Research Article
An Improved Distance Matrix Computation Algorithm for Multicore Clusters
Algorithm 1
DistVect1: Hybrid DistVect Algorithm.
Input: Number of sequences N, average sequences’ length L, sequences’ dataset | , substitution matrix sbt, gab cost g, Number of Nodes M, | Number of cores P | Output: Distance Vector DV | (1) Let | (2) Let | (3) ▹ Distributing splits over M nodes | (4) for do in parallel | (5) Identify Split | (6) for do | (7) Get and from Split | (8) Initialize and | (9) for do | (10) ▹ Distributing distance computation over P cores | (11) for do in parallel | (12) Compute using (3) | (13) if then Let | (14) else Let | (15) end if | (16) Compute using (4) | (17) end for | (18) Let and | (19) Let and | (20) end for | (21) Identify | (22) Let | (23) Increment | (24) end for Pairs | (25) end for Nodes | (26) return DV |
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