Experiences with developing and deploying dynamic BLAST

Authors:
Enis Afgan;Purushotham Bangalore
Affiliations:
University of Alabama at Birmingham, Campbell Hall;University of Alabama at Birmingham, Campbell Hall
Venue:
Proceedings of the 15th ACM Mardi Gras conference: From lightweight mash-ups to lambda grids: Understanding the spectrum of distributed computing requirements, applications, tools, infrastructures, interoperability, and the incremental adoption of key capabilities
Year:
2008

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Abstract

Basic Local Alignment Search Tool (BLAST) is a heavily used bioinformatics application that has gotten significant attention from the high performance computing community. The authors have taken BLAST execution a step further and enabled it to execute on grid resources. Adapting BLAST to execute on the grid brings up concerns regarding grid resource heterogeneity, which inevitably cause difficulty with application availability, fault tolerance, interoperability, and variability in performance of individual segments that are being distributed throughout grid resources. In addition difficulties arise because of tools, technologies, and middleware dependencies that an application developer must deal with. This paper describes Dynamic BLAST and experiences with developing and deploying the application on grid resources over a two year period. Dynamic BLAST is a BLAST-specific metascheduler, a multithreaded, master-worker type application that handles all aspects of a BLAST job submission on the grid for the user. It was developed with the goal of bringing the grid closer to a typical scientist by eliminating the initial learning curve necessary for use of many grid applications. Associated research and development have resulted in the authors' extensive experience in dealing with grid related issues with respect to available tools and technologies. Lessons learned and suggestions are also presented in this paper.