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 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 9 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 11 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: Globus Toolkit 4 Java CoG Jetspeed Portal Tomcat Jboss Postgresql Condor G GridPort4 GridSphere Framework with JSR168-compatible Portlet Container 14 BioScience Gird Portal Resource monitoring in a grid Proxy management File management Job specification and execution Building Bioinformatics tools with Grid Technology apply on Grid Portal: 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 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. 46