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TeraGrid Science Gateways in Barcelona. Nancy Wilkins-Diehr TeraGrid Area Director for Science Gateways wilkinsn@sdsc.edu. A technical talk about gateways No videos!.

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teragrid science gateways in barcelona

TeraGrid Science Gatewaysin Barcelona

Nancy Wilkins-Diehr

TeraGrid Area Director for Science Gateways


EGEE 2009, September 21-25, 2009


A technical talk about gateways

    • No videos!

EGEE 2009, September 21-25, 2009

How did the Gateway program develop?A natural result of the impact of the internet on worldwide communication and information retrieval
  • Implications on the conduct of science are still evolving
    • 1980’s, Early gateways, National Center for Biotechnology Information BLAST server, search results sent by email, still a working portal today
    • 1992 Mosaic web browser developed
    • 1995 “International Protein Data Bank Enhanced by Computer Browser”
    • 2004 TeraGrid project director Rick Stevens recognized growth in scientific portal development and proposed the Science Gateway Program
    • Today, Web 3.0 and programmatic exchange of data between web pages
  • Simultaneous explosion of digital information
    • Growing analysis needs in many, many scientific areas
    • Sensors, telescopes, satellites, digital images and video,
    • #1 machine on Top500 today is 1000x more powerful than all combined entries on the first list in 1993

Only 17 years since the release of Mosaic!

EGEE 2009, September 21-25, 2009

why are gateways worth the effort
Why are gateways worth the effort?


# Full path to executable


# Working directory, where Condor-G will write

# its output and error files on the local machine.


# To set the working directory of the remote job, we

# specify it in this globus RSL, which will be appended

# to the RSL that Condor-G generates


# Arguments to pass to executable.


# Condor-G can stage the executable


# Specify the globus resource to execute the job


# Condor has multiple universes, but Condor-G always uses globus


# Files to receive sdout and stderr.



# Specify the number of copies of the job to submit to the condor queue.

queue 1

  • Increasing range of expertise needed to tackle the most challenging scientific problems
    • How many details do you want each individual scientist to need to know?
      • PBS, RSL, Condor
      • Coupling multi-scale codes
      • Assembling data from multiple sources
      • Collaboration frameworks

#! /bin/sh

#PBS -q dque

#PBS -l nodes=1:ppn=2

#PBS -l walltime=00:02:00

#PBS -o pbs.out

#PBS -e pbs.err


cd /users/wilkinsn/tutorial/exercise_3

../bin/mcell nmj_recon.main.mdl












EGEE 2009, September 21-25, 2009

gateways democratize access to high end resources
Gateways democratize access to high end resources
  • Almost anyone can investigate scientific questions using high end resources
    • Not just those in the research groups of those who request allocations
    • Gateways allow anyone with a web browser to explore
      • Opportunities can be uncovered via google
        • My 11-year-old son discovered nanoHUB.org himself while his class was studying Bucky Balls
  • Foster new ideas, cross-disciplinary approaches
    • Encourage students to experiment
  • But used in production too
    • Significant number of papers resulting from gateways including GridChem, nanoHUB
      • Over 600 Google Scholar references to Robetta
    • Scientists can focus on challenging science problems rather than challenging infrastructure problems

EGEE 2009, September 21-25, 2009

today there are approximately 35 gateways using the teragrid
Today, there are approximately 35 gateways using the TeraGrid

EGEE 2009, September 21-25, 2009

not just ease of use what can scientists do that they couldn t do previously
Not just ease of useWhat can scientists do that they couldn’t do previously?
  • Linked Environments for Atmospheric Discovery (LEAD) - access to radar data
  • National Virtual Observatory (NVO) – access to sky surveys
  • Ocean Observing Initiative (OOI) – access to sensor data
  • PolarGrid – access to polar ice sheet data
  • SIDGrid – expensive datasets, analysis tools
  • GridChem –coupling multiscale codes
  • How would this have been done before gateways?

EGEE 2009, September 21-25, 2009

what makes a gateway a teragrid gateway
What makes a gateway a TeraGrid gateway?
  • TeraGrid gateways that use TeraGrid resources
  • Are they all developed by TeraGrid?
    • No, we don’t make gateways the gateways you use, we make the gateways you use better
    • The strength of the program lies in the development of end user interfaces by those in the community
      • We work to provide flexible services to meet a variety of needs in a scalable way
  • TeraGrid does provide staff to assist with gateway use of the resources
    • Anyone can request support via the same peer review process used to request CPU hours or a data allocation
  • Are gateways required to be developed with a certain software stack?
    • No, gateways can be developed using any front end technology
    • In general, they will use TeraGrid’s common software stack (CTSS) to interact with the TeraGrid
      • Condor, Globus, myproxy particularly relevant for gateways
      • http://www.teragrid.org/userinfo/software/ctss_results.php

EGEE 2009, September 21-25, 2009

what kinds of technologies do we see in use today
What kinds of technologies do we see in use today?
  • http://www.teragridforum.org/mediawiki/index.php?title=Science_Gateway_Use_Cases
    • Not really meant to be a public link, but created as the result of a spring, 2009 survey of gateways to provide feedback to Globus

EGEE 2009, September 21-25, 2009

EGEE 2009, September 21-25, 2009

CC=community credential, UC=user credential, DA=dynamic accounts

  • Lots of gridsphere
    • Support has decreased, I expect to see transitions away from this
      • TeraGrid User Portal moving from gridsphere to liferay.com
  • Some JaveCoG
  • Open Grid Computing Environments (OGCE)
    • http://www.collab-ogce.org
  • SimpleGrid
    • Developed to quickly demonstrate the moving parts of a gateway
    • Build a gateway in an afternoon
  • HUBzero
    • http://www.hubzero.org
  • See less and less patience from potential developers for complicated deployments
    • Movement toward Django, Drupal, gadgets

EGEE 2009, September 21-25, 2009

ogce and simplegrid tutorials featured at doe scidac meeting june 2009
OGCE and SimpleGrid tutorialsFeatured at DOE SciDAC meeting, June, 2009

EGEE 2009, September 21-25, 2009

ogce and gateways
OGCE and Gateways
  • We develop and package software for use by TeraGrid Science Gateways and other resources
    • BioVLAB use OGCE tools to run on Amazon
  • A lot of this comes from active Gateways.
    • Information Services (GPIR, QBETS): TeraGrid User Portal
    • Workflow tools: LEAD
    • Resource Discovery Service, File Browser Applet: TGUP, GridChem
    • SIDGrid, OLSG
  • We contribute codes back to these projects.




EGEE 2009, September 21-25, 2009



  • Create a user-centric Web 2.0 environment as science gateway interface
  • Use TeraGrid to support domain-specific scientific computing
  • Develop Grid-enabled application services to access TeraGrid capabilities
  • Understand a GISolve-based workflow to steer analyses on TeraGrid





  • Web 2.0 development
    • JavaScript
    • AJAX
    • Yahoo UI (YUI)
    • Twitter API
    • Google Map
  • PHP-based server-side code development
    • Web service client programming
    • MySQL database programming
recent additional technical requirement for gateways
Recent additional technical requirement for gateways
  • Community accounts used as service accounts to launch jobs for gateway users
    • Scalable, but doesn’t let TeraGrid discover the number of end users
  • Must add unique user-identifying attributes, attribute-based authentication
  • Allows programmatic counting of end gateway users as required by the NSF
    • Goal is to have this work complete by September, 2009
      • We won’t quite make it
      • http://www.teragridforum.org/mediawiki/index.php?title=Science_Gateway_Credential_with_Attributes

EGEE 2009, September 21-25, 2009

recent area of technical focus gram5
Recent area of technical focus:GRAM5
  • Stability and scalability are of supreme importance for gateways using TeraGrid
  • Many improvements to GRAM as a result of heavy gateway utilization on TeraGrid
    • Led to development of GRAM5
    • TeraGrid platform size (60,000 processors on Ranger) also motivate scalability improvements

EGEE 2009, September 21-25, 2009

3 steps to connect a gateway to teragrid
3 steps to connect a gateway to TeraGrid
  • Request an allocation
    • Only a 1 paragraph abstract required for up to 200k CPU hours
  • Register your gateway
    • Visibility on public TeraGrid


  • Request a community account
    • Run jobs for others via your portal
  • Staff support is available!
  • www.teragrid.org/gateways

EGEE 2009, September 21-25, 2009

gce09 at sc09 in portland grid computing environments workshop
GCE09 at SC09 in PortlandGrid Computing Environments Workshop
  • Friday November 20, 2009
    • http://www.collab-ogce.org/gce09
  • Topics include
    • Integration of Web 2.0 technologies with science gateways
    • Gateways to cloud computing services
    • Applications of virtual world technologies to science and education gateways
    • Grid portals and gateways deployments, including User Portals, Application Portals, Science Gateways, Education Portals, User interface/usability studies
    • Design and architecture of Grid portals, portal containers, and gateways
    • Tools and frameworks that make developing Grid Portals and gateways easier
    • Portal security models and solutions
    • Middleware solutions in support of scientific portals and Gateways including Web Services, workflow and mashup composers and engines, and similar capabilities
    • Non-browser gateways: desktops and mobile computing gateways
    • Summary and survey papers.

EGEE2009, September 21-25, 2009

tremendous opportunities using the largest shared resources challenges too
Tremendous Opportunities Using the Largest Shared Resources - Challenges too!
  • What’s different when the resource doesn’t belong just to me?
    • Resource discovery
    • Accounting
    • Security
    • Proposal-based requests for resources (peer-reviewed access)
      • Code scaling and performance numbers
      • Justification of resources
      • Gateway citations
  • Tremendous benefits at the high end, but even more work for the developers
  • Potential impact on science is huge
    • Small number of developers can impact thousands of scientists
    • But need a way to train and fund those developers and provide them with appropriate tools

EGEE 2009, September 21-25, 2009

thank you for your attention questions
Thank you for your attention!Questions?

Nancy Wilkins-Diehr, wilkinsn@sdsc.edu


EGEE 2009, September 21-25, 2009