Serwery, klastry, gridy

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Chemomentum - Grid Services Based Environment to
Enable Innovative Research
Krzysztof Nowinski, Piotr Bala ICM Warsaw
University know, bala_at_icm.edu.pl.pl
CCSW 3-4.4.2006
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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 develops high level services (visualization,
  database access, access to remote instruments)
• Strong collaboration with FZJ in all projects.

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Unicore plugins

• UNICORE Client (5.3, 5.6)
• Example tasks
• Quantum Chemistry Gaussian, TBDFT
• Molecular Dynamics Amber, Gromos
• Application specific plugins
• Quantum Chemistry Gaussian, Gamess
• Molecular Dynamics AMBER , MolDyAna
• BioInformatics BLAST (new)
• DataBase Access PDB Search, DBAccess
• CFD Fluent
• General use plugins
• Visualization SapphireVis, IADemo, IVis, VisNow
• Access to the instruments Adam5k
• Other ListAllJobs, PluginLoaderPlugin

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Unicore at ICM

• Production ready UNICORE 5.6
• Users can access all production systems with
  UNICORE
• Users support and training, including plugin
  development

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SapphireVis plugin A. Nowinski

• Provides quick visualization for results files
• Allows quite advanced 2D visualization
• Easy in use
• Simple sample of sapphire library power

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Sequence search plugin

• Detailed view

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Sequence search plugin

• Simple visualization based on BIOJava

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Adam5k K. Benedyczak

• Access to the external devices
• Advantech ADAM5000
• Deamon for the device running on the target
  system
• Management of the cluster hardware

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Lesson learned from UNICORE projects

• Plugin is a very good concept
• However....
• development must be easier
• configure rather than program
• Amber, GenericPlugin
• plugins too much depend on the UNICORE Client
• UNICORE was a moving target
• plugins are difficult to maintain Java object
  serialization
• need for modularity and internal workflows
• applications are changing
• UNICORE/GS

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UNIGRIDS

• UNIGRIDS - Grid services interfaces to UNICORE
• UNICORE/GS glue provided by FLE
• GPE Grid Programming Environment (Intel)
• GridBeans (previously plugins)
• Different clients
• Application client
• Expert Client
• Portal Client
• Applet Client (ICM)

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GPE (Intel) 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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GPE Application User
Grid
Application Client
Application Grid Service
WSRF
User Certificate
Lightweight Java Application

• Only one application
• Get only application specific information
• Run lightweight client on mobile devices

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Blast GridBean R.
Kluszczynski,
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Blast GridBean R.
Kluszczynski,
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Adam2k GridBean K.
Benedyczak
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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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Chemomentum

• 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

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Chemomentum participants

• University of Warsaw (coordinator)
• Research Centre Juelich
• University of Tartu
• Technical University of Dresden
• Ulster University
• University of Zurich
• Mario Negri Institute for Pharmacological
  Research
• Biochemics Consulting
• TXT e-solutions
• ExxonMobile

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Chemomentum challenges

• Create an integrated, streamlined data and
  knowledge management and discovery solution that
  provides users with the information they need for
  decision making
• Simplify Grid management, administration and
  deployment
• Primary focus on the QSAR and toxicity
  prediction.
• Dissemination by use.
• 30 months, start 1.07.2006, budget 2.5M (EU
  contrbution)

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Development Team
K. Nowinski, P. Bala know, bala_at_icm.edu.pl ICM
Warsaw University

• Krzysztof Benedyczak
• Rafal Kluszczynski
• Lukasz Korzybski

• Aleksander Nowinski
• Jakub Jurkiewicz