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 = PetscSqrtReal(PETSC_SMALL);
44: MatHtoolKernelFn *kernel = GenEntries;
45: PetscBool flg, sym = PETSC_FALSE, recompression = 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(PetscOptionsGetBool(NULL, NULL, "-recompression", &recompression, NULL));
58: PetscCall(PetscOptionsGetReal(NULL, NULL, "-mat_htool_epsilon", &epsilon, NULL));
59: PetscCallMPI(MPI_Comm_size(PETSC_COMM_WORLD, &size));
60: M = size * m;
61: PetscCall(PetscOptionsGetInt(NULL, NULL, "-M", &M, NULL));
62: PetscCall(PetscMalloc1(m * dim, &coords));
63: PetscCall(PetscRandomCreate(PETSC_COMM_WORLD, &rdm));
64: PetscCall(PetscRandomGetValuesReal(rdm, m * dim, coords));
65: PetscCall(PetscCalloc1(M * dim, &gcoords));
66: PetscCall(MatCreateDense(PETSC_COMM_WORLD, m, PETSC_DECIDE, M, K, NULL, &B));
67: PetscCall(MatSetRandom(B, rdm));
68: PetscCall(MatGetOwnershipRange(B, &begin, NULL));
69: PetscCall(PetscArraycpy(gcoords + begin * dim, coords, m * dim));
70: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, gcoords, M * dim, MPIU_REAL, MPI_SUM, PETSC_COMM_WORLD));
71: PetscCall(MatCreateHtoolFromKernel(PETSC_COMM_WORLD, m, m, M, M, dim, coords, coords, kernel, gcoords, &A));
72: PetscCall(MatSetOption(A, MAT_SYMMETRIC, sym));
73: PetscCall(MatHtoolUseRecompression(A, recompression));
74: PetscCall(MatSetFromOptions(A));
75: PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY));
76: PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY));
77: PetscCall(MatViewFromOptions(A, NULL, "-A_view"));
78: PetscCall(MatGetOwnershipIS(A, is, NULL));
79: PetscCall(ISDuplicate(is[0], is + 1));
80: PetscCall(MatIncreaseOverlap(A, 1, is, 2));
81: PetscCall(MatSetBlockSize(A, 2));
82: PetscCall(MatIncreaseOverlap(A, 1, is + 1, 1));
83: PetscCall(ISGetBlockSize(is[1], &bs));
84: PetscCheck(bs == 2, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Incorrect block size %" PetscInt_FMT " != 2", bs);
85: PetscCall(MatSetBlockSize(A, 1));
86: PetscCall(ISEqual(is[0], is[1], &flg));
87: PetscCheck(flg, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unequal index sets");
88: PetscCall(ISDestroy(is));
89: PetscCall(ISDestroy(is + 1));
90: PetscCall(MatCreateVecs(A, &right, &left));
91: PetscCall(VecSetRandom(right, rdm));
92: PetscCall(MatMult(A, right, left));
93: PetscCall(MatHtoolGetPermutationSource(A, &iss));
94: PetscCall(MatHtoolGetPermutationTarget(A, &ist));
95: PetscCall(VecDuplicate(left, &perm));
96: PetscCall(VecCopy(left, perm));
97: PetscCall(VecPermute(perm, ist, PETSC_FALSE));
98: PetscCall(VecPermute(right, iss, PETSC_FALSE));
99: PetscCall(MatHtoolUsePermutation(A, PETSC_FALSE));
100: PetscCall(MatMult(A, right, left));
101: PetscCall(VecAXPY(left, -1.0, perm));
102: PetscCall(VecNorm(left, NORM_INFINITY, &norm));
103: 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);
104: PetscCall(MatHtoolUsePermutation(A, PETSC_TRUE));
105: PetscCall(VecDestroy(&perm));
106: PetscCall(VecDestroy(&left));
107: PetscCall(VecDestroy(&right));
108: PetscCall(ISDestroy(&ist));
109: PetscCall(ISDestroy(&iss));
110: if (PetscAbsReal(epsilon) >= PETSC_SMALL) { /* when there is compression, it is more difficult to check against MATDENSE, so just compare symmetric and nonsymmetric assemblies */
111: PetscReal relative;
112: PetscCall(MatDestroy(&B));
113: PetscCall(MatCreateHtoolFromKernel(PETSC_COMM_WORLD, m, m, M, M, dim, coords, coords, kernel, gcoords, &B));
114: PetscCall(MatSetOption(B, MAT_SYMMETRIC, (PetscBool)!sym));
115: PetscCall(MatHtoolUseRecompression(B, recompression));
116: PetscCall(MatSetFromOptions(B));
117: PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
118: PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
119: PetscCall(MatViewFromOptions(B, NULL, "-B_view"));
120: PetscCall(MatConvert(A, MATDENSE, MAT_INITIAL_MATRIX, &P));
121: PetscCall(MatNorm(P, NORM_FROBENIUS, &relative));
122: PetscCall(MatConvert(B, MATDENSE, MAT_INITIAL_MATRIX, &R));
123: PetscCall(MatAXPY(R, -1.0, P, SAME_NONZERO_PATTERN));
124: PetscCall(MatNorm(R, NORM_INFINITY, &norm));
125: PetscCheck(PetscAbsReal(norm / relative) <= epsilon, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "||A(!symmetric)-A(symmetric)|| = %g (> %g)", (double)PetscAbsReal(norm / relative), (double)epsilon);
126: PetscCall(MatDestroy(&B));
127: PetscCall(MatDestroy(&R));
128: PetscCall(MatDestroy(&P));
129: } else {
130: PetscCall(MatConvert(A, MATDENSE, MAT_INITIAL_MATRIX, &D));
131: PetscCall(MatViewFromOptions(D, NULL, "-D_view"));
132: PetscCall(MatMultEqual(A, D, 10, &flg));
133: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "Ax != Dx");
134: PetscCall(MatMultTransposeEqual(A, D, 10, &flg));
135: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "A^Tx != D^Tx");
136: PetscCall(MatMultAddEqual(A, D, 10, &flg));
137: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "y+Ax != y+Dx");
138: PetscCall(MatGetOwnershipRange(B, &begin, NULL));
139: PetscCall(MatDenseGetArrayWrite(D, &ptr));
140: for (PetscInt i = begin; i < m + begin; ++i)
141: for (PetscInt j = 0; j < M; ++j) PetscCall(GenEntries(dim, 1, 1, &i, &j, ptr + i - begin + j * m, gcoords));
142: PetscCall(MatDenseRestoreArrayWrite(D, &ptr));
143: PetscCall(MatMultEqual(A, D, 10, &flg));
144: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "Ax != Dx");
145: PetscCall(MatTranspose(D, MAT_INPLACE_MATRIX, &D));
146: PetscCall(MatTranspose(A, MAT_INITIAL_MATRIX, &AT));
147: PetscCall(MatMultEqual(AT, D, 10, &flg));
148: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "A^Tx != D^Tx");
149: PetscCall(MatTranspose(A, MAT_REUSE_MATRIX, &AT));
150: PetscCall(MatMultEqual(AT, D, 10, &flg));
151: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "A^Tx != D^Tx");
152: PetscCall(MatAXPY(D, -1.0, AT, SAME_NONZERO_PATTERN));
153: PetscCall(MatNorm(D, NORM_INFINITY, &norm));
154: PetscCheck(PetscAbsReal(norm) <= PETSC_SMALL, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "||A-D|| = %g (> %g)", (double)norm, (double)PETSC_SMALL);
155: PetscCall(MatDestroy(&AT));
156: PetscCall(MatDestroy(&D));
157: PetscCall(MatMatMult(A, B, MAT_INITIAL_MATRIX, PETSC_DETERMINE, &P));
158: PetscCall(MatAssemblyBegin(P, MAT_FINAL_ASSEMBLY));
159: PetscCall(MatAssemblyEnd(P, MAT_FINAL_ASSEMBLY));
160: PetscCall(MatMatMultEqual(A, B, P, 10, &flg));
161: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "ABx != Px");
162: PetscCall(MatTransposeMatMultEqual(A, B, P, 10, &flg));
163: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "A^TBx != P^Tx");
164: PetscCall(MatDestroy(&B));
165: PetscCall(MatDestroy(&P));
166: if (n) {
167: PetscCall(PetscMalloc1(n * dim, &scoords));
168: PetscCall(PetscRandomGetValuesReal(rdm, n * dim, scoords));
169: N = n;
170: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &N, 1, MPIU_INT, MPI_SUM, PETSC_COMM_WORLD));
171: PetscCall(PetscCalloc1(N * dim, &gscoords));
172: PetscCallMPI(MPI_Exscan(&n, &begin, 1, MPIU_INT, MPI_SUM, PETSC_COMM_WORLD));
173: PetscCall(PetscArraycpy(gscoords + begin * dim, scoords, n * dim));
174: PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, gscoords, N * dim, MPIU_REAL, MPI_SUM, PETSC_COMM_WORLD));
175: kernel = GenEntriesRectangular;
176: ctx[0] = gcoords;
177: ctx[1] = gscoords;
178: PetscCall(MatCreateHtoolFromKernel(PETSC_COMM_WORLD, m, n, M, N, dim, coords, scoords, kernel, ctx, &R));
179: PetscCall(MatSetFromOptions(R));
180: PetscCall(MatHtoolUseRecompression(R, recompression));
181: PetscCall(MatAssemblyBegin(R, MAT_FINAL_ASSEMBLY));
182: PetscCall(MatAssemblyEnd(R, MAT_FINAL_ASSEMBLY));
183: PetscCall(MatViewFromOptions(R, NULL, "-R_view"));
184: PetscCall(MatConvert(R, MATDENSE, MAT_INITIAL_MATRIX, &D));
185: PetscCall(MatViewFromOptions(D, NULL, "-D_view"));
186: PetscCall(MatMultEqual(R, D, 10, &flg));
187: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "Rx != Dx");
188: PetscCall(MatTranspose(D, MAT_INPLACE_MATRIX, &D));
189: PetscCall(MatTranspose(R, MAT_INITIAL_MATRIX, &RT));
190: PetscCall(MatMultEqual(RT, D, 10, &flg));
191: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "R^Tx != D^Tx");
192: PetscCall(MatTranspose(R, MAT_REUSE_MATRIX, &RT));
193: PetscCall(MatMultEqual(RT, D, 10, &flg));
194: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "R^Tx != D^Tx");
195: PetscCall(MatDestroy(&RT));
196: PetscCall(MatDestroy(&D));
197: PetscCall(MatCreateDense(PETSC_COMM_WORLD, n, PETSC_DECIDE, PETSC_DETERMINE, K, NULL, &B));
198: PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY));
199: PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY));
200: PetscCall(MatSetRandom(B, rdm));
201: PetscCall(MatMatMult(R, B, MAT_INITIAL_MATRIX, PETSC_DETERMINE, &P));
202: PetscCall(MatAssemblyBegin(P, MAT_FINAL_ASSEMBLY));
203: PetscCall(MatAssemblyEnd(P, MAT_FINAL_ASSEMBLY));
204: PetscCall(MatMatMultEqual(R, B, P, 10, &flg));
205: PetscCheck(flg, PETSC_COMM_WORLD, PETSC_ERR_PLIB, "RBx != Px");
206: PetscCall(MatDestroy(&B));
207: PetscCall(MatDestroy(&P));
208: PetscCall(MatCreateVecs(R, &right, &left));
209: PetscCall(VecSetRandom(right, rdm));
210: PetscCall(MatMult(R, right, left));
211: PetscCall(MatHtoolGetPermutationSource(R, &iss));
212: PetscCall(MatHtoolGetPermutationTarget(R, &ist));
213: PetscCall(VecDuplicate(left, &perm));
214: PetscCall(VecCopy(left, perm));
215: PetscCall(VecPermute(perm, ist, PETSC_FALSE));
216: PetscCall(VecPermute(right, iss, PETSC_FALSE));
217: PetscCall(MatHtoolUsePermutation(R, PETSC_FALSE));
218: PetscCall(MatMult(R, right, left));
219: PetscCall(VecAXPY(left, -1.0, perm));
220: PetscCall(VecNorm(left, NORM_INFINITY, &norm));
221: 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);
222: PetscCall(MatHtoolUsePermutation(R, PETSC_TRUE));
223: PetscCall(VecDestroy(&perm));
224: PetscCall(VecDestroy(&left));
225: PetscCall(VecDestroy(&right));
226: PetscCall(ISDestroy(&ist));
227: PetscCall(ISDestroy(&iss));
228: PetscCall(MatDestroy(&R));
229: PetscCall(PetscFree(gscoords));
230: PetscCall(PetscFree(scoords));
231: }
232: }
233: PetscCall(PetscRandomDestroy(&rdm));
234: PetscCall(MatDestroy(&A));
235: PetscCall(PetscFree(gcoords));
236: PetscCall(PetscFree(coords));
237: PetscCall(PetscFinalize());
238: return 0;
239: }
241: /*TEST
243: build:
244: requires: htool
246: test:
247: requires: htool
248: suffix: 1
249: nsize: 4
250: args: -m_local 80 -n_local 25 -mat_htool_epsilon 1.0e-11 -symmetric {{false true}shared output} -recompression {{false true}shared output}
251: output_file: output/empty.out
253: test:
254: requires: htool
255: suffix: 2
256: nsize: 4
257: 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}
258: output_file: output/empty.out
260: TEST*/