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Last modified 8 years ago Last modified on 04/30/12 09:47:52

Overview

Condor is a high throughput computing (HTC) software framework, developed by the Condor team at the University of Wisconsin, Madison. Condor is a tool to help researchers efficiently process large amounts of data by distributing their analysis tasks across a dynamic pool of compute resources.

UAB Condor Pilot Study

Condor Pilot study is a project taken up by UAB IT-Research Computing to study the potential utility of harvesting spare computing capacity from ordinary desktop computers spread across the UAB campus. The focus is a comparison of the utility of various compute resources on an real scientific workflow. The results of these performance measures are used to discuss the potential utility of a scientific compute platform that leverages unused compute cycles harvested from idle computers on campus.

Autodock and High Throughput Docking

The application chosen for the condor pilot study was Autodock, a docking software used to study the best possible match between two molecules, a ligand and a receptor.

Docking is computationally difficult because there are many ways of putting two molecules together (three translational and three rotational degrees of freedom). The number of possibilities grows exponentially with the size of the components. Combining all patches of the surface of one protein molecule with all patches of a second molecule takes on the order of 107 trials. The computational problem is even more profound when considering protein flexibility and the increasing demand to screen large databases (of protein structures and of potential drugs). - Halperin, I., Ma, B., Wolfson, H. and Nussinov, R. (2002), Principles of docking: An overview of search algorithms and a guide to scoring functions . Proteins, 47: 409–443. doi: 10.1002/prot.10115.

High Throughput Docking (HTD) or Hight Throughput Screening (HTS) is the use of high performance computing to analyze large databases of chemical compounds in order to identify possible drug candidates.

UAB IT-RC in collaboration with CIS department and IT-Desktop Services, performed analysis of HTD with Autodock on campus compute fabrics (SGE and Condor). These performances were compared against runs on UW CHTC and OSG Engage VO Condor pools. The performance analysis on the various compute fabrics is found here.

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