Department of EECS
Northwestern University
2145 Sheridan Road
Office L460
Evanston, IL 60208-3118

Office: 847.467.2299
Mobile: 847.445.4846
Email: aching AT ece DOT northwestern DOT edu


S3aSim is a sequence similarity search algorithm framework for testing and evaluating various I/O strategies using MPI-IO. It has been optimized for PVFS2 ROMIO hints, but can be augmented to use MPI-IO hints for other file systems. S3aSim uses a master-slave parallel programming model with database segmentation, which mimics the mpiBLAST access pattern. A referring publication can be found here from HPDC 2006. Contact me for any additional information and/or suggestions.

2007.05.20 - Download here (s3asim-1.00.tar.gz). Added error checks to all arguments. Improved documentation in the 'doc' directory and with the README.

2007.04.19 - Download here (s3asim-0.98.tar.gz). Cleaned up memory leaks. Fixed compiler problems against mpich2-1.0.5p3. Changed MPI-IO hints to use the -H option.

Parallel-Search Database Segmentation