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Bioinformatics Grid-based Bioinformatics Grid-based Applications and IOIT-HCM GridApplications and IOIT-HCM Grid
Tran Van Lang, Do Van LongTran Van Lang, Do Van LongMembers of VNGrid ProjectMembers of VNGrid Project
HCM City Institute of Information HCM City Institute of Information Technology (IOIT-HCM, VAST)Technology (IOIT-HCM, VAST)
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IOIT-HCM IntroductionIOIT-HCM Introduction
Ho Chi Minh City Institute of Ho Chi Minh City Institute of Information Technology Information Technology
(IOIT-HCM, VAST)(IOIT-HCM, VAST)
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History of IOIT-HCM GridHistory of IOIT-HCM Grid
2003 2004 20052001-2002
Conference on HPC and Grid Computing, in HCM City, held by Ministry of Science
and Technology
The Centers and systems for HPC were
founded
IOIT-HCM Grid Project
HCM City UT Grid Project
BK Grid Group,
Hanoi UT
Grid Group of HCM City College Natural
Sciences
BioGrid, IOIT-HCM
2006-2007
IOIT-HCM connect to
Pragma
VNGrid Project
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IOIT-HCM join to PragmaIOIT-HCM join to Pragma
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PHÂN VIỆN CÔNG NGHỆ PHÂN VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)MINH (IOIT-HCM) 55
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PHÂN VIỆN CÔNG NGHỆ PHÂN VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)MINH (IOIT-HCM) 66
IOIT-HCM Grid resource IOIT-HCM Grid resource monitormonitor
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PHÂN VIỆN CÔNG NGHỆ PHÂN VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)MINH (IOIT-HCM) 77
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PHÂN VIỆN CÔNG NGHỆ PHÂN VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)MINH (IOIT-HCM) 88
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99
Applications and Middleware Applications and Middleware in Pragma testbedin Pragma testbed
http://goc.pragma-grid.net/applications/default.html
Real science applications pair and drive Real science applications pair and drive middleware developmentmiddleware development
Achieve long-run and scientific resultsAchieve long-run and scientific results Open to applications of all scientific disciplinesOpen to applications of all scientific disciplines
Climate simulationClimate simulation Savannah/Nimrod (MU, Australia)Savannah/Nimrod (MU, Australia) MM5/Mpich-Gx (CICESE, Mexico; KISTI, MM5/Mpich-Gx (CICESE, Mexico; KISTI,
Korea)Korea) Quantum-mechanics, quantum-chemistry:Quantum-mechanics, quantum-chemistry:
TDDFT, QM-MD, FMO/Ninf-G (AIST, Japan)TDDFT, QM-MD, FMO/Ninf-G (AIST, Japan) GenomicsGenomics
iGAP/Gfarm/CSF (UCSD, USA; AIST, Japan; iGAP/Gfarm/CSF (UCSD, USA; AIST, Japan; JLU, China)JLU, China)
HPM: genomics (IOIT-HCM, Vietnam)HPM: genomics (IOIT-HCM, Vietnam) mpiBlast/Mpich-G2 (ASGC, Taiwan)mpiBlast/Mpich-G2 (ASGC, Taiwan)
Organic chemistryOrganic chemistry Gamess-APBS/Nimrod (UZurich, Gamess-APBS/Nimrod (UZurich,
Switzerland)Switzerland) Molecular simulationMolecular simulation
Siesta/Nimrod (UZurich, Switzerland; MU, Siesta/Nimrod (UZurich, Switzerland; MU, Australia)Australia)
Amber/Rsh ( USM, Malaysia)Amber/Rsh ( USM, Malaysia) Computer ScienceComputer Science
Load Balancer (IOIT-HCM, Vietnam)Load Balancer (IOIT-HCM, Vietnam) GriddLeS (MU, Australia)GriddLeS (MU, Australia)
2 applications from Vietnam2 applications from Vietnam
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IOIT-HCM Grid MembersIOIT-HCM Grid Members
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PHÂN VIỆN CÔNG NGHỆ PHÂN VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)MINH (IOIT-HCM) 1111
Infrastructure of IOIT-HCM Grid SystemInfrastructure of IOIT-HCM Grid System
Ethernet – 1 GbpsEthernet –10 Mbps
Ethernet 1 Gbps
Internet
172.25.100.2 172.25.100.3 172.25.100.5
172.25.100.1
172.25.101.2 172.25.101.3
172.25.101.1
172.25.97.28203.162.99.117
172.25.97.30203.162.99.98
172.25.98.118203.162.99.118
172.25.97.10203.162.99.116
biogrid.ioit-hcm.ac.vn bio.ioit-hcm.ac.vn
moon.ioit-hcm.ac.vn
Head Node (Condor)
Head Node(Condor)
Grid Portal Database
Compute Node Compute Node
CA
Ethernet – 100 Mbps
Head NodeCA (SGE)
172.25.97.29
Compute Node
172.25.102.2 172.25.102.3
172.25.102.4
172.25.102.5
172.25.102.1
venus.ioit-hcm.ac.vn
IOIT-HCM LAN
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PHÂN VIỆN CÔNG NGHỆ PHÂN VIỆN CÔNG NGHỆ THÔNG TIN TẠI TP. HỒ CHÍ THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)MINH (IOIT-HCM) 1212
Network architecture of Grid System Network architecture of Grid System connect to KISTI, PRAGMA and VASTconnect to KISTI, PRAGMA and VAST
Internet
Compute Nodes
Ethernet
PBS
Ethernet
SGE
proliant.vast-hcm.ac.vn
198.202.88.52
150.183.249.14
rocks-52.sdsc.edu
Compute Nodes
Ethernet
Ethernet
jupiter.gridcenter.or.kr
210.86.238.85
SGE
IOIT-HCM Grid
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Grid-based applicationsGrid-based applications
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1414
IOIT-HCM Grid PortalIOIT-HCM Grid Portal
Our Grid Portal based on Our Grid Portal based on opensource packages:opensource packages: Globus Toolkit 4 Globus Toolkit 4 Java CoGJava CoG Jetspeed PortalJetspeed Portal Tomcat Tomcat Jboss Jboss PostgresqlPostgresql Condor GCondor G GridPort4GridPort4 GridSphere Framework with GridSphere Framework with
JSR168-compatible Portlet JSR168-compatible Portlet ContainerContainer
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BioScienceBioScience Gird Portal Gird Portal
Resource monitoring in a gridResource monitoring in a grid Proxy managementProxy management File managementFile management Job specification and execution Job specification and execution
Building Bioinformatics tools with Grid Technology Building Bioinformatics tools with Grid Technology apply on Grid Portal: apply on Grid Portal: Multiple sequences alignmentMultiple sequences alignment Phylogenetics TreePhylogenetics Tree BlastBlast Motif findingMotif finding Protein Structure PredictionProtein Structure Prediction
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Grid PortalGrid Portal
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Gird computing apply for generating the Phylogenetic Tree
1
2
3
4
5
3
2
Align a sequence to a profile
Align a profile to a profile
Align a sequence to a sequence
11
2
3
4
5
3
2
Align a sequence to a profile
Align a profile to a profile
Align a sequence to a sequence
1
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IOIT-HCM Grid Portal - Blast deploying
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Motif findingMotif finding Programming in MPI-2 apply on IOIT-HCM Grid Sys
tem
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Protein Structure predictionProtein Structure prediction Programming in MPI-2 with Molecular Dynamic (MD)
Algorithm
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Access Grid deploymentAccess Grid deployment
Access Grid for Access Grid for collaboration the collaboration the multimedia data multimedia data ((IOIT-HCMIOIT-HCM):):Support ting to the Support ting to the Conference on IT and Conference on IT and Communication in Communication in Haiphong, Vietnam Haiphong, Vietnam (10/2005)(10/2005)
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Meeting Room 1 2nd Floor – Block 1
Meeting Room 32nd Floor – Block 2
Meeting Room 21st Floor – Block 2
Center Room1st Floor – Block 1
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TelemedicineTelemedicine
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Telemedicine Conference on 05/05/05 Telemedicine Conference on 05/05/05 Hospital of Medical (HCM) vs. VietDuc Hospital (Ha Hospital of Medical (HCM) vs. VietDuc Hospital (Ha
Noi)Noi)
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Conference between BenTre Province Leaders with University of Medical (HCM)Conference between BenTre Province Leaders with University of Medical (HCM)Deploying Telemedicine with AccessGrid Technology from IOIT-HCMDeploying Telemedicine with AccessGrid Technology from IOIT-HCM
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Telemedicine between Nhi Dong 1 Hospital (HCM) Telemedicine between Nhi Dong 1 Hospital (HCM) and Nguyen Dinh Chieu (Ben Tre Province)and Nguyen Dinh Chieu (Ben Tre Province)
Deploying Telemedicine with Video Conferencing Technology from IOIT-HCMDeploying Telemedicine with Video Conferencing Technology from IOIT-HCM
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Setup the e-Learning system for Setup the e-Learning system for training on Girdtraining on Gird
2nd Training Course on Functional Genomics of Insect Vector of Human diseases - Oct 2005, Malaria Research Center, Bamako, Africa (support from NIH, US)
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Elearning system of IOIT-HCM deploy in Bamako, Mali, AficaElearning system of IOIT-HCM deploy in Bamako, Mali, Afica
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Bioinformatics Courses with NCBI
NLM – National Library Medical Training ClassNIH, US
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Research for deploy Grid System in Research for deploy Grid System in South Provinces of VietnamSouth Provinces of Vietnam
Connecting from HCM to Can Tho University
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Connecting from HCM to An Giang University
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Avian Flu Observer research to deploy on Avian Flu Observer research to deploy on GridGrid
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Vietnam Digital Map research to deploy on Vietnam Digital Map research to deploy on GridGrid
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Join to the Grid CommunitiesJoin to the Grid Communities
1.1. GeoGrid, Pragma 12: GeoGrid, Pragma 12: ThailandThailand (03/2007) (03/2007)
2.2. ISGC 07: ISGC 07: TaipeiTaipei (03/2007) (03/2007)
3.3. EGEE User Forum: EGEE User Forum: ManchesterManchester (05/2007) (05/2007)
4.4. AsiaGrid: AsiaGrid: SingaporeSingapore (06/2007) (06/2007)
5.5. APAN Meeting: APAN Meeting: ChinaChina (08/2007) (08/2007)
6.6. EGEE Meeting: EGEE Meeting: PudapestPudapest (10/2007) (10/2007)
7.7. Grid Camp: Grid Camp: TaipeiTaipei (11/2007) (11/2007)
8.8. Do Son School: Do Son School: VietnamVietnam (11/2007) (11/2007)
9.9. ……
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Join to the Grid Communities (cont.)Join to the Grid Communities (cont.)
Fragma 12 – Thailand, Mar 2007
ISGC 2007 – Taipei, Apr 2007
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EGEE User Forum, England ,EGEE User Forum, England ,
May 2007May 2007AsiaGrid – Singapore, AsiaGrid – Singapore,
Jun 2007Jun 2007
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International IT Conference 10th ,Vietnam, Sep 200724th APAN Meeting- Xian, China
Aug 2007
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EGEE Meeting: EGEE Meeting: PudapestPudapest (10/2007)(10/2007) Grid Camp: Grid Camp: TaipeiTaipei (11/2007) (11/2007)
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Future step: Setup Grid on VinaRen Future step: Setup Grid on VinaRen NetworkNetwork
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Finished test TEIN2 Connection from VNU Ha Noi to IOIT-HCM
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4646
ConclusionConclusion Studying Grid Technology and try to Studying Grid Technology and try to
apply to Science and Education. apply to Science and Education. Will invest more for the networking and Will invest more for the networking and
infrastructure infrastructure Need to connect to the other Grid Need to connect to the other Grid
System for expand the collaboration.System for expand the collaboration. Need more supporting to developNeed more supporting to develop
Our next step is connecting to EGEE Asia Federation (EAF) Our next step is connecting to EGEE Asia Federation (EAF) to receive the operations technology and experience for to receive the operations technology and experience for deploying e-Science on our Grid Resource Centers.deploying e-Science on our Grid Resource Centers.