Running Molecular Dynamics Simulations in a Grid Environment

Grid computing enables resources in different administrative domains to be shared. Researchers are able to collaborate more easily and can gain access to more computing power, enabling more studies to be run and larger problems to be considered. A common middleware employed by grid projects is the Globus Toolkit. Recently, a new version of the Globus Toolkit (GT4), based on standards that build on Web Services, has been released. However, most grid projects using the Globus Toolkit still employ GT2. This paper presents an approach for running molecular dynamics simulations in a mixed GT2/GT4 grid environment. Simulations are automatically checkpointed and migrated between sites as needed, increasing fault tolerance should a site fail. Users do not need to manually discover what resources are available and do not need to learn the potentially different approaches for submitting jobs at different sites. All jobs are submitted to a metascheduler which handles the site specific details. Simulations have been successfully run in a grid environment comprised of resources from across Canada, including resources from the Grid Research Centre at the University of Calgary, WestGrid and ACEnet.