steve crouch, omii-uk southampton stephen mcgough , imperial college london

Web: www.omii.ac.uk Email: [email protected]

OMII-UK: progressing from adopting open specifications to sustainable open development

by fostering Asia-Pacific collaborations and creating

communities Steve Crouch, OMII-UK Southampton

A.Stephen McGough, Imperial College LondonShantenu Jha, Louisiana State University

17/09/08


Introduction to the Session

• OMII-UK: who we are and how we can help

• Reducing the gap between e-Researchers and e-Infrastructure

• Creating communities – users and developers

• OGF standards - where/how are they used?

• Highlight Asia Pacific collaborations


OMII-UK: Supporting e-Research

OMII-UK provides software and services to help the UK research community adopt e-Research practices and

technologyhttp://www.omii.ac.uk

• Teams from Southampton, Manchesterand Edinburgh universities

• Funding from EPSRC from 2004 to 2010• Software, e.g.

o Workflow design and execution – Tavernao Access/integrate data – OGSA-DAI - tutorial session today at

4pm, here!o Manage and access computational resources – GridSAM; Campus

Grid Toolkit, OMII-SAGA

• Build active, sustainable communities around developed open source products that use appropriate accepted/emerging open standards


OMII-UK: Adding benefit to e-Science

• More than just the middleware

o go above the components to provide added value

• Skilled team to help the community

o putting the right things together, integrating components

o providing consultancy and support to improve uptake

o developing, commissioning and improving software


From Open Standards to Sustainable Open Development

Internal DevelopmentInternal Development

Internal development

Satisfy initial requirements

Open Standards

Developer community involvement

User community involvement

Open DevelopmentOpen Development

Host development on community development infrastructure

Active open engagement from developer community

Satisfy further requirements to increase uptake

Open Standards

Sustainable Open DevelopmentSustainable Open Development

Complete the open cycle

Active open engagement from developer community

Active open engagement from user communities

Sustainable, user-driven development

Open Standards


Bridging the Gaps

SOFTWARE CSPs

ENGAGEDevelopers

e-Researchers

Support,Expertise


Commissioned Software Programme• Funded projects to address identified gaps in

e-Research software and e-Infrastructure• Further development of existing prototypes

and improvement of existing softwareo To increase user uptake, where interest existso Open source, accessible to community developers

• Proposals evaluated reactively, or in response to a call for software

• Software evaluated at intervals throughout project


CSP Projects and OGF Standards

• Funding/funded variety of projects that use OGF standards:

o Application Hosting Environment (AHE) – JSDLo OGRSH (GenesisII) – ByteIO, RNS, BES, JSDL,

HPC-Profileo RAPID – JSDLo JSDL Application Repository – JSDLo OMII-SAGA – SAGA, JSDLo GridSAM, ICTGridSAM – BES, JSDL, HPC-

Profile, DRMAAo OMII-AuthZ – AuthZo Grimoires – GLUE


OMII-Europe Component Exchange

• OMII-Europe: re-engineering of Grid middleware components to support interoperability through appropriate open standards

o Middleware components sourced across six areas• Virtual Organisation Management: OGSA-AuthZ, SAML• Accounting: OGSA-RUS and OGSA-UR• Data Access: WS-DAI*• Job Submission, Component Exchange: OGSA-BES, JSDL, HPC-Profile• Portals: much of the above

o Globus, gLite and UNICORE - primary infrastructures• Facilitated a two-way exchange of components

between OMII-Europe and our project partners in China

o Beihang University: Meta Scheduler within CROWNo Coordinated implementation of BES interface to the

Scheduler


The CROWN BES Meta Scheduler

ContainerContainer

BES

Client

BES

Client

OMII containerOMII container

CROWN Meta-SchedulerCROWN Meta-Scheduler

Internal RegistryInternal Registry

BES endpointBES endpoint

Resource availability

BES job submission and query

BES job submission and query

e.g. GridSAM, UNICORE-BES, CREAM-BES …


Engaging Research with e-Infrastructure

• Interviewing researchers to identify what works and what’s needed

• Analysing requirements and proposing interventions

• Developing solutions and disseminating best practice

www.engage.ac.uk


The ENGAGE philosophy

• What do people do?• What do people want to do?

o not how can they use what we’ve got to do it

• Trivial barriers are sometimes insurmountable

o what’s easy for us is often frustrating for otherso don’t assume the last step’s easy for everyoneo let’s celebrate success in the community

• Try to extend beyond the “usual suspects”• Solve specific technical issues for specific

users


ENGAGE Interviews by domain


ENGAGE preliminary, non-empirical qualitative finding

People will tend to prioritise ease of use, support and continued development over a complete feature set

This requires a sustainable community around the software and trust by the users in the e-Infrastructure providers (and vice-versa)

Don’t agree? Sign up for an interview to correct the bias! [email protected]


High Throughput Humanities for e-Research

• Improve the accessibility and usability of digitised texts

o 19th Century Serials Edition

• Calculate similarity measures to allow comparisons to be made

o computationally intensive

• Gerhard Brey


Exposing Bioinformatic Programs as Web Services

• Develop better approaches for detecting Protein – Protein Interaction Motifs in protein datasets

• Improve repeatability, collaboration and increase available resources

• Richard Edwards


Docking and Molecular Dynamics Simulations

• Aid the understanding of the nature of glycans

o devise vaccines which reduce undesired events

• Improve the use and efficiency of molecular dynamics simulation packages on NGS

• Babak Afrough, Hans Heidl


Addressing the Issues of Uptake

• Number of issues identified by user community and Campus Grid SIG

• Issues need to be resolved e.g. for University College London:

o Already using GridSAM in Theoretical Chemistry group & Centre for Computational Science

o Number of research domains with own applications, in neurological modelling, Markov models/genetics, chemistry, nanoscale electronics, gene search

o Legion cluster: PBS/Torque, Lustre shared filesystemo With Applications Hosting Environment (AHE), use

GridSAM to access resources• Challenges in supporting platforms, accounting,

security, job management• How do we organise resources and manage an

approach to this?

steve crouch, omii-uk southampton stephen mcgough , imperial college london

Documents