Building the e-Minerals Minigrid

Rik Tyer, Lisa Blanshard, Kerstin Kleese(Data Management Group)

Rob Allan, Andrew Richards(Grid Technology Group)

AHM, Nottingham 2003

Royal Institution

University of

Reading

Project Members

AHM, Nottingham 2003

Who we are

• One of Europe’s largest Research Support Organisations

• Provides large scale experimental, data and computing facilities

• Serves the UK research community both in academia and industry

• Annually support 12000 scientists from all major scientific domains

• 1800 members of staff over three sites:

Rutherford Appleton Laboratory in Oxfordshire

Daresbury Laboratory in Cheshire

Chilbolton Observatory in Hampshire

• Large quantities of data associated with the various facilities

• Major e-Science centre in the UK

http://www.cclrc.ac.uk

Council for the Central Laboratory of the Research Councils

AHM, Nottingham 2003

Environmental Issues

Radioactive waste disposal

Crystal growth and scale inhibition

Pollution: molecules and atoms on mineral surfaces

Crystal dissolution and weathering

AHM, Nottingham 2003

Examples of Codes

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)

SURFACE SIMULATIONS: New developments aimed at efficient scanning of many configurations of complex fluid-mineral interfaces, for studies of crystal growth and dissolution (Bath)

AHM, Nottingham 2003

Data Management Requirements

• Many output files produced from each simulation run

• Each set of input and output files is a dataset

• Need to keep information about each simulation – metadata

• Other scientists need access to this information and datasets

• Need to search different metadata repositories at once

• Access could be from anywhere in the world

• Need to categorise data so it can be found by someone else

• These requirements are same for all scientists

AHM, Nottingham 2003

Integrated Portals using web services

External Applications

DataPortal

HPCPortal

High Performance

Computers on the GRID

Metadata databases

Web Services

Web Services

Web Services

AHM, Nottingham 2003

DataPortal

Metadata Object

Topic

Study Description

Access Conditions

Data Location

Data Description

Related Material

Discipline e.g. Earth Sciences/Soil Contamination/Heavy Metals/Arsenic

Provenance about what the study is, who did it and when.

Conditions of use providing information on who and how the data can be accessed.

Detailed description of the organisation of the data into datasets and files.

Locations providing a navigational to where the data on the study can be found.References into the literature and community providing context about the study.

Scientific Metadata Model

AHM, Nottingham 2003

DataPortal – Use Cases

DATA PORTAL

Request Metadata

Store AssociatedData Files

Transfer Data Files

Multiple Metadata Repositories

Scientist

External ApplicationRemote Machines

AHM, Nottingham 2003

Plan of Work

High-requirement science

High-performance codes

Collaborative environment

AHM, Nottingham 2003

e-Minerals Minigrid and Portal

• Minigrid makes the shared computing resources available to the project through the UK e-Science grid (built using globus, incorporating storage resource broker)

• The e-Minerals minigrid is accessed through the e-Minerals portal, based on the HPCPortal and Dataportal developed at the Daresbury Laboratory

• The e-Minerals minigrid links to a storage resource broker to store the outputs of simulation runs

AHM, Nottingham 2003

e-Minerals Portal

AHM, Nottingham 2003

DataPortal Results

AHM, Nottingham 2003

Condor Technologies

Condor:

Mature-ish technology to build small or large distributed computing systems from standard desktop computers

The important point is that condor can allow you to use idle time on desktops, and hence harness the potential of powerful processors

AHM, Nottingham 2003

The UCL Windows Condor Pool

• Runs WTS (Windows Terminal Server)

• Approximately 750 cpu’s in 30 clusters.

• Most are 1GHz Pentium 4, with 256/512Mb ram and 40Gb hard disks.

• All 90%+ underutilised and running 24/7…

• We are using condor to use this pool as a massive distributed computing system

AHM, Nottingham 2003

Technology Used

• Operating system: SuSE Linux 8.1 (kernel 2.4.19-4GB)

• Sun Microsystems J2SDK version 1.4

• All Data Portal web services built and deployed under Apache Tomcat version 4.1.18 using Apache Ant version 1.5.1

• Apache Axis as the SOAP engine

• For authentication MyProxy server used

• Systinet UDDI Server version 4.5 for Lookup Web Service

• PostgreSQL (version 7.2.2-16) databases for Lookup, Session Manager, Access & Control, Shopping Cart Web Services

• HPCPortal services built using Globus 2 toolkit with GSoap2 libraries. Deployed under standard Apache http server 1.3.27

AHM, Nottingham 2003

Further Information

Environment from the Molecular Levelhttp://www.e-science.clrc.ac.uk/web/projects/emineralshttp://eminerals.org/

E-minerals Mini Grid (need a X.509 certificate)http://wk-pc1.dl.ac.uk:8080/dataportal/eminerals.html

Integrated e-Science Environment Portalhttp://esc.dl.ac.uk/IeSE/

HPC Grid Services Portalhttp://esc.dl.ac.uk/HPCPortal/

DataPortal demonstrationhttp://esc.dl.ac.uk:9000/index.html

UK CCLRC e-Science Centrehttp://www.e-science.clrc.ac.uk