Collaborative grid infrastructure for molecular simulations: TheeMinerals minigrid as a prototype integrated compute and data grid

Abstract

This paper describes a prototype grid infrastructure, called the "eMinerals minigrid", for molecular simulation scientists. which is based on an integration of shared compute and data resources. We describe the key components, namely the use of Condor pools, Linux/Unix clusters with PBS and IBM's LoadLeveller job handling tools, the use of Globus for security handling, the use of Condor-G tools for wrapping globus job submit commands, Condor's DAGman tool for handling workflow, the Storage Resource Broker for handling data, and the CCLRC dataportal and associated tools for both archiving data with metadata and making data available to other workers.

Grid computing and molecular simulations: the vision of theeMinerals project

“…Integrated data grid infrastructure. Computing and data go hand in hand, and the vision for the eMinerals project has at its core the integration of computing resources and data management [19,20,22]. When jobs run on distributed computing resources, the data generated will need to be managed in ways that hide the distribution from the user.…”

“…The science applications concern issues such as nuclear waste encapsulation [16,17,27,28], adsorption of organic pollutants on soil particles [18,19], and surface processes, weathering and precipitation of minerals [29 -33]. The wider aim of the project is to develop a cross-institute collaborative infrastructure that can be used by the scientists to accomplish the scientific objectives [20].…”

An adiabatic model for calculating overtone spectra of dimers such as (H 2 O) 2

“…However, in this scheme, the memory required for each average becomes quite small, shown by the space required per point in table 1. We have implemented a procedure for performing these calculations using the CONDOR [39,40] protocol which allows the effective interaction potential calculations at each dimer grid point to be evaluated in a completely delocalized fashion across a large number of essentially uncoupled personal computers.…”

eScience for molecular-scale simulations and the e Minerals project

“…We use the GLOBUS TOOLKIT, with user authentication handled by X.509 certificates. However, GLOBUS commands are not easy for researchers to work with, and so we originally developed a grid job submission tool called my_condor_submit (MCS; Calleja et al 2005;Bruin et al 2008), which uses the CONDOR_G interface to GLOBUS and CONDOR's DAGMAN workflow system. This tool required the user to supply a simple script that closely resembles the scripts used with the CONDOR system, and which our experience showed users were more comfortable with.…”