Computational Chemistry and NanoMaterial GRID

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Computational Chemistry and Nano-Material GRID
Grid Forum Korea 2003 2003/12/02

• Y.S.Lee, J.Kwak, Quantum Chemistry Laboratory
• Department of Chemistry, KAIST

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Table of Contents

• Objective
• Activities
• Plan Result
• Scope
• Request
• Future work

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Objective

• Practical GRID system for computational chemists
• Scalability of problem
• Extensibility of system
• Feedback to GRID infra-structure developers

4
Objective

• Practical GRID system for computational chemists
• Scalability of problem
• Extensibility of system
• Feedback to GRID infra-structure developers

• Providing computational resources to
  collaborating research groups _at_ Hardware
  resources _at_ Software resources (various
  computational chemistry packages)
• Educational purpose

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Objective

• Practical GRID system for computational chemists
• Scalability of problem
• Extensibility of system
• Feedback to GRID infra-structure developers

• Finding computational chemistry problems which
  are scalable to GRID system

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Objective

• Practical GRID system for computational chemists
• Scalability of problem
• Extensibility of system
• Feedback to GRID infra-structure developers

• GRID infra-structure functionalities
• User interface
• Standardization

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Activities

• Practical GRID system for computational
  chemists- Development of WWW portal, which is
  easy to use- GRID system applets for easy
  installation- Field test with real world
  computational chemistry problems

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Activities

• Scalability of problem- High Throughput
  Computing problems rather than HPC/parallel
  processing.- Field test with the developed GRID
  system

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Activities

• Extensibility of problem
• Study on OGSA/Globus 3.0
• Study on DB connection
• Study on ECCE connection to get more precise user
  interface
• Study on more GRID infrastructure functionalities
  and Gridsphere

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Activities

• Extensibility of problem
• Study on OGSA/Globus 3.0
• Study on DB connection
• Study on ECCE connection to get more precise user
  interface
• Study on more GRID infrastructure functionalities
  and Gridsphere

Database
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Activities

• Extensibility of problem
• Study on OGSA/Globus 3.0
• Study on DB connection
• Study on ECCE connection to get more precise user
  interface
• Study on more GRID infrastructure functionalities
  and Gridsphere

Database
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Activities

• Extensibility of problem
• Study on OGSA/Globus 3.0
• Study on DB connection
• Study on ECCE connection to get more precise user
  interface
• Study on more GRID infrastructure functionalities
  and Gridsphere

Database
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Activities

• Feedback- Open web site- Documentation

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Plan and Result

• Development and set-up
• AAOGS2 GRID system
• AAOGS2 WWW console
• Field study
• AAOGS2 GRID system Ge surface cluster model
• AAOGS2 WWW consoleC60 cage with N atom
• HIO CCSD calculation with ECP etc.
• Extensibility
• OGSA/Globus 3.0 test
• ECCE 3.1 set-up and architecture design
• Architecture design of Gridsphere and DB
  connection
• Documentation
• Documentation http//aaogs.kaist.ac.kr/grid
  Wikiwiki website
• Problems and solution models of computational
  chemistry applications for GRID computing
  environment
• Introduction of OGSA and Globus 3.0 and its
  reality to computational chemistry
• Etc.

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Scope ScalabilityGRID vs.Chemistry

• Characteristics of computational chemistry
  calculation
• Different software packages for various molecular
  systems
• Various scales of calculations on research groups
  with different conditions
• Repeated calculation with gradual progress in
  many cases
• Computational resource collaboration and
  High-Throughput-Computing

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Scope AAOGS2 GRID system

• Focus on easy installation and easy usage
• Direct job launcher/Multiple input generator/FTP
  input catcher
• JAVA molecular structure viewer and Network map
  viewer
• Simple WWW output analyzer/MS Excel connectivity

Input Generator
End user
Select resources (program and arguments)
Submit a job
View result
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AAOGS2 GRID system

• Designed for a organization of 36 academic
  research groups
• 16 testbed nodes, 40 cluster CPUs, 6 workstation
  in KISTI, KAIST and WKU currently connected.
• Applied for
• Scanning along various geometries
• Discovery among a large number of candidate
  molecules
• Sharing computational resources
• Sharing computational chemistry software package
• Educational usage

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Field study with AAOGS2

• Ge surface cluster model
• Study on top dimer structure and dangling bonds
• Getting potential energy curve along various bond
  length
• Trying on various sizes of models
• PM3 method
• Presented KCS Meeting (2003)

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Field study with AAOGS2

• Fullerene with N atom
• Study on N atom capturing pathway
• Potential energy calculation along selected
  entering pat way
• PM3 calculation completed
• DFT calculation proceeding
• Dynamic view
• http//aaogs.kaist.ac.kr/grid/c60withn_ani.htm

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Field study with AAOGS2

• Other routine calculations with collaborating
  resources
• Ex) HIO molecule spin--orbit correction term
  calculation with effective core potential
• Proceeding
• Now, at the stage of getting optimized geometry
  without spin--orbit effect
• Iodine atom with ECP

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Extensibility - NTGP GRID system

• Test GRID system for studying extensibility of
  CCNM GRID
• Tested with OLED material candidates

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Extensibility OGSA/Globus3 test

• IBM/KISTI OGSA Workshop and Group seminar
• to study OGSA structure and its practicality of
  application to chemistry
• Globus 3.0 Gridsphere OLED material discovery
  problem tested on NTGP
• Globus 3.0 instability, Heavy overhead,
  Difficulties of debugging

System Management Services
Grid Services
ResourceManagement
Cluster Management
Policy
ProblemDetermination
Logging
Service Collections
JobScheduling
FileTransfer
DataReplication
Provisioning
OGSI Open Grid Services Infrastructure
Management
Registry
Lifecycle
Discovery
HandleMap
Notification
Factory
Web Services
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Extensibility ECCE

• ECCE 3.1 set up / install know-how
• GSISSH remote shell processing structure

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Extensibility ECCE

• To be connected to GRID system for advanced user
  interface

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Extensibility More Globus functions

• Design of system to adopt advanced features of
  Globus
• Finding optimal resources with MDS/GRIS/GIIS
• Studied on NTGP

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Extensibility More Globus functions

• Design of Database connectivity
• Studied on NTGP

WebServer (GridsphereandECCEsupport)
Portal Service
Users
???
Qury Generator
Resource 1
MDS
Resource 2
HTTP
Input Generator
GSI
GRAM
Job Manager
Resource N
Users
???
GridFTP
Remote Storage
Monitoring
Grid Portal
Globus Toolkit
CCNM GRID
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Feedback

• CCNM GRID project Website
• Project/research reports
• GRID introduction
• Document archive
• http//aaogs.kaist.ac.kr/grid

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Request

• Standardized and convenient resource information
  service tool
• By-passing message-passing-tool support
• Intentional job migration tool rather than
  accidental job migration service

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Request Bypassing message-passing

• Based on study on network load of computational
  chemistry calculation parallel processing
• Adoption of NetPIPE or MP_Lite giving efficient
  High Performance Computing application

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Request Intentional job migration

• Computational chemistry systems are very various.

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Request Intentional job migration
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Request Intentional job migration
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Presentation and Publication

• Presentation
• 2003.4.KCS(WWW Based Distributed Computing
  System For Computational Chemistry)
• 2003.6. The 3rd Symposium of material design and
  development with computer modeling(Quantum
  Chemistry Study on Acetylene Adsorption on Ge
  Surface Study and Fullerene Metal Complex)
• 2003.6. KAIST-Princeton Joint Symposium(Developme
  nt of Fault Tolerant Distributed Computing System
  For Computational Chemistry)
• 2003.10. KCS(Parallel Processing and Distributed
  Computing for Computational Chemistry on GRID
  environment)
• 4th International Conference on
  Electroluminescence of Molecular Materials and
  Related Phenomena(Theoretical Study for the
  Structural and Optical Properties of
  Metalloporphyrin Complexes)
• Publication
• Spin-Orbit Density Functional Theory Calculations
  for TlAt with Relativistic Effective Core
  Potentials, Bulletin of the Korean Chemical
  Society Vol.24, No.6

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Future Work

• System packaging
• Application researches with GRID system
• Education support
• Extended features implementation

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Collaborating groups
KAIST Yoon Sup Lee
KNU Sang Yeon Lee KNU Cheol-ho Choi SSU See-year
Seong SSU Myung-ho Kim WKU Ki-hak
Lee http//aaogs.kaist.ac.kr/grid