-agnostic website. Ideal for college-level, introductory astronomy courses, Teach Astronomy can be a valuable reference for astronomers at all levels, especially informal learners. Over the past year, multiple changes have been made to the infrastructure behind Teach Astronomy to provide high availability to our tens of thousands of monthly, unique users, as well as fostering in new features. Teach Astronomy contains interactive tools which supplement the free textbook, such as a Quiz Tool with real-time feedback. The site also provides a searchable collection of Chris Impey’s responses to questions frequently asked by our users. The developers and educators behind Teach Astronomy are working to create an environment which encourages astronomy students of all levels to continue to increase their knowledge and help others learn.

Toward Scalable Trustworthy Computing Using the Human-Physiology-Immunity Metaphor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hively, Lee M; Sheldon, Frederick T

The cybersecurity landscape consists of an ad hoc patchwork of solutions. Optimal cybersecurity is difficult for various reasons: complexity, immense data and processing requirements, resource-agnostic cloud computing, practical time-space-energy constraints, inherent flaws in 'Maginot Line' defenses, and the growing number and sophistication of cyberattacks. This article defines the high-priority problems and examines the potential solution space. In that space, achieving scalable trustworthy computing and communications is possible through real-time knowledge-based decisions about cyber trust. This vision is based on the human-physiology-immunity metaphor and the human brain's ability to extract knowledge from data and information. The article outlines future steps towardmore » scalable trustworthy systems requiring a long-term commitment to solve the well-known challenges.« less

Building a Generic Virtual Research Environment Framework for Multiple Earth and Space Science Domains and a Diversity of Users.

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Fraser, R.; Evans, B. J. K.; Friedrich, C.; Klump, J. F.; Lescinsky, D. T.

2017-12-01

Virtual Research Environments (VREs) are now part of academic infrastructures. Online research workflows can be orchestrated whereby data can be accessed from multiple external repositories with processing taking place on public or private clouds, and centralised supercomputers using a mixture of user codes, and well-used community software and libraries. VREs enable distributed members of research teams to actively work together to share data, models, tools, software, workflows, best practices, infrastructures, etc. These environments and their components are increasingly able to support the needs of undergraduate teaching. External to the research sector, they can also be reused by citizen scientists, and be repurposed for industry users to help accelerate the diffusion and hence enable the translation of research innovations. The Virtual Geophysics Laboratory (VGL) in Australia was started in 2012, built using a collaboration between CSIRO, the National Computational Infrastructure (NCI) and Geoscience Australia, with support funding from the Australian Government Department of Education. VGL comprises three main modules that provide an interface to enable users to first select their required data; to choose a tool to process that data; and then access compute infrastructure for execution. VGL was initially built to enable a specific set of researchers in government agencies access to specific data sets and a limited number of tools. Over the years it has evolved into a multi-purpose Earth science platform with access to an increased variety of data (e.g., Natural Hazards, Geochemistry), a broader range of software packages, and an increasing diversity of compute infrastructures. This expansion has been possible because of the approach to loosely couple data, tools and compute resources via interfaces that are built on international standards and accessed as network-enabled services wherever possible. Built originally for researchers that were not fussy about general usability, increasing emphasis on User Interfaces (UIs) and stability will lead to increased uptake in the education and industry sectors. Simultaneously, improvements are being added to facilitate access to data and tools by experienced researchers who want direct access to both data and flexible workflows.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

PubMed

Burdick, David B; Cavnor, Chris C; Handcock, Jeremy; Killcoyne, Sarah; Lin, Jake; Marzolf, Bruz; Ramsey, Stephen A; Rovira, Hector; Bressler, Ryan; Shmulevich, Ilya; Boyle, John

2010-07-14

High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services.

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments

PubMed Central

2010-01-01

Background High throughput sequencing has become an increasingly important tool for biological research. However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires. Results Existing software solutions provide static and well-established algorithms in a restrictive package. However as high throughput sequencing is a rapidly evolving field, such static approaches lack the ability to readily adopt the latest advances and techniques which are often required by researchers. We have used a loosely coupled, service-oriented infrastructure to develop SeqAdapt. This system streamlines data management and allows for rapid integration of novel algorithms. Our approach also allows computational biologists to focus on developing and applying new methods instead of writing boilerplate infrastructure code. Conclusion The system is based around the Addama service architecture and is available at our website as a demonstration web application, an installable single download and as a collection of individual customizable services. PMID:20630057

OpenCMISS: a multi-physics & multi-scale computational infrastructure for the VPH/Physiome project.

PubMed

Bradley, Chris; Bowery, Andy; Britten, Randall; Budelmann, Vincent; Camara, Oscar; Christie, Richard; Cookson, Andrew; Frangi, Alejandro F; Gamage, Thiranja Babarenda; Heidlauf, Thomas; Krittian, Sebastian; Ladd, David; Little, Caton; Mithraratne, Kumar; Nash, Martyn; Nickerson, David; Nielsen, Poul; Nordbø, Oyvind; Omholt, Stig; Pashaei, Ali; Paterson, David; Rajagopal, Vijayaraghavan; Reeve, Adam; Röhrle, Oliver; Safaei, Soroush; Sebastián, Rafael; Steghöfer, Martin; Wu, Tim; Yu, Ting; Zhang, Heye; Hunter, Peter

2011-10-01

The VPH/Physiome Project is developing the model encoding standards CellML (cellml.org) and FieldML (fieldml.org) as well as web-accessible model repositories based on these standards (models.physiome.org). Freely available open source computational modelling software is also being developed to solve the partial differential equations described by the models and to visualise results. The OpenCMISS code (opencmiss.org), described here, has been developed by the authors over the last six years to replace the CMISS code that has supported a number of organ system Physiome projects. OpenCMISS is designed to encompass multiple sets of physical equations and to link subcellular and tissue-level biophysical processes into organ-level processes. In the Heart Physiome project, for example, the large deformation mechanics of the myocardial wall need to be coupled to both ventricular flow and embedded coronary flow, and the reaction-diffusion equations that govern the propagation of electrical waves through myocardial tissue need to be coupled with equations that describe the ion channel currents that flow through the cardiac cell membranes. In this paper we discuss the design principles and distributed memory architecture behind the OpenCMISS code. We also discuss the design of the interfaces that link the sets of physical equations across common boundaries (such as fluid-structure coupling), or between spatial fields over the same domain (such as coupled electromechanics), and the concepts behind CellML and FieldML that are embodied in the OpenCMISS data structures. We show how all of these provide a flexible infrastructure for combining models developed across the VPH/Physiome community. Copyright © 2011 Elsevier Ltd. All rights reserved.

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology.

PubMed

Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E; Troein, Carl; Millar, Andrew J; Goryanin, Igor; Gilmore, Stephen

2013-03-01

Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI's use of standard data formats. All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials.

Computational analysis of water entry of a circular section at constant velocity based on Reynold's averaged Navier-Stokes method

NASA Astrophysics Data System (ADS)

Uddin, M. Maruf; Fuad, Muzaddid-E.-Zaman; Rahaman, Md. Mashiur; Islam, M. Rabiul

2017-12-01

With the rapid decrease in the cost of computational infrastructure with more efficient algorithm for solving non-linear problems, Reynold's averaged Navier-Stokes (RaNS) based Computational Fluid Dynamics (CFD) has been used widely now-a-days. As a preliminary evaluation tool, CFD is used to calculate the hydrodynamic loads on offshore installations, ships, and other structures in the ocean at initial design stages. Traditionally, wedges have been studied more than circular cylinders because cylinder section has zero deadrise angle at the instant of water impact, which increases with increase of submergence. In Present study, RaNS based commercial code ANSYS Fluent is used to simulate the water entry of a circular section at constant velocity. It is seen that present computational results were compared with experiment and other numerical method.

LHC@Home: a BOINC-based volunteer computing infrastructure for physics studies at CERN

NASA Astrophysics Data System (ADS)

Barranco, Javier; Cai, Yunhai; Cameron, David; Crouch, Matthew; Maria, Riccardo De; Field, Laurence; Giovannozzi, Massimo; Hermes, Pascal; Høimyr, Nils; Kaltchev, Dobrin; Karastathis, Nikos; Luzzi, Cinzia; Maclean, Ewen; McIntosh, Eric; Mereghetti, Alessio; Molson, James; Nosochkov, Yuri; Pieloni, Tatiana; Reid, Ivan D.; Rivkin, Lenny; Segal, Ben; Sjobak, Kyrre; Skands, Peter; Tambasco, Claudia; Veken, Frederik Van der; Zacharov, Igor

2017-12-01

The LHC@Home BOINC project has provided computing capacity for numerical simulations to researchers at CERN since 2004, and has since 2011 been expanded with a wider range of applications. The traditional CERN accelerator physics simulation code SixTrack enjoys continuing volunteers support, and thanks to virtualisation a number of applications from the LHC experiment collaborations and particle theory groups have joined the consolidated LHC@Home BOINC project. This paper addresses the challenges related to traditional and virtualized applications in the BOINC environment, and how volunteer computing has been integrated into the overall computing strategy of the laboratory through the consolidated LHC@Home service. Thanks to the computing power provided by volunteers joining LHC@Home, numerous accelerator beam physics studies have been carried out, yielding an improved understanding of charged particle dynamics in the CERN Large Hadron Collider (LHC) and its future upgrades. The main results are highlighted in this paper.

MEMOPS: data modelling and automatic code generation.

PubMed

Fogh, Rasmus H; Boucher, Wayne; Ionides, John M C; Vranken, Wim F; Stevens, Tim J; Laue, Ernest D

2010-03-25

In recent years the amount of biological data has exploded to the point where much useful information can only be extracted by complex computational analyses. Such analyses are greatly facilitated by metadata standards, both in terms of the ability to compare data originating from different sources, and in terms of exchanging data in standard forms, e.g. when running processes on a distributed computing infrastructure. However, standards thrive on stability whereas science tends to constantly move, with new methods being developed and old ones modified. Therefore maintaining both metadata standards, and all the code that is required to make them useful, is a non-trivial problem. Memops is a framework that uses an abstract definition of the metadata (described in UML) to generate internal data structures and subroutine libraries for data access (application programming interfaces--APIs--currently in Python, C and Java) and data storage (in XML files or databases). For the individual project these libraries obviate the need for writing code for input parsing, validity checking or output. Memops also ensures that the code is always internally consistent, massively reducing the need for code reorganisation. Across a scientific domain a Memops-supported data model makes it easier to support complex standards that can capture all the data produced in a scientific area, share them among all programs in a complex software pipeline, and carry them forward to deposition in an archive. The principles behind the Memops generation code will be presented, along with example applications in Nuclear Magnetic Resonance (NMR) spectroscopy and structural biology.

The Secret Life of Quarks, Final Report for the University of North Carolina at Chapel Hill

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fowler, Robert J.

This final report summarizes activities and results at the University of North Carolina as part of the the SciDAC-2 Project The Secret Life of Quarks: National Computational Infrastructure for Lattice Quantum Chromodynamics. The overall objective of the project is to construct the software needed to study quantum chromo- dynamics (QCD), the theory of the strong interactions of subatomic physics, and similar strongly coupled gauge theories anticipated to be of importance in the LHC era. It built upon the successful efforts of the SciDAC-1 project National Computational Infrastructure for Lattice Gauge Theory, in which a QCD Applications Programming Interface (QCD API)more » was developed that enables lat- tice gauge theorists to make effective use of a wide variety of massively parallel computers. In the SciDAC-2 project, optimized versions of the QCD API were being created for the IBM Blue- Gene/L (BG/L) and BlueGene/P (BG/P), the Cray XT3/XT4 and its successors, and clusters based on multi-core processors and Infiniband communications networks. The QCD API is being used to enhance the performance of the major QCD community codes and to create new applications. Software libraries of physics tools have been expanded to contain sharable building blocks for inclusion in application codes, performance analysis and visualization tools, and software for au- tomation of physics work flow. New software tools were designed for managing the large data sets generated in lattice QCD simulations, and for sharing them through the International Lattice Data Grid consortium. As part of the overall project, researchers at UNC were funded through ASCR to work in three general areas. The main thrust has been performance instrumentation and analysis in support of the SciDAC QCD code base as it evolved and as it moved to new computation platforms. In support of the performance activities, performance data was to be collected in a database for the purpose of broader analysis. Third, the UNC work was done at RENCI (Renaissance Computing Institute), which has extensive expertise and facilities for scientific data visualization, so we acted in an ongoing consulting and support role in that area.« less

77 FR 59203 - Critical Infrastructure Partnership Advisory Council (CIPAC)

Federal Register 2010, 2011, 2012, 2013, 2014

2012-09-26

... Infrastructure Partnership Advisory Council. [FR Doc. 2012-23666 Filed 9-25-12; 8:45 am] BILLING CODE 9910-9P-P ... DEPARTMENT OF HOMELAND SECURITY [Docket No. DHS-2012-0051] Critical Infrastructure Partnership... meeting. SUMMARY: The Critical Infrastructure Partnership Advisory Council (CIPAC) Plenary Meeting will be...

Development and application of the dynamic system doctor to nuclear reactor probabilistic risk assessments.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kunsman, David Marvin; Aldemir, Tunc; Rutt, Benjamin

2008-05-01

This LDRD project has produced a tool that makes probabilistic risk assessments (PRAs) of nuclear reactors - analyses which are very resource intensive - more efficient. PRAs of nuclear reactors are being increasingly relied on by the United States Nuclear Regulatory Commission (U.S.N.R.C.) for licensing decisions for current and advanced reactors. Yet, PRAs are produced much as they were 20 years ago. The work here applied a modern systems analysis technique to the accident progression analysis portion of the PRA; the technique was a system-independent multi-task computer driver routine. Initially, the objective of the work was to fuse the accidentmore » progression event tree (APET) portion of a PRA to the dynamic system doctor (DSD) created by Ohio State University. Instead, during the initial efforts, it was found that the DSD could be linked directly to a detailed accident progression phenomenological simulation code - the type on which APET construction and analysis relies, albeit indirectly - and thereby directly create and analyze the APET. The expanded DSD computational architecture and infrastructure that was created during this effort is called ADAPT (Analysis of Dynamic Accident Progression Trees). ADAPT is a system software infrastructure that supports execution and analysis of multiple dynamic event-tree simulations on distributed environments. A simulator abstraction layer was developed, and a generic driver was implemented for executing simulators on a distributed environment. As a demonstration of the use of the methodological tool, ADAPT was applied to quantify the likelihood of competing accident progression pathways occurring for a particular accident scenario in a particular reactor type using MELCOR, an integrated severe accident analysis code developed at Sandia. (ADAPT was intentionally created with flexibility, however, and is not limited to interacting with only one code. With minor coding changes to input files, ADAPT can be linked to other such codes.) The results of this demonstration indicate that the approach can significantly reduce the resources required for Level 2 PRAs. From the phenomenological viewpoint, ADAPT can also treat the associated epistemic and aleatory uncertainties. This methodology can also be used for analyses of other complex systems. Any complex system can be analyzed using ADAPT if the workings of that system can be displayed as an event tree, there is a computer code that simulates how those events could progress, and that simulator code has switches to turn on and off system events, phenomena, etc. Using and applying ADAPT to particular problems is not human independent. While the human resources for the creation and analysis of the accident progression are significantly decreased, knowledgeable analysts are still necessary for a given project to apply ADAPT successfully. This research and development effort has met its original goals and then exceeded them.« less

Towards Reproducibility in Computational Hydrology

NASA Astrophysics Data System (ADS)

Hutton, Christopher; Wagener, Thorsten; Freer, Jim; Han, Dawei; Duffy, Chris; Arheimer, Berit

2017-04-01

Reproducibility is a foundational principle in scientific research. The ability to independently re-run an experiment helps to verify the legitimacy of individual findings, and evolve (or reject) hypotheses and models of how environmental systems function, and move them from specific circumstances to more general theory. Yet in computational hydrology (and in environmental science more widely) the code and data that produces published results are not regularly made available, and even if they are made available, there remains a multitude of generally unreported choices that an individual scientist may have made that impact the study result. This situation strongly inhibits the ability of our community to reproduce and verify previous findings, as all the information and boundary conditions required to set up a computational experiment simply cannot be reported in an article's text alone. In Hutton et al 2016 [1], we argue that a cultural change is required in the computational hydrological community, in order to advance and make more robust the process of knowledge creation and hypothesis testing. We need to adopt common standards and infrastructures to: (1) make code readable and re-useable; (2) create well-documented workflows that combine re-useable code together with data to enable published scientific findings to be reproduced; (3) make code and workflows available, easy to find, and easy to interpret, using code and code metadata repositories. To create change we argue for improved graduate training in these areas. In this talk we reflect on our progress in achieving reproducible, open science in computational hydrology, which are relevant to the broader computational geoscience community. In particular, we draw on our experience in the Switch-On (EU funded) virtual water science laboratory (http://www.switch-on-vwsl.eu/participate/), which is an open platform for collaboration in hydrological experiments (e.g. [2]). While we use computational hydrology as the example application area, we believe that our conclusions are of value to the wider environmental and geoscience community as far as the use of code and models for scientific advancement is concerned. References: [1] Hutton, C., T. Wagener, J. Freer, D. Han, C. Duffy, and B. Arheimer (2016), Most computational hydrology is not reproducible, so is it really science?, Water Resour. Res., 52, 7548-7555, doi:10.1002/2016WR019285. [2] Ceola, S., et al. (2015), Virtual laboratories: New opportunities for collaborative water science, Hydrol. Earth Syst. Sci. Discuss., 11(12), 13443-13478, doi:10.5194/hessd-11-13443-2014.

Open NASA Earth Exchange (OpenNEX): Strategies for enabling cross organization collaboration in the earth sciences

NASA Astrophysics Data System (ADS)

Michaelis, A.; Ganguly, S.; Nemani, R. R.; Votava, P.; Wang, W.; Lee, T. J.; Dungan, J. L.

2014-12-01

Sharing community-valued codes, intermediary datasets and results from individual efforts with others that are not in a direct funded collaboration can be a challenge. Cross organization collaboration is often impeded due to infrastructure security constraints, rigid financial controls, bureaucracy, and workforce nationalities, etc., which can force groups to work in a segmented fashion and/or through awkward and suboptimal web services. We show how a focused community may come together, share modeling and analysis codes, computing configurations, scientific results, knowledge and expertise on a public cloud platform; diverse groups of researchers working together at "arms length". Through the OpenNEX experimental workshop, users can view short technical "how-to" videos and explore encapsulated working environment. Workshop participants can easily instantiate Amazon Machine Images (AMI) or launch full cluster and data processing configurations within minutes. Enabling users to instantiate computing environments from configuration templates on large public cloud infrastructures, such as Amazon Web Services, may provide a mechanism for groups to easily use each others work and collaborate indirectly. Moreover, using the public cloud for this workshop allowed a single group to host a large read only data archive, making datasets of interest to the community widely available on the public cloud, enabling other groups to directly connect to the data and reduce the costs of the collaborative work by freeing other individual groups from redundantly retrieving, integrating or financing the storage of the datasets of interest.

Performance Analysis, Design Considerations, and Applications of Extreme-Scale In Situ Infrastructures

DOE PAGES

Ayachit, Utkarsh; Bauer, Andrew; Duque, Earl P. N.; ...

2016-11-01

A key trend facing extreme-scale computational science is the widening gap between computational and I/O rates, and the challenge that follows is how to best gain insight from simulation data when it is increasingly impractical to save it to persistent storage for subsequent visual exploration and analysis. One approach to this challenge is centered around the idea of in situ processing, where visualization and analysis processing is performed while data is still resident in memory. Our paper examines several key design and performance issues related to the idea of in situ processing at extreme scale on modern platforms: Scalability, overhead,more » performance measurement and analysis, comparison and contrast with a traditional post hoc approach, and interfacing with simulation codes. We illustrate these principles in practice with studies, conducted on large-scale HPC platforms, that include a miniapplication and multiple science application codes, one of which demonstrates in situ methods in use at greater than 1M-way concurrency.« less

Building A Community Focused Data and Modeling Collaborative platform with Hardware Virtualization Technology

NASA Astrophysics Data System (ADS)

Michaelis, A.; Wang, W.; Melton, F. S.; Votava, P.; Milesi, C.; Hashimoto, H.; Nemani, R. R.; Hiatt, S. H.

2009-12-01

As the length and diversity of the global earth observation data records grow, modeling and analyses of biospheric conditions increasingly requires multiple terabytes of data from a diversity of models and sensors. With network bandwidth beginning to flatten, transmission of these data from centralized data archives presents an increasing challenge, and costs associated with local storage and management of data and compute resources are often significant for individual research and application development efforts. Sharing community valued intermediary data sets, results and codes from individual efforts with others that are not in direct funded collaboration can also be a challenge with respect to time, cost and expertise. We purpose a modeling, data and knowledge center that houses NASA satellite data, climate data and ancillary data where a focused community may come together to share modeling and analysis codes, scientific results, knowledge and expertise on a centralized platform, named Ecosystem Modeling Center (EMC). With the recent development of new technologies for secure hardware virtualization, an opportunity exists to create specific modeling, analysis and compute environments that are customizable, “archiveable” and transferable. Allowing users to instantiate such environments on large compute infrastructures that are directly connected to large data archives may significantly reduce costs and time associated with scientific efforts by alleviating users from redundantly retrieving and integrating data sets and building modeling analysis codes. The EMC platform also provides the possibility for users receiving indirect assistance from expertise through prefabricated compute environments, potentially reducing study “ramp up” times.

Enabling a Scientific Cloud Marketplace: VGL (Invited)

NASA Astrophysics Data System (ADS)

Fraser, R.; Woodcock, R.; Wyborn, L. A.; Vote, J.; Rankine, T.; Cox, S. J.

2013-12-01

The Virtual Geophysics Laboratory (VGL) provides a flexible, web based environment where researchers can browse data and use a variety of scientific software packaged into tool kits that run in the Cloud. Both data and tool kits are published by multiple researchers and registered with the VGL infrastructure forming a data and application marketplace. The VGL provides the basic work flow of Discovery and Access to the disparate data sources and a Library for tool kits and scripting to drive the scientific codes. Computation is then performed on the Research or Commercial Clouds. Provenance information is collected throughout the work flow and can be published alongside the results allowing for experiment comparison and sharing with other researchers. VGL's "mix and match" approach to data, computational resources and scientific codes, enables a dynamic approach to scientific collaboration. VGL allows scientists to publish their specific contribution, be it data, code, compute or work flow, knowing the VGL framework will provide other components needed for a complete application. Other scientists can choose the pieces that suit them best to assemble an experiment. The coarse grain workflow of the VGL framework combined with the flexibility of the scripting library and computational toolkits allows for significant customisation and sharing amongst the community. The VGL utilises the cloud computational and storage resources from the Australian academic research cloud provided by the NeCTAR initiative and a large variety of data accessible from national and state agencies via the Spatial Information Services Stack (SISS - http://siss.auscope.org). VGL v1.2 screenshot - http://vgl.auscope.org

Grid Computing and Collaboration Technology in Support of Fusion Energy Sciences

NASA Astrophysics Data System (ADS)

Schissel, D. P.

2004-11-01

The SciDAC Initiative is creating a computational grid designed to advance scientific understanding in fusion research by facilitating collaborations, enabling more effective integration of experiments, theory and modeling, and allowing more efficient use of experimental facilities. The philosophy is that data, codes, analysis routines, visualization tools, and communication tools should be thought of as easy to use network available services. Access to services is stressed rather than portability. Services share the same basic security infrastructure so that stakeholders can control their own resources and helps ensure fair use of resources. The collaborative control room is being developed using the open-source Access Grid software that enables secure group-to-group collaboration with capabilities beyond teleconferencing including application sharing and control. The ability to effectively integrate off-site scientists into a dynamic control room will be critical to the success of future international projects like ITER. Grid computing, the secure integration of computer systems over high-speed networks to provide on-demand access to data analysis capabilities and related functions, is being deployed as an alternative to traditional resource sharing among institutions. The first grid computational service deployed was the transport code TRANSP and included tools for run preparation, submission, monitoring and management. This approach saves user sites from the laborious effort of maintaining a complex code while at the same time reducing the burden on developers by avoiding the support of a large number of heterogeneous installations. This tutorial will present the philosophy behind an advanced collaborative environment, give specific examples, and discuss its usage beyond FES.

Using Cloud Computing infrastructure with CloudBioLinux, CloudMan and Galaxy

PubMed Central

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-01-01

Cloud computing has revolutionized availability and access to computing and storage resources; making it possible to provision a large computational infrastructure with only a few clicks in a web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this protocol, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatics analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to setup the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command line interface, and the web-based Galaxy interface. PMID:22700313

Using cloud computing infrastructure with CloudBioLinux, CloudMan, and Galaxy.

PubMed

Afgan, Enis; Chapman, Brad; Jadan, Margita; Franke, Vedran; Taylor, James

2012-06-01

Cloud computing has revolutionized availability and access to computing and storage resources, making it possible to provision a large computational infrastructure with only a few clicks in a Web browser. However, those resources are typically provided in the form of low-level infrastructure components that need to be procured and configured before use. In this unit, we demonstrate how to utilize cloud computing resources to perform open-ended bioinformatic analyses, with fully automated management of the underlying cloud infrastructure. By combining three projects, CloudBioLinux, CloudMan, and Galaxy, into a cohesive unit, we have enabled researchers to gain access to more than 100 preconfigured bioinformatics tools and gigabytes of reference genomes on top of the flexible cloud computing infrastructure. The protocol demonstrates how to set up the available infrastructure and how to use the tools via a graphical desktop interface, a parallel command-line interface, and the Web-based Galaxy interface.

The SENSEI Generic In Situ Interface

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ayachit, Utkarsh; Whitlock, Brad; Wolf, Matthew

The SENSEI generic in situ interface is an API that promotes code portability and reusability. From the simulation view, a developer can instrument their code with the SENSEI API and then make make use of any number of in situ infrastructures. From the method view, a developer can write an in situ method using the SENSEI API, then expect it to run in any number of in situ infrastructures, or be invoked directly from a simulation code, with little or no modification. This paper presents the design principles underlying the SENSEI generic interface, along with some simplified coding examples.

77 FR 60687 - Record of Decision for the U.S. Marine Corps Basewide Water Infrastructure Project at Marine...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-04

... Water Infrastructure Project at Marine Corps Base Camp Pendleton, California AGENCY: Department of the... Environmental Policy Act (NEPA) of 1969, 42 United States Code (U.S.C.) Section 4332(2)(c), the regulations of the Council on Environmental Quality for Implementing the Procedural Provisions of NEPA (40 Code of...

National Fusion Collaboratory: Grid Computing for Simulations and Experiments

NASA Astrophysics Data System (ADS)

Greenwald, Martin

2004-05-01

The National Fusion Collaboratory Project is creating a computational grid designed to advance scientific understanding and innovation in magnetic fusion research by facilitating collaborations, enabling more effective integration of experiments, theory and modeling and allowing more efficient use of experimental facilities. The philosophy of FusionGrid is that data, codes, analysis routines, visualization tools, and communication tools should be thought of as network available services, easily used by the fusion scientist. In such an environment, access to services is stressed rather than portability. By building on a foundation of established computer science toolkits, deployment time can be minimized. These services all share the same basic infrastructure that allows for secure authentication and resource authorization which allows stakeholders to control their own resources such as computers, data and experiments. Code developers can control intellectual property, and fair use of shared resources can be demonstrated and controlled. A key goal is to shield scientific users from the implementation details such that transparency and ease-of-use are maximized. The first FusionGrid service deployed was the TRANSP code, a widely used tool for transport analysis. Tools for run preparation, submission, monitoring and management have been developed and shared among a wide user base. This approach saves user sites from the laborious effort of maintaining such a large and complex code while at the same time reducing the burden on the development team by avoiding the need to support a large number of heterogeneous installations. Shared visualization and A/V tools are being developed and deployed to enhance long-distance collaborations. These include desktop versions of the Access Grid, a highly capable multi-point remote conferencing tool and capabilities for sharing displays and analysis tools over local and wide-area networks.

Initial Coupling of the RELAP-7 and PRONGHORN Applications

DOE Office of Scientific and Technical Information (OSTI.GOV)

J. Ortensi; D. Andrs; A.A. Bingham

2012-10-01

Modern nuclear reactor safety codes require the ability to solve detailed coupled neutronic- thermal fluids problems. For larger cores, this implies fully coupled higher dimensionality spatial dynamics with appropriate feedback models that can provide enough resolution to accurately compute core heat generation and removal during steady and unsteady conditions. The reactor analysis code PRONGHORN is being coupled to RELAP-7 as a first step to extend RELAP’s current capabilities. This report details the mathematical models, the type of coupling, and the testing results from the integrated system. RELAP-7 is a MOOSE-based application that solves the continuity, momentum, and energy equations inmore » 1-D for a compressible fluid. The pipe and joint capabilities enable it to model parts of the power conversion unit. The PRONGHORN application, also developed on the MOOSE infrastructure, solves the coupled equations that define the neutron diffusion, fluid flow, and heat transfer in a full core model. The two systems are loosely coupled to simplify the transition towards a more complex infrastructure. The integration is tested on a simplified version of the OECD/NEA MHTGR-350 Coupled Neutronics-Thermal Fluids benchmark model.« less

75 FR 14454 - National Protection and Programs Directorate; National Infrastructure Advisory Council

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-25

..., National Infrastructure Advisory Council. [FR Doc. 2010-6633 Filed 3-24-10; 8:45 am] BILLING CODE 9110-9P-P ... Directorate; National Infrastructure Advisory Council AGENCY: National Protection and Programs Directorate... Infrastructure Advisory Council (NIAC) will meet on Tuesday, April 13, 2010, at the National Press Club's...

Telomerecat: A ploidy-agnostic method for estimating telomere length from whole genome sequencing data.

PubMed

Farmery, James H R; Smith, Mike L; Lynch, Andy G

2018-01-22

Telomere length is a risk factor in disease and the dynamics of telomere length are crucial to our understanding of cell replication and vitality. The proliferation of whole genome sequencing represents an unprecedented opportunity to glean new insights into telomere biology on a previously unimaginable scale. To this end, a number of approaches for estimating telomere length from whole-genome sequencing data have been proposed. Here we present Telomerecat, a novel approach to the estimation of telomere length. Previous methods have been dependent on the number of telomeres present in a cell being known, which may be problematic when analysing aneuploid cancer data and non-human samples. Telomerecat is designed to be agnostic to the number of telomeres present, making it suited for the purpose of estimating telomere length in cancer studies. Telomerecat also accounts for interstitial telomeric reads and presents a novel approach to dealing with sequencing errors. We show that Telomerecat performs well at telomere length estimation when compared to leading experimental and computational methods. Furthermore, we show that it detects expected patterns in longitudinal data, repeated measurements, and cross-species comparisons. We also apply the method to a cancer cell data, uncovering an interesting relationship with the underlying telomerase genotype.

Bottlenecks and Waiting Points in Nucleosynthesis in X-ray bursts and Novae

NASA Astrophysics Data System (ADS)

Smith, Michael S.; Sunayama, Tomomi; Hix, W. Raphael; Lingerfelt, Eric J.; Nesaraja, Caroline D.

2010-08-01

To better understand the energy generation and element synthesis occurring in novae and X-ray bursts, we give quantitative definitions to the concepts of ``bottlenecks'' and ``waiting points'' in the thermonuclear reaction flow. We use these criteria to search for bottlenecks and waiting points in post-processing element synthesis explosion simulations. We have incorporated these into the Computational Infrastructure for Nuclear Astrophysics, a suite of nuclear astrophysics codes available online at nucastrodata.org, so that anyone may perform custom searches for bottlenecks and waiting points.

Bottlenecks and Waiting Points in Nucleosynthesis in X-ray bursts and Novae

DOE Office of Scientific and Technical Information (OSTI.GOV)

Smith, Michael S.; Hix, W. Raphael; Nesaraja, Caroline D.

2010-08-12

To better understand the energy generation and element synthesis occurring in novae and X-ray bursts, we give quantitative definitions to the concepts of ''bottlenecks'' and ''waiting points'' in the thermonuclear reaction flow. We use these criteria to search for bottlenecks and waiting points in post-processing element synthesis explosion simulations. We have incorporated these into the Computational Infrastructure for Nuclear Astrophysics, a suite of nuclear astrophysics codes available online at nucastrodata.org, so that anyone may perform custom searches for bottlenecks and waiting points.

OPserver: opacities and radiative accelerations on demand

NASA Astrophysics Data System (ADS)

Mendoza, C.; González, J.; Seaton, M. J.; Buerger, P.; Bellorín, A.; Meléndez, M.; Rodríguez, L. S.; Delahaye, F.; Zeippen, C. J.; Palacios, E.; Pradhan, A. K.

2009-05-01

We report on developments carried out within the Opacity Project (OP) to upgrade atomic database services to comply with e-infrastructure requirements. We give a detailed description of an interactive, online server for astrophysical opacities, referred to as OPserver, to be used in sophisticated stellar modelling where Rosseland mean opacities and radiative accelerations are computed at every depth point and each evolution cycle. This is crucial, for instance, in chemically peculiar stars and in the exploitation of the new asteroseismological data. OPserver, downloadable with the new OPCD_3.0 release from the Centre de Données Astronomiques de Strasbourg, France, computes mean opacities and radiative data for arbitrary chemical mixtures from the OP monochromatic opacities. It is essentially a client-server network restructuring and optimization of the suite of codes included in the earlier OPCD_2.0 release. The server can be installed locally or, alternatively, accessed remotely from the Ohio Supercomputer Center, Columbus, Ohio, USA. The client is an interactive web page or a subroutine library that can be linked to the user code. The suitability of this scheme in grid computing environments is emphasized, and its extension to other atomic database services for astrophysical purposes is discussed.

Dynamic Collaboration Infrastructure for Hydrologic Science

NASA Astrophysics Data System (ADS)

Tarboton, D. G.; Idaszak, R.; Castillo, C.; Yi, H.; Jiang, F.; Jones, N.; Goodall, J. L.

2016-12-01

Data and modeling infrastructure is becoming increasingly accessible to water scientists. HydroShare is a collaborative environment that currently offers water scientists the ability to access modeling and data infrastructure in support of data intensive modeling and analysis. It supports the sharing of and collaboration around "resources" which are social objects defined to include both data and models in a structured standardized format. Users collaborate around these objects via comments, ratings, and groups. HydroShare also supports web services and cloud based computation for the execution of hydrologic models and analysis and visualization of hydrologic data. However, the quantity and variety of data and modeling infrastructure available that can be accessed from environments like HydroShare is increasing. Storage infrastructure can range from one's local PC to campus or organizational storage to storage in the cloud. Modeling or computing infrastructure can range from one's desktop to departmental clusters to national HPC resources to grid and cloud computing resources. How does one orchestrate this vast number of data and computing infrastructure without needing to correspondingly learn each new system? A common limitation across these systems is the lack of efficient integration between data transport mechanisms and the corresponding high-level services to support large distributed data and compute operations. A scientist running a hydrology model from their desktop may require processing a large collection of files across the aforementioned storage and compute resources and various national databases. To address these community challenges a proof-of-concept prototype was created integrating HydroShare with RADII (Resource Aware Data-centric collaboration Infrastructure) to provide software infrastructure to enable the comprehensive and rapid dynamic deployment of what we refer to as "collaborative infrastructure." In this presentation we discuss the results of this proof-of-concept prototype which enabled HydroShare users to readily instantiate virtual infrastructure marshaling arbitrary combinations, varieties, and quantities of distributed data and computing infrastructure in addressing big problems in hydrology.

A Three-Phase Decision Model of Computer-Aided Coding for the Iranian Classification of Health Interventions (IRCHI).

PubMed

Azadmanjir, Zahra; Safdari, Reza; Ghazisaeedi, Marjan; Mokhtaran, Mehrshad; Kameli, Mohammad Esmail

2017-06-01

Accurate coded data in the healthcare are critical. Computer-Assisted Coding (CAC) is an effective tool to improve clinical coding in particular when a new classification will be developed and implemented. But determine the appropriate method for development need to consider the specifications of existing CAC systems, requirements for each type, our infrastructure and also, the classification scheme. The aim of the study was the development of a decision model for determining accurate code of each medical intervention in Iranian Classification of Health Interventions (IRCHI) that can be implemented as a suitable CAC system. first, a sample of existing CAC systems was reviewed. Then feasibility of each one of CAC types was examined with regard to their prerequisites for their implementation. The next step, proper model was proposed according to the structure of the classification scheme and was implemented as an interactive system. There is a significant relationship between the level of assistance of a CAC system and integration of it with electronic medical documents. Implementation of fully automated CAC systems is impossible due to immature development of electronic medical record and problems in using language for medical documenting. So, a model was proposed to develop semi-automated CAC system based on hierarchical relationships between entities in the classification scheme and also the logic of decision making to specify the characters of code step by step through a web-based interactive user interface for CAC. It was composed of three phases to select Target, Action and Means respectively for an intervention. The proposed model was suitable the current status of clinical documentation and coding in Iran and also, the structure of new classification scheme. Our results show it was practical. However, the model needs to be evaluated in the next stage of the research.

Interoperability Assets for Patient Summary Components: A Gap Analysis.

PubMed

Heitmann, Kai U; Cangioli, Giorgio; Melgara, Marcello; Chronaki, Catherine

2018-01-01

The International Patient Summary (IPS) standards aim to define the specifications for a minimal and non-exhaustive Patient Summary, which is specialty-agnostic and condition-independent, but still clinically relevant. Meanwhile, health systems are developing and implementing their own variation of a patient summary while, the eHealth Digital Services Infrastructure (eHDSI) initiative is deploying patient summary services across countries in the Europe. In the spirit of co-creation, flexible governance, and continuous alignment advocated by eStandards, the Trillum-II initiative promotes adoption of the patient summary by engaging standards organizations, and interoperability practitioners in a community of practice for digital health to share best practices, tools, data, specifications, and experiences. This paper compares operational aspects of patient summaries in 14 case studies in Europe, the United States, and across the world, focusing on how patient summary components are used in practice, to promote alignment and joint understanding that will improve quality of standards and lower costs of interoperability.

Clarity: An Open Source Manager for Laboratory Automation

PubMed Central

Delaney, Nigel F.; Echenique, José Rojas; Marx, Christopher J.

2013-01-01

Software to manage automated laboratories interfaces with hardware instruments, gives users a way to specify experimental protocols, and schedules activities to avoid hardware conflicts. In addition to these basics, modern laboratories need software that can run multiple different protocols in parallel and that can be easily extended to interface with a constantly growing diversity of techniques and instruments. We present Clarity: a laboratory automation manager that is hardware agnostic, portable, extensible and open source. Clarity provides critical features including remote monitoring, robust error reporting by phone or email, and full state recovery in the event of a system crash. We discuss the basic organization of Clarity; demonstrate an example of its implementation for the automated analysis of bacterial growth; and describe how the program can be extended to manage new hardware. Clarity is mature; well documented; actively developed; written in C# for the Common Language Infrastructure; and is free and open source software. These advantages set Clarity apart from currently available laboratory automation programs. PMID:23032169

Computation Directorate Annual Report 2003

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crawford, D L; McGraw, J R; Ashby, S F

Big computers are icons: symbols of the culture, and of the larger computing infrastructure that exists at Lawrence Livermore. Through the collective effort of Laboratory personnel, they enable scientific discovery and engineering development on an unprecedented scale. For more than three decades, the Computation Directorate has supplied the big computers that enable the science necessary for Laboratory missions and programs. Livermore supercomputing is uniquely mission driven. The high-fidelity weapon simulation capabilities essential to the Stockpile Stewardship Program compel major advances in weapons codes and science, compute power, and computational infrastructure. Computation's activities align with this vital mission of the Departmentmore » of Energy. Increasingly, non-weapons Laboratory programs also rely on computer simulation. World-class achievements have been accomplished by LLNL specialists working in multi-disciplinary research and development teams. In these teams, Computation personnel employ a wide array of skills, from desktop support expertise, to complex applications development, to advanced research. Computation's skilled professionals make the Directorate the success that it has become. These individuals know the importance of the work they do and the many ways it contributes to Laboratory missions. They make appropriate and timely decisions that move the entire organization forward. They make Computation a leader in helping LLNL achieve its programmatic milestones. I dedicate this inaugural Annual Report to the people of Computation in recognition of their continuing contributions. I am proud that we perform our work securely and safely. Despite increased cyber attacks on our computing infrastructure from the Internet, advanced cyber security practices ensure that our computing environment remains secure. Through Integrated Safety Management (ISM) and diligent oversight, we address safety issues promptly and aggressively. The safety of our employees, whether at work or at home, is a paramount concern. Even as the Directorate meets today's supercomputing requirements, we are preparing for the future. We are investigating open-source cluster technology, the basis of our highly successful Mulitprogrammatic Capability Resource (MCR). Several breakthrough discoveries have resulted from MCR calculations coupled with theory and experiment, prompting Laboratory scientists to demand ever-greater capacity and capability. This demand is being met by a new 23-TF system, Thunder, with architecture modeled on MCR. In preparation for the ''after-next'' computer, we are researching technology even farther out on the horizon--cell-based computers. Assuming that the funding and the technology hold, we will acquire the cell-based machine BlueGene/L within the next 12 months.« less

Application of Composite Mechanics to Composites Enhanced Concrete Structures

NASA Technical Reports Server (NTRS)

Chamis, Christos C.; Gotsis, Pascal K.

2006-01-01

A new and effective method is described to design composites to repair damage or enhance the overload strength of concrete infrastructures. The method is based on composite mechanics which is available in computer codes. It is used to simulate structural sections made from reinforced concrete which are typical in infrastructure as well as select reinforced concrete structures. The structural sections are represented by a number of layers through the thickness where different layers are used in concrete, and for the composite. The reinforced concrete structures are represented with finite elements where the element stiffness parameters are from the structural sections which are represented by composite mechanics. The load carrying capability of the structure is determined by progressive structural fracture. Results show up to 40 percent improvements for damage and for overload enhancement with relatively small laminate thickness for the structural sections and up to three times for the composite enhanced select structures (arches and domes).

caGrid 1.0 : an enterprise Grid infrastructure for biomedical research.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oster, S.; Langella, S.; Hastings, S.

To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. Design: An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG{trademark}) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including (1) discovery, (2) integrated and large-scale data analysis, and (3) coordinated study. Measurements: The caGrid is built as a Grid software infrastructure andmore » leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. Results: The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: .« less

Characterizing Crowd Participation and Productivity of Foldit Through Web Scraping

DTIC Science & Technology

2016-03-01

Berkeley Open Infrastructure for Network Computing CDF Cumulative Distribution Function CPU Central Processing Unit CSSG Crowdsourced Serious Game...computers at once can create a similar capacity. According to Anderson [6], principal investigator for the Berkeley Open Infrastructure for Network...extraterrestrial life. From this project, a software-based distributed computing platform called the Berkeley Open Infrastructure for Network Computing

SOCR data dashboard: an integrated big data archive mashing medicare, labor, census and econometric information.

PubMed

Husain, Syed S; Kalinin, Alexandr; Truong, Anh; Dinov, Ivo D

Intuitive formulation of informative and computationally-efficient queries on big and complex datasets present a number of challenges. As data collection is increasingly streamlined and ubiquitous, data exploration, discovery and analytics get considerably harder. Exploratory querying of heterogeneous and multi-source information is both difficult and necessary to advance our knowledge about the world around us. We developed a mechanism to integrate dispersed multi-source data and service the mashed information via human and machine interfaces in a secure, scalable manner. This process facilitates the exploration of subtle associations between variables, population strata, or clusters of data elements, which may be opaque to standard independent inspection of the individual sources. This a new platform includes a device agnostic tool (Dashboard webapp, http://socr.umich.edu/HTML5/Dashboard/) for graphical querying, navigating and exploring the multivariate associations in complex heterogeneous datasets. The paper illustrates this core functionality and serviceoriented infrastructure using healthcare data (e.g., US data from the 2010 Census, Demographic and Economic surveys, Bureau of Labor Statistics, and Center for Medicare Services) as well as Parkinson's Disease neuroimaging data. Both the back-end data archive and the front-end dashboard interfaces are continuously expanded to include additional data elements and new ways to customize the human and machine interactions. A client-side data import utility allows for easy and intuitive integration of user-supplied datasets. This completely open-science framework may be used for exploratory analytics, confirmatory analyses, meta-analyses, and education and training purposes in a wide variety of fields.

Building a Community Infrastructure for Scalable On-Line Performance Analysis Tools around Open|Speedshop

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Barton

2014-06-30

Peta-scale computing environments pose significant challenges for both system and application developers and addressing them required more than simply scaling up existing tera-scale solutions. Performance analysis tools play an important role in gaining this understanding, but previous monolithic tools with fixed feature sets have not sufficed. Instead, this project worked on the design, implementation, and evaluation of a general, flexible tool infrastructure supporting the construction of performance tools as “pipelines” of high-quality tool building blocks. These tool building blocks provide common performance tool functionality, and are designed for scalability, lightweight data acquisition and analysis, and interoperability. For this project, wemore » built on Open|SpeedShop, a modular and extensible open source performance analysis tool set. The design and implementation of such a general and reusable infrastructure targeted for petascale systems required us to address several challenging research issues. All components needed to be designed for scale, a task made more difficult by the need to provide general modules. The infrastructure needed to support online data aggregation to cope with the large amounts of performance and debugging data. We needed to be able to map any combination of tool components to each target architecture. And we needed to design interoperable tool APIs and workflows that were concrete enough to support the required functionality, yet provide the necessary flexibility to address a wide range of tools. A major result of this project is the ability to use this scalable infrastructure to quickly create tools that match with a machine architecture and a performance problem that needs to be understood. Another benefit is the ability for application engineers to use the highly scalable, interoperable version of Open|SpeedShop, which are reassembled from the tool building blocks into a flexible, multi-user interface set of tools. This set of tools targeted at Office of Science Leadership Class computer systems and selected Office of Science application codes. We describe the contributions made by the team at the University of Wisconsin. The project built on the efforts in Open|SpeedShop funded by DOE/NNSA and the DOE/NNSA Tri-Lab community, extended Open|Speedshop to the Office of Science Leadership Class Computing Facilities, and addressed new challenges found on these cutting edge systems. Work done under this project at Wisconsin can be divided into two categories, new algorithms and techniques for debugging, and foundation infrastructure work on our Dyninst binary analysis and instrumentation toolkits and MRNet scalability infrastructure.« less

Ensembl comparative genomics resources.

PubMed

Herrero, Javier; Muffato, Matthieu; Beal, Kathryn; Fitzgerald, Stephen; Gordon, Leo; Pignatelli, Miguel; Vilella, Albert J; Searle, Stephen M J; Amode, Ridwan; Brent, Simon; Spooner, William; Kulesha, Eugene; Yates, Andrew; Flicek, Paul

2016-01-01

Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org. © The Author(s) 2016. Published by Oxford University Press.

Ensembl comparative genomics resources

PubMed Central

Muffato, Matthieu; Beal, Kathryn; Fitzgerald, Stephen; Gordon, Leo; Pignatelli, Miguel; Vilella, Albert J.; Searle, Stephen M. J.; Amode, Ridwan; Brent, Simon; Spooner, William; Kulesha, Eugene; Yates, Andrew; Flicek, Paul

2016-01-01

Evolution provides the unifying framework with which to understand biology. The coherent investigation of genic and genomic data often requires comparative genomics analyses based on whole-genome alignments, sets of homologous genes and other relevant datasets in order to evaluate and answer evolutionary-related questions. However, the complexity and computational requirements of producing such data are substantial: this has led to only a small number of reference resources that are used for most comparative analyses. The Ensembl comparative genomics resources are one such reference set that facilitates comprehensive and reproducible analysis of chordate genome data. Ensembl computes pairwise and multiple whole-genome alignments from which large-scale synteny, per-base conservation scores and constrained elements are obtained. Gene alignments are used to define Ensembl Protein Families, GeneTrees and homologies for both protein-coding and non-coding RNA genes. These resources are updated frequently and have a consistent informatics infrastructure and data presentation across all supported species. Specialized web-based visualizations are also available including synteny displays, collapsible gene tree plots, a gene family locator and different alignment views. The Ensembl comparative genomics infrastructure is extensively reused for the analysis of non-vertebrate species by other projects including Ensembl Genomes and Gramene and much of the information here is relevant to these projects. The consistency of the annotation across species and the focus on vertebrates makes Ensembl an ideal system to perform and support vertebrate comparative genomic analyses. We use robust software and pipelines to produce reference comparative data and make it freely available. Database URL: http://www.ensembl.org. PMID:26896847

PyNN: A Common Interface for Neuronal Network Simulators.

PubMed

Davison, Andrew P; Brüderle, Daniel; Eppler, Jochen; Kremkow, Jens; Muller, Eilif; Pecevski, Dejan; Perrinet, Laurent; Yger, Pierre

2008-01-01

Computational neuroscience has produced a diversity of software for simulations of networks of spiking neurons, with both negative and positive consequences. On the one hand, each simulator uses its own programming or configuration language, leading to considerable difficulty in porting models from one simulator to another. This impedes communication between investigators and makes it harder to reproduce and build on the work of others. On the other hand, simulation results can be cross-checked between different simulators, giving greater confidence in their correctness, and each simulator has different optimizations, so the most appropriate simulator can be chosen for a given modelling task. A common programming interface to multiple simulators would reduce or eliminate the problems of simulator diversity while retaining the benefits. PyNN is such an interface, making it possible to write a simulation script once, using the Python programming language, and run it without modification on any supported simulator (currently NEURON, NEST, PCSIM, Brian and the Heidelberg VLSI neuromorphic hardware). PyNN increases the productivity of neuronal network modelling by providing high-level abstraction, by promoting code sharing and reuse, and by providing a foundation for simulator-agnostic analysis, visualization and data-management tools. PyNN increases the reliability of modelling studies by making it much easier to check results on multiple simulators. PyNN is open-source software and is available from http://neuralensemble.org/PyNN.

PyNN: A Common Interface for Neuronal Network Simulators

PubMed Central

Davison, Andrew P.; Brüderle, Daniel; Eppler, Jochen; Kremkow, Jens; Muller, Eilif; Pecevski, Dejan; Perrinet, Laurent; Yger, Pierre

2008-01-01

Computational neuroscience has produced a diversity of software for simulations of networks of spiking neurons, with both negative and positive consequences. On the one hand, each simulator uses its own programming or configuration language, leading to considerable difficulty in porting models from one simulator to another. This impedes communication between investigators and makes it harder to reproduce and build on the work of others. On the other hand, simulation results can be cross-checked between different simulators, giving greater confidence in their correctness, and each simulator has different optimizations, so the most appropriate simulator can be chosen for a given modelling task. A common programming interface to multiple simulators would reduce or eliminate the problems of simulator diversity while retaining the benefits. PyNN is such an interface, making it possible to write a simulation script once, using the Python programming language, and run it without modification on any supported simulator (currently NEURON, NEST, PCSIM, Brian and the Heidelberg VLSI neuromorphic hardware). PyNN increases the productivity of neuronal network modelling by providing high-level abstraction, by promoting code sharing and reuse, and by providing a foundation for simulator-agnostic analysis, visualization and data-management tools. PyNN increases the reliability of modelling studies by making it much easier to check results on multiple simulators. PyNN is open-source software and is available from http://neuralensemble.org/PyNN. PMID:19194529

The Next Generation of Lab and Classroom Computing - The Silver Lining

DTIC Science & Technology

2016-12-01

desktop infrastructure (VDI) solution, as well as the computing solutions at three universities, was selected as the basis for comparison. The research... infrastructure , VDI, hardware cost, software cost, manpower, availability, cloud computing, private cloud, bring your own device, BYOD, thin client...virtual desktop infrastructure (VDI) solution, as well as the computing solutions at three universities, was selected as the basis for comparison. The

Executable research compendia in geoscience research infrastructures

NASA Astrophysics Data System (ADS)

Nüst, Daniel

2017-04-01

From generation through analysis and collaboration to communication, scientific research requires the right tools. Scientists create their own software using third party libraries and platforms. Cloud computing, Open Science, public data infrastructures, and Open Source enable scientists with unprecedented opportunites, nowadays often in a field "Computational X" (e.g. computational seismology) or X-informatics (e.g. geoinformatics) [0]. This increases complexity and generates more innovation, e.g. Environmental Research Infrastructures (environmental RIs [1]). Researchers in Computational X write their software relying on both source code (e.g. from https://github.com) and binary libraries (e.g. from package managers such as APT, https://wiki.debian.org/Apt, or CRAN, https://cran.r-project.org/). They download data from domain specific (cf. https://re3data.org) or generic (e.g. https://zenodo.org) data repositories, and deploy computations remotely (e.g. European Open Science Cloud). The results themselves are archived, given persistent identifiers, connected to other works (e.g. using https://orcid.org/), and listed in metadata catalogues. A single researcher, intentionally or not, interacts with all sub-systems of RIs: data acquisition, data access, data processing, data curation, and community support [3]. To preserve computational research [3] proposes the Executable Research Compendium (ERC), a container format closing the gap of dependency preservation by encapsulating the runtime environment. ERCs and RIs can be integrated for different uses: (i) Coherence: ERC services validate completeness, integrity and results (ii) Metadata: ERCs connect the different parts of a piece of research and faciliate discovery (iii) Exchange and Preservation: ERC as usable building blocks are the shared and archived entity (iv) Self-consistency: ERCs remove dependence on ephemeral sources (v) Execution: ERC services create and execute a packaged analysis but integrate with existing platforms for display and control These integrations are vital for capturing workflows in RIs and connect key stakeholders (scientists, publishers, librarians). They are demonstrated using developments by the DFG-funded project Opening Reproducible Research (http://o2r.info). Semi-automatic creation of ERCs based on research workflows is a core goal of the project. References [0] Tony Hey, Stewart Tansley, Kristin Tolle (eds), 2009. The Fourth Paradigm: Data-Intensive Scientific Discovery. Microsoft Research. [1] P. Martin et al., Open Information Linking for Environmental Research Infrastructures, 2015 IEEE 11th International Conference on e-Science, Munich, 2015, pp. 513-520. doi: 10.1109/eScience.2015.66 [2] Y. Chen et al., Analysis of Common Requirements for Environmental Science Research Infrastructures, The International Symposium on Grids and Clouds (ISGC) 2013, Taipei, 2013, http://pos.sissa.it/archive/conferences/179/032/ISGC [3] Opening Reproducible Research, Geophysical Research Abstracts Vol. 18, EGU2016-7396, 2016, http://meetingorganizer.copernicus.org/EGU2016/EGU2016-7396.pdf

The Electrolyte Genome project: A big data approach in battery materials discovery

DOE Office of Scientific and Technical Information (OSTI.GOV)

Qu, Xiaohui; Jain, Anubhav; Rajput, Nav Nidhi

2015-06-01

We present a high-throughput infrastructure for the automated calculation of molecular properties with a focus on battery electrolytes. The infrastructure is largely open-source and handles both practical aspects (input file generation, output file parsing, and information management) as well as more complex problems (structure matching, salt complex generation, and failure recovery). Using this infrastructure, we have computed the ionization potential (IP) and electron affinities (EA) of 4830 molecules relevant to battery electrolytes (encompassing almost 55,000 quantum mechanics calculations) at the B3LYP/6-31+G(*) level. We describe automated workflows for computing redox potential, dissociation constant, and salt-molecule binding complex structure generation. We presentmore » routines for automatic recovery from calculation errors, which brings the failure rate from 9.2% to 0.8% for the QChem DFT code. Automated algorithms to check duplication between two arbitrary molecules and structures are described. We present benchmark data on basis sets and functionals on the G2-97 test set; one finding is that a IP/EA calculation method that combines PBE geometry optimization and B3LYP energy evaluation requires less computational cost and yields nearly identical results as compared to a full B3LYP calculation, and could be suitable for the calculation of large molecules. Our data indicates that among the 8 functionals tested, XYGJ-OS and B3LYP are the two best functionals to predict IP/EA with an RMSE of 0.12 and 0.27 eV, respectively. Application of our automated workflow to a large set of quinoxaline derivative molecules shows that functional group effect and substitution position effect can be separated for IP/EA of quinoxaline derivatives, and the most sensitive position is different for IP and EA. Published by Elsevier B.V« less

SBSI: an extensible distributed software infrastructure for parameter estimation in systems biology

PubMed Central

Adams, Richard; Clark, Allan; Yamaguchi, Azusa; Hanlon, Neil; Tsorman, Nikos; Ali, Shakir; Lebedeva, Galina; Goltsov, Alexey; Sorokin, Anatoly; Akman, Ozgur E.; Troein, Carl; Millar, Andrew J.; Goryanin, Igor; Gilmore, Stephen

2013-01-01

Summary: Complex computational experiments in Systems Biology, such as fitting model parameters to experimental data, can be challenging to perform. Not only do they frequently require a high level of computational power, but the software needed to run the experiment needs to be usable by scientists with varying levels of computational expertise, and modellers need to be able to obtain up-to-date experimental data resources easily. We have developed a software suite, the Systems Biology Software Infrastructure (SBSI), to facilitate the parameter-fitting process. SBSI is a modular software suite composed of three major components: SBSINumerics, a high-performance library containing parallelized algorithms for performing parameter fitting; SBSIDispatcher, a middleware application to track experiments and submit jobs to back-end servers; and SBSIVisual, an extensible client application used to configure optimization experiments and view results. Furthermore, we have created a plugin infrastructure to enable project-specific modules to be easily installed. Plugin developers can take advantage of the existing user-interface and application framework to customize SBSI for their own uses, facilitated by SBSI’s use of standard data formats. Availability and implementation: All SBSI binaries and source-code are freely available from http://sourceforge.net/projects/sbsi under an Apache 2 open-source license. The server-side SBSINumerics runs on any Unix-based operating system; both SBSIVisual and SBSIDispatcher are written in Java and are platform independent, allowing use on Windows, Linux and Mac OS X. The SBSI project website at http://www.sbsi.ed.ac.uk provides documentation and tutorials. Contact: stg@inf.ed.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23329415

Continuous Codes and Standards Improvement (CCSI)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivkin, Carl H; Burgess, Robert M; Buttner, William J

2015-10-21

As of 2014, the majority of the codes and standards required to initially deploy hydrogen technologies infrastructure in the United States have been promulgated. These codes and standards will be field tested through their application to actual hydrogen technologies projects. Continuous codes and standards improvement (CCSI) is a process of identifying code issues that arise during project deployment and then developing codes solutions to these issues. These solutions would typically be proposed amendments to codes and standards. The process is continuous because as technology and the state of safety knowledge develops there will be a need to monitor the applicationmore » of codes and standards and improve them based on information gathered during their application. This paper will discuss code issues that have surfaced through hydrogen technologies infrastructure project deployment and potential code changes that would address these issues. The issues that this paper will address include (1) setback distances for bulk hydrogen storage, (2) code mandated hazard analyses, (3) sensor placement and communication, (4) the use of approved equipment, and (5) system monitoring and maintenance requirements.« less

Use of information and communication technology and retention of health workers in rural post-war conflict Northern Uganda: findings from a qualitative study.

PubMed

Yagos, Walter Onen; Tabo Olok, Geoffrey; Ovuga, Emilio

2017-01-10

Information and communication technologies have become a vital infrastructural asset for use in the retention of rural health workers. However, little is known about the potential influence of ICT use, perceptions of health workers on ICT in healthcare delivery, and contribution of ICT to health care providers' retention in rural and remote areas in rural post-war and conflict situations of northern Uganda. Data from interviews were transcribed, coded and thematically analysed. Participants generally exhibited low confidence, knowledge and low ICT skills. Majority of participants, however, perceived ICT as beneficial in relation to job performance and health care provider retention in rural areas. Common barriers for the implementation and use of ICT in health centres were inadequate ICT knowledge and skills, poor Internet networks, inadequate computers, inadequate power supply, lack of Internet Modems and expensive access to outside computer centres. This qualitative study showed low confidence, poor knowledge and skills in ICT usage but positive perceptions about the benefits and contributions of ICT. These findings suggest the need for specific investment in ICT infrastructural development for health care providers in remote rural areas of northern Uganda.

A Unified Data-Driven Approach for Programming In Situ Analysis and Visualization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aiken, Alex

The placement and movement of data is becoming the key limiting factor on both performance and energy efficiency of high performance computations. As systems generate more data, it is becoming increasingly difficult to actually move that data elsewhere for post-processing, as the rate of improvements in supporting I/O infrastructure is not keeping pace. Together, these trends are creating a shift in how we think about exascale computations, from a viewpoint that focuses on FLOPS to one that focuses on data and data-centric operations as fundamental to the reasoning about, and optimization of, scientific workflows on extreme-scale architectures. The overarching goalmore » of our effort was the study of a unified data-driven approach for programming applications and in situ analysis and visualization. Our work was to understand the interplay between data-centric programming model requirements at extreme-scale and the overall impact of those requirements on the design, capabilities, flexibility, and implementation details for both applications and the supporting in situ infrastructure. In this context, we made many improvements to the Legion programming system (one of the leading data-centric models today) and demonstrated in situ analyses on real application codes using these improvements.« less

Nbody Simulations and Weak Gravitational Lensing using new HPC-Grid resources: the PI2S2 project

NASA Astrophysics Data System (ADS)

Becciani, U.; Antonuccio-Delogu, V.; Costa, A.; Comparato, M.

2008-08-01

We present the main project of the new grid infrastructure and the researches, that have been already started in Sicily and will be completed by next year. The PI2S2 project of the COMETA consortium is funded by the Italian Ministry of University and Research and will be completed in 2009. Funds are from the European Union Structural Funds for Objective 1 regions. The project, together with a similar project called Trinacria GRID Virtual Laboratory (Trigrid VL), aims to create in Sicily a computational grid for e-science and e-commerce applications with the main goal of increasing the technological innovation of local enterprises and their competition on the global market. PI2S2 project aims to build and develop an e-Infrastructure in Sicily, based on the grid paradigm, mainly for research activity using the grid environment and High Performance Computer systems. As an example we present the first results of a new grid version of FLY a tree Nbody code developed by INAF Astrophysical Observatory of Catania, already published in the CPC program Library, that will be used in the Weak Gravitational Lensing field.

Green Infrastructure Barriers and Opportunities in Dallas, Texas

EPA Pesticide Factsheets

This report will assist other municipalities with recognizing barriers and inconsistencies in municipal codes and ordinances which may be impeding the implementation of green infrastructure practices in their communities.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rodgers, Arthur J.; Dreger, Douglas S.; Pitarka, Arben

We performed three-dimensional (3D) anelastic ground motion simulations of the South Napa earthquake to investigate the performance of different finite rupture models and the effects of 3D structure on the observed wavefield. We considered rupture models reported by Dreger et al. (2015), Ji et al., (2015), Wei et al. (2015) and Melgar et al. (2015). We used the SW4 anelastic finite difference code developed at Lawrence Livermore National Laboratory (Petersson and Sjogreen, 2013) and distributed by the Computational Infrastructure for Geodynamics. This code can compute the seismic response for fully 3D sub-surface models, including surface topography and linear anelasticity. Wemore » use the 3D geologic/seismic model of the San Francisco Bay Area developed by the United States Geological Survey (Aagaard et al., 2008, 2010). Evaluation of earlier versions of this model indicated that the structure can reproduce main features of observed waveforms from moderate earthquakes (Rodgers et al., 2008; Kim et al., 2010). Simulations were performed for a domain covering local distances (< 25 km) and resolution providing simulated ground motions valid to 1 Hz.« less

The dependence of educational infrastructure on clinical infrastructure.

PubMed Central

Cimino, C.

1998-01-01

The Albert Einstein College of Medicine needed to assess the growth of its infrastructure for educational computing as a first step to determining if student needs were being met. Included in computing infrastructure are space, equipment, software, and computing services. The infrastructure was assessed by reviewing purchasing and support logs for a six year period from 1992 to 1998. This included equipment, software, and e-mail accounts provided to students and to faculty for educational purposes. Student space has grown at a constant rate (averaging 14% increase each year respectively). Student equipment on campus has grown by a constant amount each year (average 8.3 computers each year). Student infrastructure off campus and educational support of faculty has not kept pace. It has either declined or remained level over the six year period. The availability of electronic mail clearly demonstrates this with accounts being used by 99% of students, 78% of Basic Science Course Leaders, 38% of Clerkship Directors, 18% of Clerkship Site Directors, and 8% of Clinical Elective Directors. The collection of the initial descriptive infrastructure data has revealed problems that may generalize to other medical schools. The discrepancy between infrastructure available to students and faculty on campus and students and faculty off campus creates a setting where students perceive a paradoxical declining support for computer use as they progress through medical school. While clinical infrastructure may be growing, it is at the expense of educational infrastructure at affiliate hospitals. PMID:9929262

Advanced Computational Methods for Optimization of Non-Periodic Inspection Intervals for Aging Infrastructure

DTIC Science & Technology

2017-01-05

AFRL-AFOSR-JP-TR-2017-0002 Advanced Computational Methods for Optimization of Non-Periodic Inspection Intervals for Aging Infrastructure Manabu...Computational Methods for Optimization of Non-Periodic Inspection Intervals for Aging Infrastructure 5a.  CONTRACT NUMBER 5b.  GRANT NUMBER FA2386...UNLIMITED: PB Public Release 13. SUPPLEMENTARY NOTES 14. ABSTRACT This report for the project titled ’Advanced Computational Methods for Optimization of

Application of large-scale computing infrastructure for diverse environmental research applications using GC3Pie

NASA Astrophysics Data System (ADS)

Maffioletti, Sergio; Dawes, Nicholas; Bavay, Mathias; Sarni, Sofiane; Lehning, Michael

2013-04-01

The Swiss Experiment platform (SwissEx: http://www.swiss-experiment.ch) provides a distributed storage and processing infrastructure for environmental research experiments. The aim of the second phase project (the Open Support Platform for Environmental Research, OSPER, 2012-2015) is to develop the existing infrastructure to provide scientists with an improved workflow. This improved workflow will include pre-defined, documented and connected processing routines. A large-scale computing and data facility is required to provide reliable and scalable access to data for analysis, and it is desirable that such an infrastructure should be free of traditional data handling methods. Such an infrastructure has been developed using the cloud-based part of the Swiss national infrastructure SMSCG (http://www.smscg.ch) and Academic Cloud. The infrastructure under construction supports two main usage models: 1) Ad-hoc data analysis scripts: These scripts are simple processing scripts, written by the environmental researchers themselves, which can be applied to large data sets via the high power infrastructure. Examples of this type of script are spatial statistical analysis scripts (R-based scripts), mostly computed on raw meteorological and/or soil moisture data. These provide processed output in the form of a grid, a plot, or a kml. 2) Complex models: A more intense data analysis pipeline centered (initially) around the physical process model, Alpine3D, and the MeteoIO plugin; depending on the data set, this may require a tightly coupled infrastructure. SMSCG already supports Alpine3D executions as both regular grid jobs and as virtual software appliances. A dedicated appliance with the Alpine3D specific libraries has been created and made available through the SMSCG infrastructure. The analysis pipelines are activated and supervised by simple control scripts that, depending on the data fetched from the meteorological stations, launch new instances of the Alpine3D appliance, execute location-based subroutines at each grid point and store the results back into the central repository for post-processing. An optional extension of this infrastructure will be to provide a 'ring buffer'-type database infrastructure, such that model results (e.g. test runs made to check parameter dependency or for development) can be visualised and downloaded after completion without submitting them to a permanent storage infrastructure. Data organization Data collected from sensors are archived and classified in distributed sites connected with an open-source software middleware, GSN. Publicly available data are available through common web services and via a cloud storage server (based on Swift). Collocation of the data and processing in the cloud would eventually eliminate data transfer requirements. Execution control logic Execution of the data analysis pipelines (for both the R-based analysis and the Alpine3D simulations) has been implemented using the GC3Pie framework developed by UZH. (https://code.google.com/p/gc3pie/). This allows large-scale, fault-tolerant execution of the pipelines to be described in terms of software appliances. GC3Pie also allows supervision of the execution of large campaigns of appliances as a single simulation. This poster will present the fundamental architectural components of the data analysis pipelines together with initial experimental results.

Software and the Scientist: Coding and Citation Practices in Geodynamics

NASA Astrophysics Data System (ADS)

Hwang, Lorraine; Fish, Allison; Soito, Laura; Smith, MacKenzie; Kellogg, Louise H.

2017-11-01

In geodynamics as in other scientific areas, computation has become a core component of research, complementing field observation, laboratory analysis, experiment, and theory. Computational tools for data analysis, mapping, visualization, modeling, and simulation are essential for all aspects of the scientific workflow. Specialized scientific software is often developed by geodynamicists for their own use, and this effort represents a distinctive intellectual contribution. Drawing on a geodynamics community that focuses on developing and disseminating scientific software, we assess the current practices of software development and attribution, as well as attitudes about the need and best practices for software citation. We analyzed publications by participants in the Computational Infrastructure for Geodynamics and conducted mixed method surveys of the solid earth geophysics community. From this we learned that coding skills are typically learned informally. Participants considered good code as trusted, reusable, readable, and not overly complex and considered a good coder as one that participates in the community in an open and reasonable manor contributing to both long- and short-term community projects. Participants strongly supported citing software reflected by the high rate a software package was named in the literature and the high rate of citations in the references. However, lacking are clear instructions from developers on how to cite and education of users on what to cite. In addition, citations did not always lead to discoverability of the resource. A unique identifier to the software package itself, community education, and citation tools would contribute to better attribution practices.

Photoplus: auxiliary information for printed images based on distributed source coding

NASA Astrophysics Data System (ADS)

Samadani, Ramin; Mukherjee, Debargha

2008-01-01

A printed photograph is difficult to reuse because the digital information that generated the print may no longer be available. This paper describes a mechanism for approximating the original digital image by combining a scan of the printed photograph with small amounts of digital auxiliary information kept together with the print. The auxiliary information consists of a small amount of digital data to enable accurate registration and color-reproduction, followed by a larger amount of digital data to recover residual errors and lost frequencies by distributed Wyner-Ziv coding techniques. Approximating the original digital image enables many uses, including making good quality reprints from the original print, even when they are faded many years later. In essence, the print itself becomes the currency for archiving and repurposing digital images, without requiring computer infrastructure.

Atheists, agnostics and Alcoholics Anonymous.

PubMed

Tonigan, J Scott; Miller, W R; Schermer, Carol

2002-09-01

In spite of the strong emphasis in AA on spiritual beliefs and practices, findings are mixed about the importance of such beliefs in predicting AA affiliation. This study of the Project MATCH outpatient (N = 952) and aftercare (N = 774) samples tested three hypotheses about the role of client God belief and subsequent AA attendance and benefit, taking into account that some individuals may, in fact, deny the existence of a God. Longitudinal analyses were conducted (N = 1,526) investigating client God beliefs, AA attendance, patterns of AA attendance and alcohol use. Assessments were conducted at intake and in 3-month intervals using the Form 90, Religious Behaviors and Background, and the Alcoholics Anonymous Inventory. 12-Step treatment was significantly more likely to promote pre-post shifts in client God beliefs, and atheist and agnostic clients attended AA significantly less often throughout follow-up relative to clients self-labeled as spiritual and religious. AA attendance, however, was significantly associated with increased abstinence and reductions in drinking intensity regardless of God belief. Finally, no differences in percent days abstinence and drinking intensity were found between atheist and agnostic versus spiritual and religious clients, but clients unsure about their God belief reported significantly higher drinking frequency relative to the other groups. God belief appears to be relatively unimportant in deriving AA-related benefit, but atheist and agnostic clients are less likely to initiate and sustain AA attendance relative to spiritual and religious clients. This apparent reticence to affiliate with AA ought to be clinically recognized when encouraging AA participation.

The QUANTGRID Project (RO)—Quantum Security in GRID Computing Applications

NASA Astrophysics Data System (ADS)

Dima, M.; Dulea, M.; Petre, M.; Petre, C.; Mitrica, B.; Stoica, M.; Udrea, M.; Sterian, R.; Sterian, P.

2010-01-01

The QUANTGRID Project, financed through the National Center for Programme Management (CNMP-Romania), is the first attempt at using Quantum Crypted Communications (QCC) in large scale operations, such as GRID Computing, and conceivably in the years ahead in the banking sector and other security tight communications. In relation with the GRID activities of the Center for Computing & Communications (Nat.'l Inst. Nucl. Phys.—IFIN-HH), the Quantum Optics Lab. (Nat.'l Inst. Plasma and Lasers—INFLPR) and the Physics Dept. (University Polytechnica—UPB) the project will build a demonstrator infrastructure for this technology. The status of the project in its incipient phase is reported, featuring tests for communications in classical security mode: socket level communications under AES (Advanced Encryption Std.), both proprietary code in C++ technology. An outline of the planned undertaking of the project is communicated, highlighting its impact in quantum physics, coherent optics and information technology.

Infrastructures for Distributed Computing: the case of BESIII

NASA Astrophysics Data System (ADS)

Pellegrino, J.

2018-05-01

The BESIII is an electron-positron collision experiment hosted at BEPCII in Beijing and aimed to investigate Tau-Charm physics. Now BESIII has been running for several years and gathered more than 1PB raw data. In order to analyze these data and perform massive Monte Carlo simulations, a large amount of computing and storage resources is needed. The distributed computing system is based up on DIRAC and it is in production since 2012. It integrates computing and storage resources from different institutes and a variety of resource types such as cluster, grid, cloud or volunteer computing. About 15 sites from BESIII Collaboration from all over the world joined this distributed computing infrastructure, giving a significant contribution to the IHEP computing facility. Nowadays cloud computing is playing a key role in the HEP computing field, due to its scalability and elasticity. Cloud infrastructures take advantages of several tools, such as VMDirac, to manage virtual machines through cloud managers according to the job requirements. With the virtually unlimited resources from commercial clouds, the computing capacity could scale accordingly in order to deal with any burst demands. General computing models have been discussed in the talk and are addressed herewith, with particular focus on the BESIII infrastructure. Moreover new computing tools and upcoming infrastructures will be addressed.

Medical reliable network using concatenated channel codes through GSM network.

PubMed

Ahmed, Emtithal; Kohno, Ryuji

2013-01-01

Although the 4(th) generation (4G) of global mobile communication network, i.e. Long Term Evolution (LTE) coexisting with the 3(rd) generation (3G) has successfully started; the 2(nd) generation (2G), i.e. Global System for Mobile communication (GSM) still playing an important role in many developing countries. Without any other reliable network infrastructure, GSM can be applied for tele-monitoring applications, where high mobility and low cost are necessary. A core objective of this paper is to introduce the design of a more reliable and dependable Medical Network Channel Code system (MNCC) through GSM Network. MNCC design based on simple concatenated channel code, which is cascade of an inner code (GSM) and an extra outer code (Convolution Code) in order to protect medical data more robust against channel errors than other data using the existing GSM network. In this paper, the MNCC system will provide Bit Error Rate (BER) equivalent to the BER for medical tele monitoring of physiological signals, which is 10(-5) or less. The performance of the MNCC has been proven and investigated using computer simulations under different channels condition such as, Additive White Gaussian Noise (AWGN), Rayleigh noise and burst noise. Generally the MNCC system has been providing better performance as compared to GSM.

Workflow Management Systems for Molecular Dynamics on Leadership Computers

NASA Astrophysics Data System (ADS)

Wells, Jack; Panitkin, Sergey; Oleynik, Danila; Jha, Shantenu

Molecular Dynamics (MD) simulations play an important role in a range of disciplines from Material Science to Biophysical systems and account for a large fraction of cycles consumed on computing resources. Increasingly science problems require the successful execution of ''many'' MD simulations as opposed to a single MD simulation. There is a need to provide scalable and flexible approaches to the execution of the workload. We present preliminary results on the Titan computer at the Oak Ridge Leadership Computing Facility that demonstrate a general capability to manage workload execution agnostic of a specific MD simulation kernel or execution pattern, and in a manner that integrates disparate grid-based and supercomputing resources. Our results build upon our extensive experience of distributed workload management in the high-energy physics ATLAS project using PanDA (Production and Distributed Analysis System), coupled with recent conceptual advances in our understanding of workload management on heterogeneous resources. We will discuss how we will generalize these initial capabilities towards a more production level service on DOE leadership resources. This research is sponsored by US DOE/ASCR and used resources of the OLCF computing facility.

Software engineering and automatic continuous verification of scientific software

NASA Astrophysics Data System (ADS)

Piggott, M. D.; Hill, J.; Farrell, P. E.; Kramer, S. C.; Wilson, C. R.; Ham, D.; Gorman, G. J.; Bond, T.

2011-12-01

Software engineering of scientific code is challenging for a number of reasons including pressure to publish and a lack of awareness of the pitfalls of software engineering by scientists. The Applied Modelling and Computation Group at Imperial College is a diverse group of researchers that employ best practice software engineering methods whilst developing open source scientific software. Our main code is Fluidity - a multi-purpose computational fluid dynamics (CFD) code that can be used for a wide range of scientific applications from earth-scale mantle convection, through basin-scale ocean dynamics, to laboratory-scale classic CFD problems, and is coupled to a number of other codes including nuclear radiation and solid modelling. Our software development infrastructure consists of a number of free tools that could be employed by any group that develops scientific code and has been developed over a number of years with many lessons learnt. A single code base is developed by over 30 people for which we use bazaar for revision control, making good use of the strong branching and merging capabilities. Using features of Canonical's Launchpad platform, such as code review, blueprints for designing features and bug reporting gives the group, partners and other Fluidity uers an easy-to-use platform to collaborate and allows the induction of new members of the group into an environment where software development forms a central part of their work. The code repositoriy are coupled to an automated test and verification system which performs over 20,000 tests, including unit tests, short regression tests, code verification and large parallel tests. Included in these tests are build tests on HPC systems, including local and UK National HPC services. The testing of code in this manner leads to a continuous verification process; not a discrete event performed once development has ceased. Much of the code verification is done via the "gold standard" of comparisons to analytical solutions via the method of manufactured solutions. By developing and verifying code in tandem we avoid a number of pitfalls in scientific software development and advocate similar procedures for other scientific code applications.

Decaf: Decoupled Dataflows for In Situ High-Performance Workflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dreher, M.; Peterka, T.

Decaf is a dataflow system for the parallel communication of coupled tasks in an HPC workflow. The dataflow can perform arbitrary data transformations ranging from simply forwarding data to complex data redistribution. Decaf does this by allowing the user to allocate resources and execute custom code in the dataflow. All communication through the dataflow is efficient parallel message passing over MPI. The runtime for calling tasks is entirely message-driven; Decaf executes a task when all messages for the task have been received. Such a messagedriven runtime allows cyclic task dependencies in the workflow graph, for example, to enact computational steeringmore » based on the result of downstream tasks. Decaf includes a simple Python API for describing the workflow graph. This allows Decaf to stand alone as a complete workflow system, but Decaf can also be used as the dataflow layer by one or more other workflow systems to form a heterogeneous task-based computing environment. In one experiment, we couple a molecular dynamics code with a visualization tool using the FlowVR and Damaris workflow systems and Decaf for the dataflow. In another experiment, we test the coupling of a cosmology code with Voronoi tessellation and density estimation codes using MPI for the simulation, the DIY programming model for the two analysis codes, and Decaf for the dataflow. Such workflows consisting of heterogeneous software infrastructures exist because components are developed separately with different programming models and runtimes, and this is the first time that such heterogeneous coupling of diverse components was demonstrated in situ on HPC systems.« less

Edge Simulation Laboratory Progress and Plans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cohen, R

The Edge Simulation Laboratory (ESL) is a project to develop a gyrokinetic code for MFE edge plasmas based on continuum (Eulerian) techniques. ESL is a base-program activity of OFES, with an allied algorithm research activity funded by the OASCR base math program. ESL OFES funds directly support about 0.8 FTE of career staff at LLNL, a postdoc and a small fraction of an FTE at GA, and a graduate student at UCSD. In addition the allied OASCR program funds about 1/2 FTE each in the computations directorates at LBNL and LLNL. OFES ESL funding for LLNL and UCSD began inmore » fall 2005, while funding for GA and the math team began about a year ago. ESL's continuum approach is a complement to the PIC-based methods of the CPES Project, and was selected (1) because of concerns about noise issues associated with PIC in the high-density-contrast environment of the edge pedestal, (2) to be able to exploit advanced numerical methods developed for fluid codes, and (3) to build upon the successes of core continuum gyrokinetic codes such as GYRO, GS2 and GENE. The ESL project presently has three components: TEMPEST, a full-f, full-geometry (single-null divertor, or arbitrary-shape closed flux surfaces) code in E, {mu} (energy, magnetic-moment) coordinates; EGK, a simple-geometry rapid-prototype code, presently of; and the math component, which is developing and implementing algorithms for a next-generation code. Progress would be accelerated if we could find funding for a fourth, computer science, component, which would develop software infrastructure, provide user support, and address needs for data handing and analysis. We summarize the status and plans for the three funded activities.« less

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser

PubMed Central

Almeida, Jonas S.; Iriabho, Egiebade E.; Gorrepati, Vijaya L.; Wilkinson, Sean R.; Grüneberg, Alexander; Robbins, David E.; Hackney, James R.

2012-01-01

Background: Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. Materials and Methods: ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Results: Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. Conclusions: The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local “download and installation”. PMID:22934238

ImageJS: Personalized, participated, pervasive, and reproducible image bioinformatics in the web browser.

PubMed

Almeida, Jonas S; Iriabho, Egiebade E; Gorrepati, Vijaya L; Wilkinson, Sean R; Grüneberg, Alexander; Robbins, David E; Hackney, James R

2012-01-01

Image bioinformatics infrastructure typically relies on a combination of server-side high-performance computing and client desktop applications tailored for graphic rendering. On the server side, matrix manipulation environments are often used as the back-end where deployment of specialized analytical workflows takes place. However, neither the server-side nor the client-side desktop solution, by themselves or combined, is conducive to the emergence of open, collaborative, computational ecosystems for image analysis that are both self-sustained and user driven. ImageJS was developed as a browser-based webApp, untethered from a server-side backend, by making use of recent advances in the modern web browser such as a very efficient compiler, high-end graphical rendering capabilities, and I/O tailored for code migration. Multiple versioned code hosting services were used to develop distinct ImageJS modules to illustrate its amenability to collaborative deployment without compromise of reproducibility or provenance. The illustrative examples include modules for image segmentation, feature extraction, and filtering. The deployment of image analysis by code migration is in sharp contrast with the more conventional, heavier, and less safe reliance on data transfer. Accordingly, code and data are loaded into the browser by exactly the same script tag loading mechanism, which offers a number of interesting applications that would be hard to attain with more conventional platforms, such as NIH's popular ImageJ application. The modern web browser was found to be advantageous for image bioinformatics in both the research and clinical environments. This conclusion reflects advantages in deployment scalability and analysis reproducibility, as well as the critical ability to deliver advanced computational statistical procedures machines where access to sensitive data is controlled, that is, without local "download and installation".

A Development of Lightweight Grid Interface

NASA Astrophysics Data System (ADS)

Iwai, G.; Kawai, Y.; Sasaki, T.; Watase, Y.

2011-12-01

In order to help a rapid development of Grid/Cloud aware applications, we have developed API to abstract the distributed computing infrastructures based on SAGA (A Simple API for Grid Applications). SAGA, which is standardized in the OGF (Open Grid Forum), defines API specifications to access distributed computing infrastructures, such as Grid, Cloud and local computing resources. The Universal Grid API (UGAPI), which is a set of command line interfaces (CLI) and APIs, aims to offer simpler API to combine several SAGA interfaces with richer functionalities. These CLIs of the UGAPI offer typical functionalities required by end users for job management and file access to the different distributed computing infrastructures as well as local computing resources. We have also built a web interface for the particle therapy simulation and demonstrated the large scale calculation using the different infrastructures at the same time. In this paper, we would like to present how the web interface based on UGAPI and SAGA achieve more efficient utilization of computing resources over the different infrastructures with technical details and practical experiences.

Hardness Results for Agnostically Learning Low-Degree Polynomial Threshold Functions

DTIC Science & Technology

2011-01-01

S∩[n](ri + δ) ∙ ∏ j∈S∩[n+1,2n]rj − ∏ i∈ Sri ) | 6 ∑ 16|S|6d|cS | ∙ (∑ ∅6=T⊆S∩[n]δ |T | ∙ ∏ i∈S\\T |ri| ) 6 ∑ 16|S|6d|cS | ∙ 2 |S| ∙ ( δ ∙ ∏ i∈S:ri>1...Diakonikolas, P. Harsha, A. Klivans, R. Meka, P. Raghavendra, R. A. Servedio, and L.-Y. Tan . Bounding the average sensitivity and noise sensitiv- ity of...applications. Information and Computation, 100(1):78–150, 1992. [12] J. Jackson . An efficient membership-query algo- rithm for learning DNF with respect to

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community.

PubMed

Krampis, Konstantinos; Booth, Tim; Chapman, Brad; Tiwari, Bela; Bicak, Mesude; Field, Dawn; Nelson, Karen E

2012-03-19

A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them.

Cloud BioLinux: pre-configured and on-demand bioinformatics computing for the genomics community

PubMed Central

2012-01-01

Background A steep drop in the cost of next-generation sequencing during recent years has made the technology affordable to the majority of researchers, but downstream bioinformatic analysis still poses a resource bottleneck for smaller laboratories and institutes that do not have access to substantial computational resources. Sequencing instruments are typically bundled with only the minimal processing and storage capacity required for data capture during sequencing runs. Given the scale of sequence datasets, scientific value cannot be obtained from acquiring a sequencer unless it is accompanied by an equal investment in informatics infrastructure. Results Cloud BioLinux is a publicly accessible Virtual Machine (VM) that enables scientists to quickly provision on-demand infrastructures for high-performance bioinformatics computing using cloud platforms. Users have instant access to a range of pre-configured command line and graphical software applications, including a full-featured desktop interface, documentation and over 135 bioinformatics packages for applications including sequence alignment, clustering, assembly, display, editing, and phylogeny. Each tool's functionality is fully described in the documentation directly accessible from the graphical interface of the VM. Besides the Amazon EC2 cloud, we have started instances of Cloud BioLinux on a private Eucalyptus cloud installed at the J. Craig Venter Institute, and demonstrated access to the bioinformatic tools interface through a remote connection to EC2 instances from a local desktop computer. Documentation for using Cloud BioLinux on EC2 is available from our project website, while a Eucalyptus cloud image and VirtualBox Appliance is also publicly available for download and use by researchers with access to private clouds. Conclusions Cloud BioLinux provides a platform for developing bioinformatics infrastructures on the cloud. An automated and configurable process builds Virtual Machines, allowing the development of highly customized versions from a shared code base. This shared community toolkit enables application specific analysis platforms on the cloud by minimizing the effort required to prepare and maintain them. PMID:22429538

Mining Software Usage with the Automatic Library Tracking Database (ALTD)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hadri, Bilel; Fahey, Mark R

2013-01-01

Tracking software usage is important for HPC centers, computer vendors, code developers and funding agencies to provide more efficient and targeted software support, and to forecast needs and guide HPC software effort towards the Exascale era. However, accurately tracking software usage on HPC systems has been a challenging task. In this paper, we present a tool called Automatic Library Tracking Database (ALTD) that has been developed and put in production on several Cray systems. The ALTD infrastructure prototype automatically and transparently stores information about libraries linked into an application at compilation time and also the executables launched in a batchmore » job. We will illustrate the usage of libraries, compilers and third party software applications on a system managed by the National Institute for Computational Sciences.« less

Semantic Web Infrastructure Supporting NextFrAMES Modeling Platform

NASA Astrophysics Data System (ADS)

Lakhankar, T.; Fekete, B. M.; Vörösmarty, C. J.

2008-12-01

Emerging modeling frameworks offer new ways to modelers to develop model applications by offering a wide range of software components to handle common modeling tasks such as managing space and time, distributing computational tasks in parallel processing environment, performing input/output and providing diagnostic facilities. NextFrAMES, the next generation updates to the Framework for Aquatic Modeling of the Earth System originally developed at University of New Hampshire and currently hosted at The City College of New York takes a step further by hiding most of these services from modeler behind a platform agnostic modeling platform that allows scientists to focus on the implementation of scientific concepts in the form of a new modeling markup language and through a minimalist application programming interface that provide means to implement model processes. At the core of the NextFrAMES modeling platform there is a run-time engine that interprets the modeling markup language loads the module plugins establishes the model I/O and executes the model defined by the modeling XML and the accompanying plugins. The current implementation of the run-time engine is designed for single processor or symmetric multi processing (SMP) systems but future implementation of the run-time engine optimized for different hardware architectures are anticipated. The modeling XML and the accompanying plugins define the model structure and the computational processes in a highly abstract manner, which is not only suitable for the run-time engine, but has the potential to integrate into semantic web infrastructure, where intelligent parsers can extract information about the model configurations such as input/output requirements applicable space and time scales and underlying modeling processes. The NextFrAMES run-time engine itself is also designed to tap into web enabled data services directly, therefore it can be incorporated into complex workflow to implement End-to-End application from observation to the delivery of highly aggregated information. Our presentation will discuss the web services ranging from OpenDAP and WaterOneFlow data services to metadata provided through catalog services that could serve NextFrAMES modeling applications. We will also discuss the support infrastructure needed to streamline the integration of NextFrAMES into an End-to-End application to deliver highly processed information to end users. The End-to-End application will be demonstrated through examples from the State-of-the Global Water System effort that builds on data services provided through WMO's Global Terrestrial Network for Hydrology to deliver water resources related information to policy makers for better water management. Key components of this E2E system are promoted as Community of Practice examples for the Global Observing System of Systems therefore the State-of-the Global Water System can be viewed as test case for the interoperability of the incorporated web service components.

GAMERA - The New Magnetospheric Code

NASA Astrophysics Data System (ADS)

Lyon, J.; Sorathia, K.; Zhang, B.; Merkin, V. G.; Wiltberger, M. J.; Daldorff, L. K. S.

2017-12-01

The Lyon-Fedder-Mobarry (LFM) code has been a main-line magnetospheric simulation code for 30 years. The code base, designed in the age of memory to memory vector ma- chines,is still in wide use for science production but needs upgrading to ensure the long term sustainability. In this presentation, we will discuss our recent efforts to update and improve that code base and also highlight some recent results. The new project GAM- ERA, Grid Agnostic MHD for Extended Research Applications, has kept the original design characteristics of the LFM and made significant improvements. The original de- sign included high order numerical differencing with very aggressive limiting, the ability to use arbitrary, but logically rectangular, grids, and maintenance of div B = 0 through the use of the Yee grid. Significant improvements include high-order upwinding and a non-clipping limiter. One other improvement with wider applicability is an im- proved averaging technique for the singularities in polar and spherical grids. The new code adopts a hybrid structure - multi-threaded OpenMP with an overarching MPI layer for large scale and coupled applications. The MPI layer uses a combination of standard MPI and the Global Array Toolkit from PNL to provide a lightweight mechanism for coupling codes together concurrently. The single processor code is highly efficient and can run magnetospheric simulations at the default CCMC resolution faster than real time on a MacBook pro. We have run the new code through the Athena suite of tests, and the results compare favorably with the codes available to the astrophysics community. LFM/GAMERA has been applied to many different situations ranging from the inner and outer heliosphere and magnetospheres of Venus, the Earth, Jupiter and Saturn. We present example results the Earth's magnetosphere including a coupled ring current (RCM), the magnetospheres of Jupiter and Saturn, and the inner heliosphere.

Validation of Storm Water Management Model Storm Control Measures Modules

NASA Astrophysics Data System (ADS)

Simon, M. A.; Platz, M. C.

2017-12-01

EPA's Storm Water Management Model (SWMM) is a computational code heavily relied upon by industry for the simulation of wastewater and stormwater infrastructure performance. Many municipalities are relying on SWMM results to design multi-billion-dollar, multi-decade infrastructure upgrades. Since the 1970's, EPA and others have developed five major releases, the most recent ones containing storm control measures modules for green infrastructure. The main objective of this study was to quantify the accuracy with which SWMM v5.1.10 simulates the hydrologic activity of previously monitored low impact developments. Model performance was evaluated with a mathematical comparison of outflow hydrographs and total outflow volumes, using empirical data and a multi-event, multi-objective calibration method. The calibration methodology utilized PEST++ Version 3, a parameter estimation tool, which aided in the selection of unmeasured hydrologic parameters. From the validation study and sensitivity analysis, several model improvements were identified to advance SWMM LID Module performance for permeable pavements, infiltration units and green roofs, and these were performed and reported herein. Overall, it was determined that SWMM can successfully simulate low impact development controls given accurate model confirmation, parameter measurement, and model calibration.

Cloud Computing in Support of Applied Learning: A Baseline Study of Infrastructure Design at Southern Polytechnic State University

ERIC Educational Resources Information Center

Conn, Samuel S.; Reichgelt, Han

2013-01-01

Cloud computing represents an architecture and paradigm of computing designed to deliver infrastructure, platforms, and software as constructible computing resources on demand to networked users. As campuses are challenged to better accommodate academic needs for applications and computing environments, cloud computing can provide an accommodating…

Heterogeneous scalable framework for multiphase flows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Morris, Karla Vanessa

2013-09-01

Two categories of challenges confront the developer of computational spray models: those related to the computation and those related to the physics. Regarding the computation, the trend towards heterogeneous, multi- and many-core platforms will require considerable re-engineering of codes written for the current supercomputing platforms. Regarding the physics, accurate methods for transferring mass, momentum and energy from the dispersed phase onto the carrier fluid grid have so far eluded modelers. Significant challenges also lie at the intersection between these two categories. To be competitive, any physics model must be expressible in a parallel algorithm that performs well on evolving computermore » platforms. This work created an application based on a software architecture where the physics and software concerns are separated in a way that adds flexibility to both. The develop spray-tracking package includes an application programming interface (API) that abstracts away the platform-dependent parallelization concerns, enabling the scientific programmer to write serial code that the API resolves into parallel processes and threads of execution. The project also developed the infrastructure required to provide similar APIs to other application. The API allow object-oriented Fortran applications direct interaction with Trilinos to support memory management of distributed objects in central processing units (CPU) and graphic processing units (GPU) nodes for applications using C++.« less

An Object-Oriented Network-Centric Software Architecture for Physical Computing

NASA Astrophysics Data System (ADS)

Palmer, Richard

1997-08-01

Recent developments in object-oriented computer languages and infrastructure such as the Internet, Web browsers, and the like provide an opportunity to define a more productive computational environment for scientific programming that is based more closely on the underlying mathematics describing physics than traditional programming languages such as FORTRAN or C++. In this talk I describe an object-oriented software architecture for representing physical problems that includes classes for such common mathematical objects as geometry, boundary conditions, partial differential and integral equations, discretization and numerical solution methods, etc. In practice, a scientific program written using this architecture looks remarkably like the mathematics used to understand the problem, is typically an order of magnitude smaller than traditional FORTRAN or C++ codes, and hence easier to understand, debug, describe, etc. All objects in this architecture are ``network-enabled,'' which means that components of a software solution to a physical problem can be transparently loaded from anywhere on the Internet or other global network. The architecture is expressed as an ``API,'' or application programmers interface specification, with reference embeddings in Java, Python, and C++. A C++ class library for an early version of this API has been implemented for machines ranging from PC's to the IBM SP2, meaning that phidentical codes run on all architectures.

Increasing Road Infrastructure Capacity Through the Use of Autonomous Vehicles

DTIC Science & Technology

2016-12-01

NAVAL POSTGRADUATE SCHOOL MONTEREY, CALIFORNIA THESIS Approved for public release. Distribution is unlimited. INCREASING ROAD ...DATES COVERED Master’s thesis 4. TITLE AND SUBTITLE INCREASING ROAD INFRASTRUCTURE CAPACITY THROUGH THE USE OF AUTONOMOUS VEHICLES 5. FUNDING...driverless vehicles, road infrastructure 15. NUMBER OF PAGES 65 16. PRICE CODE 17. SECURITY CLASSIFICATION OF REPORT Unclassified 18. SECURITY

Applying a rateless code in content delivery networks

NASA Astrophysics Data System (ADS)

Suherman; Zarlis, Muhammad; Parulian Sitorus, Sahat; Al-Akaidi, Marwan

2017-09-01

Content delivery network (CDN) allows internet providers to locate their services, to map their coverage into networks without necessarily to own them. CDN is part of the current internet infrastructures, supporting multi server applications especially social media. Various works have been proposed to improve CDN performances. Since accesses on social media servers tend to be short but frequent, providing redundant to the transmitted packets to ensure lost packets not degrade the information integrity may improve service performances. This paper examines the implementation of rateless code in the CDN infrastructure. The NS-2 evaluations show that rateless code is able to reduce packet loss up to 50%.

Towards energy-efficient nonoscillatory forward-in-time integrations on lat-lon grids

NASA Astrophysics Data System (ADS)

Polkowski, Marcin; Piotrowski, Zbigniew; Ryczkowski, Adam

2017-04-01

The design of the next-generation weather prediction models calls for new algorithmic approaches allowing for robust integrations of atmospheric flow over complex orography at sub-km resolutions. These need to be accompanied by efficient implementations exposing multi-level parallelism, capable to run on modern supercomputing architectures. Here we present the recent advances in the energy-efficient implementation of the consistent soundproof/implicit compressible EULAG dynamical core of the COSMO weather prediction framework. Based on the experiences of the atmospheric dwarfs developed within H2020 ESCAPE project, we develop efficient, architecture agnostic implementations of fully three-dimensional MPDATA advection schemes and generalized diffusion operator in curvilinear coordinates and spherical geometry. We compare optimized Fortran implementation with preliminary C++ implementation employing the Gridtools library, allowing for integrations on CPU and GPU while maintaining single source code.

VERCE: a productive e-Infrastructure and e-Science environment for data-intensive seismology research

NASA Astrophysics Data System (ADS)

Vilotte, J. P.; Atkinson, M.; Spinuso, A.; Rietbrock, A.; Michelini, A.; Igel, H.; Frank, A.; Carpené, M.; Schwichtenberg, H.; Casarotti, E.; Filgueira, R.; Garth, T.; Germünd, A.; Klampanos, I.; Krause, A.; Krischer, L.; Leong, S. H.; Magnoni, F.; Matser, J.; Moguilny, G.

2015-12-01

Seismology addresses both fundamental problems in understanding the Earth's internal wave sources and structures and augmented societal applications, like earthquake and tsunami hazard assessment and risk mitigation; and puts a premium on open-data accessible by the Federated Digital Seismological Networks. The VERCE project, "Virtual Earthquake and seismology Research Community e-science environment in Europe", has initiated a virtual research environment to support complex orchestrated workflows combining state-of-art wave simulation codes and data analysis tools on distributed computing and data infrastructures (DCIs) along with multiple sources of observational data and new capabilities to combine simulation results with observational data. The VERCE Science Gateway provides a view of all the available resources, supporting collaboration with shared data and methods, with data access controls. The mapping to DCIs handles identity management, authority controls, transformations between representations and controls, and access to resources. The framework for computational science that provides simulation codes, like SPECFEM3D, democratizes their use by getting data from multiple sources, managing Earth models and meshes, distilling them as input data, and capturing results with meta-data. The dispel4py data-intensive framework allows for developing data-analysis applications using Python and the ObsPy library, which can be executed on different DCIs. A set of tools allows coupling with seismology and external data services. Provenance driven tools validate results and show relationships between data to facilitate method improvement. Lessons learned from VERCE training lead us to conclude that solid-Earth scientists could make significant progress by using VERCE e-science environment. VERCE has already contributed to the European Plate Observation System (EPOS), and is part of the EPOS implementation phase. Its cross-disciplinary capabilities are being extended for the EPOS implantation phase.

High-Performance First-Principles Molecular Dynamics for Predictive Theory and Modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gygi, Francois; Galli, Giulia; Schwegler, Eric

This project focused on developing high-performance software tools for First-Principles Molecular Dynamics (FPMD) simulations, and applying them in investigations of materials relevant to energy conversion processes. FPMD is an atomistic simulation method that combines a quantum-mechanical description of electronic structure with the statistical description provided by molecular dynamics (MD) simulations. This reliance on fundamental principles allows FPMD simulations to provide a consistent description of structural, dynamical and electronic properties of a material. This is particularly useful in systems for which reliable empirical models are lacking. FPMD simulations are increasingly used as a predictive tool for applications such as batteries, solarmore » energy conversion, light-emitting devices, electro-chemical energy conversion devices and other materials. During the course of the project, several new features were developed and added to the open-source Qbox FPMD code. The code was further optimized for scalable operation of large-scale, Leadership-Class DOE computers. When combined with Many-Body Perturbation Theory (MBPT) calculations, this infrastructure was used to investigate structural and electronic properties of liquid water, ice, aqueous solutions, nanoparticles and solid-liquid interfaces. Computing both ionic trajectories and electronic structure in a consistent manner enabled the simulation of several spectroscopic properties, such as Raman spectra, infrared spectra, and sum-frequency generation spectra. The accuracy of the approximations used allowed for direct comparisons of results with experimental data such as optical spectra, X-ray and neutron diffraction spectra. The software infrastructure developed in this project, as applied to various investigations of solids, liquids and interfaces, demonstrates that FPMD simulations can provide a detailed, atomic-scale picture of structural, vibrational and electronic properties of complex systems relevant to energy conversion devices.« less

Computational Science in Armenia (Invited Talk)

NASA Astrophysics Data System (ADS)

Marandjian, H.; Shoukourian, Yu.

This survey is devoted to the development of informatics and computer science in Armenia. The results in theoretical computer science (algebraic models, solutions to systems of general form recursive equations, the methods of coding theory, pattern recognition and image processing), constitute the theoretical basis for developing problem-solving-oriented environments. As examples can be mentioned: a synthesizer of optimized distributed recursive programs, software tools for cluster-oriented implementations of two-dimensional cellular automata, a grid-aware web interface with advanced service trading for linear algebra calculations. In the direction of solving scientific problems that require high-performance computing resources, examples of completed projects include the field of physics (parallel computing of complex quantum systems), astrophysics (Armenian virtual laboratory), biology (molecular dynamics study of human red blood cell membrane), meteorology (implementing and evaluating the Weather Research and Forecast Model for the territory of Armenia). The overview also notes that the Institute for Informatics and Automation Problems of the National Academy of Sciences of Armenia has established a scientific and educational infrastructure, uniting computing clusters of scientific and educational institutions of the country and provides the scientific community with access to local and international computational resources, that is a strong support for computational science in Armenia.

Moving Virtual Research Environments from high maintenance Stovepipes to Multi-purpose Sustainable Service-oriented Science Platforms

NASA Astrophysics Data System (ADS)

Klump, Jens; Fraser, Ryan; Wyborn, Lesley; Friedrich, Carsten; Squire, Geoffrey; Barker, Michelle; Moloney, Glenn

2017-04-01

The researcher of today is likely to be part of a team distributed over multiple sites that will access data from an external repository and then process the data on a public or private cloud or even on a large centralised supercomputer. They are increasingly likely to use a mixture of their own code, third party software and libraries, or even access global community codes. These components will be connected into a Virtual Research Environments (VREs) that will enable members of the research team who are not co-located to actively work together at various scales to share data, models, tools, software, workflows, best practices, infrastructures, etc. Many VRE's are built in isolation: designed to meet a specific research program with components tightly coupled and not capable of being repurposed for other use cases - they are becoming 'stovepipes'. The limited number of users of some VREs also means that the cost of maintenance per researcher can be unacceptably high. The alternative is to develop service-oriented Science Platforms that enable multiple communities to develop specialised solutions for specific research programs. The platforms can offer access to data, software tools and processing infrastructures (cloud, supercomputers) through globally distributed, interconnected modules. In Australia, the Virtual Geophysics Laboratory (VGL) was initially built to enable a specific set of researchers in government agencies access to specific data sets and a limited number of tools, that is now rapidly evolving into a multi-purpose Earth science platform with access to an increased variety of data, a broader range of tools, users from more sectors and a diversity of computational infrastructures. The expansion has been relatively easy, because of the architecture whereby data, tools and compute resources are loosely coupled via interfaces that are built on international standards and accessed as services wherever possible. In recent years, investments in discoverability and accessibility of data via online services in Australia mean that data resources can be easily added to the virtual environments as and when required. Another key to increasing to reusability and uptake of the VRE is the capability to capturing workflows so that they can be reused and repurposed both within and beyond the community that that defined the original use case. Unfortunately, Software-as-a-Service in the research sector is not yet mature. In response, we developed a Scientific Software solutions Center (SSSC) that enables researchers to discover, deploy and then share computational codes, code snippets or processes both in a human and machine-readable manner. Growth has come not only from within the Earth science community but from the Australian Virtual Laboratory community which is building VREs for a diversity of communities such as astronomy, genomics, environment, humanities, climate etc. Components such as access control, provenance, visualisation, accounting etc. are common to all scientific domains and sharing of these across multiple domains reduces costs, but more importantly increases the ability to undertake interdisciplinary science. These efforts are transitioning VREs to more sustainable Service-oriented Science Platforms that can be delivered in an agile, adaptable manner for broader community interests.

Signal and noise extraction from analog memory elements for neuromorphic computing.

PubMed

Gong, N; Idé, T; Kim, S; Boybat, I; Sebastian, A; Narayanan, V; Ando, T

2018-05-29

Dense crossbar arrays of non-volatile memory (NVM) can potentially enable massively parallel and highly energy-efficient neuromorphic computing systems. The key requirements for the NVM elements are continuous (analog-like) conductance tuning capability and switching symmetry with acceptable noise levels. However, most NVM devices show non-linear and asymmetric switching behaviors. Such non-linear behaviors render separation of signal and noise extremely difficult with conventional characterization techniques. In this study, we establish a practical methodology based on Gaussian process regression to address this issue. The methodology is agnostic to switching mechanisms and applicable to various NVM devices. We show tradeoff between switching symmetry and signal-to-noise ratio for HfO 2 -based resistive random access memory. Then, we characterize 1000 phase-change memory devices based on Ge 2 Sb 2 Te 5 and separate total variability into device-to-device variability and inherent randomness from individual devices. These results highlight the usefulness of our methodology to realize ideal NVM devices for neuromorphic computing.

Real-space processing of helical filaments in SPARX

PubMed Central

Behrmann, Elmar; Tao, Guozhi; Stokes, David L.; Egelman, Edward H.; Raunser, Stefan; Penczek, Pawel A.

2012-01-01

We present a major revision of the iterative helical real-space refinement (IHRSR) procedure and its implementation in the SPARX single particle image processing environment. We built on over a decade of experience with IHRSR helical structure determination and we took advantage of the flexible SPARX infrastructure to arrive at an implementation that offers ease of use, flexibility in designing helical structure determination strategy, and high computational efficiency. We introduced the 3D projection matching code which now is able to work with non-cubic volumes, the geometry better suited for long helical filaments, we enhanced procedures for establishing helical symmetry parameters, and we parallelized the code using distributed memory paradigm. Additional feature includes a graphical user interface that facilitates entering and editing of parameters controlling the structure determination strategy of the program. In addition, we present a novel approach to detect and evaluate structural heterogeneity due to conformer mixtures that takes advantage of helical structure redundancy. PMID:22248449

Sustaining a Community Computing Infrastructure for Online Teacher Professional Development: A Case Study of Designing Tapped In

NASA Astrophysics Data System (ADS)

Farooq, Umer; Schank, Patricia; Harris, Alexandra; Fusco, Judith; Schlager, Mark

Community computing has recently grown to become a major research area in human-computer interaction. One of the objectives of community computing is to support computer-supported cooperative work among distributed collaborators working toward shared professional goals in online communities of practice. A core issue in designing and developing community computing infrastructures — the underlying sociotechnical layer that supports communitarian activities — is sustainability. Many community computing initiatives fail because the underlying infrastructure does not meet end user requirements; the community is unable to maintain a critical mass of users consistently over time; it generates insufficient social capital to support significant contributions by members of the community; or, as typically happens with funded initiatives, financial and human capital resource become unavailable to further maintain the infrastructure. On the basis of more than 9 years of design experience with Tapped In-an online community of practice for education professionals — we present a case study that discusses four design interventions that have sustained the Tapped In infrastructure and its community to date. These interventions represent broader design strategies for developing online environments for professional communities of practice.

A Cloud-based Infrastructure and Architecture for Environmental System Research

NASA Astrophysics Data System (ADS)

Wang, D.; Wei, Y.; Shankar, M.; Quigley, J.; Wilson, B. E.

2016-12-01

The present availability of high-capacity networks, low-cost computers and storage devices, and the widespread adoption of hardware virtualization and service-oriented architecture provide a great opportunity to enable data and computing infrastructure sharing between closely related research activities. By taking advantage of these approaches, along with the world-class high computing and data infrastructure located at Oak Ridge National Laboratory, a cloud-based infrastructure and architecture has been developed to efficiently deliver essential data and informatics service and utilities to the environmental system research community, and will provide unique capabilities that allows terrestrial ecosystem research projects to share their software utilities (tools), data and even data submission workflow in a straightforward fashion. The infrastructure will minimize large disruptions from current project-based data submission workflows for better acceptances from existing projects, since many ecosystem research projects already have their own requirements or preferences for data submission and collection. The infrastructure will eliminate scalability problems with current project silos by provide unified data services and infrastructure. The Infrastructure consists of two key components (1) a collection of configurable virtual computing environments and user management systems that expedite data submission and collection from environmental system research community, and (2) scalable data management services and system, originated and development by ORNL data centers.

Building an infrastructure at PICKSC for the educational use of kinetic software tools

NASA Astrophysics Data System (ADS)

Mori, W. B.; Decyk, V. K.; Tableman, A.; Fonseca, R. A.; Tsung, F. S.; Hu, Q.; Winjum, B. J.; Amorim, L. D.; An, W.; Dalichaouch, T. N.; Davidson, A.; Joglekar, A.; Li, F.; May, J.; Touati, M.; Xu, X. L.; Yu, P.

2016-10-01

One aim of the Particle-In-Cell and Kinetic Simulation Center (PICKSC) at UCLA is to coordinate a community development of educational software for undergraduate and graduate courses in plasma physics and computer science. The rich array of physical behaviors exhibited by plasmas can be difficult to grasp by students. If they are given the ability to quickly and easily explore plasma physics through kinetic simulations, and to make illustrative visualizations of plasma waves, particle motion in electromagnetic fields, instabilities, or other phenomena, then they can be equipped with first-hand experiences that inform and contextualize conventional texts and lectures. We are developing an infrastructure for any interested persons to take our kinetic codes, run them without any prerequisite knowledge, and explore desired scenarios. Furthermore, we are actively interested in any ideas or input from other plasma physicists. This poster aims to illustrate what we have developed and gather a community of interested users and developers. Supported by NSF under Grant ACI-1339893.

OpenSoC Fabric

DOE Office of Scientific and Technical Information (OSTI.GOV)

2014-08-21

Recent advancements in technology scaling have shown a trend towards greater integration with large-scale chips containing thousands of processors connected to memories and other I/O devices using non-trivial network topologies. Software simulation proves insufficient to study the tradeoffs in such complex systems due to slow execution time, whereas hardware RTL development is too time-consuming. We present OpenSoC Fabric, an on-chip network generation infrastructure which aims to provide a parameterizable and powerful on-chip network generator for evaluating future high performance computing architectures based on SoC technology. OpenSoC Fabric leverages a new hardware DSL, Chisel, which contains powerful abstractions provided by itsmore » base language, Scala, and generates both software (C++) and hardware (Verilog) models from a single code base. The OpenSoC Fabric2 infrastructure is modeled after existing state-of-the-art simulators, offers large and powerful collections of configuration options, and follows object-oriented design and functional programming to make functionality extension as easy as possible.« less

Removing a barrier to computer-based outbreak and disease surveillance--the RODS Open Source Project.

PubMed

Espino, Jeremy U; Wagner, M; Szczepaniak, C; Tsui, F C; Su, H; Olszewski, R; Liu, Z; Chapman, W; Zeng, X; Ma, L; Lu, Z; Dara, J

2004-09-24

Computer-based outbreak and disease surveillance requires high-quality software that is well-supported and affordable. Developing software in an open-source framework, which entails free distribution and use of software and continuous, community-based software development, can produce software with such characteristics, and can do so rapidly. The objective of the Real-Time Outbreak and Disease Surveillance (RODS) Open Source Project is to accelerate the deployment of computer-based outbreak and disease surveillance systems by writing software and catalyzing the formation of a community of users, developers, consultants, and scientists who support its use. The University of Pittsburgh seeded the Open Source Project by releasing the RODS software under the GNU General Public License. An infrastructure was created, consisting of a website, mailing lists for developers and users, designated software developers, and shared code-development tools. These resources are intended to encourage growth of the Open Source Project community. Progress is measured by assessing website usage, number of software downloads, number of inquiries, number of system deployments, and number of new features or modules added to the code base. During September--November 2003, users generated 5,370 page views of the project website, 59 software downloads, 20 inquiries, one new deployment, and addition of four features. Thus far, health departments and companies have been more interested in using the software as is than in customizing or developing new features. The RODS laboratory anticipates that after initial installation has been completed, health departments and companies will begin to customize the software and contribute their enhancements to the public code base.

Managing a tier-2 computer centre with a private cloud infrastructure

NASA Astrophysics Data System (ADS)

Bagnasco, Stefano; Berzano, Dario; Brunetti, Riccardo; Lusso, Stefano; Vallero, Sara

2014-06-01

In a typical scientific computing centre, several applications coexist and share a single physical infrastructure. An underlying Private Cloud infrastructure eases the management and maintenance of such heterogeneous applications (such as multipurpose or application-specific batch farms, Grid sites, interactive data analysis facilities and others), allowing dynamic allocation resources to any application. Furthermore, the maintenance of large deployments of complex and rapidly evolving middleware and application software is eased by the use of virtual images and contextualization techniques. Such infrastructures are being deployed in some large centres (see e.g. the CERN Agile Infrastructure project), but with several open-source tools reaching maturity this is becoming viable also for smaller sites. In this contribution we describe the Private Cloud infrastructure at the INFN-Torino Computer Centre, that hosts a full-fledged WLCG Tier-2 centre, an Interactive Analysis Facility for the ALICE experiment at the CERN LHC and several smaller scientific computing applications. The private cloud building blocks include the OpenNebula software stack, the GlusterFS filesystem and the OpenWRT Linux distribution (used for network virtualization); a future integration into a federated higher-level infrastructure is made possible by exposing commonly used APIs like EC2 and OCCI.

General Mission Analysis Tool (GMAT) Architectural Specification. Draft

NASA Technical Reports Server (NTRS)

Hughes, Steven P.; Conway, Darrel, J.

2007-01-01

Early in 2002, Goddard Space Flight Center (GSFC) began to identify requirements for the flight dynamics software needed to fly upcoming missions that use formations of spacecraft to collect data. These requirements ranged from low level modeling features to large scale interoperability requirements. In 2003 we began work on a system designed to meet these requirement; this system is GMAT. The General Mission Analysis Tool (GMAT) is a general purpose flight dynamics modeling tool built on open source principles. The GMAT code is written in C++, and uses modern C++ constructs extensively. GMAT can be run through either a fully functional Graphical User Interface (GUI) or as a command line program with minimal user feedback. The system is built and runs on Microsoft Windows, Linux, and Macintosh OS X platforms. The GMAT GUI is written using wxWidgets, a cross platform library of components that streamlines the development and extension of the user interface Flight dynamics modeling is performed in GMAT by building components that represent the players in the analysis problem that is being modeled. These components interact through the sequential execution of instructions, embodied in the GMAT Mission Sequence. A typical Mission Sequence will model the trajectories of a set of spacecraft evolving over time, calculating relevant parameters during this propagation, and maneuvering individual spacecraft to maintain a set of mission constraints as established by the mission analyst. All of the elements used in GMAT for mission analysis can be viewed in the GMAT GUI or through a custom scripting language. Analysis problems modeled in GMAT are saved as script files, and these files can be read into GMAT. When a script is read into the GMAT GUI, the corresponding user interface elements are constructed in the GMAT GUI. The GMAT system was developed from the ground up to run in a platform agnostic environment. The source code compiles on numerous different platforms, and is regularly exercised running on Windows, Linux and Macintosh computers by the development and analysis teams working on the project. The system can be run using either a graphical user interface, written using the open source wxWidgets framework, or from a text console. The GMAT source code was written using open source tools. GSFC has released the code using the NASA open source license.

Simulating electron wave dynamics in graphene superlattices exploiting parallel processing advantages

NASA Astrophysics Data System (ADS)

Rodrigues, Manuel J.; Fernandes, David E.; Silveirinha, Mário G.; Falcão, Gabriel

2018-01-01

This work introduces a parallel computing framework to characterize the propagation of electron waves in graphene-based nanostructures. The electron wave dynamics is modeled using both "microscopic" and effective medium formalisms and the numerical solution of the two-dimensional massless Dirac equation is determined using a Finite-Difference Time-Domain scheme. The propagation of electron waves in graphene superlattices with localized scattering centers is studied, and the role of the symmetry of the microscopic potential in the electron velocity is discussed. The computational methodologies target the parallel capabilities of heterogeneous multi-core CPU and multi-GPU environments and are built with the OpenCL parallel programming framework which provides a portable, vendor agnostic and high throughput-performance solution. The proposed heterogeneous multi-GPU implementation achieves speedup ratios up to 75x when compared to multi-thread and multi-core CPU execution, reducing simulation times from several hours to a couple of minutes.

Improving Remote Voting Security with CodeVoting

NASA Astrophysics Data System (ADS)

Joaquim, Rui; Ribeiro, Carlos; Ferreira, Paulo

One of the major problems that prevents the spread of elections with the possibility of remote voting over electronic networks, also called Internet Voting, is the use of unreliable client platforms, such as the voter's computer and the Internet infrastructure connecting it to the election server. A computer connected to the Internet is exposed to viruses, worms, Trojans, spyware, malware and other threats that can compromise the election's integrity. For instance, it is possible to write a virus that changes the voter's vote to a predetermined vote on election's day. Another possible attack is the creation of a fake election web site where the voter uses a malicious vote program on the web site that manipulates the voter's vote (phishing/pharming attack). Such attacks may not disturb the election protocol, therefore can remain undetected in the eyes of the election auditors.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurth, Thorsten; Pochinsky, Andrew; Sarje, Abhinav

Practitioners of lattice QCD/QFT have been some of the primary pioneer users of the state-of-the-art high-performance-computing systems, and contribute towards the stress tests of such new machines as soon as they become available. As with all aspects of high-performance-computing, I/O is becoming an increasingly specialized component of these systems. In order to take advantage of the latest available high-performance I/O infrastructure, to ensure reliability and backwards compatibility of data files, and to help unify the data structures used in lattice codes, we have incorporated parallel HDF5 I/O into the SciDAC supported USQCD software stack. Here we present the design andmore » implementation of this I/O framework. Our HDF5 implementation outperforms optimized QIO at the 10-20% level and leaves room for further improvement by utilizing appropriate dataset chunking.« less

A Three-Phase Decision Model of Computer-Aided Coding for the Iranian Classification of Health Interventions (IRCHI)

PubMed Central

Azadmanjir, Zahra; Safdari, Reza; Ghazisaeedi, Marjan; Mokhtaran, Mehrshad; Kameli, Mohammad Esmail

2017-01-01

Introduction: Accurate coded data in the healthcare are critical. Computer-Assisted Coding (CAC) is an effective tool to improve clinical coding in particular when a new classification will be developed and implemented. But determine the appropriate method for development need to consider the specifications of existing CAC systems, requirements for each type, our infrastructure and also, the classification scheme. Aim: The aim of the study was the development of a decision model for determining accurate code of each medical intervention in Iranian Classification of Health Interventions (IRCHI) that can be implemented as a suitable CAC system. Methods: first, a sample of existing CAC systems was reviewed. Then feasibility of each one of CAC types was examined with regard to their prerequisites for their implementation. The next step, proper model was proposed according to the structure of the classification scheme and was implemented as an interactive system. Results: There is a significant relationship between the level of assistance of a CAC system and integration of it with electronic medical documents. Implementation of fully automated CAC systems is impossible due to immature development of electronic medical record and problems in using language for medical documenting. So, a model was proposed to develop semi-automated CAC system based on hierarchical relationships between entities in the classification scheme and also the logic of decision making to specify the characters of code step by step through a web-based interactive user interface for CAC. It was composed of three phases to select Target, Action and Means respectively for an intervention. Conclusion: The proposed model was suitable the current status of clinical documentation and coding in Iran and also, the structure of new classification scheme. Our results show it was practical. However, the model needs to be evaluated in the next stage of the research. PMID:28883671

Modernizing the ATLAS simulation infrastructure

NASA Astrophysics Data System (ADS)

Di Simone, A.; CollaborationAlbert-Ludwigs-Universitt Freiburg, ATLAS; Institut, Physikalisches; Br., 79104 Freiburg i.; Germany

2017-10-01

The ATLAS Simulation infrastructure has been used to produce upwards of 50 billion proton-proton collision events for analyses ranging from detailed Standard Model measurements to searches for exotic new phenomena. In the last several years, the infrastructure has been heavily revised to allow intuitive multithreading and significantly improved maintainability. Such a massive update of a legacy code base requires careful choices about what pieces of code to completely rewrite and what to wrap or revise. The initialization of the complex geometry was generalized to allow new tools and geometry description languages, popular in some detector groups. The addition of multithreading requires Geant4-MT and GaudiHive, two frameworks with fundamentally different approaches to multithreading, to work together. It also required enforcing thread safety throughout a large code base, which required the redesign of several aspects of the simulation, including truth, the record of particle interactions with the detector during the simulation. These advances were possible thanks to close interactions with the Geant4 developers.

Value-Range Analysis of C Programs

NASA Astrophysics Data System (ADS)

Simon, Axel

In 1988, Robert T. Morris exploited a so-called buffer-overflow bug in finger (a dæmon whose job it is to return information on local users) to mount a denial-of-service attack on hundreds of VAX and Sun-3 computers [159]. He created what is nowadays called a worm; that is, a crafted stream of bytes that, when sent to a computer over the network, utilises a buffer-overflow bug in the software of that computer to execute code encoded in the byte stream. In the case of a worm, this code will send the very same byte stream to other computers on the network, thereby creating an avalanche of network traffic that ultimately renders the network and all computers involved in replicating the worm inaccessible. Besides duplicating themselves, worms can alter data on the host that they are running on. The most famous example in recent years was the MSBlaster32 worm, which altered the configuration database on many Microsoft Windows machines, thereby forcing the computers to reboot incessantly. Although this worm was rather benign, it caused huge damage to businesses who were unable to use their IT infrastructure for hours or even days after the appearance of the worm. A more malicious worm is certainly conceivable [187] due to the fact that worms are executed as part of a dæmon (also known as "service" on Windows machines) and thereby run at a privileged level, allowing access to any data stored on the remote computer. While the deletion of data presents a looming threat to valuable information, even more serious uses are espionage and theft, in particular because worms do not have to affect the running system and hence may be impossible to detect.

Mobile Transactional Modelling: From Concepts to Incremental Knowledge

NASA Astrophysics Data System (ADS)

Launders, Ivan; Polovina, Simon; Hill, Richard

In 1988, Robert T. Morris exploited a so-called buffer-overflow bug in finger (a dæmon whose job it is to return information on local users) to mount a denial-of-service attack on hundreds of VAX and Sun-3 computers [159]. He created what is nowadays called a worm; that is, a crafted stream of bytes that, when sent to a computer over the network, utilises a buffer-overflow bug in the software of that computer to execute code encoded in the byte stream. In the case of a worm, this code will send the very same byte stream to other computers on the network, thereby creating an avalanche of network traffic that ultimately renders the network and all computers involved in replicating the worm inaccessible. Besides duplicating themselves, worms can alter data on the host that they are running on. The most famous example in recent years was the MSBlaster32 worm, which altered the configuration database on many Microsoft Windows machines, thereby forcing the computers to reboot incessantly. Although this worm was rather benign, it caused huge damage to businesses who were unable to use their IT infrastructure for hours or even days after the appearance of the worm. A more malicious worm is certainly conceivable [187] due to the fact that worms are executed as part of a dæmon (also known as "service" on Windows machines) and thereby run at a privileged level, allowing access to any data stored on the remote computer. While the deletion of data presents a looming threat to valuable information, even more serious uses are espionage and theft, in particular because worms do not have to affect the running system and hence may be impossible to detect.

Dragon pulse information management system (DPIMS): A unique model-based approach to implementing domain agnostic system of systems and behaviors

NASA Astrophysics Data System (ADS)

Anderson, Thomas S.

2016-05-01

The Global Information Network Architecture is an information technology based on Vector Relational Data Modeling, a unique computational paradigm, DoD network certified by USARMY as the Dragon Pulse Informa- tion Management System. This network available modeling environment for modeling models, where models are configured using domain relevant semantics and use network available systems, sensors, databases and services as loosely coupled component objects and are executable applications. Solutions are based on mission tactics, techniques, and procedures and subject matter input. Three recent ARMY use cases are discussed a) ISR SoS. b) Modeling and simulation behavior validation. c) Networked digital library with behaviors.

DIVE: A Graph-based Visual Analytics Framework for Big Data

PubMed Central

Rysavy, Steven J.; Bromley, Dennis; Daggett, Valerie

2014-01-01

The need for data-centric scientific tools is growing; domains like biology, chemistry, and physics are increasingly adopting computational approaches. As a result, scientists must now deal with the challenges of big data. To address these challenges, we built a visual analytics platform named DIVE: Data Intensive Visualization Engine. DIVE is a data-agnostic, ontologically-expressive software framework capable of streaming large datasets at interactive speeds. Here we present the technical details of the DIVE platform, multiple usage examples, and a case study from the Dynameomics molecular dynamics project. We specifically highlight our novel contributions to structured data model manipulation and high-throughput streaming of large, structured datasets. PMID:24808197

Molecular Genetics Information System (MOLGENIS): alternatives in developing local experimental genomics databases.

PubMed

Swertz, Morris A; De Brock, E O; Van Hijum, Sacha A F T; De Jong, Anne; Buist, Girbe; Baerends, Richard J S; Kok, Jan; Kuipers, Oscar P; Jansen, Ritsert C

2004-09-01

Genomic research laboratories need adequate infrastructure to support management of their data production and research workflow. But what makes infrastructure adequate? A lack of appropriate criteria makes any decision on buying or developing a system difficult. Here, we report on the decision process for the case of a molecular genetics group establishing a microarray laboratory. Five typical requirements for experimental genomics database systems were identified: (i) evolution ability to keep up with the fast developing genomics field; (ii) a suitable data model to deal with local diversity; (iii) suitable storage of data files in the system; (iv) easy exchange with other software; and (v) low maintenance costs. The computer scientists and the researchers of the local microarray laboratory considered alternative solutions for these five requirements and chose the following options: (i) use of automatic code generation; (ii) a customized data model based on standards; (iii) storage of datasets as black boxes instead of decomposing them in database tables; (iv) loosely linking to other programs for improved flexibility; and (v) a low-maintenance web-based user interface. Our team evaluated existing microarray databases and then decided to build a new system, Molecular Genetics Information System (MOLGENIS), implemented using code generation in a period of three months. This case can provide valuable insights and lessons to both software developers and a user community embarking on large-scale genomic projects. http://www.molgenis.nl

22 CFR 139.4 - Responsibilities of the Program Administrator.

Code of Federal Regulations, 2010 CFR

2010-04-01

... of living, support infrastructure, and other relevant factors. The Program Administrator, from time... program regulations, including rules of the Program Administrator and the code of code of conduct; or the...

A study to compute integrated dpa for neutron and ion irradiation environments using SRIM-2013

NASA Astrophysics Data System (ADS)

Saha, Uttiyoarnab; Devan, K.; Ganesan, S.

2018-05-01

Displacements per atom (dpa), estimated based on the standard Norgett-Robinson-Torrens (NRT) model, is used for assessing radiation damage effects in fast reactor materials. A computer code CRaD has been indigenously developed towards establishing the infrastructure to perform improved radiation damage studies in Indian fast reactors. We propose a method for computing multigroup neutron NRT dpa cross sections based on SRIM-2013 simulations. In this method, for each neutron group, the recoil or primary knock-on atom (PKA) spectrum and its average energy are first estimated with CRaD code from ENDF/B-VII.1. This average PKA energy forms the input for SRIM simulation, wherein the recoil atom is taken as the incoming ion on the target. The NRT-dpa cross section of iron computed with "Quick" Kinchin-Pease (K-P) option of SRIM-2013 is found to agree within 10% with the standard NRT-dpa values, if damage energy from SRIM simulation is used. SRIM-2013 NRT-dpa cross sections applied to estimate the integrated dpa for Fe, Cr and Ni are in good agreement with established computer codes and data. A similar study carried out for polyatomic material, SiC, shows encouraging results. In this case, it is observed that the NRT approach with average lattice displacement energy of 25 eV coupled with the damage energies from the K-P option of SRIM-2013 gives reliable displacement cross sections and integrated dpa for various reactor spectra. The source term of neutron damage can be equivalently determined in the units of dpa by simulating self-ion bombardment. This shows that the information of primary recoils obtained from CRaD can be reliably applied to estimate the integrated dpa and damage assessment studies in accelerator-based self-ion irradiation experiments of structural materials. This study would help to advance the investigation of possible correlations between the damages induced by ions and reactor neutrons.

Flexible services for the support of research.

PubMed

Turilli, Matteo; Wallom, David; Williams, Chris; Gough, Steve; Curran, Neal; Tarrant, Richard; Bretherton, Dan; Powell, Andy; Johnson, Matt; Harmer, Terry; Wright, Peter; Gordon, John

2013-01-28

Cloud computing has been increasingly adopted by users and providers to promote a flexible, scalable and tailored access to computing resources. Nonetheless, the consolidation of this paradigm has uncovered some of its limitations. Initially devised by corporations with direct control over large amounts of computational resources, cloud computing is now being endorsed by organizations with limited resources or with a more articulated, less direct control over these resources. The challenge for these organizations is to leverage the benefits of cloud computing while dealing with limited and often widely distributed computing resources. This study focuses on the adoption of cloud computing by higher education institutions and addresses two main issues: flexible and on-demand access to a large amount of storage resources, and scalability across a heterogeneous set of cloud infrastructures. The proposed solutions leverage a federated approach to cloud resources in which users access multiple and largely independent cloud infrastructures through a highly customizable broker layer. This approach allows for a uniform authentication and authorization infrastructure, a fine-grained policy specification and the aggregation of accounting and monitoring. Within a loosely coupled federation of cloud infrastructures, users can access vast amount of data without copying them across cloud infrastructures and can scale their resource provisions when the local cloud resources become insufficient.

Space Telecommunications Radio System (STRS) Compliance Testing

NASA Technical Reports Server (NTRS)

Handler, Louis M.

2011-01-01

The Space Telecommunications Radio System (STRS) defines an open architecture for software defined radios. This document describes the testing methodology to aid in determining the degree of compliance to the STRS architecture. Non-compliances are reported to the software and hardware developers as well as the NASA project manager so that any non-compliances may be fixed or waivers issued. Since the software developers may be divided into those that provide the operating environment including the operating system and STRS infrastructure (OE) and those that supply the waveform applications, the tests are divided accordingly. The static tests are also divided by the availability of an automated tool that determines whether the source code and configuration files contain the appropriate items. Thus, there are six separate step-by-step test procedures described as well as the corresponding requirements that they test. The six types of STRS compliance tests are: STRS application automated testing, STRS infrastructure automated testing, STRS infrastructure testing by compiling WFCCN with the infrastructure, STRS configuration file testing, STRS application manual code testing, and STRS infrastructure manual code testing. Examples of the input and output of the scripts are shown in the appendices as well as more specific information about what to configure and test in WFCCN for non-compliance. In addition, each STRS requirement is listed and the type of testing briefly described. Attached is also a set of guidelines on what to look for in addition to the requirements to aid in the document review process.

Implementing Computer-Aided Instruction in Distance Education: An Infrastructure. RR/89-06.

ERIC Educational Resources Information Center

Kotze, Paula

The infrastructure required for the implementation of computer aided instruction is described with particular reference to the distance education environment at the University of South Africa. A review of the state of the art of online distance education in the United States and Europe is followed by an outline of the proposed infrastructure for…

Data Center Consolidation: A Step towards Infrastructure Clouds

NASA Astrophysics Data System (ADS)

Winter, Markus

Application service providers face enormous challenges and rising costs in managing and operating a growing number of heterogeneous system and computing landscapes. Limitations of traditional computing environments force IT decision-makers to reorganize computing resources within the data center, as continuous growth leads to an inefficient utilization of the underlying hardware infrastructure. This paper discusses a way for infrastructure providers to improve data center operations based on the findings of a case study on resource utilization of very large business applications and presents an outlook beyond server consolidation endeavors, transforming corporate data centers into compute clouds.

Elastic Cloud Computing Infrastructures in the Open Cirrus Testbed Implemented via Eucalyptus

NASA Astrophysics Data System (ADS)

Baun, Christian; Kunze, Marcel

Cloud computing realizes the advantages and overcomes some restrictionsof the grid computing paradigm. Elastic infrastructures can easily be createdand managed by cloud users. In order to accelerate the research ondata center management and cloud services the OpenCirrusTM researchtestbed has been started by HP, Intel and Yahoo!. Although commercialcloud offerings are proprietary, Open Source solutions exist in the field ofIaaS with Eucalyptus, PaaS with AppScale and at the applications layerwith Hadoop MapReduce. This paper examines the I/O performance ofcloud computing infrastructures implemented with Eucalyptus in contrastto Amazon S3.

Network and computing infrastructure for scientific applications in Georgia

NASA Astrophysics Data System (ADS)

Kvatadze, R.; Modebadze, Z.

2016-09-01

Status of network and computing infrastructure and available services for research and education community of Georgia are presented. Research and Educational Networking Association - GRENA provides the following network services: Internet connectivity, network services, cyber security, technical support, etc. Computing resources used by the research teams are located at GRENA and at major state universities. GE-01-GRENA site is included in European Grid infrastructure. Paper also contains information about programs of Learning Center and research and development projects in which GRENA is participating.

Development and validation of chemistry agnostic flow battery cost performance model and application to nonaqueous electrolyte systems: Chemistry agnostic flow battery cost performance model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Crawford, Alasdair; Thomsen, Edwin; Reed, David

2016-04-20

A chemistry agnostic cost performance model is described for a nonaqueous flow battery. The model predicts flow battery performance by estimating the active reaction zone thickness at each electrode as a function of current density, state of charge, and flow rate using measured data for electrode kinetics, electrolyte conductivity, and electrode-specific surface area. Validation of the model is conducted using a 4kW stack data at various current densities and flow rates. This model is used to estimate the performance of a nonaqueous flow battery with electrode and electrolyte properties used from the literature. The optimized cost for this system ismore » estimated for various power and energy levels using component costs provided by vendors. The model allows optimization of design parameters such as electrode thickness, area, flow path design, and operating parameters such as power density, flow rate, and operating SOC range for various application duty cycles. A parametric analysis is done to identify components and electrode/electrolyte properties with the highest impact on system cost for various application durations. A pathway to 100$kWh -1 for the storage system is identified.« less

Towards a Multi-Mission, Airborne Science Data System Environment

NASA Astrophysics Data System (ADS)

Crichton, D. J.; Hardman, S.; Law, E.; Freeborn, D.; Kay-Im, E.; Lau, G.; Oswald, J.

2011-12-01

NASA earth science instruments are increasingly relying on airborne missions. However, traditionally, there has been limited common infrastructure support available to principal investigators in the area of science data systems. As a result, each investigator has been required to develop their own computing infrastructures for the science data system. Typically there is little software reuse and many projects lack sufficient resources to provide a robust infrastructure to capture, process, distribute and archive the observations acquired from airborne flights. At NASA's Jet Propulsion Laboratory (JPL), we have been developing a multi-mission data system infrastructure for airborne instruments called the Airborne Cloud Computing Environment (ACCE). ACCE encompasses the end-to-end lifecycle covering planning, provisioning of data system capabilities, and support for scientific analysis in order to improve the quality, cost effectiveness, and capabilities to enable new scientific discovery and research in earth observation. This includes improving data system interoperability across each instrument. A principal characteristic is being able to provide an agile infrastructure that is architected to allow for a variety of configurations of the infrastructure from locally installed compute and storage services to provisioning those services via the "cloud" from cloud computer vendors such as Amazon.com. Investigators often have different needs that require a flexible configuration. The data system infrastructure is built on the Apache's Object Oriented Data Technology (OODT) suite of components which has been used for a number of spaceborne missions and provides a rich set of open source software components and services for constructing science processing and data management systems. In 2010, a partnership was formed between the ACCE team and the Carbon in Arctic Reservoirs Vulnerability Experiment (CARVE) mission to support the data processing and data management needs. A principal goal is to provide support for the Fourier Transform Spectrometer (FTS) instrument which will produce over 700,000 soundings over the life of their three-year mission. The cost to purchase and operate a cluster-based system in order to generate Level 2 Full Physics products from this data was prohibitive. Through an evaluation of cloud computing solutions, Amazon's Elastic Compute Cloud (EC2) was selected for the CARVE deployment. As the ACCE infrastructure is developed and extended to form an infrastructure for airborne missions, the experience of working with CARVE has provided a number of lessons learned and has proven to be important in reinforcing the unique aspects of airborne missions and the importance of the ACCE infrastructure in developing a cost effective, flexible multi-mission capability that leverages emerging capabilities in cloud computing, workflow management, and distributed computing.

The NSF Arctic Data Center: Leveraging the DataONE Federation to Build a Sustainable Archive for the NSF Arctic Research Community

NASA Astrophysics Data System (ADS)

Budden, A. E.; Arzayus, K. M.; Baker-Yeboah, S.; Casey, K. S.; Dozier, J.; Jones, C. S.; Jones, M. B.; Schildhauer, M.; Walker, L.

2016-12-01

The newly established NSF Arctic Data Center plays a critical support role in archiving and curating the data and software generated by Arctic researchers from diverse disciplines. The Arctic community, comprising Earth science, archaeology, geography, anthropology, and other social science researchers, are supported through data curation services and domain agnostic tools and infrastructure, ensuring data are accessible in the most transparent and usable way possible. This interoperability across diverse disciplines within the Arctic community facilitates collaborative research and is mirrored by interoperability between the Arctic Data Center infrastructure and other large scale cyberinfrastructure initiatives. The Arctic Data Center leverages the DataONE federation to standardize access to and replication of data and metadata to other repositories, specifically the NOAA's National Centers for Environmental Information (NCEI). This approach promotes long-term preservation of the data and metadata, as well as opening the door for other data repositories to leverage this replication infrastructure with NCEI and other DataONE member repositories. The Arctic Data Center uses rich, detailed metadata following widely recognized standards. Particularly, measurement-level and provenance metadata provide scientists the details necessary to integrate datasets across studies and across repositories while enabling a full understanding of the provenance of data used in the system. The Arctic Data Center gains this deep metadata and provenance support by simply adopting DataONE services, which results in significant efficiency gains by eliminating the need to develop systems de novo. Similarly, the advanced search tool developed by the Knowledge Network for Biocomplexity and extended for data submission by the Arctic Data Center, can be used by other DataONE-compliant repositories without further development. By standardizing interfaces and leveraging the DataONE federation, the Arctic Data Center has advanced rapidly and can itself contribute to raising the capabilities of all members of the federation.

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pinski, Peter; Riplinger, Christoph; Neese, Frank, E-mail: evaleev@vt.edu, E-mail: frank.neese@cec.mpg.de

2015-07-21

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implementsmore » sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.« less

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. I. An efficient and simple linear scaling local MP2 method that uses an intermediate basis of pair natural orbitals.

PubMed

Pinski, Peter; Riplinger, Christoph; Valeev, Edward F; Neese, Frank

2015-07-21

In this work, a systematic infrastructure is described that formalizes concepts implicit in previous work and greatly simplifies computer implementation of reduced-scaling electronic structure methods. The key concept is sparse representation of tensors using chains of sparse maps between two index sets. Sparse map representation can be viewed as a generalization of compressed sparse row, a common representation of a sparse matrix, to tensor data. By combining few elementary operations on sparse maps (inversion, chaining, intersection, etc.), complex algorithms can be developed, illustrated here by a linear-scaling transformation of three-center Coulomb integrals based on our compact code library that implements sparse maps and operations on them. The sparsity of the three-center integrals arises from spatial locality of the basis functions and domain density fitting approximation. A novel feature of our approach is the use of differential overlap integrals computed in linear-scaling fashion for screening products of basis functions. Finally, a robust linear scaling domain based local pair natural orbital second-order Möller-Plesset (DLPNO-MP2) method is described based on the sparse map infrastructure that only depends on a minimal number of cutoff parameters that can be systematically tightened to approach 100% of the canonical MP2 correlation energy. With default truncation thresholds, DLPNO-MP2 recovers more than 99.9% of the canonical resolution of the identity MP2 (RI-MP2) energy while still showing a very early crossover with respect to the computational effort. Based on extensive benchmark calculations, relative energies are reproduced with an error of typically <0.2 kcal/mol. The efficiency of the local MP2 (LMP2) method can be drastically improved by carrying out the LMP2 iterations in a basis of pair natural orbitals. While the present work focuses on local electron correlation, it is of much broader applicability to computation with sparse tensors in quantum chemistry and beyond.

COMMUNITY-ORIENTED DESIGN AND EVALUATION PROCESS FOR SUSTAINABLE INFRASTRUCTURE

EPA Science Inventory

We met our first objective by completing the physical infrastructure of the La Fortuna-Tule water and sanitation project using the CODE-PSI method. This physical component of the project was important in providing a real, relevant, community-scale test case for the methods ...

RAPTOR. I. Time-dependent radiative transfer in arbitrary spacetimes

NASA Astrophysics Data System (ADS)

Bronzwaer, T.; Davelaar, J.; Younsi, Z.; Mościbrodzka, M.; Falcke, H.; Kramer, M.; Rezzolla, L.

2018-05-01

Context. Observational efforts to image the immediate environment of a black hole at the scale of the event horizon benefit from the development of efficient imaging codes that are capable of producing synthetic data, which may be compared with observational data. Aims: We aim to present RAPTOR, a new public code that produces accurate images, animations, and spectra of relativistic plasmas in strong gravity by numerically integrating the equations of motion of light rays and performing time-dependent radiative transfer calculations along the rays. The code is compatible with any analytical or numerical spacetime. It is hardware-agnostic and may be compiled and run both on GPUs and CPUs. Methods: We describe the algorithms used in RAPTOR and test the code's performance. We have performed a detailed comparison of RAPTOR output with that of other radiative-transfer codes and demonstrate convergence of the results. We then applied RAPTOR to study accretion models of supermassive black holes, performing time-dependent radiative transfer through general relativistic magneto-hydrodynamical (GRMHD) simulations and investigating the expected observational differences between the so-called fast-light and slow-light paradigms. Results: Using RAPTOR to produce synthetic images and light curves of a GRMHD model of an accreting black hole, we find that the relative difference between fast-light and slow-light light curves is less than 5%. Using two distinct radiative-transfer codes to process the same data, we find integrated flux densities with a relative difference less than 0.01%. Conclusions: For two-dimensional GRMHD models, such as those examined in this paper, the fast-light approximation suffices as long as errors of a few percent are acceptable. The convergence of the results of two different codes demonstrates that they are, at a minimum, consistent. The public version of RAPTOR is available at the following URL: http://https://github.com/tbronzwaer/raptor

High-Performance I/O: HDF5 for Lattice QCD

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kurth, Thorsten; Pochinsky, Andrew; Sarje, Abhinav

2015-01-01

Practitioners of lattice QCD/QFT have been some of the primary pioneer users of the state-of-the-art high-performance-computing systems, and contribute towards the stress tests of such new machines as soon as they become available. As with all aspects of high-performance-computing, I/O is becoming an increasingly specialized component of these systems. In order to take advantage of the latest available high-performance I/O infrastructure, to ensure reliability and backwards compatibility of data files, and to help unify the data structures used in lattice codes, we have incorporated parallel HDF5 I/O into the SciDAC supported USQCD software stack. Here we present the design andmore » implementation of this I/O framework. Our HDF5 implementation outperforms optimized QIO at the 10-20% level and leaves room for further improvement by utilizing appropriate dataset chunking.« less

High-Performance I/O: HDF5 for Lattice QCD

DOE PAGES

Kurth, Thorsten; Pochinsky, Andrew; Sarje, Abhinav; ...

2017-05-09

Practitioners of lattice QCD/QFT have been some of the primary pioneer users of the state-of-the-art high-performance-computing systems, and contribute towards the stress tests of such new machines as soon as they become available. As with all aspects of high-performance-computing, I/O is becoming an increasingly specialized component of these systems. In order to take advantage of the latest available high-performance I/O infrastructure, to ensure reliability and backwards compatibility of data files, and to help unify the data structures used in lattice codes, we have incorporated parallel HDF5 I/O into the SciDAC supported USQCD software stack. Here we present the design andmore » implementation of this I/O framework. Our HDF5 implementation outperforms optimized QIO at the 10-20% level and leaves room for further improvement by utilizing appropriate dataset chunking.« less

Idea Paper: The Lifecycle of Software for Scientific Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dubey, Anshu; McInnes, Lois C.

The software lifecycle is a well researched topic that has produced many models to meet the needs of different types of software projects. However, one class of projects, software development for scientific computing, has received relatively little attention from lifecycle researchers. In particular, software for end-to-end computations for obtaining scientific results has received few lifecycle proposals and no formalization of a development model. An examination of development approaches employed by the teams implementing large multicomponent codes reveals a great deal of similarity in their strategies. This idea paper formalizes these related approaches into a lifecycle model for end-to-end scientific applicationmore » software, featuring loose coupling between submodels for development of infrastructure and scientific capability. We also invite input from stakeholders to converge on a model that captures the complexity of this development processes and provides needed lifecycle guidance to the scientific software community.« less

Geoinformatics in the public service: building a cyberinfrastructure across the geological surveys

USGS Publications Warehouse

Allison, M. Lee; Gundersen, Linda C.; Richard, Stephen M.; Keller, G. Randy; Baru, Chaitanya

2011-01-01

Advanced information technology infrastructure is increasingly being employed in the Earth sciences to provide researchers with efficient access to massive central databases and to integrate diversely formatted information from a variety of sources. These geoinformatics initiatives enable manipulation, modeling and visualization of data in a consistent way, and are helping to develop integrated Earth models at various scales, and from the near surface to the deep interior. This book uses a series of case studies to demonstrate computer and database use across the geosciences. Chapters are thematically grouped into sections that cover data collection and management; modeling and community computational codes; visualization and data representation; knowledge management and data integration; and web services and scientific workflows. Geoinformatics is a fascinating and accessible introduction to this emerging field for readers across the solid Earth sciences and an invaluable reference for researchers interested in initiating new cyberinfrastructure projects of their own.

Modeling the Cloud to Enhance Capabilities for Crises and Catastrophe Management

DTIC Science & Technology

2016-11-16

order for cloud computing infrastructures to be successfully deployed in real world scenarios as tools for crisis and catastrophe management, where...Statement of the Problem Studied As cloud computing becomes the dominant computational infrastructure[1] and cloud technologies make a transition to hosting...1. Formulate rigorous mathematical models representing technological capabilities and resources in cloud computing for performance modeling and

Infrastructure Systems for Advanced Computing in E-science applications

NASA Astrophysics Data System (ADS)

Terzo, Olivier

2013-04-01

In the e-science field are growing needs for having computing infrastructure more dynamic and customizable with a model of use "on demand" that follow the exact request in term of resources and storage capacities. The integration of grid and cloud infrastructure solutions allows us to offer services that can adapt the availability in terms of up scaling and downscaling resources. The main challenges for e-sciences domains will on implement infrastructure solutions for scientific computing that allow to adapt dynamically the demands of computing resources with a strong emphasis on optimizing the use of computing resources for reducing costs of investments. Instrumentation, data volumes, algorithms, analysis contribute to increase the complexity for applications who require high processing power and storage for a limited time and often exceeds the computational resources that equip the majority of laboratories, research Unit in an organization. Very often it is necessary to adapt or even tweak rethink tools, algorithms, and consolidate existing applications through a phase of reverse engineering in order to adapt them to a deployment on Cloud infrastructure. For example, in areas such as rainfall monitoring, meteorological analysis, Hydrometeorology, Climatology Bioinformatics Next Generation Sequencing, Computational Electromagnetic, Radio occultation, the complexity of the analysis raises several issues such as the processing time, the scheduling of tasks of processing, storage of results, a multi users environment. For these reasons, it is necessary to rethink the writing model of E-Science applications in order to be already adapted to exploit the potentiality of cloud computing services through the uses of IaaS, PaaS and SaaS layer. An other important focus is on create/use hybrid infrastructure typically a federation between Private and public cloud, in fact in this way when all resources owned by the organization are all used it will be easy with a federate cloud infrastructure to add some additional resources form the Public cloud for following the needs in term of computational and storage resources and release them where process are finished. Following the hybrid model, the scheduling approach is important for managing both cloud models. Thanks to this model infrastructure every time resources are available for additional request in term of IT capacities that can used "on demand" for a limited time without having to proceed to purchase additional servers.

The Future of ECHO: Evaluating Open Source Possibilities

NASA Astrophysics Data System (ADS)

Pilone, D.; Gilman, J.; Baynes, K.; Mitchell, A. E.

2012-12-01

NASA's Earth Observing System ClearingHOuse (ECHO) is a format agnostic metadata repository supporting over 3000 collections and 100M science granules. ECHO exposes FTP and RESTful Data Ingest APIs in addition to both SOAP and RESTful search and order capabilities. Built on top of ECHO is a human facing search and order web application named Reverb. ECHO processes hundreds of orders, tens of thousands of searches, and 1-2M ingest actions each week. As ECHO's holdings, metadata format support, and visibility have increased, the ECHO team has received requests by non-NASA entities for copies of ECHO that can be run locally against their data holdings. ESDIS and the ECHO Team have begun investigations into various deployment and Open Sourcing models that can balance the real constraints faced by the ECHO project with the benefits of providing ECHO capabilities to a broader set of users and providers. This talk will discuss several release and Open Source models being investigated by the ECHO team along with the impacts those models are expected to have on the project. We discuss: - Addressing complex deployment or setup issues for potential users - Models of vetting code contributions - Balancing external (public) user requests versus our primary partners - Preparing project code for public release, including navigating licensing issues related to leveraged libraries - Dealing with non-free project dependencies such as commercial databases - Dealing with sensitive aspects of project code such as database passwords, authentication approaches, security through obscurity, etc. - Ongoing support for the released code including increased testing demands, bug fixes, security fixes, and new features.

Cloud Infrastructure & Applications - CloudIA

NASA Astrophysics Data System (ADS)

Sulistio, Anthony; Reich, Christoph; Doelitzscher, Frank

The idea behind Cloud Computing is to deliver Infrastructure-as-a-Services and Software-as-a-Service over the Internet on an easy pay-per-use business model. To harness the potentials of Cloud Computing for e-Learning and research purposes, and to small- and medium-sized enterprises, the Hochschule Furtwangen University establishes a new project, called Cloud Infrastructure & Applications (CloudIA). The CloudIA project is a market-oriented cloud infrastructure that leverages different virtualization technologies, by supporting Service-Level Agreements for various service offerings. This paper describes the CloudIA project in details and mentions our early experiences in building a private cloud using an existing infrastructure.

Cloud access to interoperable IVOA-compliant VOSpace storage

NASA Astrophysics Data System (ADS)

Bertocco, S.; Dowler, P.; Gaudet, S.; Major, B.; Pasian, F.; Taffoni, G.

2018-07-01

Handling, processing and archiving the huge amount of data produced by the new generation of experiments and instruments in Astronomy and Astrophysics are among the more exciting challenges to address in designing the future data management infrastructures and computing services. We investigated the feasibility of a data management and computation infrastructure, available world-wide, with the aim of merging the FAIR data management provided by IVOA standards with the efficiency and reliability of a cloud approach. Our work involved the Canadian Advanced Network for Astronomy Research (CANFAR) infrastructure and the European EGI federated cloud (EFC). We designed and deployed a pilot data management and computation infrastructure that provides IVOA-compliant VOSpace storage resources and wide access to interoperable federated clouds. In this paper, we detail the main user requirements covered, the technical choices and the implemented solutions and we describe the resulting Hybrid cloud Worldwide infrastructure, its benefits and limitations.

A cyber infrastructure for the SKA Telescope Manager

NASA Astrophysics Data System (ADS)

Barbosa, Domingos; Barraca, João. P.; Carvalho, Bruno; Maia, Dalmiro; Gupta, Yashwant; Natarajan, Swaminathan; Le Roux, Gerhard; Swart, Paul

2016-07-01

The Square Kilometre Array Telescope Manager (SKA TM) will be responsible for assisting the SKA Operations and Observation Management, carrying out System diagnosis and collecting Monitoring and Control data from the SKA subsystems and components. To provide adequate compute resources, scalability, operation continuity and high availability, as well as strict Quality of Service, the TM cyber-infrastructure (embodied in the Local Infrastructure - LINFRA) consists of COTS hardware and infrastructural software (for example: server monitoring software, host operating system, virtualization software, device firmware), providing a specially tailored Infrastructure as a Service (IaaS) and Platform as a Service (PaaS) solution. The TM infrastructure provides services in the form of computational power, software defined networking, power, storage abstractions, and high level, state of the art IaaS and PaaS management interfaces. This cyber platform will be tailored to each of the two SKA Phase 1 telescopes (SKA_MID in South Africa and SKA_LOW in Australia) instances, each presenting different computational and storage infrastructures and conditioned by location. This cyber platform will provide a compute model enabling TM to manage the deployment and execution of its multiple components (observation scheduler, proposal submission tools, MandC components, Forensic tools and several Databases, etc). In this sense, the TM LINFRA is primarily focused towards the provision of isolated instances, mostly resorting to virtualization technologies, while defaulting to bare hardware if specifically required due to performance, security, availability, or other requirement.

48 CFR 52.212-1 - Instructions to Offerors-Commercial Items.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Classification System (NAICS) code and small business size standard. The NAICS code and small business size... Government infrastructure not later than 5:00 p.m. one working day prior to the date specified for receipt of...

The High-Performance Computing and Communications program, the national information infrastructure and health care.

PubMed Central

Lindberg, D A; Humphreys, B L

1995-01-01

The High-Performance Computing and Communications (HPCC) program is a multiagency federal effort to advance the state of computing and communications and to provide the technologic platform on which the National Information Infrastructure (NII) can be built. The HPCC program supports the development of high-speed computers, high-speed telecommunications, related software and algorithms, education and training, and information infrastructure technology and applications. The vision of the NII is to extend access to high-performance computing and communications to virtually every U.S. citizen so that the technology can be used to improve the civil infrastructure, lifelong learning, energy management, health care, etc. Development of the NII will require resolution of complex economic and social issues, including information privacy. Health-related applications supported under the HPCC program and NII initiatives include connection of health care institutions to the Internet; enhanced access to gene sequence data; the "Visible Human" Project; and test-bed projects in telemedicine, electronic patient records, shared informatics tool development, and image systems. PMID:7614116

NCI HPC Scaling and Optimisation in Climate, Weather, Earth system science and the Geosciences

NASA Astrophysics Data System (ADS)

Evans, B. J. K.; Bermous, I.; Freeman, J.; Roberts, D. S.; Ward, M. L.; Yang, R.

2016-12-01

The Australian National Computational Infrastructure (NCI) has a national focus in the Earth system sciences including climate, weather, ocean, water management, environment and geophysics. NCI leads a Program across its partners from the Australian science agencies and research communities to identify priority computational models to scale-up. Typically, these cases place a large overall demand on the available computer time, need to scale to higher resolutions, use excessive scarce resources such as large memory or bandwidth that limits, or in some cases, need to meet requirements for transition to a separate operational forecasting system, with set time-windows. The model codes include the UK Met Office Unified Model atmospheric model (UM), GFDL's Modular Ocean Model (MOM), both the UK Met Office's GC3 and Australian ACCESS coupled-climate systems (including sea ice), 4D-Var data assimilation and satellite processing, the Regional Ocean Model (ROMS), and WaveWatch3 as well as geophysics codes including hazards, magentuellerics, seismic inversions, and geodesy. Many of these codes use significant compute resources both for research applications as well as within the operational systems. Some of these models are particularly complex, and their behaviour had not been critically analysed for effective use of the NCI supercomputer or how they could be improved. As part of the Program, we have established a common profiling methodology that uses a suite of open source tools for performing scaling analyses. The most challenging cases are profiling multi-model coupled systems where the component models have their own complex algorithms and performance issues. We have also found issues within the current suite of profiling tools, and no single tool fully exposes the nature of the code performance. As a result of this work, international collaborations are now in place to ensure that improvements are incorporated within the community models, and our effort can be targeted in a coordinated way. The coordinations have involved user stakeholders, the model developer community, and dependent software libraries. For example, we have spent significant time characterising I/O scalability, and improving the use of libraries such as NetCDF and HDF5.

49 CFR 260.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... appropriations and which must be paid by Applicant or its non-Federal infrastructure partner before that direct... provisions of this part. (j) Including means including but not limited to. (k) Infrastructure partner means... subtitle IV of title 49, United States Code. (s) Subsidy cost of a direct loan means the net present value...

Seismo-Live: Training in Seismology with Jupyter Notebooks

NASA Astrophysics Data System (ADS)

Krischer, Lion; Tape, Carl; Igel, Heiner

2016-04-01

Seismological training tends to occur within the isolation of a particular institution with a limited set of tools (codes, libraries) that are often not transferrable outside. Here, we propose to overcome these limitations with a community-driven library of Jupyter notebooks dedicated to training on any aspect of seismology for purposes of education and outreach, on-site or archived tutorials for codes, classroom instruction, and research. A Jupyter notebook (jupyter.org) is an open-source interactive computational environment that allows combining code execution, rich text, mathematics, and plotting. It can be considered a platform that supports reproducible research, as all inputs and outputs may be stored. Text, external graphics, equations can be handled using Markdown (incl. LaTeX) format. Jupyter notebooks are driven by standard web browsers, can be easily exchanged in text format, or converted to other documents (e.g. PDF, slide shows). They provide an ideal format for practical training in seismology. A pilot-platform was setup with a dedicated server such that the Jupyter notebooks can be run in any browser (PC, notepad, smartphone). We show the functionalities of the Seismo-Live platform with examples from computational seismology, seismic data access and processing using the ObsPy library, seismic inverse problems, and others. The current examples are all using the Python programming language but any free language can be used. Potentially, such community platforms could be integrated with the EPOS-IT infrastructure and extended to other fields of Earth sciences.

THE PLUTO CODE FOR ADAPTIVE MESH COMPUTATIONS IN ASTROPHYSICAL FLUID DYNAMICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mignone, A.; Tzeferacos, P.; Zanni, C.

We present a description of the adaptive mesh refinement (AMR) implementation of the PLUTO code for solving the equations of classical and special relativistic magnetohydrodynamics (MHD and RMHD). The current release exploits, in addition to the static grid version of the code, the distributed infrastructure of the CHOMBO library for multidimensional parallel computations over block-structured, adaptively refined grids. We employ a conservative finite-volume approach where primary flow quantities are discretized at the cell center in a dimensionally unsplit fashion using the Corner Transport Upwind method. Time stepping relies on a characteristic tracing step where piecewise parabolic method, weighted essentially non-oscillatory,more » or slope-limited linear interpolation schemes can be handily adopted. A characteristic decomposition-free version of the scheme is also illustrated. The solenoidal condition of the magnetic field is enforced by augmenting the equations with a generalized Lagrange multiplier providing propagation and damping of divergence errors through a mixed hyperbolic/parabolic explicit cleaning step. Among the novel features, we describe an extension of the scheme to include non-ideal dissipative processes, such as viscosity, resistivity, and anisotropic thermal conduction without operator splitting. Finally, we illustrate an efficient treatment of point-local, potentially stiff source terms over hierarchical nested grids by taking advantage of the adaptivity in time. Several multidimensional benchmarks and applications to problems of astrophysical relevance assess the potentiality of the AMR version of PLUTO in resolving flow features separated by large spatial and temporal disparities.« less

HAlign-II: efficient ultra-large multiple sequence alignment and phylogenetic tree reconstruction with distributed and parallel computing.

PubMed

Wan, Shixiang; Zou, Quan

2017-01-01

Multiple sequence alignment (MSA) plays a key role in biological sequence analyses, especially in phylogenetic tree construction. Extreme increase in next-generation sequencing results in shortage of efficient ultra-large biological sequence alignment approaches for coping with different sequence types. Distributed and parallel computing represents a crucial technique for accelerating ultra-large (e.g. files more than 1 GB) sequence analyses. Based on HAlign and Spark distributed computing system, we implement a highly cost-efficient and time-efficient HAlign-II tool to address ultra-large multiple biological sequence alignment and phylogenetic tree construction. The experiments in the DNA and protein large scale data sets, which are more than 1GB files, showed that HAlign II could save time and space. It outperformed the current software tools. HAlign-II can efficiently carry out MSA and construct phylogenetic trees with ultra-large numbers of biological sequences. HAlign-II shows extremely high memory efficiency and scales well with increases in computing resource. THAlign-II provides a user-friendly web server based on our distributed computing infrastructure. HAlign-II with open-source codes and datasets was established at http://lab.malab.cn/soft/halign.

Future Naval Use of COTS Networking Infrastructure

DTIC Science & Technology

2009-07-01

user to benefit from Google’s vast databases and computational resources. Obviously, the ability to harness the full power of the Cloud could be... Computing Impact Findings Action Items Take-Aways Appendices: Pages 54-68 A. Terms of Reference Document B. Sample Definitions of Cloud ...and definition of Cloud Computing . While Cloud Computing is developing in many variations – including Infrastructure as a Service (IaaS), Platform as

An Infrastructure for UML-Based Code Generation Tools

NASA Astrophysics Data System (ADS)

Wehrmeister, Marco A.; Freitas, Edison P.; Pereira, Carlos E.

The use of Model-Driven Engineering (MDE) techniques in the domain of distributed embedded real-time systems are gain importance in order to cope with the increasing design complexity of such systems. This paper discusses an infrastructure created to build GenERTiCA, a flexible tool that supports a MDE approach, which uses aspect-oriented concepts to handle non-functional requirements from embedded and real-time systems domain. GenERTiCA generates source code from UML models, and also performs weaving of aspects, which have been specified within the UML model. Additionally, this paper discusses the Distributed Embedded Real-Time Compact Specification (DERCS), a PIM created to support UML-based code generation tools. Some heuristics to transform UML models into DERCS, which have been implemented in GenERTiCA, are also discussed.

'Toxgnostics': an unmet need in cancer medicine.

PubMed

Church, David; Kerr, Rachel; Domingo, Enric; Rosmarin, Dan; Palles, Claire; Maskell, Kevin; Tomlinson, Ian; Kerr, David

2014-06-01

If we were to summarize the rationale that underpins medical oncology in a Latin aphorism, it might be 'veneno ergo sum'; that is, I poison, therefore I am. The burden of chemotherapy-associated toxicity is well recognized, but we have relatively few tools that increase the precision of anticancer drug prescribing. We propose a shift in emphasis from the focussed study of polymorphisms in drug metabolic pathways in small sets of patients to broader agnostic analyses to systematically correlate germline genetic variants with adverse events in large, well-defined cancer populations. Thus, we propose the new science of 'toxgnostics' (that is, the systematic, agnostic study of genetic predictors of toxicity from anticancer therapy).

Web-based reactive transport modeling using PFLOTRAN

NASA Astrophysics Data System (ADS)

Zhou, H.; Karra, S.; Lichtner, P. C.; Versteeg, R.; Zhang, Y.

2017-12-01

Actionable understanding of system behavior in the subsurface is required for a wide spectrum of societal and engineering needs by both commercial firms and government entities and academia. These needs include, for example, water resource management, precision agriculture, contaminant remediation, unconventional energy production, CO2 sequestration monitoring, and climate studies. Such understanding requires the ability to numerically model various coupled processes that occur across different temporal and spatial scales as well as multiple physical domains (reservoirs - overburden, surface-subsurface, groundwater-surface water, saturated-unsaturated zone). Currently, this ability is typically met through an in-house approach where computational resources, model expertise, and data for model parameterization are brought together to meet modeling needs. However, such an approach has multiple drawbacks which limit the application of high-end reactive transport codes such as the Department of Energy funded[?] PFLOTRAN code. In addition, while many end users have a need for the capabilities provided by high-end reactive transport codes, they do not have the expertise - nor the time required to obtain the expertise - to effectively use these codes. We have developed and are actively enhancing a cloud-based software platform through which diverse users are able to easily configure, execute, visualize, share, and interpret PFLOTRAN models. This platform consists of a web application and available on-demand HPC computational infrastructure. The web application consists of (1) a browser-based graphical user interface which allows users to configure models and visualize results interactively, and (2) a central server with back-end relational databases which hold configuration, data, modeling results, and Python scripts for model configuration, and (3) a HPC environment for on-demand model execution. We will discuss lessons learned in the development of this platform, the rationale for different interfaces, implementation choices, as well as the planned path forward.

Scientific Services on the Cloud

NASA Astrophysics Data System (ADS)

Chapman, David; Joshi, Karuna P.; Yesha, Yelena; Halem, Milt; Yesha, Yaacov; Nguyen, Phuong

Scientific Computing was one of the first every applications for parallel and distributed computation. To this date, scientific applications remain some of the most compute intensive, and have inspired creation of petaflop compute infrastructure such as the Oak Ridge Jaguar and Los Alamos RoadRunner. Large dedicated hardware infrastructure has become both a blessing and a curse to the scientific community. Scientists are interested in cloud computing for much the same reason as businesses and other professionals. The hardware is provided, maintained, and administrated by a third party. Software abstraction and virtualization provide reliability, and fault tolerance. Graduated fees allow for multi-scale prototyping and execution. Cloud computing resources are only a few clicks away, and by far the easiest high performance distributed platform to gain access to. There may still be dedicated infrastructure for ultra-scale science, but the cloud can easily play a major part of the scientific computing initiative.

High Performance Computing for Modeling Wind Farms and Their Impact

NASA Astrophysics Data System (ADS)

Mavriplis, D.; Naughton, J. W.; Stoellinger, M. K.

2016-12-01

As energy generated by wind penetrates further into our electrical system, modeling of power production, power distribution, and the economic impact of wind-generated electricity is growing in importance. The models used for this work can range in fidelity from simple codes that run on a single computer to those that require high performance computing capabilities. Over the past several years, high fidelity models have been developed and deployed on the NCAR-Wyoming Supercomputing Center's Yellowstone machine. One of the primary modeling efforts focuses on developing the capability to compute the behavior of a wind farm in complex terrain under realistic atmospheric conditions. Fully modeling this system requires the simulation of continental flows to modeling the flow over a wind turbine blade, including down to the blade boundary level, fully 10 orders of magnitude in scale. To accomplish this, the simulations are broken up by scale, with information from the larger scales being passed to the lower scale models. In the code being developed, four scale levels are included: the continental weather scale, the local atmospheric flow in complex terrain, the wind plant scale, and the turbine scale. The current state of the models in the latter three scales will be discussed. These simulations are based on a high-order accurate dynamic overset and adaptive mesh approach, which runs at large scale on the NWSC Yellowstone machine. A second effort on modeling the economic impact of new wind development as well as improvement in wind plant performance and enhancements to the transmission infrastructure will also be discussed.

Virtual Systems Pharmacology (ViSP) software for simulation from mechanistic systems-level models.

PubMed

Ermakov, Sergey; Forster, Peter; Pagidala, Jyotsna; Miladinov, Marko; Wang, Albert; Baillie, Rebecca; Bartlett, Derek; Reed, Mike; Leil, Tarek A

2014-01-01

Multiple software programs are available for designing and running large scale system-level pharmacology models used in the drug development process. Depending on the problem, scientists may be forced to use several modeling tools that could increase model development time, IT costs and so on. Therefore, it is desirable to have a single platform that allows setting up and running large-scale simulations for the models that have been developed with different modeling tools. We developed a workflow and a software platform in which a model file is compiled into a self-contained executable that is no longer dependent on the software that was used to create the model. At the same time the full model specifics is preserved by presenting all model parameters as input parameters for the executable. This platform was implemented as a model agnostic, therapeutic area agnostic and web-based application with a database back-end that can be used to configure, manage and execute large-scale simulations for multiple models by multiple users. The user interface is designed to be easily configurable to reflect the specifics of the model and the user's particular needs and the back-end database has been implemented to store and manage all aspects of the systems, such as Models, Virtual Patients, User Interface Settings, and Results. The platform can be adapted and deployed on an existing cluster or cloud computing environment. Its use was demonstrated with a metabolic disease systems pharmacology model that simulates the effects of two antidiabetic drugs, metformin and fasiglifam, in type 2 diabetes mellitus patients.

Virtual Systems Pharmacology (ViSP) software for simulation from mechanistic systems-level models

PubMed Central

Ermakov, Sergey; Forster, Peter; Pagidala, Jyotsna; Miladinov, Marko; Wang, Albert; Baillie, Rebecca; Bartlett, Derek; Reed, Mike; Leil, Tarek A.

2014-01-01

Multiple software programs are available for designing and running large scale system-level pharmacology models used in the drug development process. Depending on the problem, scientists may be forced to use several modeling tools that could increase model development time, IT costs and so on. Therefore, it is desirable to have a single platform that allows setting up and running large-scale simulations for the models that have been developed with different modeling tools. We developed a workflow and a software platform in which a model file is compiled into a self-contained executable that is no longer dependent on the software that was used to create the model. At the same time the full model specifics is preserved by presenting all model parameters as input parameters for the executable. This platform was implemented as a model agnostic, therapeutic area agnostic and web-based application with a database back-end that can be used to configure, manage and execute large-scale simulations for multiple models by multiple users. The user interface is designed to be easily configurable to reflect the specifics of the model and the user's particular needs and the back-end database has been implemented to store and manage all aspects of the systems, such as Models, Virtual Patients, User Interface Settings, and Results. The platform can be adapted and deployed on an existing cluster or cloud computing environment. Its use was demonstrated with a metabolic disease systems pharmacology model that simulates the effects of two antidiabetic drugs, metformin and fasiglifam, in type 2 diabetes mellitus patients. PMID:25374542

University of Washington/ Northwest National Marine Renewable Energy Center Tidal Current Technology Test Protocol, Instrumentation, Design Code, and Oceanographic Modeling Collaboration: Cooperative Research and Development Final Report, CRADA Number CRD-11-452

DOE Office of Scientific and Technical Information (OSTI.GOV)

Driscoll, Frederick R.

The University of Washington (UW) - Northwest National Marine Renewable Energy Center (UW-NNMREC) and the National Renewable Energy Laboratory (NREL) will collaborate to advance research and development (R&D) of Marine Hydrokinetic (MHK) renewable energy technology, specifically renewable energy captured from ocean tidal currents. UW-NNMREC is endeavoring to establish infrastructure, capabilities and tools to support in-water testing of marine energy technology. NREL is leveraging its experience and capabilities in field testing of wind systems to develop protocols and instrumentation to advance field testing of MHK systems. Under this work, UW-NNMREC and NREL will work together to develop a common instrumentation systemmore » and testing methodologies, standards and protocols. UW-NNMREC is also establishing simulation capabilities for MHK turbine and turbine arrays. NREL has extensive experience in wind turbine array modeling and is developing several computer based numerical simulation capabilities for MHK systems. Under this CRADA, UW-NNMREC and NREL will work together to augment single device and array modeling codes. As part of this effort UW NNMREC will also work with NREL to run simulations on NREL's high performance computer system.« less

Gene calling and bacterial genome annotation with BG7.

PubMed

Tobes, Raquel; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Kovach, Evdokim; Alekhin, Alexey; Pareja, Eduardo

2015-01-01

New massive sequencing technologies are providing many bacterial genome sequences from diverse taxa but a refined annotation of these genomes is crucial for obtaining scientific findings and new knowledge. Thus, bacterial genome annotation has emerged as a key point to investigate in bacteria. Any efficient tool designed specifically to annotate bacterial genomes sequenced with massively parallel technologies has to consider the specific features of bacterial genomes (absence of introns and scarcity of nonprotein-coding sequence) and of next-generation sequencing (NGS) technologies (presence of errors and not perfectly assembled genomes). These features make it convenient to focus on coding regions and, hence, on protein sequences that are the elements directly related with biological functions. In this chapter we describe how to annotate bacterial genomes with BG7, an open-source tool based on a protein-centered gene calling/annotation paradigm. BG7 is specifically designed for the annotation of bacterial genomes sequenced with NGS. This tool is sequence error tolerant maintaining their capabilities for the annotation of highly fragmented genomes or for annotating mixed sequences coming from several genomes (as those obtained through metagenomics samples). BG7 has been designed with scalability as a requirement, with a computing infrastructure completely based on cloud computing (Amazon Web Services).

Consolidation and development roadmap of the EMI middleware

NASA Astrophysics Data System (ADS)

Kónya, B.; Aiftimiei, C.; Cecchi, M.; Field, L.; Fuhrmann, P.; Nilsen, J. K.; White, J.

2012-12-01

Scientific research communities have benefited recently from the increasing availability of computing and data infrastructures with unprecedented capabilities for large scale distributed initiatives. These infrastructures are largely defined and enabled by the middleware they deploy. One of the major issues in the current usage of research infrastructures is the need to use similar but often incompatible middleware solutions. The European Middleware Initiative (EMI) is a collaboration of the major European middleware providers ARC, dCache, gLite and UNICORE. EMI aims to: deliver a consolidated set of middleware components for deployment in EGI, PRACE and other Distributed Computing Infrastructures; extend the interoperability between grids and other computing infrastructures; strengthen the reliability of the services; establish a sustainable model to maintain and evolve the middleware; fulfil the requirements of the user communities. This paper presents the consolidation and development objectives of the EMI software stack covering the last two years. The EMI development roadmap is introduced along the four technical areas of compute, data, security and infrastructure. The compute area plan focuses on consolidation of standards and agreements through a unified interface for job submission and management, a common format for accounting, the wide adoption of GLUE schema version 2.0 and the provision of a common framework for the execution of parallel jobs. The security area is working towards a unified security model and lowering the barriers to Grid usage by allowing users to gain access with their own credentials. The data area is focusing on implementing standards to ensure interoperability with other grids and industry components and to reuse already existing clients in operating systems and open source distributions. One of the highlights of the infrastructure area is the consolidation of the information system services via the creation of a common information backbone.

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community

PubMed Central

Smith, Andy; Southgate, Joel; Poplawski, Radoslaw; Bull, Matthew J.; Richardson, Emily; Ismail, Matthew; Thompson, Simon Elwood-; Kitchen, Christine; Guest, Martyn; Bakke, Marius

2016-01-01

The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data. PMID:28785418

CLIMB (the Cloud Infrastructure for Microbial Bioinformatics): an online resource for the medical microbiology community.

PubMed

Connor, Thomas R; Loman, Nicholas J; Thompson, Simon; Smith, Andy; Southgate, Joel; Poplawski, Radoslaw; Bull, Matthew J; Richardson, Emily; Ismail, Matthew; Thompson, Simon Elwood-; Kitchen, Christine; Guest, Martyn; Bakke, Marius; Sheppard, Samuel K; Pallen, Mark J

2016-09-01

The increasing availability and decreasing cost of high-throughput sequencing has transformed academic medical microbiology, delivering an explosion in available genomes while also driving advances in bioinformatics. However, many microbiologists are unable to exploit the resulting large genomics datasets because they do not have access to relevant computational resources and to an appropriate bioinformatics infrastructure. Here, we present the Cloud Infrastructure for Microbial Bioinformatics (CLIMB) facility, a shared computing infrastructure that has been designed from the ground up to provide an environment where microbiologists can share and reuse methods and data.

caGrid 1.0: An Enterprise Grid Infrastructure for Biomedical Research

PubMed Central

Oster, Scott; Langella, Stephen; Hastings, Shannon; Ervin, David; Madduri, Ravi; Phillips, Joshua; Kurc, Tahsin; Siebenlist, Frank; Covitz, Peter; Shanbhag, Krishnakant; Foster, Ian; Saltz, Joel

2008-01-01

Objective To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. Design An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG™) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including 1) discovery, 2) integrated and large-scale data analysis, and 3) coordinated study. Measurements The caGrid is built as a Grid software infrastructure and leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. Results The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. Conclusions While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community. PMID:18096909

caGrid 1.0: an enterprise Grid infrastructure for biomedical research.

PubMed

Oster, Scott; Langella, Stephen; Hastings, Shannon; Ervin, David; Madduri, Ravi; Phillips, Joshua; Kurc, Tahsin; Siebenlist, Frank; Covitz, Peter; Shanbhag, Krishnakant; Foster, Ian; Saltz, Joel

2008-01-01

To develop software infrastructure that will provide support for discovery, characterization, integrated access, and management of diverse and disparate collections of information sources, analysis methods, and applications in biomedical research. An enterprise Grid software infrastructure, called caGrid version 1.0 (caGrid 1.0), has been developed as the core Grid architecture of the NCI-sponsored cancer Biomedical Informatics Grid (caBIG) program. It is designed to support a wide range of use cases in basic, translational, and clinical research, including 1) discovery, 2) integrated and large-scale data analysis, and 3) coordinated study. The caGrid is built as a Grid software infrastructure and leverages Grid computing technologies and the Web Services Resource Framework standards. It provides a set of core services, toolkits for the development and deployment of new community provided services, and application programming interfaces for building client applications. The caGrid 1.0 was released to the caBIG community in December 2006. It is built on open source components and caGrid source code is publicly and freely available under a liberal open source license. The core software, associated tools, and documentation can be downloaded from the following URL: https://cabig.nci.nih.gov/workspaces/Architecture/caGrid. While caGrid 1.0 is designed to address use cases in cancer research, the requirements associated with discovery, analysis and integration of large scale data, and coordinated studies are common in other biomedical fields. In this respect, caGrid 1.0 is the realization of a framework that can benefit the entire biomedical community.

Minimizing Overhead for Secure Computation and Fully Homomorphic Encryption: Overhead

DTIC Science & Technology

2015-11-01

many inputs. We also improved our compiler infrastructure to handle very large circuits in a more scalable way. In Jan’13, we employed the AESNI and...Amazon’s elastic compute infrastructure , and is running under a Xen hypervisor. Since we do not have direct access to the bare metal, we cannot...creating novel opportunities for compressing au- thentication overhead. It is especially compelling that existing public key infrastructures can be used

Nuclear-specific AR-V7 Protein Localization is Necessary to Guide Treatment Selection in Metastatic Castration-resistant Prostate Cancer.

PubMed

Scher, Howard I; Graf, Ryon P; Schreiber, Nicole A; McLaughlin, Brigit; Lu, David; Louw, Jessica; Danila, Daniel C; Dugan, Lyndsey; Johnson, Ann; Heller, Glenn; Fleisher, Martin; Dittamore, Ryan

2017-06-01

Circulating tumor cells (CTCs) expressing AR-V7 protein localized to the nucleus (nuclear-specific) identify metastatic castration-resistant prostate cancer (mCRPC) patients with improved overall survival (OS) on taxane therapy relative to the androgen receptor signaling inhibitors (ARSi) abiraterone acetate, enzalutamide, and apalutamide. To evaluate if expanding the positivity criteria to include both nuclear and cytoplasmic AR-V7 localization ("nuclear-agnostic") identifies more patients who would benefit from a taxane over an ARSi. The study used a cross-sectional cohort. Between December 2012 and March 2015, 193 pretherapy blood samples, 191 of which were evaluable, were collected and processed from 161 unique mCRPC patients before starting a new line of systemic therapy for disease progression at the Memorial Sloan Kettering Cancer Center. The association between two AR-V7 scoring criteria, post-therapy prostate-specific antigen (PSA) change (PTPC) and OS following ARSi or taxane treatment, was explored. One criterion required nuclear-specific AR-V7 localization, and the other required an AR-V7 signal but was agnostic to protein localization in CTCs. Correlation of AR-V7 status to PTPC and OS was investigated. Relationships with survival were analyzed using multivariable Cox regression and log-rank analyses. A total of 34 (18%) samples were AR-V7-positive using nuclear-specific criteria, and 56 (29%) were AR-V7-positive using nuclear-agnostic criteria. Following ARSi treatment, none of the 16 nuclear-specific AR-V7-positive samples and six of the 32 (19%) nuclear-agnostic AR-V7-positive samples had ≥50% PTPC at 12 weeks. The strongest baseline factor influencing OS was the interaction between the presence of nuclear-specific AR-V7-positive CTCs and treatment with a taxane (hazard ratio 0.24, 95% confidence interval 0.078-0.79; p=0.019). This interaction was not significant when nuclear-agnostic criteria were used. To reliably inform treatment selection using an AR-V7 protein biomarker in CTCs, nuclear-specific localization is required. We analyzed outcomes for patients with metastatic castration-resistant prostate cancer on androgen receptor signaling inhibitors and standard chemotherapy. Patients with circulating tumor cells that had AR-V7 protein in the cellular nuclei were very likely to survive longer on taxane-based chemotherapy, and tests unable to distinguish where the protein is located in the cell are not as predictive of benefit. Copyright © 2016 European Association of Urology. Published by Elsevier B.V. All rights reserved.

Unbiased Rare Event Sampling in Spatial Stochastic Systems Biology Models Using a Weighted Ensemble of Trajectories

PubMed Central

Donovan, Rory M.; Tapia, Jose-Juan; Sullivan, Devin P.; Faeder, James R.; Murphy, Robert F.; Dittrich, Markus; Zuckerman, Daniel M.

2016-01-01

The long-term goal of connecting scales in biological simulation can be facilitated by scale-agnostic methods. We demonstrate that the weighted ensemble (WE) strategy, initially developed for molecular simulations, applies effectively to spatially resolved cell-scale simulations. The WE approach runs an ensemble of parallel trajectories with assigned weights and uses a statistical resampling strategy of replicating and pruning trajectories to focus computational effort on difficult-to-sample regions. The method can also generate unbiased estimates of non-equilibrium and equilibrium observables, sometimes with significantly less aggregate computing time than would be possible using standard parallelization. Here, we use WE to orchestrate particle-based kinetic Monte Carlo simulations, which include spatial geometry (e.g., of organelles, plasma membrane) and biochemical interactions among mobile molecular species. We study a series of models exhibiting spatial, temporal and biochemical complexity and show that although WE has important limitations, it can achieve performance significantly exceeding standard parallel simulation—by orders of magnitude for some observables. PMID:26845334

Semantic solutions to Heliophysics data access

NASA Astrophysics Data System (ADS)

Narock, T. W.; Vandegriff, J. D.; Weigel, R. S.

2011-12-01

Within the domain of Heliophysics, data discovery is being actively addressed. However, data diversity in the returned results has proven to be a significant barrier to integrated multi-mission analysis. Software is being actively developed (e.g. Vandergriff and Brown, 2008) that is data format and measurement type agnostic. However, such approaches rely on an a priori definition of common baseline parameters, units, and coordinate systems onto which all data will be mapped. In this work, we describe our efforts at utilizing a task ontology (Guarino, 1998) to model the steps involved in data transformation within Heliophysics. Thus, given Heliophysics logic and heterogeneous input data, we are able to develop software that is able to infer the set of steps required to compute user specified parameters. Such a framework offers flexibility by allowing users to define their own preferred sets of parameters, units, and coordinate systems they would like in their analysis. In addition, the storage of this information as ontology instances means they are external to source code and are easily shareable and extensible. The additional inclusion of a provenance ontology allows us to capture the historical record of each data analysis session for future review. We describe our use of existing task and provenance ontologies and provide example use cases as well as potential future applications. References J. Vandegriff and L. Brown, (2010), A framework for reading and unifying heliophysics time series data, Earth Science Informatics, Volume 3, Numbers 1-2, Pages 75-86 N. Guarino, (1998), Formal Ontology in Information Systems, Proceedings of FOIS'98, Trento, Italy, 6-8 June 1998. Amsterdam, IOS Press, pp. 3-15.

gsSKAT: Rapid gene set analysis and multiple testing correction for rare-variant association studies using weighted linear kernels.

PubMed

Larson, Nicholas B; McDonnell, Shannon; Cannon Albright, Lisa; Teerlink, Craig; Stanford, Janet; Ostrander, Elaine A; Isaacs, William B; Xu, Jianfeng; Cooney, Kathleen A; Lange, Ethan; Schleutker, Johanna; Carpten, John D; Powell, Isaac; Bailey-Wilson, Joan E; Cussenot, Olivier; Cancel-Tassin, Geraldine; Giles, Graham G; MacInnis, Robert J; Maier, Christiane; Whittemore, Alice S; Hsieh, Chih-Lin; Wiklund, Fredrik; Catalona, William J; Foulkes, William; Mandal, Diptasri; Eeles, Rosalind; Kote-Jarai, Zsofia; Ackerman, Michael J; Olson, Timothy M; Klein, Christopher J; Thibodeau, Stephen N; Schaid, Daniel J

2017-05-01

Next-generation sequencing technologies have afforded unprecedented characterization of low-frequency and rare genetic variation. Due to low power for single-variant testing, aggregative methods are commonly used to combine observed rare variation within a single gene. Causal variation may also aggregate across multiple genes within relevant biomolecular pathways. Kernel-machine regression and adaptive testing methods for aggregative rare-variant association testing have been demonstrated to be powerful approaches for pathway-level analysis, although these methods tend to be computationally intensive at high-variant dimensionality and require access to complete data. An additional analytical issue in scans of large pathway definition sets is multiple testing correction. Gene set definitions may exhibit substantial genic overlap, and the impact of the resultant correlation in test statistics on Type I error rate control for large agnostic gene set scans has not been fully explored. Herein, we first outline a statistical strategy for aggregative rare-variant analysis using component gene-level linear kernel score test summary statistics as well as derive simple estimators of the effective number of tests for family-wise error rate control. We then conduct extensive simulation studies to characterize the behavior of our approach relative to direct application of kernel and adaptive methods under a variety of conditions. We also apply our method to two case-control studies, respectively, evaluating rare variation in hereditary prostate cancer and schizophrenia. Finally, we provide open-source R code for public use to facilitate easy application of our methods to existing rare-variant analysis results. © 2017 WILEY PERIODICALS, INC.

[Design and study of parallel computing environment of Monte Carlo simulation for particle therapy planning using a public cloud-computing infrastructure].

PubMed

Yokohama, Noriya

2013-07-01

This report was aimed at structuring the design of architectures and studying performance measurement of a parallel computing environment using a Monte Carlo simulation for particle therapy using a high performance computing (HPC) instance within a public cloud-computing infrastructure. Performance measurements showed an approximately 28 times faster speed than seen with single-thread architecture, combined with improved stability. A study of methods of optimizing the system operations also indicated lower cost.

75 FR 70899 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-19

... submit to the Office of Management and Budget (OMB) for clearance the following proposal for collection... Annual Burden Hours: 2,952. Public Computer Center Reports (Quarterly and Annually) Number of Respondents... specific to Infrastructure and Comprehensive Community Infrastructure, Public Computer Center, and...

Defense of Cyber Infrastructures Against Cyber-Physical Attacks Using Game-Theoretic Models

DOE PAGES

Rao, Nageswara S. V.; Poole, Stephen W.; Ma, Chris Y. T.; ...

2015-04-06

The operation of cyber infrastructures relies on both cyber and physical components, which are subject to incidental and intentional degradations of different kinds. Within the context of network and computing infrastructures, we study the strategic interactions between an attacker and a defender using game-theoretic models that take into account both cyber and physical components. The attacker and defender optimize their individual utilities expressed as sums of cost and system terms. First, we consider a Boolean attack-defense model, wherein the cyber and physical sub-infrastructures may be attacked and reinforced as individual units. Second, we consider a component attack-defense model wherein theirmore » components may be attacked and defended, and the infrastructure requires minimum numbers of both to function. We show that the Nash equilibrium under uniform costs in both cases is computable in polynomial time, and it provides high-level deterministic conditions for the infrastructure survival. When probabilities of successful attack and defense, and of incidental failures are incorporated into the models, the results favor the attacker but otherwise remain qualitatively similar. This approach has been motivated and validated by our experiences with UltraScience Net infrastructure, which was built to support high-performance network experiments. In conclusion, the analytical results, however, are more general, and we apply them to simplified models of cloud and high-performance computing infrastructures.« less

Defense of Cyber Infrastructures Against Cyber-Physical Attacks Using Game-Theoretic Models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rao, Nageswara S. V.; Poole, Stephen W.; Ma, Chris Y. T.

The operation of cyber infrastructures relies on both cyber and physical components, which are subject to incidental and intentional degradations of different kinds. Within the context of network and computing infrastructures, we study the strategic interactions between an attacker and a defender using game-theoretic models that take into account both cyber and physical components. The attacker and defender optimize their individual utilities expressed as sums of cost and system terms. First, we consider a Boolean attack-defense model, wherein the cyber and physical sub-infrastructures may be attacked and reinforced as individual units. Second, we consider a component attack-defense model wherein theirmore » components may be attacked and defended, and the infrastructure requires minimum numbers of both to function. We show that the Nash equilibrium under uniform costs in both cases is computable in polynomial time, and it provides high-level deterministic conditions for the infrastructure survival. When probabilities of successful attack and defense, and of incidental failures are incorporated into the models, the results favor the attacker but otherwise remain qualitatively similar. This approach has been motivated and validated by our experiences with UltraScience Net infrastructure, which was built to support high-performance network experiments. In conclusion, the analytical results, however, are more general, and we apply them to simplified models of cloud and high-performance computing infrastructures.« less

Detecting long tandem duplications in genomic sequences.

PubMed

Audemard, Eric; Schiex, Thomas; Faraut, Thomas

2012-05-08

Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The usual approach to gene duplication detection, based on all-pairs protein gene comparisons, provides only a restricted view of duplication. In this paper, we introduce ReD Tandem, a software using a flow based chaining algorithm targeted at detecting tandem duplication arrays of moderate to longer length regions, with possibly locally weak similarities, directly at the DNA level. On the A. thaliana genome, using a reference set of tandem duplicated genes built using TAIR,(a) we show that ReD Tandem is able to predict a large fraction of recently duplicated genes (dS  <  1) and that it is also able to predict tandem duplications involving non coding elements such as pseudo-genes or RNA genes. ReD Tandem allows to identify large tandem duplications without any annotation, leading to agnostic identification of tandem duplications. This approach nicely complements the usual protein gene based which ignores duplications involving non coding regions. It is however inherently restricted to relatively recent duplications. By recovering otherwise ignored events, ReD Tandem gives a more comprehensive view of existing evolutionary processes and may also allow to improve existing annotations.

C3-PRO: Connecting ResearchKit to the Health System Using i2b2 and FHIR.

PubMed

Pfiffner, Pascal B; Pinyol, Isaac; Natter, Marc D; Mandl, Kenneth D

2016-01-01

A renewed interest by consumer information technology giants in the healthcare domain is focused on transforming smartphones into personal health data storage devices. With the introduction of the open source ResearchKit, Apple provides a framework for researchers to inform and consent research subjects, and to readily collect personal health data and patient reported outcomes (PRO) from distributed populations. However, being research backend agnostic, ResearchKit does not provide data transmission facilities, leaving research apps disconnected from the health system. Personal health data and PROs are of the most value when presented in context along with health system data. Our aim was to build a toolchain that allows easy and secure integration of personal health and PRO data into an open source platform widely adopted across 140 academic medical centers. We present C3-PRO: the Consent, Contact, and Community framework for Patient Reported Outcomes. This open source toolchain connects, in a standards-compliant fashion, any ResearchKit app to the widely-used clinical research infrastructure Informatics for Integrating Biology and the Bedside (i2b2). C3-PRO leverages the emerging health data standard Fast Healthcare Interoperability Resources (FHIR).

C3-PRO: Connecting ResearchKit to the Health System Using i2b2 and FHIR

PubMed Central

Pfiffner, Pascal B.; Pinyol, Isaac; Natter, Marc D.; Mandl, Kenneth D.

2016-01-01

A renewed interest by consumer information technology giants in the healthcare domain is focused on transforming smartphones into personal health data storage devices. With the introduction of the open source ResearchKit, Apple provides a framework for researchers to inform and consent research subjects, and to readily collect personal health data and patient reported outcomes (PRO) from distributed populations. However, being research backend agnostic, ResearchKit does not provide data transmission facilities, leaving research apps disconnected from the health system. Personal health data and PROs are of the most value when presented in context along with health system data. Our aim was to build a toolchain that allows easy and secure integration of personal health and PRO data into an open source platform widely adopted across 140 academic medical centers. We present C3-PRO: the Consent, Contact, and Community framework for Patient Reported Outcomes. This open source toolchain connects, in a standards-compliant fashion, any ResearchKit app to the widely-used clinical research infrastructure Informatics for Integrating Biology and the Bedside (i2b2). C3-PRO leverages the emerging health data standard Fast Healthcare Interoperability Resources (FHIR). PMID:27031856

New security infrastructure model for distributed computing systems

NASA Astrophysics Data System (ADS)

Dubenskaya, J.; Kryukov, A.; Demichev, A.; Prikhodko, N.

2016-02-01

At the paper we propose a new approach to setting up a user-friendly and yet secure authentication and authorization procedure in a distributed computing system. The security concept of the most heterogeneous distributed computing systems is based on the public key infrastructure along with proxy certificates which are used for rights delegation. In practice a contradiction between the limited lifetime of the proxy certificates and the unpredictable time of the request processing is a big issue for the end users of the system. We propose to use unlimited in time hashes which are individual for each request instead of proxy certificate. Our approach allows to avoid using of the proxy certificates. Thus the security infrastructure of distributed computing system becomes easier for development, support and use.

Critical infrastructure protection : significant challenges in developing national capabilities

DOT National Transportation Integrated Search

2001-04-01

To address the concerns about protecting the nation's critical computer-dependent infrastructure, this General Accounting Office (GOA) report describes the progress of the National Infrastructure Protection Center (NIPC) in (1) developing national ca...

Distributed Accounting on the Grid

NASA Technical Reports Server (NTRS)

Thigpen, William; Hacker, Thomas J.; McGinnis, Laura F.; Athey, Brian D.

2001-01-01

By the late 1990s, the Internet was adequately equipped to move vast amounts of data between HPC (High Performance Computing) systems, and efforts were initiated to link together the national infrastructure of high performance computational and data storage resources together into a general computational utility 'grid', analogous to the national electrical power grid infrastructure. The purpose of the Computational grid is to provide dependable, consistent, pervasive, and inexpensive access to computational resources for the computing community in the form of a computing utility. This paper presents a fully distributed view of Grid usage accounting and a methodology for allocating Grid computational resources for use on a Grid computing system.

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics

PubMed Central

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A.; Caron, Christophe

2015-01-01

Summary: The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. Availability and implementation: http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). Contact: contact@workflow4metabolomics.org PMID:25527831

Workflow4Metabolomics: a collaborative research infrastructure for computational metabolomics.

PubMed

Giacomoni, Franck; Le Corguillé, Gildas; Monsoor, Misharl; Landi, Marion; Pericard, Pierre; Pétéra, Mélanie; Duperier, Christophe; Tremblay-Franco, Marie; Martin, Jean-François; Jacob, Daniel; Goulitquer, Sophie; Thévenot, Etienne A; Caron, Christophe

2015-05-01

The complex, rapidly evolving field of computational metabolomics calls for collaborative infrastructures where the large volume of new algorithms for data pre-processing, statistical analysis and annotation can be readily integrated whatever the language, evaluated on reference datasets and chained to build ad hoc workflows for users. We have developed Workflow4Metabolomics (W4M), the first fully open-source and collaborative online platform for computational metabolomics. W4M is a virtual research environment built upon the Galaxy web-based platform technology. It enables ergonomic integration, exchange and running of individual modules and workflows. Alternatively, the whole W4M framework and computational tools can be downloaded as a virtual machine for local installation. http://workflow4metabolomics.org homepage enables users to open a private account and access the infrastructure. W4M is developed and maintained by the French Bioinformatics Institute (IFB) and the French Metabolomics and Fluxomics Infrastructure (MetaboHUB). contact@workflow4metabolomics.org. © The Author 2014. Published by Oxford University Press.

Running ATLAS workloads within massively parallel distributed applications using Athena Multi-Process framework (AthenaMP)

NASA Astrophysics Data System (ADS)

Calafiura, Paolo; Leggett, Charles; Seuster, Rolf; Tsulaia, Vakhtang; Van Gemmeren, Peter

2015-12-01

AthenaMP is a multi-process version of the ATLAS reconstruction, simulation and data analysis framework Athena. By leveraging Linux fork and copy-on-write mechanisms, it allows for sharing of memory pages between event processors running on the same compute node with little to no change in the application code. Originally targeted to optimize the memory footprint of reconstruction jobs, AthenaMP has demonstrated that it can reduce the memory usage of certain configurations of ATLAS production jobs by a factor of 2. AthenaMP has also evolved to become the parallel event-processing core of the recently developed ATLAS infrastructure for fine-grained event processing (Event Service) which allows the running of AthenaMP inside massively parallel distributed applications on hundreds of compute nodes simultaneously. We present the architecture of AthenaMP, various strategies implemented by AthenaMP for scheduling workload to worker processes (for example: Shared Event Queue and Shared Distributor of Event Tokens) and the usage of AthenaMP in the diversity of ATLAS event processing workloads on various computing resources: Grid, opportunistic resources and HPC.

Pilots 2.0: DIRAC pilots for all the skies

NASA Astrophysics Data System (ADS)

Stagni, F.; Tsaregorodtsev, A.; McNab, A.; Luzzi, C.

2015-12-01

In the last few years, new types of computing infrastructures, such as IAAS (Infrastructure as a Service) and IAAC (Infrastructure as a Client), gained popularity. New resources may come as part of pledged resources, while others are opportunistic. Most of these new infrastructures are based on virtualization techniques. Meanwhile, some concepts, such as distributed queues, lost appeal, while still supporting a vast amount of resources. Virtual Organizations are therefore facing heterogeneity of the available resources and the use of an Interware software like DIRAC to hide the diversity of underlying resources has become essential. The DIRAC WMS is based on the concept of pilot jobs that was introduced back in 2004. A pilot is what creates the possibility to run jobs on a worker node. Within DIRAC, we developed a new generation of pilot jobs, that we dubbed Pilots 2.0. Pilots 2.0 are not tied to a specific infrastructure; rather they are generic, fully configurable and extendible pilots. A Pilot 2.0 can be sent, as a script to be run, or it can be fetched from a remote location. A pilot 2.0 can run on every computing resource, e.g.: on CREAM Computing elements, on DIRAC Computing elements, on Virtual Machines as part of the contextualization script, or IAAC resources, provided that these machines are properly configured, hiding all the details of the Worker Nodes (WNs) infrastructure. Pilots 2.0 can be generated server and client side. Pilots 2.0 are the “pilots to fly in all the skies”, aiming at easy use of computing power, in whatever form it is presented. Another aim is the unification and simplification of the monitoring infrastructure for all kinds of computing resources, by using pilots as a network of distributed sensors coordinated by a central resource monitoring system. Pilots 2.0 have been developed using the command pattern. VOs using DIRAC can tune pilots 2.0 as they need, and extend or replace each and every pilot command in an easy way. In this paper we describe how Pilots 2.0 work with distributed and heterogeneous resources providing the necessary abstraction to deal with different kind of computing resources.

Evolution of the Virtualized HPC Infrastructure of Novosibirsk Scientific Center

NASA Astrophysics Data System (ADS)

Adakin, A.; Anisenkov, A.; Belov, S.; Chubarov, D.; Kalyuzhny, V.; Kaplin, V.; Korol, A.; Kuchin, N.; Lomakin, S.; Nikultsev, V.; Skovpen, K.; Sukharev, A.; Zaytsev, A.

2012-12-01

Novosibirsk Scientific Center (NSC), also known worldwide as Akademgorodok, is one of the largest Russian scientific centers hosting Novosibirsk State University (NSU) and more than 35 research organizations of the Siberian Branch of Russian Academy of Sciences including Budker Institute of Nuclear Physics (BINP), Institute of Computational Technologies, and Institute of Computational Mathematics and Mathematical Geophysics (ICM&MG). Since each institute has specific requirements on the architecture of computing farms involved in its research field, currently we've got several computing facilities hosted by NSC institutes, each optimized for a particular set of tasks, of which the largest are the NSU Supercomputer Center, Siberian Supercomputer Center (ICM&MG), and a Grid Computing Facility of BINP. A dedicated optical network with the initial bandwidth of 10 Gb/s connecting these three facilities was built in order to make it possible to share the computing resources among the research communities, thus increasing the efficiency of operating the existing computing facilities and offering a common platform for building the computing infrastructure for future scientific projects. Unification of the computing infrastructure is achieved by extensive use of virtualization technology based on XEN and KVM platforms. This contribution gives a thorough review of the present status and future development prospects for the NSC virtualized computing infrastructure and the experience gained while using it for running production data analysis jobs related to HEP experiments being carried out at BINP, especially the KEDR detector experiment at the VEPP-4M electron-positron collider.

Editorial [Special issue on software defined networks and infrastructures, network function virtualisation, autonomous systems and network management

DOE PAGES

Biswas, Amitava; Liu, Chen; Monga, Inder; ...

2016-01-01

For last few years, there has been a tremendous growth in data traffic due to high adoption rate of mobile devices and cloud computing. Internet of things (IoT) will stimulate even further growth. This is increasing scale and complexity of telecom/internet service provider (SP) and enterprise data centre (DC) compute and network infrastructures. As a result, managing these large network-compute converged infrastructures is becoming complex and cumbersome. To cope up, network and DC operators are trying to automate network and system operations, administrations and management (OAM) functions. OAM includes all non-functional mechanisms which keep the network running.

Cloud computing can simplify HIT infrastructure management.

PubMed

Glaser, John

2011-08-01

Software as a Service (SaaS), built on cloud computing technology, is emerging as the forerunner in IT infrastructure because it helps healthcare providers reduce capital investments. Cloud computing leads to predictable, monthly, fixed operating expenses for hospital IT staff. Outsourced cloud computing facilities are state-of-the-art data centers boasting some of the most sophisticated networking equipment on the market. The SaaS model helps hospitals safeguard against technology obsolescence, minimizes maintenance requirements, and simplifies management.

Progress in Machine Learning Studies for the CMS Computing Infrastructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bonacorsi, Daniele; Kuznetsov, Valentin; Magini, Nicolo

Here, computing systems for LHC experiments developed together with Grids worldwide. While a complete description of the original Grid-based infrastructure and services for LHC experiments and its recent evolutions can be found elsewhere, it is worth to mention here the scale of the computing resources needed to fulfill the needs of LHC experiments in Run-1 and Run-2 so far.

Progress in Machine Learning Studies for the CMS Computing Infrastructure

DOE PAGES

Bonacorsi, Daniele; Kuznetsov, Valentin; Magini, Nicolo; ...

2017-12-06

Here, computing systems for LHC experiments developed together with Grids worldwide. While a complete description of the original Grid-based infrastructure and services for LHC experiments and its recent evolutions can be found elsewhere, it is worth to mention here the scale of the computing resources needed to fulfill the needs of LHC experiments in Run-1 and Run-2 so far.

The EDIT-COMGEOM Code

DTIC Science & Technology

1975-09-01

This report assumes a familiarity with the GIFT and MAGIC computer codes. The EDIT-COMGEOM code is a FORTRAN computer code. The EDIT-COMGEOM code...converts the target description data which was used in the MAGIC computer code to the target description data which can be used in the GIFT computer code

Distribution-Agnostic Stochastic Optimal Power Flow for Distribution Grids: Preprint

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baker, Kyri; Dall'Anese, Emiliano; Summers, Tyler

2016-09-01

This paper outlines a data-driven, distributionally robust approach to solve chance-constrained AC optimal power flow problems in distribution networks. Uncertain forecasts for loads and power generated by photovoltaic (PV) systems are considered, with the goal of minimizing PV curtailment while meeting power flow and voltage regulation constraints. A data- driven approach is utilized to develop a distributionally robust conservative convex approximation of the chance-constraints; particularly, the mean and covariance matrix of the forecast errors are updated online, and leveraged to enforce voltage regulation with predetermined probability via Chebyshev-based bounds. By combining an accurate linear approximation of the AC power flowmore » equations with the distributionally robust chance constraint reformulation, the resulting optimization problem becomes convex and computationally tractable.« less

e-Infrastructures for e-Sciences 2013 A CHAIN-REDS Workshop organised under the aegis of the European Commission

NASA Astrophysics Data System (ADS)

The CHAIN-REDS Project is organising a workshop on "e-Infrastructures for e-Sciences" focusing on Cloud Computing and Data Repositories under the aegis of the European Commission and in co-location with the International Conference on e-Science 2013 (IEEE2013) that will be held in Beijing, P.R. of China on October 17-22, 2013. The core objective of the CHAIN-REDS project is to promote, coordinate and support the effort of a critical mass of non-European e-Infrastructures for Research and Education to collaborate with Europe addressing interoperability and interoperation of Grids and other Distributed Computing Infrastructures (DCI). From this perspective, CHAIN-REDS will optimise the interoperation of European infrastructures with those present in 6 other regions of the world, both from a development and use point of view, and catering to different communities. Overall, CHAIN-REDS will provide input for future strategies and decision-making regarding collaboration with other regions on e-Infrastructure deployment and availability of related data; it will raise the visibility of e-Infrastructures towards intercontinental audiences, covering most of the world and will provide support to establish globally connected and interoperable infrastructures, in particular between the EU and the developing regions. Organised by IHEP, INFN and Sigma Orionis with the support of all project partners, this workshop will aim at: - Presenting the state of the art of Cloud computing in Europe and in China and discussing the opportunities offered by having interoperable and federated e-Infrastructures; - Exploring the existing initiatives of Data Infrastructures in Europe and China, and highlighting the Data Repositories of interest for the Virtual Research Communities in several domains such as Health, Agriculture, Climate, etc.

A need for a code of ethics in science communication?

NASA Astrophysics Data System (ADS)

Benestad, R. E.

2009-09-01

The modern western civilization and high standard of living are to a large extent the 'fruits' of scientific endeavor over generations. Some examples include the longer life expectancy due to progress in medical sciences, and changes in infrastructure associated with the utilization of electromagnetism. Modern meteorology is not possible without the state-of-the-art digital computers, satellites, remote sensing, and communications. Science also is of relevance for policy making, e.g. the present hot topic of climate change. Climate scientists have recently become much exposed to media focus and mass communications, a task for which many are not trained. Furthermore, science, communication, and politics have different objectives, and do not necessarily mix. Scientists have an obligation to provide unbiased information, and a code of ethics is needed to give a guidance for acceptable and unacceptable conduct. Some examples of questionable conduct in Norway include using the title 'Ph.D' to imply scientific authority when the person never had obtained such an academic degree, or writing biased and one-sided articles in Norwegian encyclopedia that do not reflect the scientific consensus. It is proposed here that a set of guide lines (for the scientists and journalists) and a code of conduct could provide recommendation for regarding how to act in media - similar to a code of conduct with respect to carrying out research - to which everyone could agree, even when disagreeing on specific scientific questions.

Critical Infrastructure Protection II, The International Federation for Information Processing, Volume 290.

NASA Astrophysics Data System (ADS)

Papa, Mauricio; Shenoi, Sujeet

The information infrastructure -- comprising computers, embedded devices, networks and software systems -- is vital to day-to-day operations in every sector: information and telecommunications, banking and finance, energy, chemicals and hazardous materials, agriculture, food, water, public health, emergency services, transportation, postal and shipping, government and defense. Global business and industry, governments, indeed society itself, cannot function effectively if major components of the critical information infrastructure are degraded, disabled or destroyed. Critical Infrastructure Protection II describes original research results and innovative applications in the interdisciplinary field of critical infrastructure protection. Also, it highlights the importance of weaving science, technology and policy in crafting sophisticated, yet practical, solutions that will help secure information, computer and network assets in the various critical infrastructure sectors. Areas of coverage include: - Themes and Issues - Infrastructure Security - Control Systems Security - Security Strategies - Infrastructure Interdependencies - Infrastructure Modeling and Simulation This book is the second volume in the annual series produced by the International Federation for Information Processing (IFIP) Working Group 11.10 on Critical Infrastructure Protection, an international community of scientists, engineers, practitioners and policy makers dedicated to advancing research, development and implementation efforts focused on infrastructure protection. The book contains a selection of twenty edited papers from the Second Annual IFIP WG 11.10 International Conference on Critical Infrastructure Protection held at George Mason University, Arlington, Virginia, USA in the spring of 2008.

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCaskey, Alexander J.

Hybrid programming models for beyond-CMOS technologies will prove critical for integrating new computing technologies alongside our existing infrastructure. Unfortunately the software infrastructure required to enable this is lacking or not available. XACC is a programming framework for extreme-scale, post-exascale accelerator architectures that integrates alongside existing conventional applications. It is a pluggable framework for programming languages developed for next-gen computing hardware architectures like quantum and neuromorphic computing. It lets computational scientists efficiently off-load classically intractable work to attached accelerators through user-friendly Kernel definitions. XACC makes post-exascale hybrid programming approachable for domain computational scientists.

Galaxy CloudMan: delivering cloud compute clusters.

PubMed

Afgan, Enis; Baker, Dannon; Coraor, Nate; Chapman, Brad; Nekrutenko, Anton; Taylor, James

2010-12-21

Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is "cloud computing", which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate "as is" use by experimental biologists. We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon's EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs. The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge.

Software Reuse Methods to Improve Technological Infrastructure for e-Science

NASA Technical Reports Server (NTRS)

Marshall, James J.; Downs, Robert R.; Mattmann, Chris A.

2011-01-01

Social computing has the potential to contribute to scientific research. Ongoing developments in information and communications technology improve capabilities for enabling scientific research, including research fostered by social computing capabilities. The recent emergence of e-Science practices has demonstrated the benefits from improvements in the technological infrastructure, or cyber-infrastructure, that has been developed to support science. Cloud computing is one example of this e-Science trend. Our own work in the area of software reuse offers methods that can be used to improve new technological development, including cloud computing capabilities, to support scientific research practices. In this paper, we focus on software reuse and its potential to contribute to the development and evaluation of information systems and related services designed to support new capabilities for conducting scientific research.

An Object Oriented Extensible Architecture for Affordable Aerospace Propulsion Systems

NASA Technical Reports Server (NTRS)

Follen, Gregory J.; Lytle, John K. (Technical Monitor)

2002-01-01

Driven by a need to explore and develop propulsion systems that exceeded current computing capabilities, NASA Glenn embarked on a novel strategy leading to the development of an architecture that enables propulsion simulations never thought possible before. Full engine 3 Dimensional Computational Fluid Dynamic propulsion system simulations were deemed impossible due to the impracticality of the hardware and software computing systems required. However, with a software paradigm shift and an embracing of parallel and distributed processing, an architecture was designed to meet the needs of future propulsion system modeling. The author suggests that the architecture designed at the NASA Glenn Research Center for propulsion system modeling has potential for impacting the direction of development of affordable weapons systems currently under consideration by the Applied Vehicle Technology Panel (AVT). This paper discusses the salient features of the NPSS Architecture including its interface layer, object layer, implementation for accessing legacy codes, numerical zooming infrastructure and its computing layer. The computing layer focuses on the use and deployment of these propulsion simulations on parallel and distributed computing platforms which has been the focus of NASA Ames. Additional features of the object oriented architecture that support MultiDisciplinary (MD) Coupling, computer aided design (CAD) access and MD coupling objects will be discussed. Included will be a discussion of the successes, challenges and benefits of implementing this architecture.

RAPPORT: running scientific high-performance computing applications on the cloud.

PubMed

Cohen, Jeremy; Filippis, Ioannis; Woodbridge, Mark; Bauer, Daniela; Hong, Neil Chue; Jackson, Mike; Butcher, Sarah; Colling, David; Darlington, John; Fuchs, Brian; Harvey, Matt

2013-01-28

Cloud computing infrastructure is now widely used in many domains, but one area where there has been more limited adoption is research computing, in particular for running scientific high-performance computing (HPC) software. The Robust Application Porting for HPC in the Cloud (RAPPORT) project took advantage of existing links between computing researchers and application scientists in the fields of bioinformatics, high-energy physics (HEP) and digital humanities, to investigate running a set of scientific HPC applications from these domains on cloud infrastructure. In this paper, we focus on the bioinformatics and HEP domains, describing the applications and target cloud platforms. We conclude that, while there are many factors that need consideration, there is no fundamental impediment to the use of cloud infrastructure for running many types of HPC applications and, in some cases, there is potential for researchers to benefit significantly from the flexibility offered by cloud platforms.

Virtual Labs (Science Gateways) as platforms for Free and Open Source Science

NASA Astrophysics Data System (ADS)

Lescinsky, David; Car, Nicholas; Fraser, Ryan; Friedrich, Carsten; Kemp, Carina; Squire, Geoffrey

2016-04-01

The Free and Open Source Software (FOSS) movement promotes community engagement in software development, as well as provides access to a range of sophisticated technologies that would be prohibitively expensive if obtained commercially. However, as geoinformatics and eResearch tools and services become more dispersed, it becomes more complicated to identify and interface between the many required components. Virtual Laboratories (VLs, also known as Science Gateways) simplify the management and coordination of these components by providing a platform linking many, if not all, of the steps in particular scientific processes. These enable scientists to focus on their science, rather than the underlying supporting technologies. We describe a modular, open source, VL infrastructure that can be reconfigured to create VLs for a wide range of disciplines. Development of this infrastructure has been led by CSIRO in collaboration with Geoscience Australia and the National Computational Infrastructure (NCI) with support from the National eResearch Collaboration Tools and Resources (NeCTAR) and the Australian National Data Service (ANDS). Initially, the infrastructure was developed to support the Virtual Geophysical Laboratory (VGL), and has subsequently been repurposed to create the Virtual Hazards Impact and Risk Laboratory (VHIRL) and the reconfigured Australian National Virtual Geophysics Laboratory (ANVGL). During each step of development, new capabilities and services have been added and/or enhanced. We plan on continuing to follow this model using a shared, community code base. The VL platform facilitates transparent and reproducible science by providing access to both the data and methodologies used during scientific investigations. This is further enhanced by the ability to set up and run investigations using computational resources accessed through the VL. Data is accessed using registries pointing to catalogues within public data repositories (notably including the NCI National Environmental Research Data Interoperability Platform), or by uploading data directly from user supplied addresses or files. Similarly, scientific software is accessed through registries pointing to software repositories (e.g., GitHub). Runs are configured by using or modifying default templates designed by subject matter experts. After the appropriate computational resources are identified by the user, Virtual Machines (VMs) are spun up and jobs are submitted to service providers (currently the NeCTAR public cloud or Amazon Web Services). Following completion of the jobs the results can be reviewed and downloaded if desired. By providing a unified platform for science, the VL infrastructure enables sophisticated provenance capture and management. The source of input data (including both collection and queries), user information, software information (version and configuration details) and output information are all captured and managed as a VL resource which can be linked to output data sets. This provenance resource provides a mechanism for publication and citation for Free and Open Source Science.

Measurement Techniques for Clock Jitter

NASA Technical Reports Server (NTRS)

Lansdowne, Chatwin; Schlesinger, Adam

2012-01-01

NASA is in the process of modernizing its communications infrastructure to accompany the development of a Crew Exploration Vehicle (CEV) to replace the shuttle. With this effort comes the opportunity to infuse more advanced coded modulation techniques, including low-density parity-check (LDPC) codes that offer greater coding gains than the current capability. However, in order to take full advantage of these codes, the ground segment receiver synchronization loops must be able to operate at a lower signal-to-noise ratio (SNR) than supported by equipment currently in use.

International Symposium on Grids and Clouds (ISGC) 2016

NASA Astrophysics Data System (ADS)

The International Symposium on Grids and Clouds (ISGC) 2016 will be held at Academia Sinica in Taipei, Taiwan from 13-18 March 2016, with co-located events and workshops. The conference is hosted by the Academia Sinica Grid Computing Centre (ASGC). The theme of ISGC 2016 focuses on“Ubiquitous e-infrastructures and Applications”. Contemporary research is impossible without a strong IT component - researchers rely on the existence of stable and widely available e-infrastructures and their higher level functions and properties. As a result of these expectations, e-Infrastructures are becoming ubiquitous, providing an environment that supports large scale collaborations that deal with global challenges as well as smaller and temporal research communities focusing on particular scientific problems. To support those diversified communities and their needs, the e-Infrastructures themselves are becoming more layered and multifaceted, supporting larger groups of applications. Following the call for the last year conference, ISGC 2016 continues its aim to bring together users and application developers with those responsible for the development and operation of multi-purpose ubiquitous e-Infrastructures. Topics of discussion include Physics (including HEP) and Engineering Applications, Biomedicine & Life Sciences Applications, Earth & Environmental Sciences & Biodiversity Applications, Humanities, Arts, and Social Sciences (HASS) Applications, Virtual Research Environment (including Middleware, tools, services, workflow, etc.), Data Management, Big Data, Networking & Security, Infrastructure & Operations, Infrastructure Clouds and Virtualisation, Interoperability, Business Models & Sustainability, Highly Distributed Computing Systems, and High Performance & Technical Computing (HPTC), etc.

Defense of Cyber Infrastructures Against Cyber-Physical Attacks Using Game-Theoretic Models.

PubMed

Rao, Nageswara S V; Poole, Stephen W; Ma, Chris Y T; He, Fei; Zhuang, Jun; Yau, David K Y

2016-04-01

The operation of cyber infrastructures relies on both cyber and physical components, which are subject to incidental and intentional degradations of different kinds. Within the context of network and computing infrastructures, we study the strategic interactions between an attacker and a defender using game-theoretic models that take into account both cyber and physical components. The attacker and defender optimize their individual utilities, expressed as sums of cost and system terms. First, we consider a Boolean attack-defense model, wherein the cyber and physical subinfrastructures may be attacked and reinforced as individual units. Second, we consider a component attack-defense model wherein their components may be attacked and defended, and the infrastructure requires minimum numbers of both to function. We show that the Nash equilibrium under uniform costs in both cases is computable in polynomial time, and it provides high-level deterministic conditions for the infrastructure survival. When probabilities of successful attack and defense, and of incidental failures, are incorporated into the models, the results favor the attacker but otherwise remain qualitatively similar. This approach has been motivated and validated by our experiences with UltraScience Net infrastructure, which was built to support high-performance network experiments. The analytical results, however, are more general, and we apply them to simplified models of cloud and high-performance computing infrastructures. © 2015 Society for Risk Analysis.

S3DB core: a framework for RDF generation and management in bioinformatics infrastructures

PubMed Central

2010-01-01

Background Biomedical research is set to greatly benefit from the use of semantic web technologies in the design of computational infrastructure. However, beyond well defined research initiatives, substantial issues of data heterogeneity, source distribution, and privacy currently stand in the way towards the personalization of Medicine. Results A computational framework for bioinformatic infrastructure was designed to deal with the heterogeneous data sources and the sensitive mixture of public and private data that characterizes the biomedical domain. This framework consists of a logical model build with semantic web tools, coupled with a Markov process that propagates user operator states. An accompanying open source prototype was developed to meet a series of applications that range from collaborative multi-institution data acquisition efforts to data analysis applications that need to quickly traverse complex data structures. This report describes the two abstractions underlying the S3DB-based infrastructure, logical and numerical, and discusses its generality beyond the immediate confines of existing implementations. Conclusions The emergence of the "web as a computer" requires a formal model for the different functionalities involved in reading and writing to it. The S3DB core model proposed was found to address the design criteria of biomedical computational infrastructure, such as those supporting large scale multi-investigator research, clinical trials, and molecular epidemiology. PMID:20646315

Assessing an Effort to Promote Safe Parks, Streets and Schools in Washington Heights/Inwood: Assessing Urban Infrastructure Conditions as Determinants of Physical Activity. Program Results

ERIC Educational Resources Information Center

Nakashian, Mary

2008-01-01

Researchers from the Mailman School of Public Health at Columbia University prepared a case study of CODES (Community Outreach and Development Efforts Save). CODES is a coalition of 35 people and organizations in northern Manhattan committed to promoting safe streets, parks and schools. The case study analyzed the factors that prompted CODES'…

The Czech National Grid Infrastructure

NASA Astrophysics Data System (ADS)

Chudoba, J.; Křenková, I.; Mulač, M.; Ruda, M.; Sitera, J.

2017-10-01

The Czech National Grid Infrastructure is operated by MetaCentrum, a CESNET department responsible for coordinating and managing activities related to distributed computing. CESNET as the Czech National Research and Education Network (NREN) provides many e-infrastructure services, which are used by 94% of the scientific and research community in the Czech Republic. Computing and storage resources owned by different organizations are connected by fast enough network to provide transparent access to all resources. We describe in more detail the computing infrastructure, which is based on several different technologies and covers grid, cloud and map-reduce environment. While the largest part of CPUs is still accessible via distributed torque servers, providing environment for long batch jobs, part of infrastructure is available via standard EGI tools in EGI, subset of NGI resources is provided into EGI FedCloud environment with cloud interface and there is also Hadoop cluster provided by the same e-infrastructure.A broad spectrum of computing servers is offered; users can choose from standard 2 CPU servers to large SMP machines with up to 6 TB of RAM or servers with GPU cards. Different groups have different priorities on various resources, resource owners can even have an exclusive access. The software is distributed via AFS. Storage servers offering up to tens of terabytes of disk space to individual users are connected via NFS4 on top of GPFS and access to long term HSM storage with peta-byte capacity is also provided. Overview of available resources and recent statistics of usage will be given.

Grid and Cloud for Developing Countries

NASA Astrophysics Data System (ADS)

Petitdidier, Monique

2014-05-01

The European Grid e-infrastructure has shown the capacity to connect geographically distributed heterogeneous compute resources in a secure way taking advantages of a robust and fast REN (Research and Education Network). In many countries like in Africa the first step has been to implement a REN and regional organizations like Ubuntunet, WACREN or ASREN to coordinate the development, improvement of the network and its interconnection. The Internet connections are still exploding in those countries. The second step has been to fill up compute needs of the scientists. Even if many of them have their own multi-core or not laptops for more and more applications it is not enough because they have to face intensive computing due to the large amount of data to be processed and/or complex codes. So far one solution has been to go abroad in Europe or in America to run large applications or not to participate to international communities. The Grid is very attractive to connect geographically-distributed heterogeneous resources, aggregate new ones and create new sites on the REN with a secure access. All the users have the same servicers even if they have no resources in their institute. With faster and more robust internet they will be able to take advantage of the European Grid. There are different initiatives to provide resources and training like UNESCO/HP Brain Gain initiative, EUMEDGrid, ..Nowadays Cloud becomes very attractive and they start to be developed in some countries. In this talk challenges for those countries to implement such e-infrastructures, to develop in parallel scientific and technical research and education in the new technologies will be presented illustrated by examples.

An infrastructure with a unified control plane to integrate IP into optical metro networks to provide flexible and intelligent bandwidth on demand for cloud computing

NASA Astrophysics Data System (ADS)

Yang, Wei; Hall, Trevor

2012-12-01

The Internet is entering an era of cloud computing to provide more cost effective, eco-friendly and reliable services to consumer and business users and the nature of the Internet traffic will undertake a fundamental transformation. Consequently, the current Internet will no longer suffice for serving cloud traffic in metro areas. This work proposes an infrastructure with a unified control plane that integrates simple packet aggregation technology with optical express through the interoperation between IP routers and electrical traffic controllers in optical metro networks. The proposed infrastructure provides flexible, intelligent, and eco-friendly bandwidth on demand for cloud computing in metro areas.

The BaBar Data Reconstruction Control System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ceseracciu, A

2005-04-20

The BaBar experiment is characterized by extremely high luminosity and very large volume of data produced and stored, with increasing computing requirements each year. To fulfill these requirements a Control System has been designed and developed for the offline distributed data reconstruction system. The control system described in this paper provides the performance and flexibility needed to manage a large number of small computing farms, and takes full benefit of OO design. The infrastructure is well isolated from the processing layer, it is generic and flexible, based on a light framework providing message passing and cooperative multitasking. The system ismore » distributed in a hierarchical way: the top-level system is organized in farms, farms in services, and services in subservices or code modules. It provides a powerful Finite State Machine framework to describe custom processing models in a simple regular language. This paper describes the design and evolution of this control system, currently in use at SLAC and Padova on {approx}450 CPUs organized in 9 farms.« less

The BaBar Data Reconstruction Control System

NASA Astrophysics Data System (ADS)

Ceseracciu, A.; Piemontese, M.; Tehrani, F. S.; Pulliam, T. M.; Galeazzi, F.

2005-08-01

The BaBar experiment is characterized by extremely high luminosity and very large volume of data produced and stored, with increasing computing requirements each year. To fulfill these requirements a control system has been designed and developed for the offline distributed data reconstruction system. The control system described in this paper provides the performance and flexibility needed to manage a large number of small computing farms, and takes full benefit of object oriented (OO) design. The infrastructure is well isolated from the processing layer, it is generic and flexible, based on a light framework providing message passing and cooperative multitasking. The system is distributed in a hierarchical way: the top-level system is organized in farms, farms in services, and services in subservices or code modules. It provides a powerful finite state machine framework to describe custom processing models in a simple regular language. This paper describes the design and evolution of this control system, currently in use at SLAC and Padova on /spl sim/450 CPUs organized in nine farms.

Towards Portable Large-Scale Image Processing with High-Performance Computing.

PubMed

Huo, Yuankai; Blaber, Justin; Damon, Stephen M; Boyd, Brian D; Bao, Shunxing; Parvathaneni, Prasanna; Noguera, Camilo Bermudez; Chaganti, Shikha; Nath, Vishwesh; Greer, Jasmine M; Lyu, Ilwoo; French, William R; Newton, Allen T; Rogers, Baxter P; Landman, Bennett A

2018-05-03

High-throughput, large-scale medical image computing demands tight integration of high-performance computing (HPC) infrastructure for data storage, job distribution, and image processing. The Vanderbilt University Institute for Imaging Science (VUIIS) Center for Computational Imaging (CCI) has constructed a large-scale image storage and processing infrastructure that is composed of (1) a large-scale image database using the eXtensible Neuroimaging Archive Toolkit (XNAT), (2) a content-aware job scheduling platform using the Distributed Automation for XNAT pipeline automation tool (DAX), and (3) a wide variety of encapsulated image processing pipelines called "spiders." The VUIIS CCI medical image data storage and processing infrastructure have housed and processed nearly half-million medical image volumes with Vanderbilt Advanced Computing Center for Research and Education (ACCRE), which is the HPC facility at the Vanderbilt University. The initial deployment was natively deployed (i.e., direct installations on a bare-metal server) within the ACCRE hardware and software environments, which lead to issues of portability and sustainability. First, it could be laborious to deploy the entire VUIIS CCI medical image data storage and processing infrastructure to another HPC center with varying hardware infrastructure, library availability, and software permission policies. Second, the spiders were not developed in an isolated manner, which has led to software dependency issues during system upgrades or remote software installation. To address such issues, herein, we describe recent innovations using containerization techniques with XNAT/DAX which are used to isolate the VUIIS CCI medical image data storage and processing infrastructure from the underlying hardware and software environments. The newly presented XNAT/DAX solution has the following new features: (1) multi-level portability from system level to the application level, (2) flexible and dynamic software development and expansion, and (3) scalable spider deployment compatible with HPC clusters and local workstations.

Analysing and Rationalising Molecular and Materials Databases Using Machine-Learning

NASA Astrophysics Data System (ADS)

de, Sandip; Ceriotti, Michele

Computational materials design promises to greatly accelerate the process of discovering new or more performant materials. Several collaborative efforts are contributing to this goal by building databases of structures, containing between thousands and millions of distinct hypothetical compounds, whose properties are computed by high-throughput electronic-structure calculations. The complexity and sheer amount of information has made manual exploration, interpretation and maintenance of these databases a formidable challenge, making it necessary to resort to automatic analysis tools. Here we will demonstrate how, starting from a measure of (dis)similarity between database items built from a combination of local environment descriptors, it is possible to apply hierarchical clustering algorithms, as well as dimensionality reduction methods such as sketchmap, to analyse, classify and interpret trends in molecular and materials databases, as well as to detect inconsistencies and errors. Thanks to the agnostic and flexible nature of the underlying metric, we will show how our framework can be applied transparently to different kinds of systems ranging from organic molecules and oligopeptides to inorganic crystal structures as well as molecular crystals. Funded by National Center for Computational Design and Discovery of Novel Materials (MARVEL) and Swiss National Science Foundation.

Collaborative WorkBench (cwb): Enabling Experiment Execution, Analysis and Visualization with Increased Scientific Productivity

NASA Astrophysics Data System (ADS)

Maskey, Manil; Ramachandran, Rahul; Kuo, Kwo-Sen

2015-04-01

The Collaborative WorkBench (CWB) has been successfully developed to support collaborative science algorithm development. It incorporates many features that enable and enhance science collaboration, including the support for both asynchronous and synchronous modes of interactions in collaborations. With the former, members in a team can share a full range of research artifacts, e.g. data, code, visualizations, and even virtual machine images. With the latter, they can engage in dynamic interactions such as notification, instant messaging, file exchange, and, most notably, collaborative programming. CWB also implements behind-the-scene provenance capture as well as version control to relieve scientists of these chores. Furthermore, it has achieved a seamless integration between researchers' local compute environments and those of the Cloud. CWB has also been successfully extended to support instrument verification and validation. Adopted by almost every researcher, the current practice of downloading data to local compute resources for analysis results in much duplication and inefficiency. CWB leverages Cloud infrastructure to provide a central location for data used by an entire science team, thereby eliminating much of this duplication and waste. Furthermore, use of CWB in concert with this same Cloud infrastructure enables co-located analysis with data where opportunities of data-parallelism can be better exploited, thereby further improving efficiency. With its collaboration-enabling features apposite to steps throughout the scientific process, we expect CWB to fundamentally transform research collaboration and realize maximum science productivity.

Pegasus Workflow Management System: Helping Applications From Earth and Space

NASA Astrophysics Data System (ADS)

Mehta, G.; Deelman, E.; Vahi, K.; Silva, F.

2010-12-01

Pegasus WMS is a Workflow Management System that can manage large-scale scientific workflows across Grid, local and Cloud resources simultaneously. Pegasus WMS provides a means for representing the workflow of an application in an abstract XML form, agnostic of the resources available to run it and the location of data and executables. It then compiles these workflows into concrete plans by querying catalogs and farming computations across local and distributed computing resources, as well as emerging commercial and community cloud environments in an easy and reliable manner. Pegasus WMS optimizes the execution as well as data movement by leveraging existing Grid and cloud technologies via a flexible pluggable interface and provides advanced features like reusing existing data, automatic cleanup of generated data, and recursive workflows with deferred planning. It also captures all the provenance of the workflow from the planning stage to the execution of the generated data, helping scientists to accurately measure performance metrics of their workflow as well as data reproducibility issues. Pegasus WMS was initially developed as part of the GriPhyN project to support large-scale high-energy physics and astrophysics experiments. Direct funding from the NSF enabled support for a wide variety of applications from diverse domains including earthquake simulation, bacterial RNA studies, helioseismology and ocean modeling. Earthquake Simulation: Pegasus WMS was recently used in a large scale production run in 2009 by the Southern California Earthquake Centre to run 192 million loosely coupled tasks and about 2000 tightly coupled MPI style tasks on National Cyber infrastructure for generating a probabilistic seismic hazard map of the Southern California region. SCEC ran 223 workflows over a period of eight weeks, using on average 4,420 cores, with a peak of 14,540 cores. A total of 192 million files were produced totaling about 165TB out of which 11TB of data was saved. Astrophysics: The Laser Interferometer Gravitational-Wave Observatory (LIGO) uses Pegasus WMS to search for binary inspiral gravitational waves. A month of LIGO data requires many thousands of jobs, running for days on hundreds of CPUs on the LIGO Data Grid (LDG) and Open Science Grid (OSG). Ocean Temperature Forecast: Researchers at the Jet Propulsion Laboratory are exploring Pegasus WMS to run ocean forecast ensembles of the California coastal region. These models produce a number of daily forecasts for water temperature, salinity, and other measures. Helioseismology: The Solar Dynamics Observatory (SDO) is NASA's most important solar physics mission of this coming decade. Pegasus WMS is being used to analyze the data from SDO, which will be predominantly used to learn about solar magnetic activity and to probe the internal structure and dynamics of the Sun with helioseismology. Bacterial RNA studies: SIPHT is an application in bacterial genomics, which predicts sRNA (small non-coding RNAs)-encoding genes in bacteria. This project currently provides a web-based interface using Pegasus WMS at the backend to facilitate large-scale execution of the workflows on varied resources and provide better notifications of task/workflow completion.

Improving throughput for temporal target nomination using existing infrastructure

NASA Astrophysics Data System (ADS)

Raeth, Peter G.

2007-04-01

Earlier, we reported on predictive anomaly detection (PAD) for nominating targets within data streams generated by persistent sensing and surveillance. This technique is purely temporal and does not directly depend on the physics attendant on the sensed environment. Since PAD adapts to evolving data streams, there are no determinacy assumptions. We showed PAD to be general across sensor types, demonstrating it using synthetic chaotic data and in audio, visual, and infrared applications. Defense-oriented demonstrations included explosions, muzzle flashes, and missile and aircraft detection. Experiments were ground-based and air-to-air. As new sensors come on line, PAD offers immediate data filtering and target nomination. Its results can be taken individually, pixel by pixel, for spectral analysis and material detection/identification. They can also be grouped for shape analysis, target identification, and track development. PAD analyses reduce data volume by around 95%, depending on target number and size, while still retaining all target indicators. While PAD's code is simple when compared to physics codes, PAD tends to build a huge model. A PAD model for 512 x 640 frames may contain 19,660,800 Gaussian basis functions. (PAD models grow linearly with the number of pixels and the frequency content, in the FFT sense, of the sensed scenario's background data). PAD's complexity in terms of computational and data intensity is an example of what one sees in new algorithms now in the R&D pipeline, especially as DoD seeks capability that runs fully automatic, with little to no human interaction. Work is needed to improve algorithms' throughput while employing existing infrastructure, yet allowing for growth in the types of hardware employed. In this present paper, we discuss a generic cluster interface for legacy codes that can be partitioned at the data level. The discussion's foundation is the growth of PAD models to accommodate a particular scenario and the need to reduce false alarms while preserving all targets. The discussion closes with a view of future software and hardware opportunities.

Galaxy CloudMan: delivering cloud compute clusters

PubMed Central

2010-01-01

Background Widespread adoption of high-throughput sequencing has greatly increased the scale and sophistication of computational infrastructure needed to perform genomic research. An alternative to building and maintaining local infrastructure is “cloud computing”, which, in principle, offers on demand access to flexible computational infrastructure. However, cloud computing resources are not yet suitable for immediate “as is” use by experimental biologists. Results We present a cloud resource management system that makes it possible for individual researchers to compose and control an arbitrarily sized compute cluster on Amazon’s EC2 cloud infrastructure without any informatics requirements. Within this system, an entire suite of biological tools packaged by the NERC Bio-Linux team (http://nebc.nerc.ac.uk/tools/bio-linux) is available for immediate consumption. The provided solution makes it possible, using only a web browser, to create a completely configured compute cluster ready to perform analysis in less than five minutes. Moreover, we provide an automated method for building custom deployments of cloud resources. This approach promotes reproducibility of results and, if desired, allows individuals and labs to add or customize an otherwise available cloud system to better meet their needs. Conclusions The expected knowledge and associated effort with deploying a compute cluster in the Amazon EC2 cloud is not trivial. The solution presented in this paper eliminates these barriers, making it possible for researchers to deploy exactly the amount of computing power they need, combined with a wealth of existing analysis software, to handle the ongoing data deluge. PMID:21210983

Conditions for Ubiquitous Computing: What Can Be Learned from a Longitudinal Study

ERIC Educational Resources Information Center

Lei, Jing

2010-01-01

Based on survey data and interview data collected over four academic years, this longitudinal study examined how a ubiquitous computing project evolved along with the changes in teachers, students, the human infrastructure, and technology infrastructure in the school. This study also investigated what conditions were necessary for successful…

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management.

PubMed

Neinstein, Aaron; Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-03-01

Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application ("app"), Blip, to visualize the data. Tidepool's software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool's open source, cloud model for health data interoperability is applicable to other healthcare use cases. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

A case study in open source innovation: developing the Tidepool Platform for interoperability in type 1 diabetes management

PubMed Central

Wong, Jenise; Look, Howard; Arbiter, Brandon; Quirk, Kent; McCanne, Steve; Sun, Yao; Blum, Michael; Adi, Saleh

2016-01-01

Objective Develop a device-agnostic cloud platform to host diabetes device data and catalyze an ecosystem of software innovation for type 1 diabetes (T1D) management. Materials and Methods An interdisciplinary team decided to establish a nonprofit company, Tidepool, and build open-source software. Results Through a user-centered design process, the authors created a software platform, the Tidepool Platform, to upload and host T1D device data in an integrated, device-agnostic fashion, as well as an application (“app”), Blip, to visualize the data. Tidepool’s software utilizes the principles of modular components, modern web design including REST APIs and JavaScript, cloud computing, agile development methodology, and robust privacy and security. Discussion By consolidating the currently scattered and siloed T1D device data ecosystem into one open platform, Tidepool can improve access to the data and enable new possibilities and efficiencies in T1D clinical care and research. The Tidepool Platform decouples diabetes apps from diabetes devices, allowing software developers to build innovative apps without requiring them to design a unique back-end (e.g., database and security) or unique ways of ingesting device data. It allows people with T1D to choose to use any preferred app regardless of which device(s) they use. Conclusion The authors believe that the Tidepool Platform can solve two current problems in the T1D device landscape: 1) limited access to T1D device data and 2) poor interoperability of data from different devices. If proven effective, Tidepool’s open source, cloud model for health data interoperability is applicable to other healthcare use cases. PMID:26338218

Simulations of recoiling black holes: adaptive mesh refinement and radiative transfer

NASA Astrophysics Data System (ADS)

Meliani, Zakaria; Mizuno, Yosuke; Olivares, Hector; Porth, Oliver; Rezzolla, Luciano; Younsi, Ziri

2017-02-01

Context. In many astrophysical phenomena, and especially in those that involve the high-energy regimes that always accompany the astronomical phenomenology of black holes and neutron stars, physical conditions that are achieved are extreme in terms of speeds, temperatures, and gravitational fields. In such relativistic regimes, numerical calculations are the only tool to accurately model the dynamics of the flows and the transport of radiation in the accreting matter. Aims: We here continue our effort of modelling the behaviour of matter when it orbits or is accreted onto a generic black hole by developing a new numerical code that employs advanced techniques geared towards solving the equations of general-relativistic hydrodynamics. Methods: More specifically, the new code employs a number of high-resolution shock-capturing Riemann solvers and reconstruction algorithms, exploiting the enhanced accuracy and the reduced computational cost of adaptive mesh-refinement (AMR) techniques. In addition, the code makes use of sophisticated ray-tracing libraries that, coupled with general-relativistic radiation-transfer calculations, allow us to accurately compute the electromagnetic emissions from such accretion flows. Results: We validate the new code by presenting an extensive series of stationary accretion flows either in spherical or axial symmetry that are performed either in two or three spatial dimensions. In addition, we consider the highly nonlinear scenario of a recoiling black hole produced in the merger of a supermassive black-hole binary interacting with the surrounding circumbinary disc. In this way, we can present for the first time ray-traced images of the shocked fluid and the light curve resulting from consistent general-relativistic radiation-transport calculations from this process. Conclusions: The work presented here lays the ground for the development of a generic computational infrastructure employing AMR techniques to accurately and self-consistently calculate general-relativistic accretion flows onto compact objects. In addition to the accurate handling of the matter, we provide a self-consistent electromagnetic emission from these scenarios by solving the associated radiative-transfer problem. While magnetic fields are currently excluded from our analysis, the tools presented here can have a number of applications to study accretion flows onto black holes or neutron stars.

Plant Habitat Telemetry / Command Interface and E-MIST

NASA Technical Reports Server (NTRS)

Walker, Uriae M.

2013-01-01

Plant Habitat (PH) is an experiment to be taken to the International Space Station (ISS) in 2016. It is critical that ground support computers have the ability to uplink commands to control PH, and that ISS computers have the ability to downlink PH telemetry data to ground support. This necessitates communication software that can send, receive, and process, PH specific commands and telemetry. The objective of the Plant Habitat Telemetry/ Command Interface is to provide this communication software, and to couple it with an intuitive Graphical User Interface (GUI). Initial investigation of the project objective led to the decision that code be written in C++ because of its compatibility with existing source code infrastructures and robustness. Further investigation led to a determination that multiple Ethernet packet structures would need to be created to effectively transmit data. Setting a standard for packet structures would allow us to distinguish these packets that would range from command type packets to sub categories of telemetry packets. In order to handle this range of packet types, the conclusion was made to take an object-oriented programming approach which complemented our decision to use the C++ programming language. In addition, extensive utilization of port programming concepts was required to implement the core functionality of the communication software. Also, a concrete understanding of a packet processing software was required in order to put aU the components of ISS-to-Ground Support Equipment (GSE) communication together and complete the objective. A second project discussed in this paper is Exposing Microbes to the Stratosphere (EMIST). This project exposes microbes into the stratosphere to observe how they are impacted by atmospheric effects. This paper focuses on the electrical and software expectations of the project, specifically drafting the printed circuit board, and programming the on-board sensors. The Eagle Computer-Aided Drafting (CAD) software was used to draft the E-MIST circuit. This required several component libraries to be created. Coding the sensors and obtaining sensor data involved using the Arduino Uno developmental board and coding language, and properly wiring peripheral sensors to the microcontroller (the central control unit of the experiment).

Building Interactive Visualizations for Geochronological Data

NASA Astrophysics Data System (ADS)

Zeringue, J.; Bowring, J. F.; McLean, N. M.; Pastor, F.

2014-12-01

Since the early 1990s, Ken Ludwig's Isoplot software has been the tool of choice for visualization and analysis of isotopic data used for geochronology. The software is an add-in to Microsoft Excel that allows users to generate visual representations of data. However, recent changes to Excel have made Isoplot more difficult to use and maintain, and the software is no longer supported. In the last several years, the Cyber Infrastructure Research and Development Lab for the Earth Sciences (CIRDLES), at the College of Charleston, has worked collaboratively with geochronologists to develop U-Pb_Redux, a software product that provides some of Isoplot's functionality for U-Pb geochronology. However, the community needs a full and complete Isoplot replacement that is open source, platform independent, and not dependent on proprietary software. This temporary lapse in tooling also presents a tremendous opportunity for scientific computing in the earth sciences. When Isoplot was written for Excel, it gained much of the platform's flexibility and power but also was burdened with its limitations. For example, Isoplot could not be used outside of Excel, could not be cross-platform (so long as Excel wasn't), could not be embedded in other applications, and only static images could be produced. Nonetheless this software was and still is a powerful tool that has served the community for more than two decades and the trade-offs were more than acceptable. In 2014, we seek to gain flexibility not available with Excel. We propose that the next generation of charting software be reusable, platform-agnostic, and interactive. This new software should allow scientists to easily explore—not just passively view—their data. Beginning in the fall of 2013, researchers at CIRDLES began planning for and prototyping a 21st-century replacement for Isoplot, which we call Topsoil, an anagram of Isoplot. This work is being conducted in the public domain at https://github.com/CIRDLES/topsoil. We welcome and encourage community participation and contributions.

76 FR 32989 - Request for Certification of Compliance-Rural Industrialization Loan and Grant Program

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-07

.../Purpose: The loan, guarantee, or grant application is to obtain financing for infrastructure updates... will be located in Burlington, Iowa. The NAICS industry code for this enterprise is: 311812 (commercial..., Assistant Secretary for Employment and Training. [FR Doc. 2011-13937 Filed 6-6-11; 8:45 am] BILLING CODE...

49 CFR 80.3 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 4974(c) of the Internal Revenue Code of 1986, 26 U.S.C. 4974(c)) that is a qualified institutional buyer; and (2) A governmental plan (as defined in section 414(d) of the Internal Revenue Code of 1986... issued by an obligor and funded by a lender. Local servicer means: (1) A State infrastructure bank...

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chandra, Mani; Gammie, Charles F.; Foucart, Francois, E-mail: manic@illinois.edu, E-mail: gammie@illinois.edu, E-mail: fvfoucart@lbl.gov

Hot, diffuse, relativistic plasmas such as sub-Eddington black-hole accretion flows are expected to be collisionless, yet are commonly modeled as a fluid using ideal general relativistic magnetohydrodynamics (GRMHD). Dissipative effects such as heat conduction and viscosity can be important in a collisionless plasma and will potentially alter the dynamics and radiative properties of the flow from that in ideal fluid models; we refer to models that include these processes as Extended GRMHD. Here we describe a new conservative code, grim, that enables all of the above and additional physics to be efficiently incorporated. grim combines time evolution and primitive variablemore » inversion needed for conservative schemes into a single step using an algorithm that only requires the residuals of the governing equations as inputs. This algorithm enables the code to be physics agnostic as well as flexibility regarding time-stepping schemes. grim runs on CPUs, as well as on GPUs, using the same code. We formulate a performance model and use it to show that our implementation runs optimally on both architectures. grim correctly captures classical GRMHD test problems as well as a new suite of linear and nonlinear test problems with anisotropic conduction and viscosity in special and general relativity. As tests and example applications, we resolve the shock substructure due to the presence of dissipation, and report on relativistic versions of the magneto-thermal instability and heat flux driven buoyancy instability, which arise due to anisotropic heat conduction, and of the firehose instability, which occurs due to anisotropic pressure (i.e., viscosity). Finally, we show an example integration of an accretion flow around a Kerr black hole, using Extended GRMHD.« less

A code inspection process for security reviews

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garzoglio, Gabriele; /Fermilab

2009-05-01

In recent years, it has become more and more evident that software threat communities are taking an increasing interest in Grid infrastructures. To mitigate the security risk associated with the increased numbers of attacks, the Grid software development community needs to scale up effort to reduce software vulnerabilities. This can be achieved by introducing security review processes as a standard project management practice. The Grid Facilities Department of the Fermilab Computing Division has developed a code inspection process, tailored to reviewing security properties of software. The goal of the process is to identify technical risks associated with an application andmore » their impact. This is achieved by focusing on the business needs of the application (what it does and protects), on understanding threats and exploit communities (what an exploiter gains), and on uncovering potential vulnerabilities (what defects can be exploited). The desired outcome of the process is an improvement of the quality of the software artifact and an enhanced understanding of possible mitigation strategies for residual risks. This paper describes the inspection process and lessons learned on applying it to Grid middleware.« less

Volcano Modelling and Simulation gateway (VMSg): A new web-based framework for collaborative research in physical modelling and simulation of volcanic phenomena

NASA Astrophysics Data System (ADS)

Esposti Ongaro, T.; Barsotti, S.; de'Michieli Vitturi, M.; Favalli, M.; Longo, A.; Nannipieri, L.; Neri, A.; Papale, P.; Saccorotti, G.

2009-12-01

Physical and numerical modelling is becoming of increasing importance in volcanology and volcanic hazard assessment. However, new interdisciplinary problems arise when dealing with complex mathematical formulations, numerical algorithms and their implementations on modern computer architectures. Therefore new frameworks are needed for sharing knowledge, software codes, and datasets among scientists. Here we present the Volcano Modelling and Simulation gateway (VMSg, accessible at http://vmsg.pi.ingv.it), a new electronic infrastructure for promoting knowledge growth and transfer in the field of volcanological modelling and numerical simulation. The new web portal, developed in the framework of former and ongoing national and European projects, is based on a dynamic Content Manager System (CMS) and was developed to host and present numerical models of the main volcanic processes and relationships including magma properties, magma chamber dynamics, conduit flow, plume dynamics, pyroclastic flows, lava flows, etc. Model applications, numerical code documentation, simulation datasets as well as model validation and calibration test-cases are also part of the gateway material.

A code inspection process for security reviews

NASA Astrophysics Data System (ADS)

Garzoglio, Gabriele

2010-04-01

In recent years, it has become more and more evident that software threat communities are taking an increasing interest in Grid infrastructures. To mitigate the security risk associated with the increased numbers of attacks, the Grid software development community needs to scale up effort to reduce software vulnerabilities. This can be achieved by introducing security review processes as a standard project management practice. The Grid Facilities Department of the Fermilab Computing Division has developed a code inspection process, tailored to reviewing security properties of software. The goal of the process is to identify technical risks associated with an application and their impact. This is achieved by focusing on the business needs of the application (what it does and protects), on understanding threats and exploit communities (what an exploiter gains), and on uncovering potential vulnerabilities (what defects can be exploited). The desired outcome of the process is an improvement of the quality of the software artifact and an enhanced understanding of possible mitigation strategies for residual risks. This paper describes the inspection process and lessons learned on applying it to Grid middleware.

High-resolution multi-code implementation of unsteady Navier-Stokes flow solver based on paralleled overset adaptive mesh refinement and high-order low-dissipation hybrid schemes

NASA Astrophysics Data System (ADS)

Li, Gaohua; Fu, Xiang; Wang, Fuxin

2017-10-01

The low-dissipation high-order accurate hybrid up-winding/central scheme based on fifth-order weighted essentially non-oscillatory (WENO) and sixth-order central schemes, along with the Spalart-Allmaras (SA)-based delayed detached eddy simulation (DDES) turbulence model, and the flow feature-based adaptive mesh refinement (AMR), are implemented into a dual-mesh overset grid infrastructure with parallel computing capabilities, for the purpose of simulating vortex-dominated unsteady detached wake flows with high spatial resolutions. The overset grid assembly (OGA) process based on collection detection theory and implicit hole-cutting algorithm achieves an automatic coupling for the near-body and off-body solvers, and the error-and-try method is used for obtaining a globally balanced load distribution among the composed multiple codes. The results of flows over high Reynolds cylinder and two-bladed helicopter rotor show that the combination of high-order hybrid scheme, advanced turbulence model, and overset adaptive mesh refinement can effectively enhance the spatial resolution for the simulation of turbulent wake eddies.

A microkernel design for component-based parallel numerical software systems.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Balay, S.

1999-01-13

What is the minimal software infrastructure and what type of conventions are needed to simplify development of sophisticated parallel numerical application codes using a variety of software components that are not necessarily available as source code? We propose an opaque object-based model where the objects are dynamically loadable from the file system or network. The microkernel required to manage such a system needs to include, at most: (1) a few basic services, namely--a mechanism for loading objects at run time via dynamic link libraries, and consistent schemes for error handling and memory management; and (2) selected methods that all objectsmore » share, to deal with object life (destruction, reference counting, relationships), and object observation (viewing, profiling, tracing). We are experimenting with these ideas in the context of extensible numerical software within the ALICE (Advanced Large-scale Integrated Computational Environment) project, where we are building the microkernel to manage the interoperability among various tools for large-scale scientific simulations. This paper presents some preliminary observations and conclusions from our work with microkernel design.« less

Bar Coding and Tracking in Pathology.

PubMed

Hanna, Matthew G; Pantanowitz, Liron

2016-03-01

Bar coding and specimen tracking are intricately linked to pathology workflow and efficiency. In the pathology laboratory, bar coding facilitates many laboratory practices, including specimen tracking, automation, and quality management. Data obtained from bar coding can be used to identify, locate, standardize, and audit specimens to achieve maximal laboratory efficiency and patient safety. Variables that need to be considered when implementing and maintaining a bar coding and tracking system include assets to be labeled, bar code symbologies, hardware, software, workflow, and laboratory and information technology infrastructure as well as interoperability with the laboratory information system. This article addresses these issues, primarily focusing on surgical pathology. Copyright © 2016 Elsevier Inc. All rights reserved.

Bar Coding and Tracking in Pathology.

PubMed

Hanna, Matthew G; Pantanowitz, Liron

2015-06-01

Bar coding and specimen tracking are intricately linked to pathology workflow and efficiency. In the pathology laboratory, bar coding facilitates many laboratory practices, including specimen tracking, automation, and quality management. Data obtained from bar coding can be used to identify, locate, standardize, and audit specimens to achieve maximal laboratory efficiency and patient safety. Variables that need to be considered when implementing and maintaining a bar coding and tracking system include assets to be labeled, bar code symbologies, hardware, software, workflow, and laboratory and information technology infrastructure as well as interoperability with the laboratory information system. This article addresses these issues, primarily focusing on surgical pathology. Copyright © 2015 Elsevier Inc. All rights reserved.

Wanted: More Squares Among Professors

ERIC Educational Resources Information Center

Fisher, William H.

1969-01-01

Professors who see the world and life in a context of sincerely held religious beliefs should be given the same tolerance and understanding which atheists and agnostics used to demand for themselves. (AD)

DOE Office of Scientific and Technical Information (OSTI.GOV)

O'Malley, Kathleen; Lopez, Hugo; Cairns, Julie

An overview of the main North American codes and standards associated with hydrogen safety sensors is provided. The distinction between a code and a standard is defined, and the relationship between standards and codes is clarified, especially for those circumstances where a standard or a certification requirement is explicitly referenced within a code. The report identifies three main types of standards commonly applied to hydrogen sensors (interface and controls standards, shock and hazard standards, and performance-based standards). The certification process and a list and description of the main standards and model codes associated with the use of hydrogen safety sensorsmore » in hydrogen infrastructure are presented.« less

Dynamic VM Provisioning for TORQUE in a Cloud Environment

NASA Astrophysics Data System (ADS)

Zhang, S.; Boland, L.; Coddington, P.; Sevior, M.

2014-06-01

Cloud computing, also known as an Infrastructure-as-a-Service (IaaS), is attracting more interest from the commercial and educational sectors as a way to provide cost-effective computational infrastructure. It is an ideal platform for researchers who must share common resources but need to be able to scale up to massive computational requirements for specific periods of time. This paper presents the tools and techniques developed to allow the open source TORQUE distributed resource manager and Maui cluster scheduler to dynamically integrate OpenStack cloud resources into existing high throughput computing clusters.

VMEbus based computer and real-time UNIX as infrastructure of DAQ

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yasu, Y.; Fujii, H.; Nomachi, M.

1994-12-31

This paper describes what the authors have constructed as the infrastructure of data acquisition system (DAQ). The paper reports recent developments concerned with HP VME board computer with LynxOS (HP742rt/HP-RT) and Alpha/OSF1 with VMEbus adapter. The paper also reports current status of developing a Benchmark Suite for Data Acquisition (DAQBENCH) for measuring not only the performance of VME/CAMAC access but also that of the context switching, the inter-process communications and so on, for various computers including Workstation-based systems and VME board computers.

The Five 'R's' for Developing Trusted Software Frameworks to increase confidence in, and maximise reuse of, Open Source Software.

NASA Astrophysics Data System (ADS)

Fraser, Ryan; Gross, Lutz; Wyborn, Lesley; Evans, Ben; Klump, Jens

2015-04-01

Recent investments in HPC, cloud and Petascale data stores, have dramatically increased the scale and resolution that earth science challenges can now be tackled. These new infrastructures are highly parallelised and to fully utilise them and access the large volumes of earth science data now available, a new approach to software stack engineering needs to be developed. The size, complexity and cost of the new infrastructures mean any software deployed has to be reliable, trusted and reusable. Increasingly software is available via open source repositories, but these usually only enable code to be discovered and downloaded. As a user it is hard for a scientist to judge the suitability and quality of individual codes: rarely is there information on how and where codes can be run, what the critical dependencies are, and in particular, on the version requirements and licensing of the underlying software stack. A trusted software framework is proposed to enable reliable software to be discovered, accessed and then deployed on multiple hardware environments. More specifically, this framework will enable those who generate the software, and those who fund the development of software, to gain credit for the effort, IP, time and dollars spent, and facilitate quantification of the impact of individual codes. For scientific users, the framework delivers reviewed and benchmarked scientific software with mechanisms to reproduce results. The trusted framework will have five separate, but connected components: Register, Review, Reference, Run, and Repeat. 1) The Register component will facilitate discovery of relevant software from multiple open source code repositories. The registration process of the code should include information about licensing, hardware environments it can be run on, define appropriate validation (testing) procedures and list the critical dependencies. 2) The Review component is targeting on the verification of the software typically against a set of benchmark cases. This will be achieved by linking the code in the software framework to peer review forums such as Mozilla Science or appropriate Journals (e.g. Geoscientific Model Development Journal) to assist users to know which codes to trust. 3) Referencing will be accomplished by linking the Software Framework to groups such as Figshare or ImpactStory that help disseminate and measure the impact of scientific research, including program code. 4) The Run component will draw on information supplied in the registration process, benchmark cases described in the review and relevant information to instantiate the scientific code on the selected environment. 5) The Repeat component will tap into existing Provenance Workflow engines that will automatically capture information that relate to a particular run of that software, including identification of all input and output artefacts, and all elements and transactions within that workflow. The proposed trusted software framework will enable users to rapidly discover and access reliable code, reduce the time to deploy it and greatly facilitate sharing, reuse and reinstallation of code. Properly designed it could enable an ability to scale out to massively parallel systems and be accessed nationally/ internationally for multiple use cases, including Supercomputer centres, cloud facilities, and local computers.

Technography and Design-Actuality Gap-Analysis of Internet Computer Technologies-Assisted Education: Western Expectations and Global Education

ERIC Educational Resources Information Center

Greenhalgh-Spencer, Heather; Jerbi, Moja

2017-01-01

In this paper, we provide a design-actuality gap-analysis of the internet infrastructure that exists in developing nations and nations in the global South with the deployed internet computer technologies (ICT)-assisted programs that are designed to use internet infrastructure to provide educational opportunities. Programs that specifically…

Closing the Gap: Cybersecurity for U.S. Forces and Commands

DTIC Science & Technology

2017-03-30

Dickson, Ph.D. Professor of Military Studies , JAWS Thesis Advisor Kevin Therrien, Col, USAF Committee Member Stephen Rogers, Colonel, USA Director...infrastructures, and includes the Internet, telecommunications networks, computer systems, and embedded processors and controllers in critical industries.”5...of information technology infrastructures, including the Internet, telecommunications networks, computer systems, and embedded processors and

cual-id: Globally Unique, Correctable, and Human-Friendly Sample Identifiers for Comparative Omics Studies.

PubMed

Chase, John H; Bolyen, Evan; Rideout, Jai Ram; Caporaso, J Gregory

2016-01-01

The number of samples in high-throughput comparative "omics" studies is increasing rapidly due to declining experimental costs. To keep sample data and metadata manageable and to ensure the integrity of scientific results as the scale of these projects continues to increase, it is essential that we transition to better-designed sample identifiers. Ideally, sample identifiers should be globally unique across projects, project teams, and institutions; short (to facilitate manual transcription); correctable with respect to common types of transcription errors; opaque, meaning that they do not contain information about the samples; and compatible with existing standards. We present cual-id, a lightweight command line tool that creates, or mints, sample identifiers that meet these criteria without reliance on centralized infrastructure. cual-id allows users to assign universally unique identifiers, or UUIDs, that are globally unique to their samples. UUIDs are too long to be conveniently written on sampling materials, such as swabs or microcentrifuge tubes, however, so cual-id additionally generates human-friendly 4- to 12-character identifiers that map to their UUIDs and are unique within a project. By convention, we use "cual-id" to refer to the software, "CualID" to refer to the short, human-friendly identifiers, and "UUID" to refer to the globally unique identifiers. CualIDs are used by humans when they manually write or enter identifiers, while the longer UUIDs are used by computers to unambiguously reference a sample. Finally, cual-id optionally generates printable label sticker sheets containing Code 128 bar codes and CualIDs for labeling of sample collection and processing materials. IMPORTANCE The adoption of identifiers that are globally unique, correctable, and easily handwritten or manually entered into a computer will be a major step forward for sample tracking in comparative omics studies. As the fields transition to more-centralized sample management, for example, across labs within an institution, across projects funded under a common program, or in systems designed to facilitate meta- and/or integrated analysis, sample identifiers generated with cual-id will not need to change; thus, costly and error-prone updating of data and metadata identifiers will be avoided. Further, using cual-id will ensure that transcription errors in sample identifiers do not require the discarding of otherwise-useful samples that may have been expensive to obtain. Finally, cual-id is simple to install and use and is free for all use. No centralized infrastructure is required to ensure global uniqueness, so it is feasible for any lab to get started using these identifiers within their existing infrastructure.

The National Information Infrastructure: Agenda for Action.

ERIC Educational Resources Information Center

Department of Commerce, Washington, DC. Information Infrastructure Task Force.

The National Information Infrastructure (NII) is planned as a web of communications networks, computers, databases, and consumer electronics that will put vast amounts of information at the users' fingertips. Private sector firms are beginning to develop this infrastructure, but essential roles remain for the Federal Government. The National…

The virtual machine (VM) scaler: an infrastructure manager supporting environmental modeling on IaaS clouds

USDA-ARS?s Scientific Manuscript database

Infrastructure-as-a-service (IaaS) clouds provide a new medium for deployment of environmental modeling applications. Harnessing advancements in virtualization, IaaS clouds can provide dynamic scalable infrastructure to better support scientific modeling computational demands. Providing scientific m...

Helix Nebula: Enabling federation of existing data infrastructures and data services to an overarching cross-domain e-infrastructure

NASA Astrophysics Data System (ADS)

Lengert, Wolfgang; Farres, Jordi; Lanari, Riccardo; Casu, Francesco; Manunta, Michele; Lassalle-Balier, Gerard

2014-05-01

Helix Nebula has established a growing public private partnership of more than 30 commercial cloud providers, SMEs, and publicly funded research organisations and e-infrastructures. The Helix Nebula strategy is to establish a federated cloud service across Europe. Three high-profile flagships, sponsored by CERN (high energy physics), EMBL (life sciences) and ESA/DLR/CNES/CNR (earth science), have been deployed and extensively tested within this federated environment. The commitments behind these initial flagships have created a critical mass that attracts suppliers and users to the initiative, to work together towards an "Information as a Service" market place. Significant progress in implementing the following 4 programmatic goals (as outlined in the strategic Plan Ref.1) has been achieved: × Goal #1 Establish a Cloud Computing Infrastructure for the European Research Area (ERA) serving as a platform for innovation and evolution of the overall infrastructure. × Goal #2 Identify and adopt suitable policies for trust, security and privacy on a European-level can be provided by the European Cloud Computing framework and infrastructure. × Goal #3 Create a light-weight governance structure for the future European Cloud Computing Infrastructure that involves all the stakeholders and can evolve over time as the infrastructure, services and user-base grows. × Goal #4 Define a funding scheme involving the three stake-holder groups (service suppliers, users, EC and national funding agencies) into a Public-Private-Partnership model to implement a Cloud Computing Infrastructure that delivers a sustainable business environment adhering to European level policies. Now in 2014 a first version of this generic cross-domain e-infrastructure is ready to go into operations building on federation of European industry and contributors (data, tools, knowledge, ...). This presentation describes how Helix Nebula is being used in the domain of earth science focusing on geohazards. The so called "Supersite Exploitation Platform" (SSEP) provides scientists an overarching federated e-infrastructure with a very fast access to (i) large volume of data (EO/non-space data), (ii) computing resources (e.g. hybrid cloud/grid), (iii) processing software (e.g. toolboxes, RTMs, retrieval baselines, visualization routines), and (iv) general platform capabilities (e.g. user management and access control, accounting, information portal, collaborative tools, social networks etc.). In this federation each data provider remains in full control of the implementation of its data policy. This presentation outlines the Architecture (technical and services) supporting very heterogeneous science domains as well as the procedures for new-comers to join the Helix Nebula Market Place. Ref.1 http://cds.cern.ch/record/1374172/files/CERN-OPEN-2011-036.pdf

The Computing and Data Grid Approach: Infrastructure for Distributed Science Applications

NASA Technical Reports Server (NTRS)

Johnston, William E.

2002-01-01

With the advent of Grids - infrastructure for using and managing widely distributed computing and data resources in the science environment - there is now an opportunity to provide a standard, large-scale, computing, data, instrument, and collaboration environment for science that spans many different projects and provides the required infrastructure and services in a relatively uniform and supportable way. Grid technology has evolved over the past several years to provide the services and infrastructure needed for building 'virtual' systems and organizations. We argue that Grid technology provides an excellent basis for the creation of the integrated environments that can combine the resources needed to support the large- scale science projects located at multiple laboratories and universities. We present some science case studies that indicate that a paradigm shift in the process of science will come about as a result of Grids providing transparent and secure access to advanced and integrated information and technologies infrastructure: powerful computing systems, large-scale data archives, scientific instruments, and collaboration tools. These changes will be in the form of services that can be integrated with the user's work environment, and that enable uniform and highly capable access to these computers, data, and instruments, regardless of the location or exact nature of these resources. These services will integrate transient-use resources like computing systems, scientific instruments, and data caches (e.g., as they are needed to perform a simulation or analyze data from a single experiment); persistent-use resources. such as databases, data catalogues, and archives, and; collaborators, whose involvement will continue for the lifetime of a project or longer. While we largely address large-scale science in this paper, Grids, particularly when combined with Web Services, will address a broad spectrum of science scenarios. both large and small scale.

Genetic Constructor: An Online DNA Design Platform.

PubMed

Bates, Maxwell; Lachoff, Joe; Meech, Duncan; Zulkower, Valentin; Moisy, Anaïs; Luo, Yisha; Tekotte, Hille; Franziska Scheitz, Cornelia Johanna; Khilari, Rupal; Mazzoldi, Florencio; Chandran, Deepak; Groban, Eli

2017-12-15

Genetic Constructor is a cloud Computer Aided Design (CAD) application developed to support synthetic biologists from design intent through DNA fabrication and experiment iteration. The platform allows users to design, manage, and navigate complex DNA constructs and libraries, using a new visual language that focuses on functional parts abstracted from sequence. Features like combinatorial libraries and automated primer design allow the user to separate design from construction by focusing on functional intent, and design constraints aid iterative refinement of designs. A plugin architecture enables contributions from scientists and coders to leverage existing powerful software and connect to DNA foundries. The software is easily accessible and platform agnostic, free for academics, and available in an open-source community edition. Genetic Constructor seeks to democratize DNA design, manufacture, and access to tools and services from the synthetic biology community.

Astrophysics Source Code Library -- Now even better!

NASA Astrophysics Data System (ADS)

Allen, Alice; Schmidt, Judy; Berriman, Bruce; DuPrie, Kimberly; Hanisch, Robert J.; Mink, Jessica D.; Nemiroff, Robert J.; Shamir, Lior; Shortridge, Keith; Taylor, Mark B.; Teuben, Peter J.; Wallin, John F.

2015-01-01

The Astrophysics Source Code Library (ASCL, ascl.net) is a free online registry of codes used in astronomy research. Indexed by ADS, it now contains nearly 1,000 codes and with recent major changes, is better than ever! The resource has a new infrastructure that offers greater flexibility and functionality for users, including an easier submission process, better browsing, one-click author search, and an RSS feeder for news. The new database structure is easier to maintain and offers new possibilities for collaboration. Come see what we've done!

Autonomic Management of Application Workflows on Hybrid Computing Infrastructure

DOE PAGES

Kim, Hyunjoo; el-Khamra, Yaakoub; Rodero, Ivan; ...

2011-01-01

In this paper, we present a programming and runtime framework that enables the autonomic management of complex application workflows on hybrid computing infrastructures. The framework is designed to address system and application heterogeneity and dynamics to ensure that application objectives and constraints are satisfied. The need for such autonomic system and application management is becoming critical as computing infrastructures become increasingly heterogeneous, integrating different classes of resources from high-end HPC systems to commodity clusters and clouds. For example, the framework presented in this paper can be used to provision the appropriate mix of resources based on application requirements and constraints.more » The framework also monitors the system/application state and adapts the application and/or resources to respond to changing requirements or environment. To demonstrate the operation of the framework and to evaluate its ability, we employ a workflow used to characterize an oil reservoir executing on a hybrid infrastructure composed of TeraGrid nodes and Amazon EC2 instances of various types. Specifically, we show how different applications objectives such as acceleration, conservation and resilience can be effectively achieved while satisfying deadline and budget constraints, using an appropriate mix of dynamically provisioned resources. Our evaluations also demonstrate that public clouds can be used to complement and reinforce the scheduling and usage of traditional high performance computing infrastructure.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Marquez, Andres; Manzano Franco, Joseph B.; Song, Shuaiwen

With Exascale performance and its challenges in mind, one ubiquitous concern among architects is energy efficiency. Petascale systems projected to Exascale systems are unsustainable at current power consumption rates. One major contributor to system-wide power consumption is the number of memory operations leading to data movement and management techniques applied by the runtime system. To address this problem, we present the concept of the Architected Composite Data Types (ACDT) framework. The framework is made aware of data composites, assigning them a specific layout, transformations and operators. Data manipulation overhead is amortized over a larger number of elements and program performancemore » and power efficiency can be significantly improved. We developed the fundamentals of an ACDT framework on a massively multithreaded adaptive runtime system geared towards Exascale clusters. Showcasing the capability of ACDT, we exercised the framework with two representative processing kernels - Matrix Vector Multiply and the Cholesky Decomposition – applied to sparse matrices. As transformation modules, we applied optimized compress/decompress engines and configured invariant operators for maximum energy/performance efficiency. Additionally, we explored two different approaches based on transformation opaqueness in relation to the application. Under the first approach, the application is agnostic to compression and decompression activity. Such approach entails minimal changes to the original application code, but leaves out potential applicationspecific optimizations. The second approach exposes the decompression process to the application, hereby exposing optimization opportunities that can only be exploited with application knowledge. The experimental results show that the two approaches have their strengths in HW and SW respectively, where the SW approach can yield performance and power improvements that are an order of magnitude better than ACDT-oblivious, hand-optimized implementations.We consider the ACDT runtime framework an important component of compute nodes that will lead towards power efficient Exascale clusters.« less

32 CFR 153.4 - Responsibilities.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Code. (3) Coordinate the assistance to be provided the Department of Defense with the U.S. Attorney's... logistical support, available resources, appropriate personnel, or the communications infrastructure...

Integration of Cloud resources in the LHCb Distributed Computing

NASA Astrophysics Data System (ADS)

Úbeda García, Mario; Méndez Muñoz, Víctor; Stagni, Federico; Cabarrou, Baptiste; Rauschmayr, Nathalie; Charpentier, Philippe; Closier, Joel

2014-06-01

This contribution describes how Cloud resources have been integrated in the LHCb Distributed Computing. LHCb is using its specific Dirac extension (LHCbDirac) as an interware for its Distributed Computing. So far, it was seamlessly integrating Grid resources and Computer clusters. The cloud extension of DIRAC (VMDIRAC) allows the integration of Cloud computing infrastructures. It is able to interact with multiple types of infrastructures in commercial and institutional clouds, supported by multiple interfaces (Amazon EC2, OpenNebula, OpenStack and CloudStack) - instantiates, monitors and manages Virtual Machines running on this aggregation of Cloud resources. Moreover, specifications for institutional Cloud resources proposed by Worldwide LHC Computing Grid (WLCG), mainly by the High Energy Physics Unix Information Exchange (HEPiX) group, have been taken into account. Several initiatives and computing resource providers in the eScience environment have already deployed IaaS in production during 2013. Keeping this on mind, pros and cons of a cloud based infrasctructure have been studied in contrast with the current setup. As a result, this work addresses four different use cases which represent a major improvement on several levels of our infrastructure. We describe the solution implemented by LHCb for the contextualisation of the VMs based on the idea of Cloud Site. We report on operational experience of using in production several institutional Cloud resources that are thus becoming integral part of the LHCb Distributed Computing resources. Furthermore, we describe as well the gradual migration of our Service Infrastructure towards a fully distributed architecture following the Service as a Service (SaaS) model.

Kingdom-agnostic Metagenomics and the Importance of Complete Characterization of Enteric Microbial Communities

PubMed Central

Norman, Jason M.; Handley, Scott A.; Virgin, Herbert W.

2014-01-01

Advanced sequencing techniques have shown that bacteria are not the only complex and important microbes in the human intestine. Non-bacterial organisms, particularly the virome and the mycobiome, are important regulators of intestinal immunity and inflammation. The virome is mucosal and systemic; it can alter the host response to bacteria and interact with host genes and bacteria to contribute to disease pathogenesis. The human mycobiome is also complex and can contribute to intestinal inflammation. We review what has recently been learned about the non-bacterial and non-archaeal microbes in the gastrointestinal tract, discussing their potential effects on health and disease and analytical approaches for their study. Studies of associations between the microbiome and intestinal pathology should incorporate kingdom-agnostic approaches if we are to fully understand intestinal health and disease. PMID:24508599

Sharing environmental models: An Approach using GitHub repositories and Web Processing Services

NASA Astrophysics Data System (ADS)

Stasch, Christoph; Nuest, Daniel; Pross, Benjamin

2016-04-01

The GLUES (Global Assessment of Land Use Dynamics, Greenhouse Gas Emissions and Ecosystem Services) project established a spatial data infrastructure for scientific geospatial data and metadata (http://geoportal-glues.ufz.de), where different regional collaborative projects researching the impacts of climate and socio-economic changes on sustainable land management can share their underlying base scenarios and datasets. One goal of the project is to ease the sharing of computational models between institutions and to make them easily executable in Web-based infrastructures. In this work, we present such an approach for sharing computational models relying on GitHub repositories (http://github.com) and Web Processing Services. At first, model providers upload their model implementations to GitHub repositories in order to share them with others. The GitHub platform allows users to submit changes to the model code. The changes can be discussed and reviewed before merging them. However, while GitHub allows sharing and collaborating of model source code, it does not actually allow running these models, which requires efforts to transfer the implementation to a model execution framework. We thus have extended an existing implementation of the OGC Web Processing Service standard (http://www.opengeospatial.org/standards/wps), the 52°North Web Processing Service (http://52north.org/wps) platform to retrieve all model implementations from a git (http://git-scm.com) repository and add them to the collection of published geoprocesses. The current implementation is restricted to models implemented as R scripts using WPS4R annotations (Hinz et al.) and to Java algorithms using the 52°North WPS Java API. The models hence become executable through a standardized Web API by multiple clients such as desktop or browser GIS and modelling frameworks. If the model code is changed on the GitHub platform, the changes are retrieved by the service and the processes will be updated accordingly. The admin tool of the 52°North WPS was extended to support automated retrieval and deployment of computational models from GitHub repositories. Once the R code is available in the GitHub repo, the contained process can be easily deployed and executed by simply defining the GitHub repository URL in the WPS admin tool. We illustrate the usage of the approach by sharing and running a model for land use system archetypes developed by the Helmholtz Centre for Environmental Research (UFZ, see Vaclavik et al.). The original R code was extended and published in the 52°North WPS using both, public and non-public datasets (Nüst et al., see also https://github.com/52North/glues-wps). Hosting the analysis in a Git repository now allows WPS administrators, client developers, and modelers to easily work together on new versions or completely new web processes using the powerful GitHub collaboration platform. References: Hinz, M. et. al. (2013): Spatial Statistics on the Geospatial Web. In: The 16th AGILE International Conference on Geographic Information Science, Short Papers. http://www.agile-online.org/Conference_Paper/CDs/agile_2013/Short_Papers/SP_S3.1_Hinz.pdf Nüst, D. et. al.: (2015): Open and reproducible global land use classification. In: EGU General Assembly Conference Abstracts . Vol. 17. European Geophysical Union, 2015, p. 9125, http://meetingorganizer.copernicus. org/EGU2015/EGU2015- 9125.pdf Vaclavik, T., et. al. (2013): Mapping global land system archetypes. Global Environmental Change 23(6): 1637-1647. Online available: October 9, 2013, DOI: 10.1016/j.gloenvcha.2013.09.004

76 FR 27622 - Approval and Promulgation of State Implementation Plan Revisions; Infrastructure Requirements for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-12

...), Region 8, Mail Code 8P-AR, 1595 Wynkoop Street, Denver, Colorado 80202-1129. Hand Delivery: Director, Air Program, Environmental Protection Agency (EPA), Region 8, Mail Code 8P-AR, 1595 Wynkoop Street, Denver..., Denver, Colorado 80202-1129. EPA requests that if at all possible, you contact the individual listed in...

A Grid Infrastructure for Supporting Space-based Science Operations

NASA Technical Reports Server (NTRS)

Bradford, Robert N.; Redman, Sandra H.; McNair, Ann R. (Technical Monitor)

2002-01-01

Emerging technologies for computational grid infrastructures have the potential for revolutionizing the way computers are used in all aspects of our lives. Computational grids are currently being implemented to provide a large-scale, dynamic, and secure research and engineering environments based on standards and next-generation reusable software, enabling greater science and engineering productivity through shared resources and distributed computing for less cost than traditional architectures. Combined with the emerging technologies of high-performance networks, grids provide researchers, scientists and engineers the first real opportunity for an effective distributed collaborative environment with access to resources such as computational and storage systems, instruments, and software tools and services for the most computationally challenging applications.

The Overshoot Phenomenon in Geodynamics Codes

NASA Astrophysics Data System (ADS)

Kommu, R. K.; Heien, E. M.; Kellogg, L. H.; Bangerth, W.; Heister, T.; Studley, E. H.

2013-12-01

The overshoot phenomenon is a common occurrence in numerical software when a continuous function on a finite dimensional discretized space is used to approximate a discontinuous jump, in temperature and material concentration, for example. The resulting solution overshoots, and undershoots, the discontinuous jump. Numerical simulations play an extremely important role in mantle convection research. This is both due to the strong temperature and stress dependence of viscosity and also due to the inaccessibility of deep earth. Under these circumstances, it is essential that mantle convection simulations be extremely accurate and reliable. CitcomS and ASPECT are two finite element based mantle convection simulations developed and maintained by the Computational Infrastructure for Geodynamics. CitcomS is a finite element based mantle convection code that is designed to run on multiple high-performance computing platforms. ASPECT, an adaptive mesh refinement (AMR) code built on the Deal.II library, is also a finite element based mantle convection code that scales well on various HPC platforms. CitcomS and ASPECT both exhibit the overshoot phenomenon. One attempt at controlling the overshoot uses the Entropy Viscosity method, which introduces an artificial diffusion term in the energy equation of mantle convection. This artificial diffusion term is small where the temperature field is smooth. We present results from CitcomS and ASPECT that quantify the effect of the Entropy Viscosity method in reducing the overshoot phenomenon. In the discontinuous Galerkin (DG) finite element method, the test functions used in the method are continuous within each element but are discontinuous across inter-element boundaries. The solution space in the DG method is discontinuous. FEniCS is a collection of free software tools that automate the solution of differential equations using finite element methods. In this work we also present results from a finite element mantle convection simulation implemented in FEniCS that investigates the effect of using DG elements in reducing the overshoot problem.

Do the Right Thing.

ERIC Educational Resources Information Center

Salopek, Jennifer J.

2001-01-01

An effective ethics program can enhance an organization's recruitment and retention, work environment, and reputation. Values statements and codes of conduct are the infrastructure of an effective program. (JOW)

High-Performance Java Codes for Computational Fluid Dynamics

NASA Technical Reports Server (NTRS)

Riley, Christopher; Chatterjee, Siddhartha; Biswas, Rupak; Biegel, Bryan (Technical Monitor)

2001-01-01

The computational science community is reluctant to write large-scale computationally -intensive applications in Java due to concerns over Java's poor performance, despite the claimed software engineering advantages of its object-oriented features. Naive Java implementations of numerical algorithms can perform poorly compared to corresponding Fortran or C implementations. To achieve high performance, Java applications must be designed with good performance as a primary goal. This paper presents the object-oriented design and implementation of two real-world applications from the field of Computational Fluid Dynamics (CFD): a finite-volume fluid flow solver (LAURA, from NASA Langley Research Center), and an unstructured mesh adaptation algorithm (2D_TAG, from NASA Ames Research Center). This work builds on our previous experience with the design of high-performance numerical libraries in Java. We examine the performance of the applications using the currently available Java infrastructure and show that the Java version of the flow solver LAURA performs almost within a factor of 2 of the original procedural version. Our Java version of the mesh adaptation algorithm 2D_TAG performs within a factor of 1.5 of its original procedural version on certain platforms. Our results demonstrate that object-oriented software design principles are not necessarily inimical to high performance.

Leveraging the Power of High Performance Computing for Next Generation Sequencing Data Analysis: Tricks and Twists from a High Throughput Exome Workflow

PubMed Central

Wonczak, Stephan; Thiele, Holger; Nieroda, Lech; Jabbari, Kamel; Borowski, Stefan; Sinha, Vishal; Gunia, Wilfried; Lang, Ulrich; Achter, Viktor; Nürnberg, Peter

2015-01-01

Next generation sequencing (NGS) has been a great success and is now a standard method of research in the life sciences. With this technology, dozens of whole genomes or hundreds of exomes can be sequenced in rather short time, producing huge amounts of data. Complex bioinformatics analyses are required to turn these data into scientific findings. In order to run these analyses fast, automated workflows implemented on high performance computers are state of the art. While providing sufficient compute power and storage to meet the NGS data challenge, high performance computing (HPC) systems require special care when utilized for high throughput processing. This is especially true if the HPC system is shared by different users. Here, stability, robustness and maintainability are as important for automated workflows as speed and throughput. To achieve all of these aims, dedicated solutions have to be developed. In this paper, we present the tricks and twists that we utilized in the implementation of our exome data processing workflow. It may serve as a guideline for other high throughput data analysis projects using a similar infrastructure. The code implementing our solutions is provided in the supporting information files. PMID:25942438

A framework to evaluate the effects of small area variations in healthcare infrastructure on diagnostics and patient outcomes of rare diseases based on administrative data.

PubMed

Stargardt, Tom; Schreyögg, Jonas

2012-05-01

Small area variations in healthcare infrastructure may result in differences in early detection and outcomes for patients with rare diseases. It is our aim to provide a framework for evaluating small area variations in healthcare infrastructure on the diagnostics and health outcomes of rare diseases. We focus on administrative data as it allows (a) for relatively large sample sizes even though the prevalence of rare diseases is very low, and (b) makes it possible to link information on healthcare infrastructure to morbidity, mortality, and utilization. For identifying patients with a rare disease in a database, a combination of different classification systems has to be used due to usually multiple diseases sharing one ICD code. Outcomes should be chosen that are (a) appropriate for the disease, (b) identifiable and reliably coded in the administrative database, and (c) observable during the limited time period of the follow-up. Risk adjustment using summary scores of disease-specific or comprehensive risk adjustment instruments might be preferable over empirical weights because of the lower number of variables needed. The proposed framework will help to identify differences in time to diagnosis and treatment outcomes across areas in the context of rare diseases. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Results of comparative RBMK neutron computation using VNIIEF codes (cell computation, 3D statics, 3D kinetics). Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grebennikov, A.N.; Zhitnik, A.K.; Zvenigorodskaya, O.A.

1995-12-31

In conformity with the protocol of the Workshop under Contract {open_quotes}Assessment of RBMK reactor safety using modern Western Codes{close_quotes} VNIIEF performed a neutronics computation series to compare western and VNIIEF codes and assess whether VNIIEF codes are suitable for RBMK type reactor safety assessment computation. The work was carried out in close collaboration with M.I. Rozhdestvensky and L.M. Podlazov, NIKIET employees. The effort involved: (1) cell computations with the WIMS, EKRAN codes (improved modification of the LOMA code) and the S-90 code (VNIIEF Monte Carlo). Cell, polycell, burnup computation; (2) 3D computation of static states with the KORAT-3D and NEUmore » codes and comparison with results of computation with the NESTLE code (USA). The computations were performed in the geometry and using the neutron constants presented by the American party; (3) 3D computation of neutron kinetics with the KORAT-3D and NEU codes. These computations were performed in two formulations, both being developed in collaboration with NIKIET. Formulation of the first problem maximally possibly agrees with one of NESTLE problems and imitates gas bubble travel through a core. The second problem is a model of the RBMK as a whole with imitation of control and protection system controls (CPS) movement in a core.« less

Network Computing Infrastructure to Share Tools and Data in Global Nuclear Energy Partnership

NASA Astrophysics Data System (ADS)

Kim, Guehee; Suzuki, Yoshio; Teshima, Naoya

CCSE/JAEA (Center for Computational Science and e-Systems/Japan Atomic Energy Agency) integrated a prototype system of a network computing infrastructure for sharing tools and data to support the U.S. and Japan collaboration in GNEP (Global Nuclear Energy Partnership). We focused on three technical issues to apply our information process infrastructure, which are accessibility, security, and usability. In designing the prototype system, we integrated and improved both network and Web technologies. For the accessibility issue, we adopted SSL-VPN (Security Socket Layer-Virtual Private Network) technology for the access beyond firewalls. For the security issue, we developed an authentication gateway based on the PKI (Public Key Infrastructure) authentication mechanism to strengthen the security. Also, we set fine access control policy to shared tools and data and used shared key based encryption method to protect tools and data against leakage to third parties. For the usability issue, we chose Web browsers as user interface and developed Web application to provide functions to support sharing tools and data. By using WebDAV (Web-based Distributed Authoring and Versioning) function, users can manipulate shared tools and data through the Windows-like folder environment. We implemented the prototype system in Grid infrastructure for atomic energy research: AEGIS (Atomic Energy Grid Infrastructure) developed by CCSE/JAEA. The prototype system was applied for the trial use in the first period of GNEP.

Geospatial-enabled Data Exploration and Computation through Data Infrastructure Building Blocks

NASA Astrophysics Data System (ADS)

Song, C. X.; Biehl, L. L.; Merwade, V.; Villoria, N.

2015-12-01

Geospatial data are present everywhere today with the proliferation of location-aware computing devices and sensors. This is especially true in the scientific community where large amounts of data are driving research and education activities in many domains. Collaboration over geospatial data, for example, in modeling, data analysis and visualization, must still overcome the barriers of specialized software and expertise among other challenges. The GABBs project aims at enabling broader access to geospatial data exploration and computation by developing spatial data infrastructure building blocks that leverage capabilities of end-to-end application service and virtualized computing framework in HUBzero. Funded by NSF Data Infrastructure Building Blocks (DIBBS) initiative, GABBs provides a geospatial data architecture that integrates spatial data management, mapping and visualization and will make it available as open source. The outcome of the project will enable users to rapidly create tools and share geospatial data and tools on the web for interactive exploration of data without requiring significant software development skills, GIS expertise or IT administrative privileges. This presentation will describe the development of geospatial data infrastructure building blocks and the scientific use cases that help drive the software development, as well as seek feedback from the user communities.

Cloud Bursting with GlideinWMS: Means to satisfy ever increasing computing needs for Scientific Workflows

NASA Astrophysics Data System (ADS)

Mhashilkar, Parag; Tiradani, Anthony; Holzman, Burt; Larson, Krista; Sfiligoi, Igor; Rynge, Mats

2014-06-01

Scientific communities have been in the forefront of adopting new technologies and methodologies in the computing. Scientific computing has influenced how science is done today, achieving breakthroughs that were impossible to achieve several decades ago. For the past decade several such communities in the Open Science Grid (OSG) and the European Grid Infrastructure (EGI) have been using GlideinWMS to run complex application workflows to effectively share computational resources over the grid. GlideinWMS is a pilot-based workload management system (WMS) that creates on demand, a dynamically sized overlay HTCondor batch system on grid resources. At present, the computational resources shared over the grid are just adequate to sustain the computing needs. We envision that the complexity of the science driven by "Big Data" will further push the need for computational resources. To fulfill their increasing demands and/or to run specialized workflows, some of the big communities like CMS are investigating the use of cloud computing as Infrastructure-As-A-Service (IAAS) with GlideinWMS as a potential alternative to fill the void. Similarly, communities with no previous access to computing resources can use GlideinWMS to setup up a batch system on the cloud infrastructure. To enable this, the architecture of GlideinWMS has been extended to enable support for interfacing GlideinWMS with different Scientific and commercial cloud providers like HLT, FutureGrid, FermiCloud and Amazon EC2. In this paper, we describe a solution for cloud bursting with GlideinWMS. The paper describes the approach, architectural changes and lessons learned while enabling support for cloud infrastructures in GlideinWMS.

Cloud Bursting with GlideinWMS: Means to satisfy ever increasing computing needs for Scientific Workflows

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mhashilkar, Parag; Tiradani, Anthony; Holzman, Burt

Scientific communities have been in the forefront of adopting new technologies and methodologies in the computing. Scientific computing has influenced how science is done today, achieving breakthroughs that were impossible to achieve several decades ago. For the past decade several such communities in the Open Science Grid (OSG) and the European Grid Infrastructure (EGI) have been using GlideinWMS to run complex application workflows to effectively share computational resources over the grid. GlideinWMS is a pilot-based workload management system (WMS) that creates on demand, a dynamically sized overlay HTCondor batch system on grid resources. At present, the computational resources shared overmore » the grid are just adequate to sustain the computing needs. We envision that the complexity of the science driven by 'Big Data' will further push the need for computational resources. To fulfill their increasing demands and/or to run specialized workflows, some of the big communities like CMS are investigating the use of cloud computing as Infrastructure-As-A-Service (IAAS) with GlideinWMS as a potential alternative to fill the void. Similarly, communities with no previous access to computing resources can use GlideinWMS to setup up a batch system on the cloud infrastructure. To enable this, the architecture of GlideinWMS has been extended to enable support for interfacing GlideinWMS with different Scientific and commercial cloud providers like HLT, FutureGrid, FermiCloud and Amazon EC2. In this paper, we describe a solution for cloud bursting with GlideinWMS. The paper describes the approach, architectural changes and lessons learned while enabling support for cloud infrastructures in GlideinWMS.« less

Computational Support for Technology- Investment Decisions

NASA Technical Reports Server (NTRS)

Adumitroaie, Virgil; Hua, Hook; Lincoln, William; Block, Gary; Mrozinski, Joseph; Shelton, Kacie; Weisbin, Charles; Elfes, Alberto; Smith, Jeffrey

2007-01-01

Strategic Assessment of Risk and Technology (START) is a user-friendly computer program that assists human managers in making decisions regarding research-and-development investment portfolios in the presence of uncertainties and of non-technological constraints that include budgetary and time limits, restrictions related to infrastructure, and programmatic and institutional priorities. START facilitates quantitative analysis of technologies, capabilities, missions, scenarios and programs, and thereby enables the selection and scheduling of value-optimal development efforts. START incorporates features that, variously, perform or support a unique combination of functions, most of which are not systematically performed or supported by prior decision- support software. These functions include the following: Optimal portfolio selection using an expected-utility-based assessment of capabilities and technologies; Temporal investment recommendations; Distinctions between enhancing and enabling capabilities; Analysis of partial funding for enhancing capabilities; and Sensitivity and uncertainty analysis. START can run on almost any computing hardware, within Linux and related operating systems that include Mac OS X versions 10.3 and later, and can run in Windows under the Cygwin environment. START can be distributed in binary code form. START calls, as external libraries, several open-source software packages. Output is in Excel (.xls) file format.

Machine learning patterns for neuroimaging-genetic studies in the cloud.

PubMed

Da Mota, Benoit; Tudoran, Radu; Costan, Alexandru; Varoquaux, Gaël; Brasche, Goetz; Conrod, Patricia; Lemaitre, Herve; Paus, Tomas; Rietschel, Marcella; Frouin, Vincent; Poline, Jean-Baptiste; Antoniu, Gabriel; Thirion, Bertrand

2014-01-01

Brain imaging is a natural intermediate phenotype to understand the link between genetic information and behavior or brain pathologies risk factors. Massive efforts have been made in the last few years to acquire high-dimensional neuroimaging and genetic data on large cohorts of subjects. The statistical analysis of such data is carried out with increasingly sophisticated techniques and represents a great computational challenge. Fortunately, increasing computational power in distributed architectures can be harnessed, if new neuroinformatics infrastructures are designed and training to use these new tools is provided. Combining a MapReduce framework (TomusBLOB) with machine learning algorithms (Scikit-learn library), we design a scalable analysis tool that can deal with non-parametric statistics on high-dimensional data. End-users describe the statistical procedure to perform and can then test the model on their own computers before running the very same code in the cloud at a larger scale. We illustrate the potential of our approach on real data with an experiment showing how the functional signal in subcortical brain regions can be significantly fit with genome-wide genotypes. This experiment demonstrates the scalability and the reliability of our framework in the cloud with a 2 weeks deployment on hundreds of virtual machines.

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences.

PubMed

Warris, Sven; Boymans, Sander; Muiser, Iwe; Noback, Michiel; Krijnen, Wim; Nap, Jan-Peter

2014-01-13

Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification.

Computational simulation of concurrent engineering for aerospace propulsion systems

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Singhal, S. N.

1992-01-01

Results are summarized of an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulations methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties - fundamental in developing such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering for propulsion systems and systems in general. Benefits and facets needing early attention in the development are outlined.

Computational simulation for concurrent engineering of aerospace propulsion systems

NASA Technical Reports Server (NTRS)

Chamis, C. C.; Singhal, S. N.

1993-01-01

Results are summarized for an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulation methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties--fundamental to develop such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering of propulsion systems and systems in general. Benefits and issues needing early attention in the development are outlined.

Computational simulation for concurrent engineering of aerospace propulsion systems

NASA Astrophysics Data System (ADS)

Chamis, C. C.; Singhal, S. N.

1993-02-01

Results are summarized for an investigation to assess the infrastructure available and the technology readiness in order to develop computational simulation methods/software for concurrent engineering. These results demonstrate that development of computational simulation methods for concurrent engineering is timely. Extensive infrastructure, in terms of multi-discipline simulation, component-specific simulation, system simulators, fabrication process simulation, and simulation of uncertainties--fundamental to develop such methods, is available. An approach is recommended which can be used to develop computational simulation methods for concurrent engineering of propulsion systems and systems in general. Benefits and issues needing early attention in the development are outlined.

DTS: The NOAO Data Transport System

NASA Astrophysics Data System (ADS)

Fitzpatrick, M.; Semple, T.

2014-05-01

The NOAO Data Transport System (DTS) provides high-throughput, reliable, data transfer between telescopes, pipelines and archive centers located in the Northern and Southern hemispheres. It is a distributed application using XML-RPC for command and control, and either parallel-TCP or UDT protocols for bulk data transport. The system is data-agnostic, allowing arbitrary files or directories to be moved using the same infrastructure. Data paths are configurable in the system by connecting nodes as the source or destination of data in a queue. Each leg of a data path may be configured independently based on the network environment between the sites. A queueing model is currently implemented to manage the automatic movement of data, a streaming model is planned to support arbitrarily large transfers (e.g. as in a disk recovery scenario) or to provide a 'pass-thru' interface to minize overheads. A web-based monitor allows anyone to get a graphical overview of the DTS system as it runs, operators will be able to control individual nodes in the system. Through careful tuning of the network paths DTS is able to achieve in excess of 80-percent of the nominal wire speed using only commodity networks, making it ideal for long-haul transport of large volumes of data.

A service-based BLAST command tool supported by cloud infrastructures.

PubMed

Carrión, Abel; Blanquer, Ignacio; Hernández, Vicente

2012-01-01

Notwithstanding the benefits of distributed-computing infrastructures for empowering bioinformatics analysis tools with the needed computing and storage capability, the actual use of these infrastructures is still low. Learning curves and deployment difficulties have reduced the impact on the wide research community. This article presents a porting strategy of BLAST based on a multiplatform client and a service that provides the same interface as sequential BLAST, thus reducing learning curve and with minimal impact on their integration on existing workflows. The porting has been done using the execution and data access components from the EC project Venus-C and the Windows Azure infrastructure provided in this project. The results obtained demonstrate a low overhead on the global execution framework and reasonable speed-up and cost-efficiency with respect to a sequential version.

Grids, virtualization, and clouds at Fermilab

DOE PAGES

Timm, S.; Chadwick, K.; Garzoglio, G.; ...

2014-06-11

Fermilab supports a scientific program that includes experiments and scientists located across the globe. To better serve this community, in 2004, the (then) Computing Division undertook the strategy of placing all of the High Throughput Computing (HTC) resources in a Campus Grid known as FermiGrid, supported by common shared services. In 2007, the FermiGrid Services group deployed a service infrastructure that utilized Xen virtualization, LVS network routing and MySQL circular replication to deliver highly available services that offered significant performance, reliability and serviceability improvements. This deployment was further enhanced through the deployment of a distributed redundant network core architecture andmore » the physical distribution of the systems that host the virtual machines across multiple buildings on the Fermilab Campus. In 2010, building on the experience pioneered by FermiGrid in delivering production services in a virtual infrastructure, the Computing Sector commissioned the FermiCloud, General Physics Computing Facility and Virtual Services projects to serve as platforms for support of scientific computing (FermiCloud 6 GPCF) and core computing (Virtual Services). Lastly, this work will present the evolution of the Fermilab Campus Grid, Virtualization and Cloud Computing infrastructure together with plans for the future.« less

Grids, virtualization, and clouds at Fermilab

NASA Astrophysics Data System (ADS)

Timm, S.; Chadwick, K.; Garzoglio, G.; Noh, S.

2014-06-01

Fermilab supports a scientific program that includes experiments and scientists located across the globe. To better serve this community, in 2004, the (then) Computing Division undertook the strategy of placing all of the High Throughput Computing (HTC) resources in a Campus Grid known as FermiGrid, supported by common shared services. In 2007, the FermiGrid Services group deployed a service infrastructure that utilized Xen virtualization, LVS network routing and MySQL circular replication to deliver highly available services that offered significant performance, reliability and serviceability improvements. This deployment was further enhanced through the deployment of a distributed redundant network core architecture and the physical distribution of the systems that host the virtual machines across multiple buildings on the Fermilab Campus. In 2010, building on the experience pioneered by FermiGrid in delivering production services in a virtual infrastructure, the Computing Sector commissioned the FermiCloud, General Physics Computing Facility and Virtual Services projects to serve as platforms for support of scientific computing (FermiCloud 6 GPCF) and core computing (Virtual Services). This work will present the evolution of the Fermilab Campus Grid, Virtualization and Cloud Computing infrastructure together with plans for the future.

An Abstract Process and Metrics Model for Evaluating Unified Command and Control: A Scenario and Technology Agnostic Approach

DTIC Science & Technology

2004-06-01

18 EBO Cognitive or Memetic input type ..................................................................... 18 Unanticipated EBO generated... Memetic Effects Based COA.................................................................................... 23 Policy...41 Belief systems or Memetic Content Metrics

Toward Composable Hardware Agnostic Communications Blocks Lessons Learned

DTIC Science & Technology

2016-11-01

ad9361/products/product.html [12] Google. Protocol Buffers. [Online]. Available: https://developers.google.com/protocol-buffers/ [13] VITA, “ANSI/VITA 49.0 VITA Radio Transport ( VRT ) Standard,” VITA, Tech. Rep., 2015.

Astrophysics Source Code Library Enhancements

NASA Astrophysics Data System (ADS)

Hanisch, R. J.; Allen, A.; Berriman, G. B.; DuPrie, K.; Mink, J.; Nemiroff, R. J.; Schmidt, J.; Shamir, L.; Shortridge, K.; Taylor, M.; Teuben, P. J.; Wallin, J.

2015-09-01

The Astrophysics Source Code Library (ASCL)1 is a free online registry of codes used in astronomy research; it currently contains over 900 codes and is indexed by ADS. The ASCL has recently moved a new infrastructure into production. The new site provides a true database for the code entries and integrates the WordPress news and information pages and the discussion forum into one site. Previous capabilities are retained and permalinks to ascl.net continue to work. This improvement offers more functionality and flexibility than the previous site, is easier to maintain, and offers new possibilities for collaboration. This paper covers these recent changes to the ASCL.

Development and application of the GIM code for the Cyber 203 computer

NASA Technical Reports Server (NTRS)

Stainaker, J. F.; Robinson, M. A.; Rawlinson, E. G.; Anderson, P. G.; Mayne, A. W.; Spradley, L. W.

1982-01-01

The GIM computer code for fluid dynamics research was developed. Enhancement of the computer code, implicit algorithm development, turbulence model implementation, chemistry model development, interactive input module coding and wing/body flowfield computation are described. The GIM quasi-parabolic code development was completed, and the code used to compute a number of example cases. Turbulence models, algebraic and differential equations, were added to the basic viscous code. An equilibrium reacting chemistry model and implicit finite difference scheme were also added. Development was completed on the interactive module for generating the input data for GIM. Solutions for inviscid hypersonic flow over a wing/body configuration are also presented.

Exploring Cognition Using Software Defined Radios for NASA Missions

NASA Technical Reports Server (NTRS)

Mortensen, Dale J.; Reinhart, Richard C.

2016-01-01

NASA missions typically operate using a communication infrastructure that requires significant schedule planning with limited flexibility when the needs of the mission change. Parameters such as modulation, coding scheme, frequency, and data rate are fixed for the life of the mission. This is due to antiquated hardware and software for both the space and ground assets and a very complex set of mission profiles. Automated techniques in place by commercial telecommunication companies are being explored by NASA to determine their usability by NASA to reduce cost and increase science return. Adding cognition the ability to learn from past decisions and adjust behavior is also being investigated. Software Defined Radios are an ideal way to implement cognitive concepts. Cognition can be considered in many different aspects of the communication system. Radio functions, such as frequency, modulation, data rate, coding and filters can be adjusted based on measurements of signal degradation. Data delivery mechanisms and route changes based on past successes and failures can be made to more efficiently deliver the data to the end user. Automated antenna pointing can be added to improve gain, coverage, or adjust the target. Scheduling improvements and automation to reduce the dependence on humans provide more flexible capabilities. The Cognitive Communications project, funded by the Space Communication and Navigation Program, is exploring these concepts and using the SCaN Testbed on board the International Space Station to implement them as they evolve. The SCaN Testbed contains three Software Defined Radios and a flight computer. These four computing platforms, along with a tracking antenna system and the supporting ground infrastructure, will be used to implement various concepts in a system similar to those used by missions. Multiple universities and SBIR companies are supporting this investigation. This paper will describe the cognitive system ideas under consideration and the plan for implementing them on platforms, including the SCaN Testbed. Discussions in the paper will include how these concepts might be used to reduce cost and improve the science return for NASA missions.

Detecting Faults in Southern California using Computer-Vision Techniques and Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) Interferometry

NASA Astrophysics Data System (ADS)

Barba, M.; Rains, C.; von Dassow, W.; Parker, J. W.; Glasscoe, M. T.

2013-12-01

Knowing the location and behavior of active faults is essential for earthquake hazard assessment and disaster response. In Interferometric Synthetic Aperture Radar (InSAR) images, faults are revealed as linear discontinuities. Currently, interferograms are manually inspected to locate faults. During the summer of 2013, the NASA-JPL DEVELOP California Disasters team contributed to the development of a method to expedite fault detection in California using remote-sensing technology. The team utilized InSAR images created from polarimetric L-band data from NASA's Uninhabited Aerial Vehicle Synthetic Aperture Radar (UAVSAR) project. A computer-vision technique known as 'edge-detection' was used to automate the fault-identification process. We tested and refined an edge-detection algorithm under development through NASA's Earthquake Data Enhanced Cyber-Infrastructure for Disaster Evaluation and Response (E-DECIDER) project. To optimize the algorithm we used both UAVSAR interferograms and synthetic interferograms generated through Disloc, a web-based modeling program available through NASA's QuakeSim project. The edge-detection algorithm detected seismic, aseismic, and co-seismic slip along faults that were identified and compared with databases of known fault systems. Our optimization process was the first step toward integration of the edge-detection code into E-DECIDER to provide decision support for earthquake preparation and disaster management. E-DECIDER partners that will use the edge-detection code include the California Earthquake Clearinghouse and the US Department of Homeland Security through delivery of products using the Unified Incident Command and Decision Support (UICDS) service. Through these partnerships, researchers, earthquake disaster response teams, and policy-makers will be able to use this new methodology to examine the details of ground and fault motions for moderate to large earthquakes. Following an earthquake, the newly discovered faults can be paired with infrastructure overlays, allowing emergency response teams to identify sites that may have been exposed to damage. The faults will also be incorporated into a database for future integration into fault models and earthquake simulations, improving future earthquake hazard assessment. As new faults are mapped, they will further understanding of the complex fault systems and earthquake hazards within the seismically dynamic state of California.

NGAP: Compliance as a Service

NASA Astrophysics Data System (ADS)

McLaughlin, B. D.; Pawloski, A. W.

2015-12-01

Modern development practices require the ability to quickly and easily host an application. Small projects cannot afford to maintain a large staff for infrastructure maintenance. Rapid prototyping fosters innovation. However, maintaining the integrity of data and systems demands care, particularly in a government context. The extensive data holdings that make up much of the value of NASA's EOSDIS (Earth Observing System Data and Information System) are stored in a number of locations, across a wide variety of applications, ranging from small prototypes to large computationally-intensive operational processes.However, it is increasingly difficult for an application to implement the required security controls, perform required registrations and inventory entries, ensure logging, monitoring, patching, and then ensure that all these activities continue for the life of that application, let alone five, or ten, or fifty applications. This process often takes weeks or months to complete and requires expertise in a variety of different domains such as security, systems administration, development, etc.NGAP, the Next Generation Application Platform, is tackling this problem by investigating, automating, and resolving many of the repeatable policy hurdles that a typical application must overcome. This platform provides a relatively simple and straightforward process by which applications can commit source code to a repository and then deploy that source code to a cloud-based infrastructure, all while meeting NASA's policies for security, governance, inventory, reliability, and availability. While there is still work for the application owner for any application hosting, NGAP handles a significant portion of that work.This talk will discuss areas where we have made significant progress, areas that are complex or must remain human-intensive, and areas where we are still striving to improve this application deployment and hosting pipeline.

Strengthening Software Authentication with the ROSE Software Suite

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, G

2006-06-15

Many recent nonproliferation and arms control software projects include a software authentication regime. These include U.S. Government-sponsored projects both in the United States and in the Russian Federation (RF). This trend toward requiring software authentication is only accelerating. Demonstrating assurance that software performs as expected without hidden ''backdoors'' is crucial to a project's success. In this context, ''authentication'' is defined as determining that a software package performs only its intended purpose and performs said purpose correctly and reliably over the planned duration of an agreement. In addition to visual inspections by knowledgeable computer scientists, automated tools are needed to highlightmore » suspicious code constructs, both to aid visual inspection and to guide program development. While many commercial tools are available for portions of the authentication task, they are proprietary and not extensible. An open-source, extensible tool can be customized to the unique needs of each project (projects can have both common and custom rules to detect flaws and security holes). Any such extensible tool has to be based on a complete language compiler. ROSE is precisely such a compiler infrastructure developed within the Department of Energy (DOE) and targeted at the optimization of scientific applications and user-defined libraries within large-scale applications (typically applications of a million lines of code). ROSE is a robust, source-to-source analysis and optimization infrastructure currently addressing large, million-line DOE applications in C and C++ (handling the full C, C99, C++ languages and with current collaborations to support Fortran90). We propose to extend ROSE to address a number of security-specific requirements, and apply it to software authentication for nonproliferation and arms control projects.« less

Increasing Usability in Ocean Observing Systems

NASA Astrophysics Data System (ADS)

Chase, A. C.; Gomes, K.; O'Reilly, T.

2005-12-01

As observatory systems move to more advanced techniques for instrument configuration and data management, standardized frameworks are being developed to benefit from commodities of scale. ACE (A Configuror and Editor) is a tool that was developed for SIAM (Software Infrastructure and Application for MOOS), a framework for the seamless integration of self-describing plug-and-work instruments into the Monterey Ocean Observing System. As a comprehensive solution, the SIAM infrastructure requires a number of processes to be run to configure an instrument for use within its framework. As solutions move from the lab to the field, the steps needed to implement the solution must be made bulletproof so that they may be used in the field with confidence. Loosely defined command line interfaces don't always provide enough user feedback and business logic can be difficult to maintain over a series of scripts. ACE is a tool developed for guiding the user through a number of complicated steps, removing the reliance on command-line utilities and reducing the difficulty of completing the necessary steps, while also preventing operator error and enforcing system constraints. Utilizing the cross-platform nature of the Java programming language, ACE provides a complete solution for deploying an instrument within the SIAM infrastructure without depending on special software being installed on the users computer. Requirements such as the installation of a Unix emulator for users running Windows machines, and the installation of, and ability to use, a CVS client, have all been removed by providing the equivalent functionality from within ACE. In order to achieve a "one stop shop" for configuring instruments, ACE had to be written to handle a wide variety of functionality including: compiling java code, interacting with a CVS server and maintaining client-side CVS information, editing XML, interacting with a server side database, and negotiating serial port communications through Java. This paper will address the relative tradeoffs of including all the afore-mentioned functionality in a single tool, its affects on user adoption of the framework (SIAM) it provides access to, as well as further discussion of some of the functionality generally pertinent to data management (XML editing, source code management and compilation, etc).

Cloud computing applications for biomedical science: A perspective.

PubMed

Navale, Vivek; Bourne, Philip E

2018-06-01

Biomedical research has become a digital data-intensive endeavor, relying on secure and scalable computing, storage, and network infrastructure, which has traditionally been purchased, supported, and maintained locally. For certain types of biomedical applications, cloud computing has emerged as an alternative to locally maintained traditional computing approaches. Cloud computing offers users pay-as-you-go access to services such as hardware infrastructure, platforms, and software for solving common biomedical computational problems. Cloud computing services offer secure on-demand storage and analysis and are differentiated from traditional high-performance computing by their rapid availability and scalability of services. As such, cloud services are engineered to address big data problems and enhance the likelihood of data and analytics sharing, reproducibility, and reuse. Here, we provide an introductory perspective on cloud computing to help the reader determine its value to their own research.

Cloud computing applications for biomedical science: A perspective

PubMed Central

2018-01-01

Biomedical research has become a digital data–intensive endeavor, relying on secure and scalable computing, storage, and network infrastructure, which has traditionally been purchased, supported, and maintained locally. For certain types of biomedical applications, cloud computing has emerged as an alternative to locally maintained traditional computing approaches. Cloud computing offers users pay-as-you-go access to services such as hardware infrastructure, platforms, and software for solving common biomedical computational problems. Cloud computing services offer secure on-demand storage and analysis and are differentiated from traditional high-performance computing by their rapid availability and scalability of services. As such, cloud services are engineered to address big data problems and enhance the likelihood of data and analytics sharing, reproducibility, and reuse. Here, we provide an introductory perspective on cloud computing to help the reader determine its value to their own research. PMID:29902176

Cyberdyn supercomputer - a tool for imaging geodinamic processes

NASA Astrophysics Data System (ADS)

Pomeran, Mihai; Manea, Vlad; Besutiu, Lucian; Zlagnean, Luminita

2014-05-01

More and more physical processes developed within the deep interior of our planet, but with significant impact on the Earth's shape and structure, become subject to numerical modelling by using high performance computing facilities. Nowadays, worldwide an increasing number of research centers decide to make use of such powerful and fast computers for simulating complex phenomena involving fluid dynamics and get deeper insight to intricate problems of Earth's evolution. With the CYBERDYN cybernetic infrastructure (CCI), the Solid Earth Dynamics Department in the Institute of Geodynamics of the Romanian Academy boldly steps into the 21st century by entering the research area of computational geodynamics. The project that made possible this advancement, has been jointly supported by EU and Romanian Government through the Structural and Cohesion Funds. It lasted for about three years, ending October 2013. CCI is basically a modern high performance Beowulf-type supercomputer (HPCC), combined with a high performance visualization cluster (HPVC) and a GeoWall. The infrastructure is mainly structured around 1344 cores and 3 TB of RAM. The high speed interconnect is provided by a Qlogic InfiniBand switch, able to transfer up to 40 Gbps. The CCI storage component is a 40 TB Panasas NAS. The operating system is Linux (CentOS). For control and maintenance, the Bright Cluster Manager package is used. The SGE job scheduler manages the job queues. CCI has been designed for a theoretical peak performance up to 11.2 TFlops. Speed tests showed that a high resolution numerical model (256 × 256 × 128 FEM elements) could be resolved with a mean computational speed of 1 time step at 30 seconds, by employing only a fraction of the computing power (20%). After passing the mandatory tests, the CCI has been involved in numerical modelling of various scenarios related to the East Carpathians tectonic and geodynamic evolution, including the Neogene magmatic activity, and the intriguing intermediate-depth seismicity within the so-called Vrancea zone. The CFD code for numerical modelling is CitcomS, a widely employed open source package specifically developed for earth sciences. Several preliminary 3D geodynamic models for simulating an assumed subduction or the effect of a mantle plume will be presented and discussed.

National Computational Infrastructure for Lattice Gauge Theory SciDAC-2 Closeout Report Indiana University Component

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gottlieb, Steven Arthur; DeTar, Carleton; Tousaint, Doug

This is the closeout report for the Indiana University portion of the National Computational Infrastructure for Lattice Gauge Theory project supported by the United States Department of Energy under the SciDAC program. It includes information about activities at Indian University, the University of Arizona, and the University of Utah, as those three universities coordinated their activities.

Deploying Crowd-Sourced Formal Verification Systems in a DoD Network

DTIC Science & Technology

2013-09-01

INTENTIONALLY LEFT BLANK 1 I. INTRODUCTION A. INTRODUCTION In 2014 cyber attacks on critical infrastructure are expected to increase...CSFV systems on the Internet‒‒possibly using cloud infrastructure (Dean, 2013). By using Amazon Compute Cloud (EC2) systems, DARPA will use ordinary...through standard access methods. Those clients could be mobile phones, laptops, netbooks, tablet computers or personal digital assistants (PDAs) (Smoot

75 FR 78229 - Record of Decision for the U.S. Marine Corps East Coast Basing of the F-35B Aircraft

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-15

... States Code (U.S.C.) Section 4332(2)(c), the regulations of the Council on Environmental Quality (CEQ) for Implementing the Procedural Provisions of NEPA (40 Code of Federal Regulations [CFR] parts 1500... action, the Marine Corps will: (1) Construct and/or renovate airfield facilities and infrastructure...

75 FR 78229 - Record of Decision for the U.S. Marine Corps West Coast Basing of the F-35B Aircraft

Federal Register 2010, 2011, 2012, 2013, 2014

2010-12-15

... States Code (U.S.C.) Section 4332(2)(c), the regulations of the Council on Environmental Quality (CEQ) for Implementing the Procedural Provisions of NEPA (40 Code of Federal Regulations [CFR] parts 1500...) Construct and/or renovate airfield facilities and infrastructure necessary to accommodate and maintain the F...

75 FR 5290 - Notice of the Record of Decision for the United States Marine Corps Grow the Force at Marine...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-02

...) of 1969, 42 United States Code (U.S.C.) Section 4332(2)(c), the regulations of the Council on Environmental Quality (CEQ) for Implementing the Procedural Provisions of NEPA (40 Code of Federal Regulations... infrastructure construction (e.g. buildings, roads, utility lines); (2) demolition and/or upgrades to existing...

[Rethinking criminal responsibility: practical application of operational diagnosis and gnostic into expert testimony].

PubMed

Okada, Takayuki

2005-01-01

There had been argument concerning the difference between the agnostic approach and the gnostic approach to the psychiatric perspective of criminal responsibility until the landmark ruling by the 3rd court of the Japanese Supreme Court in 1984. The decision upheld the gnostic approach and affirmed that the defendant's criminal responsibility should be based on such factors as psychopathology, motive, modus operandi, situation surrounding the crime, and pre-morbid personality, as long as the offense was not directly motivated by the delusion or hallucination. The gnostic explanation includes so many various factors that the psychiatric testimony cannot easily be objective, while agnostic experts can find a conclusion about criminal responsibility only by psychiatric diagnosis. To establish a standard, the authors summarized the means of determination of criminal responsibility. The authors also discussed various topics related to criminal responsibility including Asperger's syndrome, illicit drug intoxication, and prescribed drug intoxication.

Fiber-Optic Array Scanning Technology (FAST) for Detection and Molecular Characterization of Circulating Tumor Cells.

PubMed

Ao, Zheng; Liu, Xiaohe

2017-01-01

Circulating tumor cell (CTC) as an important component in "liquid biopsy" holds crucial clinical relevance in cancer prognosis, treatment efficiency evaluation, prediction and potentially early detection. Here, we present a Fiber-optic Array Scanning Technology (FAST) that enables antigen-agnostic, size-agnostic detection of CTC. By immunofluorescence staining detection of a combination of a panel of markers, FAST technology can be applied to detect rare CTC in non-small cell lung cancer (NSCLC) setting with high sensitivity and specificity. In combination with Automated Digital Microscopy (ADM) platform, companion markers on CTC such as Vimentin and Programmed death-ligand 1 (PD-L1) can also be analyzed to further characterize these CTCs. FAST data output is also compatible with downstream single cell picking platforms. Single cell can be isolated post ADM confirmation and used for "actionable" genetic mutations analysis.

Surface-agnostic highly stretchable and bendable conductive MXene multilayers

PubMed Central

An, Hyosung; Habib, Touseef; Shah, Smit; Gao, Huili; Radovic, Miladin; Green, Micah J.; Lutkenhaus, Jodie L.

2018-01-01

Stretchable, bendable, and foldable conductive coatings are crucial for wearable electronics and biometric sensors. These coatings should maintain functionality while simultaneously interfacing with different types of surfaces undergoing mechanical deformation. MXene sheets as conductive two-dimensional nanomaterials are promising for this purpose, but it is still extremely difficult to form surface-agnostic MXene coatings that can withstand extreme mechanical deformation. We report on conductive and conformal MXene multilayer coatings that can undergo large-scale mechanical deformation while maintaining a conductivity as high as 2000 S/m. MXene multilayers are successfully deposited onto flexible polymer sheets, stretchable poly(dimethylsiloxane), nylon fiber, glass, and silicon. The coating shows a recoverable resistance response to bending (up to 2.5-mm bending radius) and stretching (up to 40% tensile strain), which was leveraged for detecting human motion and topographical scanning. We anticipate that this discovery will allow for the implementation of MXene-based coatings onto mechanically deformable objects. PMID:29536044

A robust dataset-agnostic heart disease classifier from Phonocardiogram.

PubMed

Banerjee, Rohan; Dutta Choudhury, Anirban; Deshpande, Parijat; Bhattacharya, Sakyajit; Pal, Arpan; Mandana, K M

2017-07-01

Automatic classification of normal and abnormal heart sounds is a popular area of research. However, building a robust algorithm unaffected by signal quality and patient demography is a challenge. In this paper we have analysed a wide list of Phonocardiogram (PCG) features in time and frequency domain along with morphological and statistical features to construct a robust and discriminative feature set for dataset-agnostic classification of normal and cardiac patients. The large and open access database, made available in Physionet 2016 challenge was used for feature selection, internal validation and creation of training models. A second dataset of 41 PCG segments, collected using our in-house smart phone based digital stethoscope from an Indian hospital was used for performance evaluation. Our proposed methodology yielded sensitivity and specificity scores of 0.76 and 0.75 respectively on the test dataset in classifying cardiovascular diseases. The methodology also outperformed three popular prior art approaches, when applied on the same dataset.

Reducing the complexity of NASA's space communications infrastructure

NASA Technical Reports Server (NTRS)

Miller, Raymond E.; Liu, Hong; Song, Junehwa

1995-01-01

This report describes the range of activities performed during the annual reporting period in support of the NASA Code O Success Team - Lifecycle Effectiveness for Strategic Success (COST LESS) team. The overall goal of the COST LESS team is to redefine success in a constrained fiscal environment and reduce the cost of success for end-to-end mission operations. This goal is more encompassing than the original proposal made to NASA for reducing complexity of NASA's Space Communications Infrastructure. The COST LESS team approach for reengineering the space operations infrastructure has a focus on reversing the trend of engineering special solutions to similar problems.

NEON: Contributing continental-scale long-term environmental data for the benefit of society

NASA Astrophysics Data System (ADS)

Wee, B.; Aulenbach, S.

2011-12-01

The National Ecological Observatory Network (NEON) is a NSF funded national investment in physical and information infrastructure. Large-scale environmental changes pose challenges that straddle environmental, economic, and social boundaries. As we develop climate adaptation strategies at the Federal, state, local, and tribal levels, accessible and usable data are essential for implementing actions that are informed by the best available information. NEON's goal is to enable understanding and forecasting of the impacts of climate change, land use change and invasive species on continental-scale ecology by providing physical and information infrastructure. The NEON framework will take standardized, long-term, coordinated measurements of related environmental variables at each of its 62 sites across the nation. These observations, collected by automated instruments, field crews, and airborne instruments, will be processed into more than 700 data products that are provided freely over the web to support research, education, and environmental management. NEON is envisioned to be an integral component of an interoperable ecosystem of credible data and information sources. Other members of this information ecosystem include Federal, commercial, and non-profit entities. NEON is actively involved with the interoperability community via forums like the Foundation for Earth Science Information Partners and the USGS Community for Data Integration in a collective effort to identify the technical standards, best practices, and organizational principles that enable the emergence of such an information ecosystem. These forums have proven to be effective innovation engines for the experimentation of new techniques that evolve into emergent standards. These standards are, for the most part, discipline agnostic. It is becoming increasingly evident that we need to include socio-economic and public health data sources in interoperability initiatives, because the dynamics of coupled natural-human systems cannot be understood in the absence of data about the human dimension. Another essential element is the community of tool and platform developers who create the infrastructure for scientists, educators, resource managers, and policy analysts to discover, analyze, and collaborate on problems using the diverse data that are required to address emerging large-scale environmental challenges. These challenges are very unlikely to be problems confined to this generation: they are urgent, compelling, and long-term problems that require a sustained effort to generate and curate data and information from observations, models, and experiments. NEON's long-term national physical and information infrastructure for environmental observation is one of the cornerstones of a framework that transforms science and information for the benefit of society.

Scaling the CERN OpenStack cloud

NASA Astrophysics Data System (ADS)

Bell, T.; Bompastor, B.; Bukowiec, S.; Castro Leon, J.; Denis, M. K.; van Eldik, J.; Fermin Lobo, M.; Fernandez Alvarez, L.; Fernandez Rodriguez, D.; Marino, A.; Moreira, B.; Noel, B.; Oulevey, T.; Takase, W.; Wiebalck, A.; Zilli, S.

2015-12-01

CERN has been running a production OpenStack cloud since July 2013 to support physics computing and infrastructure services for the site. In the past year, CERN Cloud Infrastructure has seen a constant increase in nodes, virtual machines, users and projects. This paper will present what has been done in order to make the CERN cloud infrastructure scale out.

Science of Security Lablet - Scalability and Usability

DTIC Science & Technology

2014-12-16

mobile computing [19]. However, the high-level infrastructure design and our own implementation (both described throughout this paper) can easily...critical and infrastructural systems demands high levels of sophistication in the technical aspects of cybersecurity, software and hardware design...Forget, S. Komanduri, Alessandro Acquisti, Nicolas Christin, Lorrie Cranor, Rahul Telang. "Security Behavior Observatory: Infrastructure for Long-term

Performance measurement and modeling of component applications in a high performance computing environment : a case study.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Armstrong, Robert C.; Ray, Jaideep; Malony, A.

2003-11-01

We present a case study of performance measurement and modeling of a CCA (Common Component Architecture) component-based application in a high performance computing environment. We explore issues peculiar to component-based HPC applications and propose a performance measurement infrastructure for HPC based loosely on recent work done for Grid environments. A prototypical implementation of the infrastructure is used to collect data for a three components in a scientific application and construct performance models for two of them. Both computational and message-passing performance are addressed.

Role of Computational Fluid Dynamics and Wind Tunnels in Aeronautics R and D

NASA Technical Reports Server (NTRS)

Malik, Murjeeb R.; Bushnell, Dennis M.

2012-01-01

The purpose of this report is to investigate the status and future projections for the question of supplantation of wind tunnels by computation in design and to intuit the potential impact of computation approaches on wind-tunnel utilization all with an eye toward reducing the infrastructure cost at aeronautics R&D centers. Wind tunnels have been closing for myriad reasons, and such closings have reduced infrastructure costs. Further cost reductions are desired, and the work herein attempts to project which wind-tunnel capabilities can be replaced in the future and, if possible, the timing of such. If the possibility exists to project when a facility could be closed, then maintenance and other associated costs could be rescheduled accordingly (i.e., before the fact) to obtain an even greater infrastructure cost reduction.

A Computational framework for telemedicine.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foster, I.; von Laszewski, G.; Thiruvathukal, G. K.

1998-07-01

Emerging telemedicine applications require the ability to exploit diverse and geographically distributed resources. Highspeed networks are used to integrate advanced visualization devices, sophisticated instruments, large databases, archival storage devices, PCs, workstations, and supercomputers. This form of telemedical environment is similar to networked virtual supercomputers, also known as metacomputers. Metacomputers are already being used in many scientific application areas. In this article, we analyze requirements necessary for a telemedical computing infrastructure and compare them with requirements found in a typical metacomputing environment. We will show that metacomputing environments can be used to enable a more powerful and unified computational infrastructure formore » telemedicine. The Globus metacomputing toolkit can provide the necessary low level mechanisms to enable a large scale telemedical infrastructure. The Globus toolkit components are designed in a modular fashion and can be extended to support the specific requirements for telemedicine.« less

46 CFR 393.2 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-10-01

... Act, as set forth in Chapter 551 of Title 46, United States Code. (d) Corridor Sponsor. An entity that... emissions, energy savings, improved safety, system resiliency, and/or reduced infrastructure costs. Routes...

Evolution of a Materials Data Infrastructure

NASA Astrophysics Data System (ADS)

Warren, James A.; Ward, Charles H.

2018-06-01

The field of materials science and engineering is writing a new chapter in its evolution, one of digitally empowered materials discovery, development, and deployment. The 2008 Integrated Computational Materials Engineering (ICME) study report helped usher in this paradigm shift, making a compelling case and strong recommendations for an infrastructure supporting ICME that would enable access to precompetitive materials data for both scientific and engineering applications. With the launch of the Materials Genome Initiative in 2011, which drew substantial inspiration from the ICME study, digital data was highlighted as a core component of a Materials Innovation Infrastructure, along with experimental and computational tools. Over the past 10 years, our understanding of what it takes to provide accessible materials data has matured and rapid progress has been made in establishing a Materials Data Infrastructure (MDI). We are learning that the MDI is essential to eliminating the seams between experiment and computation by providing a means for them to connect effortlessly. Additionally, the MDI is becoming an enabler, allowing materials engineering to tie into a much broader model-based engineering enterprise for product design.

Information Power Grid: Distributed High-Performance Computing and Large-Scale Data Management for Science and Engineering

NASA Technical Reports Server (NTRS)

Johnston, William E.; Gannon, Dennis; Nitzberg, Bill; Feiereisen, William (Technical Monitor)

2000-01-01

The term "Grid" refers to distributed, high performance computing and data handling infrastructure that incorporates geographically and organizationally dispersed, heterogeneous resources that are persistent and supported. The vision for NASN's Information Power Grid - a computing and data Grid - is that it will provide significant new capabilities to scientists and engineers by facilitating routine construction of information based problem solving environments / frameworks that will knit together widely distributed computing, data, instrument, and human resources into just-in-time systems that can address complex and large-scale computing and data analysis problems. IPG development and deployment is addressing requirements obtained by analyzing a number of different application areas, in particular from the NASA Aero-Space Technology Enterprise. This analysis has focussed primarily on two types of users: The scientist / design engineer whose primary interest is problem solving (e.g., determining wing aerodynamic characteristics in many different operating environments), and whose primary interface to IPG will be through various sorts of problem solving frameworks. The second type of user if the tool designer: The computational scientists who convert physics and mathematics into code that can simulate the physical world. These are the two primary users of IPG, and they have rather different requirements. This paper describes the current state of IPG (the operational testbed), the set of capabilities being put into place for the operational prototype IPG, as well as some of the longer term R&D tasks.

Toward a Proof of Concept Cloud Framework for Physics Applications on Blue Gene Supercomputers

NASA Astrophysics Data System (ADS)

Dreher, Patrick; Scullin, William; Vouk, Mladen

2015-09-01

Traditional high performance supercomputers are capable of delivering large sustained state-of-the-art computational resources to physics applications over extended periods of time using batch processing mode operating environments. However, today there is an increasing demand for more complex workflows that involve large fluctuations in the levels of HPC physics computational requirements during the simulations. Some of the workflow components may also require a richer set of operating system features and schedulers than normally found in a batch oriented HPC environment. This paper reports on progress toward a proof of concept design that implements a cloud framework onto BG/P and BG/Q platforms at the Argonne Leadership Computing Facility. The BG/P implementation utilizes the Kittyhawk utility and the BG/Q platform uses an experimental heterogeneous FusedOS operating system environment. Both platforms use the Virtual Computing Laboratory as the cloud computing system embedded within the supercomputer. This proof of concept design allows a cloud to be configured so that it can capitalize on the specialized infrastructure capabilities of a supercomputer and the flexible cloud configurations without resorting to virtualization. Initial testing of the proof of concept system is done using the lattice QCD MILC code. These types of user reconfigurable environments have the potential to deliver experimental schedulers and operating systems within a working HPC environment for physics computations that may be different from the native OS and schedulers on production HPC supercomputers.

The future of PanDA in ATLAS distributed computing

NASA Astrophysics Data System (ADS)

De, K.; Klimentov, A.; Maeno, T.; Nilsson, P.; Oleynik, D.; Panitkin, S.; Petrosyan, A.; Schovancova, J.; Vaniachine, A.; Wenaus, T.

2015-12-01

Experiments at the Large Hadron Collider (LHC) face unprecedented computing challenges. Heterogeneous resources are distributed worldwide at hundreds of sites, thousands of physicists analyse the data remotely, the volume of processed data is beyond the exabyte scale, while data processing requires more than a few billion hours of computing usage per year. The PanDA (Production and Distributed Analysis) system was developed to meet the scale and complexity of LHC distributed computing for the ATLAS experiment. In the process, the old batch job paradigm of locally managed computing in HEP was discarded in favour of a far more automated, flexible and scalable model. The success of PanDA in ATLAS is leading to widespread adoption and testing by other experiments. PanDA is the first exascale workload management system in HEP, already operating at more than a million computing jobs per day, and processing over an exabyte of data in 2013. There are many new challenges that PanDA will face in the near future, in addition to new challenges of scale, heterogeneity and increasing user base. PanDA will need to handle rapidly changing computing infrastructure, will require factorization of code for easier deployment, will need to incorporate additional information sources including network metrics in decision making, be able to control network circuits, handle dynamically sized workload processing, provide improved visualization, and face many other challenges. In this talk we will focus on the new features, planned or recently implemented, that are relevant to the next decade of distributed computing workload management using PanDA.

Neo-deterministic seismic hazard scenarios for India—a preventive tool for disaster mitigation

NASA Astrophysics Data System (ADS)

Parvez, Imtiyaz A.; Magrin, Andrea; Vaccari, Franco; Ashish; Mir, Ramees R.; Peresan, Antonella; Panza, Giuliano Francesco

2017-11-01

Current computational resources and physical knowledge of the seismic wave generation and propagation processes allow for reliable numerical and analytical models of waveform generation and propagation. From the simulation of ground motion, it is easy to extract the desired earthquake hazard parameters. Accordingly, a scenario-based approach to seismic hazard assessment has been developed, namely the neo-deterministic seismic hazard assessment (NDSHA), which allows for a wide range of possible seismic sources to be used in the definition of reliable scenarios by means of realistic waveforms modelling. Such reliable and comprehensive characterization of expected earthquake ground motion is essential to improve building codes, particularly for the protection of critical infrastructures and for land use planning. Parvez et al. (Geophys J Int 155:489-508, 2003) published the first ever neo-deterministic seismic hazard map of India by computing synthetic seismograms with input data set consisting of structural models, seismogenic zones, focal mechanisms and earthquake catalogues. As described in Panza et al. (Adv Geophys 53:93-165, 2012), the NDSHA methodology evolved with respect to the original formulation used by Parvez et al. (Geophys J Int 155:489-508, 2003): the computer codes were improved to better fit the need of producing realistic ground shaking maps and ground shaking scenarios, at different scale levels, exploiting the most significant pertinent progresses in data acquisition and modelling. Accordingly, the present study supplies a revised NDSHA map for India. The seismic hazard, expressed in terms of maximum displacement (Dmax), maximum velocity (Vmax) and design ground acceleration (DGA), has been extracted from the synthetic signals and mapped on a regular grid over the studied territory.

Information technology developments within the national biological information infrastructure

USGS Publications Warehouse

Cotter, G.; Frame, M.T.

2000-01-01

Looking out an office window or exploring a community park, one can easily see the tremendous challenges that biological information presents the computer science community. Biological information varies in format and content depending whether or not it is information pertaining to a particular species (i.e. Brown Tree Snake), or a specific ecosystem, which often includes multiple species, land use characteristics, and geospatially referenced information. The complexity and uniqueness of each individual species or ecosystem do not easily lend themselves to today's computer science tools and applications. To address the challenges that the biological enterprise presents the National Biological Information Infrastructure (NBII) (http://www.nbii.gov) was established in 1993. The NBII is designed to address these issues on a National scale within the United States, and through international partnerships abroad. This paper discusses current computer science efforts within the National Biological Information Infrastructure Program and future computer science research endeavors that are needed to address the ever-growing issues related to our Nation's biological concerns.

Use of agents to implement an integrated computing environment

NASA Technical Reports Server (NTRS)

Hale, Mark A.; Craig, James I.

1995-01-01

Integrated Product and Process Development (IPPD) embodies the simultaneous application to both system and quality engineering methods throughout an iterative design process. The use of IPPD results in the time-conscious, cost-saving development of engineering systems. To implement IPPD, a Decision-Based Design perspective is encapsulated in an approach that focuses on the role of the human designer in product development. The approach has two parts and is outlined in this paper. First, an architecture, called DREAMS, is being developed that facilitates design from a decision-based perspective. Second, a supporting computing infrastructure, called IMAGE, is being designed. Agents are used to implement the overall infrastructure on the computer. Successful agent utilization requires that they be made of three components: the resource, the model, and the wrap. Current work is focused on the development of generalized agent schemes and associated demonstration projects. When in place, the technology independent computing infrastructure will aid the designer in systematically generating knowledge used to facilitate decision-making.

Multimodal Classification of Mild Cognitive Impairment Based on Partial Least Squares.

PubMed

Wang, Pingyue; Chen, Kewei; Yao, Li; Hu, Bin; Wu, Xia; Zhang, Jiacai; Ye, Qing; Guo, Xiaojuan

2016-08-10

In recent years, increasing attention has been given to the identification of the conversion of mild cognitive impairment (MCI) to Alzheimer's disease (AD). Brain neuroimaging techniques have been widely used to support the classification or prediction of MCI. The present study combined magnetic resonance imaging (MRI), 18F-fluorodeoxyglucose PET (FDG-PET), and 18F-florbetapir PET (florbetapir-PET) to discriminate MCI converters (MCI-c, individuals with MCI who convert to AD) from MCI non-converters (MCI-nc, individuals with MCI who have not converted to AD in the follow-up period) based on the partial least squares (PLS) method. Two types of PLS models (informed PLS and agnostic PLS) were built based on 64 MCI-c and 65 MCI-nc from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. The results showed that the three-modality informed PLS model achieved better classification accuracy of 81.40%, sensitivity of 79.69%, and specificity of 83.08% compared with the single-modality model, and the three-modality agnostic PLS model also achieved better classification compared with the two-modality model. Moreover, combining the three modalities with clinical test score (ADAS-cog), the agnostic PLS model (independent data: florbetapir-PET; dependent data: FDG-PET and MRI) achieved optimal accuracy of 86.05%, sensitivity of 81.25%, and specificity of 90.77%. In addition, the comparison of PLS, support vector machine (SVM), and random forest (RF) showed greater diagnostic power of PLS. These results suggested that our multimodal PLS model has the potential to discriminate MCI-c from the MCI-nc and may therefore be helpful in the early diagnosis of AD.

Spiral-shaped piezoelectric sensors for Lamb waves direction of arrival (DoA) estimation

NASA Astrophysics Data System (ADS)

De Marchi, L.; Testoni, N.; Marzani, A.

2018-04-01

A novel strategy to design piezoelectric sensors suited for direction of arrival (DoA) estimation of incoming Lamb waves is presented in this work. The designed sensor is composed by two piezoelectric patches (P1, P2) bonded on the structure to be inspected. In particular, by exploiting the Radon transform, the proposed procedure computes the shape of P2 given the shape of P1 so that the difference in time of arrival (DToA) of the Lamb waves at the two patches is linearly related to the DoA while being agnostic of the waveguide dispersion curves. With a dedicated processing procedure, the waveforms acquired from the two electrodes and digitized can be used to retrieve the DoA information. Numerical and experimental results show that DoA estimation performed by means of the proposed shaped transducers is extremely robust.

Reducing the number of templates for aligned-spin compact binary coalescence gravitational wave searches using metric-agnostic template nudging

NASA Astrophysics Data System (ADS)

Indik, Nathaniel; Fehrmann, Henning; Harke, Franz; Krishnan, Badri; Nielsen, Alex B.

2018-06-01

Efficient multidimensional template placement is crucial in computationally intensive matched-filtering searches for gravitational waves (GWs). Here, we implement the neighboring cell algorithm (NCA) to improve the detection volume of an existing compact binary coalescence (CBC) template bank. This algorithm has already been successfully applied for a binary millisecond pulsar search in data from the Fermi satellite. It repositions templates from overdense regions to underdense regions and reduces the number of templates that would have been required by a stochastic method to achieve the same detection volume. Our method is readily generalizable to other CBC parameter spaces. Here we apply this method to the aligned-single-spin neutron star-black hole binary coalescence inspiral-merger-ringdown gravitational wave parameter space. We show that the template nudging algorithm can attain the equivalent effectualness of the stochastic method with 12% fewer templates.

EGI-EUDAT integration activity - Pair data and high-throughput computing resources together

NASA Astrophysics Data System (ADS)

Scardaci, Diego; Viljoen, Matthew; Vitlacil, Dejan; Fiameni, Giuseppe; Chen, Yin; sipos, Gergely; Ferrari, Tiziana

2016-04-01

EGI (www.egi.eu) is a publicly funded e-infrastructure put together to give scientists access to more than 530,000 logical CPUs, 200 PB of disk capacity and 300 PB of tape storage to drive research and innovation in Europe. The infrastructure provides both high throughput computing and cloud compute/storage capabilities. Resources are provided by about 350 resource centres which are distributed across 56 countries in Europe, the Asia-Pacific region, Canada and Latin America. EUDAT (www.eudat.eu) is a collaborative Pan-European infrastructure providing research data services, training and consultancy for researchers, research communities, research infrastructures and data centres. EUDAT's vision is to enable European researchers and practitioners from any research discipline to preserve, find, access, and process data in a trusted environment, as part of a Collaborative Data Infrastructure (CDI) conceived as a network of collaborating, cooperating centres, combining the richness of numerous community-specific data repositories with the permanence and persistence of some of Europe's largest scientific data centres. EGI and EUDAT, in the context of their flagship projects, EGI-Engage and EUDAT2020, started in March 2015 a collaboration to harmonise the two infrastructures, including technical interoperability, authentication, authorisation and identity management, policy and operations. The main objective of this work is to provide end-users with a seamless access to an integrated infrastructure offering both EGI and EUDAT services and, then, pairing data and high-throughput computing resources together. To define the roadmap of this collaboration, EGI and EUDAT selected a set of relevant user communities, already collaborating with both infrastructures, which could bring requirements and help to assign the right priorities to each of them. In this way, from the beginning, this activity has been really driven by the end users. The identified user communities are relevant European Research infrastructure in the field of Earth Science (EPOS and ICOS), Bioinformatics (BBMRI and ELIXIR) and Space Physics (EISCAT-3D). The first outcome of this activity has been the definition of a generic use case that captures the typical user scenario with respect the integrated use of the EGI and EUDAT infrastructures. This generic use case allows a user to instantiate a set of Virtual Machine images on the EGI Federated Cloud to perform computational jobs that analyse data previously stored on EUDAT long-term storage systems. The results of such analysis can be staged back to EUDAT storages, and if needed, allocated with Permanent identifyers (PIDs) for future use. The implementation of this generic use case requires the following integration activities between EGI and EUDAT: (1) harmonisation of the user authentication and authorisation models, (2) implementing interface connectors between the relevant EGI and EUDAT services, particularly EGI Cloud compute facilities and EUDAT long-term storage and PID systems. In the presentation, the collected user requirements and the implementation status of the universal use case will be showed. Furthermore, how the universal use case is currently applied to satisfy EPOS and ICOS needs will be described.

Implementation of a 3D mixing layer code on parallel computers

NASA Technical Reports Server (NTRS)

Roe, K.; Thakur, R.; Dang, T.; Bogucz, E.

1995-01-01

This paper summarizes our progress and experience in the development of a Computational-Fluid-Dynamics code on parallel computers to simulate three-dimensional spatially-developing mixing layers. In this initial study, the three-dimensional time-dependent Euler equations are solved using a finite-volume explicit time-marching algorithm. The code was first programmed in Fortran 77 for sequential computers. The code was then converted for use on parallel computers using the conventional message-passing technique, while we have not been able to compile the code with the present version of HPF compilers.

Benchmarking infrastructure for mutation text mining

PubMed Central

2014-01-01

Background Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation text mining systems. Results We propose a community-oriented annotation and benchmarking infrastructure to support development, testing, benchmarking, and comparison of mutation text mining systems. The design is based on semantic standards, where RDF is used to represent annotations, an OWL ontology provides an extensible schema for the data and SPARQL is used to compute various performance metrics, so that in many cases no programming is needed to analyze results from a text mining system. While large benchmark corpora for biological entity and relation extraction are focused mostly on genes, proteins, diseases, and species, our benchmarking infrastructure fills the gap for mutation information. The core infrastructure comprises (1) an ontology for modelling annotations, (2) SPARQL queries for computing performance metrics, and (3) a sizeable collection of manually curated documents, that can support mutation grounding and mutation impact extraction experiments. Conclusion We have developed the principal infrastructure for the benchmarking of mutation text mining tasks. The use of RDF and OWL as the representation for corpora ensures extensibility. The infrastructure is suitable for out-of-the-box use in several important scenarios and is ready, in its current state, for initial community adoption. PMID:24568600

Benchmarking infrastructure for mutation text mining.

PubMed

Klein, Artjom; Riazanov, Alexandre; Hindle, Matthew M; Baker, Christopher Jo

2014-02-25

Experimental research on the automatic extraction of information about mutations from texts is greatly hindered by the lack of consensus evaluation infrastructure for the testing and benchmarking of mutation text mining systems. We propose a community-oriented annotation and benchmarking infrastructure to support development, testing, benchmarking, and comparison of mutation text mining systems. The design is based on semantic standards, where RDF is used to represent annotations, an OWL ontology provides an extensible schema for the data and SPARQL is used to compute various performance metrics, so that in many cases no programming is needed to analyze results from a text mining system. While large benchmark corpora for biological entity and relation extraction are focused mostly on genes, proteins, diseases, and species, our benchmarking infrastructure fills the gap for mutation information. The core infrastructure comprises (1) an ontology for modelling annotations, (2) SPARQL queries for computing performance metrics, and (3) a sizeable collection of manually curated documents, that can support mutation grounding and mutation impact extraction experiments. We have developed the principal infrastructure for the benchmarking of mutation text mining tasks. The use of RDF and OWL as the representation for corpora ensures extensibility. The infrastructure is suitable for out-of-the-box use in several important scenarios and is ready, in its current state, for initial community adoption.

BigDataScript: a scripting language for data pipelines.

PubMed

Cingolani, Pablo; Sladek, Rob; Blanchette, Mathieu

2015-01-01

The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. © The Author 2014. Published by Oxford University Press.

Integrating the Allen Brain Institute Cell Types Database into Automated Neuroscience Workflow.

PubMed

Stockton, David B; Santamaria, Fidel

2017-10-01

We developed software tools to download, extract features, and organize the Cell Types Database from the Allen Brain Institute (ABI) in order to integrate its whole cell patch clamp characterization data into the automated modeling/data analysis cycle. To expand the potential user base we employed both Python and MATLAB. The basic set of tools downloads selected raw data and extracts cell, sweep, and spike features, using ABI's feature extraction code. To facilitate data manipulation we added a tool to build a local specialized database of raw data plus extracted features. Finally, to maximize automation, we extended our NeuroManager workflow automation suite to include these tools plus a separate investigation database. The extended suite allows the user to integrate ABI experimental and modeling data into an automated workflow deployed on heterogeneous computer infrastructures, from local servers, to high performance computing environments, to the cloud. Since our approach is focused on workflow procedures our tools can be modified to interact with the increasing number of neuroscience databases being developed to cover all scales and properties of the nervous system.

BigDataScript: a scripting language for data pipelines

PubMed Central

Cingolani, Pablo; Sladek, Rob; Blanchette, Mathieu

2015-01-01

Motivation: The analysis of large biological datasets often requires complex processing pipelines that run for a long time on large computational infrastructures. We designed and implemented a simple script-like programming language with a clean and minimalist syntax to develop and manage pipeline execution and provide robustness to various types of software and hardware failures as well as portability. Results: We introduce the BigDataScript (BDS) programming language for data processing pipelines, which improves abstraction from hardware resources and assists with robustness. Hardware abstraction allows BDS pipelines to run without modification on a wide range of computer architectures, from a small laptop to multi-core servers, server farms, clusters and clouds. BDS achieves robustness by incorporating the concepts of absolute serialization and lazy processing, thus allowing pipelines to recover from errors. By abstracting pipeline concepts at programming language level, BDS simplifies implementation, execution and management of complex bioinformatics pipelines, resulting in reduced development and debugging cycles as well as cleaner code. Availability and implementation: BigDataScript is available under open-source license at http://pcingola.github.io/BigDataScript. Contact: pablo.e.cingolani@gmail.com PMID:25189778

High-throughput neuroimaging-genetics computational infrastructure

PubMed Central

Dinov, Ivo D.; Petrosyan, Petros; Liu, Zhizhong; Eggert, Paul; Hobel, Sam; Vespa, Paul; Woo Moon, Seok; Van Horn, John D.; Franco, Joseph; Toga, Arthur W.

2014-01-01

Many contemporary neuroscientific investigations face significant challenges in terms of data management, computational processing, data mining, and results interpretation. These four pillars define the core infrastructure necessary to plan, organize, orchestrate, validate, and disseminate novel scientific methods, computational resources, and translational healthcare findings. Data management includes protocols for data acquisition, archival, query, transfer, retrieval, and aggregation. Computational processing involves the necessary software, hardware, and networking infrastructure required to handle large amounts of heterogeneous neuroimaging, genetics, clinical, and phenotypic data and meta-data. Data mining refers to the process of automatically extracting data features, characteristics and associations, which are not readily visible by human exploration of the raw dataset. Result interpretation includes scientific visualization, community validation of findings and reproducible findings. In this manuscript we describe the novel high-throughput neuroimaging-genetics computational infrastructure available at the Institute for Neuroimaging and Informatics (INI) and the Laboratory of Neuro Imaging (LONI) at University of Southern California (USC). INI and LONI include ultra-high-field and standard-field MRI brain scanners along with an imaging-genetics database for storing the complete provenance of the raw and derived data and meta-data. In addition, the institute provides a large number of software tools for image and shape analysis, mathematical modeling, genomic sequence processing, and scientific visualization. A unique feature of this architecture is the Pipeline environment, which integrates the data management, processing, transfer, and visualization. Through its client-server architecture, the Pipeline environment provides a graphical user interface for designing, executing, monitoring validating, and disseminating of complex protocols that utilize diverse suites of software tools and web-services. These pipeline workflows are represented as portable XML objects which transfer the execution instructions and user specifications from the client user machine to remote pipeline servers for distributed computing. Using Alzheimer's and Parkinson's data, we provide several examples of translational applications using this infrastructure1. PMID:24795619

Accelerating Adverse Outcome Pathway Development via Systems Approaches

EPA Science Inventory

The Adverse Outcome Pathway has emerged as an internationally harmonized mechanism for organizing biological information in a chemical agnostic manner. This construct is valuable for interpreting the results from high-throughput toxicity (HTT) assessment by providing a mechanisti...

Location Based Service in Indoor Environment Using Quick Response Code Technology

NASA Astrophysics Data System (ADS)

Hakimpour, F.; Zare Zardiny, A.

2014-10-01

Today by extensive use of intelligent mobile phones, increased size of screens and enriching the mobile phones by Global Positioning System (GPS) technology use of location based services have been considered by public users more than ever.. Based on the position of users, they can receive the desired information from different LBS providers. Any LBS system generally includes five main parts: mobile devices, communication network, positioning system, service provider and data provider. By now many advances have been gained in relation to any of these parts; however the users positioning especially in indoor environments is propounded as an essential and critical issue in LBS. It is well known that GPS performs too poorly inside buildings to provide usable indoor positioning. On the other hand, current indoor positioning technologies such as using RFID or WiFi network need different hardware and software infrastructures. In this paper, we propose a new method to overcome these challenges. This method is using the Quick Response (QR) Code Technology. QR Code is a 2D encrypted barcode with a matrix structure which consists of black modules arranged in a square grid. Scanning and data retrieving process from QR Code is possible by use of different camera-enabled mobile phones only by installing the barcode reader software. This paper reviews the capabilities of QR Code technology and then discusses the advantages of using QR Code in Indoor LBS (ILBS) system in comparison to other technologies. Finally, some prospects of using QR Code are illustrated through implementation of a scenario. The most important advantages of using this new technology in ILBS are easy implementation, spending less expenses, quick data retrieval, possibility of printing the QR Code on different products and no need for complicated hardware and software infrastructures.

Mobile Security Enclaves

DTIC Science & Technology

2011-09-01

LAI Location Area Identity MANET Mobile Ad - hoc Network MCC Mobile Country Code MCD Mobile Communications Device MNC Mobile Network Code ...tower or present within a geographical area. These conditions relate directly to users who often operate with mobile ad - hoc networks. These types of...infrastructures. First responders can use these mobile base stations to set up their own networks on the fly, similar to mobile ad - hoc networks

32 CFR 240.4 - Policy.

Code of Federal Regulations, 2012 CFR

2012-07-01

... enterprise information infrastructure requirements. (c) The academic disciplines, with concentrations in IA..., computer systems analysis, cyber operations, cybersecurity, database administration, data management... infrastructure development and academic research to support the DoD IA/IT critical areas of interest. ...

32 CFR 240.4 - Policy.

Code of Federal Regulations, 2013 CFR

2013-07-01

... enterprise information infrastructure requirements. (c) The academic disciplines, with concentrations in IA..., computer systems analysis, cyber operations, cybersecurity, database administration, data management... infrastructure development and academic research to support the DoD IA/IT critical areas of interest. ...

32 CFR 240.4 - Policy.

Code of Federal Regulations, 2014 CFR

2014-07-01

... enterprise information infrastructure requirements. (c) The academic disciplines, with concentrations in IA..., computer systems analysis, cyber operations, cybersecurity, database administration, data management... infrastructure development and academic research to support the DoD IA/IT critical areas of interest. ...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 26 2013-07-01 2013-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 26 2012-07-01 2011-07-01 true Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 25 2014-07-01 2014-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 24 2010-07-01 2010-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

40 CFR 194.23 - Models and computer codes.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 25 2011-07-01 2011-07-01 false Models and computer codes. 194.23... General Requirements § 194.23 Models and computer codes. (a) Any compliance application shall include: (1... obtain stable solutions; (iv) Computer models accurately implement the numerical models; i.e., computer...

Integrated Service Provisioning in an Ipv6 over ATM Research Network

DOE Office of Scientific and Technical Information (OSTI.GOV)

Eli Dart; Helen Chen; Jerry Friesen

1999-02-01

During the past few years, the worldwide Internet has grown at a phenomenal rate, which has spurred the proposal of innovative network technologies to support the fast, efficient and low-latency transport of a wide spectrum of multimedia traffic types. Existing network infrastructures have been plagued by their inability to provide for real-time application traffic as well as their general lack of resources and resilience to congestion. This work proposes to address these issues by implementing a prototype high-speed network infrastructure consisting of Internet Protocol Version 6 (IPv6) on top of an Asynchronous Transfer Mode (ATM) transport medium. Since ATM ismore » connection-oriented whereas IP uses a connection-less paradigm, the efficient integration of IPv6 over ATM is especially challenging and has generated much interest in the research community. We propose, in collaboration with an industry partner, to implement IPv6 over ATM using a unique approach that integrates IP over fast A TM hardware while still preserving IP's connection-less paradigm. This is achieved by replacing ATM's control software with IP's routing code and by caching IP's forwarding decisions in ATM's VPI/VCI translation tables. Prototype ''VR'' and distributed-parallel-computing applications will also be developed to exercise the realtime capability of our IPv6 over ATM network.« less

Probability Distributome: A Web Computational Infrastructure for Exploring the Properties, Interrelations, and Applications of Probability Distributions.

PubMed

Dinov, Ivo D; Siegrist, Kyle; Pearl, Dennis K; Kalinin, Alexandr; Christou, Nicolas

2016-06-01

Probability distributions are useful for modeling, simulation, analysis, and inference on varieties of natural processes and physical phenomena. There are uncountably many probability distributions. However, a few dozen families of distributions are commonly defined and are frequently used in practice for problem solving, experimental applications, and theoretical studies. In this paper, we present a new computational and graphical infrastructure, the Distributome , which facilitates the discovery, exploration and application of diverse spectra of probability distributions. The extensible Distributome infrastructure provides interfaces for (human and machine) traversal, search, and navigation of all common probability distributions. It also enables distribution modeling, applications, investigation of inter-distribution relations, as well as their analytical representations and computational utilization. The entire Distributome framework is designed and implemented as an open-source, community-built, and Internet-accessible infrastructure. It is portable, extensible and compatible with HTML5 and Web2.0 standards (http://Distributome.org). We demonstrate two types of applications of the probability Distributome resources: computational research and science education. The Distributome tools may be employed to address five complementary computational modeling applications (simulation, data-analysis and inference, model-fitting, examination of the analytical, mathematical and computational properties of specific probability distributions, and exploration of the inter-distributional relations). Many high school and college science, technology, engineering and mathematics (STEM) courses may be enriched by the use of modern pedagogical approaches and technology-enhanced methods. The Distributome resources provide enhancements for blended STEM education by improving student motivation, augmenting the classical curriculum with interactive webapps, and overhauling the learning assessment protocols.

Probability Distributome: A Web Computational Infrastructure for Exploring the Properties, Interrelations, and Applications of Probability Distributions

PubMed Central

Dinov, Ivo D.; Siegrist, Kyle; Pearl, Dennis K.; Kalinin, Alexandr; Christou, Nicolas

2015-01-01

Probability distributions are useful for modeling, simulation, analysis, and inference on varieties of natural processes and physical phenomena. There are uncountably many probability distributions. However, a few dozen families of distributions are commonly defined and are frequently used in practice for problem solving, experimental applications, and theoretical studies. In this paper, we present a new computational and graphical infrastructure, the Distributome, which facilitates the discovery, exploration and application of diverse spectra of probability distributions. The extensible Distributome infrastructure provides interfaces for (human and machine) traversal, search, and navigation of all common probability distributions. It also enables distribution modeling, applications, investigation of inter-distribution relations, as well as their analytical representations and computational utilization. The entire Distributome framework is designed and implemented as an open-source, community-built, and Internet-accessible infrastructure. It is portable, extensible and compatible with HTML5 and Web2.0 standards (http://Distributome.org). We demonstrate two types of applications of the probability Distributome resources: computational research and science education. The Distributome tools may be employed to address five complementary computational modeling applications (simulation, data-analysis and inference, model-fitting, examination of the analytical, mathematical and computational properties of specific probability distributions, and exploration of the inter-distributional relations). Many high school and college science, technology, engineering and mathematics (STEM) courses may be enriched by the use of modern pedagogical approaches and technology-enhanced methods. The Distributome resources provide enhancements for blended STEM education by improving student motivation, augmenting the classical curriculum with interactive webapps, and overhauling the learning assessment protocols. PMID:27158191

49 CFR 236.909 - Minimum performance standard.

Code of Federal Regulations, 2010 CFR

2010-10-01

...://www.archives.gov/federal_register/code_of_federal_regulations/ibr_locations.html; (ii) The product is... exposure must be expressed as total train miles traveled per year over the relevant railroad infrastructure...

Soil Monitor: an open source web application for real-time soil sealing monitoring and assessment

NASA Astrophysics Data System (ADS)

Langella, Giuliano; Basile, Angelo; Giannecchini, Simone; Iamarino, Michela; Munafò, Michele; Terribile, Fabio

2016-04-01

Soil sealing is one of the most important causes of land degradation and desertification. In Europe, soil covered by impermeable materials has increased by about 80% from the Second World War till nowadays, while population has only grown by one third. There is an increasing concern at the high political levels about the need to attenuate imperviousness itself and its effects on soil functions. European Commission promulgated a roadmap (COM(2011) 571) by which the net land take would be zero by 2050. Furthermore, European Commission also published a report in 2011 providing best practices and guidelines for limiting soil sealing and imperviousness. In this scenario, we developed an open source and an open source based Soil Sealing Geospatial Cyber Infrastructure (SS-GCI) named as "Soil Monitor". This tool merges a webGIS with parallel geospatial computation in a fast and dynamic fashion in order to provide real-time assessments of soil sealing at high spatial resolution (20 meters and below) over the whole Italy. Common open source webGIS packages are used to implement both the data management and visualization infrastructures, such as GeoServer and MapStore. The high-speed geospatial computation is ensured by a GPU parallelism using the CUDA (Computing Unified Device Architecture) framework by NVIDIA®. This kind of parallelism required the writing - from scratch - all codes needed to fulfil the geospatial computation built behind the soil sealing toolbox. The combination of GPU computing with webGIS infrastructures is relatively novel and required particular attention at the Java-CUDA programming interface. As a result, Soil Monitor is smart because it can perform very high time-consuming calculations (querying for instance an Italian administrative region as area of interest) in less than one minute. The web application is embedded in a web browser and nothing must be installed before using it. Potentially everybody can use it, but the main targets are the stakeholders dealing with sealing, such as policy makers, land owners and asphalt/cement companies. As a matter of fact, Soil Monitor can be used to improve the spatial planning therefore limiting the progression of disordered soil sealing which causes both the direct loss of soils due to imperviousness but also the indirect loss caused by fragmentation of soils (which has different negative effects on the durability of soil functions, such as habitat corridors). Further, in a future version, Soil Monitor would estimate the best location for a new building or help compensating soil losses by actions in other areas to offset drawbacks at zero. The presented SS-GCI dealing with soil sealing - if opportunely scaled - would aid the implementation of best practices for limiting soil sealing or mitigating its effects on soil functions.

INFN-Pisa scientific computation environment (GRID, HPC and Interactive Analysis)

NASA Astrophysics Data System (ADS)

Arezzini, S.; Carboni, A.; Caruso, G.; Ciampa, A.; Coscetti, S.; Mazzoni, E.; Piras, S.

2014-06-01

The INFN-Pisa Tier2 infrastructure is described, optimized not only for GRID CPU and Storage access, but also for a more interactive use of the resources in order to provide good solutions for the final data analysis step. The Data Center, equipped with about 6700 production cores, permits the use of modern analysis techniques realized via advanced statistical tools (like RooFit and RooStat) implemented in multicore systems. In particular a POSIX file storage access integrated with standard SRM access is provided. Therefore the unified storage infrastructure is described, based on GPFS and Xrootd, used both for SRM data repository and interactive POSIX access. Such a common infrastructure allows a transparent access to the Tier2 data to the users for their interactive analysis. The organization of a specialized many cores CPU facility devoted to interactive analysis is also described along with the login mechanism integrated with the INFN-AAI (National INFN Infrastructure) to extend the site access and use to a geographical distributed community. Such infrastructure is used also for a national computing facility in use to the INFN theoretical community, it enables a synergic use of computing and storage resources. Our Center initially developed for the HEP community is now growing and includes also HPC resources fully integrated. In recent years has been installed and managed a cluster facility (1000 cores, parallel use via InfiniBand connection) and we are now updating this facility that will provide resources for all the intermediate level HPC computing needs of the INFN theoretical national community.

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.

PubMed

Wimalaratne, Sarala M; Grenon, Pierre; Hoehndorf, Robert; Gkoutos, Georgios V; de Bono, Bernard

2012-02-01

The article presents an infrastructure for supporting the semantic interoperability of biomedical resources based on the management (storing and inference-based querying) of their ontology-based annotations. This infrastructure consists of: (i) a repository to store and query ontology-based annotations; (ii) a knowledge base server with an inference engine to support the storage of and reasoning over ontologies used in the annotation of resources; (iii) a set of applications and services allowing interaction with the integrated repository and knowledge base. The infrastructure is being prototyped and developed and evaluated by the RICORDO project in support of the knowledge management of biomedical resources, including physiology and pharmacology models and associated clinical data. The RICORDO toolkit and its source code are freely available from http://ricordo.eu/relevant-resources. sarala@ebi.ac.uk.

Advanced Artificial Science. The development of an artificial science and engineering research infrastructure to facilitate innovative computational modeling, analysis, and application to interdisciplinary areas of scientific investigation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Saffer, Shelley

2014-12-01

This is a final report of the DOE award DE-SC0001132, Advanced Artificial Science. The development of an artificial science and engineering research infrastructure to facilitate innovative computational modeling, analysis, and application to interdisciplinary areas of scientific investigation. This document describes the achievements of the goals, and resulting research made possible by this award.

Ubiquitous Green Computing Techniques for High Demand Applications in Smart Environments

PubMed Central

Zapater, Marina; Sanchez, Cesar; Ayala, Jose L.; Moya, Jose M.; Risco-Martín, José L.

2012-01-01

Ubiquitous sensor network deployments, such as the ones found in Smart cities and Ambient intelligence applications, require constantly increasing high computational demands in order to process data and offer services to users. The nature of these applications imply the usage of data centers. Research has paid much attention to the energy consumption of the sensor nodes in WSNs infrastructures. However, supercomputing facilities are the ones presenting a higher economic and environmental impact due to their very high power consumption. The latter problem, however, has been disregarded in the field of smart environment services. This paper proposes an energy-minimization workload assignment technique, based on heterogeneity and application-awareness, that redistributes low-demand computational tasks from high-performance facilities to idle nodes with low and medium resources in the WSN infrastructure. These non-optimal allocation policies reduce the energy consumed by the whole infrastructure and the total execution time. PMID:23112621

GSDC: A Unique Data Center in Korea for HEP research

NASA Astrophysics Data System (ADS)

Ahn, Sang-Un

2017-04-01

Global Science experimental Data hub Center (GSDC) at Korea Institute of Science and Technology Information (KISTI) is a unique data center in South Korea established for promoting the fundamental research fields by supporting them with the expertise on Information and Communication Technology (ICT) and the infrastructure for High Performance Computing (HPC), High Throughput Computing (HTC) and Networking. GSDC has supported various research fields in South Korea dealing with the large scale of data, e.g. RENO experiment for neutrino research, LIGO experiment for gravitational wave detection, Genome sequencing project for bio-medical, and HEP experiments such as CDF at FNAL, Belle at KEK, and STAR at BNL. In particular, GSDC has run a Tier-1 center for ALICE experiment using the LHC at CERN since 2013. In this talk, we present the overview on computing infrastructure that GSDC runs for the research fields and we discuss on the data center infrastructure management system deployed at GSDC.

First results from a combined analysis of CERN computing infrastructure metrics

NASA Astrophysics Data System (ADS)

Duellmann, Dirk; Nieke, Christian

2017-10-01

The IT Analysis Working Group (AWG) has been formed at CERN across individual computing units and the experiments to attempt a cross cutting analysis of computing infrastructure and application metrics. In this presentation we will describe the first results obtained using medium/long term data (1 months — 1 year) correlating box level metrics, job level metrics from LSF and HTCondor, IO metrics from the physics analysis disk pools (EOS) and networking and application level metrics from the experiment dashboards. We will cover in particular the measurement of hardware performance and prediction of job duration, the latency sensitivity of different job types and a search for bottlenecks with the production job mix in the current infrastructure. The presentation will conclude with the proposal of a small set of metrics to simplify drawing conclusions also in the more constrained environment of public cloud deployments.

Ubiquitous green computing techniques for high demand applications in Smart environments.

PubMed

Zapater, Marina; Sanchez, Cesar; Ayala, Jose L; Moya, Jose M; Risco-Martín, José L

2012-01-01

Ubiquitous sensor network deployments, such as the ones found in Smart cities and Ambient intelligence applications, require constantly increasing high computational demands in order to process data and offer services to users. The nature of these applications imply the usage of data centers. Research has paid much attention to the energy consumption of the sensor nodes in WSNs infrastructures. However, supercomputing facilities are the ones presenting a higher economic and environmental impact due to their very high power consumption. The latter problem, however, has been disregarded in the field of smart environment services. This paper proposes an energy-minimization workload assignment technique, based on heterogeneity and application-awareness, that redistributes low-demand computational tasks from high-performance facilities to idle nodes with low and medium resources in the WSN infrastructure. These non-optimal allocation policies reduce the energy consumed by the whole infrastructure and the total execution time.

NCI's High Performance Computing (HPC) and High Performance Data (HPD) Computing Platform for Environmental and Earth System Data Science

NASA Astrophysics Data System (ADS)

Evans, Ben; Allen, Chris; Antony, Joseph; Bastrakova, Irina; Gohar, Kashif; Porter, David; Pugh, Tim; Santana, Fabiana; Smillie, Jon; Trenham, Claire; Wang, Jingbo; Wyborn, Lesley

2015-04-01

The National Computational Infrastructure (NCI) has established a powerful and flexible in-situ petascale computational environment to enable both high performance computing and Data-intensive Science across a wide spectrum of national environmental and earth science data collections - in particular climate, observational data and geoscientific assets. This paper examines 1) the computational environments that supports the modelling and data processing pipelines, 2) the analysis environments and methods to support data analysis, and 3) the progress so far to harmonise the underlying data collections for future interdisciplinary research across these large volume data collections. NCI has established 10+ PBytes of major national and international data collections from both the government and research sectors based on six themes: 1) weather, climate, and earth system science model simulations, 2) marine and earth observations, 3) geosciences, 4) terrestrial ecosystems, 5) water and hydrology, and 6) astronomy, social and biosciences. Collectively they span the lithosphere, crust, biosphere, hydrosphere, troposphere, and stratosphere. The data is largely sourced from NCI's partners (which include the custodians of many of the major Australian national-scale scientific collections), leading research communities, and collaborating overseas organisations. New infrastructures created at NCI mean the data collections are now accessible within an integrated High Performance Computing and Data (HPC-HPD) environment - a 1.2 PFlop supercomputer (Raijin), a HPC class 3000 core OpenStack cloud system and several highly connected large-scale high-bandwidth Lustre filesystems. The hardware was designed at inception to ensure that it would allow the layered software environment to flexibly accommodate the advancement of future data science. New approaches to software technology and data models have also had to be developed to enable access to these large and exponentially increasing data volumes at NCI. Traditional HPC and data environments are still made available in a way that flexibly provides the tools, services and supporting software systems on these new petascale infrastructures. But to enable the research to take place at this scale, the data, metadata and software now need to evolve together - creating a new integrated high performance infrastructure. The new infrastructure at NCI currently supports a catalogue of integrated, reusable software and workflows from earth system and ecosystem modelling, weather research, satellite and other observed data processing and analysis. One of the challenges for NCI has been to support existing techniques and methods, while carefully preparing the underlying infrastructure for the transition needed for the next class of Data-intensive Science. In doing so, a flexible range of techniques and software can be made available for application across the corpus of data collections available, and to provide a new infrastructure for future interdisciplinary research.

NAS infrastructure management system build 1.5 computer-human interface

DOT National Transportation Integrated Search

2001-01-01

Human factors engineers from the National Airspace System (NAS) Human Factors Branch (ACT-530) of the Federal Aviation Administration William J. Hughes Technical Center conducted an evaluation of the NAS Infrastructure Management System (NIMS) Build ...

33 CFR 105.205 - Facility Security Officer (FSO).

Code of Federal Regulations, 2010 CFR

2010-07-01

... training in the following, as appropriate: (i) Relevant international laws and codes, and recommendations... well as any plans to change the facility or facility infrastructure prior to amending the FSP; and (18...

Nuclear Energy Advanced Modeling and Simulation (NEAMS) Waste Integrated Performance and Safety Codes (IPSC) : FY10 development and integration.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Criscenti, Louise Jacqueline; Sassani, David Carl; Arguello, Jose Guadalupe, Jr.

2011-02-01

This report describes the progress in fiscal year 2010 in developing the Waste Integrated Performance and Safety Codes (IPSC) in support of the U.S. Department of Energy (DOE) Office of Nuclear Energy Advanced Modeling and Simulation (NEAMS) Campaign. The goal of the Waste IPSC is to develop an integrated suite of computational modeling and simulation capabilities to quantitatively assess the long-term performance of waste forms in the engineered and geologic environments of a radioactive waste storage or disposal system. The Waste IPSC will provide this simulation capability (1) for a range of disposal concepts, waste form types, engineered repository designs,more » and geologic settings, (2) for a range of time scales and distances, (3) with appropriate consideration of the inherent uncertainties, and (4) in accordance with robust verification, validation, and software quality requirements. Waste IPSC activities in fiscal year 2010 focused on specifying a challenge problem to demonstrate proof of concept, developing a verification and validation plan, and performing an initial gap analyses to identify candidate codes and tools to support the development and integration of the Waste IPSC. The current Waste IPSC strategy is to acquire and integrate the necessary Waste IPSC capabilities wherever feasible, and develop only those capabilities that cannot be acquired or suitably integrated, verified, or validated. This year-end progress report documents the FY10 status of acquisition, development, and integration of thermal-hydrologic-chemical-mechanical (THCM) code capabilities, frameworks, and enabling tools and infrastructure.« less

Computer Description of Black Hawk Helicopter

DTIC Science & Technology

1979-06-01

Model Combinatorial Geometry Models Black Hawk Helicopter Helicopter GIFT Computer Code Geometric Description of Targets 20. ABSTRACT...description was made using the technique of combinatorial geometry (COM-GEOM) and will be used as input to the GIFT computer code which generates Tliic...rnHp The data used bv the COVART comtmter code was eenerated bv the Geometric Information for Targets ( GIFT )Z computer code. This report documents

Infrastructure sensing.

PubMed

Soga, Kenichi; Schooling, Jennifer

2016-08-06

Design, construction, maintenance and upgrading of civil engineering infrastructure requires fresh thinking to minimize use of materials, energy and labour. This can only be achieved by understanding the performance of the infrastructure, both during its construction and throughout its design life, through innovative monitoring. Advances in sensor systems offer intriguing possibilities to radically alter methods of condition assessment and monitoring of infrastructure. In this paper, it is hypothesized that the future of infrastructure relies on smarter information; the rich information obtained from embedded sensors within infrastructure will act as a catalyst for new design, construction, operation and maintenance processes for integrated infrastructure systems linked directly with user behaviour patterns. Some examples of emerging sensor technologies for infrastructure sensing are given. They include distributed fibre-optics sensors, computer vision, wireless sensor networks, low-power micro-electromechanical systems, energy harvesting and citizens as sensors.

Infrastructure sensing

PubMed Central

Soga, Kenichi; Schooling, Jennifer

2016-01-01

Design, construction, maintenance and upgrading of civil engineering infrastructure requires fresh thinking to minimize use of materials, energy and labour. This can only be achieved by understanding the performance of the infrastructure, both during its construction and throughout its design life, through innovative monitoring. Advances in sensor systems offer intriguing possibilities to radically alter methods of condition assessment and monitoring of infrastructure. In this paper, it is hypothesized that the future of infrastructure relies on smarter information; the rich information obtained from embedded sensors within infrastructure will act as a catalyst for new design, construction, operation and maintenance processes for integrated infrastructure systems linked directly with user behaviour patterns. Some examples of emerging sensor technologies for infrastructure sensing are given. They include distributed fibre-optics sensors, computer vision, wireless sensor networks, low-power micro-electromechanical systems, energy harvesting and citizens as sensors. PMID:27499845

Primary care access barriers as reported by nonurgent emergency department users: implications for the US primary care infrastructure.

PubMed

Hefner, Jennifer L; Wexler, Randy; McAlearney, Ann Scheck

2015-01-01

The objective was to explore variation by insurance status in patient-reported barriers to accessing primary care. The authors fielded a brief, anonymous, voluntary survey of nonurgent emergency department (ED) visits at a large academic medical center and conducted descriptive analysis and thematic coding of 349 open-ended survey responses. The privately insured predominantly reported primary care infrastructure barriers-wait time in clinic and for an appointment, constraints related to conventional business hours, and difficulty finding a primary care provider (because of geography or lack of new patient openings). Half of those insured by Medicaid and/or Medicare also reported these infrastructure barriers. In contrast, the uninsured predominantly reported insurance, income, and transportation barriers. Given that insured nonurgent ED users frequently report infrastructure barriers, these should be the focus of patient-level interventions to reduce nonurgent ED use and of health system-level policies to enhance the capacity of the US primary care infrastructure. © 2014 by the American College of Medical Quality.

Grid computing technology for hydrological applications

NASA Astrophysics Data System (ADS)

Lecca, G.; Petitdidier, M.; Hluchy, L.; Ivanovic, M.; Kussul, N.; Ray, N.; Thieron, V.

2011-06-01

SummaryAdvances in e-Infrastructure promise to revolutionize sensing systems and the way in which data are collected and assimilated, and complex water systems are simulated and visualized. According to the EU Infrastructure 2010 work-programme, data and compute infrastructures and their underlying technologies, either oriented to tackle scientific challenges or complex problem solving in engineering, are expected to converge together into the so-called knowledge infrastructures, leading to a more effective research, education and innovation in the next decade and beyond. Grid technology is recognized as a fundamental component of e-Infrastructures. Nevertheless, this emerging paradigm highlights several topics, including data management, algorithm optimization, security, performance (speed, throughput, bandwidth, etc.), and scientific cooperation and collaboration issues that require further examination to fully exploit it and to better inform future research policies. The paper illustrates the results of six different surface and subsurface hydrology applications that have been deployed on the Grid. All the applications aim to answer to strong requirements from the Civil Society at large, relatively to natural and anthropogenic risks. Grid technology has been successfully tested to improve flood prediction, groundwater resources management and Black Sea hydrological survey, by providing large computing resources. It is also shown that Grid technology facilitates e-cooperation among partners by means of services for authentication and authorization, seamless access to distributed data sources, data protection and access right, and standardization.

The ORAC-DR data reduction pipeline

NASA Astrophysics Data System (ADS)

Cavanagh, B.; Jenness, T.; Economou, F.; Currie, M. J.

2008-03-01

The ORAC-DR data reduction pipeline has been used by the Joint Astronomy Centre since 1998. Originally developed for an infrared spectrometer and a submillimetre bolometer array, it has since expanded to support twenty instruments from nine different telescopes. By using shared code and a common infrastructure, rapid development of an automated data reduction pipeline for nearly any astronomical data is possible. This paper discusses the infrastructure available to developers and estimates the development timescales expected to reduce data for new instruments using ORAC-DR.

User manual for semi-circular compact range reflector code: Version 2

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Burnside, Walter D.

1987-01-01

A computer code has been developed at the Ohio State University ElectroScience Laboratory to analyze a semi-circular paraboloidal reflector with or without a rolled edge at the top and a skirt at the bottom. The code can be used to compute the total near field of the reflector or its individual components at a given distance from the center of the paraboloid. The code computes the fields along a radial, horizontal, vertical or axial cut at that distance. Thus, it is very effective in computing the size of the sweet spot for a semi-circular compact range reflector. This report describes the operation of the code. Various input and output statements are explained. Some results obtained using the computer code are presented to illustrate the code's capability as well as being samples of input/output sets.

Transportation Infrastructure Design and Construction \\0x16 Virtual Training Tools

DOT National Transportation Integrated Search

2003-09-01

This project will develop 3D interactive computer-training environments for a major element of transportation infrastructure : hot mix asphalt paving. These tools will include elements of hot mix design (including laboratory equipment) and constructi...

Putting the Information Infrastructure to Work. Report of the Information Infrastructure Task Force Committee on Applications and Technology. NIST Special Publication 857.

ERIC Educational Resources Information Center

National Inst. of Standards and Technology, Gaithersburg, MD.

An interconnection of computer networks, telecommunications services, and applications, the National Information Infrastructure (NII) can open up new vistas and profoundly change much of American life. This report explores some of the opportunities and obstacles to the use of the NII by people and organizations. The goal is to express how…

Integrating Network Management for Cloud Computing Services

DTIC Science & Technology

2015-06-01

abstraction and system design. In this dissertation, we make three major contributions. We rst propose to consolidate the tra c and infrastructure management...abstraction and system design. In this dissertation, we make three major contributions. We first propose to consolidate the traffic and infrastructure ...1.3.1 Safe Datacenter Traffic/ Infrastructure Management . . . . . . 9 1.3.2 End-host/Network Cooperative Traffic Management . . . . . . 10 1.3.3 Direct

Distributed Coding/Decoding Complexity in Video Sensor Networks

PubMed Central

Cordeiro, Paulo J.; Assunção, Pedro

2012-01-01

Video Sensor Networks (VSNs) are recent communication infrastructures used to capture and transmit dense visual information from an application context. In such large scale environments which include video coding, transmission and display/storage, there are several open problems to overcome in practical implementations. This paper addresses the most relevant challenges posed by VSNs, namely stringent bandwidth usage and processing time/power constraints. In particular, the paper proposes a novel VSN architecture where large sets of visual sensors with embedded processors are used for compression and transmission of coded streams to gateways, which in turn transrate the incoming streams and adapt them to the variable complexity requirements of both the sensor encoders and end-user decoder terminals. Such gateways provide real-time transcoding functionalities for bandwidth adaptation and coding/decoding complexity distribution by transferring the most complex video encoding/decoding tasks to the transcoding gateway at the expense of a limited increase in bit rate. Then, a method to reduce the decoding complexity, suitable for system-on-chip implementation, is proposed to operate at the transcoding gateway whenever decoders with constrained resources are targeted. The results show that the proposed method achieves good performance and its inclusion into the VSN infrastructure provides an additional level of complexity control functionality. PMID:22736972

Distributed coding/decoding complexity in video sensor networks.

PubMed

Cordeiro, Paulo J; Assunção, Pedro

2012-01-01

Video Sensor Networks (VSNs) are recent communication infrastructures used to capture and transmit dense visual information from an application context. In such large scale environments which include video coding, transmission and display/storage, there are several open problems to overcome in practical implementations. This paper addresses the most relevant challenges posed by VSNs, namely stringent bandwidth usage and processing time/power constraints. In particular, the paper proposes a novel VSN architecture where large sets of visual sensors with embedded processors are used for compression and transmission of coded streams to gateways, which in turn transrate the incoming streams and adapt them to the variable complexity requirements of both the sensor encoders and end-user decoder terminals. Such gateways provide real-time transcoding functionalities for bandwidth adaptation and coding/decoding complexity distribution by transferring the most complex video encoding/decoding tasks to the transcoding gateway at the expense of a limited increase in bit rate. Then, a method to reduce the decoding complexity, suitable for system-on-chip implementation, is proposed to operate at the transcoding gateway whenever decoders with constrained resources are targeted. The results show that the proposed method achieves good performance and its inclusion into the VSN infrastructure provides an additional level of complexity control functionality.

Hanford meteorological station computer codes: Volume 9, The quality assurance computer codes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Burk, K.W.; Andrews, G.L.

1989-02-01

The Hanford Meteorological Station (HMS) was established in 1944 on the Hanford Site to collect and archive meteorological data and provide weather forecasts and related services for Hanford Site approximately 1/2 mile east of the 200 West Area and is operated by PNL for the US Department of Energy. Meteorological data are collected from various sensors and equipment located on and off the Hanford Site. These data are stored in data bases on the Digital Equipment Corporation (DEC) VAX 11/750 at the HMS (hereafter referred to as the HMS computer). Files from those data bases are routinely transferred to themore » Emergency Management System (EMS) computer at the Unified Dose Assessment Center (UDAC). To ensure the quality and integrity of the HMS data, a set of Quality Assurance (QA) computer codes has been written. The codes will be routinely used by the HMS system manager or the data base custodian. The QA codes provide detailed output files that will be used in correcting erroneous data. The following sections in this volume describe the implementation and operation of QA computer codes. The appendices contain detailed descriptions, flow charts, and source code listings of each computer code. 2 refs.« less

Architecture for the Interdisciplinary Earth Data Alliance

NASA Astrophysics Data System (ADS)

Richard, S. M.

2016-12-01

The Interdisciplinary Earth Data Alliance (IEDA) is leading an EarthCube (EC) Integrative Activity to develop a governance structure and technology framework that enables partner data systems to share technology, infrastructure, and practice for documenting, curating, and accessing heterogeneous geoscience data. The IEDA data facility provides capabilities in an extensible framework that enables domain-specific requirements for each partner system in the Alliance to be integrated into standardized cross-domain workflows. The shared technology infrastructure includes a data submission hub, a domain-agnostic file-based repository, an integrated Alliance catalog and a Data Browser for data discovery across all partner holdings, as well as services for registering identifiers for datasets (DOI) and samples (IGSN). The submission hub will be a platform that facilitates acquisition of cross-domain resource documentation and channels users into domain and resource-specific workflows tailored for each partner community. We are exploring an event-based message bus architecture with a standardized plug-in interface for adding capabilities. This architecture builds on the EC CINERGI metadata pipeline as well as the message-based architecture of the SEAD project. Plug-in components for file introspection to match entities to a data type registry (extending EC Digital Crust and Research Data Alliance work), extract standardized keywords (using CINERGI components), location, cruise, personnel and other metadata linkage information (building on GeoLink and existing IEDA partner components). The submission hub will feed submissions to appropriate partner repositories and service endpoints targeted by domain and resource type for distribution. The Alliance governance will adopt patterns (vocabularies, operations, resource types) for self-describing data services using standard HTTP protocol for simplified data access (building on EC GeoWS and other `RESTful' approaches). Exposure of resource descriptions (datasets and service distributions) for harvesting by commercial search engines as well as geoscience-data focused crawlers (like EC B-Cube crawler) will increase discoverability of IEDA resources with minimal effort by curators.

IBM Demonstrates a General-Purpose, High-Performance, High-Availability Cloud-Hosted Data Distribution System With Live GOES-16 Weather Satellite Data

NASA Astrophysics Data System (ADS)

Snyder, P. L.; Brown, V. W.

2017-12-01

IBM has created a general purpose, data-agnostic solution that provides high performance, low data latency, high availability, scalability, and persistent access to the captured data, regardless of source or type. This capability is hosted on commercially available cloud environments and uses much faster, more efficient, reliable, and secure data transfer protocols than the more typically used FTP. The design incorporates completely redundant data paths at every level, including at the cloud data center level, in order to provide the highest assurance of data availability to the data consumers. IBM has been successful in building and testing a Proof of Concept instance on our IBM Cloud platform to receive and disseminate actual GOES-16 data as it is being downlinked. This solution leverages the inherent benefits of a cloud infrastructure configured and tuned for continuous, stable, high-speed data dissemination to data consumers worldwide at the downlink rate. It also is designed to ingest data from multiple simultaneous sources and disseminate data to multiple consumers. Nearly linear scalability is achieved by adding servers and storage.The IBM Proof of Concept system has been tested with our partners to achieve in excess of 5 Gigabits/second over public internet infrastructure. In tests with live GOES-16 data, the system routinely achieved 2.5 Gigabits/second pass-through to The Weather Company from the University of Wisconsin-Madison SSEC. Simulated data was also transferred from the Cooperative Institute for Climate and Satellites — North Carolina to The Weather Company, as well. The storage node allocated to our Proof of Concept system as tested was sized at 480 Terabytes of RAID protected disk as a worst case sizing to accommodate the data from four GOES-16 class satellites for 30 days in a circular buffer. This shows that an abundance of performance and capacity headroom exists in the IBM design that can be applied to additional missions.

The CARMEN software as a service infrastructure.

PubMed

Weeks, Michael; Jessop, Mark; Fletcher, Martyn; Hodge, Victoria; Jackson, Tom; Austin, Jim

2013-01-28

The CARMEN platform allows neuroscientists to share data, metadata, services and workflows, and to execute these services and workflows remotely via a Web portal. This paper describes how we implemented a service-based infrastructure into the CARMEN Virtual Laboratory. A Software as a Service framework was developed to allow generic new and legacy code to be deployed as services on a heterogeneous execution framework. Users can submit analysis code typically written in Matlab, Python, C/C++ and R as non-interactive standalone command-line applications and wrap them as services in a form suitable for deployment on the platform. The CARMEN Service Builder tool enables neuroscientists to quickly wrap their analysis software for deployment to the CARMEN platform, as a service without knowledge of the service framework or the CARMEN system. A metadata schema describes each service in terms of both system and user requirements. The search functionality allows services to be quickly discovered from the many services available. Within the platform, services may be combined into more complicated analyses using the workflow tool. CARMEN and the service infrastructure are targeted towards the neuroscience community; however, it is a generic platform, and can be targeted towards any discipline.

Reproducible Earth observation analytics: challenges, ideas, and a study case on containerized land use change detection

NASA Astrophysics Data System (ADS)

Appel, Marius; Nüst, Daniel; Pebesma, Edzer

2017-04-01

Geoscientific analyses of Earth observation data typically involve a long path from data acquisition to scientific results and conclusions. Before starting the actual processing, scenes must be downloaded from the providers' platforms and the computing infrastructure needs to be prepared. The computing environment often requires specialized software, which in turn might have lots of dependencies. The software is often highly customized and provided without commercial support, which leads to rather ad-hoc systems and irreproducible results. To let other scientists reproduce the analyses, the full workspace including data, code, the computing environment, and documentation must be bundled and shared. Technologies such as virtualization or containerization allow for the creation of identical computing environments with relatively little effort. Challenges, however, arise when the volume of the data is too large, when computations are done in a cluster environment, or when complex software components such as databases are used. We discuss these challenges for the example of scalable Land use change detection on Landsat imagery. We present a reproducible implementation that runs R and the scalable data management and analytical system SciDB within a Docker container. Thanks to an explicit container recipe (the Dockerfile), this enables the all-in-one reproduction including the installation of software components, the ingestion of the data, and the execution of the analysis in a well-defined environment. We furthermore discuss possibilities how the implementation could be transferred to multi-container environments in order to support reproducibility on large cluster environments.

23 CFR 505.17 - Applicability of Title 23, U.S. Code.

Code of Federal Regulations, 2010 CFR

2010-04-01

... INFRASTRUCTURE MANAGEMENT PROJECTS OF NATIONAL AND REGIONAL SIGNIFICANCE EVALUATION AND RATING § 505.17... until expended and the Federal share of the cost of a Project of National and Regional Significance...

6 CFR 29.9 - Investigation and reporting of violation of PCII procedures.

Code of Federal Regulations, 2010 CFR

2010-01-01

... PROTECTED CRITICAL INFRASTRUCTURE INFORMATION § 29.9 Investigation and reporting of violation of PCII... or employee thereof, shall be fined under title 18 of the United States Code, imprisoned not more...

Development & Use of Adverse Outcome Pathways for 21st Century Decision Support

EPA Science Inventory

The Adverse Outcome Pathway has emerged as an internationally harmonized mechanism for organizing biological information in a chemical agnostic manner. This construct is valuable for interpreting the results from high-throughput toxicity (HTT) assessment by providing a mechanisti...

A Post-Intentional Exploration of Agnostic College Students' Experiences

ERIC Educational Resources Information Center

Armstrong, Amanda

2017-01-01

Scholars have adapted college student identity development models to examine and highlight the unique, laborious, and varied experiences of marginalized populations. However, researchers have minimally explored the perspectives of nontheistic and nonreligious college students using poststructural methodologies. I followed a post-intentional…

Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences

PubMed Central

2014-01-01

Background Small RNAs are important regulators of genome function, yet their prediction in genomes is still a major computational challenge. Statistical analyses of pre-miRNA sequences indicated that their 2D structure tends to have a minimal free energy (MFE) significantly lower than MFE values of equivalently randomized sequences with the same nucleotide composition, in contrast to other classes of non-coding RNA. The computation of many MFEs is, however, too intensive to allow for genome-wide screenings. Results Using a local grid infrastructure, MFE distributions of random sequences were pre-calculated on a large scale. These distributions follow a normal distribution and can be used to determine the MFE distribution for any given sequence composition by interpolation. It allows on-the-fly calculation of the normal distribution for any candidate sequence composition. Conclusion The speedup achieved makes genome-wide screening with this characteristic of a pre-miRNA sequence practical. Although this particular property alone will not be able to distinguish miRNAs from other sequences sufficiently discriminative, the MFE-based P-value should be added to the parameters of choice to be included in the selection of potential miRNA candidates for experimental verification. PMID:24418292

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis

PubMed Central

Duarte, Afonso M. S.; Psomopoulos, Fotis E.; Blanchet, Christophe; Bonvin, Alexandre M. J. J.; Corpas, Manuel; Franc, Alain; Jimenez, Rafael C.; de Lucas, Jesus M.; Nyrönen, Tommi; Sipos, Gergely; Suhr, Stephanie B.

2015-01-01

With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners. Here we aim to provide the state of the art of Grid/Cloud computing in EU research as viewed from within the field of life sciences, focusing on key infrastructures and projects within the life sciences community. Rather than focusing purely on the technical aspects underlying the currently provided solutions, we outline the design aspects and key characteristics that can be identified across major research approaches. Overall, we aim to provide significant insights into the road ahead by establishing ever-strengthening connections between EGI as a whole and the life sciences community. PMID:26157454

Future opportunities and trends for e-infrastructures and life sciences: going beyond the grid to enable life science data analysis.

PubMed

Duarte, Afonso M S; Psomopoulos, Fotis E; Blanchet, Christophe; Bonvin, Alexandre M J J; Corpas, Manuel; Franc, Alain; Jimenez, Rafael C; de Lucas, Jesus M; Nyrönen, Tommi; Sipos, Gergely; Suhr, Stephanie B

2015-01-01

With the increasingly rapid growth of data in life sciences we are witnessing a major transition in the way research is conducted, from hypothesis-driven studies to data-driven simulations of whole systems. Such approaches necessitate the use of large-scale computational resources and e-infrastructures, such as the European Grid Infrastructure (EGI). EGI, one of key the enablers of the digital European Research Area, is a federation of resource providers set up to deliver sustainable, integrated and secure computing services to European researchers and their international partners. Here we aim to provide the state of the art of Grid/Cloud computing in EU research as viewed from within the field of life sciences, focusing on key infrastructures and projects within the life sciences community. Rather than focusing purely on the technical aspects underlying the currently provided solutions, we outline the design aspects and key characteristics that can be identified across major research approaches. Overall, we aim to provide significant insights into the road ahead by establishing ever-strengthening connections between EGI as a whole and the life sciences community.

GLIDE: a grid-based light-weight infrastructure for data-intensive environments

NASA Technical Reports Server (NTRS)

Mattmann, Chris A.; Malek, Sam; Beckman, Nels; Mikic-Rakic, Marija; Medvidovic, Nenad; Chrichton, Daniel J.

2005-01-01

The promise of the grid is that it will enable public access and sharing of immense amounts of computational and data resources among dynamic coalitions of individuals and institutions. However, the current grid solutions make several limiting assumptions that curtail their widespread adoption. To address these limitations, we present GLIDE, a prototype light-weight, data-intensive middleware infrastructure that enables access to the robust data and computational power of the grid on DREAM platforms.

Integrating multiple scientific computing needs via a Private Cloud infrastructure

NASA Astrophysics Data System (ADS)

Bagnasco, S.; Berzano, D.; Brunetti, R.; Lusso, S.; Vallero, S.

2014-06-01

In a typical scientific computing centre, diverse applications coexist and share a single physical infrastructure. An underlying Private Cloud facility eases the management and maintenance of heterogeneous use cases such as multipurpose or application-specific batch farms, Grid sites catering to different communities, parallel interactive data analysis facilities and others. It allows to dynamically and efficiently allocate resources to any application and to tailor the virtual machines according to the applications' requirements. Furthermore, the maintenance of large deployments of complex and rapidly evolving middleware and application software is eased by the use of virtual images and contextualization techniques; for example, rolling updates can be performed easily and minimizing the downtime. In this contribution we describe the Private Cloud infrastructure at the INFN-Torino Computer Centre, that hosts a full-fledged WLCG Tier-2 site and a dynamically expandable PROOF-based Interactive Analysis Facility for the ALICE experiment at the CERN LHC and several smaller scientific computing applications. The Private Cloud building blocks include the OpenNebula software stack, the GlusterFS filesystem (used in two different configurations for worker- and service-class hypervisors) and the OpenWRT Linux distribution (used for network virtualization). A future integration into a federated higher-level infrastructure is made possible by exposing commonly used APIs like EC2 and by using mainstream contextualization tools like CloudInit.

Reproducible Research in the Geosciences at Scale: Achievable Goal or Elusive Dream?

NASA Astrophysics Data System (ADS)

Wyborn, L. A.; Evans, B. J. K.

2016-12-01

Reproducibility is a fundamental tenant of the scientific method: it implies that any researcher, or a third party working independently, can duplicate any experiment or investigation and produce the same results. Historically computationally based research involved an individual using their own data and processing it in their own private area, often using software they wrote or inherited from close collaborators. Today, a researcher is likely to be part of a large team that will use a subset of data from an external repository and then process the data on a public or private cloud or on a large centralised supercomputer, using a mixture of their own code, third party software and libraries, or global community codes. In 'Big Geoscience' research it is common for data inputs to be extracts from externally managed dynamic data collections, where new data is being regularly appended, or existing data is revised when errors are detected and/or as processing methods are improved. New workflows increasingly use services to access data dynamically to create subsets on-the-fly from distributed sources, each of which can have a complex history. At major computational facilities, underlying systems, libraries, software and services are being constantly tuned and optimised, or as new or replacement infrastructure being installed. Likewise code used from a community repository is continually being refined, re-packaged and ported to the target platform. To achieve reproducibility, today's researcher increasingly needs to track their workflow, including querying information on the current or historical state of facilities used. Versioning methods are standard practice for software repositories or packages, but it is not common for either data repositories or data services to provide information about their state, or for systems to provide query-able access to changes in the underlying software. While a researcher can achieve transparency and describe steps in their workflow so that others can repeat them and replicate processes undertaken, they cannot achieve exact reproducibility or even transparency of results generated. In Big Geoscience, full reproducibiliy will be an elusive dream until data repositories and compute facilities can provide provenance information in a standards compliant, machine query-able way.

User's manual for semi-circular compact range reflector code

NASA Technical Reports Server (NTRS)

Gupta, Inder J.; Burnside, Walter D.

1986-01-01

A computer code was developed to analyze a semi-circular paraboloidal reflector antenna with a rolled edge at the top and a skirt at the bottom. The code can be used to compute the total near field of the antenna or its individual components at a given distance from the center of the paraboloid. Thus, it is very effective in computing the size of the sweet spot for RCS or antenna measurement. The operation of the code is described. Various input and output statements are explained. Some results obtained using the computer code are presented to illustrate the code's capability as well as being samples of input/output sets.

Highly fault-tolerant parallel computation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spielman, D.A.

We re-introduce the coded model of fault-tolerant computation in which the input and output of a computational device are treated as words in an error-correcting code. A computational device correctly computes a function in the coded model if its input and output, once decoded, are a valid input and output of the function. In the coded model, it is reasonable to hope to simulate all computational devices by devices whose size is greater by a constant factor but which are exponentially reliable even if each of their components can fail with some constant probability. We consider fine-grained parallel computations inmore » which each processor has a constant probability of producing the wrong output at each time step. We show that any parallel computation that runs for time t on w processors can be performed reliably on a faulty machine in the coded model using w log{sup O(l)} w processors and time t log{sup O(l)} w. The failure probability of the computation will be at most t {center_dot} exp(-w{sup 1/4}). The codes used to communicate with our fault-tolerant machines are generalized Reed-Solomon codes and can thus be encoded and decoded in O(n log{sup O(1)} n) sequential time and are independent of the machine they are used to communicate with. We also show how coded computation can be used to self-correct many linear functions in parallel with arbitrarily small overhead.« less

An emulator for minimizing computer resources for finite element analysis

NASA Technical Reports Server (NTRS)

Melosh, R.; Utku, S.; Islam, M.; Salama, M.

1984-01-01

A computer code, SCOPE, has been developed for predicting the computer resources required for a given analysis code, computer hardware, and structural problem. The cost of running the code is a small fraction (about 3 percent) of the cost of performing the actual analysis. However, its accuracy in predicting the CPU and I/O resources depends intrinsically on the accuracy of calibration data that must be developed once for the computer hardware and the finite element analysis code of interest. Testing of the SCOPE code on the AMDAHL 470 V/8 computer and the ELAS finite element analysis program indicated small I/O errors (3.2 percent), larger CPU errors (17.8 percent), and negligible total errors (1.5 percent).

A Hybrid Algorithm for Period Analysis from Multiband Data with Sparse and Irregular Sampling for Arbitrary Light-curve Shapes

NASA Astrophysics Data System (ADS)

Saha, Abhijit; Vivas, A. Katherina

2017-12-01

Ongoing and future surveys with repeat imaging in multiple bands are producing (or will produce) time-spaced measurements of brightness, resulting in the identification of large numbers of variable sources in the sky. A large fraction of these are periodic variables: compilations of these are of scientific interest for a variety of purposes. Unavoidably, the data sets from many such surveys not only have sparse sampling, but also have embedded frequencies in the observing cadence that beat against the natural periodicities of any object under investigation. Such limitations can make period determination ambiguous and uncertain. For multiband data sets with asynchronous measurements in multiple passbands, we wish to maximally use the information on periodicity in a manner that is agnostic of differences in the light-curve shapes across the different channels. Given large volumes of data, computational efficiency is also at a premium. This paper develops and presents a computationally economic method for determining periodicity that combines the results from two different classes of period-determination algorithms. The underlying principles are illustrated through examples. The effectiveness of this approach for combining asynchronously sampled measurements in multiple observables that share an underlying fundamental frequency is also demonstrated.

Spatial probabilistic pulsatility model for enhancing photoplethysmographic imaging systems

NASA Astrophysics Data System (ADS)

Amelard, Robert; Clausi, David A.; Wong, Alexander

2016-11-01

Photoplethysmographic imaging (PPGI) is a widefield noncontact biophotonic technology able to remotely monitor cardiovascular function over anatomical areas. Although spatial context can provide insight into physiologically relevant sampling locations, existing PPGI systems rely on coarse spatial averaging with no anatomical priors for assessing arterial pulsatility. Here, we developed a continuous probabilistic pulsatility model for importance-weighted blood pulse waveform extraction. Using a data-driven approach, the model was constructed using a 23 participant sample with a large demographic variability (11/12 female/male, age 11 to 60 years, BMI 16.4 to 35.1 kg·m-2). Using time-synchronized ground-truth blood pulse waveforms, spatial correlation priors were computed and projected into a coaligned importance-weighted Cartesian space. A modified Parzen-Rosenblatt kernel density estimation method was used to compute the continuous resolution-agnostic probabilistic pulsatility model. The model identified locations that consistently exhibited pulsatility across the sample. Blood pulse waveform signals extracted with the model exhibited significantly stronger temporal correlation (W=35,p<0.01) and spectral SNR (W=31,p<0.01) compared to uniform spatial averaging. Heart rate estimation was in strong agreement with true heart rate [r2=0.9619, error (μ,σ)=(0.52,1.69) bpm].

Reactive documentation system

NASA Astrophysics Data System (ADS)

Boehnlein, Thomas R.; Kramb, Victoria

2018-04-01

Proper formal documentation of computer acquired NDE experimental data generated during research is critical to the longevity and usefulness of the data. Without documentation describing how and why the data was acquired, NDE research teams lose capability such as their ability to generate new information from previously collected data or provide adequate information so that their work can be replicated by others seeking to validate their research. Despite the critical nature of this issue, NDE data is still being generated in research labs without appropriate documentation. By generating documentation in series with data, equal priority is given to both activities during the research process. One way to achieve this is to use a reactive documentation system (RDS). RDS prompts an operator to document the data as it is generated rather than relying on the operator to decide when and what to document. This paper discusses how such a system can be implemented in a dynamic environment made up of in-house and third party NDE data acquisition systems without creating additional burden on the operator. The reactive documentation approach presented here is agnostic enough that the principles can be applied to any operator controlled, computer based, data acquisition system.

Computation and application of tissue-specific gene set weights.

PubMed

Frost, H Robert

2018-04-06

Gene set testing, or pathway analysis, has become a critical tool for the analysis of highdimensional genomic data. Although the function and activity of many genes and higher-level processes is tissue-specific, gene set testing is typically performed in a tissue agnostic fashion, which impacts statistical power and the interpretation and replication of results. To address this challenge, we have developed a bioinformatics approach to compute tissuespecific weights for individual gene sets using information on tissue-specific gene activity from the Human Protein Atlas (HPA). We used this approach to create a public repository of tissue-specific gene set weights for 37 different human tissue types from the HPA and all collections in the Molecular Signatures Database (MSigDB). To demonstrate the validity and utility of these weights, we explored three different applications: the functional characterization of human tissues, multi-tissue analysis for systemic diseases and tissue-specific gene set testing. All data used in the reported analyses is publicly available. An R implementation of the method and tissue-specific weights for MSigDB gene set collections can be downloaded at http://www.dartmouth.edu/∼hrfrost/TissueSpecificGeneSets. rob.frost@dartmouth.edu.

Joint Knowledge Generation Between Climate Science and Infrastructure Engineering

NASA Astrophysics Data System (ADS)

Stoner, A. M. K.; Hayhoe, K.; Jacobs, J. M.

2015-12-01

Over the past decade the engineering community has become increasingly aware of the need to incorporate climate projections into the planning and design of sensitive infrastructure. However, this is a task that is easier said than done. This presentation will discuss some of the successes and hurdles experiences through the past year, from a climate scientist's perspective, working with engineers in infrastructure research and applied engineering through the Infrastructure & Climate Network (ICNet). Engineers rely on strict building codes and ordinances, and can be the subject of lawsuits if those codes are not followed. Matters are further complicated by the uncertainty inherent to climate projections, which include short-term natural variability, as well as the influence of scientific uncertainty and even human behavior on the rate and magnitude of change. Climate scientists typically address uncertainty by creating projections based on multiple models following different future scenarios. This uncertainty is difficult to incorporate into engineering projects, however, due to the fact that they cannot build two different bridges, one allowing for a lower amount of change, and another for a higher. More often than not there is a considerable difference between the costs of building two such bridges, which means that available funds often are the deciding factor. Discussions of climate science are often well received with engineers who work in the research area of infrastructure; going a step further, however, and implementing it in applied engineering projects can be challenging. This presentation will discuss some of the challenges and opportunities inherent to collaborations between climate scientists and transportation engineers, drawing from a range of studies including truck weight restrictions on roads during the spring thaw, and bridge deck performance due to environmental forcings.

VisIVO: A Library and Integrated Tools for Large Astrophysical Dataset Exploration

NASA Astrophysics Data System (ADS)

Becciani, U.; Costa, A.; Ersotelos, N.; Krokos, M.; Massimino, P.; Petta, C.; Vitello, F.

2012-09-01

VisIVO provides an integrated suite of tools and services that can be used in many scientific fields. VisIVO development starts in the Virtual Observatory framework. VisIVO allows users to visualize meaningfully highly-complex, large-scale datasets and create movies of these visualizations based on distributed infrastructures. VisIVO supports high-performance, multi-dimensional visualization of large-scale astrophysical datasets. Users can rapidly obtain meaningful visualizations while preserving full and intuitive control of the relevant parameters. VisIVO consists of VisIVO Desktop - a stand-alone application for interactive visualization on standard PCs, VisIVO Server - a platform for high performance visualization, VisIVO Web - a custom designed web portal, VisIVOSmartphone - an application to exploit the VisIVO Server functionality and the latest VisIVO features: VisIVO Library allows a job running on a computational system (grid, HPC, etc.) to produce movies directly with the code internal data arrays without the need to produce intermediate files. This is particularly important when running on large computational facilities, where the user wants to have a look at the results during the data production phase. For example, in grid computing facilities, images can be produced directly in the grid catalogue while the user code is running in a system that cannot be directly accessed by the user (a worker node). The deployment of VisIVO on the DG and gLite is carried out with the support of EDGI and EGI-Inspire projects. Depending on the structure and size of datasets under consideration, the data exploration process could take several hours of CPU for creating customized views and the production of movies could potentially last several days. For this reason an MPI parallel version of VisIVO could play a fundamental role in increasing performance, e.g. it could be automatically deployed on nodes that are MPI aware. A central concept in our development is thus to produce unified code that can run either on serial nodes or in parallel by using HPC oriented grid nodes. Another important aspect, to obtain as high performance as possible, is the integration of VisIVO processes with grid nodes where GPUs are available. We have selected CUDA for implementing a range of computationally heavy modules. VisIVO is supported by EGI-Inspire, EDGI and SCI-BUS projects.

A generalized one-dimensional computer code for turbomachinery cooling passage flow calculations

NASA Technical Reports Server (NTRS)

Kumar, Ganesh N.; Roelke, Richard J.; Meitner, Peter L.

1989-01-01

A generalized one-dimensional computer code for analyzing the flow and heat transfer in the turbomachinery cooling passages was developed. This code is capable of handling rotating cooling passages with turbulators, 180 degree turns, pin fins, finned passages, by-pass flows, tip cap impingement flows, and flow branching. The code is an extension of a one-dimensional code developed by P. Meitner. In the subject code, correlations for both heat transfer coefficient and pressure loss computations were developed to model each of the above mentioned type of coolant passages. The code has the capability of independently computing the friction factor and heat transfer coefficient on each side of a rectangular passage. Either the mass flow at the inlet to the channel or the exit plane pressure can be specified. For a specified inlet total temperature, inlet total pressure, and exit static pressure, the code computers the flow rates through the main branch and the subbranches, flow through tip cap for impingement cooling, in addition to computing the coolant pressure, temperature, and heat transfer coefficient distribution in each coolant flow branch. Predictions from the subject code for both nonrotating and rotating passages agree well with experimental data. The code was used to analyze the cooling passage of a research cooled radial rotor.

PRACE - The European HPC Infrastructure

NASA Astrophysics Data System (ADS)

Stadelmeyer, Peter

2014-05-01

The mission of PRACE (Partnership for Advanced Computing in Europe) is to enable high impact scientific discovery and engineering research and development across all disciplines to enhance European competitiveness for the benefit of society. PRACE seeks to realize this mission by offering world class computing and data management resources and services through a peer review process. This talk gives a general overview about PRACE and the PRACE research infrastructure (RI). PRACE is established as an international not-for-profit association and the PRACE RI is a pan-European supercomputing infrastructure which offers access to computing and data management resources at partner sites distributed throughout Europe. Besides a short summary about the organization, history, and activities of PRACE, it is explained how scientists and researchers from academia and industry from around the world can access PRACE systems and which education and training activities are offered by PRACE. The overview also contains a selection of PRACE contributions to societal challenges and ongoing activities. Examples of the latter are beside others petascaling, application benchmark suite, best practice guides for efficient use of key architectures, application enabling / scaling, new programming models, and industrial applications. The Partnership for Advanced Computing in Europe (PRACE) is an international non-profit association with its seat in Brussels. The PRACE Research Infrastructure provides a persistent world-class high performance computing service for scientists and researchers from academia and industry in Europe. The computer systems and their operations accessible through PRACE are provided by 4 PRACE members (BSC representing Spain, CINECA representing Italy, GCS representing Germany and GENCI representing France). The Implementation Phase of PRACE receives funding from the EU's Seventh Framework Programme (FP7/2007-2013) under grant agreements RI-261557, RI-283493 and RI-312763. For more information, see www.prace-ri.eu

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis

PubMed Central

Simonyan, Vahan; Chumakov, Konstantin; Dingerdissen, Hayley; Faison, William; Goldweber, Scott; Golikov, Anton; Gulzar, Naila; Karagiannis, Konstantinos; Vinh Nguyen Lam, Phuc; Maudru, Thomas; Muravitskaja, Olesja; Osipova, Ekaterina; Pan, Yang; Pschenichnov, Alexey; Rostovtsev, Alexandre; Santana-Quintero, Luis; Smith, Krista; Thompson, Elaine E.; Tkachenko, Valery; Torcivia-Rodriguez, John; Wan, Quan; Wang, Jing; Wu, Tsung-Jung; Wilson, Carolyn; Mazumder, Raja

2016-01-01

The High-performance Integrated Virtual Environment (HIVE) is a distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized users to deposit, retrieve, annotate and compute on NGS data, and to analyse the outcomes using web interface visual environments appropriately built in collaboration with research and regulatory scientists and other end users. Unlike many massively parallel computing environments, HIVE uses a cloud control server which virtualizes services, not processes. It is both very robust and flexible due to the abstraction layer introduced between computational requests and operating system processes. The novel paradigm of moving computations to the data, instead of moving data to computational nodes, has proven to be significantly less taxing for both hardware and network infrastructure. The honeycomb data model developed for HIVE integrates metadata into an object-oriented model. Its distinction from other object-oriented databases is in the additional implementation of a unified application program interface to search, view and manipulate data of all types. This model simplifies the introduction of new data types, thereby minimizing the need for database restructuring and streamlining the development of new integrated information systems. The honeycomb model employs a highly secure hierarchical access control and permission system, allowing determination of data access privileges in a finely granular manner without flooding the security subsystem with a multiplicity of rules. HIVE infrastructure will allow engineers and scientists to perform NGS analysis in a manner that is both efficient and secure. HIVE is actively supported in public and private domains, and project collaborations are welcomed. Database URL: https://hive.biochemistry.gwu.edu PMID:26989153

High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis.

PubMed

Simonyan, Vahan; Chumakov, Konstantin; Dingerdissen, Hayley; Faison, William; Goldweber, Scott; Golikov, Anton; Gulzar, Naila; Karagiannis, Konstantinos; Vinh Nguyen Lam, Phuc; Maudru, Thomas; Muravitskaja, Olesja; Osipova, Ekaterina; Pan, Yang; Pschenichnov, Alexey; Rostovtsev, Alexandre; Santana-Quintero, Luis; Smith, Krista; Thompson, Elaine E; Tkachenko, Valery; Torcivia-Rodriguez, John; Voskanian, Alin; Wan, Quan; Wang, Jing; Wu, Tsung-Jung; Wilson, Carolyn; Mazumder, Raja

2016-01-01

The High-performance Integrated Virtual Environment (HIVE) is a distributed storage and compute environment designed primarily to handle next-generation sequencing (NGS) data. This multicomponent cloud infrastructure provides secure web access for authorized users to deposit, retrieve, annotate and compute on NGS data, and to analyse the outcomes using web interface visual environments appropriately built in collaboration with research and regulatory scientists and other end users. Unlike many massively parallel computing environments, HIVE uses a cloud control server which virtualizes services, not processes. It is both very robust and flexible due to the abstraction layer introduced between computational requests and operating system processes. The novel paradigm of moving computations to the data, instead of moving data to computational nodes, has proven to be significantly less taxing for both hardware and network infrastructure.The honeycomb data model developed for HIVE integrates metadata into an object-oriented model. Its distinction from other object-oriented databases is in the additional implementation of a unified application program interface to search, view and manipulate data of all types. This model simplifies the introduction of new data types, thereby minimizing the need for database restructuring and streamlining the development of new integrated information systems. The honeycomb model employs a highly secure hierarchical access control and permission system, allowing determination of data access privileges in a finely granular manner without flooding the security subsystem with a multiplicity of rules. HIVE infrastructure will allow engineers and scientists to perform NGS analysis in a manner that is both efficient and secure. HIVE is actively supported in public and private domains, and project collaborations are welcomed. Database URL: https://hive.biochemistry.gwu.edu. © The Author(s) 2016. Published by Oxford University Press.

Cooperative high-performance storage in the accelerated strategic computing initiative

NASA Technical Reports Server (NTRS)

Gary, Mark; Howard, Barry; Louis, Steve; Minuzzo, Kim; Seager, Mark

1996-01-01

The use and acceptance of new high-performance, parallel computing platforms will be impeded by the absence of an infrastructure capable of supporting orders-of-magnitude improvement in hierarchical storage and high-speed I/O (Input/Output). The distribution of these high-performance platforms and supporting infrastructures across a wide-area network further compounds this problem. We describe an architectural design and phased implementation plan for a distributed, Cooperative Storage Environment (CSE) to achieve the necessary performance, user transparency, site autonomy, communication, and security features needed to support the Accelerated Strategic Computing Initiative (ASCI). ASCI is a Department of Energy (DOE) program attempting to apply terascale platforms and Problem-Solving Environments (PSEs) toward real-world computational modeling and simulation problems. The ASCI mission must be carried out through a unified, multilaboratory effort, and will require highly secure, efficient access to vast amounts of data. The CSE provides a logically simple, geographically distributed, storage infrastructure of semi-autonomous cooperating sites to meet the strategic ASCI PSE goal of highperformance data storage and access at the user desktop.

Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †

PubMed Central

Murdani, Muhammad Harist; Hong, Bonghee

2018-01-01

In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes (Ad-Hoc) and neighborhood proximity (Top-K). Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space. PMID:29587366

Efficient Proximity Computation Techniques Using ZIP Code Data for Smart Cities †.

PubMed

Murdani, Muhammad Harist; Kwon, Joonho; Choi, Yoon-Ho; Hong, Bonghee

2018-03-24

In this paper, we are interested in computing ZIP code proximity from two perspectives, proximity between two ZIP codes ( Ad-Hoc ) and neighborhood proximity ( Top-K ). Such a computation can be used for ZIP code-based target marketing as one of the smart city applications. A naïve approach to this computation is the usage of the distance between ZIP codes. We redefine a distance metric combining the centroid distance with the intersecting road network between ZIP codes by using a weighted sum method. Furthermore, we prove that the results of our combined approach conform to the characteristics of distance measurement. We have proposed a general and heuristic approach for computing Ad-Hoc proximity, while for computing Top-K proximity, we have proposed a general approach only. Our experimental results indicate that our approaches are verifiable and effective in reducing the execution time and search space.

IEEE TRANSACTIONS ON CYBERNETICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Craig R. RIeger; David H. Scheidt; William D. Smart

2014-11-01

MODERN societies depend on complex and critical infrastructures for energy, transportation, sustenance, medical care, emergency response, communications security. As computers, automation, and information technology (IT) have advanced, these technologies have been exploited to enhance the efficiency of operating the processes that make up these infrastructures

The Computational Infrastructure for Geodynamics: An Example of Software Curation and Citation in the Geodynamics Community

NASA Astrophysics Data System (ADS)

Hwang, L.; Kellogg, L. H.

2017-12-01

Curation of software promotes discoverability and accessibility and works hand in hand with scholarly citation to ascribe value to, and provide recognition for software development. To meet this challenge, the Computational Infrastructure for Geodynamics (CIG) maintains a community repository built on custom and open tools to promote discovery, access, identification, credit, and provenance of research software for the geodynamics community. CIG (geodynamics.org) originated from recognition of the tremendous effort required to develop sound software and the need to reduce duplication of effort and to sustain community codes. CIG curates software across 6 domains and has developed and follows software best practices that include establishing test cases, documentation, and a citable publication for each software package. CIG software landing web pages provide access to current and past releases; many are also accessible through the CIG community repository on github. CIG has now developed abc - attribution builder for citation to enable software users to give credit to software developers. abc uses zenodo as an archive and as the mechanism to obtain a unique identifier (DOI) for scientific software. To assemble the metadata, we searched the software's documentation and research publications and then requested the primary developers to verify. In this process, we have learned that each development community approaches software attribution differently. The metadata gathered is based on guidelines established by groups such as FORCE11 and OntoSoft. The rollout of abc is gradual as developers are forward-looking, rarely willing to go back and archive prior releases in zenodo. Going forward all actively developed packages will utilize the zenodo and github integration to automate the archival process when a new release is issued. How to handle legacy software, multi-authored libraries, and assigning roles to software remain open issues.

A modular (almost) automatic set-up for elastic multi-tenants cloud (micro)infrastructures

NASA Astrophysics Data System (ADS)

Amoroso, A.; Astorino, F.; Bagnasco, S.; Balashov, N. A.; Bianchi, F.; Destefanis, M.; Lusso, S.; Maggiora, M.; Pellegrino, J.; Yan, L.; Yan, T.; Zhang, X.; Zhao, X.

2017-10-01

An auto-installing tool on an usb drive can allow for a quick and easy automatic deployment of OpenNebula-based cloud infrastructures remotely managed by a central VMDIRAC instance. A single team, in the main site of an HEP Collaboration or elsewhere, can manage and run a relatively large network of federated (micro-)cloud infrastructures, making an highly dynamic and elastic use of computing resources. Exploiting such an approach can lead to modular systems of cloud-bursting infrastructures addressing complex real-life scenarios.

System Engineering Infrastructure Evolution Galileo IOV and the Steps Beyond

NASA Astrophysics Data System (ADS)

Eickhoff, J.; Herpel, H.-J.; Steinle, T.; Birn, R.; Steiner, W.-D.; Eisenmann, H.; Ludwig, T.

2009-05-01

The trends to more and more constrained financial budgets in satellite engineering require a permanent optimization of the S/C system engineering processes and infrastructure. Astrium in the recent years already has built up a system simulation infrastructure - the "Model-based Development & Verification Environment" - which meanwhile is well known all over Europe and is established as Astrium's standard approach for ESA, DLR projects and now even the EU/ESA-Project Galileo IOV. The key feature of the MDVE / FVE approach is to provide entire S/C simulation (with full featured OBC simulation) already in early phases to start OBSW code tests on a simulated S/C and to later add hardware in the loop step by step up to an entire "Engineering Functional Model (EFM)" or "FlatSat". The subsequent enhancements to this simulator infrastructure w.r.t. spacecraft design data handling are reported in the following sections.

CAPRI (Computational Analysis PRogramming Interface): A Solid Modeling Based Infra-Structure for Engineering Analysis and Design Simulations

NASA Technical Reports Server (NTRS)

Haimes, Robert; Follen, Gregory J.

1998-01-01

CAPRI is a CAD-vendor neutral application programming interface designed for the construction of analysis and design systems. By allowing access to the geometry from within all modules (grid generators, solvers and post-processors) such tasks as meshing on the actual surfaces, node enrichment by solvers and defining which mesh faces are boundaries (for the solver and visualization system) become simpler. The overall reliance on file 'standards' is minimized. This 'Geometry Centric' approach makes multi-physics (multi-disciplinary) analysis codes much easier to build. By using the shared (coupled) surface as the foundation, CAPRI provides a single call to interpolate grid-node based data from the surface discretization in one volume to another. Finally, design systems are possible where the results can be brought back into the CAD system (and therefore manufactured) because all geometry construction and modification are performed using the CAD system's geometry kernel.

DOE unveils climate model in advance of global test

NASA Astrophysics Data System (ADS)

Popkin, Gabriel

2018-05-01

The world's growing collection of climate models has a high-profile new entry. Last week, after nearly 4 years of work, the U.S. Department of Energy (DOE) released computer code and initial results from an ambitious effort to simulate the Earth system. The new model is tailored to run on future supercomputers and designed to forecast not just how climate will change, but also how those changes might stress energy infrastructure. Results from an upcoming comparison of global models may show how well the new entrant works. But so far it is getting a mixed reception, with some questioning the need for another model and others saying the $80 million effort has yet to improve predictions of the future climate. Even the project's chief scientist, Ruby Leung of the Pacific Northwest National Laboratory in Richland, Washington, acknowledges that the model is not yet a leader.

Volume accumulator design analysis computer codes

NASA Technical Reports Server (NTRS)

Whitaker, W. D.; Shimazaki, T. T.

1973-01-01

The computer codes, VANEP and VANES, were written and used to aid in the design and performance calculation of the volume accumulator units (VAU) for the 5-kwe reactor thermoelectric system. VANEP computes the VAU design which meets the primary coolant loop VAU volume and pressure performance requirements. VANES computes the performance of the VAU design, determined from the VANEP code, at the conditions of the secondary coolant loop. The codes can also compute the performance characteristics of the VAU's under conditions of possible modes of failure which still permit continued system operation.

Sustainable access to data, products, services and software from the European seismological Research Infrastructures: the EPOS TCS Seismology

NASA Astrophysics Data System (ADS)

Haslinger, Florian; Dupont, Aurelien; Michelini, Alberto; Rietbrock, Andreas; Sleeman, Reinoud; Wiemer, Stefan; Basili, Roberto; Bossu, Rémy; Cakti, Eser; Cotton, Fabrice; Crawford, Wayne; Diaz, Jordi; Garth, Tom; Locati, Mario; Luzi, Lucia; Pinho, Rui; Pitilakis, Kyriazis; Strollo, Angelo

2016-04-01

Easy, efficient and comprehensive access to data, data products, scientific services and scientific software is a key ingredient in enabling research at the frontiers of science. Organizing this access across the European Research Infrastructures in the field of seismology, so that it best serves user needs, takes advantage of state-of-the-art ICT solutions, provides cross-domain interoperability, and is organizationally and financially sustainable in the long term, is the core challenge of the implementation phase of the Thematic Core Service (TCS) Seismology within the EPOS-IP project. Building upon the existing European-level infrastructures ORFEUS for seismological waveforms, EMSC for seismological products, and EFEHR for seismological hazard and risk information, and implementing a pilot Computational Earth Science service starting from the results of the VERCE project, the work within the EPOS-IP project focuses on improving and extending the existing services, aligning them with global developments, to at the end produce a well coordinated framework that is technically, organizationally, and financially integrated with the EPOS architecture. This framework needs to respect the roles and responsibilities of the underlying national research infrastructures that are the data owners and main providers of data and products, and allow for active input and feedback from the (scientific) user community. At the same time, it needs to remain flexible enough to cope with unavoidable challenges in the availability of resources and dynamics of contributors. The technical work during the next years is organized in four areas: - constructing the next generation software architecture for the European Integrated (waveform) Data Archive EIDA, developing advanced metadata and station information services, fully integrate strong motion waveforms and derived parametric engineering-domain data, and advancing the integration of mobile (temporary) networks and OBS deployments in EIDA; - further development and expansion of services to access seismological products of scientific interest as provided by the community by implementing a common collection and development (IT) platform, improvements in the earthquake information services e.g. by introducing more robust quality indicators and diversifying collection and dissemination mechanisms, as well as improving historical earthquake data services; - development of a comprehensive suite of earthquake hazard products, tools, and services harmonized on the European level and available through a common access platform, encompassing information on seismic sources, seismogenic faults, ground-motion prediction equations, geotechnical information, and strong-motion recordings in buildings, together with an interface to earthquake risk; - a portal implementation of computational seismology tools and services, specifically for seismic waveform propagation in complex 3D media following the results of the VERCE project, and initiating the inclusion of further suitable codes on that portal in discussion with the community, forming the basis of EPOS computational earth science infrastructure. This will be accompanied by development and implementation of integrated and interoperable metadata structures, adequate and referencable persistent identifiers, and appropriate user access and authorization mechanisms. Here we present further detail on the work plan with the attempt to foster interaction with the target user community on the spectrum of services as well as on feedback mechanisms and governance.

"Hour of Code": Can It Change Students' Attitudes toward Programming?

ERIC Educational Resources Information Center

Du, Jie; Wimmer, Hayden; Rada, Roy

2016-01-01

The Hour of Code is a one-hour introduction to computer science organized by Code.org, a non-profit dedicated to expanding participation in computer science. This study investigated the impact of the Hour of Code on students' attitudes towards computer programming and their knowledge of programming. A sample of undergraduate students from two…

Accessible high performance computing solutions for near real-time image processing for time critical applications

NASA Astrophysics Data System (ADS)

Bielski, Conrad; Lemoine, Guido; Syryczynski, Jacek

2009-09-01

High Performance Computing (HPC) hardware solutions such as grid computing and General Processing on a Graphics Processing Unit (GPGPU) are now accessible to users with general computing needs. Grid computing infrastructures in the form of computing clusters or blades are becoming common place and GPGPU solutions that leverage the processing power of the video card are quickly being integrated into personal workstations. Our interest in these HPC technologies stems from the need to produce near real-time maps from a combination of pre- and post-event satellite imagery in support of post-disaster management. Faster processing provides a twofold gain in this situation: 1. critical information can be provided faster and 2. more elaborate automated processing can be performed prior to providing the critical information. In our particular case, we test the use of the PANTEX index which is based on analysis of image textural measures extracted using anisotropic, rotation-invariant GLCM statistics. The use of this index, applied in a moving window, has been shown to successfully identify built-up areas in remotely sensed imagery. Built-up index image masks are important input to the structuring of damage assessment interpretation because they help optimise the workload. The performance of computing the PANTEX workflow is compared on two different HPC hardware architectures: (1) a blade server with 4 blades, each having dual quad-core CPUs and (2) a CUDA enabled GPU workstation. The reference platform is a dual CPU-quad core workstation and the PANTEX workflow total computing time is measured. Furthermore, as part of a qualitative evaluation, the differences in setting up and configuring various hardware solutions and the related software coding effort is presented.

In-Use and Emerging Disruptive Technology Trends

DTIC Science & Technology

2015-03-31

blog/establishing-zero-trust- infrastructure / (accessed No- vember 7, 2014) Mobile Thin Client End Points In the early days of computing, the...companies are using their network infrastructure to break into the mobile broadband market. For example, Ca- blevision recently began providing a Wi-Fi...smartphones and mobile devic- es will be used within the Pentagon. A building-wide cellular infrastructure is not the an- swer to retrieving and sending

Services and the National Information Infrastructure. Report of the Information Infrastructure Task Force Committee on Applications and Technology, Technology Policy Working Group. Draft for Public Comment.

ERIC Educational Resources Information Center

Office of Science and Technology Policy, Washington, DC.

In this report, the National Information Infrastructure (NII) services issue is addressed, and activities to advance the development of NII services are recommended. The NII is envisioned to grow into a seamless web of communications networks, computers, databases, and consumer electronics that will put vast amounts of information at users'…

Talking about Code: Integrating Pedagogical Code Reviews into Early Computing Courses

ERIC Educational Resources Information Center

Hundhausen, Christopher D.; Agrawal, Anukrati; Agarwal, Pawan

2013-01-01

Given the increasing importance of soft skills in the computing profession, there is good reason to provide students withmore opportunities to learn and practice those skills in undergraduate computing courses. Toward that end, we have developed an active learning approach for computing education called the "Pedagogical Code Review"…

The International Symposium on Grids and Clouds

NASA Astrophysics Data System (ADS)

The International Symposium on Grids and Clouds (ISGC) 2012 will be held at Academia Sinica in Taipei from 26 February to 2 March 2012, with co-located events and workshops. The conference is hosted by the Academia Sinica Grid Computing Centre (ASGC). 2012 is the decennium anniversary of the ISGC which over the last decade has tracked the convergence, collaboration and innovation of individual researchers across the Asia Pacific region to a coherent community. With the continuous support and dedication from the delegates, ISGC has provided the primary international distributed computing platform where distinguished researchers and collaboration partners from around the world share their knowledge and experiences. The last decade has seen the wide-scale emergence of e-Infrastructure as a critical asset for the modern e-Scientist. The emergence of large-scale research infrastructures and instruments that has produced a torrent of electronic data is forcing a generational change in the scientific process and the mechanisms used to analyse the resulting data deluge. No longer can the processing of these vast amounts of data and production of relevant scientific results be undertaken by a single scientist. Virtual Research Communities that span organisations around the world, through an integrated digital infrastructure that connects the trust and administrative domains of multiple resource providers, have become critical in supporting these analyses. Topics covered in ISGC 2012 include: High Energy Physics, Biomedicine & Life Sciences, Earth Science, Environmental Changes and Natural Disaster Mitigation, Humanities & Social Sciences, Operations & Management, Middleware & Interoperability, Security and Networking, Infrastructure Clouds & Virtualisation, Business Models & Sustainability, Data Management, Distributed Volunteer & Desktop Grid Computing, High Throughput Computing, and High Performance, Manycore & GPU Computing.

An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq.

PubMed

Azofeifa, Joseph G; Allen, Mary A; Lladser, Manuel E; Dowell, Robin D

2017-01-01

We present a fast and simple algorithm to detect nascent RNA transcription in global nuclear run-on sequencing (GRO-seq). GRO-seq is a relatively new protocol that captures nascent transcripts from actively engaged polymerase, providing a direct read-out on bona fide transcription. Most traditional assays, such as RNA-seq, measure steady state RNA levels which are affected by transcription, post-transcriptional processing, and RNA stability. GRO-seq data, however, presents unique analysis challenges that are only beginning to be addressed. Here, we describe a new algorithm, Fast Read Stitcher (FStitch), that takes advantage of two popular machine-learning techniques, hidden Markov models and logistic regression, to classify which regions of the genome are transcribed. Given a small user-defined training set, our algorithm is accurate, robust to varying read depth, annotation agnostic, and fast. Analysis of GRO-seq data without a priori need for annotation uncovers surprising new insights into several aspects of the transcription process.

Exploring the existential function of religion and supernatural agent beliefs among Christians, Muslims, atheists, and agnostics.

PubMed

Vail, Kenneth E; Arndt, Jamie; Abdollahi, Abdolhossein

2012-10-01

Building on research suggesting one primary function of religion is the management of death awareness, the present research explored how supernatural beliefs are influenced by the awareness of death, for whom, and how individuals' extant beliefs determine which god(s), if any, are eligible to fulfill that function. In Study 1, death reminders had no effect among Atheists, but enhanced Christians' religiosity, belief in a higher power, and belief in God/Jesus and enhanced denial of Allah and Buddha. Similarly, death reminders increased Muslims' religiosity and belief in a higher power, and led to greater belief in Allah and denial of God/Jesus and Buddha (Study 2). Finally, in Study 3, death reminders motivated Agnostics to increase their religiosity, belief in a higher power, and their faith in God/Jesus, Buddha, and Allah. The studies tested three potential theoretical explanations and were consistent with terror management theory's worldview defense hypothesis. Theoretical implications are discussed.

Association between Protestant religiosity and obsessive-compulsive symptoms and cognitions.

PubMed

Abramowitz, Jonathan S; Deacon, Brett J; Woods, Carol M; Tolin, David F

2004-01-01

There is evidence that religion and other cultural influences are associated with the presentation of obsessive-compulsive symptoms, as well as beliefs and assumptions presumed to underlie the development and maintenance of these symptoms. We sought to further examine the relationship between Protestant religiosity and (1) various symptoms of obsessive-compulsive disorder (OCD) (e.g., checking, washing) and (2) OCD-related cognitions. Using self-report questionnaires, we compared differences in these OCD-related phenomena between highly religious Protestants, moderately religious Protestants, and atheist/agnostic participants drawn from an undergraduate sample. Highly religious versus moderately religious Protestants reported greater obsessional symptoms, compulsive washing, and beliefs about the importance of thoughts. Additionally, the highly religious evinced more obsessional symptoms, compulsive washing, intolerance for uncertainty, need to control thoughts, beliefs about the importance of thoughts, and inflated responsibility, compared to atheists/agnostics. Results are discussed in terms of the relationship between religion and OCD symptoms in the context of the cognitive-behavioral conceptualization of OCD. Copyright 2004 Wiley-Liss, Inc.

Guidelines for developing vectorizable computer programs

NASA Technical Reports Server (NTRS)

Miner, E. W.

1982-01-01

Some fundamental principles for developing computer programs which are compatible with array-oriented computers are presented. The emphasis is on basic techniques for structuring computer codes which are applicable in FORTRAN and do not require a special programming language or exact a significant penalty on a scalar computer. Researchers who are using numerical techniques to solve problems in engineering can apply these basic principles and thus develop transportable computer programs (in FORTRAN) which contain much vectorizable code. The vector architecture of the ASC is discussed so that the requirements of array processing can be better appreciated. The "vectorization" of a finite-difference viscous shock-layer code is used as an example to illustrate the benefits and some of the difficulties involved. Increases in computing speed with vectorization are illustrated with results from the viscous shock-layer code and from a finite-element shock tube code. The applicability of these principles was substantiated through running programs on other computers with array-associated computing characteristics, such as the Hewlett-Packard (H-P) 1000-F.

The Helicopter Antenna Radiation Prediction Code (HARP)

NASA Technical Reports Server (NTRS)

Klevenow, F. T.; Lynch, B. G.; Newman, E. H.; Rojas, R. G.; Scheick, J. T.; Shamansky, H. T.; Sze, K. Y.

1990-01-01

The first nine months effort in the development of a user oriented computer code, referred to as the HARP code, for analyzing the radiation from helicopter antennas is described. The HARP code uses modern computer graphics to aid in the description and display of the helicopter geometry. At low frequencies the helicopter is modeled by polygonal plates, and the method of moments is used to compute the desired patterns. At high frequencies the helicopter is modeled by a composite ellipsoid and flat plates, and computations are made using the geometrical theory of diffraction. The HARP code will provide a user friendly interface, employing modern computer graphics, to aid the user to describe the helicopter geometry, select the method of computation, construct the desired high or low frequency model, and display the results.

Extensible Infrastructure for Browsing and Searching Abstracted Spacecraft Data

NASA Technical Reports Server (NTRS)

Wallick, Michael N.; Crockett, Thomas M.; Joswig, Joseph C.; Torres, Recaredo J.; Norris, Jeffrey S.; Fox, Jason M.; Powell, Mark W.; Mittman, David S.; Abramyan, Lucy; Shams, Khawaja S.;

The Path to Convergence: Design, Coordination and Social Issues in the Implementation of a Middleware Data Broker.

NASA Astrophysics Data System (ADS)

Slota, S.; Khalsa, S. J. S.

2015-12-01

Infrastructures are the result of systems, networks, and inter-networks that accrete, overlay and segment one another over time. As a result, working infrastructures represent a broad heterogeneity of elements - data types, computational resources, material substrates (computing hardware, physical infrastructure, labs, physical information resources, etc.) as well as organizational and social functions which result in divergent outputs and goals. Cyber infrastructure's engineering often defaults to a separation of the social from the technical that results in the engineering succeeding in limited ways, or the exposure of unanticipated points of failure within the system. Studying the development of middleware intended to mediate interactions among systems within an earth systems science infrastructure exposes organizational, technical and standards-focused negotiations endemic to a fundamental trait of infrastructure: its characteristic invisibility in use. Intended to perform a core function within the EarthCube cyberinfrastructure, the development, governance and maintenance of an automated brokering system is a microcosm of large-scale infrastructural efforts. Points of potential system failure, regardless of the extent to which they are more social or more technical in nature, can be considered in terms of the reverse salient: a point of social and material configuration that momentarily lags behind the progress of an emerging or maturing infrastructure. The implementation of the BCube data broker has exposed reverse salients in regards to the overall EarthCube infrastructure (and the role of middleware brokering) in the form of organizational factors such as infrastructural alignment, maintenance and resilience; differing and incompatible practices of data discovery and evaluation among users and stakeholders; and a preponderance of local variations in the implementation of standards and authentication in data access. These issues are characterized by their role in increasing tension or friction among components that are on the path to convergence and may help to predict otherwise-occluded endogenous points of failure or non-adoption in the infrastructure.