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- Andrade, Jorge, et al.
(författare)
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Applications of grid computing in genetics and proteomics
- 2007
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Ingår i: Applied Parallel Computing. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783540757542 ; , s. 791-798
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Konferensbidrag (refereegranskat)abstract
- The potential for Grid technologies in applied bioinformatics is largely unexplored. We have developed a model for solving computationally demanding bioinformatics tasks in distributed Grid environments, designed to ease the usability for scientists unfamiliar with Grid computing. With a script-based implementation that uses a strategy of temporary installations of databases and existing executables on remote nodes at submission, we propose a generic solution that do not rely on predefined Grid runtime environments and that can easily be adapted to other bioinformatics tasks suitable for parallelization. This implementation has been successfully applied to whole proteome sequence similarity analyses and to genome-wide genotype simulations, where computation time was reduced from years to weeks. We conclude that computational Grid technology is a useful resource for solving high compute tasks in genetics and proteomics using existing algorithms.
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- Eerola, Paula, et al.
(författare)
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Roadmap for the ARC Grid Middleware
- 2007
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Ingår i: Lecture Notes in Computer Science. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783540757542 ; 4699/2007, s. 471-479
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Konferensbidrag (refereegranskat)abstract
- The Advanced Resource Connector (ARC) or the NorduGrid middleware is an open source software solution enabling production quality computational and data Grids, with special emphasis on scalability, stability, reliability and performance. Since its first release in May 2002, the middleware is deployed and being used in production environments. This paper aims to present the future development directions and plans of the ARC middleware in terms of outlining the software development roadmap.
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- Kessler, Christoph, 1966-, et al.
(författare)
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NestStepModelica - Mathematical Modeling and Bulk-Synchronous Parallel Simulation
- 2007
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Ingår i: 8th International Workshop, PARA 2006, Umeå, Sweden, June 18-21, 2006, Revised Selected Papers. - Berlin, Heidelberg : Springer. - 9783540757542 - 9783540757559 ; , s. 1006-1015
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Konferensbidrag (refereegranskat)abstract
- Many parallel computing applications are used for simulation of complex engineering applications and/or for visualization. To handle their complexity, there is a need for raising the level of abstraction in specifying such applications using high level mathematical modeling techniques, such as the Modelica language and technology. However, with the increased complexity of modeled systems, it becomes increasingly important to use today-s and tomorrow-s parallel hardware efficiently. Automatic parallelization is convenient, but may need to be combined with easy-to-use methods for parallel programming. In this context, we propose to combine the abstraction power of Modelica with support for shared memory bulk-synchronous parallel programming including nested parallelism (NestStepModelica), which is both flexible (can be mapped to many different parallel architectures) and simple (offers a shared address space, structured parallelism, deterministic computation, and is deadlock-free). We describe NestStepModelica and report on first results obtained with a prototype implementation.
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- Lacoursiere, Claude
(författare)
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A parallel block iterative method for interactive contacting rigid multibody simulations on multicore PCs
- 2007
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Ingår i: Applied parallel computing. - Berlin : Springer Berlin/Heidelberg. - 9783540757542 ; , s. 956-965
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Konferensbidrag (refereegranskat)abstract
- A hybrid, asynchronous, block parallel method to approximately solve complementarity problems (CPs) in real-time on multicore CPUs is described. These problems arise from interactive real-time simulations of systems of constrained, contacting rigid bodies, which are useful in virtual operator training systems for instance. A graph analysis phase identifies components which are weakly coupled using simple heuristics. Each component is then solved in parallel using either a block principal pivot or a projected block Gauss-Seidel method running in separate threads. Couplings which generate forces between the subsystems are handled iteratively using a Gauss-Seidel process which communicates updates between the interacting subsystems asynchronously. Preliminary results show that this approach delivers good performance while keeping overhead small.
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- Nilsson, Håkan, 1971
(författare)
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Some experiences on the accuracy and parallel efficiency of OpenFOAM for CFD in water turbines
- 2007
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Ingår i: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 1611-3349 .- 0302-9743. - 9783540757542 ; 4699/2007, s. 168-176
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- 50% of the electric power in Sweden is generated by water power. Many of the power plants in Sweden are getting old and some major refurbishments are coming up. Due to the development of numerical methods and computer power the last decades Computational Fluid Dynamics (CFD) is to a large extent used as a design tool for this purpose. The general features of the flow in water turbines can be resolved with todays methods and computational power, but in order to study the flow in detail enormous HPC facilities and new methods are required.The present work presents the water turbine field with its HPC requirements, shows some state-of-the-art results from OpenFOAM CFD analysis, and presents a parallel performance analysis on a Linux cluster using an ordinary gigabit interconnect v.s. an Infiniband interconnect.
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- Parviainen, Madelene Jeanette, et al.
(författare)
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Phase Space Modulations in Magnetised Plasmas by a Mildly Relativistic Two-Stream Instability
- 2007
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Ingår i: Applied Parallel Computing. State of the Art in Scientific Computing. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783540757542 - 9783540757559 ; , s. 361-370
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Konferensbidrag (refereegranskat)abstract
- A kinetic particle-in-cell simulation and 3D point-rendering visualisation are used to investigate a two-stream plasma instability, possibly found in the accretion disc of black holes. A plasma in an oblique external magnetic field is considered. The instability gives rise to a quasi-electrostatic wave able to trap electrons and accelerate them by cross-field transport. The results of the simulation show an acceleration of the electrons to speeds similar to the bulk speed of microquasar jets.
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- Rubensson, Emanuel, et al.
(författare)
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Sparse matrix algebra for quantum modeling of large systems
- 2007
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Ingår i: Applied Parallel Computing - STATE OF THE ART IN SCIENTIFIC COMPUTING. - Berlin, Germany : Springer-Verlag. - 9783540757542 ; , s. 90-99
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Konferensbidrag (refereegranskat)abstract
- Matrices appearing in Hartree-Fock or density functional theory coming from discretization with help of atom-centered local basis sets become sparse when the separation between atoms exceeds some system-dependent threshold value. Efficient implementation of sparse matrix algebra is therefore essential in large-scale quantum calculations. We describe a unique combination of algorithms and data representation that provides high performance and strict error control in blocked sparse matrix algebra. This has applications to matrix-rnatrix multiplication, the Trace-Correcting Purification algorithm and the entire self-consistent field calculation.
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