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Linkage analysis is a statistical method used by geneticists in everyday practice for mapping disease-susceptibility genes in the study of complex diseases. An essential first step in the study of genetic diseases, linkage computations may require years of CPU time. The recent DNA sampling revolution enabled unprecedented sampling density, but made the analysis even more computationally demanding. In this paper we describe a high performance online service for genetic linkage analysis, called Super link-online. The system enables anyone with Internet access to submit genetic data and analyze it as easily and quickly as if using a supercomputer. The analyses are automatically parallelized and executed on tens of thousands distributed CPUs in multiple clouds and grids. The first version of the system, which employed up to 3,000 CPUs in UW Madison and Technion Condor pools, has been successfully used since 2006 by hundreds of geneticists worldwide, with over 40 citations in the genetics literature. Here we describe the second version, which substantially improves the scalability and performance of first: it uses over 45,000 non-dedicated hosts, in 10different grids and clouds, including EC2 and the Superlink@Technion community grid. Improved system performance is obtained through a virtual grid hierarchy with dynamic load balancing and multi-grid overlay via the Grid Bot system, parallel pruning of short tasks for overhead minimization, and cost-efficient use of cloud resources in reliability-critical execution periods. These enhancements enabled execution of many previously infeasible analyses, which can now be completed within a few hours. The new version of the system, in production since 2009, has completed over 6500 different runs of over 10 million tasks, with total consumption of 420 CPU years.
Date of Conference: 23-26 May 2011