3,042 research outputs found
High Throughput Protein Similarity Searches in the LIBI Grid Problem Solving Environment
Bioinformatics applications are naturally distributed, due to distribution of involved data sets, experimental data and biological databases. They require high computing power, owing to the large size of data sets and the complexity of basic computations, may access heterogeneous data, where heterogeneity is in data format, access policy, distribution, etc., and require a secure infrastructure, because they could access private data owned by different organizations. The Problem Solving Environment (PSE) is an approach and a technology that can fulfil such bioinformatics requirements. The PSE can be used for the definition and composition of complex applications, hiding programming and configuration details to the user that can concentrate only on the specific problem. Moreover, Grids can be used for building geographically distributed collaborative problem solving environments and Grid aware PSEs can search and use dispersed high performance computing, networking, and data resources. In this work, the PSE solution has been chosen as the integration platform of bioinformatics tools and data sources. In particular an experiment of multiple sequence alignment on large scale, supported by the LIBIPSE, is presented
MOSE': A grid-enabled software platform to solve geoprocessing problems
Grid computing has emerged as an important new field in the distributed computing arena. It focus on intensive resource sharing, innovative applications, and in some cases,
high-performance orientation. This paper describes how
grids technologies can be used to develop an infrastructure for developing geoprocessing applications. We present the MOS`E system, a grid-enabled problem solving environment (PSE) able to support the activities that concern the modelling and simulation of spatio-temporal phenomena for analyzing and managing the identification and the mitigation of natural disasters like floods, wildfires, landslides, etc. MOSE' takes advantages of the standardized resource access and workflow support for loosely coupled software components provided by the web/grid services technologies
Cooperative high-performance storage in the accelerated strategic computing initiative
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
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Leveraging legacy codes to distributed problem solving environments: A web service approach
This paper describes techniques used to leverage high performance legacy codes as CORBA components to a distributed problem solving environment. It first briefly introduces the software architecture adopted by the environment. Then it presents a CORBA oriented wrapper generator (COWG) which can be used to automatically wrap high performance legacy codes as CORBA components. Two legacy codes have been wrapped with COWG. One is an MPI-based molecular dynamic simulation (MDS) code, the other is a finite element based computational fluid dynamics (CFD) code for simulating incompressible Navier-Stokes flows. Performance comparisons between runs of the MDS CORBA component and the original MDS legacy code on a cluster of workstations and on a parallel computer are also presented. Wrapped as CORBA components, these legacy codes can be reused in a distributed computing environment. The first case shows that high performance can be maintained with the wrapped MDS component. The second case shows that a Web user can submit a task to the wrapped CFD component through a Web page without knowing the exact implementation of the component. In this way, a user’s desktop computing environment can be extended to a high performance computing environment using a cluster of workstations or a parallel computer
Mathematical Modelling of Chemical Diffusion through Skin using Grid-based PSEs
A Problem Solving Environment (PSE) with connections to remote distributed Grid processes is developed. The Grid simulation is itself a parallel process and allows steering of individual or multiple runs of the core computation of chemical diffusion through the stratum corneum, the outer layer of the skin. The effectiveness of this Grid-based approach in improving the quality of the simulation is assessed
A grid-enabled problem solving environment for parallel computational engineering design
This paper describes the development and application of a piece of engineering software that provides a problem solving environment (PSE) capable of launching, and interfacing with, computational jobs executing on remote resources on a computational grid. In particular it is demonstrated how a complex, serial, engineering optimisation code may be efficiently parallelised, grid-enabled and embedded within a PSE.
The environment is highly flexible, allowing remote users from different sites to collaborate, and permitting computational tasks to be executed in parallel across multiple grid resources, each of which may be a parallel architecture. A full working prototype has been built and successfully applied to a computationally demanding engineering optimisation problem. This particular problem stems from elastohydrodynamic lubrication and involves optimising the computational model for a lubricant based on the match between simulation results and experimentally observed data
Knowledge-based Expressive Technologies within Cloud Computing Environments
Presented paper describes the development of comprehensive approach for
knowledge processing within e-Sceince tasks. Considering the task solving
within a simulation-driven approach a set of knowledge-based procedures for
task definition and composite application processing can be identified. This
procedures could be supported by the use of domain-specific knowledge being
formalized and used for automation purpose. Within this work the developed
conceptual and technological knowledge-based toolbox for complex
multidisciplinary task solv-ing support is proposed. Using CLAVIRE cloud
computing environment as a core platform a set of interconnected expressive
technologies were developed.Comment: Proceedings of the 8th International Conference on Intelligent
Systems and Knowledge Engineering (ISKE2013). 201
BSML: A Binding Schema Markup Language for Data Interchange in Problem Solving Environments (PSEs)
We describe a binding schema markup language (BSML) for describing data
interchange between scientific codes. Such a facility is an important
constituent of scientific problem solving environments (PSEs). BSML is designed
to integrate with a PSE or application composition system that views model
specification and execution as a problem of managing semistructured data. The
data interchange problem is addressed by three techniques for processing
semistructured data: validation, binding, and conversion. We present BSML and
describe its application to a PSE for wireless communications system design
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