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Experience of the SRB in support of

collaborative grid computing

Martin DoveUniversity of Cambridge

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A voyage of discovery‣We aimed to focus on grid computing to

support molecular-scale simulations ...‣ ... but discovered the important role of

data and information delivery

‣We thought that the SRB would provide a means to archive data ...

‣ ... but discovered that it could be much more useful than that

The SRB has radically changed our view of how we should carry out the scientific

process

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My view of eScience

Computing grids

Data grids Collaborative grids

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Science beyond the lab-book‣ Management of too

many tasks

‣ Management of the resultant data deluge

‣ Sharing the information content with collaborators

‣ Maintaining accuracy and verification

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Expansion of calciteNeutron diffraction experiments

small decrease in a

5% increase in c

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5.0

5.5

6.0

6.5

7.0

7.5

8.0

0 500 1000 1500 2000 2500

Temperature (K)

Un

it c

ell

len

gth

(Å

)

abc

R3 c

R3 m

Pm3 m

BaCO3: lattice parameters

Molecular dynamics simulations on the NGS

Molecular dynamics simulations on the NGS

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Challenge for the researcher

‣ Short-term collation of the data

‣ Longer-term management of the data

‣ Sharing the data with collaborators

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SRB and grid computing

‣ It was important to build the data grid – in our case the SRB – into the heart of the computing grid environment

‣ Then we needed tools to make the integration of the data and compute grids seamless, and which are easy to use – non-intrusive

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Profile of our users‣ They want maximum control

over their work processes – they don’t want to access them through portals or GUI’s

‣ They also don’t want their applications pre-wrapped as services: they want to have complete control over their applications, e.g. to add capability

‣ They know what they are doing ...

‣ ... and they don’t want to be told how to do things!

Internet

Researcher

Compute clusters Cluster

JobMgr

Globus

Application server

Access to external facilities and grids

Desktop pools Condor

JobMgr

Globus

Campus grids Condor

JobMgr

Globus

Parallel (HPC) clusters Cluster

JobMgr

Globus

Data vault

Data vault

Data vault

Data vault

Globus is useda) to provide user authentication via digital certificatesb) job submission middleware

Our data grid is based on the San Diego Storage Resource Broker

The application server provides databases and server capabilities for the SRB, metadata tools, and job submission tool

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Job submission process‣ We have developed RMCS to run the

job submission process

‣ It integrates with the use of the data grid, specifically with the SRB

‣ RMCS can be run from the user’s desktop via a shell-command client tool

4. Job runs on grid compute resourcesApplication

server

1. Upload data files and application to

data vault

5. Metadata is sent to the application server

6. Output files are transferred

to the data vault

7. Researcher interacts with the metadata

database to extract core

output values 2. Submit job to grid via RMCS

3. Data files and application are transferred to

the grid resource

Researcher

Data vault

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Parameter sweeps

‣ implement bulk file upload to the SRB or other data grid

‣ generate set of RMCS input files

‣ submit all the RMCS jobs

We have perl programs that

Bulk job creation and submission is a one-command

procedure

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Data and information

?XML data

representation instead

Data vaultUpload XML data files to data

vault for sharing with collaborator

Researcher A

Researcher B

View information content of data files using ccViz

View information content of data files using ccViz

Access Grid with JMAST

Instant messaging

SciSpace.net

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SRB: some early positives

‣ When we started, it was the only show in town to facilitate easy data sharing

‣ It was affordable in terms of capital and person ££££

‣ It is easily extended through addition of new vaults

‣ It proved easy to use

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Anecdote: Lucy’s project

‣ Lucy learned to use the SRB-based data grid very easily

‣ Using our data tools, she was able to provide me with remote access to the information content of her data very easily

Lucy was a third-year project student, and we let her perform her project using all our grid infrastructure with no compromises

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Some caveats‣ We didn’t actually need to federate or

distribute different data sources ...

‣ ... and by distributing our data we discovered that such an approach gives an unnecessary weak link and issues of ownership

‣ We didn’t need the access-control tools, nor the data replication tools, in which case some of the infrastructure was heavier than needed

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So what is different now?‣ We now expect to be able to share their

data with collaborators ...

‣ ... and we expect this to be easy (ie not via a multi-stage process)

‣ We now routinely produce complete archives of all files associated with a study easily and automatically, rather than have stuff dumped to our desktops

‣ And we now expect a single place to deposit data, and for this process to be easy and automatic

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Summary‣ The SRB was critical to the successes of

the eMinerals project

‣ The SRB was easy to use, and affordable

‣ We have developed some tools on top of the SRB to make access, display of data, and access control easier (eg webdav access, web interface)

‣ The SRB has radically changed the way we think about managing data – but I don’t think that this was an easy change to acquire

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Credits

Cambridge: Kat Austen, Richard Bruin, Mark Calleja, Gen-Tao Chiang, Ian Frame, Peter Murray-Rust, Toby White, Andrew Walker

STFC: Kerstin Kleese van Dam, Phil Couch, Tom Mortimer-Jones, Rik Tyer

Funded by NERC