G E R E - UCL Department of Computer Science

righteousgaggleData Management

Jan 31, 2013 (4 years and 4 months ago)

134 views

UCL
-
CS GT3 Activities

Meeting 28
th

May 2003

Report on

GLOBUS GT3 @ CS_UCL

S.Street (eProtein)

S
-
A.Sorensen (eProtein, SBFP
-
P2P, GRS)

S.Jiang (6net)

GT3 Meeting


28
th

May 2003

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


28
th

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


28
th

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


28
th

May 2003

eProtein
-

GT2 Configuration

G

E

R

E

Summit48

Summit48

Summit48

FREKE

Titin

Cisco

JANET

Pioneer

GT3 Meeting


28
th

May 2003

eProtein
-

GT2 Configuration

G

E

R

E

Summit48

Summit48

Summit48

FREKE

Titin

Cisco

JANET

Pioneer

GT3 Meeting


28
th

May 2003

GenTHREADER Demo


loading...

GT3 Meeting


28
th

May 2003

GT3 STRUCTURE

G

E

R

E

Summit48

Summit48

Summit48

FREKE

Titin

Cisco

JANET

Pioneer

Biochem

GT3 Meeting


28
th

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


28
th

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


28
th

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


28
th

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


28
th

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