The CompChem VO and a Grid application for spacecraft reentry simulations

1. The CompChem VO and a Grid application for spacecraft reentry simulations Authors: 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

2. 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 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 To change: View -> Header and Footer

4. THE CROSSED BEAM EXPERIMENTof 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 To change: View -> Header and Footer

5. WORKFLOW OF GEMS.0 Input Interaction Dynamics Measurables Virtual Monitor To change: View -> Header and Footer

6. The INTERACTION module START Is there a suitable LEPS Pes? NO INTERACTION YES Import the PES parameters DYNAMICS To change: View -> Header and Footer

7. The DYNAMICS module Are quantum dynamics calculations Inappro- priate? NO DYNAMICS YES TRAJ: application using classical trajectory calculations (atom-diatom) OBSERVABLES To change: View -> Header and Footer

8. TRAJECTORY PSEUDOCODE Master: 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 SEND “ready” status message RECEIVE seed integrate trajectory update indicators SEND “ready” status message GOTO RECEIVE To change: View -> Header and Footer

9. GRIDIFYING the TRAJ kernel Define quantities of general use TRAJ Iterate over initial conditions the integration of individual trajectories (ABCTRAJ, etc.) return To change: View -> Header and Footer

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

11. THE H+ICl REACTION THE VIRTUAL MONI-TORS BUILD IN REAL TIME THE PRODUCT ANGULAR DISTRIBU-TIONS OF THE VA-RIOUS CHANNELS H+ICl→HI+Cl H+ICl→H + ICl H+ICl→HCl+I 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 To change: View -> Header and Footer

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

14. Gridified time dependent approach Define quantities of general use TD • Iterate over initial conditions • the integration over time • propagation (RWAVEPR, etc.) return To change: View -> Header and Footer

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

16. THE SERVICE APPROACH Service request Search for components Simulation Outcomes composition NO Is the answer adequate? yes Service provision To change: View -> Header and Footer

17. The N+N2 reaction Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici A QUANTUM STUDY OF To change: View -> Header and Footer

18. QUANTUM METHODS Time dependent {W} – set of position vectors of the nuclei or any other choice of coordinates Hn - nuclear Hamiltonian Factor out time and choose a different continuity va-riable (or transformation from reactants to products) Time independent To change: View -> Header and Footer

19. TIME DEPENDENT PSEUDOCODE Master: Worker: DO init_cond =1, N_initcond RECEIVE status message IF worker “ready” THEN SEND init_cond to worker ELSE GOTO RECEIVE endIF endDO SEND “ready” status message RECEIVE init_cond integrate in time generate the S matrix element SEND “ready” status message GOTO RECEIVE To change: View -> Header and Footer

20. State to state probabilities Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici E(v) 0.146 eV V=0 V=1 0.433 eV V=2 0.717 eV V=3 0.997 eV 1.270 eV V=4 V=5 1.543eV To change: View -> Header and Footer

21. Grid based molecular simulators: the nitrogen atom reactions Leonardo Pacifici Threshold energies Etr 1.359 eV V=0 V=1 0.950 eV V=2 0.772 eV V=4 0.199 eV To change: View -> Header and Footer

22. 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. Some CompChem users

24. 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. Jobs submitted per week

26. Hours of CPU per week

27. 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. Speed-ups • Performances are affected by the time sharing regime adopted by the node

29. 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

30. 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. 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. Web3d and Web/Grid Services UDDI Server Files Servers of Molecular Structures UDDI Register Search / Download mol. struct. files in/from Web sites Simulator Web Service Client Administration of the molecular structure file collection Mol Struct Files Collection S O A P WEB SERVICE Simulator X3D Client WSDL Mol Struct files to simulator input files Converter Web Service Server Simulator simulator output files to Mol Struct Converter WEB SERVICE Simulator Server Client Server

33. Slide Title THANKS FOR YOUR ATTENTION To change: View -> Header and Footer

34. Extended INTERACTION module START Take force field data and procedures from related databases Are ab initio calculations available? Are ab initio calculations feasible? NO NO Is there a suitable Pes? NO INTERACTION YES YES YES Import the PES routine CALL FITTING CALL SUPSIM DYNAMICS To change: View -> Header and Footer

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

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

37. Extended MEASURABLES module INTERACTION VM for thermal and thermodynamic pro- perties including Molecular Virtual Reality tools Is the observable a state-to-state one? Is the observable a state specific onee? NO NO OBSERVABLES Beam VM for Intensity in the Lab frame YES YES 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? NO YES END To change: View -> Header and Footer