1. Dynamic Programming on SIMD

2. SIMD (SSE)
A register has say Example
4 parts, each x:=x+y
part has 8 bits or
16 bits
x,y are memory locations of
Each part appropriate alignment and
executes the each refers to 4 different
same operation variables
but in parallel

3. Edit Distance between Strings
Q
D
Edit distance
between Q[1..j]
and D[1..i]

4. E(i,j)

5. F(i,j)

6. Summarizing
A G C T
A -1 2 2 2
G 2 -1 2 2
C 2 2 -1 2
T 2 2 2 -1

7. Parallel Computing
Find the max
value path from
Mismatch
each location to
the top left
corner
Insertion in
Q
Insertion in
D

8. Parallel Computing
Anti-
diagonal
can be
done in
parallel

9. SIMD?
One SIMD register
can handle all
values in this chunk
Partition into
chunks, each chunk
should have proper
alignment

10. Fix: Go Vertical
Partition into vertical
chunks, each chunk
should have proper
alignment

11. Problem 1: Boundaries
One value comes from
the previous chunk
Each chunk needs a
shift

12. Solution 1: Striping
x’s belong to one
chunk, y’s to another
and so on

13. Problem 2: Computing F
At most number of
blocks
Sequential Dependency

14. Problem 2: Computing F
Sequential Dependency

15. Thank You