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Www.eminerals.org Experience of the SRB in support of collaborative grid computing Martin Dove University of Cambridge.

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Presentation on theme: "Www.eminerals.org Experience of the SRB in support of collaborative grid computing Martin Dove University of Cambridge."— Presentation transcript:

1 Experience of the SRB in support of collaborative grid computing Martin Dove University of Cambridge

2 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

3 My view of eScience Computing grids Data grids Collaborative grids

4 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

5 Crystal structure of CaCO 3 ‣ Note layers of Ca cations and CO 3 carbonate molecular ions ‣ Carbonate ions start to spin and then tumble at high temperature

6 Expansion of calcite Neutron diffraction experiments small decrease in a 5% increase in c

7 Rock-salt structure of BaCO 3 Note disordered positions of oxygen atoms

8 BaCO 3 : lattice parameters Molecular dynamics simulations on the NGS

9 Challenge for the researcher ‣ Short-term collation of the data ‣ Longer-term management of the data ‣ Sharing the data with collaborators

10 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

11 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!

12 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 Globus is used a) to provide user authentication via digital certificates b) 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

13 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

14 4. Job runs on grid compute resources Application 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

15 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

16 Scientific collaboration Classical molecular dynamics methods Quantum mechanical methods

17 Data and information ? XML data representation instead

18 Data vault Upload XML data files to data vault for sharing with collaborator Researcher A Researcher B View information content of data files using ccViz Access Grid with JMAST Instant messaging SciSpace.net

19 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

20 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

21 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

22 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

23 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

24 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


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