This paper describes the Pegasus framework that can be used to map complex scientific workflows onto distributed resources. Pegasus enables users to represent the workflows at an abstract level without needing to worry about the particulars of the target execution systems. The paper describes general issues in mapping applications and the functionality of Pegasus. We present the results of improving application performance through workflow restructuring which clusters multiple tasks in a workflow into single entities. A real-life astronomy application is used as the basis for the study.

Ewa Deelman

Gurmeet Singh

Mei-Hui Su

James Blythe

Yolanda Gil

Carl Kesselman

Gaurang Mehta

Karan Vahi

G. Bruce Berriman

John Good

Anastasia Laity

Joseph C. Jacob

Daniel S. Katz

Pegasus: A Framework for Mapping Complex Scientific Workflows onto Distributed Systems

This paper describes the work of an object oriented framework designed to be used in the parallelization of a set of related algorithms. The idea behind the system we are describing is to have a re-usable framework for running several sequential algorithms in a parallel environment. The algorithms that the framework can be used with have several things in common: they have to run in cycles and the work should be possible to be split between several &#x22;processing units&#x22;. The parallel framework uses the message-passing communication paradigm and is organized as a master-slave system. Two applications are presented: an Ant Colony Optimization (ACO) parallel algorithm for the Travelling Salesman Problem (TSP) and an Image Processing (IP) parallel algorithm for the Symmetrical Neighborhood Filter (SNF). The implementations of these applications by means of the parallel framework prove to have good performances: approximatively linear speedup and low communication cost.

Mitic&#x0103; Craus

Lauren&#x0163;iu Rudeanu

Parallel Framework for Cooperative Processes

Abstract data types developed for computational science and engineering are frequently modeled after physical objects whose state variables must satisfy governing differential equations. Generalizing the associated algebraic and differential operators to operate on the abstract data types facilitates high-level program constructs that mimic standard mathematical notation. For non-trivial expressions, multiple object instantiations must occur to hold intermediate results during the expression's evaluation. When the dimension of each object's state space is not specified at compile-time, the programmer becomes responsible for dynamically allocating and de-allocating memory for each instantiation. With the advent of allocatable components in Fortran 2003 derived types, the potential exists for these intermediate results to occupy a substantial fraction of a program's footprint in memory. This issue becomes particularly acute at the highest levels of abstraction where coarse-grained data structures predominate. This paper proposes a set of rules for de-allocating memory that has been dynamically allocated for intermediate results in derived type calculus, while distinguishing that memory from more persistent objects. The new rules are applied to the design of a polymorphic time integrator for integrating evolution equations governing dynamical systems. Associated issues of efficiency and design robustness are discussed.

Damian W.I. Rouson

Karla Morris

Xiaofeng Xu

Dynamic Memory De-allocation in Fortran 95/2003 Derived Type Calculus

The statistical properties of oligonucleotide appearances within long DNA sequences often reveal useful characteristics of the corresponding DNA areas. Two algorithms to statistically analyze oligonucleotide appearances within long DNA sequences in genome banks are presented. The first algorithm determines statistical indices for arbitrary length oligonucleotides within arbitrary length DNA sequences. The critical exponent &#x3bc; of the distance distribution between consecutive occurrences of the same oligonucleotide is calculated and its value is shown to characterize the functionality of the oligonucleotide. The second algorithm searches for areas with variable homogeneity, based on the density of oligonucleotides. The two algorithms have been applied to representative eucaryotes (the animal Mus musculusand the plant Arabidopsis thaliana) and interesting results were obtained, confirmed by biological observations. All programs are open source and publicly available on our web site.

P. Katsaloulis

T. Theoharis

A. Provata

Statistical Algorithms for Long DNA Sequences: Oligonucleotide Distributions and Homogeneity Maps

Dan Nagle

High Performance Linux Clusters, by A. Joseph and D. Sloan

Agent oriented programming is often claimed to become the next breakthrough in development and implementation of large-scale complex software systems. At the same time it is rather difficult to find successful applications of agent technology, in particular when large-scale systems are considered. The aim of this paper is to investigate if one of the possible limits could be the scalability of existing agent environments. For this purpose we have selected JADE agent platform and investigated its performance in a number of test-scenarios. Results of our experiments are presented and discussed.

Krzysztof Chmiel

Maciej Gawinecki

Pawel Kaczmarek

Michal Szymczak

Marcin Paprzycki

Efficiency of JADE Agent Platform

We describe how the R-GMA (Relational Grid Monitoring Architecture) can be used to allow for instrument monitoring in a Grid environment. The R-GMA has been developed within the European DataGrid Project (EDG) as a Grid Information and Monitoring System. It is based on the Grid Monitoring Architecture (GMA) from the Global Grid Forum (GGF), which is a simple Consumer-Producer model. The special strength of this implementation comes from the power of the relational model. It offers a global view of the information as if each Virtual Organisation had one large relational database. It provides a number of different Producer types with different characteristics; for example some support streaming of information. We describe the R-GMA component that allows for instrument monitoring, the CanonicalProducer. We also describe an example use of this approach in the European CrossGrid project, SANTA-G, a network monitoring tool.

Stuart Kenny

Brian Coghlan

David O'Callaghan

John Ryan

Rob Byrom

Laurence Field

Steve Hicks

Manish Soni

Antony Wilson

Xiaomei Zhu

Roney Cordenonsi

Ari Datta

Linda Cornwall

Abdeslem Djaoui

Norbert Podhorszki

The CanonicalProducer: An Instrument Monitoring Component of the Relational Grid Monitoring Architecture (R-GMA)

One of the important issues facing the development of the grid as a computational framework of the future is availability of grid-enabled software. In this context, we discuss possible approaches to constructing a grid-enabled version of a computer algebra system. Our case study involves Maple: the proposed Maple2g package allows the connection between Maple and the computational grids based on the Globus Toolkit. We present the design of the Maple2g package and follow with a detailed discussion of its implementation. Finally, we illustrate performance of Maple2g in a number of experiments.

Dana Petcu

Diana Dubu

Design and Implementation of a Grid Extension for Maple

The aim of this paper is to present a qualitative evaluation of three state-of-the-art parallel languages: OpenMP, Unified Parallel C (UPC) and Co-Array Fortran (CAF). OpenMP and UPC are explicit parallel programming languages based on the ANSI standard. CAF is an implicit programming language. On the one hand, OpenMP designs for shared-memory architectures and extends the base-language by using compiler directives that annotate the original source-code. On the other hand, UPC and CAF designs for distribute-shared memory architectures and extends the base-language by new parallel constructs. We deconstruct each language into its basic components, show examples, make a detailed analysis, compare them, and finally draw some conclusions.

Ami Marowka

Execution Model of Three Parallel Languages: OpenMP, UPC and CAF

Amphiphiles are molecules with hydrophobic tails and hydrophilic heads. When dispersed in solvents, they self assemble into complex mesophases including the beautiful cubic gyroid phase. The goal of the TeraGyroid experiment was to study defect pathways and dynamics in these gyroids. The UK's supercomputing and USA's TeraGrid facilities were coupled together, through a dedicated high-speed network, into a single computational Grid for research work that peaked around the Supercomputing 2003 conference. The gyroids were modeled using lattice Boltzmann methods with parameter spaces explored using many 1283 and 3grid point simulations, this data being used to inform the world's largest three-dimensional time dependent simulation with 10243-grid points. The experiment generated some 2 TBytes of useful data. In terms of Grid technology the project demonstrated the migration of simulations (using Globus middleware) to and fro across the Atlantic exploiting the availability of resources. Integration of the systems accelerated the time to insight. Distributed visualisation of the output datasets enabled the parameter space of the interactions within the complex fluid to be explored from a number of sites, informed by discourse over the Access Grid. The project was sponsored by EPSRC (UK) and NSF (USA) with trans-Atlantic optical bandwidth provided by British Telecommunications.

R.J. Blake

P.V. Coveney

P. Clarke

S.M. Pickles

The TeraGyroid Experiment &#x2013; Supercomputing 2003

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Scientific Programming provides a forum for research results in, and practical experience with, software engineering environments, tools, languages, and models of computation aimed specifically at supporting scientific and engineering computing.

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Chief Editor&nbsp;Professor Tramontana&nbsp;is based at the University of Catania and his research primarily concerns the areas of software engineering and distributed systems.

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Scientific Programming - Table of contents 2005

title

Scientific Programming provides a forum for research results in, and practical experience with, software engineering environments, tools, languages, and models of computation aimed specifically at supporting scientific and engineering computing.

Scientific Programming