Performance Characterization of BLAST for the Grid

BLAST is a commonly used bioinformatics application for performing query searches and analysis of biological data. As the amount of search data increases so does job search times. As means of reducing job turnaround times, scientists are resorting to new technologies such as grid computing to obtain needed computational and storage resources. Inherent with advent of new technologies, are additional complexities that arise, forcing scientists to deal with them. Grid computing exemplifies dynamic and transient state of heterogeneous resources that become a major obstacle in realizing user-desired levels of service. Many users do not realize that techniques applied in more traditional cluster environments do not simply transition into grid environment. This paper analyzes resource and application dependencies for BLAST in terms of job parameters that result in performance tradeoffs. We present a set of examples showing performance variability and point out a set of guidelines, which lead to establishing job performance tradeoffs.