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NBCR Science Gateway: Transparent Access to Remote Resources Through Rich Desktop Clients Luca Clementi clem@sdsc.edu. Outline. NBCR/PRAGMA NBCR SOA infrastructure Opal Overview Opal Toolkit GUI Opal Integration into Existing Tools Access to Multiple Resources (TG, PRAGMA).

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slide1

NBCR Science Gateway: Transparent Access to Remote Resources Through Rich Desktop ClientsLuca Clementiclem@sdsc.edu

outline
Outline
  • NBCR/PRAGMA
  • NBCR SOA infrastructure
    • Opal Overview
    • Opal Toolkit GUI
    • Opal Integration into Existing Tools
    • Access to Multiple Resources (TG, PRAGMA)
national biomedical computational resource
National Biomedical Computational Resource
  • Funded by NIH (NCRR)
  • Its mission is to conduct, catalyze, and enable biomedical research by harnessing, developing, and deploying forefront computational, information and grid technologies
    • Develop and deploy advanced computational, data and visualization tools.
    • Integrate them in an advanced grid framework.
    • Deliver and support this grid/Cyber-infrastructure
    • Training (Summer Institute)
national biomedical computational resource1
National Biomedical Computational Resource
  • Funded by NIH (NCRR)
  • Its mission is to conduct, catalyze, and enable biomedical research by harnessing, developing, and deploying forefront computational, information and grid technologies
    • Develop and deploy advanced computational, data and visualization tools.
    • Integrate them in an advanced grid framework.
    • Deliver and support this grid/Cyber-infrastructure
    • Training (Summer Institute)
slide5

Pacific Rim Application and Grid Middleware Assembly

(PRAGMA)

A Practical Collaborative Framework

In the Pacific Rim and Globally 29 institutions

Strengthen Existing and Establish New Sustainable Collaborations

Work with Science Teams to Advance Grid Technologies and Improve the Underlying Infrastructure

  • Collaborations
  • Integration of existing applications
  • Deployment of a Grid infrastructure

http://www.pragma-grid.net

motivation
Motivation
  • Integration of different tools (client side application, workflow tools, web portals, etc.)
    • Several user interfaces
  • Seamless access to computational resources
    • Easy from the scientific user perspective
big picture
Big Picture

Web server

PMV/Vision

Kepler

State

Mgmt

Application Services

Security Services (GAMA)

Globus

Globus

Globus

PBS Cluster

Condor pool

SGE Cluster

opal toolkit
Opal Toolkit

Opal allows application developers to publish command-line applications using Web services

Minimal deployment effort: no coding, only a simple configuration file

plain web service, SOAP

Common interface: every application uses the same WSDL (same stubs on the client side)

Simple APIs (Launch job, Query job status, Get job outputs, Get output as Base64, Destroy job, etc.)

opal toolkit1
Opal Toolkit
  • Every application exposed with its own URL http://ws.nbcr.net/opal/services/Pdb2pqrService
  • It takes care of data staging
  • It supports submission via:
    • Fork
    • Globus GRAM
    • DRMAA
    • CSF4 (experimental)
  • Run all the applications under a single user account
  • Used in NBCR, CAMERA, GLEON, among other
opal toolkit client side
Opal Toolkit / Client Side

Several clients APIs available: Java, Python, PERL.

Command line generic client:

# java edu.sdsc.nbcr.opal.GenericServiceClient

-l http://localhost:8080/axis/services/PDB2PQRServicePort

-r launchJob

-a "-ipdb sample.pdb -h -opdb output.pdb“

-f etc/sample.pdb

  • Too complex for beginner users
  • Graphical User Interfaces
slide11

User

User clients

Browser

Vision

getAppMetadata

Kepler

PDB2PQR

launchJob

getOutput

getAppMetadata

MEME

launchJob

getOutput

Opal server

opal gui
Opal GUI

Main characteristics:

Working out of the box (no configuration)

Multiplatform -> Web interface

Shipped with Opal

Key features:

Access Statistics

List of services

Simple submission form

Advanced submission form

access statistics
Access Statistics

Go to http://ws.nbcr.net

NBCR production server

simple submission form
Simple Submission Form

User has to input command line!

Too error prone.

Submission form should be customized on command line arguments

advanced submission form
Advanced Submission Form

When deploying a scientific application there is an optional part to describe input and output of the application

It is a command line syntax description language

pdb2pqr advanced submission form
PDB2PQR Advanced Submission Form

Exclusive group

Input file

Group 1

String

Group 2

Exclusive enumeration

Group 3

Flag

Group 4

slide23
CSF4
  • Community Scheduler Framework:
    • Open Source project and can be accessed at http://sourceforge.net/projects/gcsf
    • Developed by Lab. of Distributed Computing and System Architecture, Jilin University, China
    • It is a metascheduler framework hosted as an Execution Component in GT4 container
    • It uses WSRF compliant services
    • It can submit jobs to Globus
slide24

CSF4 Typical Deployment

  • GT2 (gatekeeper)
  • GT4 (WS-GRAM)
csf4 new feature
CSF4 New Feature

Users want to run applications

  • Application based scheduling:
    • CSF4 keeps a table of available applications
csf4 new feature1
CSF4 New Feature

Users want to run applications

  • Application based scheduling:
    • CSF4 keeps a table of available applications

Avian Flu Grid

opal csf4 integration
Opal CSF4 Integration
  • Opal plug-in for submission to CSF4
  • Deployment architecture:
slide28

Opal Enable Clients

WS/SOAP

App A

App B

App C

Opal Server

WSRF

App A

App B

App C

CSF4

(Pre/WS)-GRAM

Globus GRAM

Globus GRAM

ClusterB

appA

appC

ClusterA

appA

appB

future directions
Future Directions
  • Opal 2.0 will be released soon
    • Improved architecture (plug-in model)
    • URL support for input and output files
    • Embedded database (Hibernate)
  • Support for other metascheduler (Gridway)
  • Opal GUI for Gridsphere (Portlet)
acknowledgments
Acknowledgments
  • Wilfred Li, Peter Arzberg (NBCR vision)
  • Sriram Krishnan (Opal)
  • Xiaohui Wei (CFS4)
  • Many other NBCR developers...
  • More information, downloads, documentation:
    • http://nbcr.net
    • http://nbcr.net/software/opal/