Environment from the Molecular Level:

1. Environment from the Molecular Level: An e-science project for modelling the atomistic processes involved in environmental issues(funded by NERC)

2. Molecular Environmental Issues Radioactive waste disposal Pollution: molecules and atoms on mineral surfaces Crystal dissolution and weathering Crystal growth and scale inhibition

3. Rocks and Mineral Structures Radioactive waste disposal Pollution: molecules and atoms on mineral surfaces Crystal dissolution and weathering Crystal growth and scale inhibition

4. Level of theory Quantum Monte Carlo Natural organic matter Linear-scaling quantum mechanics Oxides/hydroxides Aluminosilicates Clays, micas Sulphides Phosphates Carbonates Large empirical models Organic molecules Adsorbing surface Metallic elements Halogens Contaminant The “Grand Challenge”. Requires scientists to work together in teams - a Virtual Organisation

5. Design Approach taken: • Over approx 3 years we have engaged in many workshops, tutorials and prototyping with developers and users. Teaching users what e-Science can “do for them”, including security. • Cooperation between CCLRC and NIEeS in Cambridge. • Planned to integrate together some tools which had already been developed/ prototyped at CCLRC, UCL and Reading. • A service-oriented approach is used for certain aspects: Grid, data management, user interfaces, metadata management. Workflow was found to be important to users, e.g. for combinatorial studies. • Several iterations of software have enabled some usability issues to be addresses. • Originally envisaged an “Integrated Portal Architecture” linking HPCPortal, DataPortal and visualisation services. • We thought we knew what users would like, but actually they preferred a simpler incremental approach; • Workflow scripting was preferred to a single portal. There are now several separate tools in use.

6. E-Minerals Portal

7. Technical Strategy • Technology considerations: • Considered: Globus GT2, SRB, Harness, CCF, Portal, Web services, visualisation tools • Various tool sets were tried and the users “voted with their feet” • Used: Globus, Condor, SRB, AG, MAST, RCommands, Metadata Editor, Workflow scripts, Web services, XML/ RDF/ OWL for data interoperability. • Infrastructure • E-Minerals “mini-Grid” was a great success, based on earlier work at Daresbury and Manchester on Grid evaluation. Mini-Grid focuses resources of the e-Minerals VO and includes large campus Condor pools and parallel computers. Using Globus, Condor and GSI. Data managed using SRB. • Collaboration tools • Access Grid, MAST, Wiki

8. GSI GridFTP Globus Integrated Portal Architecture Generic portal design using Globus and Web Services: Data Systems DataPortal Web Services Web Services HPCPortal Web Services Visualisation HPC Systems Working with GGF Grid Computing Environments Research Group

9. Development Issues • Constraints and other issues: • Project divided from outset into: • development team; • application team; • science team. • All teams work together and collaborate on papers • Tools written in C to integrate with existing “heritage” applications, e.g. from the Collaborative Computational Projects (CCPs) • Other interoperability issues addressed using Web services, e.g. gSOAP (client) +AXIS (server), XML-based data models and Semantic Grid technologies RDF+OWL • Constraints: short term goals, no prior experience of e-Science, new technology must not disrupt current work. • High requirements on computing resources for simulation studies • This lead to a focus on workflows for repeated calculations, data management for storing and retrieving results, semantic Web technologies for data interoperability between codes

10. Evaluation • Papers presented at All Hands 2005 included: • E-Science Usability: the e-Minerals Experience (paper 425) • The e-Minerals Project: Developing the Concept of the Virtual Organisation to support Collaborative Work on Molecular-scale Environmental Simulations (paper 518) • User engagement and evaluation: • Looked at the Usability Task Force metrics. • Our approach did not readily map onto them, but there are overlaps • Key: understand the science users, their needs, and their natural ways of working. • Good and bad points summarised on next slides

11. Lessons Learnt What was usable? • Keep it simple – use effective lightweight tools for the job • Condor and Globus – Condor job scripts were accepted readily. Condor-G and DAGMan now used. RSL also embedded in scripts. • SRB – required little training and was found to be useful, SCommands in scripts. • Resource Management – Globus-based resource-monitoring tool was developed (in the Portal). A meta-scheduler is being developed. • Security – GSI proved “easy for users to work with”. The Portal uses MyProxy to ensure pervasive access. Certificates were not a problem – we offered training from Day 1. • Collaboration tools – desktop use of AG enables ad hoc meetings + MAST (Multi-cast Application Sharing Tool). Wiki and Instant Messaging also used. • Semantic technologies. CML was initially used with XSLT and SVG. This now extended in the AgentX toolkit.

12. Lessons Learnt What was not usable? • Client tools * – installation has caused difficulties, e.g. Globus. Initially used “submit machines”. Solutions investigated include: • Portal – hides the complexity behind a Web interface, user doesn’t install anything; • Web service interfaces – for Condor (Chapman et al.), GROWL for Globus and SRB (Allan et al.); • BPEL interface – work at UCL/ OMII – plug-in for Eclipse. • Firewall issues – for both users and infrastructure – changes to rules lead to instability. Portal and Web services solve this problem for users. • Meta-data – tools are available, but automatic harvesting required to avoid mistakes. RCommands developed to improve this, can be linked into the workflow scripts. * A recent workshop “Lightweight Grid Computing” was held 2-3/5/06 at Losehill Hall. Attendees from GROWL, RealityGrid, Imperial College, e-Minerals, e-CCP… Transcript of discussions on usability issues is available giving more detailed information.

13. Future Plans Current and Future development plans: • New tools are being developed, for instance recently the meta-data editor and RCommands were added to the suite . • AgentX data-interoperability tools have been added from e-CCP extending the use of CML. Such work is now timely and illustrates how existing large codes, e.g. Siesta and GULP from CCP5 can be integrated easily with visualisation tools. • Development staff also work on other projects and with other developers. E-Minerals tools are now being evaluated in other areas, e.g. Integrative Biology and e-CCP. There are key synergies and critical mass, sharing of experiences and code/ services. • Full integration via a portal interface was not initially wanted, and also could not be achieved at the start of the project as the technology was not adequate (we tried PHP, now have JSR-168). This is now being re-visited as it provides a good solution to many of the problems highlighted. • Re-usable portlet-based tools from the NGS Portal can be re-used, already done for Integrative Biology and other projects. Can be combined with Wiki etc. Some following slides show more details of some of the tools. Blatant advert: Portals and Portlets 2006 http://www.nesc.ac.uk/esi/events/686/

14. AgentX Framework - Overview Specify how to locate data (XML, CML, XLink) with a particular meaning Applications can use tools (AgentX library) that work with the specification to obtain information Classes and properties of entities are specified in an ontology (OWL, RDF/ XML) Mappings (RDF/ XML) associate classes and properties with fragment identifiers (XPointer) Fragment identifiers can be used to locate logical collections (classes) and data items (properties) Ontology Mappings Data O 0.000 0.000 0.000 H 0.000 0.757 0.587 H 0.000 -0.757 0.587 MOLECULE locator “Mol_frag_id” ATOM locator “Atom_frag_id” xCoordinate locator “xCoor_frag_id”

15. AgentX Framework - Example DL_POLY3 (CCP5) integrated with CCP1 GUI Mappings DL_POLY3 REVCON.xml CONTROL CCP1 GUI Mappings • AgentX • Core library written in C • Wrappers for Python, Perl and Fortran • Hides the complexities of dealing with XML • Simple API • Enables straightforward exchange of information AgentX core AgentX core CONFIG.xml Fortran wrapper Python wrapper Standard Ontology Standard Mappings

16. RCommands • RCommands are shell tools and associated Web services for meta-data manipulation • RCommands primary use case is within e-Minerals workflow, i.e. to allow automatic insertion of meta-data as a post processing action

17. Client Side RCommands gSOAP RCommand Server Code Axis Server Side JDBC RCommands Service-based Arch Link into workflows BPEL Engine SOAP Relational Database

18. Title • Description • Notes • Start / End Dates • Originator • Name • Description Name Value Pairs • Name • URI Subset of Schema

19. University of Reading Royal Institution