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. “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) The Grid: from dreams to reality

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

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 3Com Gigabit 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 3Com 2 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. High perfor- mance nets NetworksFiber optics Portals Security Communications Resource Management Monitoring Middleware HP Components Problem Solving Libraries Cost models Program- Ming tools Applications AstrophysicsBioinformatics Earth observation Geophysics Computational Chemistry 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 GRID INITIATIVE (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 share data (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 1.VO Registration and VO Database 2.Site Validation Tests 3.Core VO Service Provision 4.Help Desk and User Technical Support 5.Documentation 6.Help Desk for Application Porting 7.Case Studies 8.Consulting 9.Application Database 10.Development of Services (Grid Planning)

19. NGI User Community Tasks 11.Integration of Domain’s Resources 12.Feedback 13.Dissemination 14.Community-Specific Gateways and Help Desk 15.Validation of Site Resources/Services 16.Coordination 17.User Conference – User Forum Events 18.Technical Coordination Grid Planning 19.Regional Coordination

20. EGI User Community Goals 1.Gathering requirements from the user communities. 2.Carrying out a review process to integrate useful “external” software 3.Establishing Science Gateways that expose common tools and services to user communities in the various disciplines (specialized support center, SSC). 4.Establishing technical collaborations with the large ERI projects 5.Providing “umbrella” services for collaborating projects, (e.g. maintenance of repositories, FAQs, wikis, etc.) 6.Maintaining a European Grid Application Database that allows applications to be “registered” 7.Organising European events such as the User Forum meetings and topical meetings 8.Providing services for new communities 9.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 EGI.org EGI Director Non-voting Representatives extra-EU NGIs, Chair of UFSC, … Associate Members e.g. EIROforum member, … Members NGI 1, NGI 2, NGI 3, … NGI n EGI Council Advisory Committees e.g. Middleware Coordination Board (MCB) User Forum Steering Committee (UFSC) User Forum (UF) Middleware Unit Administration & PR Unit Operations Unit User Community Services CTO Middleware Maintenance CAO Admin & PR UCO User Coordination COO Operations

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) - 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). A sistematic grid approach to molecular and materials science simulations

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

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

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

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

31. SUPSIM: the concurrent Ab initio approach SUPSIM return 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 Collect single molecular geometry energy L. Storchi, F. Tarantelli, A. Lagana’, Computing Molecular energy surfaces on the grid, Lecture Notes in Computer Science 3980, 675- 683 (2006).

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 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

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

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

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

37. The concurrent 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 Collect coupling matrix elements Collect state to state S matrix elements

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

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. 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 RWAVEPR Perugia (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 WAVE Melbourne (Australia) quantum differential cross-section (work in progress) VENUS Vitoria (Spain) classical mechanics cross 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 COMPCHEM Applications

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 1.GATHER EXISTING VOs IN CHEMISTRY AND MATERIALS SCIENCE and TECHNOLOGIES (COMPCHEM, GAUSSIAN, ….) IN A SINGLE SSC (CMST) 2. ATTRACT NEW RESEARCH GROUPS AND LABORATORIES ACTIVE IN THE FIELD 3.REPRESENT THE RELATED VOs at EGI USER FORUM AND STEERING COMMITTEE LEVEL 4.INTERACT WITH THE OPERATIONAL AND USER SUPPORT UNITS OF EGI 5.DESIGN A DEVELOPMENT STRATEGY FOR THE VOS OF THE AREA 6.PROVIDE TRAINING OPPORTUNITIES AND COORDINATE DISSEMINATION ACTIVITIES

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

50. A Grid Implementation of Direct Semiclassical Calculations of Rate Coe ffi cients, 5592, 93 (2009), A. Costantini, N. Faginas Lago, A. Lagana, and F. Huarte A Grid Implementation of Direct Quantum Calculations of Rate Coe ffi cients, 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 Lecture notes in Computer Science recent papers

51. THE MCTDH METHOD Diagonalisation of the thermal flux operator defined onto a dividing surface to build a reduced Krylov subspace (iterative diagonalisation by consecutive application of the thermal flux operator on a trial wave function). The outcome is a set of eigenvalues and eigenstates of the thermal flux operator. Time propagation of the thermal flux eigenstates employing MCTDH. Calculation of observables: k(T), N(E).

52. THE FLUSS PROGRAM calculate the individual eigenfunctions

53. TIME INTEGRATION distribute the individual propagations

54. FURTHER GENERALIZATION OF QUANTUM DYNAMICS Broaden the offering of cooperating/competing packages as web services Avoid electron-nuclei separation (Born- Oppenheimer) and generalize coordinates to N- body problems Introduce easy ways of composing packages

55. GENERALIZE GEMS WORKFLOWS Inter-job workflow - Wrap the jobs - Treat the jobs as objects - Define composition rules and data links Intra-job workflows - Define tools as for inter-job workflows via directives to be inserted inside the jobs

56. PGRADE ABC workflow Gridification of ABC  classical command line interface  P-GRADE Grid Portal 2.7 Executor: executed as many times in parallel as many parameters are generated by “Generator” Collector: collects all output files into a single TAR file Generator: generates input files with different parameters

57. Execution of 4 ABC parameter study jobs for F + HD reaction varying jmax and rmax on - a local machine (P4 3.4GHz, 1GByte RAM)‏ - 4 WMS selected clusters that support COMPCHEM VO Better speed-up can be achieved with more parameter jobs Performance

58. Execution of 500 ABC parameter study jobs for F + HD reaction on - a local machine (P4 3.4GHz, 1GByte RAM)‏ - WMSs selected clusters that support COMPCHEM VO Performance

59. 6 – FORWARD LOOKING

60. DEVELOP A (COLLABORATIVE) GRID ECONOMY Service oriented approaches QoS and QoU Credit system and cost of services

61. C. Manuali – A. LaganàUniversity of Perugia (IT) CGW’09 Krakow (PL) – October 12-14, 2009 GriF: a collaborative tool for grid empowering to computational applications GriF is meant to make grid applications black box like and to push the grid computing to a higher level of transparency (Clouds Computing) in which better memory usage, reduced cpu and wall times consumption as well as an optimized distribution of tasks over the grid are automatically performed. GriF is a collaborative JAVA Service Oriented Architecture (SOA) framework which provides grid services aimed at exploiting the articulation of computational applications in sequential, concurrent or alternative paths on the EGI Grid by adopting SOA and Web Service standard technologies. GriF improves the grid by providing the VO or SSC users with standard operational modalities based on friendly user driven services. Moreover, GriF creates collaborations to add value for all parties involved also by working with service providers which can offer applications to users by composing one or more services without knowing their implementation details.

62. C. Manuali – A. LaganàUniversity of Perugia (IT) CGW’09 Krakow (PL) – October 12-14, 2009 GriF in the Grid scenario The SOA organization consists essentially of two JAVA servers and the JAVA client. The two JAVA servers are YR (Yet a Registry, used to drive the initial discovery of the Web Services offered by the VO or the SSC) and YP (Yet a Provider, used to hold the VO or SSC Web Services). The JAVA client is YC (Yet a Consumer, used to interact with GriF in Wizard/Expert mode). In the top part of the figure phases 1 and 2 show the services discovery and phases 3-7 show a typical program execution performed on the EGI Grid in which the selected YP takes care of running the job on the associated User Interface (UI). In the bottom part of the figure the grid proxy management and its YC interactions are shown.

63. C. Manuali – A. LaganàUniversity of Perugia (IT) CGW’09 Krakow (PL) – October 12-14, 2009 GriF @ Work (Wizard Mode) 1 - Using the “Framework Management” tab to create the Grid Proxy and check the GriF Status 2 - Using the “Wizard Mode” to start the Grid Job (Parametric Jobs on EGI for the ABC program), check the Job’s Status and retrieve the results

64. AIR POLLUTION SIMULATION CPM10 Concentration from CHIMERE-aerosols

65. Gas hydrates (Clathrates): water hydrogen bonded structures caging gas molecules Cl 2 Cl 2 H 2 S H 2 S CO 2 CO 2 CH 4 CH 4 H 2 H 2 etc. etc.

66. HYDROGEN HYDRATE

67. ACKNOWLEDGEMENTS CDK group, Dept. Chemistry, Perugia (Crocchianti, Faginas, Pacifici, Skouteris, Costantini, Rampino, Manuali) HPC group, Dept. Math&Inf, Perugia (Gervasi, Tasso) Qdyn group, COST D37 (Garcia, Huarte, Lendvay, Nyman, Balint-Kurti, Farantos) Other groups of COST D37 COST-ESF, EU-FP7, MIUR (It), ESA funding TANKS FOR YOUR ATTENTION