StochKit-FF: Efficient Systems Biology on Multicore Architectures

The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.Comment: 14 pages + cover pag

Toward a Formal Semantics for Autonomic Components

Autonomic management can improve the QoS provided by parallel/ distributed applications. Within the CoreGRID Component Model, the autonomic management is tailored to the automatic - monitoring-driven - alteration of the component assembly and, therefore, is defined as the effect of (distributed) management code. This work yields a semantics based on hypergraph rewriting suitable to model the dynamic evolution and non-functional aspects of Service Oriented Architectures and component-based autonomic applications. In this regard, our main goal is to provide a formal description of adaptation operations that are typically only informally specified. We contend that our approach makes easier to raise the level of abstraction of management code in autonomic and adaptive applications.Comment: 11 pages + cover pag

Two Fundamental Concepts in Skeletal Parallel Programming

We define the concepts of nesting mode and interaction mode as they arise in the description of skeletal parallel programming systems. We sugegs

Gaspar data-centric framework

This paper presents the Gaspar data-centric framework to develop high performance parallel applications in Java. Our approach is based on data iterators and on the map pattern of computation. The framework provides an efficient data Application Programming Inter-face(API) that supports flexible data layout and data tiling. Data layout and tiling enable the improvement of data locality, which is essential to foster application scalability in modern multi-core systems. The paper presents the framework data-centric concepts and shows that the performance is comparable to pure Java code.(undefined)info:eu-repo/semantics/publishedVersio

A parallel pattern for iterative stencil + reduce

We advocate the Loop-of-stencil-reduce pattern as a means of simplifying the implementation of data-parallel programs on heterogeneous multi-core platforms. Loop-of-stencil-reduce is general enough to subsume map, reduce, map-reduce, stencil, stencil-reduce, and, crucially, their usage in a loop in both data-parallel and streaming applications, or a combination of both. The pattern makes it possible to deploy a single stencil computation kernel on different GPUs. We discuss the implementation of Loop-of-stencil-reduce in FastFlow, a framework for the implementation of applications based on the parallel patterns. Experiments are presented to illustrate the use of Loop-of-stencil-reduce in developing data-parallel kernels running on heterogeneous systems

Porting Decision Tree Algorithms to Multicore using FastFlow

The whole computer hardware industry embraced multicores. For these machines, the extreme optimisation of sequential algorithms is no longer sufficient to squeeze the real machine power, which can be only exploited via thread-level parallelism. Decision tree algorithms exhibit natural concurrency that makes them suitable to be parallelised. This paper presents an approach for easy-yet-efficient porting of an implementation of the C4.5 algorithm on multicores. The parallel porting requires minimal changes to the original sequential code, and it is able to exploit up to 7X speedup on an Intel dual-quad core machine.Comment: 18 pages + cove

Pushouts in software architecture design

A classical approach to program derivation is to progressively extend a simple specification and then incrementally refine it to an implementation. We claim this approach is hard or impractical when reverse engineering legacy software architectures. We present a case study that shows optimizations and pushouts--in addition to refinements and extensions--are essential for practical stepwise development of complex software architectures.NSF CCF 0724979NSF CNS 0509338NSF CCF 0917167NSF DGE-1110007FCT SFRH/BD/47800/2008FCT UTAustin/CA/0056/200