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On the development of an a priori Grid enabled molecular simulator

On the development of an a priori Grid enabled molecular simulator. EGEE User Forum – March 1-3, 2006 Geneva, CH Antonio Laganà 1 , Osvaldo Gervasi 2 1 Dept. of Chemistry, University of Perugia 2 Dept. of Math. & Computer Science, University of Perugia. FACTS.

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On the development of an a priori Grid enabled molecular simulator

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  1. 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 Perugia 2 Dept. of Math. & Computer Science, University of Perugia

  2. 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 GEMS and CompChem VO status

  3. SUMMARY 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 GEMS and CompChem VO status

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

  5. 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 GEMS and CompChem VO status

  6. 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 GEMS and CompChem VO status

  7. Metachem: Metalaboratories for Complex Computational Applications in Chemistry DYSTS: Dynamics and Spectroscopy of Systems : Relevant to Environment and Applied Chemistry MURQM: Multireference Quantum Chemical Methods ELCHEM: E-learning Technologies for Chemistry ICAB: Integration of Codes for Ab Initio Methods GEMS and CompChem VO status

  8. EU GRID for Chemistry: D23 COST action Simbex Murqm Dirac Elchem Icab Dysts Comovit GEMS and CompChem VO status

  9. 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 GEMS and CompChem VO status

  10. SIMBEX: a research/educational tool for the simulation of elementary chemical reaction High interactivity Advanced visualization In deep insight into the chemical mechansm

  11. THE STARTING POINT: GEMS.0

  12. GEMS.0 The problem Interaction Dynamics Observables The solution GEMS and CompChem VO status

  13. The INTERACTION module START Is there a suitable LEPS Pes? NO INTERACTION YES Import the PES parameters DYNAMICS GEMS and CompChem VO status

  14. The DYNAMICS module Are quantum dynamics calculations Inappro- priate? NO DYNAMICS YES TRAJ: application using classical trajectory calculations (atom-diatom) OBSERVABLES GEMS and CompChem VO status

  15. The OBSERVABLES 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 GEMS and CompChem VO status

  16. THE ANGULAR DISTRIBUTION VIR-TUAL MONITORS FOR ATOM DIATOMS H+ICl→H+ICl H+ICl→HCl+I H+ICl→HI+Cl GEMS and CompChem VO status

  17. The GRIDified TRAJ kernel Define quantities of general use TRAJ Iterate over initial conditions the integration of individual trajectories (ABCTRAJ, etc.) return GEMS and CompChem VO status

  18. FROM WHERE DOES THE COMPUTATIONAL KNOW HOW COME FROM?

  19. NATIONAL PROJECTS • GRID.it • UNICORE • NORDUGRID GEMS and CompChem VO status

  20. The Italian GRID project GRID.IT Enabling platforms for high performance computational Grids oriented to scalable virtual organizations CNR, INFN, CNIT, ASI, Universities GEMS and CompChem VO status

  21. Earth observation Astrophysics Bioinformatics Applications Computational Chemistry Geophysics HP Components Problem Solving Program- Ming tools Libraries Cost models Portals Communications Security Middleware Monitoring Resource Management High perfor- mance nets GARR Fiber optics GEMS and CompChem VO status

  22. WHERE WE GO

  23. A priori molecular simulator Service request Interaction Dynamics Observables NO Is validation passed? YES Service delivery GEMS and CompChem VO status

  24. The 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 GEMS and CompChem VO status

  25. The SUPSIM module (atom-diatom) 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 GEMS and CompChem VO status

  26. The FITTING module (atom-diatom) 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 GEMS and CompChem VO status

  27. The 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 GEMS and CompChem VO status

  28. The TD QM module (atom-diatom) Define quantities of general use TD • Iterate over initial conditions • the integration over time • propagation (RWAVEPR, etc.) return GEMS and CompChem VO status

  29. The TI QM module (atom-diatom) 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 GEMS and CompChem VO status

  30. The OBSERVABLES module INTERACTION Is the observable a state-to-state one? Is the observable a state specific onee? RATE: virtual monitor (VM) for thermal rate coefficients 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 GEMS and CompChem VO status

  31. COMPUTER SCIENCE AND ORGANISATION

  32. The PG hardware configuration Access to Grid GEMS and CompChem VO status

  33. 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 GEMS and CompChem VO status

  34. 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 GEMS and CompChem VO status

  35. 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) GEMS and CompChem VO status

  36. GEMS and CompChem VO status

  37. wavepacket scalar pseudocode Read input data: v, j, k, masses… Perform preliminary calculations Loop on J Loop on t Loop 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 GEMS and CompChem VO status

  38. Coarse grain Master-worker parallel Model master J=0,N … slave J=0 Λ=0 J=N Λ=0 J=N Λ=1 J=N Λ=N Collect master … slave J=1 Λ=0 J=1 Λ=1 J=N-1 Λ=0 J=N-1 Λ=N-1 Collect master … END GEMS and CompChem VO status

  39. Fine grain DVR: MPI vs ASSIST GEMS and CompChem VO status

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