HPWREN and International Collaborations

1
PRAGMA A Framework For Collaborations
Cindy Zheng Peter Arzberger Philip
Papadopoulos Mason Katz Pacific Rim Application
and Grid Middleware Assembly University of
California, San Diego http//www.pragma-grid.net
http//goc.pragma-grid.net
2
Overview

• PRAGMA
• Goal and approach
• Collaborations
• In testbed
• Applications and middleware
• With science and technology teams
• With other Grids
• GIN-OPS, Peer-grids
• In education and training
• PRIME, PRIUS, NBCR institute

3
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
4
Overview and ApproachProcess to Promote Routine
Use Team Science
Application-Driven Collaborations Applications Mid
dleware
Outcomes Improved middleware Broader Use New
Collaborations Transfer Tech. Standards Publicatio
ns New Knowledge Data Access Education
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PRAGMA Grid Testbed
JLU China
UZurich Switzerland
AIST OsakaU UTsukuba TITech Japan
NCSA USA
CNIC GUCAS China
AIST
KISTI Korea
BU USA
UUtah USA
SDSC USA
SDSC
NECTEC ThaiGrid Thailand
NECTEC ThaiGrid
ASGC NCHC Taiwan
UMC USA
CICESE Mexico
UoHyd India
CUHK HongKong
UNAM Mexico
MIMOS USM Malaysia
IOIT-HCM Vietnam
ASURC Costa Rica
APAC QUT Australia
BII IHPC NGO Singapore
UCN Chile
BESTGrid New Zealand
NGO
UChile Chile
MU Australia
31 Clusters from 27 institutions in 14
countries/regions (8 in preparation)
5 gfarm sites
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Applications and Middleware http//goc.pragma-gri
d.net/applications/default.html

• Real science applications pair and drive
  middleware development
• Achieve long-run and scientific results
• Open to applications of all scientific
  disciplines
• Climate simulation
• Savannah/Nimrod (MU, Australia)
• MM5/Mpich-Gx (CICESE, Mexico KISTI, Korea)
• Quantum-mechanics, quantum-chemistry
• TDDFT, QM-MD, FMO/Ninf-G (AIST, Japan)
• Genomics
• iGAP/Gfarm/CSF (UCSD, USA AIST, Japan JLU,
  China)
• HPM genomics (IOIT-HCM, Vietnam)
• mpiBlast/Mpich-G2 (ASGC, Taiwan)
• Organic chemistry
• Gamess-APBS/Nimrod (UZurich, Switzerland)
• Molecular simulation
• Siesta/Nimrod (UZurich, Switzerland MU,
  Australia)
• Amber/Rsh ( USM, Malaysia)
• Compute Science
• Load Balancer (VAST-HCM, Vietnam)

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Application/Middleware Collaborationshttp//wiki.
pragma-grid.net http//goc.pragma-grid.net

• Mutually beneficial
• Nimrod based Gamess-APBS
• Gamess-APBS UZurich, Switzerland
• Nimrod MU, Australia
• Mpich-Gx based MM5 and WRF
• MM5 and WRF CICESE, Mexico
• Mpich-Gx KISTI, Korea
• Test/develop Gfarm and CSF with iGAP
• Gfarm AIST, Japan
• CSF JLU, China
• iGAP UCSD, USA

8
Collaborations With Science and Technology Teams

• Grid security
• Naregi (Japan), APGrid, GAMA (SDSC, USA)
• Grid infrastructure
• Monitoring - SCMSWeb (ThaiGrid, Thailand)
• Accounting - MOGAS (NTU Singapore)
• Metascheduling - Community Scheduling Forum (JLU,
  China)
• Cyber-environment - CSE-Online (UUtah, USA)
• Rocks and middleware (SDSC, USA )
• Ninf-G, SCE, Gfarm, Bio, KRocks, Condor,
• Datagrid, sensor, network
• Gfarm-fuse (AIST, Japan)
• GEON data network
• GLEON sensor network
• OptIPuter
• High performance networked TDW
• Telescience

9
Source Elaine Liu, PRIME 2006
TDW/OptIPuter Example
Viewing _at_ UCSD
Controlling _at_ CNIC
10
Collaborations in BioScience

• Avian Flu Research Project
• UCSD, CNIC, JLU, Uni. Of Tskuba/AIST, University
  of Hawaii and Konkuk University
• EGEE Academia Sinica
• Biosciences Portal
• Collaboration between Osaka University,
  University of Queensland, JLU, UCSD.
• Involves PRIME, PRIUS and summer students from
  UCSD, Osaka and JLU.
• Metagenomics Research and Genome Informatics
• Bioinformatics, computational biology software
• Gfarm/CSF4, TskubaU/JLU, Japan/China
• With University of Wisconsin, UCSD, PRIME project

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GEON-iGEON-PRAGMA
www.geongrid.org

• GEON is a coalition among IT and Earth Science
  researchers with the goal of developing advanced
  information technologies to enable new modes of
  geosciences research
• GEON is developing technologies for information
  integration and knowledge discovery

• Internationalization of GEON iGEON
• PRAGMA
• Some sites already working on geoscience
  projects
• Building a datagrid
• Welcome geoscience applications
• Seeking collaboration in grid interoperation

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PRAGMA and GEON/iGEON collaboration

• Sharing data, software know-how, interoperate
  grids
• Geoscience workgroup established at PRAGMA11,
  joint conferences with PRAGMA
• GUCAS (China)
• Setup a GEON node in PRAGMA testbed
• UMC (USA) and GUCAS
• Preparing a GEON application to run in PRAGMA
  testbed
• CNIC (China)
• Is setting up a GEON data node in PRAGMA testbed
• UoHyd (India)
• has setup a GEON node, will join PRAGMA testbed
• AIST Geogrid (Japan) plan
• Share data with GEON
• Interoperate with PRAGMA testbed

13
Collaboration in Environmental Science

• GLEON
• A grassroots network of
• People lake scientists, engineers, information
  technology experts
• Institutions universities, national
  laboratories, agencies
• Programs PRAGMA, AS-Forest Biogeochemistry,US-LTE
  R, TERN, KING, EcoGrid, etc.
• Instruments
• Data
• Linked by a common purpose and cyberinfrastructure
  
• With a goal of understanding lake dynamics at
  local, regional, continental, and global scales

14
Collaborate in Publishing Research Results

• Some published papers in 2006
• Arzberger P, Papadopoulos P. PRAGMA Example of
  Grass-Roots Grid Promoting Collaborative EScience
  Teams. CTWatch. Vol 2, No. 1 Feb 2006.
  www.ctwatch.org/quarterly/articles/2006/02/pragmae
  xample-of-grass-roots-grid-promoting-collaborative
  e-science-teams
• Abramson D, Lynch A, Takemiya H, Tanimura Y, Date
  S, Nakamura H, Jeong K, Hwang S, Zhu J, Lu Z,
  Amoreira C, Baldridge K, Lee H, Wang C, Shih HL,
  Molina T, Li, W, Arzberger P. Deploying
  Scientific Applications on the PRAGMA Grid
  testbed Ways, Means and Lessons. IEEE/CCGRID
  International Workshop on Grid Computing, 2006,
  Singapore.
• Lee B-S, Tang M, Zhang J, Soon O Y, Zheng C,
  Arzberger P. Analysis of Jobs on a
  Multi-Organizational Grid Testbed. IEEE/CCGRID
  Intl Workshop on Grid Computing, 2006,
  Singapore.
• Zheng C, Abramson D, Arzberger P, Ayuub S,
  Enticott C, Garic S, Katz M, Kwak J, Lee B S,
  Papadopoulos P, Phatanapherom S, Sriprayoonsakul
  S, Tanaka Y, Tanimura Y, Tatebe O, Uthayopas P.
  The PRAGMA Testbed Building a Multi-Application
  International Grid. 2005 IEEE/CCGRID
  International Workshop on Grid Computing, 2006,
  Singapore.
• Li WW, Arzberger PW, Yeo CL, Ang L, Tatebe O,
  Sekiguchi S, Jeong K, Wuang S, Date S, Kwak JH.
  Proteome Analysis Using iGAP in Gfarm. The Second
  International Life Science Grid Workshop 2005,
  Grid Asia 2005, Singapore 2005.
• Wei X, Ding Z, Li W W, Tatebe O, Jiang J, et al.
  GDIA A Scalable Grid Infrastructure for Data
  Intensive Applications. IEEE Intl Conference on
  Hybrid Information Technology, ICHIT 2006, Cheju
  Island, Korea.
• Krishnan S, Baldridge K K, Greenberg J. P, Stearn
  B, Bhatia K. An End-to-End Web Services-Based
  Infrastructure for Biomedical Applications.
  Proceedings of Grid 2005, 6th IEEE/ACM Intl
  Workshop on Grid Computing, November 13-14, 2005,
  Seattle, WA, U.S.

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Grid Interoperation Now (GIN)http//forge.gridfor
um.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOp
s

• OGF GIN-OPS
• GIN testbed (February, 2006 on-going)
• TDDFT/Ninf-G (PRAGMA - AIST, Japan)
• PRAGMA, TeraGrid, OSG, NorduGrid EGEE
• Savanah fire simulation (PRAGMA - MU, Australia)
• PRAGMA, TeraGrid, OSG
• Multi-Grid monitoring
• SCMSWeb probe matrix (PRAGMA - ThaiGrid,
  Thailand)
• Common schema (PRAGMA, TeraGrid, EGEE, NorduGrid)

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Peer-grid Interoperation Experimentshttp//goc.pr
agma-grid.net/wiki/index.php/Main_PageGrid_Inter-
operations

• PRAGMA-gtTeraGrid (October, 2006 on-going)
• PRAGMA member runs application across both grids
• QM/MD/Ninf-G (AIST, Japan)
• Manual reservation, 7 sites in PRAGMA, 3 sites in
  TeraGrid
• OSGlt-gtPRAGMA (January, 2007 on-going)
• Members from both grids run applications across
  both grids
• Applications
• OSG
• GISolve
• spatial Interpolation
• UIowa, USA
• PRAGMA
• FMO/Ninf-G
• quantum Chemistry
• AIST, Japan

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OSG-PRAGMA Interoperation Experimenthttp//goc.pr
agma-grid.net/wiki/index.php/OSG-PRAGMA_Grid_Inter
operation_Experiments

• Resources
• OSG
• FermilabGrid
• PRAGMA
• SDSC, USA
• NECTEC, Thailand
• NGO, Singapore
• ThaiGrid, Thailand
• Process
• Jan 4, 2007, identify who and how
• Coordinator, application drivers, resource
  supporters
• Wiki, application, requirements
• Jan 25, 2007, initial VTC
• Goals, Q/A exchange
• Start working
• Email immediately issues, solutions
• Weekly status, email, wiki
• Status
• Feb 26 - March 1, started application runs
  successfully

• Learned
• Differences in grid environment effect users and
  applications
• Job submission
• Change RSL parameter
• Remove inter-node parallel execution
• Security policy
• Take work to setup access
• Account on gatekeeper node
• Large scale calculations are possible
• Middleware fault tolerance and flexible resource
  management is important

A set of jobs are processed on the VO, collected,
and updated for the next iteration.
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PRIME http//prime.ucsd.edu

• Providing UCSD undergraduate students
  international interdisciplinary research
  internships and Cultural experiences
• Preparing the global work place of the 21st
  century
• Built on top of PRAGMA RD network and activities
  for Undergraduate Research
• A Pilot Project for Global Engagement

• Summer research abroad
• Mentors from UCSD and host institutions
• Real science and practical projects
• Learning science, technology and culture
• Demos and talks
• Continuing research involvement thereafter

PRIME Class 2006
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PRIME 2006 (Thrid Year)Host Institutions and
Projects at a Glance

• CNIC, China
• Virtual Screening of Avian Influenza H5N1
  Neuraminidase and Hemagglutinin proteins against
  two libraries of ligands
• High-resolution astronomial visualization and
  visual collaboration environment
• MU, Australia
• Computational analysis of biological structures
  using GAMESS-APBS/Nimrod programs
• Develop efficient method for large scale virtual
  screening of ligands
• More stable ionic model of ventricular myocytes
• OsakaU, Japan
• Homology modeling of the protein kinases and
  binding site prediction
• Docking simulations of protein kinases and
  virtual screening of ligands for inhibitors
• Established networked Tile Display Wall
• NCHC, Taiwan
• implementing image-processing software for neural
  networks
• Develop software tools for earthquake
  experiments, monitoring and analysis

Prime Students 2006 Hosted by CNIC, China At Lao
She Tea House
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PRIUS - Pacific Rim International UniverSity
Based at Osaka University
http//prius.ics.es.osaka-u.ac.jp/en/index.html

• Establish a consistent educational program for
  graduate students.

• On-the-Job-training and education with PRAGMA

P.D Exchange prgm produces liquidity in human
resource
P.D
Long Abroad Internship Provide skill building
chances
Doc
Research Part
Educational Part
Short Abroad Internship Offer trial opportunities
M2
Lecture course Stimulate students ambitious
M1
Source Susumu Date, Osaka University
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PRIUS (First Year)

• Internship abroad
• UCSD, USA
• Develop QM/MM hybrid simulation program for
  protein research using OPAL
• NTU, Singapore
• Design/prototype a grid security monitoring
  system as an add-on to MOGAS
• QUT, Australia
• Develop a bioscience portal for PRAGMA
• NCHC, Taiwan
• Implement high-definition-quality streaming video
  over a high-speed network with various TDW
  technologies

• 10 International instructors
• All from PRAGMA members
• UCSD, USA
• NCHC, Taiwan
• NTU, Singapore
• QUT, MU, Australia
• Grid computing/applications
• Grid and web services
• Clustering tools
• Optical network computing
• Grid accounting systems
• Biomedical grid applications
• Economic and social impact of cyberinfrastructure
• Interaction with students

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Future Meeting

• 20 22 March 2007, Bangkok Thailand
• PRAGMA 12 Hosted by NECTEC and Thai National Grid
  Center
• 18 20 March 2007 GEOGrid Workshop
• Fall 2007, Urbana-Champaign USA
• PRAGMA 13 Hosted by NCSA
• Spring 2008, Hsinchu Taiwan
• PRAGMA 14 Hosted by NCHC
• Fall 2008, Penang Malaysia
• PRAGMA 15 Hosted by USM

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• PRAGMA is supported by the National Science
  Foundation (Grant No. INT-0216895, INT-0314015,
  OCI -0627026), and member institutions
• PRIME is supported by the National Science
  Foundation under NSF INT 04007508

Thank You
http//www.pragma-grid.net http//goc.pragma-grid.
net