Slide1 : PRAGMA Grid
A Multi-Application Route-Use Global Grid Cindy Zheng
PRAGMA Grid Coordinator
Pacific Rim Application and Grid Middleware Assembly
University of California, San Diego
San Diego Supercomputer Center
http://www.pragma-grid.net
http://goc.pragma-grid.net
Overview : Overview PRAGMA
Goals, Characteristics, Working groups, Workshops
PRAGMA Grid testbed
Goals, Characteristics, Resources
Applications
Application middleware
Infrastructure middleware
Benefit summary
Multi-Grid interoperation
Goals, Resources
Applications
Infrastructure testing matrix
Lessons learned
Forward
Slide3 : PRAGMA http://www.pragma-grid.net 2002 -
Goals
Open international organization
Grid applications, practical issues
Build international scientific collaborations
Members and community
28 institutional members, 11 countries
>38 inst. >14 countries are actively involved
Characteristics
No central funding, but mutual interests
Build friendship, trust, help, community
Do, act
Working groups
Bio, data, resources, telescience, geosciences, …
Semi-annual Workshops
The PRAGMA Steering Committee : The PRAGMA Steering Committee http://www.pragma-grid.net/steering_committee.htm
Pragma Grid testbed and Routine-basis Experiements : Pragma Grid testbed and Routine-basis Experiements 2004 -
Goal – make grid easier for scientists to use, by improving
middleware interoperability
Global grid usability and productivity
Method
For applications. Let applications drive
More organized testbed operation
Full-scale and integrated testing/research
Long application runs
Learn issues, develop/research/test solutions
Manners
Grass-roots
Voluntary, contribute of resources and work
long term, persistent
Inclusion: don’t have to be PRAGMA member or pacific rim
General science grid
Slide6 : PRAGMA Grid Resources
Slide7 : PRAGMA Grid Testbed AIST
OSAKAU
TITECH
Japan CNIC
GUCAS
China KISTI
Korea ASCC
NCHC
Taiwan UoHyd
India MU
Australia BII
IHPC
NGO
Singapore KU
NECTEC
Thailand NCSA
USA SDSC
USA CICESE
Mexico UNAM
Mexico UChile
Chile QUT
Australia UZurich
Switzerland JLU
China MIMOS
USM
Malaysia IOIT-HCM
Vietnam BU
USA UMC
USA
PRAGMA Grid Software Layers : PRAGMA Grid Software Layers
Applications http://goc.pragma-grid.net : Applications http://goc.pragma-grid.net Real science, multi-applications (11)
TDDFT: quantum-chemistry, AIST, Japan
Savannah: climate model, MU, Australia
MM5: climate model, CICESE, Mexico
QM-MD, FMO: quantum-mechanics, AIST, Japan
iGAP: genomics, UCSD, USA
HPM: genomics, IOIT-HCM, Vietnam
mpiBlast: genomics, ASCC, Taiwan
Gamess-APBS: organic chemistry, UZurich, Switzerland
Siesta: molecular simulation, UZurich, Switzerland
Amber: molecular simulation, USM, Malaysia
Learn
How to grid-enable, run
Application needs, issues
Grid Application Middleware : Grid Application Middleware Why grid application middleware
Enable applications to run on grid(s)
Make easier
Example grid application middleware development/testing
Ninf-G (AIST, Japan)
Nimrod/G (Monash University, Australia)
Mpich-Gx (KISTI, Korea)
Ninf-G http://ninf.apgrid.org : Ninf-G http://ninf.apgrid.org Developed by AIST, Japan
Support GridRPC model which will be a GGF standard
Integrated to NMI release 8 (first non-US software in NMI)
Ninf roll for Rocks 4.x is also available
3 applications ran in PRAGMA grid and 1 ran on GIN testbed (multi-grids)
TDDFT
QM/MD
FMO
Achieved long runs (1 week ~ 50 days)
Improved fault-tolerance (papers) - hang
Simplified deployment procedures
Speed-up development cycles
Nimrod/G http://ninf.apgrid.org : Nimrod/G http://ninf.apgrid.org Developed by Monash University, Australia
Supports large scale parameter sweeps on Grid infrastructure
Easy user interface - portal
3 applications ran in PRAGMA grid and 1 will run in GIN testbed (multi-grids)
Savanah climate simulation (MU)
GAMESS/APBS (UZurich)
Siesta (UZurich)
Achieved long runs (90 different scenarios of 6 weeks each
Improved fault-tolerance (innovate time_step)
Speed-up enhancements
Mpich-Gx http://www.moredream.org/mpich.htm : Mpich-Gx http://www.moredream.org/mpich.htm KISTI, Korea
Grid-enabled MPI, support
Private IP
Fault tolerance
Application run on KGrid
MM5
Climate simulation
CICESE, Mexico
Infrastructure Middleware : Infrastructure Middleware Why grid infrastructure middleware
Provide grid services
Make grid easier to use and manage
Example grid infrastructure middleware
Grid file system
Gfarm (AIST, Japan)
Grid monitoring system
SCMSWeb (Kasetsart University, Thailand)
Grid accounting system
MOGAS (Nanyang Technological University, Singapore)
Gfarm – Grid Virtual File System http://datafarm.apgrid.org/ : Gfarm – Grid Virtual File System http://datafarm.apgrid.org/ Developed by AIST, Japan
High performance, scalable grid file system
Support Linux, Solaris; also scp, gridftp, SMB
Meta-server, file replication, Gfarm-FUSE
Ease user/application setup, file sharing (CSA), fault tolerance
6 sites, 3786 GBytes, 1527 MB/sec (70 I/O nodes)
Tested with iGAP, large number of files, performance up >10x
SCMSWeb http://www.opensce.org/components/SCMSWeb : SCMSWeb http://www.opensce.org/components/SCMSWeb Developed by Kasetsart University, Thailand
Web-based monitoring system for clusters and grid
System usage, functional/performance metrics, job/queue status
Easy user interface, rapid support
Testing in PRAGMA grid, get user feedbacks and sites help
Speed-up development, enhancement, platform support expansion
Improve fault tolerance, functionalities, user interface
Popularize the software
GIN, common schema
Multi-organisation Grid Accounting System http://ntu-cg.ntu.edu.sg/pragma : Multi-organisation Grid Accounting System http://ntu-cg.ntu.edu.sg/pragma Developed by NTU, Singapore
Resource usage based on project/individual/organization
Daily, weekly, monthly, yearly
Pie charts and detail job logs
Metering and charging tool, easily customizable pricing system
Database and data analysis tools
Run on 17 sites in PRAGMA testbed
Improved interface to various globus and local schedulers
PRAGMA Grid Brings Together : PRAGMA Grid Brings Together People
Hands-on learning to make grid work
Software development
Heterogeneity and reality check
Check software Integration and interface both horizontally and vertically
User feedback steers better direction
Popularize grid software
Collaborations
Naregi-CA (AIST, Japan) and Gama (SDSC, USA) Integration
Rocks (SDSC, USA) and SCE (KU, Thailand), Ninf-G (AIST, Japan), Gfarm (AIST), KRocks (KISTI, Korea)
PRAGMA and NLANR
PRAGMA and GEON
PRAGMA testbed and sensor networks (NCHC, Taiwan; Binghamton University, USA)
… GAMA
Grid Interoperation Now (GIN) http://goc.pragma-grid.net/gin/default.html : Grid Interoperation Now (GIN) http://goc.pragma-grid.net/gin/default.html GIN testbed (started Feb. 2006)
PRAGMA, TeraGrid, EGEE, OSG,
NorduGrid
Applications
TDDFT/Ninf-G
Lead: Yoshio Tanaka, Yusuke Tanimura (AIST, Japan)
Deployed and run
PRAGMA - AIST, NCSA, SDSC
TeraGrid – ANL
Working on deployment to EGEE, OSG and NorduGrid
Savanah Study
Lead: Colin Enticott (MU, Australia)
Infrastructure testing matrix
Cindy Zheng (SDSC, USA) and Somsak Sriprayoonsakul (KU, Thailand)
Use SCMSWeb
Lessons Learned : Lessons Learned Differences among grids
Organization structures
Authentication (GSI, VOMS)
Job submission (GRAM, Gridftp)
Software stacks
Takes a lot of learning to understand
Takes a lot of work to interoperate
Resolved some problems (GSI-VOM, GT2-GT4)
Stimulated new initiatives (Cross grid monitoring)
Learned some from each other (Community Software Area)
Many more still yet to work on (File sharing, easy user access, direction and standards)
Forward : Forward More resources
More computational resources
GUCAS, China; UMC, USA; …
Add data resources (geo, atro, bio, …)
Add sensor network resources
NCHC, Taiwan; BU, USA; …
More applications
Geoscience (Mian Liu, Huai Zhang)
More and better grid middleware
Credential management systems (SDSC, USA; Naregi, Japan)
Portals (NCHC, Taiwan; QUT, Australia; …)
Meta-schedulers (AIST, Japan; IHPC, Singapore; …)
More grids interoperation
More grids
More applications
More collaboration on grid technology research and development
One Possible Collaboration with AIST : One Possible Collaboration with AIST
Collaborations with GSCAS and CNIC : Collaborations with GSCAS and CNIC GSCAS (Shi Yaolin, Huai Zhang), U Missouri (Mian Liu), UCSD (Chaitan Baru, Cindy Zheng), CNIC (Kai Nan)
Develop PRAGMA/iGEON Node at GSCAS
Develop initial parallel finite element codes
Run a geodynamics models on this cluster and then the PRAGMA testbed
Ensure user-friendly, Web interfaces to access and execute finite element codes developed by China on PRAGMA grid as well as TeraGrid
Collaborations with U Hyderabad : Collaborations with U Hyderabad Collaborators A. Agarwal, K.V. Subbarao (U Hyderabad) and Chaitan Baru (UCSD)
Establish GEON node at U Hyderabad
Experiment with sharing data
Register new datasets
Other Collaborations : Other Collaborations Exchanges:
Calit2
Students (PRIME)
GEON willing to support this OptIPuter
New Paradigm: Global Team Science : New Paradigm: Global Team Science U.Waikato
D.Hamilton
Models NCHC
F.P.Lin
Maintain YYL
Parallelize Codes U.Wisconsin
T.Kratz
Maintain Trout Bog
Lake Metabolism UCSD
F.Vernon, S.Peltier,
T.Fountain P.Arzberger
ROADNet, Telescience
Moore Fnd, PRAGMA NIGLAS
B.Q Qin
Maintain Taihu
Physical Limnology Kangwon U
B.Kim
Maintain Soyang
Public Policy
Thank You : Thank You Everyone is welcome to join us!
Either to build grid and/or
to run applications. zhengc@sdsc.edu
http://goc.pragma-grid.net