Serwery, klastry, gridy

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CHEMOMENTUM Grid Services Based Environment to
Enable Innovative Research
Piotr Bala ICM Warsaw University, Warsaw N.
Copernicus University, Torun bala_at_icm.edu.pl
Cracow Grid Workshop 2006
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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)

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UNICORE architecture
Single entry point
SSL/UPL
Firewall
Gateway
AJO
UUDB
NJS
NJS
UUDB
TSI
TSI
USpace
USpace
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UNICORE Client

• Single application
• Job preparation
• Job monitoring

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Sequence comparison K. Benedyczak, S. Dydel
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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

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IVis architecture K.
Benedyczak, A. Nowinski
Still single entry point
Client
SSL/UPL
Visualization
Firewall
Gateway
IVis Extension
Visualization
IVis server
UUDB
NJS
TSI
USpace
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IVis build-in visualization K. Benedyczak, A.
Nowinski
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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

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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

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UNICORE 6 The Big Picture
Grid SDK
Deploy GridBean
Developer Workstation
Deploy GS
Expert Client
Plugins
Plugins
Grid
GridBeans
Application GS
Keystore
UNICORE
User Workstation
Application Client
Database GS
Broker GS
WSRF
G-API
Globus
GridBean
User Certificate
Application GS
Mobile Device
Condor
Application Portal
Information GS
Web Client
JSP
GridBean
Web Browser
Service Certificate
Service Provider
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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

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GPE Application Client
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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.

Rafal Kluszczynski klusi_at_mat.uni.torun.pl
UNICORE Summit 2006 Dresden (31 Aug)
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GridBean Service
Rafal Kluszczynski klusi_at_mat.uni.torun.pl
UNICORE Summit 2006 Dresden (31 Aug)
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BLAST GridBean R. Kluszczynski, M.
Borcz
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BLAST Results
R. Kluszczynski
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NAMD GridBean (ongoing work) R. Kluszczynski
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GPE Expert Client
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GPE AppletClient J.
Jurkiewicz
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GPE AppletClient J.
Jurkiewicz
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GPE AppletClient J.
Jurkiewicz
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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

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Streaming services UGSF Architecture
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Streaming services UGSF Architecture (2)
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OGSA-DAI4UnicoreGS K. Benedyczak
GridBean
Client Application
UNIGRIDS Toolkit
Client Toolkit
WSI Client Stubs
WSRF Client Stubs
WSRF Client Stubs
Client layer
SOAP
SOAP
Data Services
Data Services
Presentation layer
WSI Data Service
WSRF Data Service
WSRF Data Service
OGSA-DAI Core
Data Service Resource A
Data Service Resource B
Data Service Resource C
Business logic layer
XML Database
Relational Database
File
Data layer
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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

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OGSADAI GridBean
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OGSADAI Data Service Browser
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Overview of Project

• 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

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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

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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.