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Unformatted text preview: 8 7 8 C 0 1 4 5 8 8 11 10 9 A 0 2 3 6 7 10 10 10 12 CSEP 524: Parallel ComputaIon Winter 2013: Chamberlain Step 4: Interpret the path against the original sequences AGCACAC–A A–CACACTA How could we do this in parallel? 77 Smith- Waterman Data- Parallel Approach: Loop over diagonals serially proc computeH(H: [0..n, 0..n] int) { for upperDiag in 1..n do forall diagPos in 0..#upperDiag { const (i,j) = [diagPos+1, upperDiag-diagPos]; H[i,j] = f(H[i-1,j-1], H[i-1,j], H[i,j-1]); } for lowerDiag in 1..n-1 do forall diagPos in lowerDiag..n-1 by -1 { const (i,j) = [diagPos+1, lowerDiag+diagPos]; H[i,j] = f(H[i-1,j-1], H[i-1,j], H[i,j-1]); } Advantages: } •  Reasonably clean (if I got my Traverse each diagonal in parallel indexing correct) Disadvantages: •  Not so great in terms of...
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