AHM

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Case Study SRB and e-MineralsEnvironment from
the Molecular LevelAn UK e-science project for
modelling the atomistic processes involved in
environmental issues

• Lisa Blanshard
• Data Management Research
• CCLRC Daresbury Laboratory

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Environmental Issues
Crystal dissolution and weathering
Pollution molecules and atoms on mineral surfaces
Radioactive waste disposal
Crystal growth and scale inhibition
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Programs for large-scale simulations (millions of
atoms)
DL_POLY3 parallel molecular dynamics code.
Modifications aimed at running efficient
simulations with millions of atoms for
simulations of radiation damage (Daresbury)
SIESTA Order-N quantum mechanics code. Objective
to run with large samples and realistic fluids
(Cambridge)

• need to parallelise on UK grid
• BUT will generate lots more data files in
  different locations

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• Data Management Requirements
• Scientists want to
• store input and output files from simulations in
  different locations
• manage their own files/data via the web
• give access to other project members
• give temporary access to others

SRB
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Each user has their own collection to store their
own files
users collection for storing files
There is an eminerals collection for project files
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Files can be stored on any resource
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You can give people access to your data
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You can give other people temporary access using
MySRB tickets
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Next few months...
Upload files using MySRB on the web
Web Browser
Send files for computation
Daresbury App Server
MySRB
Application server runs SRB software
Eminerals MiniGrid
UK Grid
SRB Server
Oracle Client
Store simulation output
Database server holds locations of files
Daresbury Database server
MCAT
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Further Information
Environment from the Molecular Level http//www.e-
science.clrc.ac.uk/web/projects/eminerals http//e
minerals.org/ UK CCLRC e-Science
Centre http//www.e-science.clrc.ac.uk