SI2008 Cluster and Grid Computing and Workflow Management

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General Information

This track will cover the basic cluster and grid computing techniques, use of Opal to wrap applications as services, and use of Vision to build computational workflows.

Time: 8 am to 12 pm

Location: EBU1-5702

Schedule

  • Tuesday, Aug 5, Cluster and Grid Computing Environment Basics
    Instructors: Sriram Krishnan, Luca Clementi
    What is a cluster and a Grid, and how to effectively use cluster and Grid resources? Users will learn how to access the NBCR cluster resources, and run scientific jobs such as MEME, AutoDock http://autodock.scripps.edu using local batch schedulers such as the Sun Grid Engine (SGE). We did present the Globus toolkit for accessing Grid resources, and users will learn about the Grid Security Infrastructure (GSI), and how to submit remote Globus jobs and transfer data using GridFTP.
    Introduction to Clusters Sriram Krishnan
    Cluster Hands On Luca Clementi
    Introduction to Grids Sriram Krishnan
    Globus Hands On Luca Clementi
    Sample files for hands on session Luca Clementi
  • Wednesday, Aug 6, Rocks Cluster Environment, Application Deployment, and Virtual Rocks Clusters
    Instructors: Anoop Rajendra, Jane Ren
    This session covers the academic computing environment based on Rocks http://www.rocksclusters.org, and covers the general architecture, network requirements, storage and performance tuning. It is targeted for both administrators and users of Rocks clusters, with an emphasis on performance benchmarking of applications, and trouble shooting the bottle necks. In addition, the development of Rock'n Rolls, a software distribution mechanism for Rocks, is illustrated using the NBCR roll. Users will also learn how to build a virtual cluster within a multicore machine, with the help of a hypervisor system such as VMWare.
    Rocks presentation Anoop Rajendra
    NBCR Rocks Rolls and Virtualization presentation Jane Ren
  • Thursday, Aug 7, Service Oriented Architecture for Scientific Applications
    Instructors: Sriram Krishnan, Luca Clementi
    In this tutorial, we will present an introduction to Web services, and how they are applicable to scientific applications. We will present the NBCR Opal Web services wrapper toolkit, and show how it can be used to rapidly deploy scientific applications as Web services in a live hands-on session. We will also present the use of XML metadata to automatically generate Web interfaces for deployed Opal applications
    Introduction to Web Services Sriram Krishnan
    The Opal Toolkit Sriram Krishnan
    Hands On on Opal Luca Clementi
  • Friday, Aug 8, The Vision Environment and Advanced Workflow Management
    Instructors: Guillaume Vareille, Luca Clementi
    Location: PFBH-161
    Users will learn how to use the Vision workflow and visual programming environment to build workflows for molecular visualization, image processing, and coupling different applications into a computational pipeline through the development of Vision nodes. Uses will also learn how to develop complex workflows using remote Opal based web services for distributing long running jobs to remote resources including the TeraGrid. How to develop Vision nodes based on local applications or remote web services.
    MGLTools/Vision
    Vision Presentation

Related Materials from previous SI sessions

SI2007 Cluster and Grid Computing

SI2007 Molecular Visualization and Virtual Screening

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