Ken Meacham

ECSES – examining crystal structures using `e-science': a demonstrator employing web and grid services to enhance user participation in crystallographic experiments

An application of e-science methodology and grid networking technology is presented that opens up new possibilities to enhance the operation of large high-throughput service-crystallography facilities, exemplified by the UK National Crystallography Service (NCS). A seamless distributed computing approach is used to provide remote secure visualization, monitoring and interaction with the laboratory and the diffraction experiment, supervision and input to the data workup and analysis processes, and to enable dissemination and further use of the resulting structural data. The architecture of the system is based on web and grid services (in particular the use of Globus, v1.1.4), which provide a secure environment for two-way information flow and communication between the service users and operators. This capability will enhance operations of instrument and software automation by providing more efficient use of the resources, increasing the throughput of samples and enabling interactions with distributed chemistry information databases, computational services and networks. The viability of these interactions is assessed and directions for future crystallography services suggested. The setup would be equally applicable to protein or powder crystallography services.

Predictive resource management for meta-applications

This paper defines meta-applications as large, related collections of computational tasks, designed to achieve a specific overall result, running on a (possibly geographically) distributed, non-dedicated meta-computing platform. To carry out such applications in an industrial context, one requires resource management and job scheduling facilities (including capacity planning), to ensure that the application is feasible using the available resources, that each component job will be sent to an appropriate resource, and that everything will finish before the computing resources are needed for other purposes.

Industrial Stochastic Simulations on a European Meta-Computer

This paper outlines the experiences of running a large stochastic multi-body simulation across a pan-European meta-computer, to demonstrate the use of the PROMENVIR tool within such a large-scale WAN environment. We describe the meta-application management approach developed by PAC and discuss the technical issues raised by this experiment.

A middleware independent Grid workflow builder for scientific applications

Grid workflow authoring tools are typically specific to particular workflow engines built into Grid middleware, or are application specific and are designed to interact with specific software implementations. g-Eclipse is a middleware independent Grid workbench that aims to provide a unified abstraction of the Grid and includes a Grid workflow builder to allow users to author and deploy workflows to the Grid. This paper describes the g-Eclipse Workflow Builder and its implementations for two Grid middlewares, gLite and GRIA, and a case study utilizing the Workflow Builder in a Grid users scientific workflow deployment.

Parallelisation of the molecular dynamics code GROMOS87 for distributed memory parallel architectures

This paper describes the techniques and methodologies employed during parallelization of the Molecular Dynamics (MD) code GROMOS87, with the specific requirement that the program run efficiently on a range of distributed-memory parallel platforms. We discuss the preliminary results of our parallel port and indicate to what extent we are able to satisfy the basic requirements of industrial users with regard to code performance and scalability. We introduce a scheme which is used to dynamically allocate charge groups to processors reducing the time imbalance during the non-bonded force calculation phase from 30 – 40% to < 1%. We propose a new method for parallelizing the constraint dynamics algorithm (SHAKE) where the emphasis is placed on reducing the number and size of communicated packets during the iterative SHAKEing process.

Parallelization of the GROMOS87 Molecular Dynamics Code: An Update

In this paper, we describe the performance of the parallel GROMOS87 code, developed under the ESPRIT EUROPORT-2/PACC project, and indicate its potential impact in industry. An outline of the parallel code structure is given, followed by a discussion of the results of some industrially-relevant testcases. Conclusions are drawn as to the overall success of the project, and lessons learned from the porting and benchmarking activities, which show that the parallel code can enable more ambitious use of molecular simulation in industry.

Trust Modelling in 5G mobile networks

5G technologies will change the business landscape for mobile network operation. The use of virtualization through SDN, NFV and Cloud computing offer significant savings of CAPEX and OPEX, but they also allow new stakeholders to rent infrastructure capacity and operate mobile networks, including specialized networks supporting so-called vertical applications serving specific business sectors. In the resulting diverse stakeholder communities, the old trust assumptions between network operators will no longer apply. There is a pressing need for a far broader understanding of trust in such networks if they are to operate safely and securely for the engaged stakeholder communities. This paper describes the work carried out in the 5G-ENSURE project to address this need.

An integrated decision-support information system on the impact of extreme natural hazards on critical infrastructure

In this paper, we introduce an Integrated Decision-Support Tool (IDST v2.0) which was developed as part of the INFRARISK project (https://www.infrarisk-fp7.eu/). The IDST is an online tool which demonstrates the implementation of a risk-based stress testing methodology for analyzing the potential impact of natural hazards on transport infrastructure networks. The IDST is enabled with a set of software workflow processes that allow the definition of multiple cascading natural hazards, geospatial coverage and impact on important large infrastructure, including those which are critical to transport networks in Europe. Stress tests on these infrastructure are consequently performed together with the automated generation of useful case study reports for practitioners. An exemplar stress test study using the IDST is provided in this paper. In this study, risks and consequences of an earthquake-triggered landslide scenario in Northern Italy is described. Further, it provides a step-by-step account of the developed stress testing overarching methodology which is applied to the impact on a road network of the region of interest.

Co-creating an online TimeBank for inclusive research

Participatory and inclusive approaches to research have become more common as researchers recognize the benefits of enabling the meaningful involvement of representative community users in the development of accessible technologies. One of the major challenges in this context is how the involvement of community members can be appropriately supported in project-related activities: payment for time and contributions is a particularly difficult and longstanding issue. This paper discusses the inclusive development of an online Timebank involving community members with intellectual disabilities. The TimeBank is conceived as a tool that enables people to contribute their different expertise on the basis of time, rather than monetary reward. The development process of the TimeBank is described as well as the challenges faced by the research team. There is much potential in the Timebank idea, although considerable further research is needed to establish an accessible, usable, credible and trustworthy resource.

High-throughput structure/function screening of materials and catalysts with multiple spectroscopic techniques

High throughput screening methodologies are expanded to synchrotron based x‐ray absorption techniques. An environmental chamber, based on ultra‐high vacuum equipment, has been developed allowing in situ studies on arrays of samples while X‐ray absorption fine structure spectroscopy, Raman spectroscopy, mass spectrometry and/or X‐ray diffraction can be applied simultaneously to characterize the system under process conditions in a time‐resolved manner. The chamber accommodates a diverse range of samples from surface science to materials chemistry to heterogeneous catalysis. Data acquisition and data logging software is developed to handle large quantities of divers but related information. New data logging, processing and analysis procedures and programs are developed which will allow fast structure‐function relationships characterization.