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Highly scalable ab initio genomic motif identification
- Source :
- SC
- Publication Year :
- 2011
- Publisher :
- ACM, 2011.
-
Abstract
- We present results of scaling an ab initio motif family identification system, Dragon Motif Finder (DMF), to 65,536 processor cores of IBM Blue Gene/P. DMF seeks groups of mutually similar polynucleotide patterns within a set of genomic sequences and builds various motif families from them. Such information is of relevance to many problems in life sciences. Prior attempts to scale such ab initio motif-finding algorithms achieved limited success. We solve the scalability issues using a combination of mixed-mode MPI-OpenMP parallel programming, master-slave work assignment, multi-level workload distribution, multi-level MPI collectives, and serial optimizations. While the scalability of our algorithm was excellent (94% parallel efficiency on 65,536 cores relative to 256 cores on a modest-size problem), the final speedup with respect to the original serial code exceeded 250,000 when serial optimizations are included. This enabled us to carry out many large-scale ab initio motif-finding simulations in a few hours while the original serial code would have needed decades of execution time.
Details
- Database :
- OpenAIRE
- Journal :
- Proceedings of 2011 International Conference for High Performance Computing, Networking, Storage and Analysis
- Accession number :
- edsair.doi...........f6302c620bd1f5d3e5e0deb01e7b54e3