Concurrency Research Papers - Academia.edu (original) (raw)

... Cédric Augonnet, Samuel Thibault, Raymond Namyst, and Pierre-André Wacrenier ... To bridge the gap between such APIs and HPC applications, one crucial step is to provide optimized versions of computation kernels (BLAS routines, FFT,... more

... Cédric Augonnet, Samuel Thibault, Raymond Namyst, and Pierre-André Wacrenier ... To bridge the gap between such APIs and HPC applications, one crucial step is to provide optimized versions of computation kernels (BLAS routines, FFT, and other numerical libraries) capable ...

Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research... more

Life sciences research is based on individuals, often with diverse skills, assembled into research groups. These groups use their specialist expertise to address scientific problems. The in silico experiments undertaken by these research groups can be represented as workflows involving the co-ordinated use of analysis programs and information repositories that may be globally distributed. With regards to Grid computing, the requirements relate to the sharing of analysis and information resources rather than sharing computational power. The myGrid project has developed the Taverna Workbench for the composition and execution of workflows for the life sciences community. This experience paper describes lessons learnt during the development of Taverna. A common theme is the importance of understanding how workflows fit into the scientists' experimental context. The lessons reflect an evolving understanding of life scientists' requirements on a workflow environment, which is relevant to other areas of data intensive and exploratory science. Copyright © 2005 John Wiley & Sons, Ltd.

We define the notion of a well-separated pair decomposition of points in d -dimensional space. We then develop efficient sequential and parallel algorithms for computing such a decomposition. We apply the resulting decomposition to the... more

We define the notion of a well-separated pair decomposition of points in d -dimensional space. We then develop efficient sequential and parallel algorithms for computing such a decomposition. We apply the resulting decomposition to the efficient computation of k -nearest neighbors and n -body potential fields.

In this paper, we discuss a real-world application scenario that uses three distinct types of workflow within the Triana problem-solving environment: serial scientific workflow for the data processing of gravitational wave signals; job... more

In this paper, we discuss a real-world application scenario that uses three distinct types of workflow within the Triana problem-solving environment: serial scientific workflow for the data processing of gravitational wave signals; job submission workflows that execute Triana services on a testbed; and monitoring workflows that examine and modify the behaviour of the executing application. We briefly describe the Triana distribution mechanisms and the underlying architectures that we can support. Our middleware independent abstraction layer, called the Grid Application Prototype (GAP), enables us to advertise, discover and communicate with Web and peer-to-peer (P2P) services. We show how gravitational wave search algorithms have been implemented to distribute both the search computation and data across the European GridLab testbed, using a combination of Web services, Globus interaction and P2P infrastructures. Copyright © 2005 John Wiley & Sons, Ltd.

Transitions systems are well established as a semantic model for distributed systems. There are widely accepted preorders that serve as criteria for refinement of a more abstract transition system to a more concrete one. To reason about... more

Transitions systems are well established as a semantic model for distributed systems. There are widely accepted preorders that serve as criteria for refinement of a more abstract transition system to a more concrete one. To reason about probabilistic phenomena such as failure rates, we need to extend models and methods that have proven successful for nonprobabilistic systems to a probabilistic setting. We consider a model of probabilistic transition systems, containing probabilistic choice and nondeterministic choice as independent concepts. We present a notion of testing for these systems. Our main contributions are denotational characterizations of the testing preorders. The characterizations are given in terms of chains for may testing and refusal chains for must testing, that are analogous to traces and failures in denotational models of CSP. Refinement corresponds to inclusion between chains and refusal chains modulo closure operations. The preorders are shown to be compositional. We also show that when restricted to nonprobabilistic systems, these preorders collapse to the standard simulation and refusal simulation

This paper describes how two runtime analysis algorithms, an existing data race detection algorithm and a new deadlock detection algorithm, have been implemented to analyze Java programs. Runtime analysis is based on the idea of executing... more

This paper describes how two runtime analysis algorithms, an existing data race detection algorithm and a new deadlock detection algorithm, have been implemented to analyze Java programs. Runtime analysis is based on the idea of executing the program once, and observing the generated run to extract various kinds of information. This information can then be used to predict whether other different runs may violate some properties of interest, in addition of course to demonstrate whether the generated run itself violates such properties. These runtime analyses can be performed stand-alone to generate a set of warnings. It is furthermore demonstrated how these warnings can be used to guide a model checker, thereby reducing the search space. The described techniques have been implemented in the home grown Java model checker called Java PathFinder.

We present a theoretical model for self-assembling tiles with flexible branches motivated by DNA branched junction molecules. We encode an instance of a “problem” as a pot of such tiles, and a “solution” as an assembled complete complex... more

We present a theoretical model for self-assembling tiles with flexible branches motivated by DNA branched junction molecules. We encode an instance of a “problem” as a pot of such tiles, and a “solution” as an assembled complete complex without any free sticky ends (called ports), whose number of tiles is within predefined bounds. We develop an algebraic representation of this self-assembly process and use it to prove that this model of self-assembly precisely captures NP-computability when the number of tiles in the minimal complete complexes is bounded by a polynomial.