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Second PRAGMA Institute, 12/3/2007 Cindy Zheng, David Abramson, Peter Arzberger, Shahaan Ayyub, Colin Enticott, Slavisa Garic, Wojtek Goscinski, Mason J. Katz, Bu Sung Lee, Phil M. Papadopoulos, Sugree Phatanapherom, Somsak Sriprayoonsakul, Yoshio Tanaka, Yusuke Tanimura, Osamu Tatebe, Putchong Uthayopas and the whole PRAGMA Grid team Pacific Rim Application and Grid Middleware Assembly http://www.pragma-grid.net http://goc.pragma-grid.net PRAGMA Grid – Lessons Learned

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PRAGMA Grid – Lessons Learned. Cindy Zheng, David Abramson, Peter Arzberger, Shahaan Ayyub, Colin Enticott, Slavisa Garic, Wojtek Goscinski, Mason J. Katz, - PowerPoint PPT Presentation

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Page 1: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Cindy Zheng, David Abramson, Peter Arzberger, Shahaan Ayyub, Colin Enticott, Slavisa Garic, Wojtek Goscinski, Mason J. Katz, Bu Sung Lee, Phil M. Papadopoulos, Sugree Phatanapherom, Somsak Sriprayoonsakul, Yoshio Tanaka, Yusuke Tanimura,

Osamu Tatebe, Putchong Uthayopasand the whole

PRAGMA Grid team

Pacific Rim Application and Grid Middleware Assemblyhttp://www.pragma-grid.nethttp://goc.pragma-grid.net

PRAGMA Grid – Lessons Learned

Page 2: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Overview• PRAGMA• PRAGMA Grid

– People– Hardware– Software– Operations

• Grid Applications• Grid Middleware

– Security– Infrastructure– Services

• Education Grid• Collaborations/Integrations• Grid Interoperations

Heterogeneity People

CollaborationsIntegrations

Lessons learned

Page 3: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

http://www.pragma-grid.net

Overarching Goals

PRAGMA“A Practical Collaborative Framework”

People and applications

Strengthen Existing and Establish New Collaborations

Work with Science Teams to Advance Grid Technologies and Improve the

Underlying InfrastructureIn the Pacific Rim and Globally

Page 4: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

PRAGMA Member InstitutionsPRAGMA Member Institutions

KUNECTECTNGCThailand

UoHydIndia

MIMOSUSMMalaysia

ASGCCNCHCTaiwan

AISTCCSCMCNARCOsakaUTITechJapan

BIIIHPCNGOSingapore

MUAustralia

APACAustralia

JLUChina

CalIT2CRBSSDSCUCSDUSA CICESE

Mexico

NCSAStarLightTransPAC2USA

CNICChina

CRAYPNWGUSA

KBSIKISTIKonkukKorea

APANJapan

http://www.pragma-grid.net

33 institutions from 12 countries/regions Founded 2002Supported by Members

UUtahUSA

BeSTGRIDNew Zealand

Page 5: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

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

Page 6: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

PRAGMA Working Groups

• Bioscience• Telescience• Geo-science• Resources and data

–Grid middleware interoperability–Global grid usability and productivity

PRAGMA Grid effort is led by resources and data working group, but rely on collaborations and contributions among all working groups.

Page 7: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

PRAGMA GridPRAGMA Grid

32 institutions in 16 countries/regions, 27 compute sites, 14 Gfarm sites (+ 6 in preparation)

UZHSwitzerland

NECTECThaiGridThailand

UoHydIndia

MIMOSUSMMalaysia

CUHKHongKong

ASGCNCHCTaiwan

HCMUTIOIT-HCMVietnam

AISTOsakaUUTsukubaTITechJapan

BIIIHPCNGONTUSingapore

MUAustralia

APACQUTAustralia

KISTIKorea

JLUChina

SDSCUSA

CICESEMexico

UNAMMexico

UCNChile

UChileChile

UUtahUSA

NCSAUSA BU

USA

CeNAT-ITCRCosta Rica

BESTGridNew Zealand

CNICGUCASChina

LZUChina UPRM

Puerto Rico

AIST

SDSC

NGO

NECTECThaiGrid

ASGC

CNICGUCAS

MIMOS

NCSA

LZU

IOIT-HCM

CUHK

UZH

14 gfarm sites

Page 8: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

PRAGMA Grid Members and Teamhttp://goc.pragma-grid.net/wiki/index.php/Site_status_and_tasks

• Sites– 23 sites from PRAGMA member institutions– 15 sites from Non-PRAGMA member institutions– 27 sites contributed compute clusters

• Team members– 170 and growing– one management contact / site– 1~3 technical support contact / site– 1~4 application drivers / application– 1~5/Middleware development teams

Page 9: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

PRAGMA Grid Compute Resourceshttp://goc.pragma-grid.net/pragma-doc/computegrid.html

Page 10: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Characteristics of PRAGMA Grid• Grass-root

– Voluntary contribution– Open (PRAGMA member or not, pacific rim or not)– Long-term collaborative working experiment

• Heterogeneous– Funding– No uniform infrastructure management– Variety of sciences and applications– Site policies, system and network environments

• Realistically tough – Good for development, collaborations, integrations and

testing

Page 11: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

PRAGMA Grid Software Layershttp://goc.pragma-grid.net/pragma-doc/userguide/join.html

Local job scheduler (require one)

Globus (required)Application Middleware

Applications

Infrastructure Middleware

SGE PBS LSF SQMS …

Ninf-G Nimrod/G Mpich-GX … Gfarm SCMSWeb MOGASCSF

Phylogenetic …FMO CSTFTSavannah MM5 AMBERSiesta

Page 12: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

PRAGMA Grid Operations

Page 13: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

One of the major lessons from PRAGMA Grid, that everybody has

noticed and would agree– “You have to Grid People before

you can Grid machines” 

Rajesh ChhabraAustralia

Page 14: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Grid Operationhttp://goc.pragma-grid.net, http://wiki.pragma-grid.net

• Develop and maintain mutual beneficial and happy relationships among all people involved– Geographies, time-zones, languages– Funding, chain-of-command, priorities– Mutual benefit, consensus, active leadership– Coordinator, site contacts

• Collaboration tools– Mailing lists, VTCs, Skype, semi-annual workshops – Grid Operation Center (GOC)– Wiki, all sites and application, middleware teams collaborate

• Heterogeneity– Tolerate, technology, overcome and take advantage– Software inventory instead of software stack– Many sub-grids for applications– Recommendation instead of requirements– Software license (Amber grid-wide license)

Page 15: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Create New Ways To Operate http://goc.pragma-grid.net, http://wiki.pragma-grid.net

• Lack precedence• Everyone contributes ideas, suggestions• Evolving and improving over time • Everyone document and update (wiki)

– Create new procedures• New site setup to join PRAGMA Grid

http://goc.pragma-grid.net/pragma-doc/userguide/join.html• New user/application to run in PRAGMA grid

http://goc.pragma-grid.net/pragma-doc/userguide/pragma_user_guide.html

– Tabulate information• Application pages, site pages, resources tables, status pages

– Publish instructions• Software deployment procedures, tools

Page 16: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Application Driven

Page 17: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Applications and Middleware http://goc.pragma-grid.net/applications/default.html

• Real science applications paired with and drive middleware development

• Open to applications of all scientific disciplines• Achieve long-run and scientific results• ~30 applications in 3 years:

– 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 and meta-genomics• iGAP/Gfarm/CSF (UCSD, USA; AIST, Japan; JLU, China)• HPM: genomics (IOIT-HCM, Vietnam)• mpiBlast/Mpich-G2 (ASGC, Taiwan)• Phylogenetic/Gfarm/CFS (UWisc and UCSD, USA)

– Computational chemistry and fluid dynamics• CSE-Online (UUtah, USA)• e-AIRS (KISTI, Korea)• Gamess-APBS/Nimrod (UZurich, Switzerland)

– Molecular simulation• Siesta/Nimrod (UZurich, Switzerland; MU, Australia)• Amber/Gfarm ( USM, Malaysia; AIST, Japan)

– Environmental Science• CSTFT/Ninf-G (UPRM, Puerto Rico)

– Computer Science• Load Balancer (VAST-HCM, Vietnam)• GriddLeS (MU, Australia)

Page 18: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

• PRAGMA grid and its heterogeneous environment is great for– Testing– Collaborating– Integrating – Sharing

• Not easy– Middleware needs improvements

• Work in heterogeneous environment• Fault tolerance

– Need user friendly portals and services• Automate and integrate

– Information collections (grid monitoring, workflow)– Decisions and executions (scheduling)– Domain specific easy user interfaces (portals, CE

tools)– …

Lessons Learned From Running Applications

Page 19: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Grid Middleware

Page 20: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Ninf-G http://ninf.apgrid.org

• Developed by AIST, Japan• Based on GridRPC model• Support parallel computing • Integrated to NMI release 8 (first non-US software in NMI)• Integrate with Rocks• OGF standard• 4 applications ran in PRAGMA grid, 2 ran across multi-grid

– TDDFT– QM/MD– FMO– CSTFT (UPRM)

• Achieved long runs (50 days)• Improved fault-tolerance• Simplified deployment procedures• Speed-up development cycles

Page 21: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Nimrod/Ghttp://www.csse.monash.edu.au/~davida/nimrod

• Developed by Monash University (MU), Australia• Supports large scale parameter sweeps on Grid infrastructure• Easy user interface – Nimrod portals

– MU, Australia– UZurich, Switzerland– UCSD, USA

• 3 applications ran in PRAGMA grid and 1 runs in multi-grids– Savanah climate simulation (MU, Australia))– GAMESS/APBS (UZurich, Switzerland)– Siesta (UZurich, Switzerland)– Structure biology (MU, Australia)

• Developed interface to Unicore• Achieved long runs (90 different scenarios of 6 weeks each• Improved fault-tolerance (innovate time_step)• Enhancements in data and storage handling

Job 1 Job 2 Job 3Job 4 Job 5 Job 6Job 7 Job 8 Job 9Job 10Job 11Job 12Job 13Job 14Job 15Job 16Job 17Job 18

Description of ParametersPLAN FILE

Page 22: PRAGMA Grid – Lessons Learned

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Mpich-Gxhttp://www.moredream.org/mpich.htm

• Mpich-GX– Korea Institute of Science and Technology

Information (KISTI), Korea– Based on Mpich-g2– Grid-enabled MPI, support

• Private IP• Fault tolerance

• MM5 and WRF – CICESE, Mexico– Medium scale atmospheric simulation model

• Experiment– KGrid– WRF work well with MPICH-GX– MM5 experienced scaling problems with MPICH-GX

when use more than 24 processors in a cluster– Functionality of the private IP is usable– Performance of the private IP is reasonable

Page 23: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

MM5-WRF/Mpich-GX Experiment

pluto

eolo

Hurricane Marty Simulation

Santana Winds Simulation

output

CICESE Ensenada

USA

MéxicoSDSC

Private IP support

Fault Tolerance support

Mpich-GX

KGrid

Page 24: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Education Gridhttp://prime.ucsd.edu http://prius.ics.es.osaka-u.ac.jp/en/index.html

PRIME - Pacific Rim Undergraduate Experiences, providing UCSD undergraduate students international interdisciplinary research internships and Cultural experiences, in collaboration with PRAGMA since 2004. PRIUS - Pacific Rim International UniverSity, provide Osaka University students expert lectures and internship abroad, in collaboration with PRAGMA since 2005

Sample middleware projects– MOGAS– Grid security analysis

Sample applications ran in PRAGMA grid this year:– 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

Page 25: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Science

Technologies

Collaborations

Integrations

Page 26: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

PRAGMA is a great model and needs to be emulated. Has helped weaken barriers between different research

groups across different continents and allowed people to trust and collaborate

rather than compete.

Arun AgarwalUoHyd, India

Page 27: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

• Grid security– Naregi (Japan), APGrid, GAMA (SDSC, USA)

• Grid infrastructure– Monitoring - SCMSWeb (ThaiGrid, Thailand)– Accounting - MOGAS (NTU Singapore)– Metascheduling - Community Scheduler

Framework (JLU, China)– Cyber-environment - CSE-Online (UUtah,

USA)– Rocks and middleware (SDSC, USA; …)

• Ninf-G, SCE, Gfarm, Bio, K*Rocks, Condor, …• Science, datagrid, sensor, network

– Biosciences – Avian Flu, portal, …– Gfarm-fuse (AIST, Japan)– GEON data network– GLEON sensor network– OptIPuter

• High performance networked TDW• Telescience

Collaborations With Science and Technology Teams

Page 28: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Grid Security• Trust in PRAGMA grid,

http://goc.pragma-grid.net/pragma-doc/certificates.html– IGTF distribution– Non-IGTF distribution (trust all PRAGMA Grid sites)

• APGrid PMA– One of three IGTF founding PMAs– Many PRAGMA grid sites are members– PRAGMA CA

• Naregi-CA– AIST, UCSD, UChile, UoHyd, UPRM

• PRAGMA CA (experimental and production)– Based on Naregi-CA– Catch-all CA for PRAGMA– Production CA is IGTF compliant

• MyProxy and VOMS services– APAC

• Work with GAMA– Integrate with Naregi-CA (Naregi, UCSD)– Integration with VOMS (AIST)– Add servelet for account management (UChile)

Lessons learned • Leverage resources,

setups and expertise• Balance and consider

both security and easy access and use

• Get more user communities involved with grid security

Page 29: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Gfarm Grid File Systemhttp://datafarm.apgrid.org

• AIST, UTsukuba, Open source development at SourceForge.net• Grid file system that Federates storage of each site• Meta-server keeps track of file copies and locations• Can be mounted from cluster nodes and clients (GfarmFS-FUSE)• Parallel I/O, near site copy for scalable performance• Replication for fault tolerance• Use GSI authentication• Easy application deployment, file sharing

Page 30: PRAGMA Grid – Lessons Learned

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PRAGMA Gfarm Datagridhttp://goc.pragma-grid.net/pragma-doc/datagrid.html

- Compute Cluster

Page 31: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Testing with applications• Igap (Gfarm, Japan, UCSD, USA; JLU, China)

– Huge number of small files– High meta-data access overhead– Meta-data cache server– Dramatic improvements (44sec -> 3.54sec)

• AMBER (USM, Malaysia; Gfarm, Japan)– Remote Gfarm meta-server– Meta-server is bottle-neck– File sharing permission, security– 2.0 improved performance– Use as a shared storage only

Version 1.4 works well in local or regional grid• GeoGrid, Japan• CLGrid, ChileIntegration• SCMSWeb (ThaiGrid, Thailand)• Rocks (SDSC, USA; UZH, Switzerland)

Develop and Test GfarmFS-FUSE in PRAGMA Gridhttp://goc.pragma-grid.net/wiki/index.php/Resources_and_Data

Page 32: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

SCMSWebhttp://www.opensce.org/components/SCMSWeb

• Developed by Kasetsart University and ThaiGrid• Web-based real-time grid monitoring system

– System usage, Job/queue status– Probe – Globus authentication, job submission, gridftp,

Gfarm access, …– Network bandwidth measurements with Iperf– PRAGMA grid geo map

• Support Linux, Solaris. Good meta-view, easy user interface, excellent user support

• Develop and test in PRAGMA grid– Deployed in 27 sites, improve scalability and

performance– Sites help with porting to ia64 and Solaris– Demands push fast expansion of functionalities

• More regional/national grids learned and adopted

Page 33: PRAGMA Grid – Lessons Learned

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SCMSWeb Collaborations and Integrations• Grid Interoperation Now (GIN, OGF)

http://forge.gridforum.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOps – Worked with PRAGMA grid, TeraGrid, OSG, NorduGrid and EGEE on GIN testbed

monitoring http://goc.pragma-grid.net/cgi-bin/scmsweb/probe.cgi, added probes to handle various grid service configurations/tests.

– Worked with CERN and Implemented a XML-> LDIF translator for GIN geo map http://maps.google.com/maps?q=http://lfield.home.cern.ch/lfield/gin.kml

– Worked with many grid monitor software developers on a common schema for cross-grid monitoring http://wiki.pragma-grid.net/index.php?title=GIN_%28Grid_Inter-operation_Now%29_Monitoring

• Software integration and interoperations– Rocks – SCE roll– MOGAS – grid accounting– Condor, CSF, … – provide resource info

• Things are being worked on and planned– Data federator for grid applications

• Provide site software information• Standardize data extractions and formats• Improve data storage with RDBMS

– Interoperate with other monitoring software• Ganglia support

Page 34: PRAGMA Grid – Lessons Learned

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MOGAShttp://ntu-cg.ntu.edu.sg/pragma/index.jsp

• Multi-Organization Grid Accounting System (MOGAS)– Lead by NanYang University, funded by National Grid Office in Singapore– Build on globus core (gridftp, GRAM, GSI) – Support GT2,3,4; SGE, PBS– Job/user/cluster/OU/grid levels usages; job logs; metering and charging tools

• Develop and test in PRAGMA grid– Deployed on 14 sites: different GT versions, job schedulers, GRAM scripts,

security policies– Feedbacks, improve, automate deployment procedure– Decentralized servers and better database to improve scalability and

performance– Collaborations and integrations with applications and other middleware teams

push the development of easy database interface

Page 35: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

• Community Scheduler Framework, v4 – meta-scheduler– Developed by Jilin University, China– Grid services host in GT4, WSRF compliant, execution Component in Globus

Toolkit 4– Open Source, http://sourceforge.net/projects/gcsf– Support GT2&4, LSF, PBS, SGE, Condor– Easy user interface - portal

• Testing and collaborating in PRAGMA– Testing with application iGAP (UCSD, AIST, KISTI, …) – Collaborate and integrate with Gfarm on data staging (AIST, Japan)– Setup a CSF server and portal (SDSC, USA)– Collaborate/integrate with SCMSWeb for resource information (Thaigrid, Thailand)– Leverage resources and global grid testing environment

CSF4http://goc.pragma-grid.net/wiki/index.php/CSF_server_and_portal

Page 36: PRAGMA Grid – Lessons Learned

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Computational Science & Engineering Onlinehttp://cse-online.net

• Developed by University of Utah, USA (Thanh N. Truong)• Desktop tool, user friendly interface enables seamless access to

remote data, tools and grid computing resources• Currently support computational Chemistry• Can be customized for other domain science• Developed interface to TeraGrid• Collaborate with ThaiGrid as case study

– Used for Computational workshop– Extend grid access to portal architecture– Improved security

• Working on interface PRAGMA grid– Heterogeneity

Quantum Chemistry

Nano-materialsDrug Design

Page 37: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Collaborations with OptIPuter, GLIF and CAMERAhttp://www.optiputer.net

• OptIPuter (Optical networking, Internet Protocol, computer storage, processing and visualization technologies)– Infrastructure that will tightly couple computational resources over

parallel optical networks using the IP communication mechanism– central architectural element is optical networking, not computers – enable scientists who are generating terabytes and petabytes of

data to interactively visualize, analyze, and correlate their data from multiple storage sites connected to optical networks

• Rocks/SAGE VIS-roll (SDSC)• Networked Tile Display Walls (TDW)

– Low cost– For research collaboration– For remote education and conferencing– Deployed at many PRAGMA grid sites

Page 38: PRAGMA Grid – Lessons Learned

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Build a Rocks / SAGE OptIPortal

NCMIR@UCSD SIO@UCSD

UIC

Calit2@UCI

KISTI

NCSA & TRECC

Calit2@UCSD

AIST UZurich CNIC

NCHC

Osaka U

Page 39: PRAGMA Grid – Lessons Learned

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Global Lambda Integrated Facility (GLIF)http://www.glif.is

Visualization courtesy of Bob Patterson, NCSA.

– Map to many PRAGMA grid sites

– PRAGMA grid use GLIF to solve grid application bandwidth problem

Page 40: PRAGMA Grid – Lessons Learned

Second PRAGMA Institute, 12/3/2007

Intergrate CAMERA and PRAGMA Grid Microbial Metagenomicist Userbase

Over 1300 Registered Users From 48 Countries

Page 41: PRAGMA Grid – Lessons Learned

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Calit2/PRAGMA/CAMERA/LambdaGrid Collaborations

USA 761China 24Australia 20India 15Mexico 14J apan 14Chile* 6Switzerland* 5Taiwan 4Singapore 3New Zealand* 2Malaysia 2Korea 1Vietnam* 0Thailand 0Costa Rica* 0

• Add CAMERA Server to PRAGMA Grid Testbed– Ad hoc Supercomputing– NIMROD?– New Bioinformatics Apps

• Set up PRAGMA OptIPortal LambdaGrid for several PRAGMA Sites– KISTI, Konkuk U (Korea)– AIST, Osaka U (Japan)– CNIC (China)– NCHC (Taiwan)– APAC, UMelbourne,

Monash U, U Queensland (Australia)

– CICESE (Mexico)– UZurich (Switzerland)– Plus Other Volunteers!Source: Paul Gilna,

Kayo Arima, Calit2

PRAGMA Countries with CAMERA Registered Users

Page 42: PRAGMA Grid – Lessons Learned

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Grid Interoperation

Page 43: PRAGMA Grid – Lessons Learned

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• Open Grid Forum and GIN• GIN-OPS (lead by PRAGMA)• GIN testbed (February, 2006 – On

going)– One or more clusters from each grid– Still part of each production grid– Running real science applications– Explore interoperation issues– Develop solutions– Provide insight to standardization

effort• Application driven

– TDDFT/Ninf-G (PRAGMA - AIST, Japan)

• PRAGMA, TeraGrid, OSG, NorduGrid; EGEE

– Savanah fire simulation (PRAGMA – Monash University, Australia)

• PRAGMA, TeraGrid, OSG

Grid Interoperation Now (GIN)http://forge.gridforum.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOps

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• Software interface and integration– Ninf-G (AIST/PRAGMA) - NorduGrid– Nimrod/G (MU-PRIME/PRAGMA) – Unicore– SCMSWeb (ThaiGrid/PRAGMA) – Condor (UWisc/OSG)– SCMSWeb (ThaiGrid/PRAGMA) – BDII (CERN)– VDT (OSG) and Rocks (SDSC/PRAGMA) integration

• Multi-Grid monitoring– Lead by ThaiGrid/PRAGMA– SCMSWeb probe matrix (PRAGMA - ThaiGrid, Thailand)– Common schema (http://goc.pragma-grid.net/wiki/index.php?title=GIN_

%28Grid_Inter-operation_Now%29_Monitoring)• PRAGMA – SCMSWeb, MOGAS• TeraGrid – Globus Gt4.0.1, Ganglia, NAGIOS• EGEE – MonAlisa• NorduGrid/ARC – NorduGrid/MDS2, NorduGrid/Grid Monitor

Grid Interoperation Now (GIN)http://forge.gridforum.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOps

Page 46: PRAGMA Grid – Lessons Learned

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• Different from GIN testbed– More resources and support from each grid– Either uni-directional or bi-directional application run– Long run to achieve scientific results

• OSG<->PRAGMA (January, 2007 – on-going)– How

• Each grid identify management, application drivers, resources supporters

• All participants document application requirements, meetings, issues, solutions, status, results, … at wiki.pragma-grid.net

– Resources• OSG – FermilabGrid, will add UWisc• PRAGMA grid - any sites application driver choose to use

– Applications• OSG – GISolve, spatial Interpolation (UIowa, USA)• PRAGMA

– FMO/Ninf-G, quantum Chemistry (AIST, Japan) – completed– Structure biology (MU, Australia) – start soon

Peer-grid Interoperation Experimentshttp://goc.pragma-grid.net/wiki/index.php/Main_Page#Grid_Inter-operations

Page 47: PRAGMA Grid – Lessons Learned

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OSG-PRAGMA Grid Interoperation Experimentshttp://goc.pragma-grid.net/wiki/index.php/Main_Page#Grid_Inter-operations

• More resources and support from each grid, but no special arrangements

• Application long-run– GridFMO/Ninf-G – Large scale quantum Chemistry (Tsutomo Ikegami,

AIST, Japan)– 240 CPUs from OSG and PRAGMA grid, 10 days x 7 calculations– Fault-tolerance enabled long-run– Meaningful and usable scientific results

Page 48: PRAGMA Grid – Lessons Learned

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• Start a series of three workshops– First – March~April 2008

• Organized by UZurich• Swiss Grid, European Federated Grid

(Euro-Grid), and PRAGMA• Goal

– Inform and learn from each other– Seek ways to collaborate

• Collaboration work started summer 2007– Nimrod interface to UNICORE

PRAGMA Summit

Page 49: PRAGMA Grid – Lessons Learned

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Lessons Learned From Grid Interoperation http://forge.gridforum.org/sf/wiki/do/viewPage/projects.gin/wiki/GinOps

• Grid interoperation make large scale calculations possible• Differences among grids provide learning, collaboration and integration

opportunities– IGTF, VOMS (GIN)– Common Software Area (TeraGrid)– Ninf-G – NorduGrid– Nimrod/G – Unicore– SCMSWeb – Condor– SCMSWeb – BDII– SCMSWeb probe matrix for GIN testbed monitoring– Common schema among many grid monitoring software– VDT (OSG) and Rocks (SDSC/PRAGMA) integration

• Differences in grid environment are source of difficulties for users and applications

– Different user access setup procedure - take extra effort– Different job submission protocols

• GRAM, Sandbox, gridftp, modified GRAM, …• One-to-one interface - is it scalable? Possible standards?

• Middleware fault tolerance and flexible resource management is important– Cope with unfamiliar fault conditions, lack of parallel computation support, …

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Collaborate in Publishing Research Results

Some published papers in 2007:• Amaro, RE, Minh DDL, Cheng LS, Lindstrom, WM Jr, Olson AJ, Lin JH, Li WW, and McCammon JA. Remarkable

Loop Flexibility in Avian Influenza N1 and Its Implications for Antiviral Drug Design . J. AM. CHEM. SOC. 2007, 129, 7764-7765 (PRIME)

• Choi Y, Jung S, Kim D, Lee J, Jeong K, Lim SB, Heo D, Hwang S, and Byeon OH."Glyco-MGrid: A Collaborative Molecular Simulation Grid for e-Glycomics," in 3rd IEEE International Conference on e-Science and Grid Computing, Banglore, India, 2007. Accepted.

• Ding Z, Wei W, Luo Y, Ma D, Arzberger PW, and Li WW, "Customized Plug-in Modules in Metascheduler CSF4 for Life Sciences Applications," New Generation Computing, p. In Press, 2007.

• Ding Z, Wei S, Ma, D and Li WW, "VJM -- A Deadlock Free Resource Co-allocation Model for Cross Domain Parallel Jobs," in HPC Asia 2007, Seoul, Korea, 2007, p. In Press.

• Görgen K, Lynch H, Abramson D, Beringer J and Uotila P. "Savanna fires increase monsoon rainfall as simulated using a distributed computing environment", to appear, Geophysical Research Letters.

• Ichikawa K, Date S, Krishnan S, Li W, Nakata K, Yonezawa Y, Nakamura H, and Shimojo S, "Opal OP: An extensible Grid-enabling wrapping approach for legacy applications", GCA2007 - Proceedings of the 3rd workshop on Grid Computing & Applications -, pp.117-127 , Singapore, June 2007 a. (PRIUS)

• Ichikawa K, Date S, and Shimojo S. “A Framework for Meta-Scheduling WSRF Based Services”, Proceedings of 2007 IEEE Pacific Rim Conference on Communications, Computers and Signal Processing (PACRIM 2007), Victoria, Canada, pp. 481-484, Aug. 2007 b. (PRIUS)

• Kuwabara S, Ichikawa K, Date S, and Shimojo S. “A Built-in Application Control Module for SAGE”, Proceedings of 2007 IEEE Pacific Rim Conference on Communications, Computers and Signal Processing (PACRIM 2007), Victoria, Canada, pp. 117-120, Aug. 2007. (PRIUS)

• Takeda S, Date S, Zhang J, Lee BU, and Shimojo S. “Security Monitoring Extension For MOGAS”, GCA2007 - Proceedings of the 3rd workshop on Grid Computing & Applications - , pp.128-137 Singapore, June 2007. (PRIUS)

• Tilak S, Hubbard P, Miller M, and Fountain T, ``The Ring Buffer Network Bus (RBNB) DataTurbine Streaming Data Middleware for Environmental Observing Systems," to appear in the Proceedings of the e-Science 2007

• Zheng C, Katz M, Papadopoulos P, Abramson D, Ayyub S, Enticott C, Garic S, Goscinski W, Arzberger P, Lee B S, Phatanapherom S, Sriprayoonsakul S, Uthayopas P, Tanaka Y, Tanimura Y, Tatebe O. Lesson Learned Through Driving Science Applications in the PRAGMA Grid. Int. J. Web and Grid Servies, Vol.3, No.3, pp287-312. 2007 …

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Summary• PRAGMA grid

– Shared vision lower resistance to use others software, test on others resources

– Formed new development collaborations– Size and heterogeneity, explore issues which functional grid must resolve

• Management, resources and software coordination• Identity and fault management• Scalability and performance• Feedback between application and middleware help improve software and

promote software integration• Heterogeneous global grid

– Is realistic and challenging– Can be good for middleware development and testing– Can be useful for real science

• Impact– Software dissemination (Rocks, Ninf-G, Nimrod, SCMSWeb, Naregi-CA, …)– Help new national/regional grids (Chile, Vietnam, Hong kong, …)

• Key is people, is collaboration

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How Can I Participate?

• Get involved now– PRAGMA or similar collaborative communities

• Cost a little• Benefit a lot

– Being a part of larger grid effort – Learn from doing– Build collaborations– Develop bigger/better ideas/projects– Push the use of network and other infrastructure

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A Grass Roots Effort

“One of the most important lessons of the Internet is that it grows most successfully where grass roots initiatives are encouraged and enabled. The Internet has historically grown from the bottom up, and this aspect continues to fuel its continued growth in the academic and commercial sectors.”

– Vint Cert, UN Economic and Social Council in 2000

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http://www.pragma-grid.nethttp://goc.pragma-grid.nethttp://wiki.pragma-grid.net

Thank You

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

• PRIME is supported by the National Science Foundation under NSF INT 04007508

• PRAGMA grid is the result of contributions and support from all PRAGMA grid team members