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Benchmark Report: Univa Grid Engine, Nextflow, and Docker for running Genomic Analysis Workflows

Summary of testing by The Centre for Genomic Regulation utilizing new virtualization technology.

Abstract


Computing environments frequently change in an effort to increase efficiency. Docker has emerged recently as a new type of virtualization technology that allows an organization to create a self-contained runtime environment. CRG tested the capabilities of Docker for the deployment of scientific data analysis pipelines on distributed clusters by incorporating Univa Grid Engine resource manager and CRG's Nextflow toolkit. The ability to virtualize a single process or the execution of a bunch of applications in a Docker container resulted in reduced configuration and deployment problems and produced an increase in task run times and ease of replication.

Running jobs in a Docker container combined with Univa Grid Engine resulted in minimal performance loss of execution time as well as in simplified and optimized Docker image deployments. The fast start-up time for Docker containers technology allows one to virtualize a single process or the execution of a bunch of applications, instead of a complete operating system.

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