Data grid services for biodiversity informatics

The infrastructure provided by Grid computing, in particular Data Grids, allows a systematic approach to the process of discovering, accessing, analysing and integrating huge amounts of data. Most data grid software and applications assume the data is in files, although recently tools such as OGSA-DAI have been developed to provide grid services for interfacing to databases. This paper investigates the use of Data Grid technologies (Web Services, Grid Services and Grid tool) for applications that store all their data in databases, in particular, applications in biodiversity informatics. The aim of this work is to analyse the benefit (or otherwise) of these approaches. Web Service and Grid Service prototypes of the Global Biodiversity Information Facility (GBIF), a distributed web-based biodiversity information system, were developed as part of the evaluation process.Lester K.W. Leong, Paul Coddington, Andrew Wendelbor

Extensible job managers for grid computing

Copyright © 2003, Australian Computer Society, Inc. This paper appeared at the Twenty-Sixth Australasian Computer Science Conference (ACSC2003), Adelaide, Australia. Conferences in Research and Practice in Information Technology, Vol. 16. Michael Oudshoorn, Ed. Reproduction for academic, not-for profit purposes permitted provided this text is included.Grid computing is becoming an important framework for enabling applications to utilize widely distributed collections of computational and data resources, however current grid software is still immature and rather difficult to use. The Globus Grid Toolkit is a set of low-level tools, protocols and services that has become a defacto standard for basic grid computing infrastructure. The Globus Resource Allocation and Management (GRAM) service provides for the management and remote execution of jobs defined using a standard Resource Specification Language (RSL). Currently, the GRAM has very limited functionality, which makes it more difficult to develop grid applications. One limitation is the lack of support for applications that require a special execution environment, such as Java applications that run within a Java Virtual Machine. Cumbersome workarounds are necessary to run such applications. The current GRAM addresses these problems in a rather ad hoc way for certain specific cases, however there is no general, well- defined mechanism for supporting arbitrary execution environments. Here we outline some of the problems with the current Globus GRAM specification and provide a proposal for how they might be addressed by defining some extensions to the standard RSL supported by the GRAM, as well as some modifications to the design of the GRAM that would enable it to support arbitrary execution environments. We give examples of how our proposed system can provide improved support for Java applications and cluster management systems, and describe our ongoing work in implementing prototypes of these proposed GRAM extensions.Coddington, P.D., Lu, L., Webb, D. and Wendelborn, A.

Optimizing Sisal Programs: a Formal Approach

We formally describe optimization techniques for the com pilation of the language Sisal 2.0. More precisely, we translate Sisal programs into data-flow IF1 graphs and optimize these graphs. An in teractive visualization environment for IF1 graphs is also provided

An ATM-based distributed high performance computing system

We describe the distributed high performance computing system we have developed to integrate together a heterogeneous set of high performance computers, high capacity storage systems and fast communications hardware. Our system is based upon Asynchronous Transfer Mode (ATM) communications technology and we routinely operate between the geographically distant sites of Adelaide and Canberra (separated by some 1100km) using Telstra’s ATMbased Experimental Broadband Network (EBN). We discuss some of the latency and performance issues that result from running day-to-day operations across such a long distance network. In addition to reviewing the hardware and systems software we have used, we relate some of the experience we have gained from integrating this technology into our working environment. We believe this type of distributed computing system has great potential for a range of distributed applications which we also present