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Application Porting activities @ INFN. Giuseppe LA ROCCA INFN Catania EGEE’08 Conference Istanbul, 22-26 September 2008. CNR - ITB. Porting the „ MrBayes ” application to EGEE. Case study from INFN. General Introduction /1.

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Application Porting activities @ INFN

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Application Porting activities @ INFN

Giuseppe LA ROCCA

INFN Catania

EGEE’08 ConferenceIstanbul, 22-26 September 2008


Porting the „MrBayes” application to EGEE

Case study from INFN

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.

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.

Worker Node(s)

Worker Node(s)

Worker Node(s)

Job SubmissionTool

MrBayes’ application workflow

LFC Catalog

Computing Element(s)

LCG Resource Broker


Start video

User’s workstation

Robot Certificate

gLite UI +

Dissemination & outreach

Links and references

  • JST :


  • MrBayes + JST Implementation :


  • For further information :

    • Giacinto DONVITO []

    • Giuseppe LA ROCCA []

Porting the

Case study from INFN

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 thephysical 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.

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.

Some reconstructed instruments..


  • 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.

Worker Node(s)

Worker Node(s)

Worker Node(s)

ASTRA application workflow

ASTRA software experiment

Computing Element(s)

Resource Broker

gLite UI +

VOMS Server

User’s workstation

Implementation details

  • Packing the following packages :



    • alsa-oss-1.0.4-1.cvs.rh90.ccrma.i386.rpm


    • festival-1.4.2-16.i386.rpm

    • festival-devel-1.4.2-16.i386.rpm




  • Install the software experiment using SoftwareManager privilege under {VO_EUMED_SW_DIR} and publish the following software tag : VO-eumed-ASTRA

ASTRA user interfaces

Dissemination & outreach


  • 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

    • 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

Links and Credits

  • The ASTRA Project website :

    • []

  • For further information :

    • Domenico VICINANZA


    • Responsible for testing and modeling:

      Mariapaola SORRENTINO (Conservatory of Music of Salerno)


    • Responsible for development activities:

      Salvatore AVANZO (University of Salerno - Italy)


    • Responsible for gridification activities:

      Giuseppe LA ROCCA (INFN – Catania)


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