Parallelization of molecular dynamics program in a grid computing environment

Khawaja , Mohammad Ali Qamar (2007) Parallelization of molecular dynamics program in a grid computing environment. Masters thesis, University of Malaya.

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Abstract

This thesis describes the building of two Beowulf clusters in a grid computing environment and parallelization of molecular dynamics program EQMOL/NEMD by using Message Passing Interface (MPI) library. Linux (Red Hat 9) was used as a base operating system for the development of Beowulf clusters, Grid and MPI-enabled EQMOL program. The Beowulf clusters were built by setting up Network Information Server (NIS), Network File Server (NFS), firewall and modification of the base operating system. Sun Grid Engine software (version 5.3) from Sun Microsystems was used to encapsulate the Beowulf clusters in order to provide a single interface to control job/resource management and cluster configuration. The serial version of EQMOL/NEMD coded in standard FORTRAN 77 was parallelized and implemented on Intel Beowulf Linux cluster using the Message Passing Interface (MPI) library. In this thesis, strategies of designing the parallel version of EQMOL are discussed; detailed implementation of parallel EQMOL is reported, and performance oriented time measurement data of parallel EQMOL on Beowulf clusters in a grid computing environment is presented. The EQMOL program was parallelized using the most common approach to parallelism, called data parallelism, and also referred to as Single Program Multiple data (SMPD) parallelism. Comparisons of wallclock time of EQMOL are made on increasing number of execution nodes (1-7). The parallelized EQMOL gives speedup by a factor of 1.06, which reduces the total execution time of running the application. The comparison of the numerical accuracy of serial EQMOL molecular dynamics program with parallel version was also made and the results of serial and parallel EQMOL were similar.

Item Type: Thesis (Masters)
Subjects: Z Bibliography. Library Science. Information Resources > Z665 Library Science. Information Science
Depositing User: MS NOOR ZAKIRA ZULRIMI
Date Deposited: 11 Jul 2013 01:01
Last Modified: 11 Jul 2013 01:01
URI: http://repository.um.edu.my/id/eprint/139

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