Uniform Access to the Distributed Resources for the Computational Chemistry Using UNICORE

Abstract

In this paper we describe deployment of qunatum chemical and biomolecular applications on the grid. We have used UNICORE infrastructure as framework for development dedicated user interface to the number of existing computational chemistry codes as well as molecular bilogy databases. The user interface is integrated with the UNICORE client based on plugin mechanism which provides general grid functionality such as single login, job submission and control mechanism.

Automatic distributed workflow generation with GridMD library

“…Currently the interfaces exist for Portable Batch System (PBS), Grid manager of Joint Supercomputer Center of Russian Academy of Sciences [19] based on Globus 4 [20] and for the DEISA Grid environment [21] based on UNICORE [1]. In the future we plan to add interfaces for other workflow middleware such as Nimrod [4] and Kepler [5].…”

“…It uses the traditional programming (C++), no special languages, code preprocessing, manual scripting tools or even the knowledge of Grid functionality and middleware are required to describe the GridMD workflow. From the existing Grid instrumentation tools [1,[3][4][5][6], the Grid Superscalar [6] project follows the approach most similar to the one of GridMD [7,15]. Since there are significant differences, we will briefly indicate and dis- cuss them in the following sections.…”

“…This requires some workflow specifications from the application designer. Usually this is done by the explicit indication of the application subtasks as separate executables or services and of the data flow between these subtasks [1,[3][4][5].…”

“…The abbreviation GridMD stands for Grid-enabled Molecular Dynamics, however the part of the library responsible for workflow definitions may be used in all kinds of numerical simulation, not limited to the Molecular Dynamics (MD) method. The problem of the workflow definition for large scientific applications is widely discussed [1][2][3][4][5][6][7]. For an application that can be split into separate stages logically linked between each other, one needs a scenario to specify the correct execution order and the dataflow.…”

Development of Chemistry Portal for Grid-enabled Molecular Science

“…Some computational chemistry programs which provide graphic user interface, such as GaussView [2], are able to run user applications only on local workstations and access to remote distributed resources is limited. A dedicated user interface [3] that uses UNICORE infrastructure [4] provided an access to a number of computational chemistry codes on distributed computer resources. However, to use this interface, users need to install the UNICORE client together with the plugin software on to their workstations or PC machines.…”