| 1. |
- 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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| 2. |
- 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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| 3. |
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| 4. |
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| 5. |
- 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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| 6. |
- 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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| 7. |
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| 8. |
- 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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| 9. |
- 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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| 10. |
- 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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| 11. |
- Shafaat, Tallat M., et al.
(författare)
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A method of adaptive coarsening for compressing scientific datasets
- 2007
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Ingår i: Applied Parallel Computing. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783540757542 ; , s. 774-780
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Konferensbidrag (refereegranskat)abstract
- We present adaptive coarsening, a multi-resolution lossy compression algorithm for scientific datasets. The algorithm provides guaranteed error bounds according to the user's requirements for subsequent post-processing. We demonstrate compression factors of up to an order of magnitude with datasets coming from solutions to time-dependent partial differential equations in one and two dimensions.
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| 12. |
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| 13. |
- Smirnova, Oxana
(författare)
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Grids for scientific computing: Minisymposium abstract
- 2007
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Ingår i: Applied Parallel Computing - State of the Art in Scientific Computing. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 1611-3349 .- 0302-9743. - 9783540757542 ; 4699, s. 470-470
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Konferensbidrag (refereegranskat)abstract
- Grid technologies are still evolving, with standards yet to be defined and reliable production-level solutions yet to be found. Nevertheless, Grid already stepped out of the cradle and slowly but steadily finds its way to the world of the modern information technologies. Early testers and adopters of this innovative technology are researchers in various fields of science, primarily those that traditionally require massive computational resources. Destined by the virtue of their occupation to investigate new phenomena, they provide most valuable feedback to the Grid technology developers, helping to shape the designs and define the roadmaps. Historically, researchers in High Energy Physics were the first to appreciate the Grid idea, not just as the consumers, but also as the key developers of many current solutions.
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| 14. |
- Tu, Yaoquan, et al.
(författare)
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A highly efficient Ab initio tight-binding-like approximate density-functional quantum mechanical method
- 2007
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Ingår i: Applied Parallel Computing. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783540757542 ; , s. 100-108, s. 100-108
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Konferensbidrag (refereegranskat)abstract
- A highly efficient ab initio tight-binding-like approximate density-functional quantum mechanical method has recently been developed by us. In this method, the integrals related to the exchange-correlation part are obtained by higher order many-center expansions and all the integrals can be obtained by the interpolation of the look-up tables. The speed of the calculation is also enhanced by using a better way to choose the integrals in the look-up tables. It is shown that the calculated molecular equilibrium geometries and the reaction energies for hydrogenation reactions are very close to those from the usual density functional theory calculations.
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| 15. |
- Tångrot, Jeanette, et al.
(författare)
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Design, construction and use of the FISH server
- 2007
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Ingår i: Applied parallel computing. - Berlin, Heidelberg : Springer Link. - 9783540757542 ; , s. 647-657
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- At the core of the FISH (Family Identification with Structure anchored Hidden Markov models, saHMMs) server lies the midnight ASTRAL set. It is a collection of protein domains with low mutual sequence identity within homologous families, according to the structural classification of proteins, SCOP. Here, we evaluate two algorithms for creating the midnight ASTRAL set. The algorithm that limits the number of structural comparisons is about an order of magnitude faster than the all-against-all algorithm. We therefore choose the faster algorithm, although it produces slightly fewer domains in the set. We use the midnight ASTRAL set to construct the structure-anchored Hidden Markov Model data base, saHMM-db, where each saHMM represents one family. Sequence searches using saHMMs provide information about protein function, domain organization, the probable 2D and 3D structure, and can lead to the discovery of homologous domains in remotely related sequences.
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| 16. |
- Van Der Spoel, David, et al.
(författare)
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Protein Folding Properties from Molecular Dynamics Simulations
- 2007
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Ingår i: Applied Parallel Computing. - 9783540757542 ; , s. 109-115
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Konferensbidrag (refereegranskat)abstract
- Protein folding simulations have contributed significantly to our understanding of the problem, since it is difficult to study individual molecules during the folding process. We have recently performed folding simulations of Chignolin, a decapeptide (Seibert et al., J. Mol. Biol. 354 (2006) p. 173) and introduced a new algorithm for deriving kinetics information as well as thermodynamics from the trajectories (Van der Spoel & Seibert, Phys. Rev. Lett. 96 (2006), p. 238102). Here we investigate the algorithm further and show that the folding reaction for Chignolin is a two-state folding reaction, in accord with experimental data.
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| 17. |
- Vedin, Jörgen, et al.
(författare)
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Implementing a particle-fluid model of auroral electrons
- 2007
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Ingår i: Applied Parallel Computing. State of the Art in Scientific Computing. - Heidelberg : Springer Berlin/Heidelberg. - 9783540757542 ; , s. 371-379
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Konferensbidrag (refereegranskat)abstract
- The particle-fluid model of auroral electrons that is presented in [1] is a major step forward within the field of dynamic models of the auroral generation mechanisms. The model is, however, also an example where the implementation of a physical model requires a lot of knowledge from the field of computer science. Therefore, this paper contains a detailed description of the implementation behind the particle-fluid model. We present how the particles are implemented in doubly linked lists, how the fluid equations are solved in a time-efficient algorithm, and how these two parts are coupled into a single framework. We also describe how the code is parallelized with an efficiency of nearly 100%.
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| 18. |
- Vitos, Levente, et al.
(författare)
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Mechanical properties of random alloys from quantum mechanical simulations
- 2007
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Ingår i: Applied Parallel Computing. - Berlin, Heidelberg : Springer Berlin Heidelberg. - 9783540757542 ; , s. 510-519
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Konferensbidrag (refereegranskat)abstract
- Today, a direct determination of the mechanical properties of complex alloys from first-principles theory is not feasible. On the other hand, well established phenomenological models exist, which are suitable for an accurate description of materials behavior under various mechanical loads. These models involve a large set of atomic-level physical parameters. Unfortunately, in many cases the available parameters have unacceptably large experimental error bars. Here we demonstrate that computational modeling based on modern first-principles alloy theory can yield fundamental physical parameters with high accuracy. We illustrate this in the case of aluminum and transition metal alloys and austenitic stainless steels by computing the size and elastic misfit parameters, and the surface and stacking fault energies as functions of chemical composition.
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