We describe a systematic method for the design of systolic arrays. This method may be used for algorithms that can be expressed as a set of uniform recurrent equations over a convex set D ofâ€¦ (More)

The parallelization of many algorithms can be obtained using space-time transformations which are applied on nested do-loops or on recurrence equations. In this paper, we analyze systems of linearâ€¦ (More)

HMMER is a widely used tool in bioinformatic, based on Profile Hidden Markov Models. The computation kernels of HMMER i.e. MSV and P7Viterbi are very compute intensive and data dependencies restrictâ€¦ (More)

Profile based Hidden Markov Model is a widely used tool in bioinformatics. While being very valuable to biologists, it is extremely compute intensive and suffers from prohibitive execution time. Weâ€¦ (More)

Systolic arrays are locally connected parallel architectures, whose structure is well-suited to the implementation of many algorithms, in scientiic computation, signal and image processing,â€¦ (More)

We study the problem of scheduling systems of affine recurrence equations (SAREs), a convenient formalism for modeling massively parallel computations. We unify in a single framework, the two mostâ€¦ (More)