the compchem vo and a grid application for spacecraft reentry simulations

EGEE-II INFSO-RI-031688

Enabling Grids for E-sciencE

www.eu-egee.org

EGEE and gLite are registered trademarks

THE COMPCHEM VO AND A GRID APPLICATION TO SPACECRAFT REENTRY

A. Laganà1, O. Gervasi2, A. Costantini1

B. 1 Department of Chemistry, University of Perugia, Perugia (I)

C. 2 Department of Mathematics and Computer Science, University of Perugia, Perugia (I)

The CompChem VO and a Grid application for spacecraft reentry simulationsAuthors: A. Laganà1, A. Costantini1, O. Gervasi2

Location: 1) Department of Chemistry, University of Perugia, Perugia, Italy

2) Department of Mathematics and Compute Science, University of Perugia, Perugia, Italy

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A VO FOR MOLECULAR SCIENCES

WE HAVE REGISTERED THE VIRTUAL ORGANIZATION COMPCHEM (http://compchem.unipg.it) IN ORDER TO

- gather together Molecular sciences hardware and computational packages

- develop in Grid hardware and middleware specific for Molecular sciences simulations

- carry out realistic simulations based on first principles - perform extended cpu-intensive computational

campaigns - establish an open protected collaborative environment

for developing new science and technological innovation




THE STARTING POINT

WE HAVE ALSO DEVELOPEDGEMS: a grid enabled realistic simulator based on a

collaborative usage of the necessary Molecular Science packages

GEMS.0: its first implementation on the production Grid of EGEE to simulate crossed beam experiments




THE CROSSED BEAM EXPERIMENT of Perugia

MEASURABLES- Angular and time of flight product distributions

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




WORKFLOW OF GEMS.0

Interaction

Measurables

Dynamics

Virtual Monitor

Input




The INTERACTION module

INTERACTION

DYNAMICS

Is therea suitable LEPS

Pes?

Import thePES parameters

NO

YES

START




The DYNAMICS module

DYNAMICS

OBSERVABLES

Are quantumdynamics

calculationsInappro-priate?

NO

YES

TRAJ: application

using classical trajectory

calculations(atom-diatom)




TRAJECTORY PSEUDOCODE

SEND “ready” status messageRECEIVE seedintegrate trajectoryupdate indicatorsSEND “ready” status messageGOTO RECEIVE

Worker:

DO traj_index =1, traj_number RECEIVE status message IF worker “ready” THEN generate seed SEND seed to worker ELSE GOTO RECEIVE endIF endDO

Master:




GRIDIFYING the TRAJ kernel

TRAJ

return

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

Define quantities of generaluse




The MEASURABLE 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




THE VIRTUAL MONI-TORS BUILD IN REAL TIME THE PRODUCT ANGULAR DISTRIBU-TIONS OF THE VA-RIOUS CHANNELS

THE H+ICl REACTION

H+ICl→H + ICl

H+ICl→HCl+I

H+ICl→HI+Cl




PRESENT ADVANCES

EXTEND European collaboration to the development Grid empowered applications in Molecular and Matter Sciences

• WG1 PHOTODYN: Computational photochemistry and photobiology

• WG2 QDYN: Quantum dynamics engines for Grid enabled molecular simulators

• WG3 ELAMS: E-science and Learning approaches in Molecular Science

• WG4 DECIQ: Code interoperability in Computational Quantum Chemistry

• WG5 CCWF: Computational Chemistry Workflows and Data Management

• WG6 AIMD4GRID: Ab initio Molecular Dynamics for the Grid

In collaboration with the COST action D37




Extended 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)




Gridified time dependent approach

TD

return

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

Define quantities of generaluse




Gridified time independent approach

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




THE SERVICE APPROACH

Service request

Search for components

Outcomes composition

Service provision

Simulation

yes

NO Is the answer adequate?



EGEE-II INFSO-RI-031688 Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici

The N+N2 reaction

)',()(),()( 12

412

4 vNSNvNSN gg

A QUANTUM STUDY OF




QUANTUM METHODS

Time dependent

Time independent

{W} – set of position vectors of the nuclei or any other choice of coordinatesHn - nuclear Hamiltonian

Factor out time and choose a different continuity va-riable (or transformation from reactants to products)




TIME DEPENDENT PSEUDOCODE

SEND “ready” status messageRECEIVE init_condintegrate in timegenerate the S matrix elementSEND “ready” status messageGOTO RECEIVE

Worker:

DO init_cond =1, N_initcond RECEIVE status message IF worker “ready” THEN SEND init_cond to worker ELSE GOTO RECEIVE endIF endDO

Master:




State to state probabilities

0.146 eV

0.433 eV

0.717 eV

0.997 eV

E(v)

V=0

V=1

V=2

V=3

1.270 eV

1.543eV

V=4

V=5




Threshold energies

1.359 eV

0.950 eV

0.772 eV

0.199 eV

Etr

V=0

V=1

V=2

V=4

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CompChem VO

• CompChem VO is running on the EGEE production Grid from the end of 2004

• 21 active users• The VO contributes to the EGEE production grid with 2

CE:– ce.grid.unipg.it (LCG 3.0) 12 nodes (biproc) Intel PIII– cex.grid.unipg.it (Glite 3.0) 8 nodes (biproc) Intel Xeon

• Several EGEE sites are supporting the VO

– the Italian EGEE sites, CESGA (Spain), IN2P3 (France), Trinity College of Dublin (Ireland), CYFRONET and POZNAN Supercomputing Center (Poland), Hellas Grid and GRNET (Greece), University of Cyprus (Cyprus).




Some CompChem users

Organization User Contact email

University of Barcelona Margarita Alberti maw <at> qf .ub.es

University of the Basque Country (Spain) Ernesto Garcia qfpgapae <at> vc.ehu.es

University of Perugia (I taly)Dimitris Skouteris. Leonardo Arteconi,

Alessandro Costantini, Max Porrini

{dimitris, bodynet, alex, max}

<at> dyn.unipg.it

Cyf ronet (Poland) Mariusz Sterzel m.sterzel <at> cyf ronet.pl

I MI P- I talian National Research Council (I taly) Domenico Bruno d.bruno <at> area.ba.cnr.it

CESGA (Spain) J avier Lopez j lopez <at> cesga.es

University of Vienna (Austria) Hans Lishcka hans.lischka <at> univie.ac.at

University of Cyprus (Cyprus) Constantinos Zeinalipour-Yazdi zeinalip <at> ucy.ac.cy

ENEA (I taly) Carlo Scio scio <at> f rascati.enea.it

Vilius University (Lithuania) Gintaras Urbelis gintaras.urbelis <at> chf .vu.lt

Center fo Parallel Computers (Sweden) Olav Vatras vahtras <at> pdc.kth.se

University of Crete and FORTH (Greece) Stavros C Farantos f arantos <at> iesl.f orth.gr




CompChem VO in EGEE III

• In EGEE the Computational Chemistry community is represented by two VO’s:– CompChem VO (public domain, shareware software, managed

by University of Perugia, Italy)– GAUSSIAN VO (commercial software, managed by Cyfronet,

PL)

• A Center of Excellence grouping the labs of both VOs will be established in EGEE III

• CompChem participates to – the MPI working group to promote the use of MPI and parallel

software in EGEE (EGEE/int.eu.grid MPI international workshop, Dublin, Dec 11th-12th, 2006)

– the User Support working group to promote and improve the User Support systems available in EGEE (EGEE Workshop for VO’s, Karlshrue, Germany, March 1st-2nd, 2007 )




Jobs submitted per week




Hours of CPU per week




Parallel performances

Parallel performances measured on the EGEE-Grid platform

• Indications were obtained running a test case on six different EGEE-Grid clusters (which support MPICH library until Sept 2006)

• The calculations ran sequentially on one node and in parallel on 2 and 4 nodes

• Related speed-ups were evaluated




Speed-ups

• Performances are affected by the time sharing regime

adopted by the node




Failures statistics

Job status Number %

Success 37 74

Aborted 13 26

Aborted reasons Number %

Communic. Error 8 62

DL POLY error 3 23

Scheduler error 2 15

• Statistical analysis were calculated on 50 parallel jobs• More than 70% of the jobs ran properly and only 26%

were aborted




Visualization tools and Web3D based Web services

• The use of Molecular Virtual Reality (Visualization + Virtual Reality techniques applied at the nanometer level) helps to understand the molecular processes

• We have implemented some virtual monitors of GEMS creating Virtual Worlds based on atoms positions saved during the trajectory calculations (MVR animations)

• A Virtual World may be created also from a static description of the system in the initial or in the final configuration (mol2, pdb, etc).




The molecular virtual world

• Type of molecular representations:– Balls and Sticks (BS)

– Wire frame (WF)

– Space filling (SF)

– SF+WF

– Colored wire frame

• Properties

– Transparency

– Labels

• The atoms are colored using the RASMOL CPK coloring scheme




Web3d and Web/Grid Services

SimulatorSimulatorWeb

ServiceClient

Web ServiceClient

Client

UDDIRegister

WSDL

WEB SERVICE

X3DClient

X3DClient

WebServiceServer

WebServiceServer

Server

WEB SERVICEMol

Struct Files

Collection

Search / Download

mol. struct. files in/fromWeb sites

Search / Download

mol. struct. files in/fromWeb sites

Mol Struct files to simulatorinput filesConverter

Mol Struct files to simulatorinput filesConverter

simulatoroutput files

to Mol StructConverter

simulatoroutput files

to Mol StructConverter

UDDI Server

Files Servers of Molecular Structures

SOAP

SimulatorServer

SimulatorSimulator

SimulatorSimulator

Administration of the molecular structure file collection




Slide Title

THANKS FOR YOUR ATTENTION




Extended 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




Gridified Ab initio approach

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




Gridified FITTING portal

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




Extended MEASURABLES module

OBSERVABLESNO NO

YES YES

Is the observable

a state-to-stateone?

Is theobservable

a state specificonee?

VM for thermal and thermodynamic pro-

perties including Molecular Virtual

Reality tools

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

the compchem vo and a grid application for spacecraft reentry simulations

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