The CompChem VO and a Grid application for spacecraft reentry simulations
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Transcript of The CompChem VO and a Grid application for spacecraft reentry simulations
EGEE-II INFSO-RI-031688
Enabling Grids for E-sciencE
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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
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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
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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
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WORKFLOW OF GEMS.0
Interaction
Measurables
Dynamics
Virtual Monitor
Input
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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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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:
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GRIDIFYING the TRAJ kernel
TRAJ
return
Iterate over initial conditionsthe integration of individualtrajectories (ABCTRAJ, etc.)
Define quantities of generaluse
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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
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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
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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
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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)
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Gridified time dependent approach
TD
return
•Iterate over initial conditions•the integration over time•propagation (RWAVEPR, etc.)
Define quantities of generaluse
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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
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THE SERVICE APPROACH
Service request
Search for components
Outcomes composition
Service provision
Simulation
yes
NO Is the answer adequate?
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The N+N2 reaction
)',()(),()( 12
412
4 vNSNvNSN gg
A QUANTUM STUDY OF
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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)
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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:
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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
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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).
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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
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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 )
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Jobs submitted per week
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Hours of CPU per week
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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
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Speed-ups
• Performances are affected by the time sharing regime
adopted by the node
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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
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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).
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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
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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
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Slide Title
THANKS FOR YOUR ATTENTION
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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
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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
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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
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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