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Parallelization of software pipelines using the mpififo Tool

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3 Author(s)
Weeks, N.T. ; Iowa State Univ., Ames, IA, USA ; Kraeva, M. ; Luecke, G.R.

Software pipelines are often used in scientific applications in fields such as bioinformatics. Unix pipes allow processes in the pipeline to concurrently execute and communicate without disk I/O on a single shared-memory node. However, a significant number of CPU-bound, memory-bound, and I/O-bound software pipelines could benefit from the distribution of work across multiple nodes. Rewriting applications to use MPI is often time consuming. mpififo is an MPI-based tool that allows for the easy distribution of the processes in a pipeline across multiple nodes. This paper describes the design of mpififo, and presents an example of its use in a bioinformatics application. mpififo is available for download at https://bitbucket.org/nathanweeks/mpififo.

Published in:

Cluster Computing (CLUSTER), 2013 IEEE International Conference on

Date of Conference:

23-27 Sept. 2013