Definitions

1. Definitions • A Synchronous application is one where all processes must reach certain points before execution continues. • Local synchronization is a requirement that a subset of processes (usually neighbors) reach a synchronous point before execution continues. • A barrier is the basic message passing mechanism for synchronizing processes. • Deadlock occurs when groups of processors are permanently waiting for messages that cannot be satisfied because the sending processes are also permanently waiting for messages.

2. P0 P0 Barrier P0 Executing P0 Waiting P0 Barrier Illustration C: MPI_Barrier(MPI_COMM_WORLD); Processor code will reach barrier points at different times. This leads to idle time and load imbalance.

3. Counter (linear) Barrier: Implementation Barriers consist of two phases: Entry phase and departure phases Master Processor O(P) steps For (i=0; i<P; i++) // Entry Phase Receive null message from any processor For (i=0; i<P; i++) // Release Phase Send null message to release slaves Slave Processors Send null message to enter barrier Receive null message for barrier release Note: This logic avoids processors arriving before prior release

4. P0 P1 P2 P3 P4 P5 P6 P7 Tree (non-linear) Barrier The release phase uses the inverse tree construction, entry and departure each require O(lg P) steps P0 P1 P2 P3 P4 P5 P6 Release Phase P7 Entry Phase Note: Implementation logic is similar to divide and conquer

5. P0 P1 P2 P3 P4 P5 P6 P7 P0 P1 P2 P3 P4 P5 P6 P7 P0 P1 P2 P3 P4 P5 P6 P7 P0 P1 P2 P3 P4 P5 P6 P7 Butterfly Barrier • Stage 1: P0p1; p2p3; p4p5; p6p7 • Stage 2: p0p2; p1p3; p4p6; p5p7 • Stage 3: p0p4; p1p5; p2p6; p3p7 • Advantages: • requires only single parallel single send() and receive() pairs at each stage. • Completes in only O(lg P) steps Note: At stage s, processor p synchronizes with (p + 2s-1)mod P

6. Local Synchronization Synchronize with neighbors before proceeding • Even Processors Send null message to processor i-1 Receive null message from processor i-1 Send null message to processor i+1 Receive null message from processor i+1 • Odd Numbered Processors Receive null message from processor i+1 Send null message to processor i+1 Receive null message from processor i-1 Send null message to processor i-1 • Notes: • Local Synchronization is an incomplete barrier: processors exit after receiving messages from their neighbors • Reminder: Deadlock can occur with incorrrect message passing orders. MPI_Sendrecv() and MPI_Sendrecv_replace() are deadlock free

7. Local Synchronization Example • Heat Distribution Problem • Goal • Determine final temperature at each n x n grid point • Initial boundary condition • Know initial temperatures at the designated points (ex: outer rim or internal heat sink) • Cannot proceed to next iteration until local synchronization completes DO Average each grid point with its neighbors UNTIL temperature changes are small enough New Value = (∑neighbors)/4

8. Sequential Heat Distribution Code Initialize rows 0,n and columns 0,n of g and h Iteration = 0 DO FOR (i=1; i<n; i++) FOR (j=1; j<n; j++) IF (iteration %2) hi,j = (gi-1,j+gi+1,j+gi,j-1+gi,j+1)/4 ELSE gi,j = (hi-1,j+hi+1,j+hi,j-1+hi,j+1)/4 iteration++ UNTIL max (|gi – hi|)<tolerance or iteration>MAX • Notes • Even iterations update gijarray; Odd iterations iterate gijarray • Recall: Odd/Even sort

9. p0 p1 p2 p3 p4 p5 p6 p7 p8 p9 p10 p11 p12 p13 p14 p15 Block or Strip Partitioning Assign portions of the grid to processors in the topology • Block Partitioning (allocate in squares) • Eight messages exchanged at each iteration • Data exchanged per message is n/sqrt(P) • Strip Partitioning • Four messages exchanged at each iteration • Data exchanged per message is n/P • Question: Which is better? Blocks p0 p1 p2 p3 p4 p5 p6 p7 Column Strips

10. Strip versus Block Partitioning • Characteristics • Strip partitioning – generally more data, less messages • Block partitioning – generally less data, more messages • Choice: Low latency favors block; High latency favors strip • Example: Grid is 64 x 64, p = 16 • Strip Partitioning – Strips are 4x64; 4 x 64 cells transferred per iteration per processor • Block Partitioning – Blocks are 16 x 16; 8 x 16 cells transferred per iteration per processor • Example: Grid is 64 x 64, p = 4 • Strip Partitioning – Strips are 8x64, 4 x 64 cells transferred per iteration per processor • Block Partitioning – Blocks are 32 x 32, 8 x 32 cells transferred per iteration per processor

11. Cells to north Pi Cells to east Cells to west Cells to south Parallel Implementation Modifications to the sequential algorithm • Declare “ghost” rows to hold adjacent data (declare array of 10 x 10 for an 8 x 8 block) • Exchange data with neighbor processors • Perform the calculation for the local grid cells

12. Heat Distribution Partitioning Main logic For each iteration For each point compute new temperature SendRcv(row-1,col,point) SendRcv(row+1,col,point) SendRcv(row,col-1,point) SendRcv(row,col+1,point) SendRcv(row,col) if row,col is not local if myrank even Send(point,prow,col) Recv(point,prow,col) Else Recv(point,prow,col) Send(point,prow,col)

13. Full Synchronization • Data Parallel Computations • Simultaneously apply the same operation to different data • This approach models many numerical computations • They are easy to program and scale well to large data sets • Sequential Code for (i=0; i<n; i++) a[i] = someFunction(a[i]) • Shared Memory Code Forall (i=0; i<n; i++) {bodyOfInstructions} • Note: the for loop semantics imply a natural barrier • Distributed processing For local a[i]; {someFunction(a[i])} barrier();

14. Data Parallel Example A[] += k A[0] += k A[1] += k A[n-1] += k p0 p1 pn • All processors execute instructions in “lock step” • forall (i=0; i<n; i++) a[i] += k • Note: Multi-computers partition data into course grain blocks

15. Prefix-Based Operations • Definition: Given a set of n values a1, a2,…, an and an associative operation, the operation is applied to all predecessor values • Prefix Sum: {2, 7, 9, 4}  {2, 9, 18, 22} • Application: Radix Sort • Solution by Doubling: An algorithm where operations calculate in increasing powers of 2 • Example: 1, 2, 4, 8, etc., (each iteration doubles)

16. Prefix Sum by Doubling • Overview • 1. Add each data[i] is added to data[i+1] • 2. Add each data[i] is added to data[i+2] • 3. Add each data[i] is added to data[i+4] • 4. Add each data[i] is added to data[i+8] • ETC….. • Note: Skip the operation if i+increment > array length

17. Prefix Sum Illustration

18. Prefix Sum Example Sequential Time: O(n), Parallel Time: O(N/P lg N/P ) Note: * means the sum is not added at the next step

19. Prefix Sum Parallel Implementation • Sequential codefor (j=0;j<lg(n);j++) for (i=0; i<n – 2j; i++) a[i] += a[i+2j]; • Parallel shared memory fine grain logicfor (j=0; j<lg(n); j++) forall (i=0; i<n–2j; i++) a[i+2j] +=a[i]; • Parallel distributed course grain logic for (j=1; j<= log(n); j++) if (myrank>=2j-1 receive(sum, myrank – 2j-1) add sum to processor's data else send(processor's data, myrank + 2j-1)

20. Synchronous Iteration • Processes synchronize at each iteration step • Example: Simulation of Natural Processes • Shared memory code for (j=0; j<n; j++) forall (i=0; i<N; i++) algorithm(i); • Distributed memory code for (j=0; j<n; j++) algorithm(myRank); barrier();

21. Example: n equations, n unknowns an-1,0x0 + an,1x1 …+ an,n-1xn-1 = bk∙∙∙ ak,0x0 + ak,1x1 …+ ak,n-1xn-1 = bk∙∙∙ a1,0x0 + a1,1x1 …+ a1,n-1xn-1 = b1 a0,0x0 + a0,1x1 …+ a0,n-1xn-1 = b0 • Or we can rewrite the equations as follows: xk=(bk–ak,0x0-…-ak,j-1xj-1-ak,j+1xj+1-…-ak,n-1xn-1)/ak,k= (bk - ∑j≠kai,j xj)/ai,i

22. Jacobi Iteration Numerical Algorithm to solve N equations with N unknowns xi • Pseudo Code xnewi = initial guess DO xi = xnewi xnewi = Calculated next guess UNTIL ∑i|xnewi – xi|<tolerance • Jacobi iteration always converges if:ak,k > ∑i≠k ai,0(The diagonal value dominates the column sum) Error Iteration i i+1 Traditional solutions are O(N3), or O(N2) for special cases

23. xnew0 xnew1 xnewn-1 xi Allgather() xnewi into xi Parallel Jacobi Code xnewi = bi DO for each i xi = xnewi sum = -ai,i * xi FOR (j=0; j<n; j++) sum += ai,i * xj xnewi = (bi – sum)/ai,i allgather(xnewi) barrier() Until iterations>MAX or ∑i|xnewi – xi|<tolerance

24. Additional Jacobi Notes Time • If P (processor count) < n, allocate blocks of variables to processors • Block Allocation: Allocate consecutive xi to processors • Cyclic Allocation • Allocate x0, xP, … to p0 • Allocate x1, xp+1, … to p1 … etc. • Question: Which allocation scheme is better? Computation Communication 4 8 12 16 20 24 Processors Jacobi Performance

25. Cellular Automata Definition • The System has a finite grid of cells • Each cell can assume a finite number of states • Cells change state according to a well-defined rule set • All cell changes of state occur simultaneously • The system iterates through a number of generations Note: Animations of these systems can lead to interesting insights Serious Applications • Fluid and gas dynamics • Biological growth • Airplane wing airflow • Erosion modeling • Groundwater pollution Fun Applications • Game of Life • Sharks and Fishes • Foxes and Rabbits • Gaming applications

26. Conway’s Game of Life • The grid (world) is a two dimension array of cells • Note: The grid ends can optionally wrap around (like a torus) • Each cell • Can hold one “organism” • There are eight neighbor cells: North, Northeast, East, Southeast, South, Southwest, West, Northwest • Rules (run the simulation over many generations) • Organism dies (loneliness) if <2 organisms live in neighbor cells • Organism survives if 2 organisms live in adjacent cells • An empty cell with 3 living neighbors gives birth to organisms in every empty adjacent cell • Organism dies (overpopulation) >= 4 organisms live in neighbor cells

27. Sharks and Fishes • The grid (ocean) is modeled by a three dimension array • Note: The grid ends can optionally wrap around (like a torus) • Each cell • Can hold either a fish or a shark, but not both • There are twenty six adjacent cubic cells • Rules for fish • Fish move randomly to empty adjacent cells • If there are no empty adjacent cells, fish stay put • Fish of breeding age leave a baby fish in the vacating cell • Fish die after some fixed (or random) number of generations • Rules for sharks • Sharks randomly move to adjacent cells that don't contain sharks • If they enter a cell containing a fish, they eat the fish • Sharks stay put when all adjacent cells contain sharks • Sharks of breeding age leave a baby shark in a vacating cell • Sharks die (starvation) if they don’t eat a fish for some fixed (or random) number of generations