Parallel Programming: for Multicore and Cluster Systems- P41 pptx

7.2 Direct Methods for Linear Systems with Banded Structure 383 where I denotes the N × N unit matrix, which has the value 1 in the diagonal elements and the value 0 in all other entries. The matrix B has the structure B = ⎛ ⎜ ⎜ ⎜ ⎜ ⎝ 4 −10 −14 . . . . . . . . . −1 0 −14 ⎞ ⎟ ⎟ ⎟ ⎟ ⎠ . (7.19) Figure 7.9 illustrates the two-dimensional mesh with five-point stencil (above) and the sparsity structure of the corresponding coefficient matrix A of Formula (7.17). In summary, Formulas (7.15) and (7.17) represent a linear equation system with a sparse coefficient matrix, which has non-zero elements in the main diagonal and its direct neighbors as well as in the diagonals in distance N . Thus, the linear equation system resulting from the Poisson equation has a banded structure, which should be exploited when solving the system. In the following, we present solution meth- ods for linear equation systems with banded structure and start the description with tridiagonal systems. These systems have only three non-zero diagonals in the main diagonal and its two neighbors. A tridiagonal system results, for example, when discretizing the one-dimensional Poisson equation. 7.2.2 Tridiagonal Systems For the solution of a linear equation system Ax = y with a banded or tridiagonal coefficient matrix A ∈ R n×n , specific solution methods can exploit the sparse matrix structure. A matrix A = (a ij ) i, j=1, ,n ∈ R n×n is called banded when its structure takes the form of a band of non-zero elements around the principal diagonal. More precisely, this means a matrix A is a banded matrix if there exists r ∈ N, r ≤ n, with a ij = 0for|i − j| > r . The number r is called the semi-bandwidth of A.Forr = 1 a banded matrix is called tridiagonal matrix. We first consider the solution of tridiagonal systems which are linear equation systems with tridiagonal coefficient matrix. 7.2.2.1 Gaussian Elimination for Tridiagonal Systems For the solution of a linear equation system Ax = y with tridiagonal matrix A, the Gaussian elimination can be used. Step k of the forward elimination (without pivoting) results in the following computations, see also Sect. 7.1: 1. Compute l ik := a (k) ik /a (k) kk for i = k +1, ,n. 2. Subtract l ik times the kth row from the rows i = k +1, ,n, i.e., compute a (k+1) ij = a (k) ij −l ik ·a (k) kj for k ≤ j ≤ n and k < i ≤ n . 384 7 Algorithms for Systems of Linear Equations i-1 i+1i i-N i+N x 23 N1 2N y 2 N N+1 (N-1)N+1 12 n 1 2 n x x x x x x x x x x x x x x x xx x xx x x xx x x x x xx x x x x x x x x x N N Fig. 7.9 Rectangular mesh in the x–y plane of size N × N and the n × n coefficient matrix with n = N 2 of the corresponding linear equation system of the five-point formula. The sparsity structure of the matrix corresponds to the adjacency relation of the mesh points. The mesh can be considered as adjacency graph of the non-zero elements of the matrix The vector y is changed analogously. Because of the tridiagonal structure of A, all matrix elements a ik with i ≥ k +2are zero elements, i.e., a ik = 0. Thus, in each step k of the Gaussian elimination only one elimination factor l k+1 := l k+1,k and only one row with only one new element have to be computed. Using the notation 7.2 Direct Methods for Linear Systems with Banded Structure 385 A = ⎛ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎝ b 1 c 1 0 a 2 b 2 c 2 a 3 b 3 . . . . . . . . . c n−1 0 a n b n ⎞ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎠ (7.20) for the matrix elements and starting with u 1 = b 1 , these computations are l k+1 = a k+1 /u k , (7.21) u k+1 = b k+1 −l k+1 ·c k . After n − 1 steps an LU decomposition A = LU of matrix (7.20) with L = ⎛ ⎜ ⎜ ⎜ ⎝ 10 l 2 1 . . . . . . 0 l n 1 ⎞ ⎟ ⎟ ⎟ ⎠ and U = ⎛ ⎜ ⎜ ⎜ ⎝ u 1 c 1 0 . . . . . . u n−1 c n−1 0 u n ⎞ ⎟ ⎟ ⎟ ⎠ results. The right-hand side y is transformed correspondingly according to ˜ y k+1 = y k+1 −l k+1 · ˜ y k . The solution x is computed from the upper triangular matrix U by a backward sub- stitution, starting with x n = ˜ y n /u n and solving the equations u i x i +c i x i+1 = ˜ y i one after another resulting in x i = ˜ y i u i − c i u i x i+1 for i = n − 1, ,1 . The computational complexity of the Gaussian elimination is reduced to O(n)for tridiagonal systems. However, the elimination phase computing l k and u k according to Eq. (7.21) is inherently sequential, since the computation of l k+1 depends on u k and the computation of u k+1 depends on l k+1 . Thus, in this form the Gaussian elimi- nation or LU decomposition has to be computed sequentially and is not suitable for a parallel implementation. 7.2.2.2 Recursive Doubling for Tridiagonal Systems An alternative approach for solving a linear equation system with tridiagonal matrix is the method of recursive doubling or cyclic reduction. The methods of recursive doubling and cyclic reduction also use elimination steps but contain potential par- allelism [72, 71]. Both techniques can be applied if the coefficient matrix is either symmetric and positive definite or diagonal dominant [115]. The elimination steps 386 7 Algorithms for Systems of Linear Equations in both methods are applied to linear equation systems Ax = y with the matrix structure shown in (7.20), i.e., b 1 x 1 + c 1 x 2 = y 1 , a i x i−1 + b i x i + c i x i+1 = y i for i = 2, ,n − 1, a n x n−1 + b n x n = y n . The method, which was first introduced by Hockney and Golub in [91], uses two equations i − 1 and i + 1 to eliminate the variables x i−1 and x i+1 from equation i. This results in a new equivalent equation system with a coefficient matrix with three non-zero diagonals where the diagonals are moved to the outside. Recursive doubling and cyclic reduction can be considered as two implementation variants for the same numerical idea of the method of Hockney and Golub. The implementation of recursive doubling repeats the elimination step, which finally results in a matrix structure in which only the elements in the principal diagonal are non-zero and the solution vector x can be computed easily. Cyclic reduction is a variant of recursive doubling which also eliminates variables using neighboring rows. But in each step the elimination is only applied to half of the equations and, thus, less computations are performed. On the other hand, the computation of the solution vector x requires a substitution phase. We would like to mention that the terms recursive doubling and cyclic reduction are used in different ways in the literature. Cyclic reduction is sometimes used for the numerical method of Hockney and Golub in both implementation variants, see [60, 115]. On the other hand the term recursive doubling (or full recursive doubling) is sometimes used for a different method, the method of Stone [168]. This method applies the implementation variants sketched above in Eq. (7.21) resulting from the Gaussian elimination, see [61, 173]. In the following, we start the description of recursive doubling for the method of Hockney and Golub according to [61] and [13]. Recursive doubling considers three neighboring equations i − 1, i, i + 1of the equation system Ax = y with coefficient matrix A in the form (7.20) for i = 3, 4, ,n − 2. These equations are a i−1 x i−2 + b i−1 x i−1 + c i−1 x i = y i−1 , a i x i−1 + b i x i + c i x i+1 = y i , a i+1 x i + b i+1 x i+1 + c i+1 x i+2 = y i+1 . Equation i −1isusedtoeliminatex i−1 from the ith equation and equation i +1is used to eliminate x i+1 from the ith equation. This is done by reformulating equations i − 1 and i +1to x i−1 = y i−1 b i−1 − a i−1 b i−1 x i−2 − c i−1 b i−1 x i , x i+1 = y i+1 b i+1 − a i+1 b i+1 x i − c i+1 b i+1 x i+2 and inserting those descriptions of x i−1 and x i+1 into equation i. The resulting new equation i is 7.2 Direct Methods for Linear Systems with Banded Structure 387 a (1) i x i−2 +b (1) i x i +c (1) i x i+2 = y (1) i (7.22) with coefficients a (1) i = α (1) i ·a i−1 , b (1) i = b i +α (1) i ·c i−1 +β (1) i ·a i+1 , c (1) i = β (1) i ·c i+1 , (7.23) y (1) i = y i +α (1) i · y i−1 +β (1) i · y i+1 , and α (1) i :=−a i /b i−1 , β (1) i :=−c i /b i+1 . For the special cases i = 1, 2, n −1, n, the coefficients are given by b (1) 1 = b 1 +β (1) 1 ·a 2 , y (1) 1 = y 1 +β (1) 1 · y 2 , b (1) n = b n +α (1) n ·c n−1 , y (1) n = b n +α (1) n · y n−1 , a (1) 1 = a (1) 2 = 0, and c (1) n−1 = c (1) n = 0 . The values for a (1) n−1 , a (1) n , b (1) 2 , b (1) n−1 , c (1) 1 , c (1) 2 , y (1) 2 , and y (1) n−1 are defined as in Eq. (7.23). Equation (7.22) forms a linear equation system A (1) x = y (1) with a coefficient matrix A (1) = ⎛ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎝ b (1) 1 0 c (1) 1 0 0 b (1) 2 0 c (1) 2 a (1) 3 0 b (1) 3 . . . . . . a (1) 4 . . . . . . . . . c (1) n−2 . . . . . . . . . 0 0 a (1) n 0 b (1) n ⎞ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎠ . Comparing the structure of A (1) with the structure of A, it can be seen that the diagonals are moved to the outside. In the next step, this method is applied to the equations i − 2, i, i + 2ofthe equation system A (1) x = y (1) for i = 5, 6, ,n − 4. Equation i − 2isusedto eliminate x i−2 from the ith equation and equation i + 2 is used to eliminate x i+2 from the ith equation. This results in a new ith equation a (2) i x i−4 +b (2) i x i +c (2) i x i+4 = y (2) i , which contains the variables x i−4 , x i , and x i+4 . The cases i = 1, ,4, n−3, ,n are treated separately as shown for the first elimination step. Altogether a next equa- tion system A (2) x = y (2) results in which the diagonals are further moved to the outside. The structure of A (2) is 388 7 Algorithms for Systems of Linear Equations A (2) = ⎛ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎜ ⎝ b (2) 1 000c (2) 1 0 0 b (2) 2 c (2) 2 0 . . . . . . 0 . . . c (2) n−4 a (2) 5 . . . 0 a (2) 6 . . . 0 . . . . . . 0 0 a (2) n 000b (2) n ⎞ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎟ ⎠ . The following steps of the recursive doubling algorithm apply the same method to the modified equation system of the last step. Step k transfers the side diagonals 2 k −1 positions away from the main diagonal, compared to the original coefficient matrix. This is reached by considering equations i − 2 k−1 , i, i +2 k−1 : a (k−1) i−2 k−1 x i−2 k + b (k−1) i−2 k−1 x i−2 k−1 + c (k−1) i−2 k−1 x i = y (k−1) i−2 k−1 , a (k−1) i x i−2 k−1 + b (k−1) i x i + c (k−1) i x i+2 k−1 = y (k−1) i , a (k−1) i+2 k−1 x i + b (k−1) i+2 k−1 x i+2 k−1 + c (k−1) i+2 k−1 x i+2 k = y (k−1) i+2 k−1 . Equation i − 2 k−1 is used to eliminate x i−2 k−1 from the ith equation and equation i +2 k−1 is used to eliminate x i+2 k−1 from the ith equation. Again, the elimination is performed by computing the coefficients for the next equation system. These coef- ficients are a (k) i = α (k) i ·a (k−1) i−2 k−1 for i = 2 k +1, ,n, and a (k) i = 0 otherwise, c (k) i = β (k) i ·c (k−1) i+2 k−1 for i = 1, ,n − 2 k , and c (k) i = 0 otherwise, (7.24) b (k) i = α (k) i ·c (k−1) i−2 k−1 +b (k−1) i +β (k) i ·a (k−1) i+2 k−1 for i = 1, ,n , y (k) i = α (k) i · y (k−1) i−2 k−1 + y (k−1) i +β (k) i · y (k−1) i+2 k−1 for i = 1, ,n with α (k) i :=−a (k−1) i /b (k−1) i−2 k−1 for i = 2 k−1 +1, ,n , (7.25) β (k) i :=−c (k−1) i /b (k−1) i+2 k−1 for i = 1, ,n − 2 k−1 . The modified equation i results by multiplying equation i −2 k−1 from step k −1 with α (k) i , multiplying equation i + 2 k−1 from step k −1 with β (k) i , and adding both to equation i. The resulting ith equation is a (k) i x i−2 k +b (k) i x i +c (k) i x i+2 k = y (k) i (7.26) 7.2 Direct Methods for Linear Systems with Banded Structure 389 with the coefficients (7.24). The cases k = 1, 2 are special cases of this formula. The initialization for k = 0 is the following: a (0) i = a i for i = 2, ,n , b (0) i = b i for i = 1, ,n , c (0) i = c i for i = 1, ,n − 1 , y (0) i = y i for i = 1, ,n . and a (0) 1 = 0, c (0) n = 0. Also, for the steps k = 0, ,log n and i ∈ Z \{1, ,n} the values a (k) i = c (k) i = y (k) i = 0 , b (k) i = 1 , x i = 0 are set. After N =log nsteps, the original matrix A is transformed into a diagonal matrix A (N ) A (N ) = diag(b (N ) 1 , ,b (N ) n ) in which only the main diagonal contains non-zero elements. The solution x of the linear equation system can be directly computed using this matrix and the corre- spondingly modified vector y (N ) : x i = y (N ) i /b (N ) i for i = 1, 2, ,n . To summarize, the recursive doubling algorithm consists of two main phases: 1. Elimination phase: Compute the values a (k) i , b (k) i , c (k) i , and y (k) i for k =1, ,log n and i = 1, ,n according to Eqs. (7.24) and (7.25). 2. Solution phase: Compute x i = y (N ) i /b (N ) i for i = 1, ,n with N =log n. The first phase consists of log n steps where in each step O(n) values are com- puted. The sequential asymptotic runtime of the algorithm is therefore O(n ·log n) which is asymptotically slower than the O(n) runtime for the Gaussian elimination approach described earlier. The advantage is that the computations in each step of the elimination and the substitution phase are independent and can be performed in parallel. Figure 7.10 illustrates the computations of the recursive doubling algorithm and the data dependencies between different steps. 7.2.2.3 Cyclic Reduction for Tridiagonal Systems The recursive doubling algorithm offers a large degree of potential parallelism but has a larger computational complexity than the Gaussian elimination caused by 390 7 Algorithms for Systems of Linear Equations i=1 i=2 i=3 i=4 i=5 i=6 i=7 i=8 k=0 k=1 k=2 k=3 Fig. 7.10 Dependence graph for the computation steps of the recursive doubling algorithm in the case of three computation steps and eight equations. The computations of step k are shown in column k of the illustration. Column k contains one node for each equation i, thus representing the computation of all coefficients needed in step k. Column 0 represents the data of the coefficient matrix of the linear system. An edge from a node i in step k to a node j in step k + 1 means that the computation at node j needs at least one coefficient computed at node i computational redundancy. The cyclic reduction algorithm is a modification of recursive doubling which reduces the amount of computations to be performed. In each step, half the variables in the equation system are eliminated which means that only half of the values a (k) i , b (k) i , c (k) i , and y (k) i are computed. A substitution phase is needed to compute the solution vector x. The elimination and the substitution phases of cyclic reduction are described by the following two phases: 1. Elimination phase: For k = 1, ,log n compute a (k) i , b (k) i , c (k) i , and y (k) i with i = 2 k , ,n and step size 2 k . The number of equations of the form (7.26) is reduced by a factor of 1/2 in each step. In step k =logn there is only one equation left for i = 2 N with N =log n. 2. Substitution phase: For k =log n, ,0 compute x i according to Eq. (7.26) for i = 2 k , ,n with step size 2 k+1 : x i = y (k) i −a (k) i · x i−2 k −c (k) i · x i+2 k b (k) i . (7.27) Figure 7.11 illustrates the computations of the elimination and the substitution phases of cyclic reduction represented by nodes and their dependencies represented by arrows. In each computation step k, k = 1, ,log n, of the elimination phase, 7.2 Direct Methods for Linear Systems with Banded Structure 391 i=1 i=2 i=3 i=4 i=5 i=6 i=7 i=8 k=0 k=1 k=2 k=3 8 x 4 x x x x x x x 2 6 1 3 5 7 Fig. 7.11 Dependence graph illustrating the dependencies between neighboring computation steps of the cyclic reduction algorithm for the case of three computation steps and eight equations in analogy to the representation in Fig. 7.10. The first four columns represent the computations of the coefficients. The last columns in the graph represent the computation of the solution vector x in the second phase of the cyclic reduction algorithm, see (7.27) there are n/2 k nodes representing the computations for the coefficients of one equa- tion. This results in n 2 + n 4 + n 8 +···+ n 2 N = n · log n  i=1 1 2 i ≤ n computation nodes with N =log n and, therefore, the execution time of cyclic reduction is O(n). Thus, the computational complexity is the same as for the Gaussian elimination; however, the cyclic reduction offers potential parallelism which can be exploited in a parallel implementation as described in the following. The computations of the numbers α (k) i , β (k) i require a division by b (k) i and, thus, cyclic reduction as well as recursive doubling is not possible if any number b (k) i is zero. This can happen even when the original matrix is invertible and has non-zero diagonal elements or when the Gaussian elimination can be applied without pivot- ing. However, for many classes of matrices it can be shown that a division by zero is never encountered. Examples are matrices A which are symmetric and positive definite or invertible and diagonally dominant, see [61] or [115] (using the name odd–even reduction). (A matrix A is symmetric if A = A T and positive definite if x T Ax > 0 for all x. A matrix is diagonally dominant if in each row the absolute value of the diagonal element exceeds the sum of the absolute values of the other elements in the row without the diagonal in the row.) 392 7 Algorithms for Systems of Linear Equations 7.2.2.4 Parallel Implementation of Cyclic Reduction We consider a parallel algorithm for the cyclic reduction for p processors. For the description of the phases we assume n = p ·q for q ∈ N and q = 2 Q for Q ∈ N. Each processor stores a block of rows of size q, i.e., processor P i stores the rows of A with the numbers (i − 1)q +1, ,i ·q for 1 ≤ i ≤ p. We describe the parallel algorithm with data exchange operations that are needed for an implementation with a distributed address space. As data distribution a row-blockwise distribution of the matrix A is used to reduce the interaction between processors as much as possible. The parallel algorithm for the cyclic reduction comprises three phases: the elimina- tion phase stopping earlier than described above, an additional recursive doubling phase, and a substitution phase. Phase 1: Parallel reduction of the cyclic reduction in log q steps: Each pro- cessor computes the first Q = log q steps of the cyclic reduction algorithm, i.e., processor P i computes for k = 1, ,Q the values a (k) j , b (k) j , c (k) j , y (k) j for j = (i − 1) ·q + 2 k , ,i · q with step size 2 k . After each computation step, processor P i receives four data values from P i−1 (if i > 1) and from processor P i+1 (if i < n) computed in the previous step. Since each processor owns a block of rows of size q, no communication with any other processor is required. The size of data to be exchanged with the neighboring processors is a multiple of 4 since four coefficients (a (k) j , b (k) j , c (k) j , y (k) j ) are transferred. Only one data block is received per step and so there are at most 2Q messages of size 4 for each step. Phase 2: Parallel recursive doubling for tridiagonal systems of size p: Proces- sor P i is responsible for the ith equation of the following p-dimensional tridiagonal system ˜ a i ˜ x i−1 + ˜ b i ˜ x i + ˜ c i ˜ x i+1 = ˜ y i for i = 1, , p with ˜ a i = a (Q) i·q ˜ b i = b (Q) i·q ˜ c i = c (Q) i·q ˜ y i = y (Q) i·q ˜ x i = x i·q ⎫ ⎪ ⎪ ⎪ ⎪ ⎪ ⎪ ⎪ ⎬ ⎪ ⎪ ⎪ ⎪ ⎪ ⎪ ⎪ ⎭ for i = 1, ,p . For the solution of this system, we use recursive doubling. Each processor is assigned one equation. Processor P i performs log p steps of the recursive dou- bling algorithm. In step k, k = 1, ,log p, processor P i computes ˜ a (k) i , ˜ b (k) i , ˜ c (k) i , ˜ y (k) i . 2, ,n , b (0) i = b i for i = 1, ,n , c (0) i = c i for i = 1, ,n − 1 , y (0) i = y i for i = 1, ,n . and a (0) 1 = 0, c (0) n = 0. Also, for the steps k = 0, ,log n and i ∈ Z {1, ,n} the. row.) 392 7 Algorithms for Systems of Linear Equations 7.2.2.4 Parallel Implementation of Cyclic Reduction We consider a parallel algorithm for the cyclic reduction for p processors. For the description. Thus, in this form the Gaussian elimi- nation or LU decomposition has to be computed sequentially and is not suitable for a parallel implementation. 7.2.2.2 Recursive Doubling for Tridiagonal