1. 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.Laganà 1, O. Gervasi 2, A. Costantini 1 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 simulations Authors: A. Laganà 1, A. Costantini 1, O. Gervasi 2 Location: 1) Department of Chemistry, University of Perugia, Perugia, Italy 2) Department of Mathematics and Compute Science, University of Perugia, Perugia, Italy

2. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 2 A VO FOR MOLECULAR SCIENCES WE HAVE REGISTERED THE VIRTUAL ORGANIZATION COMPCHEM (http://compchem.unipg.it) IN ORDER TOhttp://compchem.unipg.it - 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

3. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 3 THE STARTING POINT WE HAVE ALSO DEVELOPED GEMS: 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

4. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 4 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

5. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 5 WORKFLOW OF GEMS.0 Interaction Measurables Dynamics Virtual Monitor Input

6. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 6 The INTERACTION module INTERACTION DYNAMICS Is there a suitable LEPS Pes? Import the PES parameters NO YES START

7. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 7 The DYNAMICS module DYNAMICS OBSERVABLES Are quantum dynamics calculations Inappro- priate? NO YES TRAJ: application using classical trajectory calculations (atom-diatom)

8. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 8 TRAJECTORY PSEUDOCODE SEND “ready” status message RECEIVE seed integrate trajectory update indicators SEND “ready” status message GOTO 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:

9. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 9 GRIDIFYING the TRAJ kernel TRAJ return Iterate over initial conditions the integration of individual trajectories (ABCTRAJ, etc.) Define quantities of general use

10. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 10 The MEASURABLE module OBSERVABLES NO YES Is the observable a state-to-state one? DISTRIBUTIONS: VM for scalar and vector product distributions, and state-to-state crosssections Do calculated and measured properties agree? END: EXTEND THE CALCULATION TO OTHER PROPERTIES YES NO END: TRY WITH ANOTHER SURFACE

11. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 11 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

12. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 12 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

13. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 13 Extended DYNAMICS module DYNAMICS OBSERVABLES Are quantum dynamics calculations Inappro- priate? Is the calculation single initial state? NO YES TI: application carrying out time-independent quantum calculations (atom-diatom) TD: application carrying out time- dependent quantum calculations (atom-diatom) TRAJ: application using classical trajectory calculations (atom-diatom) (polyatomic) (many-bodies)

14. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 14 Gridified time dependent approach TD return Iterate over initial conditions the integration over time propagation (RWAVEPR, etc.) Define quantities of general use

15. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 15 Gridified time independent approach TI return Iterate over total energy value the integration of scattering equations Define quantities of general use including the integration bed Iterate over the reaction coor- dinate to build the interaction matrix Broadcast coupling matrix

16. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 16 THE SERVICE APPROACH Service request Search for components Outcomes composition Service provision Simulation yes NO Is the answer adequate?

17. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 17 Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici The N+N 2 reaction A QUANTUM STUDY OF

18. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 18 QUANTUM METHODS Time dependent Time independent {W} – set of position vectors of the nuclei or any other choice of coordinates H n - nuclear Hamiltonian Factor out time and choose a different continuity va- riable (or transformation from reactants to products)

19. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 19 TIME DEPENDENT PSEUDOCODE SEND “ready” status message RECEIVE init_cond integrate in time generate the S matrix element SEND “ready” status message GOTO 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:

20. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 20 Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici 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

21. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 21 Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici Threshold energies 1.359 eV 0.950 eV 0.772 eV 0.199 eV Etr V=0 V=1 V=2 V=4

22. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 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).

23. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Some CompChem users

24. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 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 )

25. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Jobs submitted per week

26. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Hours of CPU per week

27. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 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

28. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Speed-ups Performances are affected by the time sharing regime adopted by the node

29. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Failures statistics Job status Number % Success 37 74 Aborted 13 26 Aborted reasons Number % Communic. Error862 DL POLY error323 Scheduler error215 Statistical analysis were calculated on 50 parallel jobs More than 70% of the jobs ran properly and only 26% were aborted

30. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 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).

31. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 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

32. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 Web3d and Web/Grid Services Simulator Web Service Client Web Service Client UDDI Register WSDL WEB SERVICE X3D Client X3D Client Web Service Server Web Service Server WEB SERVICE Mol Struct Files Collection Search / Download mol. struct. files in/from Web sites Search / Download mol. struct. files in/from Web sites Mol Struct files to simulator input files Converter Mol Struct files to simulator input files Converter simulator output files to Mol Struct Converter simulator output files to Mol Struct Converter UDDI Server Files Servers of Molecular Structures SOAPSOAP Simulator Server Simulator Administration of the molecular structure file collection

33. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 33 Slide Title THANKS FOR YOUR ATTENTION

34. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 34 Extended INTERACTION module INTERACTION DYNAMICS Is there a suitable Pes? Are ab initio calculations available? Are ab initio calculations feasible? CALL SUPSIMCALL FITTING Import the PES routine NO YES Take force field data and procedures from related databases START

35. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 35 Gridified Ab initio approach SUPSIM return Iterate over the system geometries the call of ab initio suites of codes (GAMESS, etc) Define the characteristics of the ab initio calculation, the coordinates used and the Variable’s intervals

36. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 36 Gridified FITTING portal FITTING Return Are asym- ptotic values accurate? Are remai- ning values inaccurate? Do ab initio values have the proper sym- metry? Enforce the proper symmetry Application using fitting programs to generate a PES routine Modify asym- ptotic values NO Modify short and long range values YES

37. Enabling Grids for E-sciencE EGEE-II INFSO-RI-031688 To change: View -> Header and Footer 37 Extended MEASURABLES module OBSERVABLES NO YES Is the observable a state-to-state one? Is the observable a state specific onee? VM for thermal and thermodynamic pro- perties including Molecular Virtual Reality tools CROSS: VM for state specific cross sections, rate constants and maps of product intensity DISTRIBUTIONS: VM for scalar and vector product distributions, and state-to-state crosssections Do calculated and measured properties agree? END YES INTERACTION NO Beam VM for Intensity in the Lab frame