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Parallelization of d2_cluster

Attached is some work i have done in the past for a company for the benchmarking of d2_cluster in MPI mode. I can’t provide the details as the source was revealed to me under NDA. The attached document was the best i could do.

Abstract: The increasing use of EST data for sequence analysis has lead to the parallization of such computations in order to provide for the capabilities to analyze these information at a greater rate. Coupled with the improvements and affordability of Linux clusters, new methods of parrallizing d2_cluster to aid in the sequence analysis would be beneficial. D2_cluster was parrallized using MPI in a Beowulf cluster. Results obtained in the tests shows promising results with speed up of 42.7 over a uni-processor system using 8 CPUs.

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