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UCL-CS GT3 Activities

UCL-CS GT3 Activities

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UCL-CS GT3 Activities

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  1. UCL-CS GT3 Activities Meeting 28th May 2003 Report on GLOBUS GT3 @ CS_UCL S.Street (eProtein) S-A.Sorensen (eProtein, SBFP-P2P, GRS) S.Jiang (6net)

  2. ACTIVITIES USING GT3 • eProtein • Imperial, UCL and EBI will use GRID technology to provide a structure-based annotation of the proteins in the major genomes. The high performance computational needs for the regular updates will be met by sharing resources at each site using the GRID under GLOBUS. This project will develop the prototype for a national distributed proteome annotation GRID. • 6net (Grid Activities only) • porting GT3 to be IPv6 enabled • build up IPv6 enabled Grid Infrastructure GT3 Meeting – 28th May 2003

  3. GT2 in PRATICE • Submit a job – GenTHREADER • make similar scores between a target sequence & a template fold (produces six scores) Combine potentials into one score (the result) generate alignments • Job executed using a java wrapper • Run on one or more remote machines • UCL - Computer Science & Biochemistry • Imperial GT3 Meeting – 28th May 2003

  4. GT2 in PRATICE contd... • Job controlled using GRAM • Resource requirements & parameters set using an globus-job-run or an RSL file • Job submission committed using a single shell script on local client GT3 Meeting – 28th May 2003

  5. G E R E Titin Pioneer Cisco JANET Summit48 Summit48 FREKE Summit48 eProtein - GT2 Configuration GT3 Meeting – 28th May 2003

  6. G E R E Titin Pioneer Cisco JANET Summit48 Summit48 FREKE Summit48 eProtein - GT2 Configuration GT3 Meeting – 28th May 2003

  7. GenTHREADER Demo • loading... GT3 Meeting – 28th May 2003

  8. G E R E Titin Pioneer Cisco JANET Summit48 Summit48 FREKE Summit48 GT3 STRUCTURE Biochem GT3 Meeting – 28th May 2003

  9. GT3 INSTALLATION • Documentation • Covers the major steps but overlooks detail • Using Java • Globus supports Java 1.3 • We want to use Java 1.4 for IPv6 support • Add Xalan.jar for xml security • Tomcat • GT3 has a standalone web container for testing • Use lightweight version of Tomcat • library conflicts between java 1.4 & standard Tomcat GT3 Meeting – 28th May 2003

  10. GT3 INSTALLATION contd... • JDBC – PostGreSQL (or MySQL) • For use with upper layer services • GRAM, RFT (Reliable File Transfer) • For IPv6 support – build with IPv6 patch • Certificates • Time consuming, modifications needed and similar drawbacks to previous versions GT3 Meeting – 28th May 2003

  11. GT3 IPv6-enabled Porting Activities • GT3 Stand-alone Web Container – only for tests • GT3 Server – needs some work on where IPv4 Calls are made • GT3 Client – needs some work on where IPv4 Calls are made • Tracking Globus Changes GT3 Meeting – 28th May 2003

  12. Non-web Services Considerations • OGSA is web based – little problem if correct initialisation JDK parameters are used • Some other components not yet web based, • need more detailed analysis to identify changes • Grid FTP is an example of such a service • The services needed are dependent on method of usage for specific applications GT3 Meeting – 28th May 2003

  13. FURTHER WORK with GT3 • Virtual submission environment • Provide transparent single point of access for user • Virtual execution machine • To interact with schedulers & related software • Provides easy firewall pass through between clusters • Automated process migration GT3 Meeting – 28th May 2003