FROM EGEE TO EGI: THE ROLE OF VIRTUAL RESEARCH COMMUNITIES IN MOLECULAR AND MATERIALS SCIENCE

1. FROM EGEE TO EGI: THE ROLE OF VIRTUAL RESEARCH COMMUNITIES IN MOLECULAR AND MATERIALS SCIENCE Antonio Laganà* Department of Chemistry, University of Perugia, Italy * With the collaboration of several members of the COMPCHEM Virtual Organization

2. SUMMARY THE EGEE GRID AND ITS IMPLICATIONS FOR COMPUTATIONAL MOLECULAR AND MATERIALS SCIENTISTS PAVING THE WAY TO EGI FROM SIMBEX (SIMULATOR of MOLECULAR BEAM EXPERIMENT) TO GEMS (GRID EMPOWERED MOLECULAR SIMULATOR) FROM COMPCHEM TO CMST GRIDIFICATION APPROACHES FORWARD LOOKING

3. 1 - THE EGEE GRID AND ITS IMPLICATIONS FOR COMPU-TATIONAL MOLECULAR AND MATERIALS SCIENTISTS The european seminal implementation of the Grid and the assemblage of the COMPCHEM Virtual Organization

4. The Grid: from dreams to reality “A computational Grid is a hardware and software infrastructure that provides dependable, consistent, pervasive and inexpensive access to high-end computational capabilities.” Ian Foster, The Grid: Blueprint for a future computing infrastructure (1999)

5. THE PERVASIVITY OF THE EGEE PRODUCTION GRID

6. THE EGEE PRODUCTION GRID EGEE is a European project aimed at developing a European grid infrastructure for science with links to US, Latin America, India and China grids. In the first biennium little support (NA4 Activity Application Identification and Support) was given to chemistry. Starting from the second biennium the Beam Molecular simulator (SIMBEX) was produced and the Chemistry virtual organization (VO) COMPCHEM admitted as unfunded In the third biennium a prototype version of the Grid Molecular Simulator GEMS was designed and implemented

7. THE COST EFFECTIVENESS OF THE EGEE PRODUCTION GRID • On public network • Out of shelves technology (from PC to supercomputers) • Evolutionary approach • Aggregated local nodes (the Perugia case)

8. The initial Beowulf-Mosix “GRID” • front-end + 15 nodes • 2 proc. PIII 1.0 Ghz, • 2 Gbytes RAM, • NIC Intel e1000 Gigabit Ethernet • Switch 3ComGigabit Ethernet 16 port • Hybrid architecture: • Beowulf • MOSIX

9. The additional cluster “GRID” • front-end + 40 nodes • proc. Intel Xeon Quadcore X3210 2.13 GHz, • 164 GB RAM, • 8 Mb Cache L2 MB (2x6) Level 2 RJ 45 Ethernet • Switch 3Com2 Switch Gigabit Ethernet 48 ports

10. FURTHER ESPANSION OF THE PERUGIA NODE Coordination to the original nucleus of scientists from Computer Science and Chem-dynamics with those of the local section of INFN, CNR, Chem-electronics, Drug-design. Gathering together the related hardware (different Tier3) and software tools and experimenting new ones (like GPUs, workflows and framework) Assembling the specific packages of the different scientific areas Widening the service area in grid porting, training and education.

11. FURTHER ESPANSION OF COMPCHEM Increase the number of users. Increase the number of programs Improvement of the support to users (registration, porting, training (2 schools), …) Connection with other VOs and application to INFRA-2010 as part of the ROSCOE application.

12. 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 Networks Fiber optics THE DEPENDABILITY OF THE EGEE PRODUCTION GRID

13. NO ADEQUATE BANDWIDTH and RELIABILITY of public networks NO STANDARD MIDDLEWARE (Glite, Arc, Unicore) NO EFFICIENT PARALLELIZATION TOOLS (MPI Libraries), PORTALS, WORKFLOWS NO ESTABLISHED DATA AND PACKAGE MODELS AND STANDARDS THE CONSISTENCY AND DEPENDABILITY OF THE EGEE PRODUCTION GRID

14. 2 - PAVING THE WAY TO THE EUROPEAN GRIDINITIATIVE (EGI) The structuring of a new true pan-european grid infrastructure

15. MISSION and STRUCTURE • Support international research teams and projects by means of an interna-tional infrastructure to sharedata (knowledge) and compute resources • Common infrastructure • national funding of computing research infrastructures via NGI platforms • coordination through EGI.ORG • steering by User Communities

16. EGI Basic Elements • EGI ORGANIZATION • EGI.ORG a light coordination body • Central location + decentralized bodies • Synergy for EU level added value • Coordination activities • Links with external bodies (Consortia, ..) • NGIs Stakeholders of EGI.ORG • national funding • own agenda and tasks

17. EGI Stakeholders

18. NGI User Community Tasks • VO Registration and VO Database • Site Validation Tests • Core VO Service Provision • Help Desk and User Technical Support • Documentation • Help Desk for Application Porting • Case Studies • Consulting • Application Database • Development of Services (Grid Planning)

19. NGI User Community Tasks • Integration of Domain’s Resources • Feedback • Dissemination • Community-Specific Gateways and Help Desk • Validation of Site Resources/Services • Coordination • User Conference – User Forum Events • Technical Coordination Grid Planning • Regional Coordination

20. EGI User Community Goals • Gatheringrequirements from the user communities. • Carrying out a review process to integrate useful “external” software • Establishing Science Gateways that expose common tools and services to user communities in the various disciplines (specialized support center, SSC). • Establishing technical collaborations with the large ERI projects • Providing “umbrella” services for collaborating projects, (e.g. maintenance of repositories, FAQs, wikis, etc.) • Maintaining a European Grid Application Database that allows applications to be “registered” • Organising European events such as the User Forum meetings and topical meetings • Providing services for new communities • Ensuring high quality documentation and training services.

21. OTHER ACTORS • ass. members: EIROs (Cern, Esa, Ebi, ..) - supplement NGIs for services & resources in specific sectors • partners: MiddleWare Consortia (gLite, Unicore, arc) • provide the OS middleware

22. EGI Management/Governance Members NGI1, NGI2, NGI3, … NGIn Associate Members e.g. EIROforum member, … Non-voting Representatives extra-EU NGIs, Chair of UFSC, … User Forum Steering Committee (UFSC) User Forum (UF) EGI Council EGI.org EGI Director AdvisoryCommittees e.g. Middleware Coordination Board (MCB) UCO User Coordination CTO MiddlewareMaintenance CAO Admin & PR COO Operations Administration& PR Unit OperationsUnit MiddlewareUnit User Community Services

23. FROM EGEE to EGI • January 20th 2009: Vote for approval of the EGI Blueprint by the EGI_DS Policy Board; first list of NGIs subscribing to the principles of EGI. • March 2nd 2009: Catania Workshop – Approval of AMSTERDAM as the EGI location; common work plan with EGEE on transition scenario. • Spring 2009: Transition team in place with authority to prepare key tasks and to negotiate with the EU; work on calls for EC funding • Summer 2009: The core of the EGI project transition team is agreed and confirmed by the Policy Board; latest date for formal establishment of EGI including location. • Autumn 2009: The EGI project proposal is prepared and submitted for approval to the EC. • January 1st, 2010: EGI is operational, with all key personnel being appointed (who may not yet be working for EGI, as e.g. still working for EGEE III or any other project). • April 2010: EGI takes over from EGEE-III

24. 3 – FROM SIMBEX (SIMULATOR of MOLECULAR BEAM EXPERIMENTS) TO GEMS (GRID EMPOWERED MOLECULAR SIMULATOR) A sistematic grid approach to molecular and materials science simulations • O. Gervasi, A. Lagana’, SIMBEX: a portal for the a priori • simulation of crossed beam experiments,  Future generation • Computer Systems, 20(5), 703-716 (2004) • O. Gervasi, C. Dittamo, A. Lagana’, A Grid Molecular simulator • for E-science, Lecture Notes in Computer Science 3470, • 16-22 (2005).

25. RESEARCH PROJECTS CHEMISTRY COMPUTING ON THE NETWORK EU: Data grid, Digital libraries, …… COST (D23, (1999) METACHEM Metalaboratories (virtual laboratories made of geographically dispersed laboratories) for computational chemistry complex applications; D37 (2004) GRIDCHEM computational chemistry applications for Grid computing). NATIONAL: analogous project funded on National resources.

26. 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 transient • Internal energy distribution of products • Key features of the potential

27. The concurrent TRAJECTORY kernel Define quantities of general use TRAJ Iterate over initial conditions the integration of individual trajectories (ABCTRAJ, etc.) Collect individual trajectory results return

28. VIRTUAL MONITORS FOR COMPUTED PRODUCT ANGULAR DISTRIBUTIONS OF THE VARIOUS CHANNELS H+ICl→Cl+HI H+ICl→HCl+I H+ICl→H+ICl

29. KNOWLEDGE FLOW OF GEMS A GRID EMPOWERED MOLECULAR SIMULATOR System input Interaction Dynamics Statistics Virtual Monitors

30. The INTERACTION module START Are ab initio calculations available? NO NO Are ab initio calculations feasible? Is there a suitable PES? NO INTERACTION YES YES YES SUPSIM Are dynamics calculations direct? Import the PES routine NO FITTING Take a database force field DYNAMICS

31. SUPSIM: the concurrent Ab initio approach Iterate over the system Geometries the call of ab initio suites of codes (GAMESS, GAUSSIAN, MOLPRO, etc) Define the characteristics of the ab initio calculation, the coordinates used and the Variable’s intervals SUPSIM L. Storchi, F. Tarantelli, A. Lagana’, Computing Molecular energy surfaces on the grid, Lecture Notes in Computer Science 3980, 675-683 (2006). return Collect single molecular geometry energy

32. AB INITIO CALCULATIONS • Methods • - wavefunction quantum approaches (MRCI) • - density functional theory (DFT) • Programs: often standard packages • - ACADEMIC like GAMESS US • - COMMERCIAL like GAUSSIAN

33. The FITTING Module 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

34. The DYNAMICS module Ap- proximate quantum calcula tions? Se- miclassical calcula- tions? Exact quantum calculations? NO NO NO DYNAMICS YES YES YES QDYN Integration of the exact quantum dynamics equations APPRQDYN Integration of the approximate or mixed QM and QC dynamics equations SEMICLASSICAL Integration of clas- sical equations of motion and of the associated classical action CLASSICAL Integration of the classical equations of motion OBSERVABLES

35. The QDYN PROCEDURES State specific (summed over final states) Single Initial quantum state? Multiple initial quantum states? NO Fully averaged NO QUANTUM DYNAMICS YES YES YES TD: single initial state atom diatom S matrix elements for several energies TI: single energy atom diatom S matrix elements for all Initial states MCTDH: reactive flux flux correla- tion function method CRP: cumulative reaction probabilities and Transition State theory OBSERVABLES

36. The concurrent time dependent approach • Iterate over initial conditions • the time propagation • (RWAVEPR, CYLHYP, etc.) Define quantities of general use TD • Collect single initial state • S matrix element return

37. The concurrent time independent approach Define quantities of general use including the integration bed TI Iterate over the reaction coor- dinate to build the interaction matrix Collect coupling matrix elements Broadcast coupling matrix Iterate over total energy value the integration of scattering equations return Collect state to state S matrix elements

38. The CLASSICAL PROCEDURES Many small body problem? Few single body problem? Few large body problem? NO Fully averaged NO CLASSICAL DYNAMICS YES YES YES VENUS: sfew body trajectory calculations DL_POLY, GROMACS: various ensembles calculations DLPOLY, GROMACS: reduced degrees of freedom Simplified or approaches OBSERVABLES

39. Using history files to rationalize mechanisms RECROSSING IN OH + HCl → H2O + Cl DIATOM-DIATOM REACTIVE PROCESSES

40. 4 – FROM THE COMPCHEM VO TO CMST SSC • Global approaches prompt collaboration, know how sharing and service providing • Collaboration prompts an evaluation of the commitment (including environmental care and social fairness) and of the productivity as well as the establishing of an economy • A. Lagana’, A. Riganelli, O. Gervasi,On the structuring of the computational chemistry virtual organization COMPCHEM,Lecture Notes in Computer Science 3980, 665-674 (2006).

41. COMPCHEM VO(http://compchem.unipg.it)‏ • is a virtual organization coordinated by the Perugia University running on the EGEE production Grid from the end of 2004 • 80 (system, development, application) users • 8000 CPUs (~8% of the EGEE resources)‏ • Strong ties with two COST actions: D23 (METACHEM, 1999) and D37 (GRIDCHEM, 2005) • Tight connections with other VOs of the Computational Chemistry cluster (eg. GAUSSIAN)

42. COMPCHEM ITALIAN Support sites‏ • se.grid.unipg.it (UNI-Perugia) • se-01.grid.sissa.it (SISSA-Trieste) • gridsrm.ts.infn.it (INFN-Trieste) • prod-se-01.pf.infn.it, prod-se-01.pf.infn.it Italian (INFN-Padova) • grid-e0-engine04.esrin.esa.int (ESA-esrin) • cmsdcache.pi.infn.it, gridse.pi.infn.it (INFN-Pisa) • grids.sns.it (SNS-Pisa) • aliserv1.ct.infn.it (INFN-Catania) • egse.frascati.enea.it, egse.cresco.portici.enea.it (GRISU.ENEA.Grid) • spacin-wn03.dna.unina.it (GRSU-SPACI-Napoli) • t2-dpm-01.na.infn.it (INFN-Napoli-Atlas) • grid2.fe.infn.it (INFN-Ferrara) • grid003.ca.infn.it (INFN-Cagliari)

43. COMPCHEM EUROPEAN Support sites‏ • plethon.grid.ucy.ac.cy (CY-01-Kimon) • grid05.lal.in2p3.fr, polgrid4.in2p3.fr (GRIF) • se02.marie.hellasgrid.gr, se01.marie.hellasgrid.gr (GR-06-iasa) • se01.grid.uoi.gr (GR-10-uoi) • se01.isabella.grnet.gr (HG-01-grnet) • se01.afroditi.hellasgrid.gr (HG-03-auth) • se01.kallisto.hellasgrid.gr (HG-04.cti-ceid) • se01.ariagni.hellasgrid.gr (HG-05.forth) • se01.athena.hellasgrid.gr (HG-06.ekt) • gridstore.cs.tcd.ie (csTCDie) • se.reef.man.poznan.pl (PSNC) • se2.egee.cesga.es (CESGA-EGEE) • se2.ppgrid1.rhu1.ac.uk (UKI-lt2-rhul)

44. COMPCHEM Applications • COLUMBUS Vienna (Austria) high-level ab initio molecular electronic structure calculations. • GAMESS-US Catania (Italy) high-level ab initio molecular quantum chemistry • ABC Perugia (Italy), Budapest (Hungary) quantum time-independent reactive dynamics • RWAVEPRPerugia (Italy), Vitoria (Spain) quantum time-dependent reactive dynamics • MCTDH Barcelona (Spain)multi-configurational time-dependent Hartree method • FLUSS Barcelona (Spain) Lanczos iterative diagonalisation of the thermal flux operator • DIFF REAL WAVEMelbourne (Australia)quantum differential cross-section (work in progress) • VENUS Vitoria (Spain)classical mechanicscross sections and rate coefficients • DL_POLY Iraklion (Greece), Perugia (Italy)molecular dynamics simulation of complex systems • CHIMERE Perugia (Italy)chemistry and transport eulerian model for air quality simulations

45. Millions of cpu hours consumption From the EGEE Accounting Portal at the Centro de Supercomputación de Galicia http://www3.egee.cesga.es/gridsite/accounting/CESGA/egee_view.html

46. The share of COMPCHEM

47. THE COMPCHEM MEMBERSHIP 1. USER PASSIVE: Runs other’s programs ACTIVE: Implements at least one program for personal usage 2. SW PROVIDER (from this level on one can earn credits) PASSIVE : Implements at least one program for other’s usage ACTIVE: Management at least one implemented program for cooperative usage 3. HW PROVIDER PASSIVE : Confers to the infrastructure at least a small cluster of processors ACTIVE: Contributes to deploy and manage the structure 4. MANAGER (STAKEHOLDER): Takes part to the development and the management of the virtual organization Further information at http://compchem.unipg.it

48. THE PLANNED SSC CMST GATHER EXISTING VOs IN CHEMISTRY AND MATERIALS SCIENCE and TECHNOLOGIES (COMPCHEM, GAUSSIAN, ….) IN A SINGLE SSC (CMST) ATTRACT NEW RESEARCH GROUPS AND LABORATORIES ACTIVE IN THE FIELD REPRESENT THE RELATED VOs at EGI USER FORUM AND STEERING COMMITTEE LEVEL INTERACT WITH THE OPERATIONAL AND USER SUPPORT UNITS OF EGI DESIGN A DEVELOPMENT STRATEGY FOR THE VOS OF THE AREA PROVIDE TRAINING OPPORTUNITIES AND COORDINATE DISSEMINATION ACTIVITIES

49. 5 – FURTHER GRIDIFICATION ACTIVITIES APPLY THE DECOMPOSITION METHODS TO OTHER PROGRAMS AND USE GRID PORTALS

50. Lecture notes in Computer Science recent papers A Grid Implementation of Direct Semiclassical Calculations of Rate Coefficients, 5592, 93 (2009), A. Costantini, N. Faginas Lago, A. Lagana, and F. Huarte A Grid Implementation of Direct Quantum Calculations of Rate Coefficients, 5592, 104 (2009), A. Costantini, N. Faginas Lago, A. Lagana, and F. Huarte A Grid Implementation of Chimere: Ozone Production in Central Italy, 5592, 115 (2009), A. Lagana, St. Crocchianti, Alessandro Costantini, Monica Angelucci, and Marco Vecchiocattivi Porting of the GROMACS package into the Grid Environment: testing of a new distribution strategy, 6019, 1-12 (2010), A. Costantini, E. Gutierrez, J. Lope Cacheiro, A. Rodriguez, O. Gervasi, A. Lagana, Accurate quantum dynamics on platforms: some effects of long range interactons on N+N2 reactivitiy, 6019, 41-52(2010), S. Rampino, F. Pirani, A. Lagana, E. Garcia