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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
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
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
“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
THE PERVASIVITY OF THE EGEE PRODUCTION GRID
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
• 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
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
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
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.
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.
High perfor-mance nets
Networks Fiber optics
Portals Security Communications
Resource Management MonitoringMiddleware
HP Components Problem Solving
Libraries Cost models
Program-Ming tools
Applications
Astrophysics Bioinformatics Earth observation
Geophysics Computational Chemistry
THE DEPENDABILITY OF THE EGEE PRODUCTION GRID
• 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
2 - PAVING THE WAY TO THE EUROPEAN GRID
INITIATIVE (EGI)The structuring of a new true pan-european grid
infrastructure
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
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
EGI Stakeholders
NGI2NGI 1
NGIn
…
Research InstitutesResearch InstitutesResearch TeamsResearch Teams
NGIsNGIsResource CentresResource Centres
EGI.orgEGI.org
NGI User Community Tasks
1. VO Registration and VO Database2. Site Validation Tests3. Core VO Service Provision4. Help Desk and User Technical Support5. Documentation6. Help Desk for Application Porting7. Case Studies8. Consulting9. Application Database10. Development of Services (Grid Planning)
NGI User Community Tasks
11. Integration of Domain’s Resources12. Feedback13. Dissemination14. Community-Specific Gateways and Help Desk15. Validation of Site Resources/Services16. Coordination17. User Conference – User Forum Events18. Technical Coordination Grid Planning19. Regional Coordination
EGI User Community Goals1. Gathering requirements from the user communities. 2. Carrying out a review process to integrate useful “external”
software3. 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 communities9. Ensuring high quality documentation and training services.
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
EGI Management/Governance
EGI.orgEGI Director
Non-voting Representativesextra-EU NGIs, Chair of UFSC, …
Associate Memberse.g. EIROforum member, …
MembersNGI1, NGI2, NGI3, … NGIn
EGI Council
AdvisoryCommittees
e.g.Middleware
CoordinationBoard(MCB)
User Forum Steering
Committee(UFSC)
UserForum (UF)
MiddlewareUnit
Administration& PR Unit
OperationsUnit
User Community Services
CTOMiddleware
Maintenance
CAOAdmin & PR
UCOUser Coordination
COOOperations
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
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
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.
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
The concurrent TRAJECTORY kernel
TRAJ
return
Iterate over initial conditionsthe integration of individualtrajectories (ABCTRAJ, etc.)
Define quantities of generaluse
Collect individual trajectory results
VIRTUAL MONITORS FOR COMPUTED PRODUCT ANGULAR DISTRIBUTIONS OF THE VARIOUS CHANNELS
H+ICl→Cl+HI
H+ICl→H+ICl H+ICl→HCl+I
KNOWLEDGE FLOW OF GEMS A GRID EMPOWERED MOLECULAR SIMULATOR
Interaction
Statistics
Dynamics
Virtual Monitors
System input
The INTERACTION module
INTERACTION
DYNAMICS
Is therea suitable PES?
Are ab initiocalculationsavailable?
Are ab initiocalculations
feasible?
NO NO NO
YES YES
YES
START
FITTING
SUPSIM
Are dynamics
calculationsdirect?
NOImport the PES routine
Take a databaseforce field
SUPSIM: the concurrent Ab initio approach
SUPSIM
return
Iterate over the systemGeometries 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).
AB INITIO CALCULATIONS
• Methods - wavefunction quantum approaches (MRCI) - density functional theory (DFT)
• Programs: often standard packages - ACADEMIC like GAMESS US - COMMERCIAL like GAUSSIAN
The FITTING Module
FITTING
Return
Are asym-ptotic values
accurate?
Are remai-ning valuesinaccurate?
Do ab initiovalues have the
proper sym-metry?
Enforce the propersymmetry
Application using fitting programs to
generate a PESroutine
Modify asym-ptotic values
NO NONO
Modify short andlong range values
YES YESYES
The DYNAMICS module
DYNAMICS
OBSERVABLES
Exact quantum
calculations?
NO NO
YES YES
CLASSICALIntegration of the
classicalequations of
motion
APPRQDYNIntegration of the approximate or mixed QM and QC dynamicsequations
QDYNIntegration of theexact quantum
dynamics equations
SEMICLASSICALIntegration of clas-sical equations of motion and of the
associated classicalaction
YES
NO Ap-
proximate quantumcalculations?
Se-miclassical
calcula-tions?
The QDYN PROCEDURES
QUANTUMDYNAMICS
OBSERVABLES
Single Initial
quantum state?
Multiple initial
quantum states?
NO NO
YES YES
CRP: cumulative
reaction probabilities and TransitionState theory
TI: single energyatom 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 functionmethod
Statespecific
(summed overfinal states)
YES
Fully averaged
The concurrent time dependent approach
TD
return
•Iterate over initial conditions•the time propagation •(RWAVEPR, CYLHYP, etc.)
Define quantities of generaluse
•Collect single initial state•S matrix element
The concurrent time independent approach
TI
return
Iterate over total energy value the integration of scattering
equations
Define quantities of generaluse 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
The CLASSICAL PROCEDURES
CLASSICALDYNAMICS
OBSERVABLES
Few single body
problem?
Few largebody
problem?
NO NO
YES YES
Simplified or approaches
DL_POLY, GROMACS:
variousensembles
calculations
VENUS: sfew body trajectory
calculations
DLPOLY,GROMACS:
reduceddegrees of
freedom
Manysmall body
problem?
YES
Fully averaged
Using history files to rationalize mechanisms
RECROSSING IN OH + HCl → H2O + Cl
DIATOM-DIATOM REACTIVE
PROCESSES
QuickTime™ and aCinepak decompressor
are needed to see this picture.
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).
•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)
• 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)
• 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)
• 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
Millions of cpu hours consumption
From the EGEE Accounting Portal at the Centro de Supercomputación de Galiciahttp://www3.egee.cesga.es/gridsite/accounting/CESGA/egee_view.html
The share of COMPCHEM
THE COMPCHEM MEMBERSHIP1. 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
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
5 – FURTHER GRIDIFICATION ACTIVITIES
APPLY THE DECOMPOSITION METHODS TO OTHER PROGRAMS AND USE GRID PORTALS
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. HuarteA Grid Implementation of Chimere: Ozone Production in Central Italy, 5592, 115 (2009), A. Lagana, St. Crocchianti, Alessandro Costantini, Monica Angelucci, and Marco VecchiocattiviPorting 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
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).
THE FLUSS PROGRAMcalculate the individual
eigenfunctions
TIME INTEGRATIONdistribute the individual
propagations
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
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
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
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
0
500
1000
1500
2000
2500
Results of ABC
Time grid
Time local
ABC
Tim
e (
min
)
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
0
50000
100000
150000
200000
250000
300000
Results of ABC
Time grid
Time local
ABC
Tim
e (
min
)
6 – FORWARD LOOKING
DEVELOP A (COLLABORATIVE) GRID ECONOMY
• Service oriented approaches
• QoS and QoU
• Credit system and cost of services
C. Manuali – A. Laganà University of Perugia (IT)
CGW’09 Krakow (PL) – October 12-14, 2009GriF: 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.
C. Manuali – A. Laganà University of Perugia (IT)
CGW’09 Krakow (PL) – October 12-14, 2009
GriF in the Grid scenarioThe 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 figurephases 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.
C. Manuali – A. Laganà University 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
AIR POLLUTION SIMULATION
CPM10 Concentration from CHIMERE-aerosols
Gas hydrates (Clathrates): water hydrogen bonded structures caging gas molecules
• ClCl22
• HH22SS
• COCO22
• CHCH44
• HH22
• etc.etc.
HYDROGEN HYDRATE
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