piotr bała icm warsaw university, warsaw n. copernicus university, toruń bala@icm.edu.pl...
Post on 17-Jan-2016
226 Views
Preview:
TRANSCRIPT
Piotr Bała
ICM Warsaw University, Warsaw
N. Copernicus University, Toruńbala@icm.edu.pl
CHEMOMENTUM Grid Services Based Environment
to Enable Innovative Research
Cracow Grid Workshop 2006
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
UNICORE projects at ICM
EUROGRID (Nov. 2000 – Nov 2003)• ICM develops middleware for biomolecular applications,• ICM operates European grid for molecular biology
GRIP (2002 – 2003)• ICM deployed interoperable biomolecular applications
UNIGRIDS (2004 – 2006)• ICM developed high level services• data streaming, visualization • database access, access to remote instruments
CHEMOMENTUM (2006 – 2008)
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Firewall
UNICORE architecture
Gateway
NJS
TSI
Single entrypoint
NJS
TSI
USpace
UUDB
USpace
UUDB
SSL/UPL
AJO
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
UNICORE Client
Single application Job preparation Job monitoring
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Unicore plugins
UNICORE Client (5.3, 5.6) Example tasks:
• Quantum Chemistry: Gaussian, TBDFT• Molecular Dynamics: Amber, Gromos
Plugins:• Quantum Chemistry: Gaussian, Gamess, CPMD (FZJ)• Molecular Dynamics: AMBER• BioInformatics: Smith-Waterman• DataBase Access: PDB Search, DBAccess• Visualization: SapphireVis, IADemo, IVis, UVisit• Broker: Resource Broker (UoM)• Other: ListAllJobs, PluginLoaderPlugin
• Finite element: StarCD, Nastran, Fluent
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
IVis architecture K. Benedyczak, A. Nowiński
FirewallGateway
NJS
TSI
Still single entry point
IVis server
USpace
UUDB
IVisExtension
Client
SSL/UPL Visualization
Visualization
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
IVis – build-in visualization K. Benedyczak, A. Nowiński
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Lesson learned – UNICORE 5
Stable, easy to configure, deploy and maintain solution Very powerfull user interface Still less popular than GT
• D-Grid• NAREGI• DEISA• China Grid
Main technology: UPL, AJO• Explicit Trust Delegation (EDT) • Lack of grid services approach
Limmited interoperability with GT4 UNICORE Gateway – single point of failure
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Lesson learned - plugins
Plugin is a very good concept.
development must be easier configure rather than program
• Amber, GnericPlugin
plugins too much depend on the UNICORE Client• no clean interface,
plugins are difficult to maintain need for modularity and internal workflows
• MetaPlugin
applications are changing
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
UNICORE 6: The Big Picture…
Application Client
GridBean
User Certificate
Mobile Device
Web Client
Web Browser
JSP
User Workstation
Expert Client
PluginsPluginsGridBeans
Keystore
Service Provider
Application Portal
Service Certificate
GridBean
GridGridApplication GS
Broker GS
Information GS
Application GS
Database GS
WS
RF
Developer Workstation
Grid SDK
Deploy GridBean
Deploy GS
Condor
UNICORE
GlobusG-A
PI
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
UNICORE 6 status
OpenSource project• unicore.sf.net
Fully GridServices oriented• WSRF• Atomic services
UNICORE 6 Alpha release avaliable
UNICORE interoperability• Unicoregs backend
GT4 interoperability• gpe4gtk.sf.net
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
GPE Application Client
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Interoperability
The GPE Clients can contact to TSSs available on different hosting environments like:
• Globus,• UnicoreGS,• others.
Once implemented GridBean can be used with different Grid middlewares.
Rafał Kluszczyński · klusi@mat.uni.torun.pl · UNICORE Summit 2006 · Dresden (31 Aug)
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
GridBean Service
Rafał Kluszczyński · klusi@mat.uni.torun.pl · UNICORE Summit 2006 · Dresden (31 Aug)
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
BLAST GridBean R. Kluszczyński, M. Borcz
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
BLAST Results R. Kluszczyński
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
NAMD GridBean (ongoing work) R. Kluszczyński
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
GPE AppletClient J. Jurkiewicz
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Streaming services UGSF
• Components:– Web Service (WS)– Streaming Server (SS)– Client library
• Streaming Server (SS)– Stand-alone application– Performs streaming– Client uses dedicated protocol to connect to the SS
and obtain real data stream.– WS uses RMI to communicate with SS and setup
streams• Avaliable at UNICORE SF
– Works with Unicore/GS 2.0.3
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Streaming services UGSF Architecture
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Data ServicesData Services
OGSA-DAI Core
RelationalDatabase
XMLDatabase
File
Data ServiceResource A
Data ServiceResource B
Data ServiceResource C
WSI Data Service WSRF Data Service
Client Toolkit
WSI Client Stubs WSRF Client Stubs
Client Application
SOAP
Client layer
Presentation layer
Business logic layer
Data layer
GridBean
UNIGRIDS Toolkit
WSRF Client Stubs
SOAP
WSRF Data Service
OGSA-DAI4UnicoreGS K. Benedyczak
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
• WSRF Data services deployed in the Unicore/GS Container
– Unicore/GS 2.0.3• WSRF Client Stubs accompanying the Data services
used to access services• OGSADAI GridBean
– Simple queries• OGSADAI Client
– Can be used with no source code modifications• Tested with different data sources:
– SQL database (MySQL), – XML database– Plain file
OGSA-DAI4UnicoreGS K. Benedyczak
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
OGSADAI GridBean
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
OGSADAI Data Service Browser
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
CHEMOMENTUM Workbench - Grid services based environment to enable innovative research.
Generic, flexible system for running workflow-centric, complex applications
Efficiently deal with data and knowledge
Focused on the end users
Use cases: drug discovery, toxicity prediction, environmental risk assessment
Based on the UNICORE Grid middleware
Web site: www.chemomentum.org
Overview of Project
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Project aims
Provide an integrated Grid solution for workflow-centric, complex applications with a focus on data management and knowledge. Place the end users into the focus, enabling them to use powerful tools in a natural and transparent fashion;
Provide Grid-enabled applications, data services and knowledge management solutions, offering integrated decision support services for risk assessment, toxicity prediction and drug design;
Setup and operate a stable pilot installation, accessible for external users. Proactively gather and evaluate feedback from these users. Simplify administration and management of the Grid;
CGW'06 16/10/2006 P. Bała (ICM/UMK)P. Bała (ICM/UMK)
Project aims
Spread awareness of the Chemomentum aims, scientific and technical approach, results and success stories in relevant industries and communities. Ensure maximum exploitation of the services and possible products developed in Chemomentum;
Test-drive the developed services in the context of the European regulatory initiative “Registration and Evaluation of Chemicals” (REACH), promoting the REACH initiative aimed at reducing animal testing, by developing in silico, Grid-based tools.
top related