Environment from the Molecular Level:
An e-science project for modelling the atomistic
processes involved in environmental issues
(funded by NERC)
Molecular Environmental Issues
Radioactive
waste disposal
Pollution: molecules and
atoms on mineral surfaces
Crystal growth and
scale inhibition
Crystal dissolution
and weathering
Rocks and Mineral Structures
Radioactive
waste disposal
Pollution: molecules and
atoms on mineral surfaces
Crystal growth and
scale inhibition
Crystal dissolution
and weathering
The “Grand Challenge”.
Requires scientists to work together in teams
- a Virtual Organisation
Organic molecules
Metallic elements
Halogens
Contaminant
Sulphides
Oxides/hydroxides
Phosphates
Carbonates
Large empirical
models
Aluminosilicates
Linear-scaling
quantum mechanics
Clays, micas
Quantum
Monte Carlo
Natural organic matter
Level of
theory
Adsorbing
surface
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.
•
–
Planned to integrate together some tools which had already been developed/
prototyped at CCLRC, UCL and Reading.
•
•
–
Cooperation between CCLRC and NIEeS in Cambridge.
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.
E-Minerals Portal
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
Integrated Portal Architecture
Generic portal design using Globus and Web Services:
GSI
Data Systems
DataPortal
Web Services
GridFTP
Web Services
HPCPortal
Web Services
Visualisation
HPC Systems
Globus
Working with GGF Grid
Computing Environments
Research Group
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
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
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.
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.
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.
Blatant advert: Portals and Portlets 2006
http://www.nesc.ac.uk/esi/events/686/
Some following slides show more details of some of the tools.
AgentX Framework - Overview
Ontology
MOLECULE
Mappings
locator
Data
O
0.000
0.000
0.000
“Mol_frag_id”
ATOM
locator
“Atom_frag_id”
xCoordinate
locator
“xCoor_frag_id”
H
0.000
0.757
0.587
H
0.000
-0.757
0.587
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)
AgentX Framework - Example
DL_POLY3 (CCP5) integrated with CCP1 GUI
Mappings
CONTROL
DL_POLY3
REVCON.xml
CCP1 GUI
AgentX
Mappings
CONFIG.xml
AgentX
core
AgentX
core
- Core library written in C
Fortran
wrapper
Python
wrapper
- Wrappers for Python, Perl and
Fortran
Standard
Ontology
Standard
Mappings
- Hides the complexities of dealing
with XML
- Simple API
- Enables straightforward
exchange of information
RCommands
•
•
RCommands are shell tools and
associated Web services for metadata manipulation
RCommands primary use case is
within e-Minerals workflow, i.e. to
allow automatic insertion of metadata as a post processing action
Function Domain
RCommand
Rinit
Authentication /
Session
Rexit
Rpasswd
Rls
Entity Operations
Rcreate
Rrm
Parameter
Operations
Rannotate
Permissions
Rchmod
Rsearch
RCommands Service-based Arch
RCommands
Client Side
BPEL Engine
gSOAP
SOAP
Axis
RCommand Server Code
JDBC
Server Side
Relational Database
Link into
workflows
Subset of Schema
• Title
• Description
• Notes
• Start / End Dates
• Originator
• Name
• Description
Name Value Pairs
• Name
• URI
University of
Reading
Royal Institution