1. E-infrastructure shared between Europe and Latin America www.eu-eela.org 1 E-Infraestructure shared between Europe and Latin America José Manuel Gutiérrez manuel.gutierrez@unican.es EELA is project funded by the European Union under contract 026409 EELA Applied Meteorology Group http://www.meteo.unican.es High-Performance GRID Computing. Activities within EELA Project in Biomedicine and Climate 2nd International Seminar on Genomics, Proteomics and Bioinformatics Popayán (Colombia), 25-27 oct. 2006.

2. E-infrastructure shared between Europe and Latin America www.eu-eela.org 2 Local clusters in Santander

3. E-infrastructure shared between Europe and Latin America www.eu-eela.org 3 Surgery planning & visualisation Flooding control MIS HEP data analysis weather & pollution modelling level 1 - special hardware 40 MHz (40 TB/sec) level 2 - embedded processors level 3 - PCs 75 KHz (75 GB/sec) 5 KHz (5 GB/sec) 100 Hz (100 MB/sec) data recording & offline analysis Task 1.0: Co-ordination & management Aplicaciones En distintas disciplinas existen problemas que requieren computación de alto rendimiento a través de paralelización de procesos y/o de ejecución de múltiples trabajos.

4. E-infrastructure shared between Europe and Latin America www.eu-eela.org 4 CrossGrid - International Testbed Organisation UCY NikosiaDEMO Athens Auth Thessaloniki CYFRONET Cracow ICM & IPJ Warsaw PSNC Poznan II SAS Bratislava FZK Karlsruhe UvA Amsterdam CSIC Valencia UAB Barcelona CSIC Santander CSIC Madrid LIP Lisbon USC Santiago TCD Dublin CrossGrid Project

5. E-infrastructure shared between Europe and Latin America www.eu-eela.org 5 Desarrollada a mediados de los noventa. Utilización de recursos computacionales distribuidos, heterogéneos, dinámicos y, de forma habitual, paralelos. Globus Toolkit y OGSA — software intermedio (middleware) y estándar para construir aplicaciones. Diversos proyectos de investigación y productos comerciales desarrollando esta tecnología. Sería fantástico que la potencia de cómputo estuviese disponible de la misma manera que la electricidad (grid) (Ian Foster). Computación GRID

6. E-infrastructure shared between Europe and Latin America www.eu-eela.org 6 Estructura del GRID Grid Resource Allocator Manager Monitoring and Discovering Sys. Grid Resource Inf. Service Grid Index Inf. Service GridFTP

7. E-infrastructure shared between Europe and Latin America www.eu-eela.org 7 UI Broker Optimal Resource Allocation Replica/Data Manager? WEB SERVICE FINDER? Master Slave CE SE CACHED Ejemplo de "job"

8. E-infrastructure shared between Europe and Latin America www.eu-eela.org 8 EELA. Goal and Objectives E-infrastructure shared between Europe and Latin America Goal: To build a bridge between consolidated e- Infrastructure initiatives in Europe and emerging ones in Latin America. Objectives:  Establish a human collaboration network between Europe and Latin America  Setting a pilot e-infrastructure in Latin America  Identifying and promoting a sustainable framework for e-Science in Latin America

9. E-infrastructure shared between Europe and Latin America www.eu-eela.org 9 Partners Spain: CIEMAT, CSIC, UPV, RED.ES, UC Italy: INFN Portugal: LIP International: CLARA CERN EU Latin America Venezuela: ULA Cuba: CUBAENERGIA Chile: UTFSM, REUNA, UDEC Peru: SENAMHI Mexico: UNAM Argentina: UNLP Brazil: UFRJ, CNEN, CECIERJ/CEDERJ, RNP, UFF

10. E-infrastructure shared between Europe and Latin America www.eu-eela.org 10 Structure WP2. Pilot testbed operation and support GEANT, RedCLARA and European and Latin American NRENs will provide the network infrastructure. The grid infrastructure will be based on the EGEE middleware framework. WP1. Project administrative and technical management WP3. Identification and support of Grid-Enhanced applications WP4. Dissemination activities

11. E-infrastructure shared between Europe and Latin America www.eu-eela.org 11 WP3. Applications Task 3.1. Biomed Applications Task 3.2. HEP Applications Task 3.3. Additional Applications: E-Learning Climate Deliverable D3.1.1. Selection Report Biomedicine and HEP Applications

12. E-infrastructure shared between Europe and Latin America www.eu-eela.org 12 Context: –The biomedical applications being deployed on the pilot EELA infrastructure have been identified from current existing ones already in use in EGEE, and from the expertise and research activity of the LA and EU partners in EELA. –The target of the biomedical part of EELA is to deploy Grid applications for the biomedical LA community to improve their research excellence and to foster the use of Grids in this community. –Applications are selected considering their relevance for LA partners from the portfolio of existing and new applications. Project: –Two applications from the portfolio of mature EGEE biomedical applications have been selected by LA partners: GATE and WISDOM. –Two new applications were identified from the specifics needs of LA partners: BLAST and Phylogenetics. –EELA has joined the Ibero-American Portal of Bioinformatics. Biomedical Applications

13. E-infrastructure shared between Europe and Latin America www.eu-eela.org 13 GATE GATE: Géant4 Application for Tomographic Emission –GATE is a C++ platform based on the Monte Carlo Geant4 software designed to model nuclear medicine applications (PET, SPECT). This platform is also adequate for radiotherapy and brachytherapy treatment planning. –The objective of GATE is to use the Grid environment to reduce the computing time of Monte Carlo simulations in order to provide higher accuracy in a reasonable period of time. –The main benefit of using the Grid is that it has enabled medical users to access to realistic Monte Carlo simulations for their research in radiotherapy planning. The EELA Grid provide of enough computational resources to deal with the large requirements that this processing has. –GATE is already installed on several EELA’s partners sites.

14. E-infrastructure shared between Europe and Latin America www.eu-eela.org 14 WISDOM WISDOM: Wide In Silico Docking On Malaria –The objective of WISDOM is the creation of new inhibitors for a family of proteins produced by Plasmodium falciparum. This protozoan parasite causes malaria. –This application consists on the deployment of a high throughput virtual screening in the perspective of in silico drug discovery for neglected diseases. –Interest of EELA partners: selection of new targets for malaria; study of new targets for new parasitory diseases; and contribution with resources for the WISDOM data challenge. –The benefit of Grids is the reduction of the development cycle of new drugs for neglected diseases by providing in silico simulations of the selection of the adequate reactors for specific targets and the needed infrastructure to deal with the computational power required.

15. E-infrastructure shared between Europe and Latin America www.eu-eela.org 15 PHYLOGENY (MrBayes) Phylogeny with MrBayes program: –A phylogeny is a reconstruction of the evolutionary history of a group of organisms. –Bayesian inference is a powerful mathematical method which is implemented in the MrBayes program for estimating phylogenetic trees that are based on the “a posteriori” probability distribution of the trees. –The phylogenetic tools are widely demanded by LA bioinformatics community. –A Grid service for the parallelised version of MrBayes application will be developed and a simple interface will be deployed on the Ibero-American Portal of Bioinformatics. This Grid-enabled service will make use of EELA resources to run phylogenetic studies at high performance.

16. E-infrastructure shared between Europe and Latin America www.eu-eela.org 16 BLAST BLAST: Basic Local Alignment Searching Tool –BLAST finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. –The process of finding homologous of sequences is computionally-intensive. The size of available non-redundant databases increases daily. Since databases are periodically updated, the periodically update of the previous studies is convenient. –The use of Grid will allow to increase the number of fragments to be analysed and the periodical update of this information. –A Grid service for running MPIBlast on the EELA grid, and using the Ibero-American portal of Bioinformatics (CECALC- ULA), has been developed.

17. IST-2006-026409 www.eu-eela.org E-infrastructure shared between Europe and Latin America Blast in Grids (BiG) Ignacio Blanquer Universidad Politécnica de Valencia

18. E-infrastructure shared between Europe and Latin America www.eu-eela.org 18 BLAST (Basic Local Alignment Search Tool) is a Bioinformatics Procedure Applied to Identify Compatible Protein and Nucleotids Sequences in Protein and DNA Databases. BLAST can be Applied, Among Other Uses, to Annotate the Estimated Function of Unknown Sequences. BLAST is Computationally Intensive.

19. E-infrastructure shared between Europe and Latin America www.eu-eela.org 19 BLAST in Grids (BiG) –Grid Interface to MPI Blast. –Access Through a Web Portal (http://portal-bio.ula.ve/). –Access to EELA Grid Through Gate-to-Grid Using a Web Service Rersource Framework Interface. FASTA File (Input Sequence) AGTACGTAGTAGCTGC TGCTACGTGGCTAGCT AGTACGTCAGACGTAG ATGCTAGCTGACTCGA FASTA File (Input Sequence) AGTACGTAGTAGCTGC TGCTACGTGGCTAGCT AGTACGTCAGACGTAG ATGCTAGCTGACTCGA Execution Parameters Execution Parameters Protein Database (Non Redunda nt e.g.) Output Matches Xxxxx x x x x x xxx xx xxx x Output Matches Xxxxx x x x x x xxx xx xxx x

20. E-infrastructure shared between Europe and Latin America www.eu-eela.org 20 Design Objectives –Easy Interface with High Compatibility (Web Service + NCBI Based)  Same Parameters as BLAST.  User-friendly and Intuitive. –Support to Searching Simultaneously on Multiple Databases  Parallel Process on Multiple Database Queries. –Architecture Exportable to Other Common Problems  Modular Structure of the System Components.  Fast Capability to Migrate to Other Problems. –Scalability  Data Partition in Grid Approach Gives Scalability with Huge Quantities of Data. –High Performance  Grid Computing + MPI Parallel Jobs in Dedicated Clusters. –Robust  Fault Tolerance on Server and Client.

21. E-infrastructure shared between Europe and Latin America www.eu-eela.org 21 Hosted by the Ibero-American Portal of Bioinformatics (http://portal-bio.ula.ve) installed on the National Centre for Scientific Computation of the Universidad de Los Andes in Venezuela.http://portal-bio.ula.ve –The Application is Available Through the Bioinformatics Portal of CeCalcULA, Being Accessible for Registered Users.  http://www.cecalc.ula.ve/blast/ http://www.cecalc.ula.ve/blast/ –This portal also provides several on-line applications for registered users. It currently has almost 600 registered users from 70 countries (although 90% come from 10 countries). The Service is Also Being Used by the Genomic Centre of the Valencian Institute of Research on Agriculture (Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias) Executions –309 Runs Since June 2006. –3200 CPU Hours (133) Consumed.

22. E-infrastructure shared between Europe and Latin America www.eu-eela.org 22 Alineamiento con BLAST

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26. E-infrastructure shared between Europe and Latin America www.eu-eela.org 26 demo msraalrlkipmpatmadfafpslrafsivvaldkqhgigdgesipwrvpedmaffkdqttllrnkkpp tekkrnavvmgrktwesvpvkfrplkgrlnivlsskatveellaplpegkraaaaqdvvvvngglaeal rllarppycssietaycvggaqvyadamlspcveklqevyltriyttapactrffpfppentttawdla ssqgrrkseadglefeickyvprnheerqylel 1 demo msraalrlkipmpatmadfafpslrafs ivvaldkqhgigdgesipwrvpedmaff kdqttllrnkkpptekkrnavvmgrktw esvpvkfrplkgrlnivlsskatveell aplpegkraaaaqdvvvvngglaealrl larppycssietaycvggaqvyadamls pcveklqevyltriyttapactrffpfp pentttawdlassqgrrkseadglefei ckyvprnheerqylel

27. E-infrastructure shared between Europe and Latin America www.eu-eela.org 27 demo

28. E-infrastructure shared between Europe and Latin America www.eu-eela.org 28 Vicente Hernández, Ignacio Blanquer Universidad Politécnica de Valencia Camino de Vera s/n 46022 Valencia, Spain Tel: +34-963879743 Fax. +34-963877274 E-mail:vhernand@dsic.upv.esvhernand@dsic.upv.es iblanque@dsic.upv.es

29. E-infrastructure shared between Europe and Latin America www.eu-eela.org 29 Climate Models Conservación de energía, masa, momento, vapor de agua, ecuación de estado de gases. 360x180x32 x nvar v = (u, v, w), T, p,  = 1/  y q

30. E-infrastructure shared between Europe and Latin America www.eu-eela.org 30 ESG Home

31. E-infrastructure shared between Europe and Latin America www.eu-eela.org 31 Subsetting List

32. E-infrastructure shared between Europe and Latin America www.eu-eela.org 32 Grid+OpenDAP Transparency Performance Typical Application Data (local) netCDF lib Application Data (remote) OpenDAP Client Application OpenDAP Via http Big Data (remote) ESG client Application ESG Grid + DODS OpenDAP Server ESG Server Distributed Application data OpenDAP Via Grid Security Resource Mgmt Analysis functions