Utilization of EGEE Grid as a Computational Platform for Chemistry

1
Utilization of EGEE Gridas a Computational
Platformfor Chemistry

• M. Sterzel(1), O. Gervasi(2), J. Kmunicek(3), M.
  Berger(4)
• (1)ACC CYFRONET AGH, (2)University of Perugia,
  (3)CESNET, (4)Univesity of Insbruck
• EGEE User Forum 3,
• Clermont-Ferrand, 11-14 February 2008

2
Overview

• Scientific context
• Grid added value
• Achievements
• Future plans

3
Community

• Five virtual organizations available
• compchem
• gaussian
• eenr.eu
• Trigida
• VOCE (VO for Central Europe)
• Partners
• ACC CYFRONET AGH
• University of Perugia
• CESNET
• University of Insbruck
• Royal Institute of Technology (SE-VR)
• 30 universities cooperating

4
Points of interest

• Molecular structure - a key step in almost all
  molecular studies necessarily to achieve before
  any property studies
• The aim to find the best (within given
  computational method) distance(s) (bond lengths)
  and angle(s) between atoms

• Properties of molecules

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Points of interest

• Chemical reactions - a process that results
  interconversion of molecules

HCN CNH
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Points of interest

• Chemical reactions - a process that results
  interconversion of molecules

• Studies help
• To understand chemical processes taking place
  during reaction
• To find factors having influence on reaction
  rates, product(s) etc.

Reaction path
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Computational methods

• Ab initio (plenty HF, CI, Coupled Cluster,
  CASSCF
• Density Functional theory
• Molecular Mechanics
• Molecular dynamics
• Monte Carlo
• These methods are highly demanding in terms of
  CPU power, memory requests and time consumption.
• Parallel execution is necessarily to complete
  studies

8
Grid added value

• Effective collaboration among researchers
• Exchange of knowledge between research groups
• Easy access to the software
• User just needs to join specific VO
• Easy computational job manipulation
• Target search, selection
• Input modification
• Job resubmission
• Utilization of the software by other scientific
  communities
• Allows parallel execution of many jobs

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Applications

• Chemical software on the Grid

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Chemical software

• Community accustomed to chemical packages
• Both commercial and non commercial needed

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Chemical software

• Community accustomed to chemical packages
• Both commercial and non commercial needed
• Commercial Software why bother about it?
• Used by majority of scientists to conduct
  research
• Faster implementation of new computational
  methods
• Better user support
• More frequent bug fixes
• Why Gausian?
• Large number of computational methods implemented
• One of the first ab-initio codes
• The most popular among communities
• User friendly
• Available on many platforms along with GUI

12
Gaussian VO

• Invented and operated by ACC CYFRONET
• All license issues confirmed with Gaussian, Inc.
• Open for every EGEE user
• Any compuing centre with site Gaussian license
  may support it (4 supporting centres)
• 25 users since the start in September 2006
• VO manager Mariusz Sterzel (m.sterzel_at_cyfronet.p
  l)

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Gaussian VO participation

• As a user
• Register at
• https//voms.cyf-kr.edu.pl8443/vo/gaussian/vomrs
  
• Accept Gaussian VO license requirements
• Wait for VOMRS admin acceptance
• voms-proxy-init --vo gaussian and you are ready
  to use the program...

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Gaussian VO participation

• As a user
• Register at
• https//voms.cyf-kr.edu.pl8443/vo/gaussian/vomrs
  
• Accept Gaussian VO license requirements
• Wait for VOMRS admin acceptance
• voms-proxy-init --vo gaussian and you are ready
  to use the program...
• As a participating centre
• Just sent an e-mail concerning participation to
  VO manager
• After confirmation of the license status at your
  centre with Gaussian Inc, detailed informations
  concerning set-up will be sent back to you

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Becoming a user
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Other packages

• Commercial
• Turbomole
• Wien2k
• Freely available

• GAMESS
• DALTON
• CPMD
• Newton X
• DL_POLY
• NAMD
• RWAVEP
• GROMACS
• Autodock
• Tinker
• Solvate

• PIC-DMSC
• MCGBgrid
• QMC
• ABCtraj
• VENUS
• CRBS
• LM
• COLUMBUS
• DINX
• Abinit
• Q/E

just to mention a few
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Grid Utilization

• The EGEE grid utilization by these applications
  place computational chemistry on third position
  just after HEP and Biomed.

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Applications

• Charon Extension Layer -
• a tool simplifying job management

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Charon Extension Layer Approach

• Why Charon Extension Layer (CEL)?
• many various batch systems scheduling
  components
• used in grid environment
• each batch system has unique tools and different
• philosophy of its utilization
• LCG/gLite provided tools are quite raw and simple
• many additional tasks to use computer resources
  properly

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Charon Extension Layer Approach

• Application management
• single/parallel execution without job script
  modification
• Job management
• easy job submission, monitoring, and result
  retrieving

21
Charon Extension Layer Approach

• Typical job flow

No additional arguments are required all
information about job is stored in control files
in job directory.
22
Charon GUI status and overview

• Graphical interface for Charon system
• offers simple and intuitive interface to
  predefined
• set of options in graphical, highly useable and
  reliable way
• removes the need to memorize CLI commands
• Basic cornerstones
• Charon GUI retains simplicity/usability
• Charon GUI allows access to all key
  functionalities
• adds a log of jobs and projects to which they
  belong

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Charon GUI status and overview

• Complete list of features
• key Charon Extension Layer functionality
• submit a job, monitor the job, retrieve results
• exploration of available application modules
• added values of graphical interface
• management of laboratory projects allowing
  complete
• projects and jobs manipulation (add, remove,
  edit)
• exhaustive jobs overview and jobs filtering
• (based on job state, time period, project
  assignment, job IDs)
• invocation of Xterm for further analysis
• advanced features
• internationalization, support for skins

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Projects/jobs tree and project details
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Adding new project / job
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Individual job details and management
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Individual job details and management
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Individual job details and management
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Individual job details and management
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Individual job details and management
Job submit Job monitoring Results retrieval
File management Input files modification Xterm
invocation Job control files cleaning
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Individual job details and management
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Jobs filtering
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Dropdown menu overview
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Skins and languages
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Applications

• Scientific results

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Simbex

• INFORMATION OBTAINABLE
• - Primary reaction products
• Reaction mechanisms
• Structure and life time of transient
• Internal energy distribution of products
• Key features of the potential

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Simulator
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Interaction module
CAVEATS PES not needed in on the
fly methods. Seldomly a PES already exists PESs
can be semiempirical Best if from a fit of ab
initio values Often PESs are of low accuracy
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Dynamics module
CAVEATS Implementation with
trajectories ABCtraj for atom diatom
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Observables module
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Atom - diatom simulation
The virtual monitors showed the product angular
distributions for the various channels

• The system considered was HICl
• The potential energy surface was a LEPS
• Millions of trajectories were integrated to get
  detailed information on rare events (like
  cooperative mechanisms)
• The monitor were producing in real time angular
  distributions of the 3 product channels
• History files allow the constructions of
  animations and the study of reaction mechanisms

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NN2 case study

• The calculation of the quantum efficiency of
  reactive processes relevant to spacecraft
  reentering modeling

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State probabilities
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Energy thresholds
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N2O braking on oxide surfaces
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Ion flow in nanotubes

• H/D ions flowing through a carbon nanotube
• A quantum scattering problem solved using a 3D
  time-dependent technique (the problem has been
  already solved using classical approaches)
• Implementation of a quantum scattering formalism
  based on polar cylindrical coordinates to single
  out resonances, interferences and tunneling

47
Real challenge
A life science application to the understanding
of cellular micropores
A nanotube model can be used to understand the
ionic conductivity of cations (like Na or K)
through cellular membranes.
48
Future plans

• Web portal with a plug-in for chemical software
  packages
• Grid ports of parallel version of chemical
  software
• Development of grid license models