Performance Evaluation of Shake&wARP, A Cluster Enabled Application for Macromolecular Crystallography

The deployment of Shake&wARP, an application used in macromolecular crystallography for electron density map refinement, in a computational cluster managed by SUN's N1 Grid Engine presented and its performance is evaluated.In this deployment, parallelization was introduced in the optimizati...

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Bibliographic Details
Published in2009 International Conference on Computing, Engineering and Information pp. 149 - 152
Main Authors Pimentel, H., Courellis, S., Kantardjieff, K.A., Rupp, B.
Format Conference Proceeding
LanguageEnglish
Published IEEE 01.04.2009
Subjects
application deployment
Application software
cluster
Computer architecture
Computer science
Crystallography
Educational institutions
Electrons
Engines
Grid computing
Proteins
shake&warp
Sun
sun grid engine
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Summary:The deployment of Shake&wARP, an application used in macromolecular crystallography for electron density map refinement, in a computational cluster managed by SUN's N1 Grid Engine presented and its performance is evaluated.In this deployment, parallelization was introduced in the optimization cycle, by decoupling the various optimization tasks. This implementation of Shake&wARP on a cluster improved the turnaround time of submitted jobs significantly. The performance of the implementation was evaluated using common UNIX utilities. Performance data gathered across the cluster were used to quantify the impact of the various software components of the clustered implementation of Shake&wARP on the cluster resources and to identify bottlenecks.
ISBN:9780769535388
0769535380
DOI:10.1109/ICC.2009.67