BioMed Research International / 2014 / Article / Alg 1

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 forPairs
(25) end forNodes
(26) return DV

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