Transcript Progress Since PRAGMA12.ppt

Progress Since PRAGMA 12
Framework for Collaboration
24 September 2007
PRAGMA 13 @ NCSA
PRAGMA Engagements in Cyberinfrastructure
PRAGMA 12
and two Joes
and the two Joes
PRAGMA
Launched in 2002
Overarching Goals
Strengthen Existing and Establish New
Collaborations
Work with Science Teams to Advance
Grid Technologies and Improve the
Underlying Infrastructure
In the Pacific Rim and Globally
“A Practical Collaborative Framework”.
http://www.pragma-grid.net
PRAGMA Workshops
Steps to Progress
1.
March 2002 San Diego
8.
SDSC, UCSD
2.
July 2002 Seoul
KISTI
3.
January 2003 Fukuoka
AIST, Osaka
4.
June 2003 Melbourne
Monash, APAC
5.
October 2003 Hsinchu
NCHC, NSC
6.
May 2004 Beijing
CNIC
7.
Sept 2004 San Diego
UCSD, SDSC, Calit2,
TransPac
May 2005 Singapore
BII, NGO
9.
Oct 2005 Hyderabad
U Hyderabad
10. March 2006 Townsville
APAC, JCU, AIMS, QPSF
11. October 2006 Osaka
Osaka U, NGI
12. March 2007 Bangkok
NECTEC, TNGP
13. Sept 2007 Urbana
NCSA, IACAT, UIUC
PRAGMA
Overarching Goals
Strengthen Existing and Establish New
Collaborations
Work with Science Teams to Advance
Grid Technologies and Improve the
Underlying Infrastructure
In the Pacific Rim and Globally
“A Practical Collaborative Framework”.
http://www.pragma-grid.net
Overview and Approach
Process to Promote Routine Use Team Science
Workshops and
Organization
Application-Driven Collaborations
Applications
Middleware
Information Exchange
Planning and Review
Routine Use Lab/Testbed
Testing Applications
Building Grid and GOC
New Collaborations
New Members
Expand Users
Expand Impact
Multiway Dissemination
Key Middleware
Outcomes
Improved Middleware
Broader Use
New Collaborations
Transfer Tech.
Standards
Publications
New Knowledge
Data Access
Education
PRAGMA Highlights of 2006 - 2007
The PRAGMA Steering Committee
http://www.pragma-grid.net/people/committee/
Resources and Data Working Group
Yoshio Tanaka, AIST
Mason Katz, UCSD
Cindy Zheng, UCSD
OSG-PRAGMA Grid Interoperation running GridFMO
Tsutomu Ikegami, Yoshio Tanaka; Neha Sharma; Cindy Zheng
Series of GridFMO calculations ran on a combination of PRAGMA and OSG resources.
Total of 7 calculations were conducted from 2007/02/28 - 2007/05/18, utilizing a maximum
of 240 CPUs. Fault-tolerance of GridFMO supported the stability of the calculations, each
of which took 10 days on average. This has produced meaningful and usable scientific
results in a relatively short time.
● Full electron calculation of bio
molecules by using FMO method
● Utilize vast computational resources on
the Grid
● Long-term calculations supported
by fault-tolerance
● Learning from the differences
Tsutomu IKEGAMI
Applications and Middleware
http://goc.pragma-grid.net/wiki/index.php/Applications
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Real science applications continue paired with and drive middleware
development
Some achieve long-run and scientific results
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Climate simulation
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Quantum-mechanics, quantum-chemistry:
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Siesta/Nimrod (UZurich, Switzerland; MU, Australia)
Amber/Gfarm ( USM, Malaysia; AIST, Japan)
Environmental Science
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CSE-Online (UUtah, USA)
e-AIRS (KISTI, Korea)
Molecular simulation
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Phylogenetic/Gfarm/CFS (UWisc and UCSD, USA)
Computational chemistry and fluid dynamics
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FMO/Ninf-G (AIST, Japan)
Genomics and meta-genemics
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Savannah/Nimrod (MU, Australia)
MM5/Mpich-Gx (CICESE, Mexico; KISTI, Korea)
CSTFT/Ninf-G (UPRM, Puerto Rico)
Applications run by PRIME students this year
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Climate modeling
Multi-walled carbon nanotube and polyethylene oxide composite computer
visualization model
Metabolic regulation of ionic currents and pumps in rabbit ventricular myocyte
model
Improving binding energy using quantum mechanics
Cardiac mechanics modeling
H5N1 simulation
Shp2 Protein Tyrosine Phosphatase Inhibitor simulation for cancer research
Source: C Zheng
Other Accomplishments
http://goc.pragma-grid.net/wiki
• PRAGMA production CA is in approval process to join
IGTF (http://goc.pragma-grid.net/ca)
– By SDSC/UCSD, USA and APGrid PMA
• Various portals and services setup completed
(http://goc.pragma-grid.net/wiki/index.php/Portal_Services)
– 2 condor-G servers setup completed at UCSD and MIMOS
• By SDSC/UCSD, USA and MIMOS, Malaysia
– Nimrod portal setup completed at UCSD
• By MU, Australia and SDSC/UCSD, USA
– CSF server and portal setup completed at UCSD
• By JLU, China and SDSC/UCSD, USA
• Gfarm-roll for Rocks are in final testing
– By UZH, Switzerland
Source: C Zheng
Telescience Working Group
Shinji Shimojo, Osaka University
Fang-Pang Lin, NCHC
RBNB Data Streaming Architecture
Kenting
Coral Reef
Taiwan
Ebbe Strandel, Sameer Tilak, Hsiu-Mei Chou, Jazz Wang, Sun-In Lin, Fang Pang Lin
GLEON Sites: RCN Award, Supplement
Lake site
Cyber-support
site
GLEON 5
Montreal CA
August 2007
GLEON 1
San Diego USA
March 2005
GLEON 2
Townsville AU
March 2006
GLEON 3
Hsinchu TW
October 2006
GLEON 4
Lammi FI
March 2007
Lake Erken: Deployment Visit
Building Community
25 – 29 June 2007
GOALS
• Install RBNB and
database system
• Gather unique
requirements and
document process to
inform and improve
future deployments
and developments
• Train local staff
• Understand challenges
at site level where IT
level typical of most
sites
Work on Large Displays
PRIME: David Jackson, Ava Pierce, Shinji Shimojo, Susumu Date,
Jurgen Schulze, Kohei Ichikawa
Other Highlights
Y.Chun (PRIME)
S.Shimojo
FP Lin
H.Yeom
Biosciences Working Group
Karpjoo Jeong, Konkuk University
Habibah Wahab, USM
Wilfred Li, UCSD
Team Science: Integrating Resources to
Address a Global Health Threat
• Distributed Bioinformatics Analysis of Avian
(Bird) Flu using Global Computational Data
Grid
– Provides a scientific driver for technology
integration and development of infrastructure
for drug discovery pipeline of infectious agents
• Goals:
– Characterize function of Influenza viruses using
structure based approach
– Understand interactions of major viral virulence
determinants using molecular dynamics (MD)
simulations
– Establish a large scale distributed computational
data grid among participating institutions
through multinational collaboration
Source:
L. Cheng
H5N1 related glycan
conformation analysis
using M*Grid and GlycoM*Grid
Relaxed Complex Method
Molecular Dynamics
Simulation Data Sets &
Database
Virtual Screening Data
Sets & Database
M*Grid deployed at KISTI for
PRAGMA Grid
MD Simulation available on
M*Grid Shared Data Repository
HPC
Clusters,
NBCR,
TeraGrid,
MHPCC
Virtual
Directory Tree
/gfs/$USER
databases
applications
Zinc
PRAGMA Portal
My WorkSphere
CSF4 Server
NCIDS
Gfarm File System
NAMD
AutoDock
Wilfred Li
Mr. Bayes
GEO Working Group
Ryosuke Nakamura, AIST
Guey Shin Chang, NARL
Ashraf Memon, UCSD
Sornthep Vannarat, NECTEC
Meetings with Strong GEO Leadership
• GEOGrid: 1st Global Earth Observation
Grid Workshops
– Held Meeting 20 March 2007
– Thailand Science Park
– Hosted by AIST, NECTEC, support by GEON
• 5th Taipei International Digital Earth
Symposium
– Special Session on GEO Grid, Organized by
NARL
– 17-18 May 2007
ASTER
Formosat-2
12 Sept, 2007
12 Sept, 2007
Source
R. Nakamura
GEO WG: Federate Data Archives
Ivanpah
playa
Nevada
PRAGMA’s Collaborative Framework
SCIENCE
• GLEON (and CREON)
– Global Ecological Observatory Network
– Grassroots effort to understand lake dynamics
• Avian Flu Grid
– Integrates technologies for shared infrastructure
• PRIME
EDUCATION
– Pacific Rim Experiences for Undergraduates
– Prepares globally-enabled workforce
• PRIUS
– Pacific Rim International UniverSity at Osaka University
– Prepares global workforce in context of curriculum
GRID
• PRAGMA
– Pacific Rim Application and Grid Middleware Assembly
– Catalyzes collaborations
SOFTWARE
• Gfarm,
OptIPuter:
MGrid, CSF4, GEO, …
– Optical networking, Internet Protocol, computer storage,
processing and visualization technologies
– Develops technologies for data intensive computing and
collaborations
Source: Philip Papadopoulos, Global Engagement
RENEWED by NSF
Providing students international interdisciplinary Research
Apprenticeships and Cultural Competency Learning Experiences
COMPONENTS
• Application Proc.
• Pre-dept Training
• 9 week internship
• Re-entry
MAJORS
• Bioeng.
• Comp. Sci.
• Comp. Eng.
• Mechanical Eng.
• Electrical Eng.
• Biology
• Computing and Arts
LOCATIONS
• Beijing CNIC
• Hsinchu NCHC
• Melbourne Monash
• Osaka University
Earn academic credit
TOPICS
• Cardiac modeling
• Ligand screening
• Earthquake Eng.
• Environmtl sensing
• Grid computing
• Visualization
Using or developing grid technology to create new knowledge
prime.ucsd.edu
PRIUS Expands
Demos: Working Group Activities
• X-SIGMA: XML-based Simple data Integration system for Gathering, Managing,
and Accessing Scientific Experimental Data in Grid Environments, Karpjoo Jeong,
Dongkwang Kim, Jonghyun Lee, Miran Kang, Suntae Hwang, and Sang Boem Lim, Konkuk University
• CSF4 Meta-Scheduler,
Xiaohui Wei , Zhaohui Ding , College of Computer Science and Technology,
Jilin University, China
• Account management using GAMA and VOMS, Yoshio Tanaka, AIST
• Amber 8 on PRAGMA Gfarm Datagrid, Habibah A. Wahab & Suhaini Ahmad. Universiti Sains
Malaysia
• The Avian Flu Grid project,
Rommie Amaro, Ph.D., Dong Xu, Ph.D., The Avian Flu Grid project
Department of Chemistry (RA), Calit2 (DX) UCSD
• CSE-Online with PRAGMA:
A case study on integrating CSE-Online with the Thailand National
Grid, Thanh N. Truong, University of Utah, Putchong Uthayopas, Thai National Grid Center
• 3D High-Resolution GIS Taiwan Platform, Guey-Shin Chang, Whey-Fone Tsai, NARL/NCHC
• Prompt satellite image processing on GEO Grid portal, Ryosuke NAKAMURA, AIST
• GEON: Networking Indian Geoscience Community through iGEON, Arun Agarwal,
University of Hyderabad
• Data Management at Kenting’s Underwater Ecological Observatory, Ebbe Strandell,
SameerTilak, Hsiu-Mei Chou, Yao-Tsung Wang, Fang-Pang Lin, Tony Fountain, San Diego Supercomputer
Center and National Center for High-Performance Computing
PRIZE of the
Best Demo!
Posters: A First Time
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Thermo-Mechanical Model of Steel Solidification Processes, NCSA & Corus RD&T The
Netherlands
MotifNetwork: A Grid-enabled Workflow for High-throughput Domain Analysis of
Biological Sequences, Renaissance Computing Institute and NCSA
Building Next-Generation CyberCollaboratory for Environmental Observatories, NCSA
Computational Chemistry Grid, a Production Cyber-environment through Distributed
Computing: Recent Enhancements and Application for DFT calculation of Amide I spectra
of Amyloid- Fibril, NCSA
The Development of a Grid Resource Broker, NCHC, Hsinchu, Taiwan
Life Sciences Utility Services, The National Grid Office (NGO) Singapore
The Ring Buffer Network Bus (RBNB) DataTurbine Streaming Data Middleware for
Environmental Observing Systems, SDSC, UCSD
Supporting remote collaboration for model execution and analysis of sensor data in
scientific workflow systems, NCSA
Biotechnology Research: Makmal Biokristalografi & Bioinformatik Structur, USM
Information Gathering about Decision Processes Using Geospatial Electronic Records,
National Center for Supercomputing ApplicationsOpal-Enabling the Web 2.0 Paradigm for
Biomedical and Metagenomics Applications, UCSD, NBCR, Calit2, CRBS, SDSC
Avian Flu Grid: International Collaborative Environment for Team Science on Avian
Influenza, UCSD, U Hawaii, Konkuk U, JLU, CNIC, NTU, USM, Tsukuba U, AIST, KISTI, HHMI
PRAGMA Institute
• Goal: Build the community of researchers in the Pacific Rim
who use grid technologies by providing training opportunities.
• Duration: Up to a week
• Frequency: Depends on demand
• PRAGMA Involvement:
– Hosting sites are PRAGMA members
– Lecturers are from PRAGMA institutions
– Program Committee to include PRAGMA members
• Participants: PRAGMA and non-PRAGMA
• Proposals: Steering Committee will review
• First Institute: NCSA, Illinois; 26 – 27 September 2007
1st PRAGMA Institute:
Advanced Computing Applications and
Technologies Institute
Life Sciences and Geo Sciences
Keynote and Invited Talks
• The Emerging Global Collaboratory for Microbial
Metagenomics Researchers, Larry Smarr
• The Impact of Petascale Computing on Biological Science,
Rick Stevens
• GEON: Networking the Indian Geosciences Community
through iGEON, Arun Agarwal
• High-Performance Computing and Information Technology in
the Geosciences, Don Wuebbles
• Miron Livny
1st PRAGMA Institute: Tutorials
• PRAGMA Grid—Lessons Learned (plenary), Cindy Zheng, PRAGMA Grid
• The Nimrod Family of Tools, David Abramson, Monash University,
Australia
• CSF4, Xiaohui Wei, Jilin University, China
• Opal, The Application Wrapper Web Service
Sriram Krishnan and Wes Goodman, National Biomedical Computation
Resource, UCSD
• GridChem, Sudhakar Pamidighantam, NCSA
• MOGAS
• SP2LEARN—A Framework for Geospatial Models from Sparse Field
Measurements Using Image Processing and Machine Learning, Peter
Bajcsy, NCSA
• MaeViz
• MPICH-GX Implementation: Grid Enabled MPI Implementation to
Support the Private IP and the Fault Tolerance Oh-kyoung Kwon, KISTI,
Korea
• Flood Grid
• D2k
Steering Committee Meeting
• New Members: Monash U; CSE Online;
BeSTGRID
• PRAGMA Institute 2: Proposal from NCHC
• Workshop Timing: PRAGMA 14, PRAGMA 15
• Proposal to Host PRAGMA 16 by KISTI
• Industry: New Approach for Involvement
• Interactions with Europe: Switzerland
• PRAGMA Brochure: Review and Fill Gaps
– Publications
– Pictures and Images
Currnt and Future
PRAGMA Workshops
• 23 – 25 September 2007, Urbana-Champaign
Illinois USA
– PRAGMA 13 Hosted by NCSA
• Spring 2008, Hsinchu Taiwan
– PRAGMA 14 Hosted by NCHC
• Fall 2008, Penang Malaysia
– PRAGMA 15 Hosted by USM
• Spring 2009,
– PRAGMA 16 proposed Korea
• Fall 2009,
– PRAGMA 17
www.pragma-grid.net
PRAGMA Highlights of 2006 - 2007
• Simulating the Australian Monsoon and the Effect
of Wildfires
• PRAGMA Biosciences Portal
• PRAGMA Leads Application Experiment of Grid
Interoperation in GIN Testbed
• PRAGMA Establishes Certificate Authority (CA)
Using Naregi-CA Software
• Expanding the Collaboration Grid
• Building Communities, Catalyzing Collaborations
• PRIME and PRIUS
• More accomplishments in the Working Group
sections
Collaborative Overview 2007 - 2008
• Avian Flu Grid
• Streaming Data Software, used in
Coral Reef Ecology
• OSG – PRAGMA Interoperation, using
GridFMO
• CSF4 Deployed, Portal/Server set up
• Gfarm distributed CAMERA Data
• PRAGMA Institute Launched, First at
NCSA
• PRIME and PRIUS Successes
• Working Group Activities
Thailand
Taiwan
Korea
Challenge 1: How do we make the PRAGMA
Grid usable to the researchers –
in particular in our own working groups?
• Phase 0: Getting to know each other (Mar 02)
• Phase 1: Deciding to focus on routine use (Oct 03)
• Phase 2: Gaining experience and learning how to
technically do experiments (Sept 05)
• Phase 3: Run applications routinely?
– Barriers: Application software not on all machines
– Barriers: Manual installation of software (not scalable)
– Incentives: To using resources, people
• Would the Resources working group discuss this
PRAGMA 13 Logistics
• We will take the first breakout session at 11
am (rather than report back)
• Assignment will be to identify interactions
between working groups that should take
place
– For example: Biosciences Working Group and the
Resources want to talk.
– I can imagine others.
• We will then try to schedule the interactions
to allow time for both individual working
groups, and mixtures.
Challenge2 : How do we better utilize and drive
the use of optical networks for collaboration
Would the Telescience Group discuss this?
OptIPortal Cyber Mashup Environment for
Scientific Discovery
100 Megapixel walls allows detailed viewing of data
4K CineGrid
graphics streams
Multi-site HD
Video conferencing
Ultra high resolution imagery
Middleware for “Mashing Up” (Combining)
Information on OptIPortals
Maxine Brown
Electronic Visualization Laboratory, University of Illinois at Chicago
Challenge 3: How do we engage new
applications: Environmental Metagenomics and GEO?
Source: P Gilna, L Smarr, J Ventor
Chlorophyll
NASA Aqua-MODIS satellite data
Challenge 4: How do we grow the next generation of
culturally competent researchers and citizen?
• PRIME and PRIUS
• PRAGMA Institutes
• The issue is scalability
• “Peace and prosperity around the world
depend on increasing the capacity of people to
think and work on a global and intercultural
basis. As technology opens borders,
educational and professional exchange opens
minds.”[i]
Challenge 5: How are we, as a community,
with our technology, addressing critical
global problems?
NCHC SARS Task Force
PRAGMA 4 Program
Committee / request for help
(16, May, Fri)
1st Hospital Outbreak (Taipei
Municipal Ho-Pin Hospital)
100
90
2 AG nodes + H.323
X-ray image interface +
medical information +
high speed network
Chang Gung Hospital
outbreak (South)
Developers at the NCHC Access Grid
node test the SARS Grid network links
No. of ca s e s
80
70
60
50
40
Suggest in PRAGMA
4 Draft Agenda to
help SARS relief…(15,
Apr)
2 AG nodes + …
PRAGMA 4
30
S us pe cte d
P roba ble
20
10
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14, May:SARS AG\Task Force
Da te of ons e t
Source: Fang-Pang Lin
Global Challenges
• Global Climate Change (IPCC WG1) Physical
Science Basis
– “Warming of the climate system is unequivocal, as
is now evident from observations of increases in
global average air and ocean temperatures,
widespread melting of snow and ice, and rising
global average sea level”
• IPCC: Climate Change 2007: Impacts, Adaptation
and Vulnerability.
– Stress on ocean and coral
– Increasing human-induced pressures on
coastal areas
– Stress on food growth
– Increase infectious diseases
• Population growth (ISSE)
Global Population (millions)
8
6
3000
4
2000
Population
CO2
1000
2
Nitrogen
140
120
100
80
60
40
20
360
340
320
300
Atmospheric CO2 (ppm)
4000
160
-1
– Living beyond our means: Water, Fish,
– Mortgaging the future of our children
5000
380
180
Total Reactive N (Tg N y )
• Millennium Ecosystem Assessment
Global
Change
Global
'Stability'
Energy used (Mt)
– Stress energy consumption and food stuffs
10
6000
Energy
0
1860
1880
1900
1920
Year
1940
1960
1980
0
2000
0
280
Source: S. Collins, ISSE Report
Thank You
• Local Committee
– Patty Kobel and many more
• Demo Committee
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Putchong Uthayopas
Yoshio Tanaka
Peter Bajscy
Mason Katz
J Kern
Wilfred Li
Fang-Pang Lin
Ryosuke Nakamura
Tom Roney
Cindy Zheng
• Poster Committee
– Peter Bajcsy
– Habibah Wahab
• Program Committee
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Radha Nandkumar
David Abramson
Arun Agarwal
Peter Bajcsy
Maxine Brown
Mason Katz
Francis Lee
Fang-Pang Lin
Jim Myers
Kan Nan
Phil Papadopoulos
Satoshi Sekiguchi
Yoshio Tanaka
Whey-Fone Tsai
Putchong Uthayopas
Habibah Wahab
Cindy Zheng
PRAGMA Workshops
Steps to Progress
1.
2.
3.
4.
5.
6.
7.
March 2002 San Diego
July 2002 Seoul
January 2003 Fukuoka
June 2003 Melbourne
October 2003 Hsinchu
May 2004 Beijing
Sept 2004 San Diego
8. May 2005 Singapore
9. Oct 2005 Hyderabad
10. March 2006 Townsville
11. October 2006 Osaka
12. March 2007 Bangkok
13. Sept 2007 Urbana
Demo (2)
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X-SIGMA Demonstration
CSF4 Meta-Scheduler
Account management using GAMA and VOMS
Amber 8 on PRAGMA Gfarm Datagrid
Avian Flu Grid project
CSE-Online with PRAGMA and Thailand National Grid
3D High-Resolution GIS Taiwan Platform
Prompt satellite image processing on GEO Grid portal
Data Management at Kenting's Underwater Ecological
Observatory
• GEON: Networking Indian Geoscience Community through
iGEON
New Paradigm: Global Team Science
Integrating Expertise
Jilin U
Grid
Scheduler
CSF-4
CNIC
Avian Flu
Databases
Simulation
Natural
Compound
Library
UCSD/NBCR
Distributed
File System
Gfarm
Grid Computing
Molecular Dynamics
Comp.Bio.Pipeline
KISTI
Konkuk U
NTU
USM
AIST
U Tsukuba
Distributed
Computing
M*Grid
TSRI
U Hawaii
Metabolism &
Avian Flu
Mol.Dyn.
Autodock