piotr bała icm warsaw university, warsaw n. copernicus university, toruń [email protected]...

Piotr Bała

ICM Warsaw University, Warsaw

N. Copernicus University, Toruń[email protected]

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)


Firewall

UNICORE architecture

Gateway

NJS

TSI

Single entrypoint

NJS

TSI

USpace

UUDB

USpace

UUDB

SSL/UPL

AJO


UNICORE Client

Single application Job preparation Job monitoring


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


IVis architecture K. Benedyczak, A. Nowiński

FirewallGateway

NJS

TSI

Still single entry point

IVis server

USpace

UUDB

IVisExtension

Client

SSL/UPL Visualization

Visualization


IVis – build-in visualization K. Benedyczak, A. Nowiński


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


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


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


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


GPE Application Client


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 · [email protected] · UNICORE Summit 2006 · Dresden (31 Aug)


GridBean Service

Rafał Kluszczyński · [email protected] · UNICORE Summit 2006 · Dresden (31 Aug)


BLAST GridBean R. Kluszczyński, M. Borcz


BLAST Results R. Kluszczyński


NAMD GridBean (ongoing work) R. Kluszczyński


GPE AppletClient J. Jurkiewicz


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


Streaming services UGSF Architecture


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


• 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


OGSADAI GridBean


OGSADAI Data Service Browser


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


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;


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.

piotr bała icm warsaw university, warsaw n. copernicus university, toruń [email protected]...

Documents

baa icmumklesson

baa icmumkunicore projects

baa icmumkivis architecture

baa icmumkivis build

baa icmumkblast gridbean

baa icmumksequence comparison

european grid

unicore summit