Information Technology Reference
In-Depth Information
10
AutoDock Gateway for Molecular
Docking Si
mulations in Cloud Systems
Zoltán Farkas, Péter Kacsuk, Tamás Kiss, Péter Borsody,
Ákos Hajnal, Ákos Balaskó, and Krisztián Karóczkai
CONTENTS
10.1 Introduction ................................................................................................ 217
10.2 WS-PGRADE Workflows and Parameter Sweep Application ............. 218
10.3 AutoDock Workflow .................................................................................. 220
10.3.1 The AutoDock Application ........................................................... 221
10.3.2 AutoDock Workflows .................................................................... 222
10.4 Migrating the AutoDock Workflows to the Cloud ................................ 224
10.4.1 Cloud-Based Execution in WS-PGRADE ................................... 224
10.4.2 Robot Certificates in WS-PGRADE/gUSE .................................. 226
10.4.3 Cloud-Based AutoDock Workflows ............................................ 227
10.5 AutoDock Gateway .................................................................................... 228
10.6 Execution Experiences and Performance ............................................... 231
10.7 Related Research ........................................................................................ 233
10.8 Conclusions ................................................................................................. 234
Acknowledgment ................................................................................................ 234
References ............................................................................................................. 234
10.1 Introduction
Parameter sweep applications are frequent in scientific simulations and in
other types of scientific applications. They require running the same applica-
tion with a very large number of parameters; hence, their execution time could
be long on a single computing resource. As a result, collecting resources on
demand from distributed computing infrastructures (DCIs), such as clouds
or grids, is a highly desired feature of any computing environment that is
offered for scientists to run such applications. Cloud computing infrastruc-
tures are especially suitable for such applications due to their elasticity and
easy scaling up on demand.
217
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