Integration of MATLAB with Cometa infrastructure: case study with a scientific application

G. Castiglia1, M. Cipolla 2,4, P.P. Corso1, D. La Porta3,4

1Dipartimento di Scienze Fisiche ed Astronomiche - via Archirafi 36, 90123 Palermo2Dipartimento di Matematica ed Applicazioni - via Archirafi 34, 90123 Palermo3Dipartimento di Ingegneria Informatica – viale delle Scienze, 90128 Palermo

4Conzorzio Cometa

AbstractWe have integrated the MATLAB Distributed Computing Engine (MDCE) with the gLite middleware of the Grid infrastructure of the Cometa Consortium.

Our work has been focused on the identification of the critical MATLAB functions used to set up parallel, distributed or simple programs and also on the typical environment settings involved in the integration.

MATLAB itself provides a scheduler for submitting parallel jobs, our work focused on modifying a set of MATLAB’s functions in order to set properly the information used by the LSF scheduler of the Cometa GRID. These functions consist of both MATLAB m-file and UNIX scripts. The process of submission requires to specify if we are using shared or not-shared memory, furthermore we need to set different environment variables in order to copy all the files we need on the GRID. Finally, unix scripts are used to specify all the paths for the libraries needed to run MATLAB jobs which are submitted by using the gLite middleware.

In order to test the performance of MDCE in the COMETA parallel environment, we have implemented a code which simulates a Hydrogen molecule in the presence of laser radiation. These tests mainly deal with the check of the performance of the system both in terms of memory requirements (using different numerical integration box sizes) and in terms of CPU and communication time, using up to 128 processors.

The algorithm has been tested on boxes with 2000, 4000, 8000 and 16000 points by using up to 128 processors. Each figure shows the actual elapsed time (red line), the expected theoretical execution time (blue line) and the ratio between them (red line in the small plot).

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In order to solve the Schroedinger equation of our physical system we have developed a parallel MATLAB 2D finite-difference code in which the two electrons are considered quantum-particles while the nuclei are classical, fixed or moving, particles. The electron wavefunction has been discretized over a square box by using Nx grid points. The grid-point matrix is partitioned along the columns according to the following scheme:

P0 P1 P2 P3 P4

As expected, results show that we achieve better performances when using large boxes. The communication overhead is significant into respect of the overall execution time when using small grid of points.

Description and results

Conclusions