1,777 research outputs found
The 1999 Center for Simulation of Dynamic Response in Materials Annual Technical Report
Introduction:
This annual report describes research accomplishments for FY 99 of the Center
for Simulation of Dynamic Response of Materials. The Center is constructing a
virtual shock physics facility in which the full three dimensional response of a
variety of target materials can be computed for a wide range of compressive, ten-
sional, and shear loadings, including those produced by detonation of energetic
materials. The goals are to facilitate computation of a variety of experiments
in which strong shock and detonation waves are made to impinge on targets
consisting of various combinations of materials, compute the subsequent dy-
namic response of the target materials, and validate these computations against
experimental data
T-infinity: The Dependency Inversion Principle for Rapid and Sustainable Multidisciplinary Software Development
The CFD Vision 2030 Study recommends that, NASA should develop and maintain an integrated simulation and software development infrastructure to enable rapid CFD technology maturation.... [S]oftware standards and interfaces must be emphasized and supported whenever possible, and open source models for noncritical technology components should be adopted. The current paper presents an approach to an open source development architecture, named T-infinity, for accelerated research in CFD leveraging the Dependency Inversion Principle to realize plugins that communicate through collections of functions without exposing internal data structures. Steady state flow visualization, mesh adaptation, fluid-structure interaction, and overset domain capabilities are demonstrated through compositions of plugins via standardized abstract interfaces without the need for source code dependencies between disciplines. Plugins interact through abstract interfaces thereby avoiding N 2 direct code-to-code data structure coupling where N is the number of codes. This plugin architecture enhances sustainable development by controlling the interaction between components to limit software complexity growth. The use of T-infinity abstract interfaces enables multidisciplinary application developers to leverage legacy applications alongside newly-developed capabilities. While rein, a description of interface details is deferred until the are more thoroughly tested and can be closed to modification
Restriction landmark genomic scanning (RLGS) spot identification by second generation virtual RLGS in multiple genomes with multiple enzyme combinations.
BackgroundRestriction landmark genomic scanning (RLGS) is one of the most successfully applied methods for the identification of aberrant CpG island hypermethylation in cancer, as well as the identification of tissue specific methylation of CpG islands. However, a limitation to the utility of this method has been the ability to assign specific genomic sequences to RLGS spots, a process commonly referred to as "RLGS spot cloning."ResultsWe report the development of a virtual RLGS method (vRLGS) that allows for RLGS spot identification in any sequenced genome and with any enzyme combination. We report significant improvements in predicting DNA fragment migration patterns by incorporating sequence information into the migration models, and demonstrate a median Euclidian distance between actual and predicted spot migration of 0.18 centimeters for the most complex human RLGS pattern. We report the confirmed identification of 795 human and 530 mouse RLGS spots for the most commonly used enzyme combinations. We also developed a method to filter the virtual spots to reduce the number of extra spots seen on a virtual profile for both the mouse and human genomes. We demonstrate use of this filter to simplify spot cloning and to assist in the identification of spots exhibiting tissue-specific methylation.ConclusionThe new vRLGS system reported here is highly robust for the identification of novel RLGS spots. The migration models developed are not specific to the genome being studied or the enzyme combination being used, making this tool broadly applicable. The identification of hundreds of mouse and human RLGS spot loci confirms the strong bias of RLGS studies to focus on CpG islands and provides a valuable resource to rapidly study their methylation
Comparison of leading parallel NAS file systems on commodity hardware
High performance computing has experienced tremendous gains in system performance over the past 20 years. Unfortunately other system capabilities, such as file I/O, have not grown commensurately. In this activity, we present the results of our tests of two leading file systems (GPFS and Lustre) on the same physical hardware. This hardware is the standard commodity storage solution in use at LLNL and, while much smaller in size, is intended to enable us to learn about differences between the two systems in terms of performance, ease of use and resilience. This work represents the first hardware consistent study of the two leading file systems that the authors are aware of
Survey and Analysis of Production Distributed Computing Infrastructures
This report has two objectives. First, we describe a set of the production
distributed infrastructures currently available, so that the reader has a basic
understanding of them. This includes explaining why each infrastructure was
created and made available and how it has succeeded and failed. The set is not
complete, but we believe it is representative.
Second, we describe the infrastructures in terms of their use, which is a
combination of how they were designed to be used and how users have found ways
to use them. Applications are often designed and created with specific
infrastructures in mind, with both an appreciation of the existing capabilities
provided by those infrastructures and an anticipation of their future
capabilities. Here, the infrastructures we discuss were often designed and
created with specific applications in mind, or at least specific types of
applications. The reader should understand how the interplay between the
infrastructure providers and the users leads to such usages, which we call
usage modalities. These usage modalities are really abstractions that exist
between the infrastructures and the applications; they influence the
infrastructures by representing the applications, and they influence the ap-
plications by representing the infrastructures
The 30th Anniversary of the Supercomputing Conference: Bringing the Future Closer - Supercomputing History and the Immortality of Now
A panel of experts discusses historical reflections on the past 30 years of the Supercomputing (SC) conference, its leading role for the professional community and some exciting future challenges
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