ISLAND INSTITUTE S ALTWATER C ONNECTIONS W INTER A SSEMBLY J ANUARY 2013.
OSG All Hands, 3/5/2007 Cindy Zheng Peter Arzberger Philip Papadopoulos Mason Katz P acific R im A...
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Transcript of OSG All Hands, 3/5/2007 Cindy Zheng Peter Arzberger Philip Papadopoulos Mason Katz P acific R im A...
OSG All Hands, 3/5/2007
Cindy ZhengPeter Arzberger
Philip PapadopoulosMason Katz
Pacific Rim Application and Grid Middleware AssemblyUniversity of California, San Diego
http://www.pragma-grid.nethttp://goc.pragma-grid.net
PRAGMA: A Framework For Collaborations
OSG All Hands, 3/5/2007
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
OSG All Hands, 3/5/2007http://www.pragma-grid.net
Overarching GoalsPRAGMA
“A Practical Collaborative Framework”.
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
OSG All Hands, 3/5/2007
Overview and ApproachProcess to Promote Routine Use Team Science
Application-Driven CollaborationsApplications Middleware
Routine Use Lab/TestbedTesting Applications
Building Grid and GOC
Multiway DisseminationKey Middleware
Workshops and Organization
Information Exchange
Planning and Review
New Collaborations
New Members
Expand Users
Expand Impact
Outcomes
Improved middlewareBroader Use
New CollaborationsTransfer Tech.
StandardsPublications
New KnowledgeData AccessEducation
OSG All Hands, 3/5/2007
PRAGMA Grid TestbedPRAGMA Grid Testbed
31 Clusters from 27 institutions in 14 countries/regions (+8 in preparation)
UZurichSwitzerland
NECTECThaiGridThailand
UoHydIndia
MIMOSUSMMalaysia
CUHKHongKong
ASGCNCHCTaiwan
IOIT-HCMVietnam
AISTOsakaUUTsukubaTITechJapan
BIIIHPCNGOSingapore MU
Australia
APACQUTAustralia
KISTIKorea
JLUChina
SDSCUSA
CICESEMexico
UNAMMexico
UCNChile
UChileChile
UMCUSA
UUtahUSA
NCSAUSA BU
USA
ASURCCosta Rica
BESTGridNew Zealand
CNICGUCASChina
AIST
SDSC
NGO
NECTECThaiGrid
5 gfarm sites
OSG All Hands, 3/5/2007
Applications and Middleware http://goc.pragma-grid.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)• GriddLeS (MU, Australia)
OSG All Hands, 3/5/2007
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
Application/Middleware Collaborationshttp://wiki.pragma-grid.net http://goc.pragma-grid.net
OSG All Hands, 3/5/2007
• 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, K*Rocks, Condor, …• Datagrid, sensor, network
– Gfarm-fuse (AIST, Japan)– GEON data network– GLEON sensor network– OptIPuter
• High performance networked TDW• Telescience
Collaborations With Science and Technology Teams
OSG All Hands, 3/5/2007
Controlling @ CNIC Viewing @ UCSD
TDW/OptIPuter ExampleSource: Elaine Liu, PRIME 2006
OSG All Hands, 3/5/2007
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
OSG All Hands, 3/5/2007
GEON-iGEON-PRAGMA
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
www.geongrid.org
Internationalization of GEON – iGEON PRAGMA
Some sites already working on geoscience projects Building a datagrid Welcome geoscience applications Seeking collaboration in grid interoperation
OSG All Hands, 3/5/2007
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
OSG All Hands, 3/5/2007
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-LTER, 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
OSG All Hands, 3/5/2007
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/pragmaexample-of-grass-roots-grid-promoting-collaborativee-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 Int’l 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 Int’l 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 Int’l Workshop on Grid Computing, November 13-14, 2005, Seattle, WA, U.S.
• …
OSG All Hands, 3/5/2007
Grid Interoperation Now (GIN)http://forge.gridforum.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOps
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)
OSG All Hands, 3/5/2007
• PRAGMA->TeraGrid (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
• OSG<->PRAGMA (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
Peer-grid Interoperation Experimentshttp://goc.pragma-grid.net/wiki/index.php/Main_Page#Grid_Inter-operations
OSG All Hands, 3/5/2007
OSG-PRAGMA Interoperation Experimenthttp://goc.pragma-grid.net/wiki/index.php/OSG-PRAGMA_Grid_Interoperation_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
A set of jobs are processed on the VO, collected, and updated for the next iteration.
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
OSG All Hands, 3/5/2007
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 R&D network and activities for
Undergraduate Research• A Pilot Project for Global Engagement
PRIME Class 2006
• Summer research abroad• Mentors from UCSD and
host institutions• Real science and practical
projects• Learning science,
technology and culture• Demo’s and talks• Continuing research
involvement thereafter
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 analysisPrime Students 2006Prime Students 2006Hosted by CNIC, China Hosted by CNIC, China At Lao She Tea HouseAt Lao She Tea House
OSG All Hands, 3/5/2007
PRIUS - Pacific Rim International UniverSity Based at Osaka University
• Establish a consistent educational program for graduate students.
• On-the-Job-training and education with PRAGMA
Lecture course:Stimulate students’ ambitious
Short Abroad Internship:Offer trial opportunities
Long Abroad Internship:Provide skill building chances
M1
M2
Doc
P.D Exchange prgm: produces liquidity in human resource
P.D
Educational Part
Research Part
Source: Susumu Date, Osaka University
http://prius.ics.es.osaka-u.ac.jp/en/index.html
OSG All Hands, 3/5/2007
PRIUS (First Year)
• 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
• 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
OSG All Hands, 3/5/2007
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
OSG All Hands, 3/5/2007
http://www.pragma-grid.nethttp://goc.pragma-grid.net
Thank You
• 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