Application of grid computing to parameter sweeps and optimizations in molecular modeling

Sudholt, Wibke; Baldridge, Kim K.; Abramson, David; Enticott, Colin; Garic, Slavisa; Kondric, Chris; Nguyen, Duy Duc

doi:10.1016/j.future.2004.09.010

Cited by 33 publications

(27 citation statements)

References 6 publications

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“…Unfortunately, apart from a few examples (e.g., [2,3,4]), building and using Cyberinfrastructure for computational chemistry has been lagging behind the hype. Not many applications have been ported to a Grid infrastructure, exceptions being for example the OpenMolGRID [5] and Gemstone [6].…”

Section: Distributed Scientific Computingmentioning

confidence: 99%

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Scientific Workflow Infrastructure for Computational Chemistry on the Grid

Sudholt

Altıntaş

Baldridge

2006

Computational Science – ICCS 2006

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Abstract. We present ongoing research in the Resurgence (RESearch sURGe ENabled by CyberinfrastructurE) project. This infrastructure shall enable the flexible combination of computational chemistry tools from a unified interface, with the focus on automated high-throughput processing. The implementation is based on the idea that the time-consuming parts of the calculations can be distributed onto computational Grids using the Kepler scientific workflow system and the Nimrod toolkit for distributed parametric modeling. We describe an example workflow that allows preparing, running, and displaying jobs on different molecules, employing the GAMESS quantum chemical program package.

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Section: Distributed Scientific Computingmentioning

confidence: 99%

“…It is part of the Nimrod toolkit for distributed parametric modeling and was already successfully employed previously [2]. Nimrod can perform embarrassingly parallel parameter sweeps (Nimrod/G) and optimizations (Nimrod/O) distributed on a Computational Grid.…”

Section: Nimrod Distributed Parametric Modeling Toolkitmentioning

confidence: 99%

Scientific Workflow Infrastructure for Computational Chemistry on the Grid

Sudholt

Altıntaş

Baldridge

2006

Computational Science – ICCS 2006

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“…However, the focus is not to generate complete predefined workflows, but large enough workflow chunks so that scientists can string them together according to their individual interests. With this purpose in mind, the Resurgence project became a part of the Kepler collaboration for developing common scientific workflow systems for a variety of disciplines [30,34,35]. The first target of the project is to build a pipeline from the base of Kepler composite actors, which automatically prepares and executes quantum chemical calculations for a number of molecules, with the individual input files generated on the fly (see Figure 1).…”

Section: Use Case 1: Gamess Workflow For Quantum Chemistrymentioning

confidence: 99%

A Framework for the Design and Reuse of Grid Workflows

Altıntaş

Birnbaum

Baldridge

et al. 2005

Scientific Applications of Grid Computing

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Abstract. Grid workflows can be seen as special scientific workflows involving high performance and/or high throughput computational tasks. Much work in grid workflows has focused on improving application performance through schedulers that optimize the use of computational resources and bandwidth. As high-end computing resources are becoming more of a commodity that is available to new scientific communities, there is an increasing need to also improve the design and reusability "performance" of scientific workflow systems. To this end, we are developing a framework that supports the design and reuse of grid workflows. Individual workflow components (e.g., for data movement, database querying, job scheduling, remote execution etc.) are abstracted into a set of generic, reusable tasks. Instantiations of these common tasks can be functionally equivalent atomic components (called actors) or composite components (so-called composite actors or subworkflows). In this way, a grid workflow designer does not have to commit to a particular Grid technology when developing a scientific workflow; instead different technologies (e.g. GridFTP, SRB, and scp) can be used interchangeably and in concert. We illustrate the application of our framework using two real-world Grid workflows from different scientific domains, i.e., cheminformatics and bioinformatics, respectively.

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“…The relatively few initiatives to use grid computing in computational chemistry have so far involved either the modification of an existing code to use some of the functionality of a grid middleware [1,2], such as Globus [3], or the creation of portals [4,5], user interfaces and/or specialized middleware to handle both grid-related tasks, such as authentication, as well as application-specific tasks, such as the creation of inputs and visualization of results [6,7,8]. These efforts, typically restricted to one or a few codes, have a significant drawback because they rely on a specific middleware to access grid resources (some projects use the Globus toolkit while other use UNICORE [9]), demanding major revision as the middleware evolves.…”

Section: Introductionmentioning

confidence: 99%

A Framework for Execution of Computational Chemistry Codes in Grid Environments

Gomes

Merzky

Visscher

2006

Computational Science – ICCS 2006

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Abstract. Grid computing is a promising technology for computational chemistry, due to the large volume of calculations involved in appplications such as molecular modeling, thermochemistry and other types of systematic studies. Difficulties in using computational chemistry codes in grid environments arise, however, from the fact that the application software is complex, requiring substantial effort to be installed on different platforms. Morever, these codes depend upon task-dependent sets of data files to be present at the execution nodes. Aiming to improve the usability of different quantum chemistry codes in the distributed, heterogeneous environments found in computational grids, we describe a framework capable of handling the execution of different codes on different platforms. This framework can be divided into three independent parts, one dealing with the mapping of a calculation to a set of codes and the construction of execution environments, one dealing with the management of grid resources, and one that takes care of the heterogeneity of the environment. The suitability of this framework to tackle typical quantum chemistry calculations is discussed and illustrated by a model application.

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Application of grid computing to parameter sweeps and optimizations in molecular modeling

Cited by 33 publications

References 6 publications

Scientific Workflow Infrastructure for Computational Chemistry on the Grid

Scientific Workflow Infrastructure for Computational Chemistry on the Grid

A Framework for the Design and Reuse of Grid Workflows

A Framework for Execution of Computational Chemistry Codes in Grid Environments

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