A Computational Economy for Grid Computing and its Implementation in the Nimrod-G Resource Brok

Computational Grids, coupling geographically distributed resources such as PCs, workstations, clusters, and scientific instruments, have emerged as a next generation computing platform for solving large-scale problems in science, engineering, and commerce. However, application development, resource management, and scheduling in these environments continue to be a complex undertaking. In this article, we discuss our efforts in developing a resource management system for scheduling computations on resources distributed across the world with varying quality of service. Our service-oriented grid computing system called Nimrod-G manages all operations associated with remote execution including resource discovery, trading, scheduling based on economic principles and a user defined quality of service requirement. The Nimrod-G resource broker is implemented by leveraging existing technologies such as Globus, and provides new services that are essential for constructing industrial-strength Grids. We discuss results of preliminary experiments on scheduling some parametric computations using the Nimrod-G resource broker on a world-wide grid testbed that spans five continents

Linking Heterogeneous Biodiversity Information Systems on the GRID: the GRAB Prototype

In the field of biodiversity informatics a wide range of diverse databases and tools already exists. The challenge is to integrate such resources in order to support scientists wishing to explore complex problems of relevance to biodiversity, and to create new resources where necessary. In this paper we outline the relevance of biodiversity informatics requirements to the future development of the GRID, identifying the main issues that need to be addressed in this area. We present GRAB (GRid And Biodiversity), which is a prototype demonstrator illustrating how one particular biodiversity-related task, namely bioclimatic modelling, can be supported in a Globus-based environment. We also describe a much larger-scale GRID application project that is just commencing (BiodiversityWorld) in which a flexible problem-solving environment is to be built for full-scale investigations by scientists working in a number of biodiversity research areas

LifeWatch deliverable 5.1.1: Data & Modelling Tool Structures – Showcases

Showcases are examples of the kinds of scientific studies that biodiversity and ecological researchers would like to be able to undertake within the context of themes concerned with, for example: Discovery of biodiversity, patterns of biodiversity patterns, biodiversity processes and monitoring change, systems biology, and nature conservation and management. This report collates information on 12 typical examples and illustrates some of the common underlying tasks and capabilities necessary for their performance. These capabilities could be combined to implement the documented showcases, but are also generic enough to implement other biodiversity science cases. The example showcases were primarily gathered during the the LifeWatch preparatory phase project (2008-2011) through contact with researchers via site visits to major institutions, or through the published work of biodiversity researchers

An analysis of the HIV testing cascade of a group of HIV-exposed infants from birth to 18 months in peri-urban Khayelitsha, South Africa

BACKGROUND: Despite the reduction of HIV mother-to-child transmission, there are concerns regarding transmission rate in the breastfeeding period. We describe the routine uptake of 6 or 10 (6/10) weeks, 9 months and 18 months testing, with and without tracing, in a cohort of infants who received HIV PCR testing at birth (birth PCR) (with and without point of care (POC) testing) in a peri-urban primary health care setting in Khayelitsha, South Africa. METHODS: In this cohort study conducted between November 2014 and February 2018, HIV-positive mothers and their HIV-exposed babies were recruited at birth and all babies were tested with birth PCR. Results of routine 6/10 weeks PCR, 9 months and 18 months testing were followed up by a patient tracer. We compared testing at 6/10 weeks with a subgroup from historical cohort who was not tested with birth PCR. RESULTS: We found that the uptake of 6/10 weeks testing was 77%, compared to 82% with tracing. When including all infants in the cascade and comparing to a historical cohort without birth testing, we found that infants who tested a birth were 22% more likely to have a 6/10 weeks test compared to those not tested at birth. There was no significant difference between the uptake of 6/10 weeks testing after birth PCR POC versus birth PCR testing without POC. Uptake of 9 months and 18 months testing was 39% and 24% respectively. With intense tracing efforts, uptake increased to 45% and 34% respectively. CONCLUSION: Uptake of HIV testing for HIV-exposed uninfected infants in the first 18 months of life shows good completion of the 6/10 weeks PCR but suboptimal uptake of HIV testing at 9 months and 18 months, despite tracing efforts. Birth PCR testing did not negatively affect uptake of the 6/10 weeks HIV test compared to no birth PCR testing

BioVeL : a virtual laboratory for data analysis and modelling in biodiversity science and ecology

Background: Making forecasts about biodiversity and giving support to policy relies increasingly on large collections of data held electronically, and on substantial computational capability and capacity to analyse, model, simulate and predict using such data. However, the physically distributed nature of data resources and of expertise in advanced analytical tools creates many challenges for the modern scientist. Across the wider biological sciences, presenting such capabilities on the Internet (as "Web services") and using scientific workflow systems to compose them for particular tasks is a practical way to carry out robust "in silico" science. However, use of this approach in biodiversity science and ecology has thus far been quite limited. Results: BioVeL is a virtual laboratory for data analysis and modelling in biodiversity science and ecology, freely accessible via the Internet. BioVeL includes functions for accessing and analysing data through curated Web services; for performing complex in silico analysis through exposure of R programs, workflows, and batch processing functions; for on- line collaboration through sharing of workflows and workflow runs; for experiment documentation through reproducibility and repeatability; and for computational support via seamless connections to supporting computing infrastructures. We developed and improved more than 60 Web services with significant potential in many different kinds of data analysis and modelling tasks. We composed reusable workflows using these Web services, also incorporating R programs. Deploying these tools into an easy-to-use and accessible 'virtual laboratory', free via the Internet, we applied the workflows in several diverse case studies. We opened the virtual laboratory for public use and through a programme of external engagement we actively encouraged scientists and third party application and tool developers to try out the services and contribute to the activity. Conclusions: Our work shows we can deliver an operational, scalable and flexible Internet-based virtual laboratory to meet new demands for data processing and analysis in biodiversity science and ecology. In particular, we have successfully integrated existing and popular tools and practices from different scientific disciplines to be used in biodiversity and ecological research.Peer reviewe

A Case for Economy Grid Architecture for Service Oriented Grid Computing

Computational Grids are a promising platform for executing large-scale resource intensive applications. However, resource management and scheduling in the Grid environment is a complex undertaking as resources are (geographically) distributed, heterogeneous in nature, owned by different individuals or organizations with their own policies, have differen t access and cost models, and have dynamically varying loads and availability. This introduces a number of challenging issues such as site autonomy, heterogeneous interaction, policy extensibility, resource allocation or coallocation, online control, scalability, transparency, resource brokering, and "computational economy". A number of Grid systems (such as Globus and Legion) have addressed many of these issues with exception of a computational economy. We argue that a computational economy is required in order to create a real world scalable Grid because it provides a mechanism for regulating the Grid resources demand and supply...

Nimrod-G resource broker for service-oriented grid computing

A computational economy framework for resource allocation and supply and demand regulation for resources was proposed. The new framework offers incentive to resource owners for being part of the Grid and motivates resource users to trade-off between time of results delivery and computational cost. Nimrod-G is a tool for automated modeling and execution of parameter sweep applications over global computational Grids. Nimrod tools for modeling parametric experiments are quite mature and in production use for cluster computing

An Evaluation of Economy-based Resource Trading and Scheduling on Computational Power Grids for Parameter Sweep Applications

: Computational Grids are becoming attractive and promising platforms for solving large-scale (problem solving) applications of multi-institutional interest. However, the management of resources and scheduling computations in the Grid environment is a complex undertaking as they are (geographically) distributed, heterogeneous in nature, owned by different individuals or organisations with their own policies, different access and cost models, and have dynamically varying loads and availability. This introduces a number of challenging issues such as site autonomy, heterogeneous substrate, policy extensibility, resource allocation or co-allocation, online control, scalability, transparency, and "economy of computations". Some of these issues are being addressed by system-level Grid middleware toolkits such as Globus. Our work in general focuses on economy/market driven resource management architecture for the Grid; and in particular on resource brokering and scheduling through a user-lev..