1. EGEE-III INFSO-RI-222667 Enabling Grids for E-sciencE www.eu-egee.org EGEE and gLite are registered trademarks Application Porting activities @ INFN Giuseppe LA ROCCA INFN Catania giuseppe.larocca@ct.infn.it EGEE’08 Conference Istanbul, 22-26 September 2008

2. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Porting the „MrBayes” application to EGEE Case study from INFN CNR - ITB

3. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 General Introduction /1 MrBayes is a program for the Bayesian estimation of phylogeny. Bayesian inference of phylogeny is based on the posterior probability distribution of trees, which is the probability of a tree conditioned on the observations. – To approximate the posterior probability distribution of trees MrBayes uses a simulation technique called Markov Chain Monte Carlo (or MCMC). The program takes as input a character matrix in a NEXUS file format.

4. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 General Introduction /2 The output is several files with the parameters that were sampled by the MCMC algorithm. The application is CPU demanding, especially if the MPI version of the software is used. Problem Domain DevelopersUser Community EGEE VO BiologyGiacinto DONVITO Giuseppe LA ROCCA ITB Bari BioinformaticsGILDA, EELA, BIOMED Frequency of usage Size of processed/generated data sets #Jobs Submitted Mediumfew KbytesFew hundreds

5. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Computing Element(s) LCG Resource Broker LFC Catalog SE Worker Node(s) MrBayes’ application workflow Worker Node(s) Robot Certificate gLite UI + User’s workstation Job Submission Tool Start video

6. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 User interfaces

7. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 1.Starting from Feb. 2008 also the Italian INFN CA will start to issue Robot Certificates. Thanks to these new certificates biologists will be able to access the grid sharing the certificate installed on the portal. 2.UK and NL CA are already issuing robot certificates 3.A personal credential which can perform automated tasks on behalf of the user. Robot Certificates https://security.fi.infn.it/CA/mgt/restricted/ucert_robot.php

8. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 In order to strong reduce the risks of having the portal certificate compromised and improve the security, the INFN CA has decided to issue this new certificate on board of the Aladdin eToken PRO 32K smart card. Each smart card can support several robot certificates: one for each application user wants to share with the other. – An user ’ s PIN is prompted every time user try to read the certificate on board of the smart card to generate a proxy. – A first prototype of Grid Portal using robot certificate on board of this hardware has been successfully designed. Robot Certificates

9. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Job Submission Tool: is driven by the concept of “Task” as the applications are – Each task could be independent or could be described as depended from another “Task” – Each task is described by a “status” – The task is executed by a wrapper that takes care of monitoring the task:  If the task is correctly executed the wrapper can change the status of the task from “Free” to “Done”  If a single step on the job execution fails, the whole task is considered failed and automatically rescheduled JST characteristics

10. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 JST tool takes care of submitting jobs, retrieving the output and monitoring the status of each task It is able to deal with accidental failure of grid services It is possible to change at run time the priority of each task/application JST characteristics

11. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Dissemination & outreach

12. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Links and references JST : – http://webcms.ba.infn.it/cms- software/index.html/index.php/Main/JobSubmiss ionTool http://webcms.ba.infn.it/cms- software/index.html/index.php/Main/JobSubmiss ionTool MrBayes + JST Implementation : – https://glite-tutor1.ct.infn.it https://glite-tutor1.ct.infn.it For further information : – Giacinto DONVITO [giacinto.donvito@ba.infn.it] – Giuseppe LA ROCCA [giuseppe.larocca@ct.infn.it]

13. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Porting the Case study from INFN

14. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 General introduction The ASTRA (Ancient instrument Sound/Timbre Reconstruction Application) projects aims to reconstruct the sound or timbre of ancient instruments using archaeological data as fragments from excavations, written descriptions, pictures... The technique used is the physical modeling synthesis, a complex digital audio rendering technique which allows to recreate a model of the musical instrument and produce the sound by simulating its behavior as a mechanical system.

15. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Reason for gridification Physical modeling synthesis is a really computing intensive technique since the complex models of the musical instruments are solved by integrating numerical coupled differential equations. – To have an idea of the needed time for simulation, on a Pentium IV 1.6 Ghz, 512MB RAM Personal Computer to correctly reproduce a sound lasting for 30 seconds it could be required more than 4 hours. Problem Domain OwnerDevelopersUser Community EGEE VO HumanitiesConservatorio di Musica di Salerno Salvatore AVANZO Giuseppe LA ROCCA MariaPaola SORRENTINO Domenico VICINANZA MusiciansEUMED Frequency of usage Size of processed/generated data sets #Jobs Submitted So far mainly during public demonstrations few KbytesFew hundreds

16. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Some reconstructed instruments..

17. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Benefits The benefits of this system are far-reaching. ASTRA not only makes it possible to recreate instruments that previously would have been either too expensive or too difficult to manufacture by hand, it also allows any model and its associated data to be accessed by other parties. Research data can be shared around the world, making it a truly international project of immense value to working archaeologists and historians.

18. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Computing Element(s) Resource Broker Worker Node(s) gLite UI + ASTRA application workflow Worker Node(s) User’s workstation ASTRA software experiment VOMS Server

19. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Implementation details Packing the following packages : – alsa-lib-1.0.10-1.cern.i386.rpm – alsa-lib-devel-1.0.10-1.cern.i386.rpm – alsa-oss-1.0.4-1.cvs.rh90.ccrma.i386.rpm – alsa-utils-1.0.10-1.cern.i386.rpm – festival-1.4.2-16.i386.rpm – festival-devel-1.4.2-16.i386.rpm – lame-3.95.1-1.fr.i386.rpm – lame-devel-3.95.1-1.fr.i386.rpm – libasound2-1.0.10-1.cern.i386.rpm Install the software experiment using SoftwareManager privilege under {VO_EUMED_SW_DIR} and publish the following software tag : VO-eumed-ASTRA

20. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 ASTRA user interfaces

21. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Dissemination & outreach

22. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Download Epigonion sound recostruction example (generated on the EUMEDCONNECT infrastructure) – Middle age piece (G. Dufay) played on 4 recostructed Epigonions, wooden resonant structure, plucked and hammered strings Middle age piece (G. Dufay) played on 4 recostructed Epigonions, wooden resonant structure, plucked and hammered strings – Excerpt from a XVII Century piece (C. Monteverdi) played on 4 recostructed Epigonions, wooden resonant structure, plucked and hammered strings Excerpt from a XVII Century piece (C. Monteverdi) played on 4 recostructed Epigonions, wooden resonant structure, plucked and hammered strings – Bach fugue played on a recostructed series of monochords, wooden resonant structure, plucked strings Bach fugue played on a recostructed series of monochords, wooden resonant structure, plucked strings

23. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 Links and Credits The ASTRA Project website : – www.astraproject.org [info@astraproject.org] www.astraproject.org For further information : – Domenico VICINANZA [domenico.vicinanza@dante.org.uk] – Responsible for testing and modeling: Mariapaola SORRENTINO (Conservatory of Music of Salerno) [mariapaola@astraproject.org] – Responsible for development activities: Salvatore AVANZO (University of Salerno - Italy) [salvatore.avanzo@gmail.com] – Responsible for gridification activities: Giuseppe LA ROCCA (INFN – Catania) [giuseppe.larocca@ct.infn.it]

24. Enabling Grids for E-sciencE EGEE-III INFSO-RI-222667 http://grid.ct.infn.it/egee_applications/survey/ This page will be accessible by means of personal certificate. Using credentials will be possible to update application status.