Transcript The TeraGrid: An essential tool for 21st century science Craig Stewart, Associate Dean, Research Technologies Chief Operating Officer, Pervasive Technology Labs Chair, Coalition for Academic Scientific.

The TeraGrid:
An essential tool for 21st century
science
Craig Stewart,
Associate Dean, Research Technologies
Chief Operating Officer, Pervasive Technology Labs
Chair, Coalition for Academic Scientific Computing
IU TeraGrid Resource Partner PI
Indiana University
[email protected]
17 February 2008
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License Terms
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Please cite this presentation as: Stewart, C.A. The TeraGrid:
An essential tool for 21st century science. (Presentation). 17 February 2010,
Annual Meeting American Association for Advancement of Science, Boston, MA.
Available from: http://hdl.handle.net/2022/14527
Portions of this document that originated from sources outside IU are shown
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Items indicated with a © are under copyright and used here with permission.
Such items may not be reused without permission from the holder of copyright
except where license terms noted on a slide permit reuse.
Except where otherwise noted, the contents of this presentation are copyright
2011 by the Trustees of Indiana University. This content is released under the
Creative Commons Attribution 3.0 Unported license
(http://creativecommons.org/licenses/by/3.0/). This license includes the following
terms: You are free to share – to copy, distribute and transmit the work and to
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work.
Outline
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Why this workshop may be valuable to you
– (Time consuming computations on the critical path of you
research? Need more storage? Do you provide scientific
services/resources over the Web?)
What is cyberinfrastructure?
Examples of TeraGrid uses
More detailed info about the TeraGrid
– Architecture
– Storage
– Computation
– Science Gateway use and support, including Visualization
– Data source and service hosting
How can you get going using the TeraGrid?
– Resources are available to use
– Help using the system is available
– At the end of the talk we will help those who wish (and have laptops
here) start the application process. You need your CV to finish the
whole process, but you can do some of the work and save it
NB: ‘Tufte was here’
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What is Cyberinfrastructure?
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Indiana University’s definition of Cyberinfrastructure:
“Cyberinfrastructure consists of computing systems, data storage
systems, advanced instruments and data repositories, visualization
environments, and people, all linked together by software and high
performance networks to improve research productivity and enable
breakthroughs not otherwise possible.”
This and other information in Wikipedia definition of Cyberinfrastructure
Some basic terms
– TFLOPS - Trillions of FLOating Point operations per Second
(mathematical operations) (10^12)
– Processor hour - one hour of processor (CPU) utilization
– TB - terabyte; PB - petabyte
– Parallel programming
– MPI - Message Passing Interface
– WSRF - Web Services Resource Framework
©Trustees of Indiana University. May be reused so long as IU and TeraGrid logos
remain, and any modifications to original are noted. Courtesy Craig A. Stewart, IU
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What is the TeraGrid?
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An instrument (cyberinfrastructure) that delivers high-end IT resources storage, computation, visualization, and data/service hosting - almost all of
which are UNIX-based under the covers; some hidden by Web interfaces
– A data storage and management facility: over 20 Petabytes of storage (disk
and tape), over 100 scientific data collections
– A computational facility - over 750 TFLOPS in parallel computing systems
and growing
– (Sometimes) an intuitive way to do very complex tasks, via Science
Gateways, or get data via data services
A service: help desk and consulting, Advanced Support for TeraGrid
Applications (ASTA), education and training events and resources
The largest individual cyberinfrastructure facility funded by the NSF, which
supports the national science and engineering research community
Something you can use without financial cost - allocated via peer review (and
without double jeopardy)
©Trustees of Indiana University. May be reused so long as IU and TeraGrid logos
remain, and any modifications to original are noted. Courtesy Craig A. Stewart, IU
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Examples of what you can do with the TeraGrid:
Simulation of cell membrane processes
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Simulation of TonB-dependent transporter (TBDT)
Used 400,000 processor (CPU) hours on systems
at National Center for Supercomputing Applications,
IU, Pittsburgh Supercomputing Center [45 years
with one processor]
Modeled mechanisms for allowing transport of
molecules through cell membrane
Experimental analysis not possible!
Work by Emad Tajkhorshid and James Gumbart, of
University of Illinois Urbana-Champaign. Mechanics
of Force Propagation in TonB-Dependent Outer
Membrane Transport. Biophysical Journal 93:496504 (2007).
Results of the simulation may be seen at
www.life.uiuc.edu/emad/TonB-BtuB/btub2.5Ans.mpg
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Image courtesy of Emad Tajkhorshid, UIUC
Predicting storms
• Hurricanes and tornadoes cause massive
loss of life and damage to property
• TeraGrid supported spring 2007 NOAA
and University of Oklahoma Hazardous
Weather Testbed
– Major Goal: assess how well ensemble
forecasting predicts thunderstorms,
including the supercells  tornadoes
– Nightly reservation at PSC
– Delivers “better than real time”
prediction
– Used 675,000 CPU hours for the
season
– Used 312 TB on HPSS storage at PSC
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Slide courtesy of Dennis Gannon, IU, and LEAD Collaboration
Solve any Rubik’s Cube in 26 moves?
• Rubik's Cube is perhaps the
most famous combinatorial
puzzle of its time
• > 43 quintillion states
(4.3x10^19)
• Gene Cooperman and Dan
Kunkle of Northeastern Univ.
proved any state can be
solved in 26 moves
• 7TB of distributed storage on
TeraGrid allowed them to
develop the proof
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Source: http://www.physorg.com/news99843195.html
• Resources for
many
disciplines!
• > 40,000
processors in
aggregate
• Resource
availability will
grow during
2008 at
unprecedented
rates
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The TeraGrid Map
Grid Infrastructure
Group (UChicago)
UW
PSC
UC/ANL
NCAR
PU
NCSA
IU
Caltech
UNC/RENCI
ORNL
Tennessee
USC/ISI
SDSC
LONI/LSU
TACC
Resource Provider (RP)
Software Integration Partner
Network Hub
©University of Chicago, Courtesy Dane Skow, Director, TeraGrid Grid Infrastructure Group. Used with Permission.
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But you don’t care - TeraGrid
Architecture
RP 1
RP 2
POPS
(for now)
User
Portal
Science
Gateways
TeraGrid Infrastructure
Accounting, …
(Accounting, Network,Network,
Authorization,…)
Command
Line
RP 3
©University of Chicago, Courtesy Dane Skow, Director, TeraGrid Grid Infrastructure Group.
Used with Permission and modified substantially from original by Craig A. Stewart
Compute
Service
Viz
Service
Data
Service 11
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Data storage and management: Tape
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TeraGrid provides persistent (up to Feb 2010+) storage on disk and
tape
Could you benefit from having a spare copy of your data stored
someplace removed from your home location?
Allocatable tape-based storage systems:
– IU (Indiana University) - geographically distributed
– NCAR (National Center for Atmospheric Research) - also supports
dual copy
– NCSA (National Center for Supercomputing Applications)
– SDSC (San Diego Supercomputer Center)
– Note: most sites have massive data storage systems that provide
storage in support of computation
Command line usage is reasonably straightforward with GridFTP; IU is
developing a GUI
©Trustees of Indiana University. May be reused so long as IU and TeraGrid logos
remain, and any modifications to original are noted. Courtesy Craig A. Stewart, IU
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©Trustees of Indiana University. May be reused so long as IU and TeraGrid logos
remain, and any modifications to original are noted. Courtesy Craig A. Stewart, IU
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Data storage and management: Disk
• GPFS-WAN (General Parallel File System Wide Area
Network). ~ 1 petabyte
– Home at San Diego Supercomputer Center; may be
accessed as if it were a local file system from NCAR,
NCSA, IU, UC/ANL
• IU Data Capacitor - Lustre
– 1 petabyte of spinning disk
– Primarily for short term storage of data
• Long term disk storage allocations
– Indiana University, National Center for Supercomputing
Applications, San Diego Supercomputer Center
©Trustees of Indiana University. May be reused so long as IU and TeraGrid logos
remain, and any modifications to original are noted. Courtesy Craig A. Stewart, IU
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TeraGrid High Performance Computing
Systems 2007-8
UC/ANL
NCSA
NCAR
Tennessee
SDSC
PSC
PU
IU
2008
(~1PF)
ORNL
LONI/LSU
2007
(504TF)
TACC
Computational Resources
(size approximate - not to scale)
Slide Courtesy Tommy Minyard, TACC
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Two examples of TeraGrid
supercomputers
• Newest addition to the TeraGrid Texas Advanced Computing
Center’s Ranger
– Biggest open supercomputer in
world
– 504 TFLOPS Sun Constellation
– 15,744 AMD Quad-core
“Barcelona” processors
– Disk subsystem - 1.7 petabytes
• IU’s Big Red
– 30 TFLOPS
– Particularly good for molecular
dynamics codes
– Biggest system in the TeraGrid in
summer 2006
Big Red
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Ranger info courtesy of Tommy Minyard, TACC
Science Gateways
• A Science Gateway is a domain-specific computing
environment, typically accessed via the Web, that provides a
scientific community with end-to-end support for a particular
scientific workflow
• Science Gateways are distinguished from Web portals
(http://en.wikipedia.org/wiki/Web_portal) in that portals “present
information from diverse sources in a unified way.”
• Hides complexity (pay no attention to the grid behind the
curtain…)
©Trustees of Indiana University. May be reused so long as IU and TeraGrid logos
remain, and any modifications to original are noted. Courtesy Craig A. Stewart, IU
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LEAD (portal.leadproject.org)
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Simple enough an undergraduate can use it!
National Center for Supercomputing Applications (NCSA) and IU teamed up to
support WxChallenge weather forecast competition. 64 teams, 1000 students,
~16,000 CPU hours on Big Red
XBaya is available from http://www.collab-ogce.org/
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Purdue’s NanoHUB (www.nanohub.org)
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U. Chicago SIDGrid
(sidgrid.ci.uchicago.edu)
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IU Render Portal
Image by Chris Matusek
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Image by Ralf Frieser
Supports scientific visualization
Supports education in visualization, graphics, and new media
©Trustees of Indiana University. May be reused so long as IU and TeraGrid logos
remain, and any modifications to original are noted. Courtesy Craig A. Stewart, IU
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Purdue TeraDRE
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TeraGrid Science Gateways
Accessible at http://www.teragrid.org/programs/sci_gateways/
Title
Discipline
Open Science Grid (OSG)
Advanced Scientific Computing
Special PRiority and Urgent Computing Environment (SPRUCE)
Advanced Scientific Computing
Massive Pulsar Surveys using the Arecibo L-band Feed Array (ALFA)
Astronomical Sciences
National Virtual Observatory (NVO)
Astronomical Sciences
High Resolution Daily Temperature and Precipitation Data for the
Northeast United States
Atmospheric Sciences
Linked Environments for Atmospheric Discovery (LEAD)
Atmospheric Sciences
Computational Chemistry Grid (GridChem)
Chemistry
Computational Science and Engineering Online (CSE-Online)
Chemistry
Network for Earthquake Engineering Simulation (NEES)
Earthquake Hazard Mitigation
GEON(GEOsciences Network)
Earth Sciences
NanoHUB
Nanotechnology
TeraGrid Geographic Information Science Gateway (GISolve)
Geography
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TeraGrid Science Gateways
Accessible at http://www.teragrid.org/programs/sci_gateways/
Title
Discipline
CIG Science Gateway for the Geodynamics Community
Geophysics
QuakeSim (QuakeSim)
Geophysics
The Earth System Grid (ESG)
Global Atmospheric Research
National Biomedical Computation Resource (NBCR)
Integrative Biology and Neuroscience
Developing Social Informatics Data Grid (SIDGrid)
Language, Cognition, and Social
Behavior
Neutron Science TeraGrid Gateway (NSTG)
Materials Research
Biology and Biomedicine Science Gateway
Molecular Biosciences
Open Life Sciences Gateway (OLSG)
Molecular Biosciences
The Telescience Project
Neuroscience Biology
Grid Analysis Environment (GAE)
Physics
SCEC Earthworks Project
Seismology
TeraGrid Visualization Gateway
Visualization, Image Processing
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Hosting services
• Remember that old Waffle House commercial?
• If you have a data set or a data resource that serves
a national community (or even a community that
extends beyond your home institution… or a
community you would like to extend beyond your
home institution) …
• Hosting of your service is available from Indiana
University via our Quarry system!
©Trustees of Indiana University. May be reused so long as IU and TeraGrid logos
remain, and any modifications to original are noted. Courtesy Craig A. Stewart, IU
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MutDB (www.mutdb.org)
http://www.chembiogrid.org/
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Getting an account and allocation
• Get a POPS (Partnership Online Proposal System) account
• Apply for a DAC allocation (Development Allocation Committee):
< 5 TB disk, < 25 TB tape storage, and/or < 30,000 Standard
Units (SUs - related to CPU hours - in general an SU on one of
the newer TeraGrid systems is about 0.5 CPU hours)
• Wait a month (although IU can help you shorten that!)
• Read the introductory documentation
• Use the TeraGrid KB if you need
• Ask for help ([email protected], [email protected])
• Go discover!
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Go to the POPS page https://pops-submit.teragrid.org/
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Create a POPS Login
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Indicate that you are “New” to the Teragrid
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Indicate that this is a “Start-up” Request
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Select DAC-TG (nonintuitive)
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Fill out PI information
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Skip Co-PIs probably (unless Co-PI
has current funding and you don’t)
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Fill out info on your project
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Fill out info on your funding
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Make reasonable estimates about your computing
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Upload your CV and Submit!
when ready
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Additional info
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www.researchtechnologies.iu.edu (also pervasive.iu.edu)
Getting started guide - includes examples of good proposals:
http://www.teragrid.org/userinfo/getting_started.php
Review criteria:
http://www.teragrid.org/userinfo/access/allocationspolicy.php
When you’re in a foreign country there is nothing like a guide. If you
need help with the application process contact IU consultants at
[email protected] or submit a help request via the TeraGrid
([email protected])
If you are interested in having a data collection or science gateway
hosted on the TeraGrid, definitely contact IU directly
([email protected]). Do the same if you are interested in
Advanced Support for TeraGrid Allocations
If you are anxious to get going, contact us as soon as you have your
DAC allocation request submitted and we can provide a local login for
up to 6 weeks of use
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Acknowledgements
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IU’s involvement as a TeraGrid Resource Partner is supported in part by the National Science Foundation under Grants No.
ACI-0338618l, OCI-0451237, OCI-0535258, and OCI-0504075.
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The IU Data Capacitor is supported in part by the National Science Foundation under Grant No. CNS-0521433.
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The Grid Infrastructure Group management of the TeraGrid, and Dane Skow's leadership thereof, is funded by NSF grant
0503697.
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Purdue’s involvement as a TeraGrid Resource Partner is supported in part by the National Science Foundation under Grant
No. OCI-050399.
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This research was supported in part by the Pervasive Technology Labs and the Indiana METACyt Initiative. Both Indiana
University initiatives are supported by the Lilly Endowment, Inc.
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This work was supported in part by Shared University Research grants from IBM, Inc. to Indiana University.
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The LEAD portal is developed under the leadership of IU Professors Dr. Dennis Gannon and Dr. Beth Plale, and supported by
NSF grant 331480. Marcus Christie and Surresh Marru of the Extreme! Computing Lab contributed the LEAD graphics
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The ChemBioGrid Portal is developed under the leadership of IU Professor Dr. Geoffrey C. Fox and Dr. Marlon Pierce and
funded via the Pervasive Technology Labs (supported by the Lilly Endowment, Inc.) and the National Institutes of Health grant
P20 HG003894-01.
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Many of the ideas presented in this talk were developed under a Fulbright Senior Scholar’s award to Stewart, funded by the
US Department of State and the Technische Universitaet Dresden.
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Any opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not
necessarily reflect the views of the National Science Foundation (NSF), National Institutes of Health (NIH), Lilly Endowment,
Inc., or any other funding agency.
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This work is made possible by the dedicated efforts of the expert staff of the Research Technologies Division of University
Information Technology Services, the faculty and staff of the Pervasive Technology Labs, and the staff of UITS generally.
Erik Cornet, Mike Lowe, Scott Tiege, Michael Grobe, and Malinda Lingwall helped with this presentation.
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Thanks to the faculty and staff with whom we collaborate locally at IU and globally (within the US via the TeraGrid, and
internationally via collaboration with Technische Universitaet Dresden)
Thank you! Any questions?
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