On the development of an a priori Grid enabled molecular simulator

Enabling Grids for E-sciencE

www.eu-egee.org

University of Perugia

On the development of an a priori Grid enabled molecular simulator

EGEE User Forum – March 1-3, 2006

Geneva, CH

Antonio Laganà1, Osvaldo Gervasi2

1 Dept. of Chemistry, University of Perugia2 Dept. of Math. & Computer Science, University of Perugia

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University of Perugia GEMS and CompChem VO status

FACTS

COMPCHEM is a virtual organization (VO) of Chemists and Molecular Scientists having the mission of developing cooperative computational tools for complex a priori realistic simulations

GEMS is the Grid Enabled Molecular Simulator meant to be made of all the components needed to implement on the Grid a priori molecular simulations

A prototype demo (GEMS.0) has been already implemented on the production grid of EGEE

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COMPUTATIONAL MOLECULAR SCIENCE• The starting point GEMS.0• Theoretical and computational know how • A workflow for distributed running

COMPUTER SCIENCE AND ORGANISATION• The need for a production grid infrastructure• The definition of operational modalities• A mechanism to reward cooperation

SUMMARY


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FROM WHERE DOES THE GRID ENABLED MOLECULAR SIMULATOR (GEMS) COME ?

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THE CHEMISTRY AND MOLECULAR SCIENCE METALABORATORIES

• A Cost-Chemistry Action (D23) • Called METACHEM (Metalaboratories for

complex computational applications in Chemistry)

• Started in the year 1999 (ended 2005)• Having the goal of establishing the

Metalaboratories (clusters of geographically distributed laboratories sharing expertise, hardware and software on the net) for Chemistry and Molecular Science complex computational simulations

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Metachem: Metalaboratories for Complex Computational Applications in Chemistry

MURQM: Multireference Quantum Chemical Methods

DIRAC: Four Component Relativistic Quantum Chemical Calculations

SIMBEX: Simulation of Molecular Beam Experiments

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Metachem: Metalaboratories for Complex Computational Applications in Chemistry

DYSTS: Dynamics and Spectroscopy of Systems : Relevant to Environment and Applied ChemistryMURQM: Multireference Quantum Chemical Methods

ELCHEM: E-learning Technologies for Chemistry

ICAB: Integration of Codes for Ab Initio

Methods

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EU GRID for Chemistry: D23 COST action

Simbex

Murqm

Dirac

Elchem

Dysts

Comovit

Icab

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PARTNER GROUPS FROM NATIONAL PROJECTS

1 Isr, Pl, Sk, Nl, Ch

2 Cz, Fr, Dk, A, Sw, No

3 Hu

4 Gr

5 E

6 D, Uk,

9 I


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SIMBEX: a research/educational tool for the simulation of elementary chemical reaction

•High interactivity

•Advanced visualization

•In deep insight into the chemical mechansm


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THE STARTING POINT: GEMS.0

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GEMS.0

Interaction

Observables

Dynamics

The solution

The problem

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The INTERACTION module

INTERACTION

DYNAMICS

Is therea suitable LEPS

Pes?

Import thePES parameters

NO

YES

START

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The DYNAMICS module

DYNAMICS

OBSERVABLES

Are quantumdynamics

calculationsInappro-priate?

NO

YES

TRAJ: application

using classical trajectory

calculations(atom-diatom)

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The OBSERVABLES module

OBSERVABLESNO

YES

Is the observable

a state-to-stateone?

DISTRIBUTIONS: VMfor scalar and vectorproduct distributions,

and state-to-state crosssections

Do calculated

and measuredproperties

agree?

END:EXTEND THE

CALCULATIONTO OTHER

PROPERTIES

YES NO END:TRY WITHANOTHER SURFACE

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THE ANGULAR DISTRIBUTION VIR-TUAL MONITORS FOR ATOM DIATOMSH+ICl→H+ICl

H+ICl→HI+Cl

H+ICl→HCl+I

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The GRIDified TRAJ kernel

TRAJ

return

Iterate over initial conditionsthe integration of individualtrajectories (ABCTRAJ, etc.)

Define quantities of generaluse


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FROM WHERE DOES THE COMPUTATIONAL KNOW HOW COME FROM?

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NATIONAL PROJECTS

• GRID.it

• UNICORE

• NORDUGRID

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GRID.IT

The Italian GRID project

CNR, INFN, CNIT, ASI, Universities

Enabling platforms for high performance computational Grids oriented to scalable virtual organizations

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High perfor-mance nets

GARR Fiber optics

Portals Security Communications

Resource Management MonitoringMiddleware

HP Components Problem Solving

Libraries Cost models

Program-Ming tools

Applications

Astrophysics Bioinformatics Earth observation

Geophysics Computational Chemistry


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WHERE WE GO

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A priori molecular simulator

Service request

Interaction

Observables

Service delivery

Dynamics

YES

NO Is validation passed?

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The INTERACTION module

INTERACTION

DYNAMICS

Is therea suitable Pes?

Are ab initiocalculationsavailable?

Are ab initiocalculations

feasible?

CALL SUPSIMCALL FITTING Import the

PES routine

NO NO NO

YES YES YES

Take force fielddata and

procedures from relateddatabases

START

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The SUPSIM module (atom-diatom)

SUPSIM

return

Iterate over the systemgeometries geometries

the call of ab initio suitesof codes (GAMESS, etc)

Define the characteristics of the ab initio calculation, the coordinates used and the

Variable’s intervals

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The FITTING module (atom-diatom)

FITTING

Return

Are asym-ptotic values

accurate?

Are remai-ning valuesinaccurate?

Do ab initiovalues have the

proper sym-metry?

Enforce the propersymmetry

Application using fitting programs to

generate a PESroutine

Modify asym-ptotic values

NO NONO

Modify short andlong range values

YES YESYES

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The DYNAMICS module

DYNAMICS

OBSERVABLES

Are quantumdynamics

calculationsInappro-priate?

Is the calculation

single initial state?

NO NO

YES YES

TI: application carrying out

time-independentquantum

calculations(atom-diatom)

TD: application carrying out time-

dependent quantumcalculations

(atom-diatom)

TRAJ: application

using classical trajectory

calculations(atom-diatom)(polyatomic)

(many-bodies)

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The TD QM module (atom-diatom)

TD

return

•Iterate over initial conditions•the integration over time•propagation (RWAVEPR, etc.)

Define quantities of generaluse

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The TI QM module (atom-diatom)

TI

return

Iterate over total energy value the integration of scattering

equations

Define quantities of generaluse including the integration

bed

Iterate over the reaction coor-dinate to build the interaction

matrix

Broadcast coupling matrix

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The OBSERVABLES module

OBSERVABLESNO NO

YES YES

Is the observable

a state-to-stateone?

Is theobservable

a state specificonee?

RATE: virtual monitor (VM)

for thermal ratecoefficients

CROSS: VM for statespecific cross sections,

rate constants and maps of

product intensity

DISTRIBUTIONS: VMfor scalar and vectorproduct distributions,

and state-to-state crosssections

Do calculated

and measuredproperties

agree?END

YES

INTERACTION

NO

Beam VM for Intensity in the

Lab frame


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COMPUTER SCIENCE AND ORGANISATION

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The PG hardware configuration

Access to Grid

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PRACTICAL GOALS

Perform extended computational campaigns for systems relevant to scientific and technological applications

Develop grid tools: middleware, workflow mana-gers, problem solving environments and coordi-nation languages for distributed heterogeneous environments

Specialize in some specific applications

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NEXT STEPS

Generalize GEMS to more complex research

purposes using a web service approach

Diffuse the membership among the members of the Computational Molecular Science community

Open the VO to non EU scientists

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Conditions

1. sign the consortium agreement 2. provide in due time requested information 3. (negotiable) implement locally at least a 4 node

cluster exposed outside the local firewall to the Grid (perform development on unexposed machines)

4. implement one stable code or suite of codes. This will be first only for personal use and later-on open for shared use in a coordinated way

5. (for labs of point 3) designate a person taking care of the local machines, ensuring real time Grid connections and implementation of necessary middleware

6. accept the credit policy (in progress)

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wavepacket scalar pseudocode

Read input data: v, j, k, masses…Perform preliminary calculationsLoop on J

Loop on tLoop on Λ Perform time-step propagation

Perform the asympotic analysis Calculate C(t) coefficients and update the fixed-J S matrix

End loop on Λ End loop on t

End loop on J

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Coarse grain Master-worker parallel Model

J=0,Nmaster

J=0 Λ=0 J=N Λ=0 J=N Λ=1 … J=N Λ=Nslave

master Collect

J=1 Λ=0 J=1 Λ=1 J=N-1 Λ=0 … J=N-1 Λ=N-1slave

master Collect

…

END

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Fine grain DVR: MPI vs ASSIST

On the development of an a priori Grid enabled molecular simulator

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