Thai National Grid Project

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Thai National Grid Project

• Building the next generation e-infrastructure
  for Thailand

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Thai National Grid Project

• A National Project under Software Industry
  Promotion Agency (Public Organization) , Ministry
  of Information and Communication Technology
• Started in 2005
• Start from 14 member organizations and expanded
  to 22 organizations in 2008
• Goal
• Building the next generation E-infrastructure for
  Thailand using Grid computing Technology

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Project Organizational Structure
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22 members
Asian Institute of Technology (AIT) Burapa
University (BU) Chaingmai University
(CMU) Chulalongkorn University (CU) Dhurakij
Pundit University (DPU) Kasetsart University
(KU) Khonkhan University (KKU) King Mongkuts
Institute of Technology North Bangkok
(KMITNB) King Mongkuts University of Technology
Thonburi (KMUTT) King Mongkuts Institute of
Technology Ladkrabang (KMITL) Mahidol Unversity
(MU)
NECTEC NANOTEC Prince of Songkla University
(PSU) Suranaree University of Technology
(SUT) Silpakorn University (SU) Sripatum
University (SPU) Siam University The
Meteorological Department Of Thailand
(TMD) University of Thai Chamber of Commerce
(UTCC) Ubonrajthani University (UBU) Walailak
University (WU)
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Strategy
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Strategy 1 Creating Grid human resources

• Encouraging the teaching in grid and parallel
  computing by creating the educational platform
• Community
• Equipment
• Courseware
• Standard
• Material for 3 training course
• Basic Grid Computing
• Grid Administrator
• Grid for Developers
• Material for 3 university level undergraduate and
  graduate program are being developed
• Introduction to grid computing
• Intermediate Grid computing
• Grid computing for Enterprise

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Important Statistics

• Train more than 800 people during 2006-2007
• More than 600 people passed the training workshop
  at various level
• Grid and parallel computing has been taught in 5
  major university producing more than 200
  grid-enable CSE
• We are pushing for more than 1000 people in this
  year

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Strategy 2 Building the Grid Infrastructure

• Thai Grid infrastructure is now functioning well
• TERA Cluster
• Installed at Thai National Grid Center
• Start to provide the service on July 11, 2007
• 200 nodes 800 cores of Intel Xeon 3.0GHz
• Rmax 2.5 Tflops (Rpeak 4.6Tflops)
• Satellite Cluster
• 14 clusters installed at each member institute
• Each cluster has 5 nodes 10 CPUs of Intel Xeon
  2.8GHz
• Institute Cluster
• Existing cluster owned by some institutes
• 3 institutes
• Total number of CPU core now 1,000 cores

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21 clusters from 16 sites around Thailand
ThaiGrid 2007
CMU
More than 1000 CPUs (August 2007)!
KKU
SUT
BU
WU
PSU
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Infrastructure Standard

• Define a set of services need to be enabled on
  each site
• Most are base on Globus Middleware
• Each cluster joining ThaiGrid given a class or
  certified level
• Grid network certified
• Basic Middleware certified

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Grid Middleware

• Still sticking with Pre-ws base services
• GT4 is installed in every member institutes, thus
  enable only Pre-ws for now
• Some institutes is moving to GT4
• 4 Institutes pass WS-Gram test
• Newly created services will base only on
  Web-services base technology or WSGram

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Monitoring infrastructure

• SCMS , a Grid monitoring tool, development is
  housed by TNGC

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ThaiGrid Infrastructure usage

• ThaiGrid provides more than 111 years of
  computing time for member
• 7 years on the grid
• 104 years on tera
• 31 projects from 8 areas are being support on
  Teraflop machine
• More small projects on each machines

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Strategy 3 Driving the Grid Adoption
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Building a Domain Specific Gridfor E-science
User community
NanoGrid
Drug Design Grid
Animation Grid
Collaborative Grid
CFD Grid
BioGrid
Grid Middleware
Grid Infrastructure
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Services on the Grid

• CSE Online
• Drug design Portal using Gridway
• TAVERNA
• Animation Grid using Web Services infrastructure
• Other commercial softwares provided in the
  collaboration with users
• Fluent
• Materials Studio
• LightWave 3D

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BioGrid

• Building Grid infrastructure for Bio-informatics
  researcher in Thailand
• Building network of bio-informatics researchers
• Using TAVERNA Web services to drive job
  workflow
• Partners
• Prince of Songkla University
• University of Manchester
• Mahidol University
• Kasetsart University
• Thai National Grid Center
• Result
• A web-based portal for Life-science Grid base on
  TAVERNA is being developed
• A network of Thai-International researches is
  created
• Activities

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BioGrid Architecture
User interface and workflow
Services
Applications (Blast, Amber, Gaussian)
ThaiGrid
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Bio grid
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Drug Design Grid

• Building Grid-base Drug Design infrastructure
• Platform in Drug design grid
• CSE-Online to drive drug design job
• Portal site Meta scheduler to distribute the
  job
• Partners
• Chulalongkorn University
• University of Utah
• Kasetsart University
• Thai National Grid Center

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Collaboration Grid

• Using the Grid to drive Virtual Research Group,
  making the collaboration between institutes more
  close
• Partners
• KMUTT, CU, KMITNB, KU
• Thai National Grid Center
• ConferenceXP is currently in action
• Portal site to manage meeting
• ConferenceXP is used for communication

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Computational Fluid Dynamics

• Creating an environment for driving CFD
  simulation
• Partners
• Kasetsart University
• Thai National Grid Center
• CFD for research
• Using existing software, such as FLUENT, in
  cluster level
• Collaborating with Microsoft to utilize
  WindowsHPC cluster
• CFD for industry
• Utilizing the use of virtual cluster for secured
  cluster environment
• A proof-of-concept platform is being developed

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Simulation of the Switched Reluctance Motor
using iMoose with NECTEC Design

• Vara Varavithya, Sumate Lipirodjanapong,
  Suphachai Kunasuntiworagul, Kamol
  Jutiwattananukul, KMITNB
• Somchai Chatratana, NSTDA, MOST
• Obective
• Estimate Magnetic Flux Distribution in the SRM
  based on Open Source Software
• Grid and Cluster Technology is used to accelerate
  time to result

• Flux Vector P502w, n 3000rpm

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NanoGrid

• Provide platform to help processing
  nanotechnology simulation
• Partners
• Computational Nano Science Consortium (Thailand)
• Thai National Grid Center
• Accelrys Software Inc.
• Nanotechnology usage in Thailand
• Using Materials Studio, software from Accelrys
  co. ltd. in cluster level
• Providing back-end computing infrastructure to
  help nanotechnology research in Thailand
• TNGC participate in porting Materials Studio 4.2
  for SGE

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CNC members in Thailand
CMU
KKU
SUT
UBU
AIT

• HW SW
• NANOTEC
• NECTEC
• ThaiGrid

KU
MU
CU
PSU
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N2O Reduction
Nitrous oxide (N2O) is a toxic pollutant gas in
the atmosphere and a major cause of such
greenhouse effect and global warming.
Here we investigate, computationally at nanoscale
using Dmol3, reaction mechanisms of the
decomposition of toxic N2O to a non-toxic N2 gas
over pristine- and Titanium decorated-carbon
nanotubes (Ti/CNTs). By comparing activation
barriers of such reaction on both catalysts, we
found Ti/CNTs a strong candidate as catalyst in
the removal of nitrous oxides (N2O).
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Hydrogen Storage (1)
The behavior of H2 molecule in different
nanoporous materials
Results from the Adsorption Locator calculations
show such probability to find hydrogen molecules
(H2) in nanoporous materials. For the
metal-organic frameworks-5 (MOF-5), H2
specifically prefers to locate near the metal
oxide clusters. No hydrogen molecule was found
near the phenyl ring or at the center of the pore.
MOF-5
Unlike the MOF-5, the zeolite imidazolate
framework-8 (ZIF-8) shows different behavior on
the adsorption of hydrogen molecule, which is
likely to diffuse and locate in the pore space
near the imidazole unit and infrequently settle
in the zinc metal area.
ZIF-8
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Human Intestinal Absorption
The model predicts human intestinal absorption
(HIA) after oral administration
The model of Egan et al. was selected for HIA
prediction.
Egan et al., J. Med. Chem. 2000, 43, 3867-3877
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Blood Brain Barrier
The model predicts blood-brain barrier (BBB)
after oral administration.
In 2002, Egan and Lauri reported BBB model that
used to predicts blood brain penetration after
oral administration.
Egan and Lauri., Advanced Drug Delivery Reviews ,
2002, 54, 273289
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Cytochrome P450 2D6
The cytochrome P450 2D6 model predicts CYP2D6
enzyme inhibition using 2D chemical structure as
input.
Susnow and Dixon presented the cytochrome P450
2D6 computational model for 100 training set
compounds with known cytochrome P450 2D6
inhibition constants.
Susnow and Dixon., J. Chem. Inf. Comput. Sci.
2003, 43, 1308-1315
The CYP2D6 score is the sum of the predicted
values (0 and 1) from all individual trees that
comprise the ensemble recursive partitioning
model, divided by the total number of trees in
that model.
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Animation Grid

• Provide environment for 3D animation rendering in
  Thailand
• An open-source project on Sourceforge called
  Animagrid
• Utilize web services and existing cluster and
  grid scheduler to distribute jobs
• Base on commercial-grade renderer software, such
  as Autodesk Maya or Blender
• A render farm builder base on ROCKS Cluster
• Collaboration with ROCKS team at SDSC
• ANImation STudio (ANIST) roll for ROCKS 4.3
• Support Maya and Blender

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Strategy 4 Driving Grid Research

• 2006-2007
• 2 National Conference on Grid computing
  (attendants 300-500)
• 3 International workshops
• 67 Publication papers from members
• 29 papers in 2006
• 38 papers in 2007
• Research Area
• Scientific computing in CFD, life science,
  physics, chemistry, math, Geo science
• Grid middleware, application, algorithm,
  scheduling, tools

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Collaboration with PRAGMA

• SCMS for PRAGMA monitoring
• Infrastructure
• Grid Probe
• Bandwidth
• Software catalog
• Testbed
• 1 Cluster from NECTEC (Grid64)
• 1 Cluster (Sunyata) from TNGCjoined testbed since
  2007

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Collaboration with PRAGMA

• ROCKS Roll (SDSC, UC San Diego)
• Grid Roll
• Animation Studio Roll
• Diskless Roll
• CSE On-line (U. of Utah)
• deployed and used in ThaiGrid Drug Design Project
• Condor-G (UW Madison) SCMS
• using PRAGMA monitoring data for Condor job
  scheduling
• Mogas (NTU, Singapore) SCMS
• using PRAGMA monitoring data for Job Accounting

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Collaboration with other partners

• GridWay Meta Scheduler SCMS
• Supply SCMS monitoring data as a Information MAD
  module for GridWay.
• Deployed and used in ThaiGrid
• Accelrys Inc.
• Develop Sun Grid Engine job submission adapter
  for Materials Studio
• Hewlett-Packard
• Research collaboration between member institute
  of ThaiGrid and HP research institute in India

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Strategy 5 Creating Grid Technology Awareness

• Seminar, talk, workshop
• 9 events in 2006
• 35 event in 2007 ( about 3 events monthly)
• International Participation
• APAN, PRAGMA, SC2006, SC2007, GridAsia
• News
• National newspaper, magazine
• International

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Collaboration with industry

• Microsoft - Leading Edge Competition
• Collaborate with Microsoft to boost awareness of
  Grid Technology on Windows 2003 Compute Cluster
  edition
• Intel Multi-core competition
• Boost awareness of parallel application on
  Multi-core technology
• Grid Innovation 2008
• Grid software development competition on Grid
  platform

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Where are we?
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• Production Grid and
• Cluster infrastructure
• Rich set of services
• Computational Grid
• Enterprise analysis Grid
• Data and knowledge Grid
• Collaborative Grid
• Broad commercial
• Adoption

Stable Grid and Cluster infrastructure Interope
rable Middleware and basic services Computational
Grid Data Grid Grid Portal Grid applications RE
and Non production enterprise applications Broad
academic adoption Limited commercial adoption
Pilot Grid and Cluster infrastructure Interop
erable Middleware Basic computational
Grid Basic Data Grid POC applications
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Objective 2009-2011
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Community driven model
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For more information please visit
http//www.thaigrid.or.th
Sharing the power to innovate
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Future is waiting for us
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Grid Maturity Metric (GMM)
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Thai National Grid Center

• An excellence Center under Software Industry
  Promotion Agency (SIPA)
• Mission

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From Genome to Drugs
Post Genome Gene/Protein function
analysis Protein identification and analysis by
Mass Spec and Microarrays
ADMET ADMET prediction

• Drug Discovery
• Computational chemistry
• Protein 3D structure prediction
• Receptor-ligand analysis

Phornphimon Maitarad 083-7582221 Kasetsart
University
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HIV-1 (3 main targets for AIDS therapy)

• Protease (PR)
• Reverse transcriptase (RT)
• Integrase (IN)

Figure 1 COMFA results of the HIV-1 IN.
Figure 5 Subsite of the HIV-1 PR.
Figure 4 Simulated box of the full-length HIV-1
IN.
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In-silico Mutagenesis of H5N1 Hemagglutinin

• Principle Investigator
• CHAK SANGMA, Cheminformatics Research Unit,
  Chemistry
• Department, Faculty of Science, Kasetsart
  University, THAILAND
• Problem
• Up to now, HA of H5 prefers avian receptor to
  human receptor but mutated HA found. Can mutation
  on HA cause the pandemic outbreak?
• Objective
• Structure and binding affinity prediction of
  mutated HA by molecular dynamic simulation using
• Benefit
• Need for H5 mutation monitoring and provide a
  high throughput prediction
• Challenges
• Estimated 240 selected mutations on 24 residues.
  Estimated computing time one month per mutant
  (AMBER9 on 8 nodes cluster) Or 60 months for
  240 mutations (32 nodes)
• Reference 1.Sangma C., Nunrium P., Hannongbua S.
  (2006) J. Theor. and Comp. Chem. 5, 116.
• Sponsor
• The National Science and Technology Development
  Agency (NSTDA)
• The National Center for Genetic Engineering and
  Biotechnology
• The Thailand Research Fund
• Kasetsart University Research and Development
  Institute

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Grid Infrastructure Software

• Middleware
• Operating system
• ROCKS
• WindowsHPC
• Grid Middleware
• GT4.x about 4 institutes ready
• Globus 2.x all other institutes
• Grid Scheduler
• GridWay Production used
• Condor-G experiment
• Grid monitoring
• SCMSWeb
• Grid Security
• ThaiGrid Experimental CA
• ThaiGrid PMA

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Operating system in ThaiGrid

• ROCKS 4.2.1 4.3 is installed on TERA and all
  Satellites cluster
• ThaiGrid Roll is developed, to help install
  Cluster and join ThaiGrid
• Other Linux operating system?
• Need to pass the Grid services probe status
  requirement
• A 16 nodes WindowsHPC Cluster is built in
  ThaiGrid
• Running commercial Windows-base application
• Experimental on how to interact with existing
  Grid middleware

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Grid Monitoring and Scheduling

• Using SCMSWeb to monitor and probe for Grid
  status
• Grid services probe is mainly used to categorize
  services level in ThaiGrid
• Used in resource certification system
• Grid Meta Scheduler
• Meta scheduler is installed in central site
• GridWay 5.2 is installed and experiment in some
  projects
• Drug Design Grid
• Information is pulled from SCMSWeb
• A plug-in for Condor-G is in development to
  utilize SCMSWeb in Condor base platform

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Grid Security

• ThaiGrid experimental CA
• Going to expired in mid-2008
• ThaiGrid PMA will be used as the new CA
  infrastructure in ThaiGrid
• Equipments are in-place
• CA in TNGC
• RA in each member institutes
• PMA will be in action in February 2008