e-CCP: Collaborative Computing Projects e-Science Environment

STFC Daresbury

Resources:• Funding 100k / year• Staff: Phil Couch• Resources: access to SCARF,

NGS, HPCx and NW-GRID

Start/end date/Duration• Start: October 2003• End: Ongoing• Duration: Ongoing

Contribution to NWG outputs:• Lev. Jobs: 2 • Lev. Fund. 100k/ year• Industr. Col 2• Publications several• Conferences: several CCPs

hold courses or workshops• Web sites:

http://www.ccp.ac.ukhttp://www.datarepresentation.org

Principal Investigator:• Martyn Guest (Daresbury)

Summary• Provide e-Science support to computational Science and

Engineering projects

Objectives• Grid enable codes for remote job management• Portals, GUIs and Web interfaces• Cross searching data and data retrieval• Capture of metadata• Data interoperability• Workflow• Make simulation and analysis codes available for experimental

facilities, e.g. Diamond Light Source

Progress towards deliverables• e-CCP has developed an extensive toolkit for data

interoperability called AgentX (described under middleware discussion).

• Codes from CCP1, CCP3, CCP4, CCP5 and CCP9 have been Grid-enabled and used on NW-GRID.

Scientific highlights• CCP3, CCP5 and CCP9 outputs were presented at recent

workshop on Materials Simulation, DL, 20/3/07• CCP4 suite used in e-HTPX project• CCP5 codes used in e-Minerals project

Project Partners:• Daresbury, RAL, most UK

Universities and some industrial partners

e-CCP Highlight: CCP9 - High TC Superconductor studies

STFC Daresbury

XMLdata

SimulationSimulationSimulationSimulation

XMLdataXMLdataXMLdata

AgentX Database

RGemRCommands

Distributed Computing Support Programme High End Computing Support Programme

STFC Daresbury

Principal Investigator:• Martyn Guest (Daresbury)

Summary• Specialist support to EPSRC community through DISCO

programme to keep EPSRC funded projects at forefront of world research. DISCO provides professional advice on mid-range cluster compute systems and software including application benchmarking results. An annual Machine Evaluation Workshop is held at Daresbury.

Objectives• Continuing availability of application benchmarks across a wide

range of compute systems• Advice to grant holders and EPSRC• Advice on efficient exploitation of national facilities

Progress towards deliverables• DISCO staff provided advice on NW-GRID procurement.• DISCO benchmarks have been run on NW-Grid systems.

Scientific highlights• N/A

Resources:• Funding 50k / year• Staff: Christine Kitchen• AMD and Intel support• Capital approx 100k supporting

cluster systems at DL

Start/end date/Duration• Start: October 2003• End: Ongoing• Duration: Ongoing

Contribution to NWG outputs:• Lev. Jobs: 5 • Lev. Fund. 50k/ year• Industr. Col 2• Publications: benchmark

reports• Conferences: annual MEW• Web site:

http://www.cse.clrc.ac.uk/disco/index.shtml

Project Partners:• Daresbury, Rutherford

Appleton, Warwick University

e-Minerals - Environment from the Molecular Level

STFC Daresbury

Principal Investigator:• Martin Dove (Cambridge)

Summary• Simulation of processes responsible for the transport of

pollutants, storage of nuclear waste and other environmental issues. Linking atomistic simulation tools with Grid technologies to facilitate realistic simulations across a wide range of chemical and physical parameters, length and time scales. Collaborative working of simulation scientists, application developers and computer scientists

Objectives• Web portals for access to Grid technology• Simulation using distributed resources• Enhanced data manipulation, analyses and metadata• Facilitate collaborative working

Progress towards deliverables• RMCS: Remote My-Condor-Submit, uses Condor-G, SRB,

AgentX and Rcommands. This was developed at Daresbury Laboratory and University of Cambridge as a computational framework for e-Minerals to control large-scale parametric simulations.

Scientific highlights• A number of outputs related to studies of minerals and

adsorbates presented at DL workshop 20/3/07

Resources:• Funding 220k / year• Staff: Rik Tyer• Resources: Condor pools at

UCL and Cambridge, accessto NGS and NW-GRID.

Start/end date/Duration• Start: October 2003• End: Ongoing• Duration: Ongoing

Contribution to NWG outputs:• Lev. Jobs: 3 • Lev. Fund. 220k/ year• Industr. Col 2• Publications yes• Conferences: Workshop on

Materials Simulation, DL, 20/3/07

• Web site:http://www.eminerals.org

Project Partners:• Cambridge, Daresbury, UCL,

Bath, Reading, Royal Institution, Bristol, Oxford, Manchester

Level of theory

Adsorbing surface

Contaminant

Quantum Monte Carlo

Large empirical models

Linear-scaling quantum mechanics

Organic molecules

Nitrates

Cla

ys,

mic

as

Alu

min

osili

cate

s

Nat

ura

l org

anic

mat

ter

Pho

sph

ates

Car

bona

tes

Oxi

des/

hydr

oxid

es

Sul

phi

des

Metallic elements

e-Minerals - Collaborative science and the Virtual Organisation

STFC Daresbury

Simplemodels

Empiricalmodels

Quantummechanics

Lattice models

Molecular dynamics

Monte Carlo

GULP

DL_POLY_3

CASTEP

SIESTA

SIESTA

OSSIA

Computational demands

Single processor:

high throughput

Parallel processors:

high performance

e-Minerals - Simulation models used in the project

STFC Daresbury

Single processors jobs:

high throughput

Compression of the mineral diopside:CASTEP

Compressibility anomaly in amorphous silica:DL_POLY_3

Cation ordering in layer silicates:OSSIA

Adsorption of molecules on mineral surfaces:SIESTA

e-Minerals - Scientific Highlights from NW-GRID

STFC Daresbury

e-HTPX: An e-Science Resource for High Throughput Protein Crystallography

STFC Daresbury

Principal Investigator:• Colin Nave (Daresbury)

Summary• an e-Science Resource for High-Throughput Protein

Crystallography

Objectives• Web portals for access to Grid and experimental technology• Experimental data analysis using distributed resources• Enhanced data manipulation, analyses and metadata• Facilitate collaborative working• Test and deploy services for PX on SRS, ESRF and Diamond

synchrotron facilities

Progress towards deliverables• e-HTPX has developed a suite of underpinning Web services

and user portals (hubs) for access to and control of experimental PX data collection tools and analysis codes for determining the 3D structure of proteins. Completed structures and metadata are uploaded for archival to the Protein Data Bank, EBI Hinxton. Has comprehensive data model and several spin-off projects.

Scientific highlights• Successful demonstration of e-HTPX services at annual

Scientific Advisory Board• Trial of services by Pfizer• Deployment on Diamond Light Source ongoing

Resources:• Funding 280k / year• Staff: Mihaela Dediu• Resources: 50k capital

for own small cluster. Accessto NGS and NW-GRID

Start/end date/Duration• Start: October 2003• End: January 2008• Duration: 4 ½ years

Contribution to NWG outputs:• Lev. Jobs: 4 • Lev. Fund. 280k/ year• Industr. Col 2• Publications yes• Conferences represented at• international synchrotron and

PX conferences• Web site:

http://www.e-htpx.ac.uk

Project Partners:• Cambridge, Cardiff, Oxford,

York, Grenoble

e-HTPX: Gene Expression to Structure Analysis Workflow

STFC Daresbury

Workflow Composition and Optimisation STFC Daresbury

Principal Investigator:• David Walker (Cardiff)

Summary• Using a problem solving environment to automatically define

service relationships and dependencies for applications services in a complex scientific procedure using distributed resources

• Specification and implementations of Grid Service to support logging and workflow optimisation

Objectives• Service discovery using OGSA based service architecture • Explore emerging technologies impacting on service oriented

Grid computing at application level• Utilise problem solving environments for exemplar applications

Progress towards deliverables• The Daresbury aspects of this project we concerned with the

pragmatic deployment of workflow systems for large-scale Grid problems in science and engineering. BPEL workflow descriptions and enactment were applied to Web services, WS-RF services and portal interfaces.

Scientific highlights• A workflow system was implemented to control the e-HTPX

data analysis pipeline which uses the CCP4 application suite. It allows semi-automatic testing of the analysis procedure with the opportunity for the user to interact via the e-HTPX Portal.

Resources:• Funding 150 k• Staff: Asif Akram

Start/end date/Duration• Start: Jan 2005• End: Nov 2007• Duration: 2 years

Contribution to NWG outputs:• Lev. Jobs: 1 • Lev. Fund. 150 k• Industr. Col 0• Publications 5• Conferences: at NeSC 11/07• Web

http://www.grids.ac.uk/WOSE

Project Partners:• Cardiff• Imperial College

Visualisation STFC Daresbury

Principal Investigator:• Richard Blake

Summary• Develop visualisation resource for high end data application for

support of Collaborative Computational projects

Objectives• Provide leading edge visualisation resource• Demonstrate capabilities of resource

Progress towards deliverables• Development of CCP1 GUI and CCP3 GUI (DLV) is ongoing.

GUIs have been used with numerous CCP applications with AgentX toolkit. GUIs are now accessing Grid resources including NW-GRID via GROWL and RMCS toolkits.

Scientific highlights• Demonstrated at several workshops and reviews with jobs

running on NW-GRID.

Resources:• Funding from JISC VizNet• Staff: Barry Searle­ £ 250 k capital: own SGI Prism

and stereo projects system• Other

Start/end date/Duration• Start: Apr 2004• End: ongoing• Duration: ongoing

Contribution to NWG outputs:• Lev. Jobs: 2 • Lev. Fund. x• Industr. Col 2• Publications• Conferences

Project Partners:• Daresbury

Visualisation Example -CCP1 GUI on NW-GRID

STFC Daresbury

Diamond:e-Science Infrastructure for Diamond Light Source

STFC Daresbury

Resources:• Funding 100k/ year• Staff: Michael Gleaves• Other• Access to SCARF,

NGS, NW-GRID and own cluster

Start/end date/Duration• Start: April 2006• End: Ongoing• Duration: Ongoing

Contribution to NWG outputs:• Lev. Jobs: 4 • Lev. Fund. 100k/ year• Industr. Col no• Publications no• Conferences no• Web sites:

http://www.diamond.ac.uk

Principal Investigator:• Rob Allan (Daresbury)

Summary• Create a data management and computational analysis

infrastrructure for the Diamond Light Source. Diamond is “the largest single investment in science in the UK for 30 years”.

Objectives• Deploy meta-data catalogue and meta-data collection software• Deploy data collection and migration software• Archive data and metadata for discovery and re-use• Deploy data analysis and simulation framework• Work with admin and science staff and users to develop an

appropriate portal interface

Progress towards deliverables• Data and meta-data collection and migration has been

demonstrated Feb’07. • Computational and Portal frameworks are currently being

developed.

Scientific highlights• None so far

Project Partners:• Daresbury, RAL, DLS

Services – see Reference Model

User Interface Layer

Data Broker Layer (SRB)

Co

mp

ute B

roke

r

NW-GRID

Compute pools

Localclusters

Facility hub

Laboratory hub

Mobile hub

Primary store

Secondary store

Tertiary store

GDA

LIMS

DUO

ATLAS - Castor

CDR

ICAT

Diamond:e-Science Infrastructure general architecture

STFC Daresbury