Bioinformatics Grid-based Applications
and IOIT-HCM Grid
Tran Van Lang, Do Van Long
Members of VNGrid Project
HCM City Institute of Information Technology
(IOIT-HCM, VAST)
IOIT-HCM Introduction
Ho Chi Minh City Institute of
Information Technology
(IOIT-HCM, VAST)
History of IOIT-HCM Grid
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
IOIT-HCM join to Pragma
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)
5
IOIT-HCM Grid resource monitor
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)
6
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)
7
PHÂN VIỆN CÔNG NGHỆ
THÔNG TIN TẠI TP. HỒ CHÍ
MINH (IOIT-HCM)
8
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)

Molecular simulation
 Siesta/Nimrod (UZurich, Switzerland; MU,
Australia)
 Amber/Rsh ( USM, Malaysia)

Computer Science
 Load Balancer (IOIT-HCM, Vietnam)
 GriddLeS (MU, Australia)
2 applications from Vietnam

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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
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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
12
Grid-based applications
IOIT-HCM Grid Portal

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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BioScience

Gird Portal

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Resource monitoring in a grid
Proxy management
File management
Job specification and execution
Building Bioinformatics tools with Grid Technology apply on
Grid Portal:
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Multiple sequences alignment
Phylogenetics 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

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)
and Nguyen Dinh Chieu (Ben Tre Province)
Deploying Telemedicine with Video Conferencing Technology from IOIT-HCM
Setup the e-Learning system for
training 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)
Elearning system of IOIT-HCM deploy in Bamako, Mali, Afica
Bioinformatics Courses with NCBI
NLM – National Library Medical Training Class
NIH, US
Research for deploy Grid System in South
Provinces of Vietnam
Connecting from HCM to Can Tho University
Connecting from HCM to An Giang University
Avian Flu Observer research to deploy on Grid
Vietnam Digital Map research to deploy on Grid
Join to the Grid Communities
1.
2.
3.
4.
5.
6.
7.
8.
9.
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)
Grid Camp: Taipei (11/2007)
Do Son School: Vietnam (11/2007)
…
Join to the Grid Communities (cont.)
Fragma 12 – Thailand,
Mar 2007
ISGC 2007 – Taipei,
Apr 2007
EGEE User Forum, England ,
May 2007
AsiaGrid – Singapore,
Jun 2007
24th APAN Meeting- Xian, China
Aug 2007
International IT Conference 10th ,Vietnam,
Sep 2007
EGEE Meeting: Pudapest
(10/2007)
Grid Camp: Taipei
(11/2007)
Future step: Setup Grid on VinaRen Network
Finished test TEIN2 Connection from VNU Ha Noi to IOIT-HCM
Conclusion

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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.
Need more supporting to develop
Our next step is connecting to EGEE Asia Federation (EAF) to
receive the operations technology and experience for deploying
e-Science on our Grid Resource Centers.
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