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)
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
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
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
eProtein - GT2 Configuration
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GT3 Meeting – 28th May 2003
eProtein - GT2 Configuration
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GT3 Meeting – 28th May 2003
GenTHREADER Demo
loading...
GT3 Meeting – 28th May 2003
GT3 STRUCTURE
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Biochem
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GT3 Meeting – 28th May 2003
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
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
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
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
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