Actual source code: ex241.c
1: static char help[] = "Tests MATHTOOL\n\n";
3: #include <petscmat.h>
5: static PetscErrorCode GenEntries(PetscInt sdim, PetscInt M, PetscInt N, const PetscInt *J, const PetscInt *K, PetscScalar *ptr, void *ctx)
6: {
7: PetscInt d, j, k;
8: PetscReal diff = 0.0, *coords = (PetscReal *)(ctx);
10: PetscFunctionBeginUser;
11: for (j = 0; j < M; j++) {
12: for (k = 0; k < N; k++) {
13: diff = 0.0;
14: for (d = 0; d < sdim; d++) diff += (coords[J[j] * sdim + d] - coords[K[k] * sdim + d]) * (coords[J[j] * sdim + d] - coords[K[k] * sdim + d]);
15: ptr[j + M * k] = 1.0 / (1.0e-2 + PetscSqrtReal(diff));
16: }
17: }
18: PetscFunctionReturn(PETSC_SUCCESS);
19: }
21: static PetscErrorCode GenEntriesRectangular(PetscInt sdim, PetscInt M, PetscInt N, const PetscInt *J, const PetscInt *K, PetscScalar *ptr, void *ctx)
22: {
23: PetscInt d, j, k;
24: PetscReal diff = 0.0, **coords = (PetscReal **)(ctx);
26: PetscFunctionBeginUser;
27: for (j = 0; j < M; j++) {
28: for (k = 0; k < N; k++) {
29: diff = 0.0;
30: for (d = 0; d < sdim; d++) diff += (coords[0][J[j] * sdim + d] - coords[1][K[k] * sdim + d]) * (coords[0][J[j] * sdim + d] - coords[1][K[k] * sdim + d]);
31: ptr[j + M * k] = 1.0 / (1.0e-2 + PetscSqrtReal(diff));
32: }
33: }
34: PetscFunctionReturn(PETSC_SUCCESS);
35: }
37: int main(int argc, char **argv)
38: {
39: Mat A, AT, D, B, P, R, RT;
40: PetscInt m = 100, dim = 3, M, K = 10, begin, n = 0, N, bs;
41: PetscMPIInt size;
42: PetscScalar *ptr;
43: PetscReal *coords, *gcoords, *scoords, *gscoords, *(ctx[2]), norm, epsilon;
44: MatHtoolKernel kernel = GenEntries;
45: PetscBool flg, sym = PETSC_FALSE;
46: PetscRandom rdm;
47: IS iss, ist, is[2];
48: Vec right, left, perm;
50: PetscFunctionBeginUser;
51: PetscCall(PetscInitialize(&argc, &argv, (char *)NULL, help));
52: PetscCall(PetscOptionsGetInt(NULL, NULL, "-m_local", &m, NULL));
53: PetscCall(PetscOptionsGetInt(NULL, NULL, "-n_local", &n, NULL));
54: PetscCall(PetscOptionsGetInt(NULL, NULL, "-dim", &dim, NULL));
55: PetscCall(PetscOptionsGetInt(NULL, NULL, "-K", &K, NULL));
56: PetscCall(PetscOptionsGetBool(NULL, NULL, "-symmetric", &sym, NULL));
57: PetscCall(PetscOptionsGetReal(NULL, NULL, "-mat_htool_epsilon", &epsilon, NULL));
58: PetscCallMPI(MPI_Comm_size(PETSC_COMM_WORLD, &size));
59: M = size * m;
60: PetscCall(PetscOptionsGetInt(NULL, NULL, "-M", &M, NULL));
61: PetscCall(PetscMalloc1(m * dim, &coords));
62: PetscCall(PetscRandomCreate(PETSC_COMM_WORLD, &rdm));
63: PetscCall(PetscRandomGetValuesReal(rdm, m * dim, coords));
64: PetscCall(PetscCalloc1(M * dim, &gcoords));
65: PetscCall(MatCreateDense(PETSC_COMM_WORLD, m, PETSC_DECIDE, M, K, NULL, &B));
66: PetscCall(MatSetRandom(B, rdm));
67: PetscCall(MatGetOwnershipRange(B, &begin, NULL));
68: PetscCall(PetscArraycpy(gcoords + begin * dim, coords, m * dim));
69: PetscCall(MPIU_Allreduce(MPI_IN_PLACE, gcoords, M * dim, MPIU_REAL, MPI_SUM, PETSC_COMM_WORLD));
70: PetscCall(MatCreateHtoolFromKernel(PETSC_COMM_WORLD, m, m, M, M, dim, coords, coords, kernel, gcoords, &A));
71: PetscCall(MatSetOption(A, MAT_SYMMETRIC, sym));
72: PetscCall(MatSetFromOptions(A));
73: PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY));
74: PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY));
75: PetscCall(MatViewFromOptions(A, NULL, "-A_view"));
76: PetscCall(MatGetOwnershipIS(A, is, NULL));
77: PetscCall(ISDuplicate(is[0], is + 1));
78: PetscCall(MatIncreaseOverlap(A, 1, is, 2));
79: PetscCall(MatSetBlockSize(A, 2));
80: PetscCall(MatIncreaseOverlap(A, 1, is + 1, 1));
81: PetscCall(ISGetBlockSize(is[1], &bs));
82: PetscCheck(bs == 2, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Incorrect block size %" PetscInt_FMT " != 2", bs);
83: PetscCall(MatSetBlockSize(A, 1));
84: PetscCall(ISEqual(is[0], is[1], &flg));
85: PetscCheck(flg, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unequal index sets");
86: PetscCall(ISDestroy(is));
87: PetscCall(ISDestroy(is + 1));
88: PetscCall(MatCreateVecs(A, &right, &left));
89: PetscCall(VecSetRandom(right, rdm));
90: PetscCall(MatMult(A, right, left));
91: PetscCall(MatHtoolGetPermutationSource(A, &iss));
92: PetscCall(MatHtoolGetPermutationTarget(A, &ist));
93: PetscCall(VecDuplicate(left, &perm));
94: PetscCall(VecCopy(left, perm));
95: PetscCall(VecPermute(perm, ist, PETSC_FALSE));
96: PetscCall(VecPermute(right, iss, PETSC_FALSE));
97: PetscCall(MatHtoolUsePermutation(A, PETSC_FALSE));
98: PetscCall(MatMult(A, right, left));
99: PetscCall(VecAXPY(left, -1.0, perm));
100: PetscCall(VecNorm(left, NORM_INFINITY, &norm));
101: PetscCheck(PetscAbsReal(norm) <= PETSC_SMALL, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "||y(with permutation)-y(without permutation)|| = %g (> %g)", (double)PetscAbsReal(norm), (double)PETSC_SMALL);
102: PetscCall(MatHtoolUsePermutation(A, PETSC_TRUE));
103: PetscCall(VecDestroy(&perm));
104: PetscCall(VecDestroy(&left));
105: PetscCall(VecDestroy(&right));
106: PetscCall(ISDestroy(&ist));
107: PetscCall(ISDestroy(&iss));
108: if (PetscAbsReal(epsilon) >= PETSC_SMALL) { /* when there is compression, it is more difficult to check against MATDENSE, so just compare symmetric and nonsymmetric assemblies */
109: PetscReal relative;
110: PetscCall(MatDestroy(&B));
111: PetscCall(MatCreateHtoolFromKernel(PETSC_COMM_WORLD, m, m, M, M, dim, coords, coords, kernel, gcoords, &B));
112: PetscCall(MatSetOption(B, MAT_SYMMETRIC, (PetscBool)!sym));
113: PetscCall(MatSetFromOptions(B));
114: PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
115: PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
116: PetscCall(MatViewFromOptions(B, NULL, "-B_view"));
117: PetscCall(MatConvert(A, MATDENSE, MAT_INITIAL_MATRIX, &P));
118: PetscCall(MatNorm(P, NORM_FROBENIUS, &relative));
119: PetscCall(MatConvert(B, MATDENSE, MAT_INITIAL_MATRIX, &R));
120: PetscCall(MatAXPY(R, -1.0, P, SAME_NONZERO_PATTERN));
121: PetscCall(MatNorm(R, NORM_INFINITY, &norm));
122: PetscCheck(PetscAbsReal(norm / relative) <= epsilon, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "||A(!symmetric)-A(symmetric)|| = %g (> %g)", (double)PetscAbsReal(norm / relative), (double)epsilon);
123: PetscCall(MatDestroy(&B));
124: PetscCall(MatDestroy(&R));
125: PetscCall(MatDestroy(&P));
126: } else {
127: PetscCall(MatConvert(A, MATDENSE, MAT_INITIAL_MATRIX, &D));
128: PetscCall(MatViewFromOptions(D, NULL, "-D_view"));
129: PetscCall(MatMultEqual(A, D, 10, &flg));
130: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "Ax != Dx");
131: PetscCall(MatMultTransposeEqual(A, D, 10, &flg));
132: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "A^Tx != D^Tx");
133: PetscCall(MatMultAddEqual(A, D, 10, &flg));
134: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "y+Ax != y+Dx");
135: PetscCall(MatGetOwnershipRange(B, &begin, NULL));
136: PetscCall(MatDenseGetArrayWrite(D, &ptr));
137: for (PetscInt i = begin; i < m + begin; ++i)
138: for (PetscInt j = 0; j < M; ++j) PetscCall(GenEntries(dim, 1, 1, &i, &j, ptr + i - begin + j * m, gcoords));
139: PetscCall(MatDenseRestoreArrayWrite(D, &ptr));
140: PetscCall(MatMultEqual(A, D, 10, &flg));
141: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "Ax != Dx");
142: PetscCall(MatTranspose(D, MAT_INPLACE_MATRIX, &D));
143: PetscCall(MatTranspose(A, MAT_INITIAL_MATRIX, &AT));
144: PetscCall(MatMultEqual(AT, D, 10, &flg));
145: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "A^Tx != D^Tx");
146: PetscCall(MatTranspose(A, MAT_REUSE_MATRIX, &AT));
147: PetscCall(MatMultEqual(AT, D, 10, &flg));
148: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "A^Tx != D^Tx");
149: PetscCall(MatAXPY(D, -1.0, AT, SAME_NONZERO_PATTERN));
150: PetscCall(MatNorm(D, NORM_INFINITY, &norm));
151: PetscCheck(PetscAbsReal(norm) <= PETSC_SMALL, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "||A-D|| = %g (> %g)", (double)norm, (double)PETSC_SMALL);
152: PetscCall(MatDestroy(&AT));
153: PetscCall(MatDestroy(&D));
154: PetscCall(MatMatMult(A, B, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &P));
155: PetscCall(MatAssemblyBegin(P, MAT_FINAL_ASSEMBLY));
156: PetscCall(MatAssemblyEnd(P, MAT_FINAL_ASSEMBLY));
157: PetscCall(MatMatMultEqual(A, B, P, 10, &flg));
158: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "ABx != Px");
159: PetscCall(MatTransposeMatMultEqual(A, B, P, 10, &flg));
160: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "A^TBx != P^Tx");
161: PetscCall(MatDestroy(&B));
162: PetscCall(MatDestroy(&P));
163: if (n) {
164: PetscCall(PetscMalloc1(n * dim, &scoords));
165: PetscCall(PetscRandomGetValuesReal(rdm, n * dim, scoords));
166: N = n;
167: PetscCall(MPIU_Allreduce(MPI_IN_PLACE, &N, 1, MPIU_INT, MPI_SUM, PETSC_COMM_WORLD));
168: PetscCall(PetscCalloc1(N * dim, &gscoords));
169: PetscCallMPI(MPI_Exscan(&n, &begin, 1, MPIU_INT, MPI_SUM, PETSC_COMM_WORLD));
170: PetscCall(PetscArraycpy(gscoords + begin * dim, scoords, n * dim));
171: PetscCall(MPIU_Allreduce(MPI_IN_PLACE, gscoords, N * dim, MPIU_REAL, MPI_SUM, PETSC_COMM_WORLD));
172: kernel = GenEntriesRectangular;
173: ctx[0] = gcoords;
174: ctx[1] = gscoords;
175: PetscCall(MatCreateHtoolFromKernel(PETSC_COMM_WORLD, m, n, M, N, dim, coords, scoords, kernel, ctx, &R));
176: PetscCall(MatSetFromOptions(R));
177: PetscCall(MatAssemblyBegin(R, MAT_FINAL_ASSEMBLY));
178: PetscCall(MatAssemblyEnd(R, MAT_FINAL_ASSEMBLY));
179: PetscCall(MatViewFromOptions(R, NULL, "-R_view"));
180: PetscCall(MatConvert(R, MATDENSE, MAT_INITIAL_MATRIX, &D));
181: PetscCall(MatViewFromOptions(D, NULL, "-D_view"));
182: PetscCall(MatMultEqual(R, D, 10, &flg));
183: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "Rx != Dx");
184: PetscCall(MatTranspose(D, MAT_INPLACE_MATRIX, &D));
185: PetscCall(MatTranspose(R, MAT_INITIAL_MATRIX, &RT));
186: PetscCall(MatMultEqual(RT, D, 10, &flg));
187: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "R^Tx != D^Tx");
188: PetscCall(MatTranspose(R, MAT_REUSE_MATRIX, &RT));
189: PetscCall(MatMultEqual(RT, D, 10, &flg));
190: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "R^Tx != D^Tx");
191: PetscCall(MatDestroy(&RT));
192: PetscCall(MatDestroy(&D));
193: PetscCall(MatCreateDense(PETSC_COMM_WORLD, n, PETSC_DECIDE, PETSC_DETERMINE, K, NULL, &B));
194: PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
195: PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
196: PetscCall(MatSetRandom(B, rdm));
197: PetscCall(MatMatMult(R, B, MAT_INITIAL_MATRIX, PETSC_DEFAULT, &P));
198: PetscCall(MatAssemblyBegin(P, MAT_FINAL_ASSEMBLY));
199: PetscCall(MatAssemblyEnd(P, MAT_FINAL_ASSEMBLY));
200: PetscCall(MatMatMultEqual(R, B, P, 10, &flg));
201: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "RBx != Px");
202: PetscCall(MatDestroy(&B));
203: PetscCall(MatDestroy(&P));
204: PetscCall(MatCreateVecs(R, &right, &left));
205: PetscCall(VecSetRandom(right, rdm));
206: PetscCall(MatMult(R, right, left));
207: PetscCall(MatHtoolGetPermutationSource(R, &iss));
208: PetscCall(MatHtoolGetPermutationTarget(R, &ist));
209: PetscCall(VecDuplicate(left, &perm));
210: PetscCall(VecCopy(left, perm));
211: PetscCall(VecPermute(perm, ist, PETSC_FALSE));
212: PetscCall(VecPermute(right, iss, PETSC_FALSE));
213: PetscCall(MatHtoolUsePermutation(R, PETSC_FALSE));
214: PetscCall(MatMult(R, right, left));
215: PetscCall(VecAXPY(left, -1.0, perm));
216: PetscCall(VecNorm(left, NORM_INFINITY, &norm));
217: PetscCheck(PetscAbsReal(norm) <= PETSC_SMALL, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "||y(with permutation)-y(without permutation)|| = %g (> %g)", (double)PetscAbsReal(norm), (double)PETSC_SMALL);
218: PetscCall(MatHtoolUsePermutation(R, PETSC_TRUE));
219: PetscCall(VecDestroy(&perm));
220: PetscCall(VecDestroy(&left));
221: PetscCall(VecDestroy(&right));
222: PetscCall(ISDestroy(&ist));
223: PetscCall(ISDestroy(&iss));
224: PetscCall(MatDestroy(&R));
225: PetscCall(PetscFree(gscoords));
226: PetscCall(PetscFree(scoords));
227: }
228: }
229: PetscCall(PetscRandomDestroy(&rdm));
230: PetscCall(MatDestroy(&A));
231: PetscCall(PetscFree(gcoords));
232: PetscCall(PetscFree(coords));
233: PetscCall(PetscFinalize());
234: return 0;
235: }
237: /*TEST
239: build:
240: requires: htool
242: test:
243: requires: htool
244: suffix: 1
245: nsize: 4
246: args: -m_local 80 -n_local 25 -mat_htool_epsilon 1.0e-11 -symmetric {{false true}shared output}
247: output_file: output/ex101.out
249: test:
250: requires: htool
251: suffix: 2
252: nsize: 4
253: args: -m_local 120 -mat_htool_epsilon 1.0e-2 -mat_htool_compressor {{sympartialACA fullACA SVD}shared output} -mat_htool_clustering {{PCARegular PCAGeometric BoundingBox1Regular BoundingBox1Geometric}shared output}
254: output_file: output/ex101.out
256: TEST*/