e-Science on
VNGrid Project
Tran Van Lang, Do Van Long
Members of VNGrid Project
HCM City Institute of Information Technology
(IOIT-HCM, VAST)
24th APAN Meeting,
Xian, China - August 2007
Contents
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VNGrid Introduction
IOIT-HCM Grid
E-Science Activities
Plan for Future e-Science in VNGrid
Conclusion
VNGrid Introduction
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IOIT-HCM Introduction
History of Grid in Vietnam
Organizations in VNGrid
Goal of VNGrid project
IOIT-HCM Grid Activities
IOIT-HCM Introduction
Ho Chi Minh City Institute of
Information Technology (IOIT-HCM)
VIETNAMESE ACADEMY OF SCIENCE AND
TECHNOLOGY (VAST)
History of Grid in Vietnam
2001-2002
2003
2004
IOIT-HCM Grid
Project
The Centers
Grid
and systems
Group of Conference on HPC
for HPC were
HCM City and Grid Computing,
founded
College in HCM City, held by
Ministry of Science
Natural
and Technology
Sciences
2005
BioGrid,
IOIT-HCM
BK Grid
Group,
Hanoi UT
2006-2007
IOIT-HCM
connect to
Pragma
HCM City UT
Grid Project
VNGrid
Project
Organizations in VNGrid
Five Universities and Institutes
were collected to lead and
execute VNGrid project:
1.
2.
3.
4.
5.
Vietnamese Institute of
Information Technology
(IOIT, VAST)
Hanoi University of Technology
(HUT)
Vietnamese National University
in Hanoi (VNU – Hanoi)
Vietnamese Military Technical
Academy (VMTA)
HCM City Institute of
Information Technology
(IOIT-HCM, VAST)
6
Goals of VNGrid project
1.
Establishing the Grid infrastructure in Vietnam:

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2.
3.
Be connected by five institutions
Connecting to other Grid systems
Studying to deploy the middleware: gLite, Globus,…
Building the Grid-based, e-Science Applications:
Bioinformatics, Meteorology, Virtual Reality, Cryptography,…

Other scientific applications on Grid system will be encouraged to
build and apply to VNGrid

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Create the environment for the collaborating and
sharing resources for Science and Education
Make Grid more easy to use.
IOIT-HCM Grid Activities
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)
9
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)
10
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)
11
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)
12
Applications and Middleware
in Pragma testbed
http://goc.pragma-grid.net/applications/default.html
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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)
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Molecular simulation
 Siesta/Nimrod (UZurich, Switzerland; MU,
Australia)
 Amber/Rsh ( USM, Malaysia)
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Computer Science
 Load Balancer (IOIT-HCM, Vietnam)
 GriddLeS (MU, Australia)
2 applications from Vietnam
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IOIT-HCM Grid
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Grid members
Infrastructure of IOIT-HCM Grid system
Network architecture of Grid System
connect to KISTI, PRAGMA and VAST
Grid Portal
IOIT-HCM Grid Members
Infrastructure of IOIT-HCM Grid System
Compute Node
Compute Node
Compute Node
CA
172.25.100.2
172.25.100.3
172.25.101.2
172.25.100.5
172.25.101.3
172.25.102.2
Ethernet –10 Mbps
Ethernet – 1 Gbps
172.25.100.1
Ethernet – 100 Mbps
172.25.101.1
Head Node
(Condor)
172.25.102.3
172.25.102.5
172.25.102.4
172.25.102.1
Head Node
CA
(SGE)
Head Node
(Condor)
moon.ioit-hcm.ac.vn
venus.ioit-hcm.ac.vn
172.25.97.28
203.162.99.117
172.25.97.30
203.162.99.98
172.25.97.29
Ethernet 1 Gbps
IOIT-HCM LAN
172.25.98.118
203.162.99.118
Grid Portal
biogrid.ioit-hcm.ac.vn
172.25.97.10
203.162.99.116
Database
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
bio.ioit-hcm.ac.vn MINH (IOIT-HCM)
Internet
256 kbps
16
Network architecture of Grid System
connect to KISTI, PRAGMA and VAST
PBS
Compute Nodes
Ethernet
Ethernet
IOIT-HCM Grid
jupiter.gridcenter.or.kr
150.183.249.14
Internet
198.202.88.52
rocks-52.sdsc.edu
210.86.238.85
proliant.vast-hcm.ac.vn
Ethernet
Ethernet
Compute Nodes
SGE
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)
SGE
17
IOIT-HCM Grid Portal
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Our Grid Portal based on
opensource packages:
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Globus Toolkit 4
Java CoG
Jetspeed Portal
Tomcat
Jboss
Postgresql
Condor G
GridPort4
GridSphere Framework
with JSR168-compatible
Portlet Container
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E-Science Activities in IOIT-HCM
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Grid and BioScience – BioGrid Portal
AccessGrid deployment
Telemedicine
Grid and BioScience
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Gird Portal
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Account and Authentication
GPIR - Grid Portals Information Repository
File Management
Job Submission
Job Sequence
GRAM Job
Condor Job Submission
Building Bioinformatics tools with Grid Technology apply on
Grid Portal:
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Phylogenetic Tree
Blast
Motif finding
Protein Structure Prediction
…
Grid Portal
Gird computing apply for generating the Phylogenetic Tree
Align a sequence to a sequence
1
1
5
2
3
3
4
2
Align a profile to a profile
Align a sequence to a profile
IOIT-HCM Grid Portal - Blast deploying
Motif finding

Programming in MPI-2 apply on IOIT-HCM Grid System
Protein Structure prediction
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Programming in MPI-2 with Molecular Dynamic (MD)
Algorithm
Access Grid deployment

Access Grid for
collaboration the
multimedia data
(IOIT-HCM):
Support ting to the
Conference on IT and
Communication in
Haiphong, Vietnam
(10/2005)
Meeting Room 1
2nd Floor – Block 1
Center Room
1st Floor – Block 1
Meeting Room 3
2nd Floor – Block 2
Meeting Room 2
1st Floor – Block 2
Telemedicine
Telemedicine Conference on 05/05/05
Hospital of Medical (HCM) vs. VietDuc Hospital (Ha Noi)
Conference between BenTre Province Leaders with University of Medical (HCM)
Deploying Telemedicine with AccessGrid Technology from IOIT-HCM
Telemedicine between Nhi Dong 1 Hospital (HCM)
with Nguyen Dinh Chieu (Ben Tre Province)
Deploying Telemedicine with Video Conferencing Technology from IOIT-HCM
Future E-Science deployment and
Other Grid applies on VNGrid
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Applying the HPC and Grid
Computing for climate forecast
(Hanoi UT and Center for HPC,
Hanoi UNS)
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Using MM5 model
Simulating some biomedical
problems (Hanoi College
of Technology)
Setup the e-Learning system for
training on Gird
Eleanring system of IOIT-HCM deploy in Bamako, Mali, Afica
Research for deploy System in South Provinces of Vietnam
Connecting from HCM to Can Tho Provinces
Connecting from HCM to An Giang Province
BirdFlu Observer
Vietnam Digital Map deploying
Join to the Grid Communities
EGEE User Forum
AsiaGrid - Singapore
Join to the Grid Communities (cont.)
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GeoGrid, Pragma 12: Thailand (03/2007)
ISGC 07: Taipei (03/2007)
EGEE User Forum: Manchester (05/2007)
AsiaGrid: Singapore (06/2007)
APAN Meeting: China (08/2007)
EGEE Meeting: Pudapest (10/2007)
Do Son School: Vietnam (11/2007)
…
Future step: Setup Grid on VinaRen Network
Conclusion
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We are studying Grid Technology and try to
apply to Science and Education.
Will invest more for the networking and
infrastructure
Need to connect to the other Grid System for
expand the collaboration.
Our next step is connecting to EGEE Asia
Federation (EAF) to receive the operations
technology and experience for deploying eScience on our Grid Resource Centers.
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Thank for your Attention