Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated computer and data grid

This paper describes a prototype grid infrastructure, called the eMinerals minigrid, for molecular simulation scientists. which is based on an integration of shared compute and data resources. We describe the key components, namely the use of Condor pools, Linux/Unix clusters with PBS and IBM's LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condor's DAGman tool for handling workflow, the Storage Resource Broker for handling data, and the CCLRC dataportal and associated tools for both archiving data with metadata and making data available to other workers.

Modeling the effects of node heterogeneity on the performance of grid applications

The performance benefit when using grid systems comes from different strategies, among which partitioning the applications into parallel tasks is the most important. However, in most cases the enhancement coming from partitioning is smoothed by the effects of synchronization overheads, mainly due to the high variability in the execution times of the different tasks, which, in turn, is accentuated by the large heterogeneity of grid nodes. In this paper we design hierarchical, queuing network performance models able to accurately analyze grid architectures and applications. Thanks to the model results, we introduce a new allocation policy based on a combination between task partitioning and task replication. The models are used to study two real applications and to evaluate the performance benefits obtained with allocation policies based on task replication.

Error analysis of a Monte Carlo algorithm for computing bilinear forms of matrix powers

In this paper we present error analysis for a Monte Carlo algorithm for evaluating bilinear forms of matrix powers. An almost Optimal Monte Carlo (MAO) algorithm for solving this problem is formulated. Results for the structure of the probability error are presented and the construction of robust and interpolation Monte Carlo algorithms are discussed. Results are presented comparing the performance of the Monte Carlo algorithm with that of a corresponding deterministic algorithm. The two algorithms are tested on a well balanced matrix and then the effects of perturbing this matrix, by small and large amounts, is studied.

Femtosecond evolution of spatially inhomogeneous carrier excitations: part 2: stochastic approach and GRID implementation

We present a stochastic approach for solving the quantum-kinetic equation introduced in Part I. A Monte Carlo method based on backward time evolution of the numerical trajectories is developed. The computational complexity and the stochastic error are investigated numerically. Variance reduction techniques are applied, which demonstrate a clear advantage with respect to the approaches based on symmetry transformation. Parallel implementation is realized on a GRID infrastructure.

The collaborative P-GRADE grid portal

Grid portals are increasingly used to provide uniform access to the grid infrastructure. This paper describes how the P-GRADE Grid Portal could be used in a collaborative manner to facilitate group work and support the notion of Virtual Organisations. We describe the development issues involved in the construction of a collaborative portal, including ensuring a consistent view between participants of a collaborative workflow and management of proxy credentials to allow separate nodes of the workflow to be submitted to different grids.

Maximizing revenue in Grid markets using an economically enhanced resource manager

Traditional resource management has had as its main objective the optimization of throughput, based on parameters such as CPU, memory, and network bandwidth. With the appearance of Grid markets, new variables that determine economic expenditure, benefit and opportunity must be taken into account. The Self-organizing ICT Resource Management (SORMA) project aims at allowing resource owners and consumers to exploit market mechanisms to sell and buy resources across the Grid. SORMA's motivation is to achieve efficient resource utilization by maximizing revenue for resource providers and minimizing the cost of resource consumption within a market environment. An overriding factor in Grid markets is the need to ensure that the desired quality of service levels meet the expectations of market participants. This paper explains the proposed use of an economically enhanced resource manager (EERM) for resource provisioning based on economic models. In particular, this paper describes techniques used by the EERM to support revenue maximization across multiple service level agreements and provides an application scenario to demonstrate its usefulness and effectiveness. Copyright © 2008 John Wiley & Sons, Ltd.

An assessment of eye-gaze potential within immersive virtual environments

In collaborative situations, eye gaze is a critical element of behavior which supports and fulfills many activities and roles. In current computer-supported collaboration systems, eye gaze is poorly supported. Even in a state-of-the-art video conferencing system such as the access grid, although one can see the face of the user, much of the communicative power of eye gaze is lost. This article gives an overview of some preliminary work that looks towards integrating eye gaze into an immersive collaborative virtual environment and assessing the impact that this would have on interaction between the users of such a system. Three experiments were conducted to assess the efficacy of eye gaze within immersive virtual environments. In each experiment, subjects observed on a large screen the eye-gaze behavior of an avatar. The eye-gaze behavior of that avatar had previously been recorded from a user with the use of a head-mounted eye tracker. The first experiment was conducted to assess the difference between users' abilities to judge what objects an avatar is looking at with only head gaze being viewed and also with eye- and head-gaze data being displayed. The results from the experiment show that eye gaze is of vital importance to the subjects, correctly identifying what a person is looking at in an immersive virtual environment. The second experiment examined whether a monocular or binocular eye-tracker would be required. This was examined by testing subjects' ability to identify where an avatar was looking from their eye direction alone, or by eye direction combined with convergence. This experiment showed that convergence had a significant impact on the subjects' ability to identify where the avatar was looking. The final experiment looked at the effects of stereo and mono-viewing of the scene, with the subjects being asked to identify where the avatar was looking. This experiment showed that there was no difference in the subjects' ability to detect where the avatar was gazing. This is followed by a description of how the eye-tracking system has been integrated into an immersive collaborative virtual environment and some preliminary results from the use of such a system.

A grouped P2P network for scalable grid information services

Information services play a crucial role in grid environments in that the state information can be used to facilitate the discovery of resources and the services available to meet user requirements, and also to help tune the performance of a grid system. However, the large size and dynamic nature of the grid brings forth a number of challenges for information services. This paper presents PIndex, a grouped peer-to-peer network that can be used for scalable grid information services. PIndex builds on Globus MDS4, but introduces peer groups to dynamically split the large grid information search space into many small sections to enhance its scalability and resilience. PIndex is subsequently modeled with Colored Petri Nets for performance evaluation. The simulation results show that PIndex is scalable and resilient in dealing with a large number of peer nodes.

Applying autonomic computing concepts to parallel computing using intelligent agents

The work reported in this paper is motivated by the fact that there is a need to apply autonomic computing concepts to parallel computing systems. Advancing on prior work based on intelligent cores [36], a swarm-array computing approach, this paper focuses on ‘Intelligent agents’ another swarm-array computing approach in which the task to be executed on a parallel computing core is considered as a swarm of autonomous agents. A task is carried to a computing core by carrier agents and is seamlessly transferred between cores in the event of a predicted failure, thereby achieving self-ware objectives of autonomic computing. The feasibility of the proposed swarm-array computing approach is validated on a multi-agent simulator.