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Environment from the Molecular Level

A NERC eScience testbed project

Storage Resource Broker

The Storage Resource Broker (SRB), developed at the San Diego Supercomputing Center, provides access to distributed data from any single point of access [29–31]. From the viewpoint of the user, the SRB gives a virtual file system, with access to data being based on data attributes and logical names rather than on physical location or real names. Physical location is seen as a file characteristic only. One of the features of the SRB is that it allows users to easily replicate data across different physical file systems in order to provide an additional level of file protection.

The SRB is a client-server middleware tool that works in conjunction with the Metadata Catalogue (MCAT). The MCAT server preserves the information about files as they are moved between different physical files systems. The SRB configuration employed within the eMinerals minigrid consists of the MCAT server held at CCLRC Daresbury, and 5 data storage systems (the SRB vaults) located in Cambridge (2 instances), Bath, UCL and Reading, giving a total storage capacity to the minigrid of around 3 TB. The Linux clusters use a RAID array on standard PCs with Intel Pentium 4 processors, with each vault on the Lake clusters providing 720 GB of storage and a further 500 GB on the Pond cluster. The Reading SRB vault is on a Dell Poweredge 700 server running SuSE Linux 9.0, providing 400 GB of storage. We will shortly be adding a sixth vault installed on the Xserve cluster, with an additional 500 GB of storage.

The use of the SRB overcomes some of the limitations experienced when using the Globus toolkit for retrieval of files generated by applications running on the minigrid. As we will discuss below, the approach we take is to handle the interaction of the user and the minigrid with data through a job lifecyle entirely through the SRB.

Application server

The eMinerals minigrid application server is an IBM Bladecentre with a dual Xeon 2.8 GHz architecture and 2 GB memory per node, and is located at CCLRC Daresbury. The application server has a number of functions. It runs the MCAT server for the SRB, the web server for the eMinerals portals, the MySRB web interface for the SRB, and the metadata editor that runs alongside the data portal and the SRB.

Database cluster

The database cluster consists of two mirror systems acting as a failover server. Again, this is located at CCLRC Daresbury. It runs the Oracle Real Application Cluster Technology to hold the SRB MCAT relational database containing data file locations and the metadata database. The use of the Oracle Dataguard system is currently being implemented with an equivalent database cluster at the CCLRC Rutherford Appleton Laboratory in order to further increase the resilience of the database cluster.

Useful links

http://www.sdsc.edu/srb/index.php/Main_Page

General references

Papers that describe the eMinerals science areas are:

  1. Environment from the molecular level: an escience testbed project.
    MT Dove, M Calleja, J Wakelin, K Trachenko, G Ferlat, P Murray-Rust, NH de Leeuw, Z Du, GD Price, PB Wilson, JP Brodholt, M Alfredsson, A Marmier, RP Tyer, LJ Blanshard, RJ Allan, K Kleese van Dam, IT Todorov, W Smith, VN Alexandrov, GJ Lewis, A Thandavan, SM Hasan.
    Proceedings of UK e-Science All Hands Meeting 2003, (EPSRC, ISBN 1-904425-11-9) pp 302–305

  2. Grid computing and molecular simulations: the vision of the eMinerals project.
    MT Dove and NH de Leeuw.
    Molecular Simulations 31, 297–301, 2005

  3. Collaborative grid infrastructure for molecular simulations: The eMinerals minigrid as a prototype integrated compute and data grid.
    M Calleja, R Bruin, MG Tucker, MT Dove, RP Tyer, LJ Blanshard, K Kleese van Dam, RJ Allan, C Chapman, W Emmerich, PB Wilson, JP Brodholt, A Thandavan, VN Alexandrov.
    Molecular Simulations 31, 303–313, 2005

  4. eMinerals: Science Outcomes enabled by new Grid Tools.
    M Alfredsson, E Artacho, M Blanchard, JP Brodholt, CRA Catlow, DJ Cooke, MT Dove, Z Du, NH de Leeuw, A Marmier, SC Parker, GD Price, JMA Pruneda, W Smith, I Todorov, K Trachenko, and K Wright.
    Proceedings of All Hands 2005 (ISBN 1-904425-53-4), pp 788–795, 2005