Paper Citing NAMD - Abstract
Malawski, Maciej; Bartynski, Tomasz; Bubak, Marian
Invocation of operations from script-based Grid applications
FUTURE GENERATION COMPUTER SYSTEMS-THE INTERNATIONAL JOURNAL OF GRID COMPUTING AND ESCIENCE, 26:138-146, JAN 2010
In this paper we address the complexity of building and running modern scientific applications on various Grid systems with heterogeneous middleware. As a solution we have proposed the Grid Operation Invoker (GOI) which offers an object-oriented method invocation semantics for interacting with diverse computational services. GOI forms the core of the ViroLab virtual laboratory and it is used to invoke operations from within in-silico experiments described using a scripting notation. We describe the details of GOI (including architecture, technology adapters and asynchronous invocations) focusing on a mechanism which allows adding high-level support for batch job processing middleware, e.g. EGEE LCG/gLite. As an example, we present the NAMD molecular dynamics program, deployed on EGEE infrastructure. The main achievement is the creation of the Grid Object abstraction, which can be used to represent and access such diverse technologies as Web Services, distributed components and job processing systems. Such an application model, based on high-level scripting, is an interesting alternative to graphical workflow-based tools. (C) 2009 Elsevier B.V. All rights reserved.
