1 #include <../src/mat/impls/aij/mpi/mpiaij.h> /*I "petscmat.h" I*/ 2 #include <petsc/private/vecimpl.h> 3 #include <petsc/private/sfimpl.h> 4 #include <petsc/private/isimpl.h> 5 #include <petscblaslapack.h> 6 #include <petscsf.h> 7 #include <petsc/private/hashmapi.h> 8 9 /* defines MatSetValues_MPI_Hash(), MatAssemblyBegin_MPI_Hash(), and MatAssemblyEnd_MPI_Hash() */ 10 #define TYPE AIJ 11 #define TYPE_AIJ 12 #include "../src/mat/impls/aij/mpi/mpihashmat.h" 13 #undef TYPE 14 #undef TYPE_AIJ 15 16 static PetscErrorCode MatReset_MPIAIJ(Mat mat) 17 { 18 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 19 20 PetscFunctionBegin; 21 PetscCall(PetscLogObjectState((PetscObject)mat, "Rows=%" PetscInt_FMT ", Cols=%" PetscInt_FMT, mat->rmap->N, mat->cmap->N)); 22 PetscCall(MatStashDestroy_Private(&mat->stash)); 23 PetscCall(VecDestroy(&aij->diag)); 24 PetscCall(MatDestroy(&aij->A)); 25 PetscCall(MatDestroy(&aij->B)); 26 #if defined(PETSC_USE_CTABLE) 27 PetscCall(PetscHMapIDestroy(&aij->colmap)); 28 #else 29 PetscCall(PetscFree(aij->colmap)); 30 #endif 31 PetscCall(PetscFree(aij->garray)); 32 PetscCall(VecDestroy(&aij->lvec)); 33 PetscCall(VecScatterDestroy(&aij->Mvctx)); 34 PetscCall(PetscFree2(aij->rowvalues, aij->rowindices)); 35 PetscCall(PetscFree(aij->ld)); 36 PetscFunctionReturn(PETSC_SUCCESS); 37 } 38 39 static PetscErrorCode MatResetHash_MPIAIJ(Mat mat) 40 { 41 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 42 /* Save the nonzero states of the component matrices because those are what are used to determine 43 the nonzero state of mat */ 44 PetscObjectState Astate = aij->A->nonzerostate, Bstate = aij->B->nonzerostate; 45 46 PetscFunctionBegin; 47 PetscCall(MatReset_MPIAIJ(mat)); 48 PetscCall(MatSetUp_MPI_Hash(mat)); 49 aij->A->nonzerostate = ++Astate, aij->B->nonzerostate = ++Bstate; 50 PetscFunctionReturn(PETSC_SUCCESS); 51 } 52 53 PetscErrorCode MatDestroy_MPIAIJ(Mat mat) 54 { 55 PetscFunctionBegin; 56 PetscCall(MatReset_MPIAIJ(mat)); 57 58 PetscCall(PetscFree(mat->data)); 59 60 /* may be created by MatCreateMPIAIJSumSeqAIJSymbolic */ 61 PetscCall(PetscObjectCompose((PetscObject)mat, "MatMergeSeqsToMPI", NULL)); 62 63 PetscCall(PetscObjectChangeTypeName((PetscObject)mat, NULL)); 64 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatStoreValues_C", NULL)); 65 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatRetrieveValues_C", NULL)); 66 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatIsTranspose_C", NULL)); 67 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatMPIAIJSetPreallocation_C", NULL)); 68 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatResetPreallocation_C", NULL)); 69 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatResetHash_C", NULL)); 70 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatMPIAIJSetPreallocationCSR_C", NULL)); 71 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatDiagonalScaleLocal_C", NULL)); 72 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpibaij_C", NULL)); 73 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpisbaij_C", NULL)); 74 #if defined(PETSC_HAVE_CUDA) 75 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpiaijcusparse_C", NULL)); 76 #endif 77 #if defined(PETSC_HAVE_HIP) 78 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpiaijhipsparse_C", NULL)); 79 #endif 80 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 81 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpiaijkokkos_C", NULL)); 82 #endif 83 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpidense_C", NULL)); 84 #if defined(PETSC_HAVE_ELEMENTAL) 85 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_elemental_C", NULL)); 86 #endif 87 #if defined(PETSC_HAVE_SCALAPACK) 88 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_scalapack_C", NULL)); 89 #endif 90 #if defined(PETSC_HAVE_HYPRE) 91 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_hypre_C", NULL)); 92 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatProductSetFromOptions_transpose_mpiaij_mpiaij_C", NULL)); 93 #endif 94 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_is_C", NULL)); 95 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatProductSetFromOptions_is_mpiaij_C", NULL)); 96 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatProductSetFromOptions_mpiaij_mpiaij_C", NULL)); 97 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatMPIAIJSetUseScalableIncreaseOverlap_C", NULL)); 98 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpiaijperm_C", NULL)); 99 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpiaijsell_C", NULL)); 100 #if defined(PETSC_HAVE_MKL_SPARSE) 101 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpiaijmkl_C", NULL)); 102 #endif 103 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpiaijcrl_C", NULL)); 104 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_is_C", NULL)); 105 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatConvert_mpiaij_mpisell_C", NULL)); 106 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatSetPreallocationCOO_C", NULL)); 107 PetscCall(PetscObjectComposeFunction((PetscObject)mat, "MatSetValuesCOO_C", NULL)); 108 PetscFunctionReturn(PETSC_SUCCESS); 109 } 110 111 static PetscErrorCode MatGetRowIJ_MPIAIJ(Mat A, PetscInt oshift, PetscBool symmetric, PetscBool inodecompressed, PetscInt *m, const PetscInt *ia[], const PetscInt *ja[], PetscBool *done) 112 { 113 Mat B; 114 115 PetscFunctionBegin; 116 PetscCall(MatMPIAIJGetLocalMat(A, MAT_INITIAL_MATRIX, &B)); 117 PetscCall(PetscObjectCompose((PetscObject)A, "MatGetRowIJ_MPIAIJ", (PetscObject)B)); 118 PetscCall(MatGetRowIJ(B, oshift, symmetric, inodecompressed, m, ia, ja, done)); 119 PetscCall(MatDestroy(&B)); 120 PetscFunctionReturn(PETSC_SUCCESS); 121 } 122 123 static PetscErrorCode MatRestoreRowIJ_MPIAIJ(Mat A, PetscInt oshift, PetscBool symmetric, PetscBool inodecompressed, PetscInt *m, const PetscInt *ia[], const PetscInt *ja[], PetscBool *done) 124 { 125 Mat B; 126 127 PetscFunctionBegin; 128 PetscCall(PetscObjectQuery((PetscObject)A, "MatGetRowIJ_MPIAIJ", (PetscObject *)&B)); 129 PetscCall(MatRestoreRowIJ(B, oshift, symmetric, inodecompressed, m, ia, ja, done)); 130 PetscCall(PetscObjectCompose((PetscObject)A, "MatGetRowIJ_MPIAIJ", NULL)); 131 PetscFunctionReturn(PETSC_SUCCESS); 132 } 133 134 /*MC 135 MATAIJ - MATAIJ = "aij" - A matrix type to be used for sparse matrices. 136 137 This matrix type is identical to` MATSEQAIJ` when constructed with a single process communicator, 138 and `MATMPIAIJ` otherwise. As a result, for single process communicators, 139 `MatSeqAIJSetPreallocation()` is supported, and similarly `MatMPIAIJSetPreallocation()` is supported 140 for communicators controlling multiple processes. It is recommended that you call both of 141 the above preallocation routines for simplicity. 142 143 Options Database Key: 144 . -mat_type aij - sets the matrix type to `MATAIJ` during a call to `MatSetFromOptions()` 145 146 Developer Note: 147 Level: beginner 148 149 Subclasses include `MATAIJCUSPARSE`, `MATAIJPERM`, `MATAIJSELL`, `MATAIJMKL`, `MATAIJCRL`, `MATAIJKOKKOS`,and also automatically switches over to use inodes when 150 enough exist. 151 152 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MATSEQAIJ`, `MatCreateAIJ()`, `MatCreateSeqAIJ()`, `MATSEQAIJ`, `MATMPIAIJ` 153 M*/ 154 155 /*MC 156 MATAIJCRL - MATAIJCRL = "aijcrl" - A matrix type to be used for sparse matrices. 157 158 This matrix type is identical to `MATSEQAIJCRL` when constructed with a single process communicator, 159 and `MATMPIAIJCRL` otherwise. As a result, for single process communicators, 160 `MatSeqAIJSetPreallocation()` is supported, and similarly `MatMPIAIJSetPreallocation()` is supported 161 for communicators controlling multiple processes. It is recommended that you call both of 162 the above preallocation routines for simplicity. 163 164 Options Database Key: 165 . -mat_type aijcrl - sets the matrix type to `MATMPIAIJCRL` during a call to `MatSetFromOptions()` 166 167 Level: beginner 168 169 .seealso: [](ch_matrices), `Mat`, `MatCreateMPIAIJCRL`, `MATSEQAIJCRL`, `MATMPIAIJCRL`, `MATSEQAIJCRL`, `MATMPIAIJCRL` 170 M*/ 171 172 static PetscErrorCode MatBindToCPU_MPIAIJ(Mat A, PetscBool flg) 173 { 174 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 175 176 PetscFunctionBegin; 177 #if defined(PETSC_HAVE_CUDA) || defined(PETSC_HAVE_HIP) || defined(PETSC_HAVE_VIENNACL) 178 A->boundtocpu = flg; 179 #endif 180 if (a->A) PetscCall(MatBindToCPU(a->A, flg)); 181 if (a->B) PetscCall(MatBindToCPU(a->B, flg)); 182 183 /* In addition to binding the diagonal and off-diagonal matrices, bind the local vectors used for matrix-vector products. 184 * This maybe seems a little odd for a MatBindToCPU() call to do, but it makes no sense for the binding of these vectors 185 * to differ from the parent matrix. */ 186 if (a->lvec) PetscCall(VecBindToCPU(a->lvec, flg)); 187 if (a->diag) PetscCall(VecBindToCPU(a->diag, flg)); 188 PetscFunctionReturn(PETSC_SUCCESS); 189 } 190 191 static PetscErrorCode MatSetBlockSizes_MPIAIJ(Mat M, PetscInt rbs, PetscInt cbs) 192 { 193 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)M->data; 194 195 PetscFunctionBegin; 196 if (mat->A) { 197 PetscCall(MatSetBlockSizes(mat->A, rbs, cbs)); 198 PetscCall(MatSetBlockSizes(mat->B, rbs, 1)); 199 } 200 PetscFunctionReturn(PETSC_SUCCESS); 201 } 202 203 static PetscErrorCode MatFindNonzeroRows_MPIAIJ(Mat M, IS *keptrows) 204 { 205 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)M->data; 206 Mat_SeqAIJ *a = (Mat_SeqAIJ *)mat->A->data; 207 Mat_SeqAIJ *b = (Mat_SeqAIJ *)mat->B->data; 208 const PetscInt *ia, *ib; 209 const MatScalar *aa, *bb, *aav, *bav; 210 PetscInt na, nb, i, j, *rows, cnt = 0, n0rows; 211 PetscInt m = M->rmap->n, rstart = M->rmap->rstart; 212 213 PetscFunctionBegin; 214 *keptrows = NULL; 215 216 ia = a->i; 217 ib = b->i; 218 PetscCall(MatSeqAIJGetArrayRead(mat->A, &aav)); 219 PetscCall(MatSeqAIJGetArrayRead(mat->B, &bav)); 220 for (i = 0; i < m; i++) { 221 na = ia[i + 1] - ia[i]; 222 nb = ib[i + 1] - ib[i]; 223 if (!na && !nb) { 224 cnt++; 225 goto ok1; 226 } 227 aa = aav + ia[i]; 228 for (j = 0; j < na; j++) { 229 if (aa[j] != 0.0) goto ok1; 230 } 231 bb = PetscSafePointerPlusOffset(bav, ib[i]); 232 for (j = 0; j < nb; j++) { 233 if (bb[j] != 0.0) goto ok1; 234 } 235 cnt++; 236 ok1:; 237 } 238 PetscCallMPI(MPIU_Allreduce(&cnt, &n0rows, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)M))); 239 if (!n0rows) { 240 PetscCall(MatSeqAIJRestoreArrayRead(mat->A, &aav)); 241 PetscCall(MatSeqAIJRestoreArrayRead(mat->B, &bav)); 242 PetscFunctionReturn(PETSC_SUCCESS); 243 } 244 PetscCall(PetscMalloc1(M->rmap->n - cnt, &rows)); 245 cnt = 0; 246 for (i = 0; i < m; i++) { 247 na = ia[i + 1] - ia[i]; 248 nb = ib[i + 1] - ib[i]; 249 if (!na && !nb) continue; 250 aa = aav + ia[i]; 251 for (j = 0; j < na; j++) { 252 if (aa[j] != 0.0) { 253 rows[cnt++] = rstart + i; 254 goto ok2; 255 } 256 } 257 bb = PetscSafePointerPlusOffset(bav, ib[i]); 258 for (j = 0; j < nb; j++) { 259 if (bb[j] != 0.0) { 260 rows[cnt++] = rstart + i; 261 goto ok2; 262 } 263 } 264 ok2:; 265 } 266 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)M), cnt, rows, PETSC_OWN_POINTER, keptrows)); 267 PetscCall(MatSeqAIJRestoreArrayRead(mat->A, &aav)); 268 PetscCall(MatSeqAIJRestoreArrayRead(mat->B, &bav)); 269 PetscFunctionReturn(PETSC_SUCCESS); 270 } 271 272 static PetscErrorCode MatDiagonalSet_MPIAIJ(Mat Y, Vec D, InsertMode is) 273 { 274 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)Y->data; 275 PetscBool cong; 276 277 PetscFunctionBegin; 278 PetscCall(MatHasCongruentLayouts(Y, &cong)); 279 if (Y->assembled && cong) { 280 PetscCall(MatDiagonalSet(aij->A, D, is)); 281 } else { 282 PetscCall(MatDiagonalSet_Default(Y, D, is)); 283 } 284 PetscFunctionReturn(PETSC_SUCCESS); 285 } 286 287 static PetscErrorCode MatFindZeroDiagonals_MPIAIJ(Mat M, IS *zrows) 288 { 289 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)M->data; 290 PetscInt i, rstart, nrows, *rows; 291 292 PetscFunctionBegin; 293 *zrows = NULL; 294 PetscCall(MatFindZeroDiagonals_SeqAIJ_Private(aij->A, &nrows, &rows)); 295 PetscCall(MatGetOwnershipRange(M, &rstart, NULL)); 296 for (i = 0; i < nrows; i++) rows[i] += rstart; 297 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)M), nrows, rows, PETSC_OWN_POINTER, zrows)); 298 PetscFunctionReturn(PETSC_SUCCESS); 299 } 300 301 static PetscErrorCode MatGetColumnReductions_MPIAIJ(Mat A, PetscInt type, PetscReal *reductions) 302 { 303 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)A->data; 304 PetscInt i, m, n, *garray = aij->garray; 305 Mat_SeqAIJ *a_aij = (Mat_SeqAIJ *)aij->A->data; 306 Mat_SeqAIJ *b_aij = (Mat_SeqAIJ *)aij->B->data; 307 PetscReal *work; 308 const PetscScalar *dummy; 309 310 PetscFunctionBegin; 311 PetscCall(MatGetSize(A, &m, &n)); 312 PetscCall(PetscCalloc1(n, &work)); 313 PetscCall(MatSeqAIJGetArrayRead(aij->A, &dummy)); 314 PetscCall(MatSeqAIJRestoreArrayRead(aij->A, &dummy)); 315 PetscCall(MatSeqAIJGetArrayRead(aij->B, &dummy)); 316 PetscCall(MatSeqAIJRestoreArrayRead(aij->B, &dummy)); 317 if (type == NORM_2) { 318 for (i = 0; i < a_aij->i[aij->A->rmap->n]; i++) work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i] * a_aij->a[i]); 319 for (i = 0; i < b_aij->i[aij->B->rmap->n]; i++) work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i] * b_aij->a[i]); 320 } else if (type == NORM_1) { 321 for (i = 0; i < a_aij->i[aij->A->rmap->n]; i++) work[A->cmap->rstart + a_aij->j[i]] += PetscAbsScalar(a_aij->a[i]); 322 for (i = 0; i < b_aij->i[aij->B->rmap->n]; i++) work[garray[b_aij->j[i]]] += PetscAbsScalar(b_aij->a[i]); 323 } else if (type == NORM_INFINITY) { 324 for (i = 0; i < a_aij->i[aij->A->rmap->n]; i++) work[A->cmap->rstart + a_aij->j[i]] = PetscMax(PetscAbsScalar(a_aij->a[i]), work[A->cmap->rstart + a_aij->j[i]]); 325 for (i = 0; i < b_aij->i[aij->B->rmap->n]; i++) work[garray[b_aij->j[i]]] = PetscMax(PetscAbsScalar(b_aij->a[i]), work[garray[b_aij->j[i]]]); 326 } else if (type == REDUCTION_SUM_REALPART || type == REDUCTION_MEAN_REALPART) { 327 for (i = 0; i < a_aij->i[aij->A->rmap->n]; i++) work[A->cmap->rstart + a_aij->j[i]] += PetscRealPart(a_aij->a[i]); 328 for (i = 0; i < b_aij->i[aij->B->rmap->n]; i++) work[garray[b_aij->j[i]]] += PetscRealPart(b_aij->a[i]); 329 } else if (type == REDUCTION_SUM_IMAGINARYPART || type == REDUCTION_MEAN_IMAGINARYPART) { 330 for (i = 0; i < a_aij->i[aij->A->rmap->n]; i++) work[A->cmap->rstart + a_aij->j[i]] += PetscImaginaryPart(a_aij->a[i]); 331 for (i = 0; i < b_aij->i[aij->B->rmap->n]; i++) work[garray[b_aij->j[i]]] += PetscImaginaryPart(b_aij->a[i]); 332 } else SETERRQ(PetscObjectComm((PetscObject)A), PETSC_ERR_ARG_WRONG, "Unknown reduction type"); 333 if (type == NORM_INFINITY) { 334 PetscCallMPI(MPIU_Allreduce(work, reductions, n, MPIU_REAL, MPIU_MAX, PetscObjectComm((PetscObject)A))); 335 } else { 336 PetscCallMPI(MPIU_Allreduce(work, reductions, n, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)A))); 337 } 338 PetscCall(PetscFree(work)); 339 if (type == NORM_2) { 340 for (i = 0; i < n; i++) reductions[i] = PetscSqrtReal(reductions[i]); 341 } else if (type == REDUCTION_MEAN_REALPART || type == REDUCTION_MEAN_IMAGINARYPART) { 342 for (i = 0; i < n; i++) reductions[i] /= m; 343 } 344 PetscFunctionReturn(PETSC_SUCCESS); 345 } 346 347 static PetscErrorCode MatFindOffBlockDiagonalEntries_MPIAIJ(Mat A, IS *is) 348 { 349 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 350 IS sis, gis; 351 const PetscInt *isis, *igis; 352 PetscInt n, *iis, nsis, ngis, rstart, i; 353 354 PetscFunctionBegin; 355 PetscCall(MatFindOffBlockDiagonalEntries(a->A, &sis)); 356 PetscCall(MatFindNonzeroRows(a->B, &gis)); 357 PetscCall(ISGetSize(gis, &ngis)); 358 PetscCall(ISGetSize(sis, &nsis)); 359 PetscCall(ISGetIndices(sis, &isis)); 360 PetscCall(ISGetIndices(gis, &igis)); 361 362 PetscCall(PetscMalloc1(ngis + nsis, &iis)); 363 PetscCall(PetscArraycpy(iis, igis, ngis)); 364 PetscCall(PetscArraycpy(iis + ngis, isis, nsis)); 365 n = ngis + nsis; 366 PetscCall(PetscSortRemoveDupsInt(&n, iis)); 367 PetscCall(MatGetOwnershipRange(A, &rstart, NULL)); 368 for (i = 0; i < n; i++) iis[i] += rstart; 369 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)A), n, iis, PETSC_OWN_POINTER, is)); 370 371 PetscCall(ISRestoreIndices(sis, &isis)); 372 PetscCall(ISRestoreIndices(gis, &igis)); 373 PetscCall(ISDestroy(&sis)); 374 PetscCall(ISDestroy(&gis)); 375 PetscFunctionReturn(PETSC_SUCCESS); 376 } 377 378 /* 379 Local utility routine that creates a mapping from the global column 380 number to the local number in the off-diagonal part of the local 381 storage of the matrix. When PETSC_USE_CTABLE is used this is scalable at 382 a slightly higher hash table cost; without it it is not scalable (each processor 383 has an order N integer array but is fast to access. 384 */ 385 PetscErrorCode MatCreateColmap_MPIAIJ_Private(Mat mat) 386 { 387 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 388 PetscInt n = aij->B->cmap->n, i; 389 390 PetscFunctionBegin; 391 PetscCheck(!n || aij->garray, PETSC_COMM_SELF, PETSC_ERR_PLIB, "MPIAIJ Matrix was assembled but is missing garray"); 392 #if defined(PETSC_USE_CTABLE) 393 PetscCall(PetscHMapICreateWithSize(n, &aij->colmap)); 394 for (i = 0; i < n; i++) PetscCall(PetscHMapISet(aij->colmap, aij->garray[i] + 1, i + 1)); 395 #else 396 PetscCall(PetscCalloc1(mat->cmap->N + 1, &aij->colmap)); 397 for (i = 0; i < n; i++) aij->colmap[aij->garray[i]] = i + 1; 398 #endif 399 PetscFunctionReturn(PETSC_SUCCESS); 400 } 401 402 #define MatSetValues_SeqAIJ_A_Private(row, col, value, addv, orow, ocol) \ 403 do { \ 404 if (col <= lastcol1) low1 = 0; \ 405 else high1 = nrow1; \ 406 lastcol1 = col; \ 407 while (high1 - low1 > 5) { \ 408 t = (low1 + high1) / 2; \ 409 if (rp1[t] > col) high1 = t; \ 410 else low1 = t; \ 411 } \ 412 for (_i = low1; _i < high1; _i++) { \ 413 if (rp1[_i] > col) break; \ 414 if (rp1[_i] == col) { \ 415 if (addv == ADD_VALUES) { \ 416 ap1[_i] += value; \ 417 /* Not sure LogFlops will slow dow the code or not */ \ 418 (void)PetscLogFlops(1.0); \ 419 } else ap1[_i] = value; \ 420 goto a_noinsert; \ 421 } \ 422 } \ 423 if (value == 0.0 && ignorezeroentries && row != col) { \ 424 low1 = 0; \ 425 high1 = nrow1; \ 426 goto a_noinsert; \ 427 } \ 428 if (nonew == 1) { \ 429 low1 = 0; \ 430 high1 = nrow1; \ 431 goto a_noinsert; \ 432 } \ 433 PetscCheck(nonew != -1, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Inserting a new nonzero at global row/column (%" PetscInt_FMT ", %" PetscInt_FMT ") into matrix", orow, ocol); \ 434 MatSeqXAIJReallocateAIJ(A, am, 1, nrow1, row, col, rmax1, aa, ai, aj, rp1, ap1, aimax, nonew, MatScalar); \ 435 N = nrow1++ - 1; \ 436 a->nz++; \ 437 high1++; \ 438 /* shift up all the later entries in this row */ \ 439 PetscCall(PetscArraymove(rp1 + _i + 1, rp1 + _i, N - _i + 1)); \ 440 PetscCall(PetscArraymove(ap1 + _i + 1, ap1 + _i, N - _i + 1)); \ 441 rp1[_i] = col; \ 442 ap1[_i] = value; \ 443 a_noinsert:; \ 444 ailen[row] = nrow1; \ 445 } while (0) 446 447 #define MatSetValues_SeqAIJ_B_Private(row, col, value, addv, orow, ocol) \ 448 do { \ 449 if (col <= lastcol2) low2 = 0; \ 450 else high2 = nrow2; \ 451 lastcol2 = col; \ 452 while (high2 - low2 > 5) { \ 453 t = (low2 + high2) / 2; \ 454 if (rp2[t] > col) high2 = t; \ 455 else low2 = t; \ 456 } \ 457 for (_i = low2; _i < high2; _i++) { \ 458 if (rp2[_i] > col) break; \ 459 if (rp2[_i] == col) { \ 460 if (addv == ADD_VALUES) { \ 461 ap2[_i] += value; \ 462 (void)PetscLogFlops(1.0); \ 463 } else ap2[_i] = value; \ 464 goto b_noinsert; \ 465 } \ 466 } \ 467 if (value == 0.0 && ignorezeroentries) { \ 468 low2 = 0; \ 469 high2 = nrow2; \ 470 goto b_noinsert; \ 471 } \ 472 if (nonew == 1) { \ 473 low2 = 0; \ 474 high2 = nrow2; \ 475 goto b_noinsert; \ 476 } \ 477 PetscCheck(nonew != -1, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Inserting a new nonzero at global row/column (%" PetscInt_FMT ", %" PetscInt_FMT ") into matrix", orow, ocol); \ 478 MatSeqXAIJReallocateAIJ(B, bm, 1, nrow2, row, col, rmax2, ba, bi, bj, rp2, ap2, bimax, nonew, MatScalar); \ 479 N = nrow2++ - 1; \ 480 b->nz++; \ 481 high2++; \ 482 /* shift up all the later entries in this row */ \ 483 PetscCall(PetscArraymove(rp2 + _i + 1, rp2 + _i, N - _i + 1)); \ 484 PetscCall(PetscArraymove(ap2 + _i + 1, ap2 + _i, N - _i + 1)); \ 485 rp2[_i] = col; \ 486 ap2[_i] = value; \ 487 b_noinsert:; \ 488 bilen[row] = nrow2; \ 489 } while (0) 490 491 static PetscErrorCode MatSetValuesRow_MPIAIJ(Mat A, PetscInt row, const PetscScalar v[]) 492 { 493 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)A->data; 494 Mat_SeqAIJ *a = (Mat_SeqAIJ *)mat->A->data, *b = (Mat_SeqAIJ *)mat->B->data; 495 PetscInt l, *garray = mat->garray, diag; 496 PetscScalar *aa, *ba; 497 498 PetscFunctionBegin; 499 /* code only works for square matrices A */ 500 501 /* find size of row to the left of the diagonal part */ 502 PetscCall(MatGetOwnershipRange(A, &diag, NULL)); 503 row = row - diag; 504 for (l = 0; l < b->i[row + 1] - b->i[row]; l++) { 505 if (garray[b->j[b->i[row] + l]] > diag) break; 506 } 507 if (l) { 508 PetscCall(MatSeqAIJGetArray(mat->B, &ba)); 509 PetscCall(PetscArraycpy(ba + b->i[row], v, l)); 510 PetscCall(MatSeqAIJRestoreArray(mat->B, &ba)); 511 } 512 513 /* diagonal part */ 514 if (a->i[row + 1] - a->i[row]) { 515 PetscCall(MatSeqAIJGetArray(mat->A, &aa)); 516 PetscCall(PetscArraycpy(aa + a->i[row], v + l, a->i[row + 1] - a->i[row])); 517 PetscCall(MatSeqAIJRestoreArray(mat->A, &aa)); 518 } 519 520 /* right of diagonal part */ 521 if (b->i[row + 1] - b->i[row] - l) { 522 PetscCall(MatSeqAIJGetArray(mat->B, &ba)); 523 PetscCall(PetscArraycpy(ba + b->i[row] + l, v + l + a->i[row + 1] - a->i[row], b->i[row + 1] - b->i[row] - l)); 524 PetscCall(MatSeqAIJRestoreArray(mat->B, &ba)); 525 } 526 PetscFunctionReturn(PETSC_SUCCESS); 527 } 528 529 PetscErrorCode MatSetValues_MPIAIJ(Mat mat, PetscInt m, const PetscInt im[], PetscInt n, const PetscInt in[], const PetscScalar v[], InsertMode addv) 530 { 531 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 532 PetscScalar value = 0.0; 533 PetscInt i, j, rstart = mat->rmap->rstart, rend = mat->rmap->rend; 534 PetscInt cstart = mat->cmap->rstart, cend = mat->cmap->rend, row, col; 535 PetscBool roworiented = aij->roworiented; 536 537 /* Some Variables required in the macro */ 538 Mat A = aij->A; 539 Mat_SeqAIJ *a = (Mat_SeqAIJ *)A->data; 540 PetscInt *aimax = a->imax, *ai = a->i, *ailen = a->ilen, *aj = a->j; 541 PetscBool ignorezeroentries = a->ignorezeroentries; 542 Mat B = aij->B; 543 Mat_SeqAIJ *b = (Mat_SeqAIJ *)B->data; 544 PetscInt *bimax = b->imax, *bi = b->i, *bilen = b->ilen, *bj = b->j, bm = aij->B->rmap->n, am = aij->A->rmap->n; 545 MatScalar *aa, *ba; 546 PetscInt *rp1, *rp2, ii, nrow1, nrow2, _i, rmax1, rmax2, N, low1, high1, low2, high2, t, lastcol1, lastcol2; 547 PetscInt nonew; 548 MatScalar *ap1, *ap2; 549 550 PetscFunctionBegin; 551 PetscCall(MatSeqAIJGetArray(A, &aa)); 552 PetscCall(MatSeqAIJGetArray(B, &ba)); 553 for (i = 0; i < m; i++) { 554 if (im[i] < 0) continue; 555 PetscCheck(im[i] < mat->rmap->N, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Row too large: row %" PetscInt_FMT " max %" PetscInt_FMT, im[i], mat->rmap->N - 1); 556 if (im[i] >= rstart && im[i] < rend) { 557 row = im[i] - rstart; 558 lastcol1 = -1; 559 rp1 = PetscSafePointerPlusOffset(aj, ai[row]); 560 ap1 = PetscSafePointerPlusOffset(aa, ai[row]); 561 rmax1 = aimax[row]; 562 nrow1 = ailen[row]; 563 low1 = 0; 564 high1 = nrow1; 565 lastcol2 = -1; 566 rp2 = PetscSafePointerPlusOffset(bj, bi[row]); 567 ap2 = PetscSafePointerPlusOffset(ba, bi[row]); 568 rmax2 = bimax[row]; 569 nrow2 = bilen[row]; 570 low2 = 0; 571 high2 = nrow2; 572 573 for (j = 0; j < n; j++) { 574 if (v) value = roworiented ? v[i * n + j] : v[i + j * m]; 575 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && im[i] != in[j]) continue; 576 if (in[j] >= cstart && in[j] < cend) { 577 col = in[j] - cstart; 578 nonew = a->nonew; 579 MatSetValues_SeqAIJ_A_Private(row, col, value, addv, im[i], in[j]); 580 } else if (in[j] < 0) { 581 continue; 582 } else { 583 PetscCheck(in[j] < mat->cmap->N, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Column too large: col %" PetscInt_FMT " max %" PetscInt_FMT, in[j], mat->cmap->N - 1); 584 if (mat->was_assembled) { 585 if (!aij->colmap) PetscCall(MatCreateColmap_MPIAIJ_Private(mat)); 586 #if defined(PETSC_USE_CTABLE) 587 PetscCall(PetscHMapIGetWithDefault(aij->colmap, in[j] + 1, 0, &col)); /* map global col ids to local ones */ 588 col--; 589 #else 590 col = aij->colmap[in[j]] - 1; 591 #endif 592 if (col < 0 && !((Mat_SeqAIJ *)aij->B->data)->nonew) { /* col < 0 means in[j] is a new col for B */ 593 PetscCall(MatDisAssemble_MPIAIJ(mat, PETSC_FALSE)); /* Change aij->B from reduced/local format to expanded/global format */ 594 col = in[j]; 595 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 596 B = aij->B; 597 b = (Mat_SeqAIJ *)B->data; 598 bimax = b->imax; 599 bi = b->i; 600 bilen = b->ilen; 601 bj = b->j; 602 ba = b->a; 603 rp2 = PetscSafePointerPlusOffset(bj, bi[row]); 604 ap2 = PetscSafePointerPlusOffset(ba, bi[row]); 605 rmax2 = bimax[row]; 606 nrow2 = bilen[row]; 607 low2 = 0; 608 high2 = nrow2; 609 bm = aij->B->rmap->n; 610 ba = b->a; 611 } else if (col < 0 && !(ignorezeroentries && value == 0.0)) { 612 if (1 == ((Mat_SeqAIJ *)aij->B->data)->nonew) { 613 PetscCall(PetscInfo(mat, "Skipping of insertion of new nonzero location in off-diagonal portion of matrix %g(%" PetscInt_FMT ",%" PetscInt_FMT ")\n", (double)PetscRealPart(value), im[i], in[j])); 614 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Inserting a new nonzero at global row/column (%" PetscInt_FMT ", %" PetscInt_FMT ") into matrix", im[i], in[j]); 615 } 616 } else col = in[j]; 617 nonew = b->nonew; 618 MatSetValues_SeqAIJ_B_Private(row, col, value, addv, im[i], in[j]); 619 } 620 } 621 } else { 622 PetscCheck(!mat->nooffprocentries, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Setting off process row %" PetscInt_FMT " even though MatSetOption(,MAT_NO_OFF_PROC_ENTRIES,PETSC_TRUE) was set", im[i]); 623 if (!aij->donotstash) { 624 mat->assembled = PETSC_FALSE; 625 if (roworiented) { 626 PetscCall(MatStashValuesRow_Private(&mat->stash, im[i], n, in, PetscSafePointerPlusOffset(v, i * n), (PetscBool)(ignorezeroentries && (addv == ADD_VALUES)))); 627 } else { 628 PetscCall(MatStashValuesCol_Private(&mat->stash, im[i], n, in, PetscSafePointerPlusOffset(v, i), m, (PetscBool)(ignorezeroentries && (addv == ADD_VALUES)))); 629 } 630 } 631 } 632 } 633 PetscCall(MatSeqAIJRestoreArray(A, &aa)); /* aa, bb might have been free'd due to reallocation above. But we don't access them here */ 634 PetscCall(MatSeqAIJRestoreArray(B, &ba)); 635 PetscFunctionReturn(PETSC_SUCCESS); 636 } 637 638 /* 639 This function sets the j and ilen arrays (of the diagonal and off-diagonal part) of an MPIAIJ-matrix. 640 The values in mat_i have to be sorted and the values in mat_j have to be sorted for each row (CSR-like). 641 No off-processor parts off the matrix are allowed here and mat->was_assembled has to be PETSC_FALSE. 642 */ 643 PetscErrorCode MatSetValues_MPIAIJ_CopyFromCSRFormat_Symbolic(Mat mat, const PetscInt mat_j[], const PetscInt mat_i[]) 644 { 645 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 646 Mat A = aij->A; /* diagonal part of the matrix */ 647 Mat B = aij->B; /* off-diagonal part of the matrix */ 648 Mat_SeqAIJ *a = (Mat_SeqAIJ *)A->data; 649 Mat_SeqAIJ *b = (Mat_SeqAIJ *)B->data; 650 PetscInt cstart = mat->cmap->rstart, cend = mat->cmap->rend, col; 651 PetscInt *ailen = a->ilen, *aj = a->j; 652 PetscInt *bilen = b->ilen, *bj = b->j; 653 PetscInt am = aij->A->rmap->n, j; 654 PetscInt diag_so_far = 0, dnz; 655 PetscInt offd_so_far = 0, onz; 656 657 PetscFunctionBegin; 658 /* Iterate over all rows of the matrix */ 659 for (j = 0; j < am; j++) { 660 dnz = onz = 0; 661 /* Iterate over all non-zero columns of the current row */ 662 for (col = mat_i[j]; col < mat_i[j + 1]; col++) { 663 /* If column is in the diagonal */ 664 if (mat_j[col] >= cstart && mat_j[col] < cend) { 665 aj[diag_so_far++] = mat_j[col] - cstart; 666 dnz++; 667 } else { /* off-diagonal entries */ 668 bj[offd_so_far++] = mat_j[col]; 669 onz++; 670 } 671 } 672 ailen[j] = dnz; 673 bilen[j] = onz; 674 } 675 PetscFunctionReturn(PETSC_SUCCESS); 676 } 677 678 /* 679 This function sets the local j, a and ilen arrays (of the diagonal and off-diagonal part) of an MPIAIJ-matrix. 680 The values in mat_i have to be sorted and the values in mat_j have to be sorted for each row (CSR-like). 681 No off-processor parts off the matrix are allowed here, they are set at a later point by MatSetValues_MPIAIJ. 682 Also, mat->was_assembled has to be false, otherwise the statement aj[rowstart_diag+dnz_row] = mat_j[col] - cstart; 683 would not be true and the more complex MatSetValues_MPIAIJ has to be used. 684 */ 685 PetscErrorCode MatSetValues_MPIAIJ_CopyFromCSRFormat(Mat mat, const PetscInt mat_j[], const PetscInt mat_i[], const PetscScalar mat_a[]) 686 { 687 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 688 Mat A = aij->A; /* diagonal part of the matrix */ 689 Mat B = aij->B; /* off-diagonal part of the matrix */ 690 Mat_SeqAIJ *aijd = (Mat_SeqAIJ *)aij->A->data, *aijo = (Mat_SeqAIJ *)aij->B->data; 691 Mat_SeqAIJ *a = (Mat_SeqAIJ *)A->data; 692 Mat_SeqAIJ *b = (Mat_SeqAIJ *)B->data; 693 PetscInt cstart = mat->cmap->rstart, cend = mat->cmap->rend; 694 PetscInt *ailen = a->ilen, *aj = a->j; 695 PetscInt *bilen = b->ilen, *bj = b->j; 696 PetscInt am = aij->A->rmap->n, j; 697 PetscInt *full_diag_i = aijd->i, *full_offd_i = aijo->i; /* These variables can also include non-local elements, which are set at a later point. */ 698 PetscInt col, dnz_row, onz_row, rowstart_diag, rowstart_offd; 699 PetscScalar *aa = a->a, *ba = b->a; 700 701 PetscFunctionBegin; 702 /* Iterate over all rows of the matrix */ 703 for (j = 0; j < am; j++) { 704 dnz_row = onz_row = 0; 705 rowstart_offd = full_offd_i[j]; 706 rowstart_diag = full_diag_i[j]; 707 /* Iterate over all non-zero columns of the current row */ 708 for (col = mat_i[j]; col < mat_i[j + 1]; col++) { 709 /* If column is in the diagonal */ 710 if (mat_j[col] >= cstart && mat_j[col] < cend) { 711 aj[rowstart_diag + dnz_row] = mat_j[col] - cstart; 712 aa[rowstart_diag + dnz_row] = mat_a[col]; 713 dnz_row++; 714 } else { /* off-diagonal entries */ 715 bj[rowstart_offd + onz_row] = mat_j[col]; 716 ba[rowstart_offd + onz_row] = mat_a[col]; 717 onz_row++; 718 } 719 } 720 ailen[j] = dnz_row; 721 bilen[j] = onz_row; 722 } 723 PetscFunctionReturn(PETSC_SUCCESS); 724 } 725 726 static PetscErrorCode MatGetValues_MPIAIJ(Mat mat, PetscInt m, const PetscInt idxm[], PetscInt n, const PetscInt idxn[], PetscScalar v[]) 727 { 728 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 729 PetscInt i, j, rstart = mat->rmap->rstart, rend = mat->rmap->rend; 730 PetscInt cstart = mat->cmap->rstart, cend = mat->cmap->rend, row, col; 731 732 PetscFunctionBegin; 733 for (i = 0; i < m; i++) { 734 if (idxm[i] < 0) continue; /* negative row */ 735 PetscCheck(idxm[i] < mat->rmap->N, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Row too large: row %" PetscInt_FMT " max %" PetscInt_FMT, idxm[i], mat->rmap->N - 1); 736 PetscCheck(idxm[i] >= rstart && idxm[i] < rend, PETSC_COMM_SELF, PETSC_ERR_SUP, "Only local values currently supported, row requested %" PetscInt_FMT " range [%" PetscInt_FMT " %" PetscInt_FMT ")", idxm[i], rstart, rend); 737 row = idxm[i] - rstart; 738 for (j = 0; j < n; j++) { 739 if (idxn[j] < 0) continue; /* negative column */ 740 PetscCheck(idxn[j] < mat->cmap->N, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Column too large: col %" PetscInt_FMT " max %" PetscInt_FMT, idxn[j], mat->cmap->N - 1); 741 if (idxn[j] >= cstart && idxn[j] < cend) { 742 col = idxn[j] - cstart; 743 PetscCall(MatGetValues(aij->A, 1, &row, 1, &col, v + i * n + j)); 744 } else { 745 if (!aij->colmap) PetscCall(MatCreateColmap_MPIAIJ_Private(mat)); 746 #if defined(PETSC_USE_CTABLE) 747 PetscCall(PetscHMapIGetWithDefault(aij->colmap, idxn[j] + 1, 0, &col)); 748 col--; 749 #else 750 col = aij->colmap[idxn[j]] - 1; 751 #endif 752 if ((col < 0) || (aij->garray[col] != idxn[j])) *(v + i * n + j) = 0.0; 753 else PetscCall(MatGetValues(aij->B, 1, &row, 1, &col, v + i * n + j)); 754 } 755 } 756 } 757 PetscFunctionReturn(PETSC_SUCCESS); 758 } 759 760 static PetscErrorCode MatAssemblyBegin_MPIAIJ(Mat mat, MatAssemblyType mode) 761 { 762 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 763 PetscInt nstash, reallocs; 764 765 PetscFunctionBegin; 766 if (aij->donotstash || mat->nooffprocentries) PetscFunctionReturn(PETSC_SUCCESS); 767 768 PetscCall(MatStashScatterBegin_Private(mat, &mat->stash, mat->rmap->range)); 769 PetscCall(MatStashGetInfo_Private(&mat->stash, &nstash, &reallocs)); 770 PetscCall(PetscInfo(aij->A, "Stash has %" PetscInt_FMT " entries, uses %" PetscInt_FMT " mallocs.\n", nstash, reallocs)); 771 PetscFunctionReturn(PETSC_SUCCESS); 772 } 773 774 PetscErrorCode MatAssemblyEnd_MPIAIJ(Mat mat, MatAssemblyType mode) 775 { 776 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 777 PetscMPIInt n; 778 PetscInt i, j, rstart, ncols, flg; 779 PetscInt *row, *col; 780 PetscBool other_disassembled; 781 PetscScalar *val; 782 783 /* do not use 'b = (Mat_SeqAIJ*)aij->B->data' as B can be reset in disassembly */ 784 785 PetscFunctionBegin; 786 if (!aij->donotstash && !mat->nooffprocentries) { 787 while (1) { 788 PetscCall(MatStashScatterGetMesg_Private(&mat->stash, &n, &row, &col, &val, &flg)); 789 if (!flg) break; 790 791 for (i = 0; i < n;) { 792 /* Now identify the consecutive vals belonging to the same row */ 793 for (j = i, rstart = row[j]; j < n; j++) { 794 if (row[j] != rstart) break; 795 } 796 if (j < n) ncols = j - i; 797 else ncols = n - i; 798 /* Now assemble all these values with a single function call */ 799 PetscCall(MatSetValues_MPIAIJ(mat, 1, row + i, ncols, col + i, val + i, mat->insertmode)); 800 i = j; 801 } 802 } 803 PetscCall(MatStashScatterEnd_Private(&mat->stash)); 804 } 805 #if defined(PETSC_HAVE_DEVICE) 806 if (mat->offloadmask == PETSC_OFFLOAD_CPU) aij->A->offloadmask = PETSC_OFFLOAD_CPU; 807 /* We call MatBindToCPU() on aij->A and aij->B here, because if MatBindToCPU_MPIAIJ() is called before assembly, it cannot bind these. */ 808 if (mat->boundtocpu) { 809 PetscCall(MatBindToCPU(aij->A, PETSC_TRUE)); 810 PetscCall(MatBindToCPU(aij->B, PETSC_TRUE)); 811 } 812 #endif 813 PetscCall(MatAssemblyBegin(aij->A, mode)); 814 PetscCall(MatAssemblyEnd(aij->A, mode)); 815 816 /* determine if any processor has disassembled, if so we must 817 also disassemble ourself, in order that we may reassemble. */ 818 /* 819 if nonzero structure of submatrix B cannot change then we know that 820 no processor disassembled thus we can skip this stuff 821 */ 822 if (!((Mat_SeqAIJ *)aij->B->data)->nonew) { 823 PetscCallMPI(MPIU_Allreduce(&mat->was_assembled, &other_disassembled, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)mat))); 824 if (mat->was_assembled && !other_disassembled) { /* mat on this rank has reduced off-diag B with local col ids, but globally it does not */ 825 PetscCall(MatDisAssemble_MPIAIJ(mat, PETSC_FALSE)); 826 } 827 } 828 if (!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) PetscCall(MatSetUpMultiply_MPIAIJ(mat)); 829 PetscCall(MatSetOption(aij->B, MAT_USE_INODES, PETSC_FALSE)); 830 #if defined(PETSC_HAVE_DEVICE) 831 if (mat->offloadmask == PETSC_OFFLOAD_CPU && aij->B->offloadmask != PETSC_OFFLOAD_UNALLOCATED) aij->B->offloadmask = PETSC_OFFLOAD_CPU; 832 #endif 833 PetscCall(MatAssemblyBegin(aij->B, mode)); 834 PetscCall(MatAssemblyEnd(aij->B, mode)); 835 836 PetscCall(PetscFree2(aij->rowvalues, aij->rowindices)); 837 838 aij->rowvalues = NULL; 839 840 PetscCall(VecDestroy(&aij->diag)); 841 842 /* if no new nonzero locations are allowed in matrix then only set the matrix state the first time through */ 843 if ((!mat->was_assembled && mode == MAT_FINAL_ASSEMBLY) || !((Mat_SeqAIJ *)aij->A->data)->nonew) { 844 PetscObjectState state = aij->A->nonzerostate + aij->B->nonzerostate; 845 PetscCallMPI(MPIU_Allreduce(&state, &mat->nonzerostate, 1, MPIU_INT64, MPI_SUM, PetscObjectComm((PetscObject)mat))); 846 } 847 #if defined(PETSC_HAVE_DEVICE) 848 mat->offloadmask = PETSC_OFFLOAD_BOTH; 849 #endif 850 PetscFunctionReturn(PETSC_SUCCESS); 851 } 852 853 static PetscErrorCode MatZeroEntries_MPIAIJ(Mat A) 854 { 855 Mat_MPIAIJ *l = (Mat_MPIAIJ *)A->data; 856 857 PetscFunctionBegin; 858 PetscCall(MatZeroEntries(l->A)); 859 PetscCall(MatZeroEntries(l->B)); 860 PetscFunctionReturn(PETSC_SUCCESS); 861 } 862 863 static PetscErrorCode MatZeroRows_MPIAIJ(Mat A, PetscInt N, const PetscInt rows[], PetscScalar diag, Vec x, Vec b) 864 { 865 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)A->data; 866 PetscInt *lrows; 867 PetscInt r, len; 868 PetscBool cong; 869 870 PetscFunctionBegin; 871 /* get locally owned rows */ 872 PetscCall(MatZeroRowsMapLocal_Private(A, N, rows, &len, &lrows)); 873 PetscCall(MatHasCongruentLayouts(A, &cong)); 874 /* fix right-hand side if needed */ 875 if (x && b) { 876 const PetscScalar *xx; 877 PetscScalar *bb; 878 879 PetscCheck(cong, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Need matching row/col layout"); 880 PetscCall(VecGetArrayRead(x, &xx)); 881 PetscCall(VecGetArray(b, &bb)); 882 for (r = 0; r < len; ++r) bb[lrows[r]] = diag * xx[lrows[r]]; 883 PetscCall(VecRestoreArrayRead(x, &xx)); 884 PetscCall(VecRestoreArray(b, &bb)); 885 } 886 887 if (diag != 0.0 && cong) { 888 PetscCall(MatZeroRows(mat->A, len, lrows, diag, NULL, NULL)); 889 PetscCall(MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL)); 890 } else if (diag != 0.0) { /* non-square or non congruent layouts -> if keepnonzeropattern is false, we allow for new insertion */ 891 Mat_SeqAIJ *aijA = (Mat_SeqAIJ *)mat->A->data; 892 Mat_SeqAIJ *aijB = (Mat_SeqAIJ *)mat->B->data; 893 PetscInt nnwA, nnwB; 894 PetscBool nnzA, nnzB; 895 896 nnwA = aijA->nonew; 897 nnwB = aijB->nonew; 898 nnzA = aijA->keepnonzeropattern; 899 nnzB = aijB->keepnonzeropattern; 900 if (!nnzA) { 901 PetscCall(PetscInfo(mat->A, "Requested to not keep the pattern and add a nonzero diagonal; may encounter reallocations on diagonal block.\n")); 902 aijA->nonew = 0; 903 } 904 if (!nnzB) { 905 PetscCall(PetscInfo(mat->B, "Requested to not keep the pattern and add a nonzero diagonal; may encounter reallocations on off-diagonal block.\n")); 906 aijB->nonew = 0; 907 } 908 /* Must zero here before the next loop */ 909 PetscCall(MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL)); 910 PetscCall(MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL)); 911 for (r = 0; r < len; ++r) { 912 const PetscInt row = lrows[r] + A->rmap->rstart; 913 if (row >= A->cmap->N) continue; 914 PetscCall(MatSetValues(A, 1, &row, 1, &row, &diag, INSERT_VALUES)); 915 } 916 aijA->nonew = nnwA; 917 aijB->nonew = nnwB; 918 } else { 919 PetscCall(MatZeroRows(mat->A, len, lrows, 0.0, NULL, NULL)); 920 PetscCall(MatZeroRows(mat->B, len, lrows, 0.0, NULL, NULL)); 921 } 922 PetscCall(PetscFree(lrows)); 923 PetscCall(MatAssemblyBegin(A, MAT_FINAL_ASSEMBLY)); 924 PetscCall(MatAssemblyEnd(A, MAT_FINAL_ASSEMBLY)); 925 926 /* only change matrix nonzero state if pattern was allowed to be changed */ 927 if (!((Mat_SeqAIJ *)mat->A->data)->keepnonzeropattern || !((Mat_SeqAIJ *)mat->A->data)->nonew) { 928 PetscObjectState state = mat->A->nonzerostate + mat->B->nonzerostate; 929 PetscCallMPI(MPIU_Allreduce(&state, &A->nonzerostate, 1, MPIU_INT64, MPI_SUM, PetscObjectComm((PetscObject)A))); 930 } 931 PetscFunctionReturn(PETSC_SUCCESS); 932 } 933 934 static PetscErrorCode MatZeroRowsColumns_MPIAIJ(Mat A, PetscInt N, const PetscInt rows[], PetscScalar diag, Vec x, Vec b) 935 { 936 Mat_MPIAIJ *l = (Mat_MPIAIJ *)A->data; 937 PetscInt n = A->rmap->n; 938 PetscInt i, j, r, m, len = 0; 939 PetscInt *lrows, *owners = A->rmap->range; 940 PetscMPIInt p = 0; 941 PetscSFNode *rrows; 942 PetscSF sf; 943 const PetscScalar *xx; 944 PetscScalar *bb, *mask, *aij_a; 945 Vec xmask, lmask; 946 Mat_SeqAIJ *aij = (Mat_SeqAIJ *)l->B->data; 947 const PetscInt *aj, *ii, *ridx; 948 PetscScalar *aa; 949 950 PetscFunctionBegin; 951 /* Create SF where leaves are input rows and roots are owned rows */ 952 PetscCall(PetscMalloc1(n, &lrows)); 953 for (r = 0; r < n; ++r) lrows[r] = -1; 954 PetscCall(PetscMalloc1(N, &rrows)); 955 for (r = 0; r < N; ++r) { 956 const PetscInt idx = rows[r]; 957 PetscCheck(idx >= 0 && A->rmap->N > idx, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Row %" PetscInt_FMT " out of range [0,%" PetscInt_FMT ")", idx, A->rmap->N); 958 if (idx < owners[p] || owners[p + 1] <= idx) { /* short-circuit the search if the last p owns this row too */ 959 PetscCall(PetscLayoutFindOwner(A->rmap, idx, &p)); 960 } 961 rrows[r].rank = p; 962 rrows[r].index = rows[r] - owners[p]; 963 } 964 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)A), &sf)); 965 PetscCall(PetscSFSetGraph(sf, n, N, NULL, PETSC_OWN_POINTER, rrows, PETSC_OWN_POINTER)); 966 /* Collect flags for rows to be zeroed */ 967 PetscCall(PetscSFReduceBegin(sf, MPIU_INT, (PetscInt *)rows, lrows, MPI_LOR)); 968 PetscCall(PetscSFReduceEnd(sf, MPIU_INT, (PetscInt *)rows, lrows, MPI_LOR)); 969 PetscCall(PetscSFDestroy(&sf)); 970 /* Compress and put in row numbers */ 971 for (r = 0; r < n; ++r) 972 if (lrows[r] >= 0) lrows[len++] = r; 973 /* zero diagonal part of matrix */ 974 PetscCall(MatZeroRowsColumns(l->A, len, lrows, diag, x, b)); 975 /* handle off-diagonal part of matrix */ 976 PetscCall(MatCreateVecs(A, &xmask, NULL)); 977 PetscCall(VecDuplicate(l->lvec, &lmask)); 978 PetscCall(VecGetArray(xmask, &bb)); 979 for (i = 0; i < len; i++) bb[lrows[i]] = 1; 980 PetscCall(VecRestoreArray(xmask, &bb)); 981 PetscCall(VecScatterBegin(l->Mvctx, xmask, lmask, ADD_VALUES, SCATTER_FORWARD)); 982 PetscCall(VecScatterEnd(l->Mvctx, xmask, lmask, ADD_VALUES, SCATTER_FORWARD)); 983 PetscCall(VecDestroy(&xmask)); 984 if (x && b) { /* this code is buggy when the row and column layout don't match */ 985 PetscBool cong; 986 987 PetscCall(MatHasCongruentLayouts(A, &cong)); 988 PetscCheck(cong, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Need matching row/col layout"); 989 PetscCall(VecScatterBegin(l->Mvctx, x, l->lvec, INSERT_VALUES, SCATTER_FORWARD)); 990 PetscCall(VecScatterEnd(l->Mvctx, x, l->lvec, INSERT_VALUES, SCATTER_FORWARD)); 991 PetscCall(VecGetArrayRead(l->lvec, &xx)); 992 PetscCall(VecGetArray(b, &bb)); 993 } 994 PetscCall(VecGetArray(lmask, &mask)); 995 /* remove zeroed rows of off-diagonal matrix */ 996 PetscCall(MatSeqAIJGetArray(l->B, &aij_a)); 997 ii = aij->i; 998 for (i = 0; i < len; i++) PetscCall(PetscArrayzero(PetscSafePointerPlusOffset(aij_a, ii[lrows[i]]), ii[lrows[i] + 1] - ii[lrows[i]])); 999 /* loop over all elements of off process part of matrix zeroing removed columns*/ 1000 if (aij->compressedrow.use) { 1001 m = aij->compressedrow.nrows; 1002 ii = aij->compressedrow.i; 1003 ridx = aij->compressedrow.rindex; 1004 for (i = 0; i < m; i++) { 1005 n = ii[i + 1] - ii[i]; 1006 aj = aij->j + ii[i]; 1007 aa = aij_a + ii[i]; 1008 1009 for (j = 0; j < n; j++) { 1010 if (PetscAbsScalar(mask[*aj])) { 1011 if (b) bb[*ridx] -= *aa * xx[*aj]; 1012 *aa = 0.0; 1013 } 1014 aa++; 1015 aj++; 1016 } 1017 ridx++; 1018 } 1019 } else { /* do not use compressed row format */ 1020 m = l->B->rmap->n; 1021 for (i = 0; i < m; i++) { 1022 n = ii[i + 1] - ii[i]; 1023 aj = aij->j + ii[i]; 1024 aa = aij_a + ii[i]; 1025 for (j = 0; j < n; j++) { 1026 if (PetscAbsScalar(mask[*aj])) { 1027 if (b) bb[i] -= *aa * xx[*aj]; 1028 *aa = 0.0; 1029 } 1030 aa++; 1031 aj++; 1032 } 1033 } 1034 } 1035 if (x && b) { 1036 PetscCall(VecRestoreArray(b, &bb)); 1037 PetscCall(VecRestoreArrayRead(l->lvec, &xx)); 1038 } 1039 PetscCall(MatSeqAIJRestoreArray(l->B, &aij_a)); 1040 PetscCall(VecRestoreArray(lmask, &mask)); 1041 PetscCall(VecDestroy(&lmask)); 1042 PetscCall(PetscFree(lrows)); 1043 1044 /* only change matrix nonzero state if pattern was allowed to be changed */ 1045 if (!((Mat_SeqAIJ *)l->A->data)->nonew) { 1046 PetscObjectState state = l->A->nonzerostate + l->B->nonzerostate; 1047 PetscCallMPI(MPIU_Allreduce(&state, &A->nonzerostate, 1, MPIU_INT64, MPI_SUM, PetscObjectComm((PetscObject)A))); 1048 } 1049 PetscFunctionReturn(PETSC_SUCCESS); 1050 } 1051 1052 static PetscErrorCode MatMult_MPIAIJ(Mat A, Vec xx, Vec yy) 1053 { 1054 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 1055 PetscInt nt; 1056 VecScatter Mvctx = a->Mvctx; 1057 1058 PetscFunctionBegin; 1059 PetscCall(VecGetLocalSize(xx, &nt)); 1060 PetscCheck(nt == A->cmap->n, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Incompatible partition of A (%" PetscInt_FMT ") and xx (%" PetscInt_FMT ")", A->cmap->n, nt); 1061 PetscCall(VecScatterBegin(Mvctx, xx, a->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1062 PetscUseTypeMethod(a->A, mult, xx, yy); 1063 PetscCall(VecScatterEnd(Mvctx, xx, a->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1064 PetscUseTypeMethod(a->B, multadd, a->lvec, yy, yy); 1065 PetscFunctionReturn(PETSC_SUCCESS); 1066 } 1067 1068 static PetscErrorCode MatMultDiagonalBlock_MPIAIJ(Mat A, Vec bb, Vec xx) 1069 { 1070 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 1071 1072 PetscFunctionBegin; 1073 PetscCall(MatMultDiagonalBlock(a->A, bb, xx)); 1074 PetscFunctionReturn(PETSC_SUCCESS); 1075 } 1076 1077 static PetscErrorCode MatMultAdd_MPIAIJ(Mat A, Vec xx, Vec yy, Vec zz) 1078 { 1079 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 1080 VecScatter Mvctx = a->Mvctx; 1081 1082 PetscFunctionBegin; 1083 PetscCall(VecScatterBegin(Mvctx, xx, a->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1084 PetscCall((*a->A->ops->multadd)(a->A, xx, yy, zz)); 1085 PetscCall(VecScatterEnd(Mvctx, xx, a->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1086 PetscCall((*a->B->ops->multadd)(a->B, a->lvec, zz, zz)); 1087 PetscFunctionReturn(PETSC_SUCCESS); 1088 } 1089 1090 static PetscErrorCode MatMultTranspose_MPIAIJ(Mat A, Vec xx, Vec yy) 1091 { 1092 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 1093 1094 PetscFunctionBegin; 1095 /* do nondiagonal part */ 1096 PetscCall((*a->B->ops->multtranspose)(a->B, xx, a->lvec)); 1097 /* do local part */ 1098 PetscCall((*a->A->ops->multtranspose)(a->A, xx, yy)); 1099 /* add partial results together */ 1100 PetscCall(VecScatterBegin(a->Mvctx, a->lvec, yy, ADD_VALUES, SCATTER_REVERSE)); 1101 PetscCall(VecScatterEnd(a->Mvctx, a->lvec, yy, ADD_VALUES, SCATTER_REVERSE)); 1102 PetscFunctionReturn(PETSC_SUCCESS); 1103 } 1104 1105 static PetscErrorCode MatIsTranspose_MPIAIJ(Mat Amat, Mat Bmat, PetscReal tol, PetscBool *f) 1106 { 1107 MPI_Comm comm; 1108 Mat_MPIAIJ *Aij = (Mat_MPIAIJ *)Amat->data, *Bij = (Mat_MPIAIJ *)Bmat->data; 1109 Mat Adia = Aij->A, Bdia = Bij->A, Aoff, Boff, *Aoffs, *Boffs; 1110 IS Me, Notme; 1111 PetscInt M, N, first, last, *notme, i; 1112 PetscBool lf; 1113 PetscMPIInt size; 1114 1115 PetscFunctionBegin; 1116 /* Easy test: symmetric diagonal block */ 1117 PetscCall(MatIsTranspose(Adia, Bdia, tol, &lf)); 1118 PetscCallMPI(MPIU_Allreduce(&lf, f, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)Amat))); 1119 if (!*f) PetscFunctionReturn(PETSC_SUCCESS); 1120 PetscCall(PetscObjectGetComm((PetscObject)Amat, &comm)); 1121 PetscCallMPI(MPI_Comm_size(comm, &size)); 1122 if (size == 1) PetscFunctionReturn(PETSC_SUCCESS); 1123 1124 /* Hard test: off-diagonal block. This takes a MatCreateSubMatrix. */ 1125 PetscCall(MatGetSize(Amat, &M, &N)); 1126 PetscCall(MatGetOwnershipRange(Amat, &first, &last)); 1127 PetscCall(PetscMalloc1(N - last + first, ¬me)); 1128 for (i = 0; i < first; i++) notme[i] = i; 1129 for (i = last; i < M; i++) notme[i - last + first] = i; 1130 PetscCall(ISCreateGeneral(MPI_COMM_SELF, N - last + first, notme, PETSC_COPY_VALUES, &Notme)); 1131 PetscCall(ISCreateStride(MPI_COMM_SELF, last - first, first, 1, &Me)); 1132 PetscCall(MatCreateSubMatrices(Amat, 1, &Me, &Notme, MAT_INITIAL_MATRIX, &Aoffs)); 1133 Aoff = Aoffs[0]; 1134 PetscCall(MatCreateSubMatrices(Bmat, 1, &Notme, &Me, MAT_INITIAL_MATRIX, &Boffs)); 1135 Boff = Boffs[0]; 1136 PetscCall(MatIsTranspose(Aoff, Boff, tol, f)); 1137 PetscCall(MatDestroyMatrices(1, &Aoffs)); 1138 PetscCall(MatDestroyMatrices(1, &Boffs)); 1139 PetscCall(ISDestroy(&Me)); 1140 PetscCall(ISDestroy(&Notme)); 1141 PetscCall(PetscFree(notme)); 1142 PetscFunctionReturn(PETSC_SUCCESS); 1143 } 1144 1145 static PetscErrorCode MatMultTransposeAdd_MPIAIJ(Mat A, Vec xx, Vec yy, Vec zz) 1146 { 1147 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 1148 1149 PetscFunctionBegin; 1150 /* do nondiagonal part */ 1151 PetscCall((*a->B->ops->multtranspose)(a->B, xx, a->lvec)); 1152 /* do local part */ 1153 PetscCall((*a->A->ops->multtransposeadd)(a->A, xx, yy, zz)); 1154 /* add partial results together */ 1155 PetscCall(VecScatterBegin(a->Mvctx, a->lvec, zz, ADD_VALUES, SCATTER_REVERSE)); 1156 PetscCall(VecScatterEnd(a->Mvctx, a->lvec, zz, ADD_VALUES, SCATTER_REVERSE)); 1157 PetscFunctionReturn(PETSC_SUCCESS); 1158 } 1159 1160 /* 1161 This only works correctly for square matrices where the subblock A->A is the 1162 diagonal block 1163 */ 1164 static PetscErrorCode MatGetDiagonal_MPIAIJ(Mat A, Vec v) 1165 { 1166 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 1167 1168 PetscFunctionBegin; 1169 PetscCheck(A->rmap->N == A->cmap->N, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Supports only square matrix where A->A is diag block"); 1170 PetscCheck(A->rmap->rstart == A->cmap->rstart && A->rmap->rend == A->cmap->rend, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "row partition must equal col partition"); 1171 PetscCall(MatGetDiagonal(a->A, v)); 1172 PetscFunctionReturn(PETSC_SUCCESS); 1173 } 1174 1175 static PetscErrorCode MatScale_MPIAIJ(Mat A, PetscScalar aa) 1176 { 1177 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 1178 1179 PetscFunctionBegin; 1180 PetscCall(MatScale(a->A, aa)); 1181 PetscCall(MatScale(a->B, aa)); 1182 PetscFunctionReturn(PETSC_SUCCESS); 1183 } 1184 1185 static PetscErrorCode MatView_MPIAIJ_Binary(Mat mat, PetscViewer viewer) 1186 { 1187 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 1188 Mat_SeqAIJ *A = (Mat_SeqAIJ *)aij->A->data; 1189 Mat_SeqAIJ *B = (Mat_SeqAIJ *)aij->B->data; 1190 const PetscInt *garray = aij->garray; 1191 const PetscScalar *aa, *ba; 1192 PetscInt header[4], M, N, m, rs, cs, cnt, i, ja, jb; 1193 PetscInt64 nz, hnz; 1194 PetscInt *rowlens; 1195 PetscInt *colidxs; 1196 PetscScalar *matvals; 1197 PetscMPIInt rank; 1198 1199 PetscFunctionBegin; 1200 PetscCall(PetscViewerSetUp(viewer)); 1201 1202 M = mat->rmap->N; 1203 N = mat->cmap->N; 1204 m = mat->rmap->n; 1205 rs = mat->rmap->rstart; 1206 cs = mat->cmap->rstart; 1207 nz = A->nz + B->nz; 1208 1209 /* write matrix header */ 1210 header[0] = MAT_FILE_CLASSID; 1211 header[1] = M; 1212 header[2] = N; 1213 PetscCallMPI(MPI_Reduce(&nz, &hnz, 1, MPIU_INT64, MPI_SUM, 0, PetscObjectComm((PetscObject)mat))); 1214 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)mat), &rank)); 1215 if (rank == 0) PetscCall(PetscIntCast(hnz, &header[3])); 1216 PetscCall(PetscViewerBinaryWrite(viewer, header, 4, PETSC_INT)); 1217 1218 /* fill in and store row lengths */ 1219 PetscCall(PetscMalloc1(m, &rowlens)); 1220 for (i = 0; i < m; i++) rowlens[i] = A->i[i + 1] - A->i[i] + B->i[i + 1] - B->i[i]; 1221 PetscCall(PetscViewerBinaryWriteAll(viewer, rowlens, m, rs, M, PETSC_INT)); 1222 PetscCall(PetscFree(rowlens)); 1223 1224 /* fill in and store column indices */ 1225 PetscCall(PetscMalloc1(nz, &colidxs)); 1226 for (cnt = 0, i = 0; i < m; i++) { 1227 for (jb = B->i[i]; jb < B->i[i + 1]; jb++) { 1228 if (garray[B->j[jb]] > cs) break; 1229 colidxs[cnt++] = garray[B->j[jb]]; 1230 } 1231 for (ja = A->i[i]; ja < A->i[i + 1]; ja++) colidxs[cnt++] = A->j[ja] + cs; 1232 for (; jb < B->i[i + 1]; jb++) colidxs[cnt++] = garray[B->j[jb]]; 1233 } 1234 PetscCheck(cnt == nz, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Internal PETSc error: cnt = %" PetscInt_FMT " nz = %" PetscInt64_FMT, cnt, nz); 1235 PetscCall(PetscViewerBinaryWriteAll(viewer, colidxs, nz, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_INT)); 1236 PetscCall(PetscFree(colidxs)); 1237 1238 /* fill in and store nonzero values */ 1239 PetscCall(MatSeqAIJGetArrayRead(aij->A, &aa)); 1240 PetscCall(MatSeqAIJGetArrayRead(aij->B, &ba)); 1241 PetscCall(PetscMalloc1(nz, &matvals)); 1242 for (cnt = 0, i = 0; i < m; i++) { 1243 for (jb = B->i[i]; jb < B->i[i + 1]; jb++) { 1244 if (garray[B->j[jb]] > cs) break; 1245 matvals[cnt++] = ba[jb]; 1246 } 1247 for (ja = A->i[i]; ja < A->i[i + 1]; ja++) matvals[cnt++] = aa[ja]; 1248 for (; jb < B->i[i + 1]; jb++) matvals[cnt++] = ba[jb]; 1249 } 1250 PetscCall(MatSeqAIJRestoreArrayRead(aij->A, &aa)); 1251 PetscCall(MatSeqAIJRestoreArrayRead(aij->B, &ba)); 1252 PetscCheck(cnt == nz, PETSC_COMM_SELF, PETSC_ERR_LIB, "Internal PETSc error: cnt = %" PetscInt_FMT " nz = %" PetscInt64_FMT, cnt, nz); 1253 PetscCall(PetscViewerBinaryWriteAll(viewer, matvals, nz, PETSC_DETERMINE, PETSC_DETERMINE, PETSC_SCALAR)); 1254 PetscCall(PetscFree(matvals)); 1255 1256 /* write block size option to the viewer's .info file */ 1257 PetscCall(MatView_Binary_BlockSizes(mat, viewer)); 1258 PetscFunctionReturn(PETSC_SUCCESS); 1259 } 1260 1261 #include <petscdraw.h> 1262 static PetscErrorCode MatView_MPIAIJ_ASCIIorDraworSocket(Mat mat, PetscViewer viewer) 1263 { 1264 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 1265 PetscMPIInt rank = aij->rank, size = aij->size; 1266 PetscBool isdraw, iascii, isbinary; 1267 PetscViewer sviewer; 1268 PetscViewerFormat format; 1269 1270 PetscFunctionBegin; 1271 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw)); 1272 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii)); 1273 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &isbinary)); 1274 if (iascii) { 1275 PetscCall(PetscViewerGetFormat(viewer, &format)); 1276 if (format == PETSC_VIEWER_LOAD_BALANCE) { 1277 PetscInt i, nmax = 0, nmin = PETSC_INT_MAX, navg = 0, *nz, nzlocal = ((Mat_SeqAIJ *)aij->A->data)->nz + ((Mat_SeqAIJ *)aij->B->data)->nz; 1278 PetscCall(PetscMalloc1(size, &nz)); 1279 PetscCallMPI(MPI_Allgather(&nzlocal, 1, MPIU_INT, nz, 1, MPIU_INT, PetscObjectComm((PetscObject)mat))); 1280 for (i = 0; i < size; i++) { 1281 nmax = PetscMax(nmax, nz[i]); 1282 nmin = PetscMin(nmin, nz[i]); 1283 navg += nz[i]; 1284 } 1285 PetscCall(PetscFree(nz)); 1286 navg = navg / size; 1287 PetscCall(PetscViewerASCIIPrintf(viewer, "Load Balance - Nonzeros: Min %" PetscInt_FMT " avg %" PetscInt_FMT " max %" PetscInt_FMT "\n", nmin, navg, nmax)); 1288 PetscFunctionReturn(PETSC_SUCCESS); 1289 } 1290 PetscCall(PetscViewerGetFormat(viewer, &format)); 1291 if (format == PETSC_VIEWER_ASCII_INFO_DETAIL) { 1292 MatInfo info; 1293 PetscInt *inodes = NULL; 1294 1295 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)mat), &rank)); 1296 PetscCall(MatGetInfo(mat, MAT_LOCAL, &info)); 1297 PetscCall(MatInodeGetInodeSizes(aij->A, NULL, &inodes, NULL)); 1298 PetscCall(PetscViewerASCIIPushSynchronized(viewer)); 1299 if (!inodes) { 1300 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Local rows %" PetscInt_FMT " nz %" PetscInt_FMT " nz alloced %" PetscInt_FMT " mem %g, not using I-node routines\n", rank, mat->rmap->n, (PetscInt)info.nz_used, (PetscInt)info.nz_allocated, 1301 info.memory)); 1302 } else { 1303 PetscCall( 1304 PetscViewerASCIISynchronizedPrintf(viewer, "[%d] Local rows %" PetscInt_FMT " nz %" PetscInt_FMT " nz alloced %" PetscInt_FMT " mem %g, using I-node routines\n", rank, mat->rmap->n, (PetscInt)info.nz_used, (PetscInt)info.nz_allocated, info.memory)); 1305 } 1306 PetscCall(MatGetInfo(aij->A, MAT_LOCAL, &info)); 1307 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] on-diagonal part: nz %" PetscInt_FMT " \n", rank, (PetscInt)info.nz_used)); 1308 PetscCall(MatGetInfo(aij->B, MAT_LOCAL, &info)); 1309 PetscCall(PetscViewerASCIISynchronizedPrintf(viewer, "[%d] off-diagonal part: nz %" PetscInt_FMT " \n", rank, (PetscInt)info.nz_used)); 1310 PetscCall(PetscViewerFlush(viewer)); 1311 PetscCall(PetscViewerASCIIPopSynchronized(viewer)); 1312 PetscCall(PetscViewerASCIIPrintf(viewer, "Information on VecScatter used in matrix-vector product: \n")); 1313 PetscCall(VecScatterView(aij->Mvctx, viewer)); 1314 PetscFunctionReturn(PETSC_SUCCESS); 1315 } else if (format == PETSC_VIEWER_ASCII_INFO) { 1316 PetscInt inodecount, inodelimit, *inodes; 1317 PetscCall(MatInodeGetInodeSizes(aij->A, &inodecount, &inodes, &inodelimit)); 1318 if (inodes) { 1319 PetscCall(PetscViewerASCIIPrintf(viewer, "using I-node (on process 0) routines: found %" PetscInt_FMT " nodes, limit used is %" PetscInt_FMT "\n", inodecount, inodelimit)); 1320 } else { 1321 PetscCall(PetscViewerASCIIPrintf(viewer, "not using I-node (on process 0) routines\n")); 1322 } 1323 PetscFunctionReturn(PETSC_SUCCESS); 1324 } else if (format == PETSC_VIEWER_ASCII_FACTOR_INFO) { 1325 PetscFunctionReturn(PETSC_SUCCESS); 1326 } 1327 } else if (isbinary) { 1328 if (size == 1) { 1329 PetscCall(PetscObjectSetName((PetscObject)aij->A, ((PetscObject)mat)->name)); 1330 PetscCall(MatView(aij->A, viewer)); 1331 } else { 1332 PetscCall(MatView_MPIAIJ_Binary(mat, viewer)); 1333 } 1334 PetscFunctionReturn(PETSC_SUCCESS); 1335 } else if (iascii && size == 1) { 1336 PetscCall(PetscObjectSetName((PetscObject)aij->A, ((PetscObject)mat)->name)); 1337 PetscCall(MatView(aij->A, viewer)); 1338 PetscFunctionReturn(PETSC_SUCCESS); 1339 } else if (isdraw) { 1340 PetscDraw draw; 1341 PetscBool isnull; 1342 PetscCall(PetscViewerDrawGetDraw(viewer, 0, &draw)); 1343 PetscCall(PetscDrawIsNull(draw, &isnull)); 1344 if (isnull) PetscFunctionReturn(PETSC_SUCCESS); 1345 } 1346 1347 { /* assemble the entire matrix onto first processor */ 1348 Mat A = NULL, Av; 1349 IS isrow, iscol; 1350 1351 PetscCall(ISCreateStride(PetscObjectComm((PetscObject)mat), rank == 0 ? mat->rmap->N : 0, 0, 1, &isrow)); 1352 PetscCall(ISCreateStride(PetscObjectComm((PetscObject)mat), rank == 0 ? mat->cmap->N : 0, 0, 1, &iscol)); 1353 PetscCall(MatCreateSubMatrix(mat, isrow, iscol, MAT_INITIAL_MATRIX, &A)); 1354 PetscCall(MatMPIAIJGetSeqAIJ(A, &Av, NULL, NULL)); 1355 /* The commented code uses MatCreateSubMatrices instead */ 1356 /* 1357 Mat *AA, A = NULL, Av; 1358 IS isrow,iscol; 1359 1360 PetscCall(ISCreateStride(PetscObjectComm((PetscObject)mat),rank == 0 ? mat->rmap->N : 0,0,1,&isrow)); 1361 PetscCall(ISCreateStride(PetscObjectComm((PetscObject)mat),rank == 0 ? mat->cmap->N : 0,0,1,&iscol)); 1362 PetscCall(MatCreateSubMatrices(mat,1,&isrow,&iscol,MAT_INITIAL_MATRIX,&AA)); 1363 if (rank == 0) { 1364 PetscCall(PetscObjectReference((PetscObject)AA[0])); 1365 A = AA[0]; 1366 Av = AA[0]; 1367 } 1368 PetscCall(MatDestroySubMatrices(1,&AA)); 1369 */ 1370 PetscCall(ISDestroy(&iscol)); 1371 PetscCall(ISDestroy(&isrow)); 1372 /* 1373 Everyone has to call to draw the matrix since the graphics waits are 1374 synchronized across all processors that share the PetscDraw object 1375 */ 1376 PetscCall(PetscViewerGetSubViewer(viewer, PETSC_COMM_SELF, &sviewer)); 1377 if (rank == 0) { 1378 if (((PetscObject)mat)->name) PetscCall(PetscObjectSetName((PetscObject)Av, ((PetscObject)mat)->name)); 1379 PetscCall(MatView_SeqAIJ(Av, sviewer)); 1380 } 1381 PetscCall(PetscViewerRestoreSubViewer(viewer, PETSC_COMM_SELF, &sviewer)); 1382 PetscCall(MatDestroy(&A)); 1383 } 1384 PetscFunctionReturn(PETSC_SUCCESS); 1385 } 1386 1387 PetscErrorCode MatView_MPIAIJ(Mat mat, PetscViewer viewer) 1388 { 1389 PetscBool iascii, isdraw, issocket, isbinary; 1390 1391 PetscFunctionBegin; 1392 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERASCII, &iascii)); 1393 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERDRAW, &isdraw)); 1394 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &isbinary)); 1395 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERSOCKET, &issocket)); 1396 if (iascii || isdraw || isbinary || issocket) PetscCall(MatView_MPIAIJ_ASCIIorDraworSocket(mat, viewer)); 1397 PetscFunctionReturn(PETSC_SUCCESS); 1398 } 1399 1400 static PetscErrorCode MatSOR_MPIAIJ(Mat matin, Vec bb, PetscReal omega, MatSORType flag, PetscReal fshift, PetscInt its, PetscInt lits, Vec xx) 1401 { 1402 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)matin->data; 1403 Vec bb1 = NULL; 1404 PetscBool hasop; 1405 1406 PetscFunctionBegin; 1407 if (flag == SOR_APPLY_UPPER) { 1408 PetscCall((*mat->A->ops->sor)(mat->A, bb, omega, flag, fshift, lits, 1, xx)); 1409 PetscFunctionReturn(PETSC_SUCCESS); 1410 } 1411 1412 if (its > 1 || ~flag & SOR_ZERO_INITIAL_GUESS || flag & SOR_EISENSTAT) PetscCall(VecDuplicate(bb, &bb1)); 1413 1414 if ((flag & SOR_LOCAL_SYMMETRIC_SWEEP) == SOR_LOCAL_SYMMETRIC_SWEEP) { 1415 if (flag & SOR_ZERO_INITIAL_GUESS) { 1416 PetscCall((*mat->A->ops->sor)(mat->A, bb, omega, flag, fshift, lits, 1, xx)); 1417 its--; 1418 } 1419 1420 while (its--) { 1421 PetscCall(VecScatterBegin(mat->Mvctx, xx, mat->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1422 PetscCall(VecScatterEnd(mat->Mvctx, xx, mat->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1423 1424 /* update rhs: bb1 = bb - B*x */ 1425 PetscCall(VecScale(mat->lvec, -1.0)); 1426 PetscCall((*mat->B->ops->multadd)(mat->B, mat->lvec, bb, bb1)); 1427 1428 /* local sweep */ 1429 PetscCall((*mat->A->ops->sor)(mat->A, bb1, omega, SOR_SYMMETRIC_SWEEP, fshift, lits, 1, xx)); 1430 } 1431 } else if (flag & SOR_LOCAL_FORWARD_SWEEP) { 1432 if (flag & SOR_ZERO_INITIAL_GUESS) { 1433 PetscCall((*mat->A->ops->sor)(mat->A, bb, omega, flag, fshift, lits, 1, xx)); 1434 its--; 1435 } 1436 while (its--) { 1437 PetscCall(VecScatterBegin(mat->Mvctx, xx, mat->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1438 PetscCall(VecScatterEnd(mat->Mvctx, xx, mat->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1439 1440 /* update rhs: bb1 = bb - B*x */ 1441 PetscCall(VecScale(mat->lvec, -1.0)); 1442 PetscCall((*mat->B->ops->multadd)(mat->B, mat->lvec, bb, bb1)); 1443 1444 /* local sweep */ 1445 PetscCall((*mat->A->ops->sor)(mat->A, bb1, omega, SOR_FORWARD_SWEEP, fshift, lits, 1, xx)); 1446 } 1447 } else if (flag & SOR_LOCAL_BACKWARD_SWEEP) { 1448 if (flag & SOR_ZERO_INITIAL_GUESS) { 1449 PetscCall((*mat->A->ops->sor)(mat->A, bb, omega, flag, fshift, lits, 1, xx)); 1450 its--; 1451 } 1452 while (its--) { 1453 PetscCall(VecScatterBegin(mat->Mvctx, xx, mat->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1454 PetscCall(VecScatterEnd(mat->Mvctx, xx, mat->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1455 1456 /* update rhs: bb1 = bb - B*x */ 1457 PetscCall(VecScale(mat->lvec, -1.0)); 1458 PetscCall((*mat->B->ops->multadd)(mat->B, mat->lvec, bb, bb1)); 1459 1460 /* local sweep */ 1461 PetscCall((*mat->A->ops->sor)(mat->A, bb1, omega, SOR_BACKWARD_SWEEP, fshift, lits, 1, xx)); 1462 } 1463 } else if (flag & SOR_EISENSTAT) { 1464 Vec xx1; 1465 1466 PetscCall(VecDuplicate(bb, &xx1)); 1467 PetscCall((*mat->A->ops->sor)(mat->A, bb, omega, (MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_BACKWARD_SWEEP), fshift, lits, 1, xx)); 1468 1469 PetscCall(VecScatterBegin(mat->Mvctx, xx, mat->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1470 PetscCall(VecScatterEnd(mat->Mvctx, xx, mat->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1471 if (!mat->diag) { 1472 PetscCall(MatCreateVecs(matin, &mat->diag, NULL)); 1473 PetscCall(MatGetDiagonal(matin, mat->diag)); 1474 } 1475 PetscCall(MatHasOperation(matin, MATOP_MULT_DIAGONAL_BLOCK, &hasop)); 1476 if (hasop) { 1477 PetscCall(MatMultDiagonalBlock(matin, xx, bb1)); 1478 } else { 1479 PetscCall(VecPointwiseMult(bb1, mat->diag, xx)); 1480 } 1481 PetscCall(VecAYPX(bb1, (omega - 2.0) / omega, bb)); 1482 1483 PetscCall(MatMultAdd(mat->B, mat->lvec, bb1, bb1)); 1484 1485 /* local sweep */ 1486 PetscCall((*mat->A->ops->sor)(mat->A, bb1, omega, (MatSORType)(SOR_ZERO_INITIAL_GUESS | SOR_LOCAL_FORWARD_SWEEP), fshift, lits, 1, xx1)); 1487 PetscCall(VecAXPY(xx, 1.0, xx1)); 1488 PetscCall(VecDestroy(&xx1)); 1489 } else SETERRQ(PetscObjectComm((PetscObject)matin), PETSC_ERR_SUP, "Parallel SOR not supported"); 1490 1491 PetscCall(VecDestroy(&bb1)); 1492 1493 matin->factorerrortype = mat->A->factorerrortype; 1494 PetscFunctionReturn(PETSC_SUCCESS); 1495 } 1496 1497 static PetscErrorCode MatPermute_MPIAIJ(Mat A, IS rowp, IS colp, Mat *B) 1498 { 1499 Mat aA, aB, Aperm; 1500 const PetscInt *rwant, *cwant, *gcols, *ai, *bi, *aj, *bj; 1501 PetscScalar *aa, *ba; 1502 PetscInt i, j, m, n, ng, anz, bnz, *dnnz, *onnz, *tdnnz, *tonnz, *rdest, *cdest, *work, *gcdest; 1503 PetscSF rowsf, sf; 1504 IS parcolp = NULL; 1505 PetscBool done; 1506 1507 PetscFunctionBegin; 1508 PetscCall(MatGetLocalSize(A, &m, &n)); 1509 PetscCall(ISGetIndices(rowp, &rwant)); 1510 PetscCall(ISGetIndices(colp, &cwant)); 1511 PetscCall(PetscMalloc3(PetscMax(m, n), &work, m, &rdest, n, &cdest)); 1512 1513 /* Invert row permutation to find out where my rows should go */ 1514 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)A), &rowsf)); 1515 PetscCall(PetscSFSetGraphLayout(rowsf, A->rmap, A->rmap->n, NULL, PETSC_OWN_POINTER, rwant)); 1516 PetscCall(PetscSFSetFromOptions(rowsf)); 1517 for (i = 0; i < m; i++) work[i] = A->rmap->rstart + i; 1518 PetscCall(PetscSFReduceBegin(rowsf, MPIU_INT, work, rdest, MPI_REPLACE)); 1519 PetscCall(PetscSFReduceEnd(rowsf, MPIU_INT, work, rdest, MPI_REPLACE)); 1520 1521 /* Invert column permutation to find out where my columns should go */ 1522 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)A), &sf)); 1523 PetscCall(PetscSFSetGraphLayout(sf, A->cmap, A->cmap->n, NULL, PETSC_OWN_POINTER, cwant)); 1524 PetscCall(PetscSFSetFromOptions(sf)); 1525 for (i = 0; i < n; i++) work[i] = A->cmap->rstart + i; 1526 PetscCall(PetscSFReduceBegin(sf, MPIU_INT, work, cdest, MPI_REPLACE)); 1527 PetscCall(PetscSFReduceEnd(sf, MPIU_INT, work, cdest, MPI_REPLACE)); 1528 PetscCall(PetscSFDestroy(&sf)); 1529 1530 PetscCall(ISRestoreIndices(rowp, &rwant)); 1531 PetscCall(ISRestoreIndices(colp, &cwant)); 1532 PetscCall(MatMPIAIJGetSeqAIJ(A, &aA, &aB, &gcols)); 1533 1534 /* Find out where my gcols should go */ 1535 PetscCall(MatGetSize(aB, NULL, &ng)); 1536 PetscCall(PetscMalloc1(ng, &gcdest)); 1537 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)A), &sf)); 1538 PetscCall(PetscSFSetGraphLayout(sf, A->cmap, ng, NULL, PETSC_OWN_POINTER, gcols)); 1539 PetscCall(PetscSFSetFromOptions(sf)); 1540 PetscCall(PetscSFBcastBegin(sf, MPIU_INT, cdest, gcdest, MPI_REPLACE)); 1541 PetscCall(PetscSFBcastEnd(sf, MPIU_INT, cdest, gcdest, MPI_REPLACE)); 1542 PetscCall(PetscSFDestroy(&sf)); 1543 1544 PetscCall(PetscCalloc4(m, &dnnz, m, &onnz, m, &tdnnz, m, &tonnz)); 1545 PetscCall(MatGetRowIJ(aA, 0, PETSC_FALSE, PETSC_FALSE, &anz, &ai, &aj, &done)); 1546 PetscCall(MatGetRowIJ(aB, 0, PETSC_FALSE, PETSC_FALSE, &bnz, &bi, &bj, &done)); 1547 for (i = 0; i < m; i++) { 1548 PetscInt row = rdest[i]; 1549 PetscMPIInt rowner; 1550 PetscCall(PetscLayoutFindOwner(A->rmap, row, &rowner)); 1551 for (j = ai[i]; j < ai[i + 1]; j++) { 1552 PetscInt col = cdest[aj[j]]; 1553 PetscMPIInt cowner; 1554 PetscCall(PetscLayoutFindOwner(A->cmap, col, &cowner)); /* Could build an index for the columns to eliminate this search */ 1555 if (rowner == cowner) dnnz[i]++; 1556 else onnz[i]++; 1557 } 1558 for (j = bi[i]; j < bi[i + 1]; j++) { 1559 PetscInt col = gcdest[bj[j]]; 1560 PetscMPIInt cowner; 1561 PetscCall(PetscLayoutFindOwner(A->cmap, col, &cowner)); 1562 if (rowner == cowner) dnnz[i]++; 1563 else onnz[i]++; 1564 } 1565 } 1566 PetscCall(PetscSFBcastBegin(rowsf, MPIU_INT, dnnz, tdnnz, MPI_REPLACE)); 1567 PetscCall(PetscSFBcastEnd(rowsf, MPIU_INT, dnnz, tdnnz, MPI_REPLACE)); 1568 PetscCall(PetscSFBcastBegin(rowsf, MPIU_INT, onnz, tonnz, MPI_REPLACE)); 1569 PetscCall(PetscSFBcastEnd(rowsf, MPIU_INT, onnz, tonnz, MPI_REPLACE)); 1570 PetscCall(PetscSFDestroy(&rowsf)); 1571 1572 PetscCall(MatCreateAIJ(PetscObjectComm((PetscObject)A), A->rmap->n, A->cmap->n, A->rmap->N, A->cmap->N, 0, tdnnz, 0, tonnz, &Aperm)); 1573 PetscCall(MatSeqAIJGetArray(aA, &aa)); 1574 PetscCall(MatSeqAIJGetArray(aB, &ba)); 1575 for (i = 0; i < m; i++) { 1576 PetscInt *acols = dnnz, *bcols = onnz; /* Repurpose now-unneeded arrays */ 1577 PetscInt j0, rowlen; 1578 rowlen = ai[i + 1] - ai[i]; 1579 for (j0 = j = 0; j < rowlen; j0 = j) { /* rowlen could be larger than number of rows m, so sum in batches */ 1580 for (; j < PetscMin(rowlen, j0 + m); j++) acols[j - j0] = cdest[aj[ai[i] + j]]; 1581 PetscCall(MatSetValues(Aperm, 1, &rdest[i], j - j0, acols, aa + ai[i] + j0, INSERT_VALUES)); 1582 } 1583 rowlen = bi[i + 1] - bi[i]; 1584 for (j0 = j = 0; j < rowlen; j0 = j) { 1585 for (; j < PetscMin(rowlen, j0 + m); j++) bcols[j - j0] = gcdest[bj[bi[i] + j]]; 1586 PetscCall(MatSetValues(Aperm, 1, &rdest[i], j - j0, bcols, ba + bi[i] + j0, INSERT_VALUES)); 1587 } 1588 } 1589 PetscCall(MatAssemblyBegin(Aperm, MAT_FINAL_ASSEMBLY)); 1590 PetscCall(MatAssemblyEnd(Aperm, MAT_FINAL_ASSEMBLY)); 1591 PetscCall(MatRestoreRowIJ(aA, 0, PETSC_FALSE, PETSC_FALSE, &anz, &ai, &aj, &done)); 1592 PetscCall(MatRestoreRowIJ(aB, 0, PETSC_FALSE, PETSC_FALSE, &bnz, &bi, &bj, &done)); 1593 PetscCall(MatSeqAIJRestoreArray(aA, &aa)); 1594 PetscCall(MatSeqAIJRestoreArray(aB, &ba)); 1595 PetscCall(PetscFree4(dnnz, onnz, tdnnz, tonnz)); 1596 PetscCall(PetscFree3(work, rdest, cdest)); 1597 PetscCall(PetscFree(gcdest)); 1598 if (parcolp) PetscCall(ISDestroy(&colp)); 1599 *B = Aperm; 1600 PetscFunctionReturn(PETSC_SUCCESS); 1601 } 1602 1603 static PetscErrorCode MatGetGhosts_MPIAIJ(Mat mat, PetscInt *nghosts, const PetscInt *ghosts[]) 1604 { 1605 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 1606 1607 PetscFunctionBegin; 1608 PetscCall(MatGetSize(aij->B, NULL, nghosts)); 1609 if (ghosts) *ghosts = aij->garray; 1610 PetscFunctionReturn(PETSC_SUCCESS); 1611 } 1612 1613 static PetscErrorCode MatGetInfo_MPIAIJ(Mat matin, MatInfoType flag, MatInfo *info) 1614 { 1615 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)matin->data; 1616 Mat A = mat->A, B = mat->B; 1617 PetscLogDouble isend[5], irecv[5]; 1618 1619 PetscFunctionBegin; 1620 info->block_size = 1.0; 1621 PetscCall(MatGetInfo(A, MAT_LOCAL, info)); 1622 1623 isend[0] = info->nz_used; 1624 isend[1] = info->nz_allocated; 1625 isend[2] = info->nz_unneeded; 1626 isend[3] = info->memory; 1627 isend[4] = info->mallocs; 1628 1629 PetscCall(MatGetInfo(B, MAT_LOCAL, info)); 1630 1631 isend[0] += info->nz_used; 1632 isend[1] += info->nz_allocated; 1633 isend[2] += info->nz_unneeded; 1634 isend[3] += info->memory; 1635 isend[4] += info->mallocs; 1636 if (flag == MAT_LOCAL) { 1637 info->nz_used = isend[0]; 1638 info->nz_allocated = isend[1]; 1639 info->nz_unneeded = isend[2]; 1640 info->memory = isend[3]; 1641 info->mallocs = isend[4]; 1642 } else if (flag == MAT_GLOBAL_MAX) { 1643 PetscCallMPI(MPIU_Allreduce(isend, irecv, 5, MPIU_PETSCLOGDOUBLE, MPI_MAX, PetscObjectComm((PetscObject)matin))); 1644 1645 info->nz_used = irecv[0]; 1646 info->nz_allocated = irecv[1]; 1647 info->nz_unneeded = irecv[2]; 1648 info->memory = irecv[3]; 1649 info->mallocs = irecv[4]; 1650 } else if (flag == MAT_GLOBAL_SUM) { 1651 PetscCallMPI(MPIU_Allreduce(isend, irecv, 5, MPIU_PETSCLOGDOUBLE, MPI_SUM, PetscObjectComm((PetscObject)matin))); 1652 1653 info->nz_used = irecv[0]; 1654 info->nz_allocated = irecv[1]; 1655 info->nz_unneeded = irecv[2]; 1656 info->memory = irecv[3]; 1657 info->mallocs = irecv[4]; 1658 } 1659 info->fill_ratio_given = 0; /* no parallel LU/ILU/Cholesky */ 1660 info->fill_ratio_needed = 0; 1661 info->factor_mallocs = 0; 1662 PetscFunctionReturn(PETSC_SUCCESS); 1663 } 1664 1665 PetscErrorCode MatSetOption_MPIAIJ(Mat A, MatOption op, PetscBool flg) 1666 { 1667 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 1668 1669 PetscFunctionBegin; 1670 switch (op) { 1671 case MAT_NEW_NONZERO_LOCATIONS: 1672 case MAT_NEW_NONZERO_ALLOCATION_ERR: 1673 case MAT_UNUSED_NONZERO_LOCATION_ERR: 1674 case MAT_KEEP_NONZERO_PATTERN: 1675 case MAT_NEW_NONZERO_LOCATION_ERR: 1676 case MAT_USE_INODES: 1677 case MAT_IGNORE_ZERO_ENTRIES: 1678 case MAT_FORM_EXPLICIT_TRANSPOSE: 1679 MatCheckPreallocated(A, 1); 1680 PetscCall(MatSetOption(a->A, op, flg)); 1681 PetscCall(MatSetOption(a->B, op, flg)); 1682 break; 1683 case MAT_ROW_ORIENTED: 1684 MatCheckPreallocated(A, 1); 1685 a->roworiented = flg; 1686 1687 PetscCall(MatSetOption(a->A, op, flg)); 1688 PetscCall(MatSetOption(a->B, op, flg)); 1689 break; 1690 case MAT_IGNORE_OFF_PROC_ENTRIES: 1691 a->donotstash = flg; 1692 break; 1693 /* Symmetry flags are handled directly by MatSetOption() and they don't affect preallocation */ 1694 case MAT_SPD: 1695 case MAT_SYMMETRIC: 1696 case MAT_STRUCTURALLY_SYMMETRIC: 1697 case MAT_HERMITIAN: 1698 case MAT_SYMMETRY_ETERNAL: 1699 case MAT_STRUCTURAL_SYMMETRY_ETERNAL: 1700 case MAT_SPD_ETERNAL: 1701 /* if the diagonal matrix is square it inherits some of the properties above */ 1702 if (a->A && A->rmap->n == A->cmap->n) PetscCall(MatSetOption(a->A, op, flg)); 1703 break; 1704 case MAT_SUBMAT_SINGLEIS: 1705 A->submat_singleis = flg; 1706 break; 1707 default: 1708 break; 1709 } 1710 PetscFunctionReturn(PETSC_SUCCESS); 1711 } 1712 1713 PetscErrorCode MatGetRow_MPIAIJ(Mat matin, PetscInt row, PetscInt *nz, PetscInt **idx, PetscScalar **v) 1714 { 1715 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)matin->data; 1716 PetscScalar *vworkA, *vworkB, **pvA, **pvB, *v_p; 1717 PetscInt i, *cworkA, *cworkB, **pcA, **pcB, cstart = matin->cmap->rstart; 1718 PetscInt nztot, nzA, nzB, lrow, rstart = matin->rmap->rstart, rend = matin->rmap->rend; 1719 PetscInt *cmap, *idx_p; 1720 1721 PetscFunctionBegin; 1722 PetscCheck(!mat->getrowactive, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Already active"); 1723 mat->getrowactive = PETSC_TRUE; 1724 1725 if (!mat->rowvalues && (idx || v)) { 1726 /* 1727 allocate enough space to hold information from the longest row. 1728 */ 1729 Mat_SeqAIJ *Aa = (Mat_SeqAIJ *)mat->A->data, *Ba = (Mat_SeqAIJ *)mat->B->data; 1730 PetscInt max = 1, tmp; 1731 for (i = 0; i < matin->rmap->n; i++) { 1732 tmp = Aa->i[i + 1] - Aa->i[i] + Ba->i[i + 1] - Ba->i[i]; 1733 if (max < tmp) max = tmp; 1734 } 1735 PetscCall(PetscMalloc2(max, &mat->rowvalues, max, &mat->rowindices)); 1736 } 1737 1738 PetscCheck(row >= rstart && row < rend, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Only local rows"); 1739 lrow = row - rstart; 1740 1741 pvA = &vworkA; 1742 pcA = &cworkA; 1743 pvB = &vworkB; 1744 pcB = &cworkB; 1745 if (!v) { 1746 pvA = NULL; 1747 pvB = NULL; 1748 } 1749 if (!idx) { 1750 pcA = NULL; 1751 if (!v) pcB = NULL; 1752 } 1753 PetscCall((*mat->A->ops->getrow)(mat->A, lrow, &nzA, pcA, pvA)); 1754 PetscCall((*mat->B->ops->getrow)(mat->B, lrow, &nzB, pcB, pvB)); 1755 nztot = nzA + nzB; 1756 1757 cmap = mat->garray; 1758 if (v || idx) { 1759 if (nztot) { 1760 /* Sort by increasing column numbers, assuming A and B already sorted */ 1761 PetscInt imark = -1; 1762 if (v) { 1763 *v = v_p = mat->rowvalues; 1764 for (i = 0; i < nzB; i++) { 1765 if (cmap[cworkB[i]] < cstart) v_p[i] = vworkB[i]; 1766 else break; 1767 } 1768 imark = i; 1769 for (i = 0; i < nzA; i++) v_p[imark + i] = vworkA[i]; 1770 for (i = imark; i < nzB; i++) v_p[nzA + i] = vworkB[i]; 1771 } 1772 if (idx) { 1773 *idx = idx_p = mat->rowindices; 1774 if (imark > -1) { 1775 for (i = 0; i < imark; i++) idx_p[i] = cmap[cworkB[i]]; 1776 } else { 1777 for (i = 0; i < nzB; i++) { 1778 if (cmap[cworkB[i]] < cstart) idx_p[i] = cmap[cworkB[i]]; 1779 else break; 1780 } 1781 imark = i; 1782 } 1783 for (i = 0; i < nzA; i++) idx_p[imark + i] = cstart + cworkA[i]; 1784 for (i = imark; i < nzB; i++) idx_p[nzA + i] = cmap[cworkB[i]]; 1785 } 1786 } else { 1787 if (idx) *idx = NULL; 1788 if (v) *v = NULL; 1789 } 1790 } 1791 *nz = nztot; 1792 PetscCall((*mat->A->ops->restorerow)(mat->A, lrow, &nzA, pcA, pvA)); 1793 PetscCall((*mat->B->ops->restorerow)(mat->B, lrow, &nzB, pcB, pvB)); 1794 PetscFunctionReturn(PETSC_SUCCESS); 1795 } 1796 1797 PetscErrorCode MatRestoreRow_MPIAIJ(Mat mat, PetscInt row, PetscInt *nz, PetscInt **idx, PetscScalar **v) 1798 { 1799 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 1800 1801 PetscFunctionBegin; 1802 PetscCheck(aij->getrowactive, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "MatGetRow() must be called first"); 1803 aij->getrowactive = PETSC_FALSE; 1804 PetscFunctionReturn(PETSC_SUCCESS); 1805 } 1806 1807 static PetscErrorCode MatNorm_MPIAIJ(Mat mat, NormType type, PetscReal *norm) 1808 { 1809 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 1810 Mat_SeqAIJ *amat = (Mat_SeqAIJ *)aij->A->data, *bmat = (Mat_SeqAIJ *)aij->B->data; 1811 PetscInt i, j, cstart = mat->cmap->rstart; 1812 PetscReal sum = 0.0; 1813 const MatScalar *v, *amata, *bmata; 1814 1815 PetscFunctionBegin; 1816 if (aij->size == 1) { 1817 PetscCall(MatNorm(aij->A, type, norm)); 1818 } else { 1819 PetscCall(MatSeqAIJGetArrayRead(aij->A, &amata)); 1820 PetscCall(MatSeqAIJGetArrayRead(aij->B, &bmata)); 1821 if (type == NORM_FROBENIUS) { 1822 v = amata; 1823 for (i = 0; i < amat->nz; i++) { 1824 sum += PetscRealPart(PetscConj(*v) * (*v)); 1825 v++; 1826 } 1827 v = bmata; 1828 for (i = 0; i < bmat->nz; i++) { 1829 sum += PetscRealPart(PetscConj(*v) * (*v)); 1830 v++; 1831 } 1832 PetscCallMPI(MPIU_Allreduce(&sum, norm, 1, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)mat))); 1833 *norm = PetscSqrtReal(*norm); 1834 PetscCall(PetscLogFlops(2.0 * amat->nz + 2.0 * bmat->nz)); 1835 } else if (type == NORM_1) { /* max column norm */ 1836 PetscReal *tmp; 1837 PetscInt *jj, *garray = aij->garray; 1838 PetscCall(PetscCalloc1(mat->cmap->N + 1, &tmp)); 1839 *norm = 0.0; 1840 v = amata; 1841 jj = amat->j; 1842 for (j = 0; j < amat->nz; j++) { 1843 tmp[cstart + *jj++] += PetscAbsScalar(*v); 1844 v++; 1845 } 1846 v = bmata; 1847 jj = bmat->j; 1848 for (j = 0; j < bmat->nz; j++) { 1849 tmp[garray[*jj++]] += PetscAbsScalar(*v); 1850 v++; 1851 } 1852 PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, tmp, mat->cmap->N, MPIU_REAL, MPIU_SUM, PetscObjectComm((PetscObject)mat))); 1853 for (j = 0; j < mat->cmap->N; j++) { 1854 if (tmp[j] > *norm) *norm = tmp[j]; 1855 } 1856 PetscCall(PetscFree(tmp)); 1857 PetscCall(PetscLogFlops(PetscMax(amat->nz + bmat->nz - 1, 0))); 1858 } else if (type == NORM_INFINITY) { /* max row norm */ 1859 PetscReal ntemp = 0.0; 1860 for (j = 0; j < aij->A->rmap->n; j++) { 1861 v = PetscSafePointerPlusOffset(amata, amat->i[j]); 1862 sum = 0.0; 1863 for (i = 0; i < amat->i[j + 1] - amat->i[j]; i++) { 1864 sum += PetscAbsScalar(*v); 1865 v++; 1866 } 1867 v = PetscSafePointerPlusOffset(bmata, bmat->i[j]); 1868 for (i = 0; i < bmat->i[j + 1] - bmat->i[j]; i++) { 1869 sum += PetscAbsScalar(*v); 1870 v++; 1871 } 1872 if (sum > ntemp) ntemp = sum; 1873 } 1874 PetscCallMPI(MPIU_Allreduce(&ntemp, norm, 1, MPIU_REAL, MPIU_MAX, PetscObjectComm((PetscObject)mat))); 1875 PetscCall(PetscLogFlops(PetscMax(amat->nz + bmat->nz - 1, 0))); 1876 } else SETERRQ(PetscObjectComm((PetscObject)mat), PETSC_ERR_SUP, "No support for two norm"); 1877 PetscCall(MatSeqAIJRestoreArrayRead(aij->A, &amata)); 1878 PetscCall(MatSeqAIJRestoreArrayRead(aij->B, &bmata)); 1879 } 1880 PetscFunctionReturn(PETSC_SUCCESS); 1881 } 1882 1883 static PetscErrorCode MatTranspose_MPIAIJ(Mat A, MatReuse reuse, Mat *matout) 1884 { 1885 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data, *b; 1886 Mat_SeqAIJ *Aloc = (Mat_SeqAIJ *)a->A->data, *Bloc = (Mat_SeqAIJ *)a->B->data, *sub_B_diag; 1887 PetscInt M = A->rmap->N, N = A->cmap->N, ma, na, mb, nb, row, *cols, *cols_tmp, *B_diag_ilen, i, ncol, A_diag_ncol; 1888 const PetscInt *ai, *aj, *bi, *bj, *B_diag_i; 1889 Mat B, A_diag, *B_diag; 1890 const MatScalar *pbv, *bv; 1891 1892 PetscFunctionBegin; 1893 if (reuse == MAT_REUSE_MATRIX) PetscCall(MatTransposeCheckNonzeroState_Private(A, *matout)); 1894 ma = A->rmap->n; 1895 na = A->cmap->n; 1896 mb = a->B->rmap->n; 1897 nb = a->B->cmap->n; 1898 ai = Aloc->i; 1899 aj = Aloc->j; 1900 bi = Bloc->i; 1901 bj = Bloc->j; 1902 if (reuse == MAT_INITIAL_MATRIX || *matout == A) { 1903 PetscInt *d_nnz, *g_nnz, *o_nnz; 1904 PetscSFNode *oloc; 1905 PETSC_UNUSED PetscSF sf; 1906 1907 PetscCall(PetscMalloc4(na, &d_nnz, na, &o_nnz, nb, &g_nnz, nb, &oloc)); 1908 /* compute d_nnz for preallocation */ 1909 PetscCall(PetscArrayzero(d_nnz, na)); 1910 for (i = 0; i < ai[ma]; i++) d_nnz[aj[i]]++; 1911 /* compute local off-diagonal contributions */ 1912 PetscCall(PetscArrayzero(g_nnz, nb)); 1913 for (i = 0; i < bi[ma]; i++) g_nnz[bj[i]]++; 1914 /* map those to global */ 1915 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)A), &sf)); 1916 PetscCall(PetscSFSetGraphLayout(sf, A->cmap, nb, NULL, PETSC_USE_POINTER, a->garray)); 1917 PetscCall(PetscSFSetFromOptions(sf)); 1918 PetscCall(PetscArrayzero(o_nnz, na)); 1919 PetscCall(PetscSFReduceBegin(sf, MPIU_INT, g_nnz, o_nnz, MPI_SUM)); 1920 PetscCall(PetscSFReduceEnd(sf, MPIU_INT, g_nnz, o_nnz, MPI_SUM)); 1921 PetscCall(PetscSFDestroy(&sf)); 1922 1923 PetscCall(MatCreate(PetscObjectComm((PetscObject)A), &B)); 1924 PetscCall(MatSetSizes(B, A->cmap->n, A->rmap->n, N, M)); 1925 PetscCall(MatSetBlockSizes(B, A->cmap->bs, A->rmap->bs)); 1926 PetscCall(MatSetType(B, ((PetscObject)A)->type_name)); 1927 PetscCall(MatMPIAIJSetPreallocation(B, 0, d_nnz, 0, o_nnz)); 1928 PetscCall(PetscFree4(d_nnz, o_nnz, g_nnz, oloc)); 1929 } else { 1930 B = *matout; 1931 PetscCall(MatSetOption(B, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_TRUE)); 1932 } 1933 1934 b = (Mat_MPIAIJ *)B->data; 1935 A_diag = a->A; 1936 B_diag = &b->A; 1937 sub_B_diag = (Mat_SeqAIJ *)(*B_diag)->data; 1938 A_diag_ncol = A_diag->cmap->N; 1939 B_diag_ilen = sub_B_diag->ilen; 1940 B_diag_i = sub_B_diag->i; 1941 1942 /* Set ilen for diagonal of B */ 1943 for (i = 0; i < A_diag_ncol; i++) B_diag_ilen[i] = B_diag_i[i + 1] - B_diag_i[i]; 1944 1945 /* Transpose the diagonal part of the matrix. In contrast to the off-diagonal part, this can be done 1946 very quickly (=without using MatSetValues), because all writes are local. */ 1947 PetscCall(MatTransposeSetPrecursor(A_diag, *B_diag)); 1948 PetscCall(MatTranspose(A_diag, MAT_REUSE_MATRIX, B_diag)); 1949 1950 /* copy over the B part */ 1951 PetscCall(PetscMalloc1(bi[mb], &cols)); 1952 PetscCall(MatSeqAIJGetArrayRead(a->B, &bv)); 1953 pbv = bv; 1954 row = A->rmap->rstart; 1955 for (i = 0; i < bi[mb]; i++) cols[i] = a->garray[bj[i]]; 1956 cols_tmp = cols; 1957 for (i = 0; i < mb; i++) { 1958 ncol = bi[i + 1] - bi[i]; 1959 PetscCall(MatSetValues(B, ncol, cols_tmp, 1, &row, pbv, INSERT_VALUES)); 1960 row++; 1961 if (pbv) pbv += ncol; 1962 if (cols_tmp) cols_tmp += ncol; 1963 } 1964 PetscCall(PetscFree(cols)); 1965 PetscCall(MatSeqAIJRestoreArrayRead(a->B, &bv)); 1966 1967 PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY)); 1968 PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY)); 1969 if (reuse == MAT_INITIAL_MATRIX || reuse == MAT_REUSE_MATRIX) { 1970 *matout = B; 1971 } else { 1972 PetscCall(MatHeaderMerge(A, &B)); 1973 } 1974 PetscFunctionReturn(PETSC_SUCCESS); 1975 } 1976 1977 static PetscErrorCode MatDiagonalScale_MPIAIJ(Mat mat, Vec ll, Vec rr) 1978 { 1979 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 1980 Mat a = aij->A, b = aij->B; 1981 PetscInt s1, s2, s3; 1982 1983 PetscFunctionBegin; 1984 PetscCall(MatGetLocalSize(mat, &s2, &s3)); 1985 if (rr) { 1986 PetscCall(VecGetLocalSize(rr, &s1)); 1987 PetscCheck(s1 == s3, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "right vector non-conforming local size"); 1988 /* Overlap communication with computation. */ 1989 PetscCall(VecScatterBegin(aij->Mvctx, rr, aij->lvec, INSERT_VALUES, SCATTER_FORWARD)); 1990 } 1991 if (ll) { 1992 PetscCall(VecGetLocalSize(ll, &s1)); 1993 PetscCheck(s1 == s2, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "left vector non-conforming local size"); 1994 PetscUseTypeMethod(b, diagonalscale, ll, NULL); 1995 } 1996 /* scale the diagonal block */ 1997 PetscUseTypeMethod(a, diagonalscale, ll, rr); 1998 1999 if (rr) { 2000 /* Do a scatter end and then right scale the off-diagonal block */ 2001 PetscCall(VecScatterEnd(aij->Mvctx, rr, aij->lvec, INSERT_VALUES, SCATTER_FORWARD)); 2002 PetscUseTypeMethod(b, diagonalscale, NULL, aij->lvec); 2003 } 2004 PetscFunctionReturn(PETSC_SUCCESS); 2005 } 2006 2007 static PetscErrorCode MatSetUnfactored_MPIAIJ(Mat A) 2008 { 2009 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2010 2011 PetscFunctionBegin; 2012 PetscCall(MatSetUnfactored(a->A)); 2013 PetscFunctionReturn(PETSC_SUCCESS); 2014 } 2015 2016 static PetscErrorCode MatEqual_MPIAIJ(Mat A, Mat B, PetscBool *flag) 2017 { 2018 Mat_MPIAIJ *matB = (Mat_MPIAIJ *)B->data, *matA = (Mat_MPIAIJ *)A->data; 2019 Mat a, b, c, d; 2020 PetscBool flg; 2021 2022 PetscFunctionBegin; 2023 a = matA->A; 2024 b = matA->B; 2025 c = matB->A; 2026 d = matB->B; 2027 2028 PetscCall(MatEqual(a, c, &flg)); 2029 if (flg) PetscCall(MatEqual(b, d, &flg)); 2030 PetscCallMPI(MPIU_Allreduce(&flg, flag, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)A))); 2031 PetscFunctionReturn(PETSC_SUCCESS); 2032 } 2033 2034 static PetscErrorCode MatCopy_MPIAIJ(Mat A, Mat B, MatStructure str) 2035 { 2036 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2037 Mat_MPIAIJ *b = (Mat_MPIAIJ *)B->data; 2038 2039 PetscFunctionBegin; 2040 /* If the two matrices don't have the same copy implementation, they aren't compatible for fast copy. */ 2041 if ((str != SAME_NONZERO_PATTERN) || (A->ops->copy != B->ops->copy)) { 2042 /* because of the column compression in the off-processor part of the matrix a->B, 2043 the number of columns in a->B and b->B may be different, hence we cannot call 2044 the MatCopy() directly on the two parts. If need be, we can provide a more 2045 efficient copy than the MatCopy_Basic() by first uncompressing the a->B matrices 2046 then copying the submatrices */ 2047 PetscCall(MatCopy_Basic(A, B, str)); 2048 } else { 2049 PetscCall(MatCopy(a->A, b->A, str)); 2050 PetscCall(MatCopy(a->B, b->B, str)); 2051 } 2052 PetscCall(PetscObjectStateIncrease((PetscObject)B)); 2053 PetscFunctionReturn(PETSC_SUCCESS); 2054 } 2055 2056 /* 2057 Computes the number of nonzeros per row needed for preallocation when X and Y 2058 have different nonzero structure. 2059 */ 2060 PetscErrorCode MatAXPYGetPreallocation_MPIX_private(PetscInt m, const PetscInt *xi, const PetscInt *xj, const PetscInt *xltog, const PetscInt *yi, const PetscInt *yj, const PetscInt *yltog, PetscInt *nnz) 2061 { 2062 PetscInt i, j, k, nzx, nzy; 2063 2064 PetscFunctionBegin; 2065 /* Set the number of nonzeros in the new matrix */ 2066 for (i = 0; i < m; i++) { 2067 const PetscInt *xjj = PetscSafePointerPlusOffset(xj, xi[i]), *yjj = PetscSafePointerPlusOffset(yj, yi[i]); 2068 nzx = xi[i + 1] - xi[i]; 2069 nzy = yi[i + 1] - yi[i]; 2070 nnz[i] = 0; 2071 for (j = 0, k = 0; j < nzx; j++) { /* Point in X */ 2072 for (; k < nzy && yltog[yjj[k]] < xltog[xjj[j]]; k++) nnz[i]++; /* Catch up to X */ 2073 if (k < nzy && yltog[yjj[k]] == xltog[xjj[j]]) k++; /* Skip duplicate */ 2074 nnz[i]++; 2075 } 2076 for (; k < nzy; k++) nnz[i]++; 2077 } 2078 PetscFunctionReturn(PETSC_SUCCESS); 2079 } 2080 2081 /* This is the same as MatAXPYGetPreallocation_SeqAIJ, except that the local-to-global map is provided */ 2082 static PetscErrorCode MatAXPYGetPreallocation_MPIAIJ(Mat Y, const PetscInt *yltog, Mat X, const PetscInt *xltog, PetscInt *nnz) 2083 { 2084 PetscInt m = Y->rmap->N; 2085 Mat_SeqAIJ *x = (Mat_SeqAIJ *)X->data; 2086 Mat_SeqAIJ *y = (Mat_SeqAIJ *)Y->data; 2087 2088 PetscFunctionBegin; 2089 PetscCall(MatAXPYGetPreallocation_MPIX_private(m, x->i, x->j, xltog, y->i, y->j, yltog, nnz)); 2090 PetscFunctionReturn(PETSC_SUCCESS); 2091 } 2092 2093 static PetscErrorCode MatAXPY_MPIAIJ(Mat Y, PetscScalar a, Mat X, MatStructure str) 2094 { 2095 Mat_MPIAIJ *xx = (Mat_MPIAIJ *)X->data, *yy = (Mat_MPIAIJ *)Y->data; 2096 2097 PetscFunctionBegin; 2098 if (str == SAME_NONZERO_PATTERN) { 2099 PetscCall(MatAXPY(yy->A, a, xx->A, str)); 2100 PetscCall(MatAXPY(yy->B, a, xx->B, str)); 2101 } else if (str == SUBSET_NONZERO_PATTERN) { /* nonzeros of X is a subset of Y's */ 2102 PetscCall(MatAXPY_Basic(Y, a, X, str)); 2103 } else { 2104 Mat B; 2105 PetscInt *nnz_d, *nnz_o; 2106 2107 PetscCall(PetscMalloc1(yy->A->rmap->N, &nnz_d)); 2108 PetscCall(PetscMalloc1(yy->B->rmap->N, &nnz_o)); 2109 PetscCall(MatCreate(PetscObjectComm((PetscObject)Y), &B)); 2110 PetscCall(PetscObjectSetName((PetscObject)B, ((PetscObject)Y)->name)); 2111 PetscCall(MatSetLayouts(B, Y->rmap, Y->cmap)); 2112 PetscCall(MatSetType(B, ((PetscObject)Y)->type_name)); 2113 PetscCall(MatAXPYGetPreallocation_SeqAIJ(yy->A, xx->A, nnz_d)); 2114 PetscCall(MatAXPYGetPreallocation_MPIAIJ(yy->B, yy->garray, xx->B, xx->garray, nnz_o)); 2115 PetscCall(MatMPIAIJSetPreallocation(B, 0, nnz_d, 0, nnz_o)); 2116 PetscCall(MatAXPY_BasicWithPreallocation(B, Y, a, X, str)); 2117 PetscCall(MatHeaderMerge(Y, &B)); 2118 PetscCall(PetscFree(nnz_d)); 2119 PetscCall(PetscFree(nnz_o)); 2120 } 2121 PetscFunctionReturn(PETSC_SUCCESS); 2122 } 2123 2124 PETSC_INTERN PetscErrorCode MatConjugate_SeqAIJ(Mat); 2125 2126 static PetscErrorCode MatConjugate_MPIAIJ(Mat mat) 2127 { 2128 PetscFunctionBegin; 2129 if (PetscDefined(USE_COMPLEX)) { 2130 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 2131 2132 PetscCall(MatConjugate_SeqAIJ(aij->A)); 2133 PetscCall(MatConjugate_SeqAIJ(aij->B)); 2134 } 2135 PetscFunctionReturn(PETSC_SUCCESS); 2136 } 2137 2138 static PetscErrorCode MatRealPart_MPIAIJ(Mat A) 2139 { 2140 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2141 2142 PetscFunctionBegin; 2143 PetscCall(MatRealPart(a->A)); 2144 PetscCall(MatRealPart(a->B)); 2145 PetscFunctionReturn(PETSC_SUCCESS); 2146 } 2147 2148 static PetscErrorCode MatImaginaryPart_MPIAIJ(Mat A) 2149 { 2150 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2151 2152 PetscFunctionBegin; 2153 PetscCall(MatImaginaryPart(a->A)); 2154 PetscCall(MatImaginaryPart(a->B)); 2155 PetscFunctionReturn(PETSC_SUCCESS); 2156 } 2157 2158 static PetscErrorCode MatGetRowMaxAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2159 { 2160 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2161 PetscInt i, *idxb = NULL, m = A->rmap->n; 2162 PetscScalar *vv; 2163 Vec vB, vA; 2164 const PetscScalar *va, *vb; 2165 2166 PetscFunctionBegin; 2167 PetscCall(MatCreateVecs(a->A, NULL, &vA)); 2168 PetscCall(MatGetRowMaxAbs(a->A, vA, idx)); 2169 2170 PetscCall(VecGetArrayRead(vA, &va)); 2171 if (idx) { 2172 for (i = 0; i < m; i++) { 2173 if (PetscAbsScalar(va[i])) idx[i] += A->cmap->rstart; 2174 } 2175 } 2176 2177 PetscCall(MatCreateVecs(a->B, NULL, &vB)); 2178 PetscCall(PetscMalloc1(m, &idxb)); 2179 PetscCall(MatGetRowMaxAbs(a->B, vB, idxb)); 2180 2181 PetscCall(VecGetArrayWrite(v, &vv)); 2182 PetscCall(VecGetArrayRead(vB, &vb)); 2183 for (i = 0; i < m; i++) { 2184 if (PetscAbsScalar(va[i]) < PetscAbsScalar(vb[i])) { 2185 vv[i] = vb[i]; 2186 if (idx) idx[i] = a->garray[idxb[i]]; 2187 } else { 2188 vv[i] = va[i]; 2189 if (idx && PetscAbsScalar(va[i]) == PetscAbsScalar(vb[i]) && idxb[i] != -1 && idx[i] > a->garray[idxb[i]]) idx[i] = a->garray[idxb[i]]; 2190 } 2191 } 2192 PetscCall(VecRestoreArrayWrite(v, &vv)); 2193 PetscCall(VecRestoreArrayRead(vA, &va)); 2194 PetscCall(VecRestoreArrayRead(vB, &vb)); 2195 PetscCall(PetscFree(idxb)); 2196 PetscCall(VecDestroy(&vA)); 2197 PetscCall(VecDestroy(&vB)); 2198 PetscFunctionReturn(PETSC_SUCCESS); 2199 } 2200 2201 static PetscErrorCode MatGetRowSumAbs_MPIAIJ(Mat A, Vec v) 2202 { 2203 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2204 Vec vB, vA; 2205 2206 PetscFunctionBegin; 2207 PetscCall(MatCreateVecs(a->A, NULL, &vA)); 2208 PetscCall(MatGetRowSumAbs(a->A, vA)); 2209 PetscCall(MatCreateVecs(a->B, NULL, &vB)); 2210 PetscCall(MatGetRowSumAbs(a->B, vB)); 2211 PetscCall(VecAXPY(vA, 1.0, vB)); 2212 PetscCall(VecDestroy(&vB)); 2213 PetscCall(VecCopy(vA, v)); 2214 PetscCall(VecDestroy(&vA)); 2215 PetscFunctionReturn(PETSC_SUCCESS); 2216 } 2217 2218 static PetscErrorCode MatGetRowMinAbs_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2219 { 2220 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)A->data; 2221 PetscInt m = A->rmap->n, n = A->cmap->n; 2222 PetscInt cstart = A->cmap->rstart, cend = A->cmap->rend; 2223 PetscInt *cmap = mat->garray; 2224 PetscInt *diagIdx, *offdiagIdx; 2225 Vec diagV, offdiagV; 2226 PetscScalar *a, *diagA, *offdiagA; 2227 const PetscScalar *ba, *bav; 2228 PetscInt r, j, col, ncols, *bi, *bj; 2229 Mat B = mat->B; 2230 Mat_SeqAIJ *b = (Mat_SeqAIJ *)B->data; 2231 2232 PetscFunctionBegin; 2233 /* When a process holds entire A and other processes have no entry */ 2234 if (A->cmap->N == n) { 2235 PetscCall(VecGetArrayWrite(v, &diagA)); 2236 PetscCall(VecCreateSeqWithArray(PETSC_COMM_SELF, 1, m, diagA, &diagV)); 2237 PetscCall(MatGetRowMinAbs(mat->A, diagV, idx)); 2238 PetscCall(VecDestroy(&diagV)); 2239 PetscCall(VecRestoreArrayWrite(v, &diagA)); 2240 PetscFunctionReturn(PETSC_SUCCESS); 2241 } else if (n == 0) { 2242 if (m) { 2243 PetscCall(VecGetArrayWrite(v, &a)); 2244 for (r = 0; r < m; r++) { 2245 a[r] = 0.0; 2246 if (idx) idx[r] = -1; 2247 } 2248 PetscCall(VecRestoreArrayWrite(v, &a)); 2249 } 2250 PetscFunctionReturn(PETSC_SUCCESS); 2251 } 2252 2253 PetscCall(PetscMalloc2(m, &diagIdx, m, &offdiagIdx)); 2254 PetscCall(VecCreateSeq(PETSC_COMM_SELF, m, &diagV)); 2255 PetscCall(VecCreateSeq(PETSC_COMM_SELF, m, &offdiagV)); 2256 PetscCall(MatGetRowMinAbs(mat->A, diagV, diagIdx)); 2257 2258 /* Get offdiagIdx[] for implicit 0.0 */ 2259 PetscCall(MatSeqAIJGetArrayRead(B, &bav)); 2260 ba = bav; 2261 bi = b->i; 2262 bj = b->j; 2263 PetscCall(VecGetArrayWrite(offdiagV, &offdiagA)); 2264 for (r = 0; r < m; r++) { 2265 ncols = bi[r + 1] - bi[r]; 2266 if (ncols == A->cmap->N - n) { /* Brow is dense */ 2267 offdiagA[r] = *ba; 2268 offdiagIdx[r] = cmap[0]; 2269 } else { /* Brow is sparse so already KNOW maximum is 0.0 or higher */ 2270 offdiagA[r] = 0.0; 2271 2272 /* Find first hole in the cmap */ 2273 for (j = 0; j < ncols; j++) { 2274 col = cmap[bj[j]]; /* global column number = cmap[B column number] */ 2275 if (col > j && j < cstart) { 2276 offdiagIdx[r] = j; /* global column number of first implicit 0.0 */ 2277 break; 2278 } else if (col > j + n && j >= cstart) { 2279 offdiagIdx[r] = j + n; /* global column number of first implicit 0.0 */ 2280 break; 2281 } 2282 } 2283 if (j == ncols && ncols < A->cmap->N - n) { 2284 /* a hole is outside compressed Bcols */ 2285 if (ncols == 0) { 2286 if (cstart) { 2287 offdiagIdx[r] = 0; 2288 } else offdiagIdx[r] = cend; 2289 } else { /* ncols > 0 */ 2290 offdiagIdx[r] = cmap[ncols - 1] + 1; 2291 if (offdiagIdx[r] == cstart) offdiagIdx[r] += n; 2292 } 2293 } 2294 } 2295 2296 for (j = 0; j < ncols; j++) { 2297 if (PetscAbsScalar(offdiagA[r]) > PetscAbsScalar(*ba)) { 2298 offdiagA[r] = *ba; 2299 offdiagIdx[r] = cmap[*bj]; 2300 } 2301 ba++; 2302 bj++; 2303 } 2304 } 2305 2306 PetscCall(VecGetArrayWrite(v, &a)); 2307 PetscCall(VecGetArrayRead(diagV, (const PetscScalar **)&diagA)); 2308 for (r = 0; r < m; ++r) { 2309 if (PetscAbsScalar(diagA[r]) < PetscAbsScalar(offdiagA[r])) { 2310 a[r] = diagA[r]; 2311 if (idx) idx[r] = cstart + diagIdx[r]; 2312 } else if (PetscAbsScalar(diagA[r]) == PetscAbsScalar(offdiagA[r])) { 2313 a[r] = diagA[r]; 2314 if (idx) { 2315 if (cstart + diagIdx[r] <= offdiagIdx[r]) { 2316 idx[r] = cstart + diagIdx[r]; 2317 } else idx[r] = offdiagIdx[r]; 2318 } 2319 } else { 2320 a[r] = offdiagA[r]; 2321 if (idx) idx[r] = offdiagIdx[r]; 2322 } 2323 } 2324 PetscCall(MatSeqAIJRestoreArrayRead(B, &bav)); 2325 PetscCall(VecRestoreArrayWrite(v, &a)); 2326 PetscCall(VecRestoreArrayRead(diagV, (const PetscScalar **)&diagA)); 2327 PetscCall(VecRestoreArrayWrite(offdiagV, &offdiagA)); 2328 PetscCall(VecDestroy(&diagV)); 2329 PetscCall(VecDestroy(&offdiagV)); 2330 PetscCall(PetscFree2(diagIdx, offdiagIdx)); 2331 PetscFunctionReturn(PETSC_SUCCESS); 2332 } 2333 2334 static PetscErrorCode MatGetRowMin_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2335 { 2336 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)A->data; 2337 PetscInt m = A->rmap->n, n = A->cmap->n; 2338 PetscInt cstart = A->cmap->rstart, cend = A->cmap->rend; 2339 PetscInt *cmap = mat->garray; 2340 PetscInt *diagIdx, *offdiagIdx; 2341 Vec diagV, offdiagV; 2342 PetscScalar *a, *diagA, *offdiagA; 2343 const PetscScalar *ba, *bav; 2344 PetscInt r, j, col, ncols, *bi, *bj; 2345 Mat B = mat->B; 2346 Mat_SeqAIJ *b = (Mat_SeqAIJ *)B->data; 2347 2348 PetscFunctionBegin; 2349 /* When a process holds entire A and other processes have no entry */ 2350 if (A->cmap->N == n) { 2351 PetscCall(VecGetArrayWrite(v, &diagA)); 2352 PetscCall(VecCreateSeqWithArray(PETSC_COMM_SELF, 1, m, diagA, &diagV)); 2353 PetscCall(MatGetRowMin(mat->A, diagV, idx)); 2354 PetscCall(VecDestroy(&diagV)); 2355 PetscCall(VecRestoreArrayWrite(v, &diagA)); 2356 PetscFunctionReturn(PETSC_SUCCESS); 2357 } else if (n == 0) { 2358 if (m) { 2359 PetscCall(VecGetArrayWrite(v, &a)); 2360 for (r = 0; r < m; r++) { 2361 a[r] = PETSC_MAX_REAL; 2362 if (idx) idx[r] = -1; 2363 } 2364 PetscCall(VecRestoreArrayWrite(v, &a)); 2365 } 2366 PetscFunctionReturn(PETSC_SUCCESS); 2367 } 2368 2369 PetscCall(PetscCalloc2(m, &diagIdx, m, &offdiagIdx)); 2370 PetscCall(VecCreateSeq(PETSC_COMM_SELF, m, &diagV)); 2371 PetscCall(VecCreateSeq(PETSC_COMM_SELF, m, &offdiagV)); 2372 PetscCall(MatGetRowMin(mat->A, diagV, diagIdx)); 2373 2374 /* Get offdiagIdx[] for implicit 0.0 */ 2375 PetscCall(MatSeqAIJGetArrayRead(B, &bav)); 2376 ba = bav; 2377 bi = b->i; 2378 bj = b->j; 2379 PetscCall(VecGetArrayWrite(offdiagV, &offdiagA)); 2380 for (r = 0; r < m; r++) { 2381 ncols = bi[r + 1] - bi[r]; 2382 if (ncols == A->cmap->N - n) { /* Brow is dense */ 2383 offdiagA[r] = *ba; 2384 offdiagIdx[r] = cmap[0]; 2385 } else { /* Brow is sparse so already KNOW maximum is 0.0 or higher */ 2386 offdiagA[r] = 0.0; 2387 2388 /* Find first hole in the cmap */ 2389 for (j = 0; j < ncols; j++) { 2390 col = cmap[bj[j]]; /* global column number = cmap[B column number] */ 2391 if (col > j && j < cstart) { 2392 offdiagIdx[r] = j; /* global column number of first implicit 0.0 */ 2393 break; 2394 } else if (col > j + n && j >= cstart) { 2395 offdiagIdx[r] = j + n; /* global column number of first implicit 0.0 */ 2396 break; 2397 } 2398 } 2399 if (j == ncols && ncols < A->cmap->N - n) { 2400 /* a hole is outside compressed Bcols */ 2401 if (ncols == 0) { 2402 if (cstart) { 2403 offdiagIdx[r] = 0; 2404 } else offdiagIdx[r] = cend; 2405 } else { /* ncols > 0 */ 2406 offdiagIdx[r] = cmap[ncols - 1] + 1; 2407 if (offdiagIdx[r] == cstart) offdiagIdx[r] += n; 2408 } 2409 } 2410 } 2411 2412 for (j = 0; j < ncols; j++) { 2413 if (PetscRealPart(offdiagA[r]) > PetscRealPart(*ba)) { 2414 offdiagA[r] = *ba; 2415 offdiagIdx[r] = cmap[*bj]; 2416 } 2417 ba++; 2418 bj++; 2419 } 2420 } 2421 2422 PetscCall(VecGetArrayWrite(v, &a)); 2423 PetscCall(VecGetArrayRead(diagV, (const PetscScalar **)&diagA)); 2424 for (r = 0; r < m; ++r) { 2425 if (PetscRealPart(diagA[r]) < PetscRealPart(offdiagA[r])) { 2426 a[r] = diagA[r]; 2427 if (idx) idx[r] = cstart + diagIdx[r]; 2428 } else if (PetscRealPart(diagA[r]) == PetscRealPart(offdiagA[r])) { 2429 a[r] = diagA[r]; 2430 if (idx) { 2431 if (cstart + diagIdx[r] <= offdiagIdx[r]) { 2432 idx[r] = cstart + diagIdx[r]; 2433 } else idx[r] = offdiagIdx[r]; 2434 } 2435 } else { 2436 a[r] = offdiagA[r]; 2437 if (idx) idx[r] = offdiagIdx[r]; 2438 } 2439 } 2440 PetscCall(MatSeqAIJRestoreArrayRead(B, &bav)); 2441 PetscCall(VecRestoreArrayWrite(v, &a)); 2442 PetscCall(VecRestoreArrayRead(diagV, (const PetscScalar **)&diagA)); 2443 PetscCall(VecRestoreArrayWrite(offdiagV, &offdiagA)); 2444 PetscCall(VecDestroy(&diagV)); 2445 PetscCall(VecDestroy(&offdiagV)); 2446 PetscCall(PetscFree2(diagIdx, offdiagIdx)); 2447 PetscFunctionReturn(PETSC_SUCCESS); 2448 } 2449 2450 static PetscErrorCode MatGetRowMax_MPIAIJ(Mat A, Vec v, PetscInt idx[]) 2451 { 2452 Mat_MPIAIJ *mat = (Mat_MPIAIJ *)A->data; 2453 PetscInt m = A->rmap->n, n = A->cmap->n; 2454 PetscInt cstart = A->cmap->rstart, cend = A->cmap->rend; 2455 PetscInt *cmap = mat->garray; 2456 PetscInt *diagIdx, *offdiagIdx; 2457 Vec diagV, offdiagV; 2458 PetscScalar *a, *diagA, *offdiagA; 2459 const PetscScalar *ba, *bav; 2460 PetscInt r, j, col, ncols, *bi, *bj; 2461 Mat B = mat->B; 2462 Mat_SeqAIJ *b = (Mat_SeqAIJ *)B->data; 2463 2464 PetscFunctionBegin; 2465 /* When a process holds entire A and other processes have no entry */ 2466 if (A->cmap->N == n) { 2467 PetscCall(VecGetArrayWrite(v, &diagA)); 2468 PetscCall(VecCreateSeqWithArray(PETSC_COMM_SELF, 1, m, diagA, &diagV)); 2469 PetscCall(MatGetRowMax(mat->A, diagV, idx)); 2470 PetscCall(VecDestroy(&diagV)); 2471 PetscCall(VecRestoreArrayWrite(v, &diagA)); 2472 PetscFunctionReturn(PETSC_SUCCESS); 2473 } else if (n == 0) { 2474 if (m) { 2475 PetscCall(VecGetArrayWrite(v, &a)); 2476 for (r = 0; r < m; r++) { 2477 a[r] = PETSC_MIN_REAL; 2478 if (idx) idx[r] = -1; 2479 } 2480 PetscCall(VecRestoreArrayWrite(v, &a)); 2481 } 2482 PetscFunctionReturn(PETSC_SUCCESS); 2483 } 2484 2485 PetscCall(PetscMalloc2(m, &diagIdx, m, &offdiagIdx)); 2486 PetscCall(VecCreateSeq(PETSC_COMM_SELF, m, &diagV)); 2487 PetscCall(VecCreateSeq(PETSC_COMM_SELF, m, &offdiagV)); 2488 PetscCall(MatGetRowMax(mat->A, diagV, diagIdx)); 2489 2490 /* Get offdiagIdx[] for implicit 0.0 */ 2491 PetscCall(MatSeqAIJGetArrayRead(B, &bav)); 2492 ba = bav; 2493 bi = b->i; 2494 bj = b->j; 2495 PetscCall(VecGetArrayWrite(offdiagV, &offdiagA)); 2496 for (r = 0; r < m; r++) { 2497 ncols = bi[r + 1] - bi[r]; 2498 if (ncols == A->cmap->N - n) { /* Brow is dense */ 2499 offdiagA[r] = *ba; 2500 offdiagIdx[r] = cmap[0]; 2501 } else { /* Brow is sparse so already KNOW maximum is 0.0 or higher */ 2502 offdiagA[r] = 0.0; 2503 2504 /* Find first hole in the cmap */ 2505 for (j = 0; j < ncols; j++) { 2506 col = cmap[bj[j]]; /* global column number = cmap[B column number] */ 2507 if (col > j && j < cstart) { 2508 offdiagIdx[r] = j; /* global column number of first implicit 0.0 */ 2509 break; 2510 } else if (col > j + n && j >= cstart) { 2511 offdiagIdx[r] = j + n; /* global column number of first implicit 0.0 */ 2512 break; 2513 } 2514 } 2515 if (j == ncols && ncols < A->cmap->N - n) { 2516 /* a hole is outside compressed Bcols */ 2517 if (ncols == 0) { 2518 if (cstart) { 2519 offdiagIdx[r] = 0; 2520 } else offdiagIdx[r] = cend; 2521 } else { /* ncols > 0 */ 2522 offdiagIdx[r] = cmap[ncols - 1] + 1; 2523 if (offdiagIdx[r] == cstart) offdiagIdx[r] += n; 2524 } 2525 } 2526 } 2527 2528 for (j = 0; j < ncols; j++) { 2529 if (PetscRealPart(offdiagA[r]) < PetscRealPart(*ba)) { 2530 offdiagA[r] = *ba; 2531 offdiagIdx[r] = cmap[*bj]; 2532 } 2533 ba++; 2534 bj++; 2535 } 2536 } 2537 2538 PetscCall(VecGetArrayWrite(v, &a)); 2539 PetscCall(VecGetArrayRead(diagV, (const PetscScalar **)&diagA)); 2540 for (r = 0; r < m; ++r) { 2541 if (PetscRealPart(diagA[r]) > PetscRealPart(offdiagA[r])) { 2542 a[r] = diagA[r]; 2543 if (idx) idx[r] = cstart + diagIdx[r]; 2544 } else if (PetscRealPart(diagA[r]) == PetscRealPart(offdiagA[r])) { 2545 a[r] = diagA[r]; 2546 if (idx) { 2547 if (cstart + diagIdx[r] <= offdiagIdx[r]) { 2548 idx[r] = cstart + diagIdx[r]; 2549 } else idx[r] = offdiagIdx[r]; 2550 } 2551 } else { 2552 a[r] = offdiagA[r]; 2553 if (idx) idx[r] = offdiagIdx[r]; 2554 } 2555 } 2556 PetscCall(MatSeqAIJRestoreArrayRead(B, &bav)); 2557 PetscCall(VecRestoreArrayWrite(v, &a)); 2558 PetscCall(VecRestoreArrayRead(diagV, (const PetscScalar **)&diagA)); 2559 PetscCall(VecRestoreArrayWrite(offdiagV, &offdiagA)); 2560 PetscCall(VecDestroy(&diagV)); 2561 PetscCall(VecDestroy(&offdiagV)); 2562 PetscCall(PetscFree2(diagIdx, offdiagIdx)); 2563 PetscFunctionReturn(PETSC_SUCCESS); 2564 } 2565 2566 PetscErrorCode MatGetSeqNonzeroStructure_MPIAIJ(Mat mat, Mat *newmat) 2567 { 2568 Mat *dummy; 2569 2570 PetscFunctionBegin; 2571 PetscCall(MatCreateSubMatrix_MPIAIJ_All(mat, MAT_DO_NOT_GET_VALUES, MAT_INITIAL_MATRIX, &dummy)); 2572 *newmat = *dummy; 2573 PetscCall(PetscFree(dummy)); 2574 PetscFunctionReturn(PETSC_SUCCESS); 2575 } 2576 2577 static PetscErrorCode MatInvertBlockDiagonal_MPIAIJ(Mat A, const PetscScalar **values) 2578 { 2579 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2580 2581 PetscFunctionBegin; 2582 PetscCall(MatInvertBlockDiagonal(a->A, values)); 2583 A->factorerrortype = a->A->factorerrortype; 2584 PetscFunctionReturn(PETSC_SUCCESS); 2585 } 2586 2587 static PetscErrorCode MatSetRandom_MPIAIJ(Mat x, PetscRandom rctx) 2588 { 2589 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)x->data; 2590 2591 PetscFunctionBegin; 2592 PetscCheck(x->assembled || x->preallocated, PetscObjectComm((PetscObject)x), PETSC_ERR_ARG_WRONGSTATE, "MatSetRandom on an unassembled and unpreallocated MATMPIAIJ is not allowed"); 2593 PetscCall(MatSetRandom(aij->A, rctx)); 2594 if (x->assembled) { 2595 PetscCall(MatSetRandom(aij->B, rctx)); 2596 } else { 2597 PetscCall(MatSetRandomSkipColumnRange_SeqAIJ_Private(aij->B, x->cmap->rstart, x->cmap->rend, rctx)); 2598 } 2599 PetscCall(MatAssemblyBegin(x, MAT_FINAL_ASSEMBLY)); 2600 PetscCall(MatAssemblyEnd(x, MAT_FINAL_ASSEMBLY)); 2601 PetscFunctionReturn(PETSC_SUCCESS); 2602 } 2603 2604 static PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ(Mat A, PetscBool sc) 2605 { 2606 PetscFunctionBegin; 2607 if (sc) A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ_Scalable; 2608 else A->ops->increaseoverlap = MatIncreaseOverlap_MPIAIJ; 2609 PetscFunctionReturn(PETSC_SUCCESS); 2610 } 2611 2612 /*@ 2613 MatMPIAIJGetNumberNonzeros - gets the number of nonzeros in the matrix on this MPI rank 2614 2615 Not Collective 2616 2617 Input Parameter: 2618 . A - the matrix 2619 2620 Output Parameter: 2621 . nz - the number of nonzeros 2622 2623 Level: advanced 2624 2625 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ` 2626 @*/ 2627 PetscErrorCode MatMPIAIJGetNumberNonzeros(Mat A, PetscCount *nz) 2628 { 2629 Mat_MPIAIJ *maij = (Mat_MPIAIJ *)A->data; 2630 Mat_SeqAIJ *aaij = (Mat_SeqAIJ *)maij->A->data, *baij = (Mat_SeqAIJ *)maij->B->data; 2631 PetscBool isaij; 2632 2633 PetscFunctionBegin; 2634 PetscCall(PetscObjectBaseTypeCompare((PetscObject)A, MATMPIAIJ, &isaij)); 2635 PetscCheck(isaij, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Not for type %s", ((PetscObject)A)->type_name); 2636 *nz = aaij->i[A->rmap->n] + baij->i[A->rmap->n]; 2637 PetscFunctionReturn(PETSC_SUCCESS); 2638 } 2639 2640 /*@ 2641 MatMPIAIJSetUseScalableIncreaseOverlap - Determine if the matrix uses a scalable algorithm to compute the overlap 2642 2643 Collective 2644 2645 Input Parameters: 2646 + A - the matrix 2647 - sc - `PETSC_TRUE` indicates use the scalable algorithm (default is not to use the scalable algorithm) 2648 2649 Level: advanced 2650 2651 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ` 2652 @*/ 2653 PetscErrorCode MatMPIAIJSetUseScalableIncreaseOverlap(Mat A, PetscBool sc) 2654 { 2655 PetscFunctionBegin; 2656 PetscTryMethod(A, "MatMPIAIJSetUseScalableIncreaseOverlap_C", (Mat, PetscBool), (A, sc)); 2657 PetscFunctionReturn(PETSC_SUCCESS); 2658 } 2659 2660 PetscErrorCode MatSetFromOptions_MPIAIJ(Mat A, PetscOptionItems PetscOptionsObject) 2661 { 2662 PetscBool sc = PETSC_FALSE, flg; 2663 2664 PetscFunctionBegin; 2665 PetscOptionsHeadBegin(PetscOptionsObject, "MPIAIJ options"); 2666 if (A->ops->increaseoverlap == MatIncreaseOverlap_MPIAIJ_Scalable) sc = PETSC_TRUE; 2667 PetscCall(PetscOptionsBool("-mat_increase_overlap_scalable", "Use a scalable algorithm to compute the overlap", "MatIncreaseOverlap", sc, &sc, &flg)); 2668 if (flg) PetscCall(MatMPIAIJSetUseScalableIncreaseOverlap(A, sc)); 2669 PetscOptionsHeadEnd(); 2670 PetscFunctionReturn(PETSC_SUCCESS); 2671 } 2672 2673 static PetscErrorCode MatShift_MPIAIJ(Mat Y, PetscScalar a) 2674 { 2675 Mat_MPIAIJ *maij = (Mat_MPIAIJ *)Y->data; 2676 Mat_SeqAIJ *aij = (Mat_SeqAIJ *)maij->A->data; 2677 2678 PetscFunctionBegin; 2679 if (!Y->preallocated) { 2680 PetscCall(MatMPIAIJSetPreallocation(Y, 1, NULL, 0, NULL)); 2681 } else if (!aij->nz) { /* It does not matter if diagonals of Y only partially lie in maij->A. We just need an estimated preallocation. */ 2682 PetscInt nonew = aij->nonew; 2683 PetscCall(MatSeqAIJSetPreallocation(maij->A, 1, NULL)); 2684 aij->nonew = nonew; 2685 } 2686 PetscCall(MatShift_Basic(Y, a)); 2687 PetscFunctionReturn(PETSC_SUCCESS); 2688 } 2689 2690 static PetscErrorCode MatMissingDiagonal_MPIAIJ(Mat A, PetscBool *missing, PetscInt *d) 2691 { 2692 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2693 2694 PetscFunctionBegin; 2695 PetscCheck(A->rmap->n == A->cmap->n, PETSC_COMM_SELF, PETSC_ERR_SUP, "Only works for square matrices"); 2696 PetscCall(MatMissingDiagonal(a->A, missing, d)); 2697 if (d) { 2698 PetscInt rstart; 2699 PetscCall(MatGetOwnershipRange(A, &rstart, NULL)); 2700 *d += rstart; 2701 } 2702 PetscFunctionReturn(PETSC_SUCCESS); 2703 } 2704 2705 static PetscErrorCode MatInvertVariableBlockDiagonal_MPIAIJ(Mat A, PetscInt nblocks, const PetscInt *bsizes, PetscScalar *diag) 2706 { 2707 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2708 2709 PetscFunctionBegin; 2710 PetscCall(MatInvertVariableBlockDiagonal(a->A, nblocks, bsizes, diag)); 2711 PetscFunctionReturn(PETSC_SUCCESS); 2712 } 2713 2714 static PetscErrorCode MatEliminateZeros_MPIAIJ(Mat A, PetscBool keep) 2715 { 2716 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 2717 2718 PetscFunctionBegin; 2719 PetscCall(MatEliminateZeros_SeqAIJ(a->A, keep)); // possibly keep zero diagonal coefficients 2720 PetscCall(MatEliminateZeros_SeqAIJ(a->B, PETSC_FALSE)); // never keep zero diagonal coefficients 2721 PetscFunctionReturn(PETSC_SUCCESS); 2722 } 2723 2724 static struct _MatOps MatOps_Values = {MatSetValues_MPIAIJ, 2725 MatGetRow_MPIAIJ, 2726 MatRestoreRow_MPIAIJ, 2727 MatMult_MPIAIJ, 2728 /* 4*/ MatMultAdd_MPIAIJ, 2729 MatMultTranspose_MPIAIJ, 2730 MatMultTransposeAdd_MPIAIJ, 2731 NULL, 2732 NULL, 2733 NULL, 2734 /*10*/ NULL, 2735 NULL, 2736 NULL, 2737 MatSOR_MPIAIJ, 2738 MatTranspose_MPIAIJ, 2739 /*15*/ MatGetInfo_MPIAIJ, 2740 MatEqual_MPIAIJ, 2741 MatGetDiagonal_MPIAIJ, 2742 MatDiagonalScale_MPIAIJ, 2743 MatNorm_MPIAIJ, 2744 /*20*/ MatAssemblyBegin_MPIAIJ, 2745 MatAssemblyEnd_MPIAIJ, 2746 MatSetOption_MPIAIJ, 2747 MatZeroEntries_MPIAIJ, 2748 /*24*/ MatZeroRows_MPIAIJ, 2749 NULL, 2750 NULL, 2751 NULL, 2752 NULL, 2753 /*29*/ MatSetUp_MPI_Hash, 2754 NULL, 2755 NULL, 2756 MatGetDiagonalBlock_MPIAIJ, 2757 NULL, 2758 /*34*/ MatDuplicate_MPIAIJ, 2759 NULL, 2760 NULL, 2761 NULL, 2762 NULL, 2763 /*39*/ MatAXPY_MPIAIJ, 2764 MatCreateSubMatrices_MPIAIJ, 2765 MatIncreaseOverlap_MPIAIJ, 2766 MatGetValues_MPIAIJ, 2767 MatCopy_MPIAIJ, 2768 /*44*/ MatGetRowMax_MPIAIJ, 2769 MatScale_MPIAIJ, 2770 MatShift_MPIAIJ, 2771 MatDiagonalSet_MPIAIJ, 2772 MatZeroRowsColumns_MPIAIJ, 2773 /*49*/ MatSetRandom_MPIAIJ, 2774 MatGetRowIJ_MPIAIJ, 2775 MatRestoreRowIJ_MPIAIJ, 2776 NULL, 2777 NULL, 2778 /*54*/ MatFDColoringCreate_MPIXAIJ, 2779 NULL, 2780 MatSetUnfactored_MPIAIJ, 2781 MatPermute_MPIAIJ, 2782 NULL, 2783 /*59*/ MatCreateSubMatrix_MPIAIJ, 2784 MatDestroy_MPIAIJ, 2785 MatView_MPIAIJ, 2786 NULL, 2787 NULL, 2788 /*64*/ NULL, 2789 MatMatMatMultNumeric_MPIAIJ_MPIAIJ_MPIAIJ, 2790 NULL, 2791 NULL, 2792 NULL, 2793 /*69*/ MatGetRowMaxAbs_MPIAIJ, 2794 MatGetRowMinAbs_MPIAIJ, 2795 NULL, 2796 NULL, 2797 NULL, 2798 NULL, 2799 /*75*/ MatFDColoringApply_AIJ, 2800 MatSetFromOptions_MPIAIJ, 2801 NULL, 2802 NULL, 2803 MatFindZeroDiagonals_MPIAIJ, 2804 /*80*/ NULL, 2805 NULL, 2806 NULL, 2807 /*83*/ MatLoad_MPIAIJ, 2808 NULL, 2809 NULL, 2810 NULL, 2811 NULL, 2812 NULL, 2813 /*89*/ NULL, 2814 NULL, 2815 MatMatMultNumeric_MPIAIJ_MPIAIJ, 2816 NULL, 2817 NULL, 2818 /*94*/ MatPtAPNumeric_MPIAIJ_MPIAIJ, 2819 NULL, 2820 NULL, 2821 NULL, 2822 MatBindToCPU_MPIAIJ, 2823 /*99*/ MatProductSetFromOptions_MPIAIJ, 2824 NULL, 2825 NULL, 2826 MatConjugate_MPIAIJ, 2827 NULL, 2828 /*104*/ MatSetValuesRow_MPIAIJ, 2829 MatRealPart_MPIAIJ, 2830 MatImaginaryPart_MPIAIJ, 2831 NULL, 2832 NULL, 2833 /*109*/ NULL, 2834 NULL, 2835 MatGetRowMin_MPIAIJ, 2836 NULL, 2837 MatMissingDiagonal_MPIAIJ, 2838 /*114*/ MatGetSeqNonzeroStructure_MPIAIJ, 2839 NULL, 2840 MatGetGhosts_MPIAIJ, 2841 NULL, 2842 NULL, 2843 /*119*/ MatMultDiagonalBlock_MPIAIJ, 2844 NULL, 2845 NULL, 2846 NULL, 2847 MatGetMultiProcBlock_MPIAIJ, 2848 /*124*/ MatFindNonzeroRows_MPIAIJ, 2849 MatGetColumnReductions_MPIAIJ, 2850 MatInvertBlockDiagonal_MPIAIJ, 2851 MatInvertVariableBlockDiagonal_MPIAIJ, 2852 MatCreateSubMatricesMPI_MPIAIJ, 2853 /*129*/ NULL, 2854 NULL, 2855 NULL, 2856 MatTransposeMatMultNumeric_MPIAIJ_MPIAIJ, 2857 NULL, 2858 /*134*/ NULL, 2859 NULL, 2860 NULL, 2861 NULL, 2862 NULL, 2863 /*139*/ MatSetBlockSizes_MPIAIJ, 2864 NULL, 2865 NULL, 2866 MatFDColoringSetUp_MPIXAIJ, 2867 MatFindOffBlockDiagonalEntries_MPIAIJ, 2868 MatCreateMPIMatConcatenateSeqMat_MPIAIJ, 2869 /*145*/ NULL, 2870 NULL, 2871 NULL, 2872 MatCreateGraph_Simple_AIJ, 2873 NULL, 2874 /*150*/ NULL, 2875 MatEliminateZeros_MPIAIJ, 2876 MatGetRowSumAbs_MPIAIJ, 2877 NULL, 2878 NULL, 2879 /*155*/ NULL, 2880 MatCopyHashToXAIJ_MPI_Hash}; 2881 2882 static PetscErrorCode MatStoreValues_MPIAIJ(Mat mat) 2883 { 2884 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 2885 2886 PetscFunctionBegin; 2887 PetscCall(MatStoreValues(aij->A)); 2888 PetscCall(MatStoreValues(aij->B)); 2889 PetscFunctionReturn(PETSC_SUCCESS); 2890 } 2891 2892 static PetscErrorCode MatRetrieveValues_MPIAIJ(Mat mat) 2893 { 2894 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 2895 2896 PetscFunctionBegin; 2897 PetscCall(MatRetrieveValues(aij->A)); 2898 PetscCall(MatRetrieveValues(aij->B)); 2899 PetscFunctionReturn(PETSC_SUCCESS); 2900 } 2901 2902 PetscErrorCode MatMPIAIJSetPreallocation_MPIAIJ(Mat B, PetscInt d_nz, const PetscInt d_nnz[], PetscInt o_nz, const PetscInt o_nnz[]) 2903 { 2904 Mat_MPIAIJ *b = (Mat_MPIAIJ *)B->data; 2905 PetscMPIInt size; 2906 2907 PetscFunctionBegin; 2908 if (B->hash_active) { 2909 B->ops[0] = b->cops; 2910 B->hash_active = PETSC_FALSE; 2911 } 2912 PetscCall(PetscLayoutSetUp(B->rmap)); 2913 PetscCall(PetscLayoutSetUp(B->cmap)); 2914 2915 #if defined(PETSC_USE_CTABLE) 2916 PetscCall(PetscHMapIDestroy(&b->colmap)); 2917 #else 2918 PetscCall(PetscFree(b->colmap)); 2919 #endif 2920 PetscCall(PetscFree(b->garray)); 2921 PetscCall(VecDestroy(&b->lvec)); 2922 PetscCall(VecScatterDestroy(&b->Mvctx)); 2923 2924 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)B), &size)); 2925 2926 MatSeqXAIJGetOptions_Private(b->B); 2927 PetscCall(MatDestroy(&b->B)); 2928 PetscCall(MatCreate(PETSC_COMM_SELF, &b->B)); 2929 PetscCall(MatSetSizes(b->B, B->rmap->n, size > 1 ? B->cmap->N : 0, B->rmap->n, size > 1 ? B->cmap->N : 0)); 2930 PetscCall(MatSetBlockSizesFromMats(b->B, B, B)); 2931 PetscCall(MatSetType(b->B, MATSEQAIJ)); 2932 MatSeqXAIJRestoreOptions_Private(b->B); 2933 2934 MatSeqXAIJGetOptions_Private(b->A); 2935 PetscCall(MatDestroy(&b->A)); 2936 PetscCall(MatCreate(PETSC_COMM_SELF, &b->A)); 2937 PetscCall(MatSetSizes(b->A, B->rmap->n, B->cmap->n, B->rmap->n, B->cmap->n)); 2938 PetscCall(MatSetBlockSizesFromMats(b->A, B, B)); 2939 PetscCall(MatSetType(b->A, MATSEQAIJ)); 2940 MatSeqXAIJRestoreOptions_Private(b->A); 2941 2942 PetscCall(MatSeqAIJSetPreallocation(b->A, d_nz, d_nnz)); 2943 PetscCall(MatSeqAIJSetPreallocation(b->B, o_nz, o_nnz)); 2944 B->preallocated = PETSC_TRUE; 2945 B->was_assembled = PETSC_FALSE; 2946 B->assembled = PETSC_FALSE; 2947 PetscFunctionReturn(PETSC_SUCCESS); 2948 } 2949 2950 static PetscErrorCode MatResetPreallocation_MPIAIJ(Mat B) 2951 { 2952 Mat_MPIAIJ *b = (Mat_MPIAIJ *)B->data; 2953 PetscBool ondiagreset, offdiagreset, memoryreset; 2954 2955 PetscFunctionBegin; 2956 PetscValidHeaderSpecific(B, MAT_CLASSID, 1); 2957 PetscCheck(B->insertmode == NOT_SET_VALUES, PETSC_COMM_SELF, PETSC_ERR_SUP, "Cannot reset preallocation after setting some values but not yet calling MatAssemblyBegin()/MatAssemblyEnd()"); 2958 if (B->num_ass == 0) PetscFunctionReturn(PETSC_SUCCESS); 2959 2960 PetscCall(MatResetPreallocation_SeqAIJ_Private(b->A, &ondiagreset)); 2961 PetscCall(MatResetPreallocation_SeqAIJ_Private(b->B, &offdiagreset)); 2962 memoryreset = (PetscBool)(ondiagreset || offdiagreset); 2963 PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &memoryreset, 1, MPIU_BOOL, MPI_LOR, PetscObjectComm((PetscObject)B))); 2964 if (!memoryreset) PetscFunctionReturn(PETSC_SUCCESS); 2965 2966 PetscCall(PetscLayoutSetUp(B->rmap)); 2967 PetscCall(PetscLayoutSetUp(B->cmap)); 2968 PetscCheck(B->assembled || B->was_assembled, PetscObjectComm((PetscObject)B), PETSC_ERR_ARG_WRONGSTATE, "Should not need to reset preallocation if the matrix was never assembled"); 2969 PetscCall(MatDisAssemble_MPIAIJ(B, PETSC_TRUE)); 2970 PetscCall(VecScatterDestroy(&b->Mvctx)); 2971 2972 B->preallocated = PETSC_TRUE; 2973 B->was_assembled = PETSC_FALSE; 2974 B->assembled = PETSC_FALSE; 2975 /* Log that the state of this object has changed; this will help guarantee that preconditioners get re-setup */ 2976 PetscCall(PetscObjectStateIncrease((PetscObject)B)); 2977 PetscFunctionReturn(PETSC_SUCCESS); 2978 } 2979 2980 PetscErrorCode MatDuplicate_MPIAIJ(Mat matin, MatDuplicateOption cpvalues, Mat *newmat) 2981 { 2982 Mat mat; 2983 Mat_MPIAIJ *a, *oldmat = (Mat_MPIAIJ *)matin->data; 2984 2985 PetscFunctionBegin; 2986 *newmat = NULL; 2987 PetscCall(MatCreate(PetscObjectComm((PetscObject)matin), &mat)); 2988 PetscCall(MatSetSizes(mat, matin->rmap->n, matin->cmap->n, matin->rmap->N, matin->cmap->N)); 2989 PetscCall(MatSetBlockSizesFromMats(mat, matin, matin)); 2990 PetscCall(MatSetType(mat, ((PetscObject)matin)->type_name)); 2991 a = (Mat_MPIAIJ *)mat->data; 2992 2993 mat->factortype = matin->factortype; 2994 mat->assembled = matin->assembled; 2995 mat->insertmode = NOT_SET_VALUES; 2996 2997 a->size = oldmat->size; 2998 a->rank = oldmat->rank; 2999 a->donotstash = oldmat->donotstash; 3000 a->roworiented = oldmat->roworiented; 3001 a->rowindices = NULL; 3002 a->rowvalues = NULL; 3003 a->getrowactive = PETSC_FALSE; 3004 3005 PetscCall(PetscLayoutReference(matin->rmap, &mat->rmap)); 3006 PetscCall(PetscLayoutReference(matin->cmap, &mat->cmap)); 3007 if (matin->hash_active) { 3008 PetscCall(MatSetUp(mat)); 3009 } else { 3010 mat->preallocated = matin->preallocated; 3011 if (oldmat->colmap) { 3012 #if defined(PETSC_USE_CTABLE) 3013 PetscCall(PetscHMapIDuplicate(oldmat->colmap, &a->colmap)); 3014 #else 3015 PetscCall(PetscMalloc1(mat->cmap->N, &a->colmap)); 3016 PetscCall(PetscArraycpy(a->colmap, oldmat->colmap, mat->cmap->N)); 3017 #endif 3018 } else a->colmap = NULL; 3019 if (oldmat->garray) { 3020 PetscInt len; 3021 len = oldmat->B->cmap->n; 3022 PetscCall(PetscMalloc1(len + 1, &a->garray)); 3023 if (len) PetscCall(PetscArraycpy(a->garray, oldmat->garray, len)); 3024 } else a->garray = NULL; 3025 3026 /* It may happen MatDuplicate is called with a non-assembled matrix 3027 In fact, MatDuplicate only requires the matrix to be preallocated 3028 This may happen inside a DMCreateMatrix_Shell */ 3029 if (oldmat->lvec) PetscCall(VecDuplicate(oldmat->lvec, &a->lvec)); 3030 if (oldmat->Mvctx) { 3031 a->Mvctx = oldmat->Mvctx; 3032 PetscCall(PetscObjectReference((PetscObject)oldmat->Mvctx)); 3033 } 3034 PetscCall(MatDuplicate(oldmat->A, cpvalues, &a->A)); 3035 PetscCall(MatDuplicate(oldmat->B, cpvalues, &a->B)); 3036 } 3037 PetscCall(PetscFunctionListDuplicate(((PetscObject)matin)->qlist, &((PetscObject)mat)->qlist)); 3038 *newmat = mat; 3039 PetscFunctionReturn(PETSC_SUCCESS); 3040 } 3041 3042 PetscErrorCode MatLoad_MPIAIJ(Mat newMat, PetscViewer viewer) 3043 { 3044 PetscBool isbinary, ishdf5; 3045 3046 PetscFunctionBegin; 3047 PetscValidHeaderSpecific(newMat, MAT_CLASSID, 1); 3048 PetscValidHeaderSpecific(viewer, PETSC_VIEWER_CLASSID, 2); 3049 /* force binary viewer to load .info file if it has not yet done so */ 3050 PetscCall(PetscViewerSetUp(viewer)); 3051 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERBINARY, &isbinary)); 3052 PetscCall(PetscObjectTypeCompare((PetscObject)viewer, PETSCVIEWERHDF5, &ishdf5)); 3053 if (isbinary) { 3054 PetscCall(MatLoad_MPIAIJ_Binary(newMat, viewer)); 3055 } else if (ishdf5) { 3056 #if defined(PETSC_HAVE_HDF5) 3057 PetscCall(MatLoad_AIJ_HDF5(newMat, viewer)); 3058 #else 3059 SETERRQ(PetscObjectComm((PetscObject)newMat), PETSC_ERR_SUP, "HDF5 not supported in this build.\nPlease reconfigure using --download-hdf5"); 3060 #endif 3061 } else { 3062 SETERRQ(PetscObjectComm((PetscObject)newMat), PETSC_ERR_SUP, "Viewer type %s not yet supported for reading %s matrices", ((PetscObject)viewer)->type_name, ((PetscObject)newMat)->type_name); 3063 } 3064 PetscFunctionReturn(PETSC_SUCCESS); 3065 } 3066 3067 PetscErrorCode MatLoad_MPIAIJ_Binary(Mat mat, PetscViewer viewer) 3068 { 3069 PetscInt header[4], M, N, m, nz, rows, cols, sum, i; 3070 PetscInt *rowidxs, *colidxs; 3071 PetscScalar *matvals; 3072 3073 PetscFunctionBegin; 3074 PetscCall(PetscViewerSetUp(viewer)); 3075 3076 /* read in matrix header */ 3077 PetscCall(PetscViewerBinaryRead(viewer, header, 4, NULL, PETSC_INT)); 3078 PetscCheck(header[0] == MAT_FILE_CLASSID, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Not a matrix object in file"); 3079 M = header[1]; 3080 N = header[2]; 3081 nz = header[3]; 3082 PetscCheck(M >= 0, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Matrix row size (%" PetscInt_FMT ") in file is negative", M); 3083 PetscCheck(N >= 0, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Matrix column size (%" PetscInt_FMT ") in file is negative", N); 3084 PetscCheck(nz >= 0, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Matrix stored in special format on disk, cannot load as MPIAIJ"); 3085 3086 /* set block sizes from the viewer's .info file */ 3087 PetscCall(MatLoad_Binary_BlockSizes(mat, viewer)); 3088 /* set global sizes if not set already */ 3089 if (mat->rmap->N < 0) mat->rmap->N = M; 3090 if (mat->cmap->N < 0) mat->cmap->N = N; 3091 PetscCall(PetscLayoutSetUp(mat->rmap)); 3092 PetscCall(PetscLayoutSetUp(mat->cmap)); 3093 3094 /* check if the matrix sizes are correct */ 3095 PetscCall(MatGetSize(mat, &rows, &cols)); 3096 PetscCheck(M == rows && N == cols, PETSC_COMM_SELF, PETSC_ERR_FILE_UNEXPECTED, "Matrix in file of different sizes (%" PetscInt_FMT ", %" PetscInt_FMT ") than the input matrix (%" PetscInt_FMT ", %" PetscInt_FMT ")", M, N, rows, cols); 3097 3098 /* read in row lengths and build row indices */ 3099 PetscCall(MatGetLocalSize(mat, &m, NULL)); 3100 PetscCall(PetscMalloc1(m + 1, &rowidxs)); 3101 PetscCall(PetscViewerBinaryReadAll(viewer, rowidxs + 1, m, PETSC_DECIDE, M, PETSC_INT)); 3102 rowidxs[0] = 0; 3103 for (i = 0; i < m; i++) rowidxs[i + 1] += rowidxs[i]; 3104 if (nz != PETSC_INT_MAX) { 3105 PetscCallMPI(MPIU_Allreduce(&rowidxs[m], &sum, 1, MPIU_INT, MPI_SUM, PetscObjectComm((PetscObject)viewer))); 3106 PetscCheck(sum == nz, PetscObjectComm((PetscObject)viewer), PETSC_ERR_FILE_UNEXPECTED, "Inconsistent matrix data in file: nonzeros = %" PetscInt_FMT ", sum-row-lengths = %" PetscInt_FMT, nz, sum); 3107 } 3108 3109 /* read in column indices and matrix values */ 3110 PetscCall(PetscMalloc2(rowidxs[m], &colidxs, rowidxs[m], &matvals)); 3111 PetscCall(PetscViewerBinaryReadAll(viewer, colidxs, rowidxs[m], PETSC_DETERMINE, PETSC_DETERMINE, PETSC_INT)); 3112 PetscCall(PetscViewerBinaryReadAll(viewer, matvals, rowidxs[m], PETSC_DETERMINE, PETSC_DETERMINE, PETSC_SCALAR)); 3113 /* store matrix indices and values */ 3114 PetscCall(MatMPIAIJSetPreallocationCSR(mat, rowidxs, colidxs, matvals)); 3115 PetscCall(PetscFree(rowidxs)); 3116 PetscCall(PetscFree2(colidxs, matvals)); 3117 PetscFunctionReturn(PETSC_SUCCESS); 3118 } 3119 3120 /* Not scalable because of ISAllGather() unless getting all columns. */ 3121 static PetscErrorCode ISGetSeqIS_Private(Mat mat, IS iscol, IS *isseq) 3122 { 3123 IS iscol_local; 3124 PetscBool isstride; 3125 PetscMPIInt gisstride = 0; 3126 3127 PetscFunctionBegin; 3128 /* check if we are grabbing all columns*/ 3129 PetscCall(PetscObjectTypeCompare((PetscObject)iscol, ISSTRIDE, &isstride)); 3130 3131 if (isstride) { 3132 PetscInt start, len, mstart, mlen; 3133 PetscCall(ISStrideGetInfo(iscol, &start, NULL)); 3134 PetscCall(ISGetLocalSize(iscol, &len)); 3135 PetscCall(MatGetOwnershipRangeColumn(mat, &mstart, &mlen)); 3136 if (mstart == start && mlen - mstart == len) gisstride = 1; 3137 } 3138 3139 PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &gisstride, 1, MPI_INT, MPI_MIN, PetscObjectComm((PetscObject)mat))); 3140 if (gisstride) { 3141 PetscInt N; 3142 PetscCall(MatGetSize(mat, NULL, &N)); 3143 PetscCall(ISCreateStride(PETSC_COMM_SELF, N, 0, 1, &iscol_local)); 3144 PetscCall(ISSetIdentity(iscol_local)); 3145 PetscCall(PetscInfo(mat, "Optimizing for obtaining all columns of the matrix; skipping ISAllGather()\n")); 3146 } else { 3147 PetscInt cbs; 3148 PetscCall(ISGetBlockSize(iscol, &cbs)); 3149 PetscCall(ISAllGather(iscol, &iscol_local)); 3150 PetscCall(ISSetBlockSize(iscol_local, cbs)); 3151 } 3152 3153 *isseq = iscol_local; 3154 PetscFunctionReturn(PETSC_SUCCESS); 3155 } 3156 3157 /* 3158 Used by MatCreateSubMatrix_MPIAIJ_SameRowColDist() to avoid ISAllGather() and global size of iscol_local 3159 (see MatCreateSubMatrix_MPIAIJ_nonscalable) 3160 3161 Input Parameters: 3162 + mat - matrix 3163 . isrow - parallel row index set; its local indices are a subset of local columns of `mat`, 3164 i.e., mat->rstart <= isrow[i] < mat->rend 3165 - iscol - parallel column index set; its local indices are a subset of local columns of `mat`, 3166 i.e., mat->cstart <= iscol[i] < mat->cend 3167 3168 Output Parameters: 3169 + isrow_d - sequential row index set for retrieving mat->A 3170 . iscol_d - sequential column index set for retrieving mat->A 3171 . iscol_o - sequential column index set for retrieving mat->B 3172 - garray - column map; garray[i] indicates global location of iscol_o[i] in `iscol` 3173 */ 3174 static PetscErrorCode ISGetSeqIS_SameColDist_Private(Mat mat, IS isrow, IS iscol, IS *isrow_d, IS *iscol_d, IS *iscol_o, PetscInt *garray[]) 3175 { 3176 Vec x, cmap; 3177 const PetscInt *is_idx; 3178 PetscScalar *xarray, *cmaparray; 3179 PetscInt ncols, isstart, *idx, m, rstart, *cmap1, count; 3180 Mat_MPIAIJ *a = (Mat_MPIAIJ *)mat->data; 3181 Mat B = a->B; 3182 Vec lvec = a->lvec, lcmap; 3183 PetscInt i, cstart, cend, Bn = B->cmap->N; 3184 MPI_Comm comm; 3185 VecScatter Mvctx = a->Mvctx; 3186 3187 PetscFunctionBegin; 3188 PetscCall(PetscObjectGetComm((PetscObject)mat, &comm)); 3189 PetscCall(ISGetLocalSize(iscol, &ncols)); 3190 3191 /* (1) iscol is a sub-column vector of mat, pad it with '-1.' to form a full vector x */ 3192 PetscCall(MatCreateVecs(mat, &x, NULL)); 3193 PetscCall(VecSet(x, -1.0)); 3194 PetscCall(VecDuplicate(x, &cmap)); 3195 PetscCall(VecSet(cmap, -1.0)); 3196 3197 /* Get start indices */ 3198 PetscCallMPI(MPI_Scan(&ncols, &isstart, 1, MPIU_INT, MPI_SUM, comm)); 3199 isstart -= ncols; 3200 PetscCall(MatGetOwnershipRangeColumn(mat, &cstart, &cend)); 3201 3202 PetscCall(ISGetIndices(iscol, &is_idx)); 3203 PetscCall(VecGetArray(x, &xarray)); 3204 PetscCall(VecGetArray(cmap, &cmaparray)); 3205 PetscCall(PetscMalloc1(ncols, &idx)); 3206 for (i = 0; i < ncols; i++) { 3207 xarray[is_idx[i] - cstart] = (PetscScalar)is_idx[i]; 3208 cmaparray[is_idx[i] - cstart] = i + isstart; /* global index of iscol[i] */ 3209 idx[i] = is_idx[i] - cstart; /* local index of iscol[i] */ 3210 } 3211 PetscCall(VecRestoreArray(x, &xarray)); 3212 PetscCall(VecRestoreArray(cmap, &cmaparray)); 3213 PetscCall(ISRestoreIndices(iscol, &is_idx)); 3214 3215 /* Get iscol_d */ 3216 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, ncols, idx, PETSC_OWN_POINTER, iscol_d)); 3217 PetscCall(ISGetBlockSize(iscol, &i)); 3218 PetscCall(ISSetBlockSize(*iscol_d, i)); 3219 3220 /* Get isrow_d */ 3221 PetscCall(ISGetLocalSize(isrow, &m)); 3222 rstart = mat->rmap->rstart; 3223 PetscCall(PetscMalloc1(m, &idx)); 3224 PetscCall(ISGetIndices(isrow, &is_idx)); 3225 for (i = 0; i < m; i++) idx[i] = is_idx[i] - rstart; 3226 PetscCall(ISRestoreIndices(isrow, &is_idx)); 3227 3228 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, m, idx, PETSC_OWN_POINTER, isrow_d)); 3229 PetscCall(ISGetBlockSize(isrow, &i)); 3230 PetscCall(ISSetBlockSize(*isrow_d, i)); 3231 3232 /* (2) Scatter x and cmap using aij->Mvctx to get their off-process portions (see MatMult_MPIAIJ) */ 3233 PetscCall(VecScatterBegin(Mvctx, x, lvec, INSERT_VALUES, SCATTER_FORWARD)); 3234 PetscCall(VecScatterEnd(Mvctx, x, lvec, INSERT_VALUES, SCATTER_FORWARD)); 3235 3236 PetscCall(VecDuplicate(lvec, &lcmap)); 3237 3238 PetscCall(VecScatterBegin(Mvctx, cmap, lcmap, INSERT_VALUES, SCATTER_FORWARD)); 3239 PetscCall(VecScatterEnd(Mvctx, cmap, lcmap, INSERT_VALUES, SCATTER_FORWARD)); 3240 3241 /* (3) create sequential iscol_o (a subset of iscol) and isgarray */ 3242 /* off-process column indices */ 3243 count = 0; 3244 PetscCall(PetscMalloc1(Bn, &idx)); 3245 PetscCall(PetscMalloc1(Bn, &cmap1)); 3246 3247 PetscCall(VecGetArray(lvec, &xarray)); 3248 PetscCall(VecGetArray(lcmap, &cmaparray)); 3249 for (i = 0; i < Bn; i++) { 3250 if (PetscRealPart(xarray[i]) > -1.0) { 3251 idx[count] = i; /* local column index in off-diagonal part B */ 3252 cmap1[count] = (PetscInt)PetscRealPart(cmaparray[i]); /* column index in submat */ 3253 count++; 3254 } 3255 } 3256 PetscCall(VecRestoreArray(lvec, &xarray)); 3257 PetscCall(VecRestoreArray(lcmap, &cmaparray)); 3258 3259 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, count, idx, PETSC_COPY_VALUES, iscol_o)); 3260 /* cannot ensure iscol_o has same blocksize as iscol! */ 3261 3262 PetscCall(PetscFree(idx)); 3263 *garray = cmap1; 3264 3265 PetscCall(VecDestroy(&x)); 3266 PetscCall(VecDestroy(&cmap)); 3267 PetscCall(VecDestroy(&lcmap)); 3268 PetscFunctionReturn(PETSC_SUCCESS); 3269 } 3270 3271 /* isrow and iscol have same processor distribution as mat, output *submat is a submatrix of local mat */ 3272 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowColDist(Mat mat, IS isrow, IS iscol, MatReuse call, Mat *submat) 3273 { 3274 Mat_MPIAIJ *a = (Mat_MPIAIJ *)mat->data, *asub; 3275 Mat M = NULL; 3276 MPI_Comm comm; 3277 IS iscol_d, isrow_d, iscol_o; 3278 Mat Asub = NULL, Bsub = NULL; 3279 PetscInt n, count, M_size, N_size; 3280 3281 PetscFunctionBegin; 3282 PetscCall(PetscObjectGetComm((PetscObject)mat, &comm)); 3283 3284 if (call == MAT_REUSE_MATRIX) { 3285 /* Retrieve isrow_d, iscol_d and iscol_o from submat */ 3286 PetscCall(PetscObjectQuery((PetscObject)*submat, "isrow_d", (PetscObject *)&isrow_d)); 3287 PetscCheck(isrow_d, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "isrow_d passed in was not used before, cannot reuse"); 3288 3289 PetscCall(PetscObjectQuery((PetscObject)*submat, "iscol_d", (PetscObject *)&iscol_d)); 3290 PetscCheck(iscol_d, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "iscol_d passed in was not used before, cannot reuse"); 3291 3292 PetscCall(PetscObjectQuery((PetscObject)*submat, "iscol_o", (PetscObject *)&iscol_o)); 3293 PetscCheck(iscol_o, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "iscol_o passed in was not used before, cannot reuse"); 3294 3295 /* Update diagonal and off-diagonal portions of submat */ 3296 asub = (Mat_MPIAIJ *)(*submat)->data; 3297 PetscCall(MatCreateSubMatrix_SeqAIJ(a->A, isrow_d, iscol_d, PETSC_DECIDE, MAT_REUSE_MATRIX, &asub->A)); 3298 PetscCall(ISGetLocalSize(iscol_o, &n)); 3299 if (n) PetscCall(MatCreateSubMatrix_SeqAIJ(a->B, isrow_d, iscol_o, PETSC_DECIDE, MAT_REUSE_MATRIX, &asub->B)); 3300 PetscCall(MatAssemblyBegin(*submat, MAT_FINAL_ASSEMBLY)); 3301 PetscCall(MatAssemblyEnd(*submat, MAT_FINAL_ASSEMBLY)); 3302 3303 } else { /* call == MAT_INITIAL_MATRIX) */ 3304 PetscInt *garray, *garray_compact; 3305 PetscInt BsubN; 3306 3307 /* Create isrow_d, iscol_d, iscol_o and isgarray (replace isgarray with array?) */ 3308 PetscCall(ISGetSeqIS_SameColDist_Private(mat, isrow, iscol, &isrow_d, &iscol_d, &iscol_o, &garray)); 3309 3310 /* Create local submatrices Asub and Bsub */ 3311 PetscCall(MatCreateSubMatrix_SeqAIJ(a->A, isrow_d, iscol_d, PETSC_DECIDE, MAT_INITIAL_MATRIX, &Asub)); 3312 PetscCall(MatCreateSubMatrix_SeqAIJ(a->B, isrow_d, iscol_o, PETSC_DECIDE, MAT_INITIAL_MATRIX, &Bsub)); 3313 3314 // Compact garray so its not of size Bn 3315 PetscCall(ISGetSize(iscol_o, &count)); 3316 PetscCall(PetscMalloc1(count, &garray_compact)); 3317 PetscCall(PetscArraycpy(garray_compact, garray, count)); 3318 3319 /* Create submatrix M */ 3320 PetscCall(ISGetSize(isrow, &M_size)); 3321 PetscCall(ISGetSize(iscol, &N_size)); 3322 PetscCall(MatCreateMPIAIJWithSeqAIJ(comm, M_size, N_size, Asub, Bsub, garray_compact, &M)); 3323 3324 /* If Bsub has empty columns, compress iscol_o such that it will retrieve condensed Bsub from a->B during reuse */ 3325 asub = (Mat_MPIAIJ *)M->data; 3326 3327 PetscCall(ISGetLocalSize(iscol_o, &BsubN)); 3328 n = asub->B->cmap->N; 3329 if (BsubN > n) { 3330 /* This case can be tested using ~petsc/src/tao/bound/tutorials/runplate2_3 */ 3331 const PetscInt *idx; 3332 PetscInt i, j, *idx_new, *subgarray = asub->garray; 3333 PetscCall(PetscInfo(M, "submatrix Bn %" PetscInt_FMT " != BsubN %" PetscInt_FMT ", update iscol_o\n", n, BsubN)); 3334 3335 PetscCall(PetscMalloc1(n, &idx_new)); 3336 j = 0; 3337 PetscCall(ISGetIndices(iscol_o, &idx)); 3338 for (i = 0; i < n; i++) { 3339 if (j >= BsubN) break; 3340 while (subgarray[i] > garray[j]) j++; 3341 3342 if (subgarray[i] == garray[j]) { 3343 idx_new[i] = idx[j++]; 3344 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "subgarray[%" PetscInt_FMT "]=%" PetscInt_FMT " cannot < garray[%" PetscInt_FMT "]=%" PetscInt_FMT, i, subgarray[i], j, garray[j]); 3345 } 3346 PetscCall(ISRestoreIndices(iscol_o, &idx)); 3347 3348 PetscCall(ISDestroy(&iscol_o)); 3349 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, n, idx_new, PETSC_OWN_POINTER, &iscol_o)); 3350 3351 } else if (BsubN < n) { 3352 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Columns of Bsub (%" PetscInt_FMT ") cannot be smaller than B's (%" PetscInt_FMT ")", BsubN, asub->B->cmap->N); 3353 } 3354 3355 PetscCall(PetscFree(garray)); 3356 *submat = M; 3357 3358 /* Save isrow_d, iscol_d and iscol_o used in processor for next request */ 3359 PetscCall(PetscObjectCompose((PetscObject)M, "isrow_d", (PetscObject)isrow_d)); 3360 PetscCall(ISDestroy(&isrow_d)); 3361 3362 PetscCall(PetscObjectCompose((PetscObject)M, "iscol_d", (PetscObject)iscol_d)); 3363 PetscCall(ISDestroy(&iscol_d)); 3364 3365 PetscCall(PetscObjectCompose((PetscObject)M, "iscol_o", (PetscObject)iscol_o)); 3366 PetscCall(ISDestroy(&iscol_o)); 3367 } 3368 PetscFunctionReturn(PETSC_SUCCESS); 3369 } 3370 3371 PetscErrorCode MatCreateSubMatrix_MPIAIJ(Mat mat, IS isrow, IS iscol, MatReuse call, Mat *newmat) 3372 { 3373 IS iscol_local = NULL, isrow_d; 3374 PetscInt csize; 3375 PetscInt n, i, j, start, end; 3376 PetscBool sameRowDist = PETSC_FALSE, sameDist[2], tsameDist[2]; 3377 MPI_Comm comm; 3378 3379 PetscFunctionBegin; 3380 /* If isrow has same processor distribution as mat, 3381 call MatCreateSubMatrix_MPIAIJ_SameRowDist() to avoid using a hash table with global size of iscol */ 3382 if (call == MAT_REUSE_MATRIX) { 3383 PetscCall(PetscObjectQuery((PetscObject)*newmat, "isrow_d", (PetscObject *)&isrow_d)); 3384 if (isrow_d) { 3385 sameRowDist = PETSC_TRUE; 3386 tsameDist[1] = PETSC_TRUE; /* sameColDist */ 3387 } else { 3388 PetscCall(PetscObjectQuery((PetscObject)*newmat, "SubIScol", (PetscObject *)&iscol_local)); 3389 if (iscol_local) { 3390 sameRowDist = PETSC_TRUE; 3391 tsameDist[1] = PETSC_FALSE; /* !sameColDist */ 3392 } 3393 } 3394 } else { 3395 /* Check if isrow has same processor distribution as mat */ 3396 sameDist[0] = PETSC_FALSE; 3397 PetscCall(ISGetLocalSize(isrow, &n)); 3398 if (!n) { 3399 sameDist[0] = PETSC_TRUE; 3400 } else { 3401 PetscCall(ISGetMinMax(isrow, &i, &j)); 3402 PetscCall(MatGetOwnershipRange(mat, &start, &end)); 3403 if (i >= start && j < end) sameDist[0] = PETSC_TRUE; 3404 } 3405 3406 /* Check if iscol has same processor distribution as mat */ 3407 sameDist[1] = PETSC_FALSE; 3408 PetscCall(ISGetLocalSize(iscol, &n)); 3409 if (!n) { 3410 sameDist[1] = PETSC_TRUE; 3411 } else { 3412 PetscCall(ISGetMinMax(iscol, &i, &j)); 3413 PetscCall(MatGetOwnershipRangeColumn(mat, &start, &end)); 3414 if (i >= start && j < end) sameDist[1] = PETSC_TRUE; 3415 } 3416 3417 PetscCall(PetscObjectGetComm((PetscObject)mat, &comm)); 3418 PetscCallMPI(MPIU_Allreduce(&sameDist, &tsameDist, 2, MPIU_BOOL, MPI_LAND, comm)); 3419 sameRowDist = tsameDist[0]; 3420 } 3421 3422 if (sameRowDist) { 3423 if (tsameDist[1]) { /* sameRowDist & sameColDist */ 3424 /* isrow and iscol have same processor distribution as mat */ 3425 PetscCall(MatCreateSubMatrix_MPIAIJ_SameRowColDist(mat, isrow, iscol, call, newmat)); 3426 PetscFunctionReturn(PETSC_SUCCESS); 3427 } else { /* sameRowDist */ 3428 /* isrow has same processor distribution as mat */ 3429 if (call == MAT_INITIAL_MATRIX) { 3430 PetscBool sorted; 3431 PetscCall(ISGetSeqIS_Private(mat, iscol, &iscol_local)); 3432 PetscCall(ISGetLocalSize(iscol_local, &n)); /* local size of iscol_local = global columns of newmat */ 3433 PetscCall(ISGetSize(iscol, &i)); 3434 PetscCheck(n == i, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "n %" PetscInt_FMT " != size of iscol %" PetscInt_FMT, n, i); 3435 3436 PetscCall(ISSorted(iscol_local, &sorted)); 3437 if (sorted) { 3438 /* MatCreateSubMatrix_MPIAIJ_SameRowDist() requires iscol_local be sorted; it can have duplicate indices */ 3439 PetscCall(MatCreateSubMatrix_MPIAIJ_SameRowDist(mat, isrow, iscol, iscol_local, MAT_INITIAL_MATRIX, newmat)); 3440 PetscFunctionReturn(PETSC_SUCCESS); 3441 } 3442 } else { /* call == MAT_REUSE_MATRIX */ 3443 IS iscol_sub; 3444 PetscCall(PetscObjectQuery((PetscObject)*newmat, "SubIScol", (PetscObject *)&iscol_sub)); 3445 if (iscol_sub) { 3446 PetscCall(MatCreateSubMatrix_MPIAIJ_SameRowDist(mat, isrow, iscol, NULL, call, newmat)); 3447 PetscFunctionReturn(PETSC_SUCCESS); 3448 } 3449 } 3450 } 3451 } 3452 3453 /* General case: iscol -> iscol_local which has global size of iscol */ 3454 if (call == MAT_REUSE_MATRIX) { 3455 PetscCall(PetscObjectQuery((PetscObject)*newmat, "ISAllGather", (PetscObject *)&iscol_local)); 3456 PetscCheck(iscol_local, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Submatrix passed in was not used before, cannot reuse"); 3457 } else { 3458 if (!iscol_local) PetscCall(ISGetSeqIS_Private(mat, iscol, &iscol_local)); 3459 } 3460 3461 PetscCall(ISGetLocalSize(iscol, &csize)); 3462 PetscCall(MatCreateSubMatrix_MPIAIJ_nonscalable(mat, isrow, iscol_local, csize, call, newmat)); 3463 3464 if (call == MAT_INITIAL_MATRIX) { 3465 PetscCall(PetscObjectCompose((PetscObject)*newmat, "ISAllGather", (PetscObject)iscol_local)); 3466 PetscCall(ISDestroy(&iscol_local)); 3467 } 3468 PetscFunctionReturn(PETSC_SUCCESS); 3469 } 3470 3471 /*@C 3472 MatCreateMPIAIJWithSeqAIJ - creates a `MATMPIAIJ` matrix using `MATSEQAIJ` matrices that contain the "diagonal" 3473 and "off-diagonal" part of the matrix in CSR format. 3474 3475 Collective 3476 3477 Input Parameters: 3478 + comm - MPI communicator 3479 . M - the global row size 3480 . N - the global column size 3481 . A - "diagonal" portion of matrix 3482 . B - if garray is `NULL`, B should be the offdiag matrix using global col ids and of size N - if garray is not `NULL`, B should be the offdiag matrix using local col ids and of size garray 3483 - garray - either `NULL` or the global index of `B` columns 3484 3485 Output Parameter: 3486 . mat - the matrix, with input `A` as its local diagonal matrix 3487 3488 Level: advanced 3489 3490 Notes: 3491 See `MatCreateAIJ()` for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3492 3493 `A` and `B` becomes part of output mat. The user cannot use `A` and `B` anymore. 3494 3495 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MATSEQAIJ`, `MatCreateMPIAIJWithSplitArrays()` 3496 @*/ 3497 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm, PetscInt M, PetscInt N, Mat A, Mat B, PetscInt *garray, Mat *mat) 3498 { 3499 PetscInt m, n; 3500 MatType mpi_mat_type; 3501 3502 PetscFunctionBegin; 3503 PetscCall(MatCreate(comm, mat)); 3504 PetscCall(MatGetSize(A, &m, &n)); 3505 PetscCheck(m == B->rmap->N, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Am %" PetscInt_FMT " != Bm %" PetscInt_FMT, m, B->rmap->N); 3506 PetscCheck(A->rmap->bs == B->rmap->bs, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "A row bs %" PetscInt_FMT " != B row bs %" PetscInt_FMT, A->rmap->bs, B->rmap->bs); 3507 3508 PetscCall(MatSetSizes(*mat, m, n, M, N)); 3509 /* Determine the type of MPI matrix that should be created from the type of matrix A, which holds the "diagonal" portion. */ 3510 PetscCall(MatGetMPIMatType_Private(A, &mpi_mat_type)); 3511 PetscCall(MatSetType(*mat, mpi_mat_type)); 3512 3513 PetscCall(MatSetBlockSizes(*mat, A->rmap->bs, A->cmap->bs)); 3514 3515 PetscCall(PetscLayoutSetUp((*mat)->rmap)); 3516 PetscCall(PetscLayoutSetUp((*mat)->cmap)); 3517 PetscCall(MatSetMPIAIJWithSplitSeqAIJ(*mat, A, B, garray)); 3518 PetscFunctionReturn(PETSC_SUCCESS); 3519 } 3520 3521 /* 3522 MatSetMPIAIJWithSplitSeqAIJ - Set the diag and offdiag matrices of a `MATMPIAIJ` matrix. 3523 It is similar to `MatCreateMPIAIJWithSplitArrays()`. This routine allows passing in 3524 B with local indices and the correct size, along with the accompanying 3525 garray, hence skipping compactification 3526 3527 Collective 3528 3529 Input Parameters: 3530 + mat - the MATMPIAIJ matrix, which should have its type and layout set, but should not have its diag, offdiag matrices set 3531 . A - the diag matrix using local col ids 3532 . B - if garray is `NULL`, B should be the offdiag matrix using global col ids and of size N - if garray is not `NULL`, B should be the offdiag matrix using local col ids and of size garray 3533 - garray - either `NULL` or the global index of `B` columns 3534 3535 Output Parameter: 3536 . mat - the updated `MATMPIAIJ` matrix 3537 3538 Level: advanced 3539 3540 Notes: 3541 See `MatCreateAIJ()` for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3542 3543 `A` and `B` become part of output mat. The user cannot use `A` and `B` anymore. 3544 3545 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MATSEQAIJ`, `MatCreateMPIAIJWithSplitArrays()` 3546 */ 3547 PETSC_INTERN PetscErrorCode MatSetMPIAIJWithSplitSeqAIJ(Mat mat, Mat A, Mat B, PetscInt *garray) 3548 { 3549 PetscFunctionBegin; 3550 Mat_MPIAIJ *mpiaij = (Mat_MPIAIJ *)mat->data; 3551 PetscInt m, n, M, N, Am, An, Bm, Bn; 3552 3553 PetscCall(MatGetSize(mat, &M, &N)); 3554 PetscCall(MatGetLocalSize(mat, &m, &n)); 3555 PetscCall(MatGetLocalSize(A, &Am, &An)); 3556 PetscCall(MatGetLocalSize(B, &Bm, &Bn)); 3557 3558 PetscCheck(m == Am && m == Bm, PETSC_COMM_SELF, PETSC_ERR_PLIB, "local number of rows do not match"); 3559 PetscCheck(n == An, PETSC_COMM_SELF, PETSC_ERR_PLIB, "local number of columns do not match"); 3560 PetscCheck(!mpiaij->A && !mpiaij->B, PETSC_COMM_SELF, PETSC_ERR_PLIB, "A, B of the MPIAIJ matrix are not empty"); 3561 mpiaij->A = A; 3562 mpiaij->B = B; 3563 mpiaij->garray = garray; 3564 3565 mat->preallocated = PETSC_TRUE; 3566 mat->nooffprocentries = PETSC_TRUE; /* See MatAssemblyBegin_MPIAIJ. In effect, making MatAssemblyBegin a nop */ 3567 3568 PetscCall(MatSetOption(mat, MAT_NO_OFF_PROC_ENTRIES, PETSC_TRUE)); 3569 PetscCall(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY)); 3570 /* MatAssemblyEnd is critical here. It sets mat->offloadmask according to A and B's, and 3571 also gets mpiaij->B compacted (if garray is NULL), with its col ids and size reduced 3572 */ 3573 PetscCall(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY)); 3574 PetscCall(MatSetOption(mat, MAT_NO_OFF_PROC_ENTRIES, PETSC_FALSE)); 3575 PetscCall(MatSetOption(mat, MAT_NEW_NONZERO_LOCATION_ERR, PETSC_TRUE)); 3576 PetscFunctionReturn(PETSC_SUCCESS); 3577 } 3578 3579 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat, PetscInt, const IS[], const IS[], MatReuse, PetscBool, Mat *); 3580 3581 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat, IS isrow, IS iscol, IS iscol_local, MatReuse call, Mat *newmat) 3582 { 3583 PetscInt i, m, n, rstart, row, rend, nz, j, bs, cbs; 3584 PetscInt *ii, *jj, nlocal, *dlens, *olens, dlen, olen, jend, mglobal; 3585 Mat_MPIAIJ *a = (Mat_MPIAIJ *)mat->data; 3586 Mat M, Msub, B = a->B; 3587 MatScalar *aa; 3588 Mat_SeqAIJ *aij; 3589 PetscInt *garray = a->garray, *colsub, Ncols; 3590 PetscInt count, Bn = B->cmap->N, cstart = mat->cmap->rstart, cend = mat->cmap->rend; 3591 IS iscol_sub, iscmap; 3592 const PetscInt *is_idx, *cmap; 3593 PetscBool allcolumns = PETSC_FALSE; 3594 MPI_Comm comm; 3595 3596 PetscFunctionBegin; 3597 PetscCall(PetscObjectGetComm((PetscObject)mat, &comm)); 3598 if (call == MAT_REUSE_MATRIX) { 3599 PetscCall(PetscObjectQuery((PetscObject)*newmat, "SubIScol", (PetscObject *)&iscol_sub)); 3600 PetscCheck(iscol_sub, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "SubIScol passed in was not used before, cannot reuse"); 3601 PetscCall(ISGetLocalSize(iscol_sub, &count)); 3602 3603 PetscCall(PetscObjectQuery((PetscObject)*newmat, "Subcmap", (PetscObject *)&iscmap)); 3604 PetscCheck(iscmap, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Subcmap passed in was not used before, cannot reuse"); 3605 3606 PetscCall(PetscObjectQuery((PetscObject)*newmat, "SubMatrix", (PetscObject *)&Msub)); 3607 PetscCheck(Msub, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Submatrix passed in was not used before, cannot reuse"); 3608 3609 PetscCall(MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat, 1, &isrow, &iscol_sub, MAT_REUSE_MATRIX, PETSC_FALSE, &Msub)); 3610 3611 } else { /* call == MAT_INITIAL_MATRIX) */ 3612 PetscBool flg; 3613 3614 PetscCall(ISGetLocalSize(iscol, &n)); 3615 PetscCall(ISGetSize(iscol, &Ncols)); 3616 3617 /* (1) iscol -> nonscalable iscol_local */ 3618 /* Check for special case: each processor gets entire matrix columns */ 3619 PetscCall(ISIdentity(iscol_local, &flg)); 3620 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3621 PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &allcolumns, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)mat))); 3622 if (allcolumns) { 3623 iscol_sub = iscol_local; 3624 PetscCall(PetscObjectReference((PetscObject)iscol_local)); 3625 PetscCall(ISCreateStride(PETSC_COMM_SELF, n, 0, 1, &iscmap)); 3626 3627 } else { 3628 /* (2) iscol_local -> iscol_sub and iscmap. Implementation below requires iscol_local be sorted, it can have duplicate indices */ 3629 PetscInt *idx, *cmap1, k; 3630 PetscCall(PetscMalloc1(Ncols, &idx)); 3631 PetscCall(PetscMalloc1(Ncols, &cmap1)); 3632 PetscCall(ISGetIndices(iscol_local, &is_idx)); 3633 count = 0; 3634 k = 0; 3635 for (i = 0; i < Ncols; i++) { 3636 j = is_idx[i]; 3637 if (j >= cstart && j < cend) { 3638 /* diagonal part of mat */ 3639 idx[count] = j; 3640 cmap1[count++] = i; /* column index in submat */ 3641 } else if (Bn) { 3642 /* off-diagonal part of mat */ 3643 if (j == garray[k]) { 3644 idx[count] = j; 3645 cmap1[count++] = i; /* column index in submat */ 3646 } else if (j > garray[k]) { 3647 while (j > garray[k] && k < Bn - 1) k++; 3648 if (j == garray[k]) { 3649 idx[count] = j; 3650 cmap1[count++] = i; /* column index in submat */ 3651 } 3652 } 3653 } 3654 } 3655 PetscCall(ISRestoreIndices(iscol_local, &is_idx)); 3656 3657 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, count, idx, PETSC_OWN_POINTER, &iscol_sub)); 3658 PetscCall(ISGetBlockSize(iscol, &cbs)); 3659 PetscCall(ISSetBlockSize(iscol_sub, cbs)); 3660 3661 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local), count, cmap1, PETSC_OWN_POINTER, &iscmap)); 3662 } 3663 3664 /* (3) Create sequential Msub */ 3665 PetscCall(MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat, 1, &isrow, &iscol_sub, MAT_INITIAL_MATRIX, allcolumns, &Msub)); 3666 } 3667 3668 PetscCall(ISGetLocalSize(iscol_sub, &count)); 3669 aij = (Mat_SeqAIJ *)Msub->data; 3670 ii = aij->i; 3671 PetscCall(ISGetIndices(iscmap, &cmap)); 3672 3673 /* 3674 m - number of local rows 3675 Ncols - number of columns (same on all processors) 3676 rstart - first row in new global matrix generated 3677 */ 3678 PetscCall(MatGetSize(Msub, &m, NULL)); 3679 3680 if (call == MAT_INITIAL_MATRIX) { 3681 /* (4) Create parallel newmat */ 3682 PetscMPIInt rank, size; 3683 PetscInt csize; 3684 3685 PetscCallMPI(MPI_Comm_size(comm, &size)); 3686 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 3687 3688 /* 3689 Determine the number of non-zeros in the diagonal and off-diagonal 3690 portions of the matrix in order to do correct preallocation 3691 */ 3692 3693 /* first get start and end of "diagonal" columns */ 3694 PetscCall(ISGetLocalSize(iscol, &csize)); 3695 if (csize == PETSC_DECIDE) { 3696 PetscCall(ISGetSize(isrow, &mglobal)); 3697 if (mglobal == Ncols) { /* square matrix */ 3698 nlocal = m; 3699 } else { 3700 nlocal = Ncols / size + ((Ncols % size) > rank); 3701 } 3702 } else { 3703 nlocal = csize; 3704 } 3705 PetscCallMPI(MPI_Scan(&nlocal, &rend, 1, MPIU_INT, MPI_SUM, comm)); 3706 rstart = rend - nlocal; 3707 PetscCheck(rank != size - 1 || rend == Ncols, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Local column sizes %" PetscInt_FMT " do not add up to total number of columns %" PetscInt_FMT, rend, Ncols); 3708 3709 /* next, compute all the lengths */ 3710 jj = aij->j; 3711 PetscCall(PetscMalloc1(2 * m + 1, &dlens)); 3712 olens = dlens + m; 3713 for (i = 0; i < m; i++) { 3714 jend = ii[i + 1] - ii[i]; 3715 olen = 0; 3716 dlen = 0; 3717 for (j = 0; j < jend; j++) { 3718 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3719 else dlen++; 3720 jj++; 3721 } 3722 olens[i] = olen; 3723 dlens[i] = dlen; 3724 } 3725 3726 PetscCall(ISGetBlockSize(isrow, &bs)); 3727 PetscCall(ISGetBlockSize(iscol, &cbs)); 3728 3729 PetscCall(MatCreate(comm, &M)); 3730 PetscCall(MatSetSizes(M, m, nlocal, PETSC_DECIDE, Ncols)); 3731 PetscCall(MatSetBlockSizes(M, bs, cbs)); 3732 PetscCall(MatSetType(M, ((PetscObject)mat)->type_name)); 3733 PetscCall(MatMPIAIJSetPreallocation(M, 0, dlens, 0, olens)); 3734 PetscCall(PetscFree(dlens)); 3735 3736 } else { /* call == MAT_REUSE_MATRIX */ 3737 M = *newmat; 3738 PetscCall(MatGetLocalSize(M, &i, NULL)); 3739 PetscCheck(i == m, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Previous matrix must be same size/layout as request"); 3740 PetscCall(MatZeroEntries(M)); 3741 /* 3742 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3743 rather than the slower MatSetValues(). 3744 */ 3745 M->was_assembled = PETSC_TRUE; 3746 M->assembled = PETSC_FALSE; 3747 } 3748 3749 /* (5) Set values of Msub to *newmat */ 3750 PetscCall(PetscMalloc1(count, &colsub)); 3751 PetscCall(MatGetOwnershipRange(M, &rstart, NULL)); 3752 3753 jj = aij->j; 3754 PetscCall(MatSeqAIJGetArrayRead(Msub, (const PetscScalar **)&aa)); 3755 for (i = 0; i < m; i++) { 3756 row = rstart + i; 3757 nz = ii[i + 1] - ii[i]; 3758 for (j = 0; j < nz; j++) colsub[j] = cmap[jj[j]]; 3759 PetscCall(MatSetValues_MPIAIJ(M, 1, &row, nz, colsub, aa, INSERT_VALUES)); 3760 jj += nz; 3761 aa += nz; 3762 } 3763 PetscCall(MatSeqAIJRestoreArrayRead(Msub, (const PetscScalar **)&aa)); 3764 PetscCall(ISRestoreIndices(iscmap, &cmap)); 3765 3766 PetscCall(MatAssemblyBegin(M, MAT_FINAL_ASSEMBLY)); 3767 PetscCall(MatAssemblyEnd(M, MAT_FINAL_ASSEMBLY)); 3768 3769 PetscCall(PetscFree(colsub)); 3770 3771 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3772 if (call == MAT_INITIAL_MATRIX) { 3773 *newmat = M; 3774 PetscCall(PetscObjectCompose((PetscObject)*newmat, "SubMatrix", (PetscObject)Msub)); 3775 PetscCall(MatDestroy(&Msub)); 3776 3777 PetscCall(PetscObjectCompose((PetscObject)*newmat, "SubIScol", (PetscObject)iscol_sub)); 3778 PetscCall(ISDestroy(&iscol_sub)); 3779 3780 PetscCall(PetscObjectCompose((PetscObject)*newmat, "Subcmap", (PetscObject)iscmap)); 3781 PetscCall(ISDestroy(&iscmap)); 3782 3783 if (iscol_local) { 3784 PetscCall(PetscObjectCompose((PetscObject)*newmat, "ISAllGather", (PetscObject)iscol_local)); 3785 PetscCall(ISDestroy(&iscol_local)); 3786 } 3787 } 3788 PetscFunctionReturn(PETSC_SUCCESS); 3789 } 3790 3791 /* 3792 Not great since it makes two copies of the submatrix, first an SeqAIJ 3793 in local and then by concatenating the local matrices the end result. 3794 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3795 3796 This requires a sequential iscol with all indices. 3797 */ 3798 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat, IS isrow, IS iscol, PetscInt csize, MatReuse call, Mat *newmat) 3799 { 3800 PetscMPIInt rank, size; 3801 PetscInt i, m, n, rstart, row, rend, nz, *cwork, j, bs, cbs; 3802 PetscInt *ii, *jj, nlocal, *dlens, *olens, dlen, olen, jend, mglobal; 3803 Mat M, Mreuse; 3804 MatScalar *aa, *vwork; 3805 MPI_Comm comm; 3806 Mat_SeqAIJ *aij; 3807 PetscBool colflag, allcolumns = PETSC_FALSE; 3808 3809 PetscFunctionBegin; 3810 PetscCall(PetscObjectGetComm((PetscObject)mat, &comm)); 3811 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 3812 PetscCallMPI(MPI_Comm_size(comm, &size)); 3813 3814 /* Check for special case: each processor gets entire matrix columns */ 3815 PetscCall(ISIdentity(iscol, &colflag)); 3816 PetscCall(ISGetLocalSize(iscol, &n)); 3817 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3818 PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &allcolumns, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)mat))); 3819 3820 if (call == MAT_REUSE_MATRIX) { 3821 PetscCall(PetscObjectQuery((PetscObject)*newmat, "SubMatrix", (PetscObject *)&Mreuse)); 3822 PetscCheck(Mreuse, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Submatrix passed in was not used before, cannot reuse"); 3823 PetscCall(MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat, 1, &isrow, &iscol, MAT_REUSE_MATRIX, allcolumns, &Mreuse)); 3824 } else { 3825 PetscCall(MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat, 1, &isrow, &iscol, MAT_INITIAL_MATRIX, allcolumns, &Mreuse)); 3826 } 3827 3828 /* 3829 m - number of local rows 3830 n - number of columns (same on all processors) 3831 rstart - first row in new global matrix generated 3832 */ 3833 PetscCall(MatGetSize(Mreuse, &m, &n)); 3834 PetscCall(MatGetBlockSizes(Mreuse, &bs, &cbs)); 3835 if (call == MAT_INITIAL_MATRIX) { 3836 aij = (Mat_SeqAIJ *)Mreuse->data; 3837 ii = aij->i; 3838 jj = aij->j; 3839 3840 /* 3841 Determine the number of non-zeros in the diagonal and off-diagonal 3842 portions of the matrix in order to do correct preallocation 3843 */ 3844 3845 /* first get start and end of "diagonal" columns */ 3846 if (csize == PETSC_DECIDE) { 3847 PetscCall(ISGetSize(isrow, &mglobal)); 3848 if (mglobal == n) { /* square matrix */ 3849 nlocal = m; 3850 } else { 3851 nlocal = n / size + ((n % size) > rank); 3852 } 3853 } else { 3854 nlocal = csize; 3855 } 3856 PetscCallMPI(MPI_Scan(&nlocal, &rend, 1, MPIU_INT, MPI_SUM, comm)); 3857 rstart = rend - nlocal; 3858 PetscCheck(rank != size - 1 || rend == n, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Local column sizes %" PetscInt_FMT " do not add up to total number of columns %" PetscInt_FMT, rend, n); 3859 3860 /* next, compute all the lengths */ 3861 PetscCall(PetscMalloc1(2 * m + 1, &dlens)); 3862 olens = dlens + m; 3863 for (i = 0; i < m; i++) { 3864 jend = ii[i + 1] - ii[i]; 3865 olen = 0; 3866 dlen = 0; 3867 for (j = 0; j < jend; j++) { 3868 if (*jj < rstart || *jj >= rend) olen++; 3869 else dlen++; 3870 jj++; 3871 } 3872 olens[i] = olen; 3873 dlens[i] = dlen; 3874 } 3875 PetscCall(MatCreate(comm, &M)); 3876 PetscCall(MatSetSizes(M, m, nlocal, PETSC_DECIDE, n)); 3877 PetscCall(MatSetBlockSizes(M, bs, cbs)); 3878 PetscCall(MatSetType(M, ((PetscObject)mat)->type_name)); 3879 PetscCall(MatMPIAIJSetPreallocation(M, 0, dlens, 0, olens)); 3880 PetscCall(PetscFree(dlens)); 3881 } else { 3882 PetscInt ml, nl; 3883 3884 M = *newmat; 3885 PetscCall(MatGetLocalSize(M, &ml, &nl)); 3886 PetscCheck(ml == m, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Previous matrix must be same size/layout as request"); 3887 PetscCall(MatZeroEntries(M)); 3888 /* 3889 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3890 rather than the slower MatSetValues(). 3891 */ 3892 M->was_assembled = PETSC_TRUE; 3893 M->assembled = PETSC_FALSE; 3894 } 3895 PetscCall(MatGetOwnershipRange(M, &rstart, &rend)); 3896 aij = (Mat_SeqAIJ *)Mreuse->data; 3897 ii = aij->i; 3898 jj = aij->j; 3899 3900 /* trigger copy to CPU if needed */ 3901 PetscCall(MatSeqAIJGetArrayRead(Mreuse, (const PetscScalar **)&aa)); 3902 for (i = 0; i < m; i++) { 3903 row = rstart + i; 3904 nz = ii[i + 1] - ii[i]; 3905 cwork = jj; 3906 jj = PetscSafePointerPlusOffset(jj, nz); 3907 vwork = aa; 3908 aa = PetscSafePointerPlusOffset(aa, nz); 3909 PetscCall(MatSetValues_MPIAIJ(M, 1, &row, nz, cwork, vwork, INSERT_VALUES)); 3910 } 3911 PetscCall(MatSeqAIJRestoreArrayRead(Mreuse, (const PetscScalar **)&aa)); 3912 3913 PetscCall(MatAssemblyBegin(M, MAT_FINAL_ASSEMBLY)); 3914 PetscCall(MatAssemblyEnd(M, MAT_FINAL_ASSEMBLY)); 3915 *newmat = M; 3916 3917 /* save submatrix used in processor for next request */ 3918 if (call == MAT_INITIAL_MATRIX) { 3919 PetscCall(PetscObjectCompose((PetscObject)M, "SubMatrix", (PetscObject)Mreuse)); 3920 PetscCall(MatDestroy(&Mreuse)); 3921 } 3922 PetscFunctionReturn(PETSC_SUCCESS); 3923 } 3924 3925 static PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B, const PetscInt Ii[], const PetscInt J[], const PetscScalar v[]) 3926 { 3927 PetscInt m, cstart, cend, j, nnz, i, d, *ld; 3928 PetscInt *d_nnz, *o_nnz, nnz_max = 0, rstart, ii, irstart; 3929 const PetscInt *JJ; 3930 PetscBool nooffprocentries; 3931 Mat_MPIAIJ *Aij = (Mat_MPIAIJ *)B->data; 3932 3933 PetscFunctionBegin; 3934 PetscCall(PetscLayoutSetUp(B->rmap)); 3935 PetscCall(PetscLayoutSetUp(B->cmap)); 3936 m = B->rmap->n; 3937 cstart = B->cmap->rstart; 3938 cend = B->cmap->rend; 3939 rstart = B->rmap->rstart; 3940 irstart = Ii[0]; 3941 3942 PetscCall(PetscCalloc2(m, &d_nnz, m, &o_nnz)); 3943 3944 if (PetscDefined(USE_DEBUG)) { 3945 for (i = 0; i < m; i++) { 3946 nnz = Ii[i + 1] - Ii[i]; 3947 JJ = PetscSafePointerPlusOffset(J, Ii[i] - irstart); 3948 PetscCheck(nnz >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Local row %" PetscInt_FMT " has a negative %" PetscInt_FMT " number of columns", i, nnz); 3949 PetscCheck(!nnz || !(JJ[0] < 0), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Row %" PetscInt_FMT " starts with negative column index %" PetscInt_FMT, i, JJ[0]); 3950 PetscCheck(!nnz || !(JJ[nnz - 1] >= B->cmap->N), PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Row %" PetscInt_FMT " ends with too large a column index %" PetscInt_FMT " (max allowed %" PetscInt_FMT ")", i, JJ[nnz - 1], B->cmap->N); 3951 } 3952 } 3953 3954 for (i = 0; i < m; i++) { 3955 nnz = Ii[i + 1] - Ii[i]; 3956 JJ = PetscSafePointerPlusOffset(J, Ii[i] - irstart); 3957 nnz_max = PetscMax(nnz_max, nnz); 3958 d = 0; 3959 for (j = 0; j < nnz; j++) { 3960 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3961 } 3962 d_nnz[i] = d; 3963 o_nnz[i] = nnz - d; 3964 } 3965 PetscCall(MatMPIAIJSetPreallocation(B, 0, d_nnz, 0, o_nnz)); 3966 PetscCall(PetscFree2(d_nnz, o_nnz)); 3967 3968 for (i = 0; i < m; i++) { 3969 ii = i + rstart; 3970 PetscCall(MatSetValues_MPIAIJ(B, 1, &ii, Ii[i + 1] - Ii[i], PetscSafePointerPlusOffset(J, Ii[i] - irstart), PetscSafePointerPlusOffset(v, Ii[i] - irstart), INSERT_VALUES)); 3971 } 3972 nooffprocentries = B->nooffprocentries; 3973 B->nooffprocentries = PETSC_TRUE; 3974 PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY)); 3975 PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY)); 3976 B->nooffprocentries = nooffprocentries; 3977 3978 /* count number of entries below block diagonal */ 3979 PetscCall(PetscFree(Aij->ld)); 3980 PetscCall(PetscCalloc1(m, &ld)); 3981 Aij->ld = ld; 3982 for (i = 0; i < m; i++) { 3983 nnz = Ii[i + 1] - Ii[i]; 3984 j = 0; 3985 while (j < nnz && J[j] < cstart) j++; 3986 ld[i] = j; 3987 if (J) J += nnz; 3988 } 3989 3990 PetscCall(MatSetOption(B, MAT_NEW_NONZERO_LOCATION_ERR, PETSC_TRUE)); 3991 PetscFunctionReturn(PETSC_SUCCESS); 3992 } 3993 3994 /*@ 3995 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in `MATAIJ` format 3996 (the default parallel PETSc format). 3997 3998 Collective 3999 4000 Input Parameters: 4001 + B - the matrix 4002 . i - the indices into `j` for the start of each local row (indices start with zero) 4003 . j - the column indices for each local row (indices start with zero) 4004 - v - optional values in the matrix 4005 4006 Level: developer 4007 4008 Notes: 4009 The `i`, `j`, and `v` arrays ARE copied by this routine into the internal format used by PETSc; 4010 thus you CANNOT change the matrix entries by changing the values of `v` after you have 4011 called this routine. Use `MatCreateMPIAIJWithSplitArrays()` to avoid needing to copy the arrays. 4012 4013 The `i` and `j` indices are 0 based, and `i` indices are indices corresponding to the local `j` array. 4014 4015 A convenience routine for this functionality is `MatCreateMPIAIJWithArrays()`. 4016 4017 You can update the matrix with new numerical values using `MatUpdateMPIAIJWithArrays()` after this call if the column indices in `j` are sorted. 4018 4019 If you do **not** use `MatUpdateMPIAIJWithArrays()`, the column indices in `j` do not need to be sorted. If you will use 4020 `MatUpdateMPIAIJWithArrays()`, the column indices **must** be sorted. 4021 4022 The format which is used for the sparse matrix input, is equivalent to a 4023 row-major ordering.. i.e for the following matrix, the input data expected is 4024 as shown 4025 .vb 4026 1 0 0 4027 2 0 3 P0 4028 ------- 4029 4 5 6 P1 4030 4031 Process0 [P0] rows_owned=[0,1] 4032 i = {0,1,3} [size = nrow+1 = 2+1] 4033 j = {0,0,2} [size = 3] 4034 v = {1,2,3} [size = 3] 4035 4036 Process1 [P1] rows_owned=[2] 4037 i = {0,3} [size = nrow+1 = 1+1] 4038 j = {0,1,2} [size = 3] 4039 v = {4,5,6} [size = 3] 4040 .ve 4041 4042 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatCreateAIJ()`, 4043 `MatCreateSeqAIJWithArrays()`, `MatCreateMPIAIJWithSplitArrays()`, `MatCreateMPIAIJWithArrays()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4044 @*/ 4045 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B, const PetscInt i[], const PetscInt j[], const PetscScalar v[]) 4046 { 4047 PetscFunctionBegin; 4048 PetscTryMethod(B, "MatMPIAIJSetPreallocationCSR_C", (Mat, const PetscInt[], const PetscInt[], const PetscScalar[]), (B, i, j, v)); 4049 PetscFunctionReturn(PETSC_SUCCESS); 4050 } 4051 4052 /*@ 4053 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in `MATMPIAIJ` format 4054 (the default parallel PETSc format). For good matrix assembly performance 4055 the user should preallocate the matrix storage by setting the parameters 4056 `d_nz` (or `d_nnz`) and `o_nz` (or `o_nnz`). 4057 4058 Collective 4059 4060 Input Parameters: 4061 + B - the matrix 4062 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4063 (same value is used for all local rows) 4064 . d_nnz - array containing the number of nonzeros in the various rows of the 4065 DIAGONAL portion of the local submatrix (possibly different for each row) 4066 or `NULL` (`PETSC_NULL_INTEGER` in Fortran), if `d_nz` is used to specify the nonzero structure. 4067 The size of this array is equal to the number of local rows, i.e 'm'. 4068 For matrices that will be factored, you must leave room for (and set) 4069 the diagonal entry even if it is zero. 4070 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4071 submatrix (same value is used for all local rows). 4072 - o_nnz - array containing the number of nonzeros in the various rows of the 4073 OFF-DIAGONAL portion of the local submatrix (possibly different for 4074 each row) or `NULL` (`PETSC_NULL_INTEGER` in Fortran), if `o_nz` is used to specify the nonzero 4075 structure. The size of this array is equal to the number 4076 of local rows, i.e 'm'. 4077 4078 Example Usage: 4079 Consider the following 8x8 matrix with 34 non-zero values, that is 4080 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4081 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4082 as follows 4083 4084 .vb 4085 1 2 0 | 0 3 0 | 0 4 4086 Proc0 0 5 6 | 7 0 0 | 8 0 4087 9 0 10 | 11 0 0 | 12 0 4088 ------------------------------------- 4089 13 0 14 | 15 16 17 | 0 0 4090 Proc1 0 18 0 | 19 20 21 | 0 0 4091 0 0 0 | 22 23 0 | 24 0 4092 ------------------------------------- 4093 Proc2 25 26 27 | 0 0 28 | 29 0 4094 30 0 0 | 31 32 33 | 0 34 4095 .ve 4096 4097 This can be represented as a collection of submatrices as 4098 .vb 4099 A B C 4100 D E F 4101 G H I 4102 .ve 4103 4104 Where the submatrices A,B,C are owned by proc0, D,E,F are 4105 owned by proc1, G,H,I are owned by proc2. 4106 4107 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4108 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4109 The 'M','N' parameters are 8,8, and have the same values on all procs. 4110 4111 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4112 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4113 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4114 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4115 part as `MATSEQAIJ` matrices. For example, proc1 will store [E] as a `MATSEQAIJ` 4116 matrix, and [DF] as another `MATSEQAIJ` matrix. 4117 4118 When `d_nz`, `o_nz` parameters are specified, `d_nz` storage elements are 4119 allocated for every row of the local DIAGONAL submatrix, and `o_nz` 4120 storage locations are allocated for every row of the OFF-DIAGONAL submatrix. 4121 One way to choose `d_nz` and `o_nz` is to use the maximum number of nonzeros over 4122 the local rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4123 In this case, the values of `d_nz`, `o_nz` are 4124 .vb 4125 proc0 dnz = 2, o_nz = 2 4126 proc1 dnz = 3, o_nz = 2 4127 proc2 dnz = 1, o_nz = 4 4128 .ve 4129 We are allocating `m`*(`d_nz`+`o_nz`) storage locations for every proc. This 4130 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4131 for proc3. i.e we are using 12+15+10=37 storage locations to store 4132 34 values. 4133 4134 When `d_nnz`, `o_nnz` parameters are specified, the storage is specified 4135 for every row, corresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4136 In the above case the values for `d_nnz`, `o_nnz` are 4137 .vb 4138 proc0 d_nnz = [2,2,2] and o_nnz = [2,2,2] 4139 proc1 d_nnz = [3,3,2] and o_nnz = [2,1,1] 4140 proc2 d_nnz = [1,1] and o_nnz = [4,4] 4141 .ve 4142 Here the space allocated is sum of all the above values i.e 34, and 4143 hence pre-allocation is perfect. 4144 4145 Level: intermediate 4146 4147 Notes: 4148 If the *_nnz parameter is given then the *_nz parameter is ignored 4149 4150 The `MATAIJ` format, also called compressed row storage (CSR), is compatible with standard Fortran 4151 storage. The stored row and column indices begin with zero. 4152 See [Sparse Matrices](sec_matsparse) for details. 4153 4154 The parallel matrix is partitioned such that the first m0 rows belong to 4155 process 0, the next m1 rows belong to process 1, the next m2 rows belong 4156 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 4157 4158 The DIAGONAL portion of the local submatrix of a processor can be defined 4159 as the submatrix which is obtained by extraction the part corresponding to 4160 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 4161 first row that belongs to the processor, r2 is the last row belonging to 4162 the this processor, and c1-c2 is range of indices of the local part of a 4163 vector suitable for applying the matrix to. This is an mxn matrix. In the 4164 common case of a square matrix, the row and column ranges are the same and 4165 the DIAGONAL part is also square. The remaining portion of the local 4166 submatrix (mxN) constitute the OFF-DIAGONAL portion. 4167 4168 If `o_nnz` and `d_nnz` are specified, then `o_nz` and `d_nz` are ignored. 4169 4170 You can call `MatGetInfo()` to get information on how effective the preallocation was; 4171 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 4172 You can also run with the option `-info` and look for messages with the string 4173 malloc in them to see if additional memory allocation was needed. 4174 4175 .seealso: [](ch_matrices), `Mat`, [Sparse Matrices](sec_matsparse), `MATMPIAIJ`, `MATAIJ`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatCreateAIJ()`, `MatMPIAIJSetPreallocationCSR()`, 4176 `MatGetInfo()`, `PetscSplitOwnership()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4177 @*/ 4178 PetscErrorCode MatMPIAIJSetPreallocation(Mat B, PetscInt d_nz, const PetscInt d_nnz[], PetscInt o_nz, const PetscInt o_nnz[]) 4179 { 4180 PetscFunctionBegin; 4181 PetscValidHeaderSpecific(B, MAT_CLASSID, 1); 4182 PetscValidType(B, 1); 4183 PetscTryMethod(B, "MatMPIAIJSetPreallocation_C", (Mat, PetscInt, const PetscInt[], PetscInt, const PetscInt[]), (B, d_nz, d_nnz, o_nz, o_nnz)); 4184 PetscFunctionReturn(PETSC_SUCCESS); 4185 } 4186 4187 /*@ 4188 MatCreateMPIAIJWithArrays - creates a `MATMPIAIJ` matrix using arrays that contain in standard 4189 CSR format for the local rows. 4190 4191 Collective 4192 4193 Input Parameters: 4194 + comm - MPI communicator 4195 . m - number of local rows (Cannot be `PETSC_DECIDE`) 4196 . n - This value should be the same as the local size used in creating the 4197 x vector for the matrix-vector product $ y = Ax$. (or `PETSC_DECIDE` to have 4198 calculated if `N` is given) For square matrices n is almost always `m`. 4199 . M - number of global rows (or `PETSC_DETERMINE` to have calculated if `m` is given) 4200 . N - number of global columns (or `PETSC_DETERMINE` to have calculated if `n` is given) 4201 . i - row indices (of length m+1); that is i[0] = 0, i[row] = i[row-1] + number of elements in that row of the matrix 4202 . j - global column indices 4203 - a - optional matrix values 4204 4205 Output Parameter: 4206 . mat - the matrix 4207 4208 Level: intermediate 4209 4210 Notes: 4211 The `i`, `j`, and `a` arrays ARE copied by this routine into the internal format used by PETSc; 4212 thus you CANNOT change the matrix entries by changing the values of `a[]` after you have 4213 called this routine. Use `MatCreateMPIAIJWithSplitArrays()` to avoid needing to copy the arrays. 4214 4215 The `i` and `j` indices are 0 based, and `i` indices are indices corresponding to the local `j` array. 4216 4217 Once you have created the matrix you can update it with new numerical values using `MatUpdateMPIAIJWithArray()` 4218 4219 If you do **not** use `MatUpdateMPIAIJWithArray()`, the column indices in `j` do not need to be sorted. If you will use 4220 `MatUpdateMPIAIJWithArrays()`, the column indices **must** be sorted. 4221 4222 The format which is used for the sparse matrix input, is equivalent to a 4223 row-major ordering, i.e., for the following matrix, the input data expected is 4224 as shown 4225 .vb 4226 1 0 0 4227 2 0 3 P0 4228 ------- 4229 4 5 6 P1 4230 4231 Process0 [P0] rows_owned=[0,1] 4232 i = {0,1,3} [size = nrow+1 = 2+1] 4233 j = {0,0,2} [size = 3] 4234 v = {1,2,3} [size = 3] 4235 4236 Process1 [P1] rows_owned=[2] 4237 i = {0,3} [size = nrow+1 = 1+1] 4238 j = {0,1,2} [size = 3] 4239 v = {4,5,6} [size = 3] 4240 .ve 4241 4242 .seealso: [](ch_matrices), `Mat`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 4243 `MATMPIAIJ`, `MatCreateAIJ()`, `MatCreateMPIAIJWithSplitArrays()`, `MatUpdateMPIAIJWithArray()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4244 @*/ 4245 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm, PetscInt m, PetscInt n, PetscInt M, PetscInt N, const PetscInt i[], const PetscInt j[], const PetscScalar a[], Mat *mat) 4246 { 4247 PetscFunctionBegin; 4248 PetscCheck(!i || !i[0], PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "i (row indices) must start with 0"); 4249 PetscCheck(m >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4250 PetscCall(MatCreate(comm, mat)); 4251 PetscCall(MatSetSizes(*mat, m, n, M, N)); 4252 /* PetscCall(MatSetBlockSizes(M,bs,cbs)); */ 4253 PetscCall(MatSetType(*mat, MATMPIAIJ)); 4254 PetscCall(MatMPIAIJSetPreallocationCSR(*mat, i, j, a)); 4255 PetscFunctionReturn(PETSC_SUCCESS); 4256 } 4257 4258 /*@ 4259 MatUpdateMPIAIJWithArrays - updates a `MATMPIAIJ` matrix using arrays that contain in standard 4260 CSR format for the local rows. Only the numerical values are updated the other arrays must be identical to what was passed 4261 from `MatCreateMPIAIJWithArrays()` 4262 4263 Deprecated: Use `MatUpdateMPIAIJWithArray()` 4264 4265 Collective 4266 4267 Input Parameters: 4268 + mat - the matrix 4269 . m - number of local rows (Cannot be `PETSC_DECIDE`) 4270 . n - This value should be the same as the local size used in creating the 4271 x vector for the matrix-vector product y = Ax. (or `PETSC_DECIDE` to have 4272 calculated if N is given) For square matrices n is almost always m. 4273 . M - number of global rows (or `PETSC_DETERMINE` to have calculated if m is given) 4274 . N - number of global columns (or `PETSC_DETERMINE` to have calculated if n is given) 4275 . Ii - row indices; that is Ii[0] = 0, Ii[row] = Ii[row-1] + number of elements in that row of the matrix 4276 . J - column indices 4277 - v - matrix values 4278 4279 Level: deprecated 4280 4281 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 4282 `MatCreateAIJ()`, `MatCreateMPIAIJWithSplitArrays()`, `MatUpdateMPIAIJWithArray()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4283 @*/ 4284 PetscErrorCode MatUpdateMPIAIJWithArrays(Mat mat, PetscInt m, PetscInt n, PetscInt M, PetscInt N, const PetscInt Ii[], const PetscInt J[], const PetscScalar v[]) 4285 { 4286 PetscInt nnz, i; 4287 PetscBool nooffprocentries; 4288 Mat_MPIAIJ *Aij = (Mat_MPIAIJ *)mat->data; 4289 Mat_SeqAIJ *Ad = (Mat_SeqAIJ *)Aij->A->data; 4290 PetscScalar *ad, *ao; 4291 PetscInt ldi, Iii, md; 4292 const PetscInt *Adi = Ad->i; 4293 PetscInt *ld = Aij->ld; 4294 4295 PetscFunctionBegin; 4296 PetscCheck(Ii[0] == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "i (row indices) must start with 0"); 4297 PetscCheck(m >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4298 PetscCheck(m == mat->rmap->n, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Local number of rows cannot change from call to MatUpdateMPIAIJWithArrays()"); 4299 PetscCheck(n == mat->cmap->n, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Local number of columns cannot change from call to MatUpdateMPIAIJWithArrays()"); 4300 4301 PetscCall(MatSeqAIJGetArrayWrite(Aij->A, &ad)); 4302 PetscCall(MatSeqAIJGetArrayWrite(Aij->B, &ao)); 4303 4304 for (i = 0; i < m; i++) { 4305 if (PetscDefined(USE_DEBUG)) { 4306 for (PetscInt j = Ii[i] + 1; j < Ii[i + 1]; ++j) { 4307 PetscCheck(J[j] >= J[j - 1], PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Column entry number %" PetscInt_FMT " (actual column %" PetscInt_FMT ") in row %" PetscInt_FMT " is not sorted", j - Ii[i], J[j], i); 4308 PetscCheck(J[j] != J[j - 1], PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Column entry number %" PetscInt_FMT " (actual column %" PetscInt_FMT ") in row %" PetscInt_FMT " is identical to previous entry", j - Ii[i], J[j], i); 4309 } 4310 } 4311 nnz = Ii[i + 1] - Ii[i]; 4312 Iii = Ii[i]; 4313 ldi = ld[i]; 4314 md = Adi[i + 1] - Adi[i]; 4315 PetscCall(PetscArraycpy(ao, v + Iii, ldi)); 4316 PetscCall(PetscArraycpy(ad, v + Iii + ldi, md)); 4317 PetscCall(PetscArraycpy(ao + ldi, v + Iii + ldi + md, nnz - ldi - md)); 4318 ad += md; 4319 ao += nnz - md; 4320 } 4321 nooffprocentries = mat->nooffprocentries; 4322 mat->nooffprocentries = PETSC_TRUE; 4323 PetscCall(MatSeqAIJRestoreArrayWrite(Aij->A, &ad)); 4324 PetscCall(MatSeqAIJRestoreArrayWrite(Aij->B, &ao)); 4325 PetscCall(PetscObjectStateIncrease((PetscObject)Aij->A)); 4326 PetscCall(PetscObjectStateIncrease((PetscObject)Aij->B)); 4327 PetscCall(PetscObjectStateIncrease((PetscObject)mat)); 4328 PetscCall(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY)); 4329 PetscCall(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY)); 4330 mat->nooffprocentries = nooffprocentries; 4331 PetscFunctionReturn(PETSC_SUCCESS); 4332 } 4333 4334 /*@ 4335 MatUpdateMPIAIJWithArray - updates an `MATMPIAIJ` matrix using an array that contains the nonzero values 4336 4337 Collective 4338 4339 Input Parameters: 4340 + mat - the matrix 4341 - v - matrix values, stored by row 4342 4343 Level: intermediate 4344 4345 Notes: 4346 The matrix must have been obtained with `MatCreateMPIAIJWithArrays()` or `MatMPIAIJSetPreallocationCSR()` 4347 4348 The column indices in the call to `MatCreateMPIAIJWithArrays()` or `MatMPIAIJSetPreallocationCSR()` must have been sorted for this call to work correctly 4349 4350 .seealso: [](ch_matrices), `Mat`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 4351 `MATMPIAIJ`, `MatCreateAIJ()`, `MatCreateMPIAIJWithSplitArrays()`, `MatUpdateMPIAIJWithArrays()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4352 @*/ 4353 PetscErrorCode MatUpdateMPIAIJWithArray(Mat mat, const PetscScalar v[]) 4354 { 4355 PetscInt nnz, i, m; 4356 PetscBool nooffprocentries; 4357 Mat_MPIAIJ *Aij = (Mat_MPIAIJ *)mat->data; 4358 Mat_SeqAIJ *Ad = (Mat_SeqAIJ *)Aij->A->data; 4359 Mat_SeqAIJ *Ao = (Mat_SeqAIJ *)Aij->B->data; 4360 PetscScalar *ad, *ao; 4361 const PetscInt *Adi = Ad->i, *Adj = Ao->i; 4362 PetscInt ldi, Iii, md; 4363 PetscInt *ld = Aij->ld; 4364 4365 PetscFunctionBegin; 4366 m = mat->rmap->n; 4367 4368 PetscCall(MatSeqAIJGetArrayWrite(Aij->A, &ad)); 4369 PetscCall(MatSeqAIJGetArrayWrite(Aij->B, &ao)); 4370 Iii = 0; 4371 for (i = 0; i < m; i++) { 4372 nnz = Adi[i + 1] - Adi[i] + Adj[i + 1] - Adj[i]; 4373 ldi = ld[i]; 4374 md = Adi[i + 1] - Adi[i]; 4375 PetscCall(PetscArraycpy(ad, v + Iii + ldi, md)); 4376 ad += md; 4377 if (ao) { 4378 PetscCall(PetscArraycpy(ao, v + Iii, ldi)); 4379 PetscCall(PetscArraycpy(ao + ldi, v + Iii + ldi + md, nnz - ldi - md)); 4380 ao += nnz - md; 4381 } 4382 Iii += nnz; 4383 } 4384 nooffprocentries = mat->nooffprocentries; 4385 mat->nooffprocentries = PETSC_TRUE; 4386 PetscCall(MatSeqAIJRestoreArrayWrite(Aij->A, &ad)); 4387 PetscCall(MatSeqAIJRestoreArrayWrite(Aij->B, &ao)); 4388 PetscCall(PetscObjectStateIncrease((PetscObject)Aij->A)); 4389 PetscCall(PetscObjectStateIncrease((PetscObject)Aij->B)); 4390 PetscCall(PetscObjectStateIncrease((PetscObject)mat)); 4391 PetscCall(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY)); 4392 PetscCall(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY)); 4393 mat->nooffprocentries = nooffprocentries; 4394 PetscFunctionReturn(PETSC_SUCCESS); 4395 } 4396 4397 /*@ 4398 MatCreateAIJ - Creates a sparse parallel matrix in `MATAIJ` format 4399 (the default parallel PETSc format). For good matrix assembly performance 4400 the user should preallocate the matrix storage by setting the parameters 4401 `d_nz` (or `d_nnz`) and `o_nz` (or `o_nnz`). 4402 4403 Collective 4404 4405 Input Parameters: 4406 + comm - MPI communicator 4407 . m - number of local rows (or `PETSC_DECIDE` to have calculated if M is given) 4408 This value should be the same as the local size used in creating the 4409 y vector for the matrix-vector product y = Ax. 4410 . n - This value should be the same as the local size used in creating the 4411 x vector for the matrix-vector product y = Ax. (or `PETSC_DECIDE` to have 4412 calculated if N is given) For square matrices n is almost always m. 4413 . M - number of global rows (or `PETSC_DETERMINE` to have calculated if m is given) 4414 . N - number of global columns (or `PETSC_DETERMINE` to have calculated if n is given) 4415 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4416 (same value is used for all local rows) 4417 . d_nnz - array containing the number of nonzeros in the various rows of the 4418 DIAGONAL portion of the local submatrix (possibly different for each row) 4419 or `NULL`, if `d_nz` is used to specify the nonzero structure. 4420 The size of this array is equal to the number of local rows, i.e 'm'. 4421 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4422 submatrix (same value is used for all local rows). 4423 - o_nnz - array containing the number of nonzeros in the various rows of the 4424 OFF-DIAGONAL portion of the local submatrix (possibly different for 4425 each row) or `NULL`, if `o_nz` is used to specify the nonzero 4426 structure. The size of this array is equal to the number 4427 of local rows, i.e 'm'. 4428 4429 Output Parameter: 4430 . A - the matrix 4431 4432 Options Database Keys: 4433 + -mat_no_inode - Do not use inodes 4434 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4435 - -matmult_vecscatter_view <viewer> - View the vecscatter (i.e., communication pattern) used in `MatMult()` of sparse parallel matrices. 4436 See viewer types in manual of `MatView()`. Of them, ascii_matlab, draw or binary cause the `VecScatter` 4437 to be viewed as a matrix. Entry (i,j) is the size of message (in bytes) rank i sends to rank j in one `MatMult()` call. 4438 4439 Level: intermediate 4440 4441 Notes: 4442 It is recommended that one use `MatCreateFromOptions()` or the `MatCreate()`, `MatSetType()` and/or `MatSetFromOptions()`, 4443 MatXXXXSetPreallocation() paradigm instead of this routine directly. 4444 [MatXXXXSetPreallocation() is, for example, `MatSeqAIJSetPreallocation()`] 4445 4446 If the *_nnz parameter is given then the *_nz parameter is ignored 4447 4448 The `m`,`n`,`M`,`N` parameters specify the size of the matrix, and its partitioning across 4449 processors, while `d_nz`,`d_nnz`,`o_nz`,`o_nnz` parameters specify the approximate 4450 storage requirements for this matrix. 4451 4452 If `PETSC_DECIDE` or `PETSC_DETERMINE` is used for a particular argument on one 4453 processor than it must be used on all processors that share the object for 4454 that argument. 4455 4456 If `m` and `n` are not `PETSC_DECIDE`, then the values determine the `PetscLayout` of the matrix and the ranges returned by 4457 `MatGetOwnershipRange()`, `MatGetOwnershipRanges()`, `MatGetOwnershipRangeColumn()`, and `MatGetOwnershipRangesColumn()`. 4458 4459 The user MUST specify either the local or global matrix dimensions 4460 (possibly both). 4461 4462 The parallel matrix is partitioned across processors such that the 4463 first `m0` rows belong to process 0, the next `m1` rows belong to 4464 process 1, the next `m2` rows belong to process 2, etc., where 4465 `m0`, `m1`, `m2`... are the input parameter `m` on each MPI process. I.e., each MPI process stores 4466 values corresponding to [m x N] submatrix. 4467 4468 The columns are logically partitioned with the n0 columns belonging 4469 to 0th partition, the next n1 columns belonging to the next 4470 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4471 4472 The DIAGONAL portion of the local submatrix on any given processor 4473 is the submatrix corresponding to the rows and columns m,n 4474 corresponding to the given processor. i.e diagonal matrix on 4475 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4476 etc. The remaining portion of the local submatrix [m x (N-n)] 4477 constitute the OFF-DIAGONAL portion. The example below better 4478 illustrates this concept. The two matrices, the DIAGONAL portion and 4479 the OFF-DIAGONAL portion are each stored as `MATSEQAIJ` matrices. 4480 4481 For a square global matrix we define each processor's diagonal portion 4482 to be its local rows and the corresponding columns (a square submatrix); 4483 each processor's off-diagonal portion encompasses the remainder of the 4484 local matrix (a rectangular submatrix). 4485 4486 If `o_nnz`, `d_nnz` are specified, then `o_nz`, and `d_nz` are ignored. 4487 4488 When calling this routine with a single process communicator, a matrix of 4489 type `MATSEQAIJ` is returned. If a matrix of type `MATMPIAIJ` is desired for this 4490 type of communicator, use the construction mechanism 4491 .vb 4492 MatCreate(..., &A); 4493 MatSetType(A, MATMPIAIJ); 4494 MatSetSizes(A, m, n, M, N); 4495 MatMPIAIJSetPreallocation(A, ...); 4496 .ve 4497 4498 By default, this format uses inodes (identical nodes) when possible. 4499 We search for consecutive rows with the same nonzero structure, thereby 4500 reusing matrix information to achieve increased efficiency. 4501 4502 Example Usage: 4503 Consider the following 8x8 matrix with 34 non-zero values, that is 4504 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4505 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4506 as follows 4507 4508 .vb 4509 1 2 0 | 0 3 0 | 0 4 4510 Proc0 0 5 6 | 7 0 0 | 8 0 4511 9 0 10 | 11 0 0 | 12 0 4512 ------------------------------------- 4513 13 0 14 | 15 16 17 | 0 0 4514 Proc1 0 18 0 | 19 20 21 | 0 0 4515 0 0 0 | 22 23 0 | 24 0 4516 ------------------------------------- 4517 Proc2 25 26 27 | 0 0 28 | 29 0 4518 30 0 0 | 31 32 33 | 0 34 4519 .ve 4520 4521 This can be represented as a collection of submatrices as 4522 4523 .vb 4524 A B C 4525 D E F 4526 G H I 4527 .ve 4528 4529 Where the submatrices A,B,C are owned by proc0, D,E,F are 4530 owned by proc1, G,H,I are owned by proc2. 4531 4532 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4533 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4534 The 'M','N' parameters are 8,8, and have the same values on all procs. 4535 4536 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4537 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4538 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4539 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4540 part as `MATSEQAIJ` matrices. For example, proc1 will store [E] as a `MATSEQAIJ` 4541 matrix, and [DF] as another SeqAIJ matrix. 4542 4543 When `d_nz`, `o_nz` parameters are specified, `d_nz` storage elements are 4544 allocated for every row of the local DIAGONAL submatrix, and `o_nz` 4545 storage locations are allocated for every row of the OFF-DIAGONAL submatrix. 4546 One way to choose `d_nz` and `o_nz` is to use the maximum number of nonzeros over 4547 the local rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4548 In this case, the values of `d_nz`,`o_nz` are 4549 .vb 4550 proc0 dnz = 2, o_nz = 2 4551 proc1 dnz = 3, o_nz = 2 4552 proc2 dnz = 1, o_nz = 4 4553 .ve 4554 We are allocating m*(`d_nz`+`o_nz`) storage locations for every proc. This 4555 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4556 for proc3. i.e we are using 12+15+10=37 storage locations to store 4557 34 values. 4558 4559 When `d_nnz`, `o_nnz` parameters are specified, the storage is specified 4560 for every row, corresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4561 In the above case the values for d_nnz,o_nnz are 4562 .vb 4563 proc0 d_nnz = [2,2,2] and o_nnz = [2,2,2] 4564 proc1 d_nnz = [3,3,2] and o_nnz = [2,1,1] 4565 proc2 d_nnz = [1,1] and o_nnz = [4,4] 4566 .ve 4567 Here the space allocated is sum of all the above values i.e 34, and 4568 hence pre-allocation is perfect. 4569 4570 .seealso: [](ch_matrices), `Mat`, [Sparse Matrix Creation](sec_matsparse), `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 4571 `MATMPIAIJ`, `MatCreateMPIAIJWithArrays()`, `MatGetOwnershipRange()`, `MatGetOwnershipRanges()`, `MatGetOwnershipRangeColumn()`, 4572 `MatGetOwnershipRangesColumn()`, `PetscLayout` 4573 @*/ 4574 PetscErrorCode MatCreateAIJ(MPI_Comm comm, PetscInt m, PetscInt n, PetscInt M, PetscInt N, PetscInt d_nz, const PetscInt d_nnz[], PetscInt o_nz, const PetscInt o_nnz[], Mat *A) 4575 { 4576 PetscMPIInt size; 4577 4578 PetscFunctionBegin; 4579 PetscCall(MatCreate(comm, A)); 4580 PetscCall(MatSetSizes(*A, m, n, M, N)); 4581 PetscCallMPI(MPI_Comm_size(comm, &size)); 4582 if (size > 1) { 4583 PetscCall(MatSetType(*A, MATMPIAIJ)); 4584 PetscCall(MatMPIAIJSetPreallocation(*A, d_nz, d_nnz, o_nz, o_nnz)); 4585 } else { 4586 PetscCall(MatSetType(*A, MATSEQAIJ)); 4587 PetscCall(MatSeqAIJSetPreallocation(*A, d_nz, d_nnz)); 4588 } 4589 PetscFunctionReturn(PETSC_SUCCESS); 4590 } 4591 4592 /*@C 4593 MatMPIAIJGetSeqAIJ - Returns the local pieces of this distributed matrix 4594 4595 Not Collective 4596 4597 Input Parameter: 4598 . A - The `MATMPIAIJ` matrix 4599 4600 Output Parameters: 4601 + Ad - The local diagonal block as a `MATSEQAIJ` matrix 4602 . Ao - The local off-diagonal block as a `MATSEQAIJ` matrix 4603 - colmap - An array mapping local column numbers of `Ao` to global column numbers of the parallel matrix 4604 4605 Level: intermediate 4606 4607 Note: 4608 The rows in `Ad` and `Ao` are in [0, Nr), where Nr is the number of local rows on this process. The columns 4609 in `Ad` are in [0, Nc) where Nc is the number of local columns. The columns are `Ao` are in [0, Nco), where Nco is 4610 the number of nonzero columns in the local off-diagonal piece of the matrix `A`. The array colmap maps these 4611 local column numbers to global column numbers in the original matrix. 4612 4613 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatMPIAIJGetLocalMat()`, `MatMPIAIJGetLocalMatCondensed()`, `MatCreateAIJ()`, `MATSEQAIJ` 4614 @*/ 4615 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A, Mat *Ad, Mat *Ao, const PetscInt *colmap[]) 4616 { 4617 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 4618 PetscBool flg; 4619 4620 PetscFunctionBegin; 4621 PetscCall(PetscStrbeginswith(((PetscObject)A)->type_name, MATMPIAIJ, &flg)); 4622 PetscCheck(flg, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "This function requires a MATMPIAIJ matrix as input"); 4623 if (Ad) *Ad = a->A; 4624 if (Ao) *Ao = a->B; 4625 if (colmap) *colmap = a->garray; 4626 PetscFunctionReturn(PETSC_SUCCESS); 4627 } 4628 4629 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm, Mat inmat, PetscInt n, MatReuse scall, Mat *outmat) 4630 { 4631 PetscInt m, N, i, rstart, nnz, Ii; 4632 PetscInt *indx; 4633 PetscScalar *values; 4634 MatType rootType; 4635 4636 PetscFunctionBegin; 4637 PetscCall(MatGetSize(inmat, &m, &N)); 4638 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4639 PetscInt *dnz, *onz, sum, bs, cbs; 4640 4641 if (n == PETSC_DECIDE) PetscCall(PetscSplitOwnership(comm, &n, &N)); 4642 /* Check sum(n) = N */ 4643 PetscCallMPI(MPIU_Allreduce(&n, &sum, 1, MPIU_INT, MPI_SUM, comm)); 4644 PetscCheck(sum == N, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Sum of local columns %" PetscInt_FMT " != global columns %" PetscInt_FMT, sum, N); 4645 4646 PetscCallMPI(MPI_Scan(&m, &rstart, 1, MPIU_INT, MPI_SUM, comm)); 4647 rstart -= m; 4648 4649 MatPreallocateBegin(comm, m, n, dnz, onz); 4650 for (i = 0; i < m; i++) { 4651 PetscCall(MatGetRow_SeqAIJ(inmat, i, &nnz, &indx, NULL)); 4652 PetscCall(MatPreallocateSet(i + rstart, nnz, indx, dnz, onz)); 4653 PetscCall(MatRestoreRow_SeqAIJ(inmat, i, &nnz, &indx, NULL)); 4654 } 4655 4656 PetscCall(MatCreate(comm, outmat)); 4657 PetscCall(MatSetSizes(*outmat, m, n, PETSC_DETERMINE, PETSC_DETERMINE)); 4658 PetscCall(MatGetBlockSizes(inmat, &bs, &cbs)); 4659 PetscCall(MatSetBlockSizes(*outmat, bs, cbs)); 4660 PetscCall(MatGetRootType_Private(inmat, &rootType)); 4661 PetscCall(MatSetType(*outmat, rootType)); 4662 PetscCall(MatSeqAIJSetPreallocation(*outmat, 0, dnz)); 4663 PetscCall(MatMPIAIJSetPreallocation(*outmat, 0, dnz, 0, onz)); 4664 MatPreallocateEnd(dnz, onz); 4665 PetscCall(MatSetOption(*outmat, MAT_NO_OFF_PROC_ENTRIES, PETSC_TRUE)); 4666 } 4667 4668 /* numeric phase */ 4669 PetscCall(MatGetOwnershipRange(*outmat, &rstart, NULL)); 4670 for (i = 0; i < m; i++) { 4671 PetscCall(MatGetRow_SeqAIJ(inmat, i, &nnz, &indx, &values)); 4672 Ii = i + rstart; 4673 PetscCall(MatSetValues(*outmat, 1, &Ii, nnz, indx, values, INSERT_VALUES)); 4674 PetscCall(MatRestoreRow_SeqAIJ(inmat, i, &nnz, &indx, &values)); 4675 } 4676 PetscCall(MatAssemblyBegin(*outmat, MAT_FINAL_ASSEMBLY)); 4677 PetscCall(MatAssemblyEnd(*outmat, MAT_FINAL_ASSEMBLY)); 4678 PetscFunctionReturn(PETSC_SUCCESS); 4679 } 4680 4681 static PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(void **data) 4682 { 4683 Mat_Merge_SeqsToMPI *merge = (Mat_Merge_SeqsToMPI *)*data; 4684 4685 PetscFunctionBegin; 4686 if (!merge) PetscFunctionReturn(PETSC_SUCCESS); 4687 PetscCall(PetscFree(merge->id_r)); 4688 PetscCall(PetscFree(merge->len_s)); 4689 PetscCall(PetscFree(merge->len_r)); 4690 PetscCall(PetscFree(merge->bi)); 4691 PetscCall(PetscFree(merge->bj)); 4692 PetscCall(PetscFree(merge->buf_ri[0])); 4693 PetscCall(PetscFree(merge->buf_ri)); 4694 PetscCall(PetscFree(merge->buf_rj[0])); 4695 PetscCall(PetscFree(merge->buf_rj)); 4696 PetscCall(PetscFree(merge->coi)); 4697 PetscCall(PetscFree(merge->coj)); 4698 PetscCall(PetscFree(merge->owners_co)); 4699 PetscCall(PetscLayoutDestroy(&merge->rowmap)); 4700 PetscCall(PetscFree(merge)); 4701 PetscFunctionReturn(PETSC_SUCCESS); 4702 } 4703 4704 #include <../src/mat/utils/freespace.h> 4705 #include <petscbt.h> 4706 4707 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat, Mat mpimat) 4708 { 4709 MPI_Comm comm; 4710 Mat_SeqAIJ *a = (Mat_SeqAIJ *)seqmat->data; 4711 PetscMPIInt size, rank, taga, *len_s; 4712 PetscInt N = mpimat->cmap->N, i, j, *owners, *ai = a->i, *aj, m; 4713 PetscMPIInt proc, k; 4714 PetscInt **buf_ri, **buf_rj; 4715 PetscInt anzi, *bj_i, *bi, *bj, arow, bnzi, nextaj; 4716 PetscInt nrows, **buf_ri_k, **nextrow, **nextai; 4717 MPI_Request *s_waits, *r_waits; 4718 MPI_Status *status; 4719 const MatScalar *aa, *a_a; 4720 MatScalar **abuf_r, *ba_i; 4721 Mat_Merge_SeqsToMPI *merge; 4722 PetscContainer container; 4723 4724 PetscFunctionBegin; 4725 PetscCall(PetscObjectGetComm((PetscObject)mpimat, &comm)); 4726 PetscCall(PetscLogEventBegin(MAT_Seqstompinum, seqmat, 0, 0, 0)); 4727 4728 PetscCallMPI(MPI_Comm_size(comm, &size)); 4729 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 4730 4731 PetscCall(PetscObjectQuery((PetscObject)mpimat, "MatMergeSeqsToMPI", (PetscObject *)&container)); 4732 PetscCheck(container, PetscObjectComm((PetscObject)mpimat), PETSC_ERR_PLIB, "Mat not created from MatCreateMPIAIJSumSeqAIJSymbolic"); 4733 PetscCall(PetscContainerGetPointer(container, (void **)&merge)); 4734 PetscCall(MatSeqAIJGetArrayRead(seqmat, &a_a)); 4735 aa = a_a; 4736 4737 bi = merge->bi; 4738 bj = merge->bj; 4739 buf_ri = merge->buf_ri; 4740 buf_rj = merge->buf_rj; 4741 4742 PetscCall(PetscMalloc1(size, &status)); 4743 owners = merge->rowmap->range; 4744 len_s = merge->len_s; 4745 4746 /* send and recv matrix values */ 4747 PetscCall(PetscObjectGetNewTag((PetscObject)mpimat, &taga)); 4748 PetscCall(PetscPostIrecvScalar(comm, taga, merge->nrecv, merge->id_r, merge->len_r, &abuf_r, &r_waits)); 4749 4750 PetscCall(PetscMalloc1(merge->nsend + 1, &s_waits)); 4751 for (proc = 0, k = 0; proc < size; proc++) { 4752 if (!len_s[proc]) continue; 4753 i = owners[proc]; 4754 PetscCallMPI(MPIU_Isend(aa + ai[i], len_s[proc], MPIU_MATSCALAR, proc, taga, comm, s_waits + k)); 4755 k++; 4756 } 4757 4758 if (merge->nrecv) PetscCallMPI(MPI_Waitall(merge->nrecv, r_waits, status)); 4759 if (merge->nsend) PetscCallMPI(MPI_Waitall(merge->nsend, s_waits, status)); 4760 PetscCall(PetscFree(status)); 4761 4762 PetscCall(PetscFree(s_waits)); 4763 PetscCall(PetscFree(r_waits)); 4764 4765 /* insert mat values of mpimat */ 4766 PetscCall(PetscMalloc1(N, &ba_i)); 4767 PetscCall(PetscMalloc3(merge->nrecv, &buf_ri_k, merge->nrecv, &nextrow, merge->nrecv, &nextai)); 4768 4769 for (k = 0; k < merge->nrecv; k++) { 4770 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4771 nrows = *buf_ri_k[k]; 4772 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4773 nextai[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recved i-structure */ 4774 } 4775 4776 /* set values of ba */ 4777 m = merge->rowmap->n; 4778 for (i = 0; i < m; i++) { 4779 arow = owners[rank] + i; 4780 bj_i = bj + bi[i]; /* col indices of the i-th row of mpimat */ 4781 bnzi = bi[i + 1] - bi[i]; 4782 PetscCall(PetscArrayzero(ba_i, bnzi)); 4783 4784 /* add local non-zero vals of this proc's seqmat into ba */ 4785 anzi = ai[arow + 1] - ai[arow]; 4786 aj = a->j + ai[arow]; 4787 aa = a_a + ai[arow]; 4788 nextaj = 0; 4789 for (j = 0; nextaj < anzi; j++) { 4790 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4791 ba_i[j] += aa[nextaj++]; 4792 } 4793 } 4794 4795 /* add received vals into ba */ 4796 for (k = 0; k < merge->nrecv; k++) { /* k-th received message */ 4797 /* i-th row */ 4798 if (i == *nextrow[k]) { 4799 anzi = *(nextai[k] + 1) - *nextai[k]; 4800 aj = buf_rj[k] + *nextai[k]; 4801 aa = abuf_r[k] + *nextai[k]; 4802 nextaj = 0; 4803 for (j = 0; nextaj < anzi; j++) { 4804 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4805 ba_i[j] += aa[nextaj++]; 4806 } 4807 } 4808 nextrow[k]++; 4809 nextai[k]++; 4810 } 4811 } 4812 PetscCall(MatSetValues(mpimat, 1, &arow, bnzi, bj_i, ba_i, INSERT_VALUES)); 4813 } 4814 PetscCall(MatSeqAIJRestoreArrayRead(seqmat, &a_a)); 4815 PetscCall(MatAssemblyBegin(mpimat, MAT_FINAL_ASSEMBLY)); 4816 PetscCall(MatAssemblyEnd(mpimat, MAT_FINAL_ASSEMBLY)); 4817 4818 PetscCall(PetscFree(abuf_r[0])); 4819 PetscCall(PetscFree(abuf_r)); 4820 PetscCall(PetscFree(ba_i)); 4821 PetscCall(PetscFree3(buf_ri_k, nextrow, nextai)); 4822 PetscCall(PetscLogEventEnd(MAT_Seqstompinum, seqmat, 0, 0, 0)); 4823 PetscFunctionReturn(PETSC_SUCCESS); 4824 } 4825 4826 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm, Mat seqmat, PetscInt m, PetscInt n, Mat *mpimat) 4827 { 4828 Mat B_mpi; 4829 Mat_SeqAIJ *a = (Mat_SeqAIJ *)seqmat->data; 4830 PetscMPIInt size, rank, tagi, tagj, *len_s, *len_si, *len_ri; 4831 PetscInt **buf_rj, **buf_ri, **buf_ri_k; 4832 PetscInt M = seqmat->rmap->n, N = seqmat->cmap->n, i, *owners, *ai = a->i, *aj = a->j; 4833 PetscInt len, *dnz, *onz, bs, cbs; 4834 PetscInt k, anzi, *bi, *bj, *lnk, nlnk, arow, bnzi; 4835 PetscInt nrows, *buf_s, *buf_si, *buf_si_i, **nextrow, **nextai; 4836 MPI_Request *si_waits, *sj_waits, *ri_waits, *rj_waits; 4837 MPI_Status *status; 4838 PetscFreeSpaceList free_space = NULL, current_space = NULL; 4839 PetscBT lnkbt; 4840 Mat_Merge_SeqsToMPI *merge; 4841 PetscContainer container; 4842 4843 PetscFunctionBegin; 4844 PetscCall(PetscLogEventBegin(MAT_Seqstompisym, seqmat, 0, 0, 0)); 4845 4846 /* make sure it is a PETSc comm */ 4847 PetscCall(PetscCommDuplicate(comm, &comm, NULL)); 4848 PetscCallMPI(MPI_Comm_size(comm, &size)); 4849 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 4850 4851 PetscCall(PetscNew(&merge)); 4852 PetscCall(PetscMalloc1(size, &status)); 4853 4854 /* determine row ownership */ 4855 PetscCall(PetscLayoutCreate(comm, &merge->rowmap)); 4856 PetscCall(PetscLayoutSetLocalSize(merge->rowmap, m)); 4857 PetscCall(PetscLayoutSetSize(merge->rowmap, M)); 4858 PetscCall(PetscLayoutSetBlockSize(merge->rowmap, 1)); 4859 PetscCall(PetscLayoutSetUp(merge->rowmap)); 4860 PetscCall(PetscMalloc1(size, &len_si)); 4861 PetscCall(PetscMalloc1(size, &merge->len_s)); 4862 4863 m = merge->rowmap->n; 4864 owners = merge->rowmap->range; 4865 4866 /* determine the number of messages to send, their lengths */ 4867 len_s = merge->len_s; 4868 4869 len = 0; /* length of buf_si[] */ 4870 merge->nsend = 0; 4871 for (PetscMPIInt proc = 0; proc < size; proc++) { 4872 len_si[proc] = 0; 4873 if (proc == rank) { 4874 len_s[proc] = 0; 4875 } else { 4876 PetscCall(PetscMPIIntCast(owners[proc + 1] - owners[proc] + 1, &len_si[proc])); 4877 PetscCall(PetscMPIIntCast(ai[owners[proc + 1]] - ai[owners[proc]], &len_s[proc])); /* num of rows to be sent to [proc] */ 4878 } 4879 if (len_s[proc]) { 4880 merge->nsend++; 4881 nrows = 0; 4882 for (i = owners[proc]; i < owners[proc + 1]; i++) { 4883 if (ai[i + 1] > ai[i]) nrows++; 4884 } 4885 PetscCall(PetscMPIIntCast(2 * (nrows + 1), &len_si[proc])); 4886 len += len_si[proc]; 4887 } 4888 } 4889 4890 /* determine the number and length of messages to receive for ij-structure */ 4891 PetscCall(PetscGatherNumberOfMessages(comm, NULL, len_s, &merge->nrecv)); 4892 PetscCall(PetscGatherMessageLengths2(comm, merge->nsend, merge->nrecv, len_s, len_si, &merge->id_r, &merge->len_r, &len_ri)); 4893 4894 /* post the Irecv of j-structure */ 4895 PetscCall(PetscCommGetNewTag(comm, &tagj)); 4896 PetscCall(PetscPostIrecvInt(comm, tagj, merge->nrecv, merge->id_r, merge->len_r, &buf_rj, &rj_waits)); 4897 4898 /* post the Isend of j-structure */ 4899 PetscCall(PetscMalloc2(merge->nsend, &si_waits, merge->nsend, &sj_waits)); 4900 4901 for (PetscMPIInt proc = 0, k = 0; proc < size; proc++) { 4902 if (!len_s[proc]) continue; 4903 i = owners[proc]; 4904 PetscCallMPI(MPIU_Isend(aj + ai[i], len_s[proc], MPIU_INT, proc, tagj, comm, sj_waits + k)); 4905 k++; 4906 } 4907 4908 /* receives and sends of j-structure are complete */ 4909 if (merge->nrecv) PetscCallMPI(MPI_Waitall(merge->nrecv, rj_waits, status)); 4910 if (merge->nsend) PetscCallMPI(MPI_Waitall(merge->nsend, sj_waits, status)); 4911 4912 /* send and recv i-structure */ 4913 PetscCall(PetscCommGetNewTag(comm, &tagi)); 4914 PetscCall(PetscPostIrecvInt(comm, tagi, merge->nrecv, merge->id_r, len_ri, &buf_ri, &ri_waits)); 4915 4916 PetscCall(PetscMalloc1(len + 1, &buf_s)); 4917 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4918 for (PetscMPIInt proc = 0, k = 0; proc < size; proc++) { 4919 if (!len_s[proc]) continue; 4920 /* form outgoing message for i-structure: 4921 buf_si[0]: nrows to be sent 4922 [1:nrows]: row index (global) 4923 [nrows+1:2*nrows+1]: i-structure index 4924 */ 4925 nrows = len_si[proc] / 2 - 1; 4926 buf_si_i = buf_si + nrows + 1; 4927 buf_si[0] = nrows; 4928 buf_si_i[0] = 0; 4929 nrows = 0; 4930 for (i = owners[proc]; i < owners[proc + 1]; i++) { 4931 anzi = ai[i + 1] - ai[i]; 4932 if (anzi) { 4933 buf_si_i[nrows + 1] = buf_si_i[nrows] + anzi; /* i-structure */ 4934 buf_si[nrows + 1] = i - owners[proc]; /* local row index */ 4935 nrows++; 4936 } 4937 } 4938 PetscCallMPI(MPIU_Isend(buf_si, len_si[proc], MPIU_INT, proc, tagi, comm, si_waits + k)); 4939 k++; 4940 buf_si += len_si[proc]; 4941 } 4942 4943 if (merge->nrecv) PetscCallMPI(MPI_Waitall(merge->nrecv, ri_waits, status)); 4944 if (merge->nsend) PetscCallMPI(MPI_Waitall(merge->nsend, si_waits, status)); 4945 4946 PetscCall(PetscInfo(seqmat, "nsend: %d, nrecv: %d\n", merge->nsend, merge->nrecv)); 4947 for (i = 0; i < merge->nrecv; i++) PetscCall(PetscInfo(seqmat, "recv len_ri=%d, len_rj=%d from [%d]\n", len_ri[i], merge->len_r[i], merge->id_r[i])); 4948 4949 PetscCall(PetscFree(len_si)); 4950 PetscCall(PetscFree(len_ri)); 4951 PetscCall(PetscFree(rj_waits)); 4952 PetscCall(PetscFree2(si_waits, sj_waits)); 4953 PetscCall(PetscFree(ri_waits)); 4954 PetscCall(PetscFree(buf_s)); 4955 PetscCall(PetscFree(status)); 4956 4957 /* compute a local seq matrix in each processor */ 4958 /* allocate bi array and free space for accumulating nonzero column info */ 4959 PetscCall(PetscMalloc1(m + 1, &bi)); 4960 bi[0] = 0; 4961 4962 /* create and initialize a linked list */ 4963 nlnk = N + 1; 4964 PetscCall(PetscLLCreate(N, N, nlnk, lnk, lnkbt)); 4965 4966 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4967 len = ai[owners[rank + 1]] - ai[owners[rank]]; 4968 PetscCall(PetscFreeSpaceGet(PetscIntMultTruncate(2, len) + 1, &free_space)); 4969 4970 current_space = free_space; 4971 4972 /* determine symbolic info for each local row */ 4973 PetscCall(PetscMalloc3(merge->nrecv, &buf_ri_k, merge->nrecv, &nextrow, merge->nrecv, &nextai)); 4974 4975 for (k = 0; k < merge->nrecv; k++) { 4976 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4977 nrows = *buf_ri_k[k]; 4978 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4979 nextai[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recved i-structure */ 4980 } 4981 4982 MatPreallocateBegin(comm, m, n, dnz, onz); 4983 len = 0; 4984 for (i = 0; i < m; i++) { 4985 bnzi = 0; 4986 /* add local non-zero cols of this proc's seqmat into lnk */ 4987 arow = owners[rank] + i; 4988 anzi = ai[arow + 1] - ai[arow]; 4989 aj = a->j + ai[arow]; 4990 PetscCall(PetscLLAddSorted(anzi, aj, N, &nlnk, lnk, lnkbt)); 4991 bnzi += nlnk; 4992 /* add received col data into lnk */ 4993 for (k = 0; k < merge->nrecv; k++) { /* k-th received message */ 4994 if (i == *nextrow[k]) { /* i-th row */ 4995 anzi = *(nextai[k] + 1) - *nextai[k]; 4996 aj = buf_rj[k] + *nextai[k]; 4997 PetscCall(PetscLLAddSorted(anzi, aj, N, &nlnk, lnk, lnkbt)); 4998 bnzi += nlnk; 4999 nextrow[k]++; 5000 nextai[k]++; 5001 } 5002 } 5003 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 5004 5005 /* if free space is not available, make more free space */ 5006 if (current_space->local_remaining < bnzi) PetscCall(PetscFreeSpaceGet(PetscIntSumTruncate(bnzi, current_space->total_array_size), ¤t_space)); 5007 /* copy data into free space, then initialize lnk */ 5008 PetscCall(PetscLLClean(N, N, bnzi, lnk, current_space->array, lnkbt)); 5009 PetscCall(MatPreallocateSet(i + owners[rank], bnzi, current_space->array, dnz, onz)); 5010 5011 current_space->array += bnzi; 5012 current_space->local_used += bnzi; 5013 current_space->local_remaining -= bnzi; 5014 5015 bi[i + 1] = bi[i] + bnzi; 5016 } 5017 5018 PetscCall(PetscFree3(buf_ri_k, nextrow, nextai)); 5019 5020 PetscCall(PetscMalloc1(bi[m] + 1, &bj)); 5021 PetscCall(PetscFreeSpaceContiguous(&free_space, bj)); 5022 PetscCall(PetscLLDestroy(lnk, lnkbt)); 5023 5024 /* create symbolic parallel matrix B_mpi */ 5025 PetscCall(MatGetBlockSizes(seqmat, &bs, &cbs)); 5026 PetscCall(MatCreate(comm, &B_mpi)); 5027 if (n == PETSC_DECIDE) { 5028 PetscCall(MatSetSizes(B_mpi, m, n, PETSC_DETERMINE, N)); 5029 } else { 5030 PetscCall(MatSetSizes(B_mpi, m, n, PETSC_DETERMINE, PETSC_DETERMINE)); 5031 } 5032 PetscCall(MatSetBlockSizes(B_mpi, bs, cbs)); 5033 PetscCall(MatSetType(B_mpi, MATMPIAIJ)); 5034 PetscCall(MatMPIAIJSetPreallocation(B_mpi, 0, dnz, 0, onz)); 5035 MatPreallocateEnd(dnz, onz); 5036 PetscCall(MatSetOption(B_mpi, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE)); 5037 5038 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 5039 B_mpi->assembled = PETSC_FALSE; 5040 merge->bi = bi; 5041 merge->bj = bj; 5042 merge->buf_ri = buf_ri; 5043 merge->buf_rj = buf_rj; 5044 merge->coi = NULL; 5045 merge->coj = NULL; 5046 merge->owners_co = NULL; 5047 5048 PetscCall(PetscCommDestroy(&comm)); 5049 5050 /* attach the supporting struct to B_mpi for reuse */ 5051 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container)); 5052 PetscCall(PetscContainerSetPointer(container, merge)); 5053 PetscCall(PetscContainerSetCtxDestroy(container, MatDestroy_MPIAIJ_SeqsToMPI)); 5054 PetscCall(PetscObjectCompose((PetscObject)B_mpi, "MatMergeSeqsToMPI", (PetscObject)container)); 5055 PetscCall(PetscContainerDestroy(&container)); 5056 *mpimat = B_mpi; 5057 5058 PetscCall(PetscLogEventEnd(MAT_Seqstompisym, seqmat, 0, 0, 0)); 5059 PetscFunctionReturn(PETSC_SUCCESS); 5060 } 5061 5062 /*@ 5063 MatCreateMPIAIJSumSeqAIJ - Creates a `MATMPIAIJ` matrix by adding sequential 5064 matrices from each processor 5065 5066 Collective 5067 5068 Input Parameters: 5069 + comm - the communicators the parallel matrix will live on 5070 . seqmat - the input sequential matrices 5071 . m - number of local rows (or `PETSC_DECIDE`) 5072 . n - number of local columns (or `PETSC_DECIDE`) 5073 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5074 5075 Output Parameter: 5076 . mpimat - the parallel matrix generated 5077 5078 Level: advanced 5079 5080 Note: 5081 The dimensions of the sequential matrix in each processor MUST be the same. 5082 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 5083 destroyed when `mpimat` is destroyed. Call `PetscObjectQuery()` to access `seqmat`. 5084 5085 .seealso: [](ch_matrices), `Mat`, `MatCreateAIJ()` 5086 @*/ 5087 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm, Mat seqmat, PetscInt m, PetscInt n, MatReuse scall, Mat *mpimat) 5088 { 5089 PetscMPIInt size; 5090 5091 PetscFunctionBegin; 5092 PetscCallMPI(MPI_Comm_size(comm, &size)); 5093 if (size == 1) { 5094 PetscCall(PetscLogEventBegin(MAT_Seqstompi, seqmat, 0, 0, 0)); 5095 if (scall == MAT_INITIAL_MATRIX) { 5096 PetscCall(MatDuplicate(seqmat, MAT_COPY_VALUES, mpimat)); 5097 } else { 5098 PetscCall(MatCopy(seqmat, *mpimat, SAME_NONZERO_PATTERN)); 5099 } 5100 PetscCall(PetscLogEventEnd(MAT_Seqstompi, seqmat, 0, 0, 0)); 5101 PetscFunctionReturn(PETSC_SUCCESS); 5102 } 5103 PetscCall(PetscLogEventBegin(MAT_Seqstompi, seqmat, 0, 0, 0)); 5104 if (scall == MAT_INITIAL_MATRIX) PetscCall(MatCreateMPIAIJSumSeqAIJSymbolic(comm, seqmat, m, n, mpimat)); 5105 PetscCall(MatCreateMPIAIJSumSeqAIJNumeric(seqmat, *mpimat)); 5106 PetscCall(PetscLogEventEnd(MAT_Seqstompi, seqmat, 0, 0, 0)); 5107 PetscFunctionReturn(PETSC_SUCCESS); 5108 } 5109 5110 /*@ 5111 MatAIJGetLocalMat - Creates a `MATSEQAIJ` from a `MATAIJ` matrix. 5112 5113 Not Collective 5114 5115 Input Parameter: 5116 . A - the matrix 5117 5118 Output Parameter: 5119 . A_loc - the local sequential matrix generated 5120 5121 Level: developer 5122 5123 Notes: 5124 The matrix is created by taking `A`'s local rows and putting them into a sequential matrix 5125 with `mlocal` rows and `n` columns. Where `mlocal` is obtained with `MatGetLocalSize()` and 5126 `n` is the global column count obtained with `MatGetSize()` 5127 5128 In other words combines the two parts of a parallel `MATMPIAIJ` matrix on each process to a single matrix. 5129 5130 For parallel matrices this creates an entirely new matrix. If the matrix is sequential it merely increases the reference count. 5131 5132 Destroy the matrix with `MatDestroy()` 5133 5134 .seealso: [](ch_matrices), `Mat`, `MatMPIAIJGetLocalMat()` 5135 @*/ 5136 PetscErrorCode MatAIJGetLocalMat(Mat A, Mat *A_loc) 5137 { 5138 PetscBool mpi; 5139 5140 PetscFunctionBegin; 5141 PetscCall(PetscObjectTypeCompare((PetscObject)A, MATMPIAIJ, &mpi)); 5142 if (mpi) { 5143 PetscCall(MatMPIAIJGetLocalMat(A, MAT_INITIAL_MATRIX, A_loc)); 5144 } else { 5145 *A_loc = A; 5146 PetscCall(PetscObjectReference((PetscObject)*A_loc)); 5147 } 5148 PetscFunctionReturn(PETSC_SUCCESS); 5149 } 5150 5151 /*@ 5152 MatMPIAIJGetLocalMat - Creates a `MATSEQAIJ` from a `MATMPIAIJ` matrix. 5153 5154 Not Collective 5155 5156 Input Parameters: 5157 + A - the matrix 5158 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5159 5160 Output Parameter: 5161 . A_loc - the local sequential matrix generated 5162 5163 Level: developer 5164 5165 Notes: 5166 The matrix is created by taking all `A`'s local rows and putting them into a sequential 5167 matrix with `mlocal` rows and `n` columns.`mlocal` is the row count obtained with 5168 `MatGetLocalSize()` and `n` is the global column count obtained with `MatGetSize()`. 5169 5170 In other words combines the two parts of a parallel `MATMPIAIJ` matrix on each process to a single matrix. 5171 5172 When `A` is sequential and `MAT_INITIAL_MATRIX` is requested, the matrix returned is the diagonal part of `A` (which contains the entire matrix), 5173 with its reference count increased by one. Hence changing values of `A_loc` changes `A`. If `MAT_REUSE_MATRIX` is requested on a sequential matrix 5174 then `MatCopy`(Adiag,*`A_loc`,`SAME_NONZERO_PATTERN`) is called to fill `A_loc`. Thus one can preallocate the appropriate sequential matrix `A_loc` 5175 and then call this routine with `MAT_REUSE_MATRIX`. In this case, one can modify the values of `A_loc` without affecting the original sequential matrix. 5176 5177 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatGetOwnershipRange()`, `MatMPIAIJGetLocalMatCondensed()`, `MatMPIAIJGetLocalMatMerge()` 5178 @*/ 5179 PetscErrorCode MatMPIAIJGetLocalMat(Mat A, MatReuse scall, Mat *A_loc) 5180 { 5181 Mat_MPIAIJ *mpimat = (Mat_MPIAIJ *)A->data; 5182 Mat_SeqAIJ *mat, *a, *b; 5183 PetscInt *ai, *aj, *bi, *bj, *cmap = mpimat->garray; 5184 const PetscScalar *aa, *ba, *aav, *bav; 5185 PetscScalar *ca, *cam; 5186 PetscMPIInt size; 5187 PetscInt am = A->rmap->n, i, j, k, cstart = A->cmap->rstart; 5188 PetscInt *ci, *cj, col, ncols_d, ncols_o, jo; 5189 PetscBool match; 5190 5191 PetscFunctionBegin; 5192 PetscCall(PetscStrbeginswith(((PetscObject)A)->type_name, MATMPIAIJ, &match)); 5193 PetscCheck(match, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Requires MATMPIAIJ matrix as input"); 5194 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)A), &size)); 5195 if (size == 1) { 5196 if (scall == MAT_INITIAL_MATRIX) { 5197 PetscCall(PetscObjectReference((PetscObject)mpimat->A)); 5198 *A_loc = mpimat->A; 5199 } else if (scall == MAT_REUSE_MATRIX) { 5200 PetscCall(MatCopy(mpimat->A, *A_loc, SAME_NONZERO_PATTERN)); 5201 } 5202 PetscFunctionReturn(PETSC_SUCCESS); 5203 } 5204 5205 PetscCall(PetscLogEventBegin(MAT_Getlocalmat, A, 0, 0, 0)); 5206 a = (Mat_SeqAIJ *)mpimat->A->data; 5207 b = (Mat_SeqAIJ *)mpimat->B->data; 5208 ai = a->i; 5209 aj = a->j; 5210 bi = b->i; 5211 bj = b->j; 5212 PetscCall(MatSeqAIJGetArrayRead(mpimat->A, &aav)); 5213 PetscCall(MatSeqAIJGetArrayRead(mpimat->B, &bav)); 5214 aa = aav; 5215 ba = bav; 5216 if (scall == MAT_INITIAL_MATRIX) { 5217 PetscCall(PetscMalloc1(1 + am, &ci)); 5218 ci[0] = 0; 5219 for (i = 0; i < am; i++) ci[i + 1] = ci[i] + (ai[i + 1] - ai[i]) + (bi[i + 1] - bi[i]); 5220 PetscCall(PetscMalloc1(1 + ci[am], &cj)); 5221 PetscCall(PetscMalloc1(1 + ci[am], &ca)); 5222 k = 0; 5223 for (i = 0; i < am; i++) { 5224 ncols_o = bi[i + 1] - bi[i]; 5225 ncols_d = ai[i + 1] - ai[i]; 5226 /* off-diagonal portion of A */ 5227 for (jo = 0; jo < ncols_o; jo++) { 5228 col = cmap[*bj]; 5229 if (col >= cstart) break; 5230 cj[k] = col; 5231 bj++; 5232 ca[k++] = *ba++; 5233 } 5234 /* diagonal portion of A */ 5235 for (j = 0; j < ncols_d; j++) { 5236 cj[k] = cstart + *aj++; 5237 ca[k++] = *aa++; 5238 } 5239 /* off-diagonal portion of A */ 5240 for (j = jo; j < ncols_o; j++) { 5241 cj[k] = cmap[*bj++]; 5242 ca[k++] = *ba++; 5243 } 5244 } 5245 /* put together the new matrix */ 5246 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, am, A->cmap->N, ci, cj, ca, A_loc)); 5247 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5248 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5249 mat = (Mat_SeqAIJ *)(*A_loc)->data; 5250 mat->free_a = PETSC_TRUE; 5251 mat->free_ij = PETSC_TRUE; 5252 mat->nonew = 0; 5253 } else if (scall == MAT_REUSE_MATRIX) { 5254 mat = (Mat_SeqAIJ *)(*A_loc)->data; 5255 ci = mat->i; 5256 cj = mat->j; 5257 PetscCall(MatSeqAIJGetArrayWrite(*A_loc, &cam)); 5258 for (i = 0; i < am; i++) { 5259 /* off-diagonal portion of A */ 5260 ncols_o = bi[i + 1] - bi[i]; 5261 for (jo = 0; jo < ncols_o; jo++) { 5262 col = cmap[*bj]; 5263 if (col >= cstart) break; 5264 *cam++ = *ba++; 5265 bj++; 5266 } 5267 /* diagonal portion of A */ 5268 ncols_d = ai[i + 1] - ai[i]; 5269 for (j = 0; j < ncols_d; j++) *cam++ = *aa++; 5270 /* off-diagonal portion of A */ 5271 for (j = jo; j < ncols_o; j++) { 5272 *cam++ = *ba++; 5273 bj++; 5274 } 5275 } 5276 PetscCall(MatSeqAIJRestoreArrayWrite(*A_loc, &cam)); 5277 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid MatReuse %d", (int)scall); 5278 PetscCall(MatSeqAIJRestoreArrayRead(mpimat->A, &aav)); 5279 PetscCall(MatSeqAIJRestoreArrayRead(mpimat->B, &bav)); 5280 PetscCall(PetscLogEventEnd(MAT_Getlocalmat, A, 0, 0, 0)); 5281 PetscFunctionReturn(PETSC_SUCCESS); 5282 } 5283 5284 /*@ 5285 MatMPIAIJGetLocalMatMerge - Creates a `MATSEQAIJ` from a `MATMPIAIJ` matrix by taking all its local rows and putting them into a sequential matrix with 5286 mlocal rows and n columns. Where n is the sum of the number of columns of the diagonal and off-diagonal part 5287 5288 Not Collective 5289 5290 Input Parameters: 5291 + A - the matrix 5292 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5293 5294 Output Parameters: 5295 + glob - sequential `IS` with global indices associated with the columns of the local sequential matrix generated (can be `NULL`) 5296 - A_loc - the local sequential matrix generated 5297 5298 Level: developer 5299 5300 Note: 5301 This is different from `MatMPIAIJGetLocalMat()` since the first columns in the returning matrix are those associated with the diagonal 5302 part, then those associated with the off-diagonal part (in its local ordering) 5303 5304 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatGetOwnershipRange()`, `MatMPIAIJGetLocalMat()`, `MatMPIAIJGetLocalMatCondensed()` 5305 @*/ 5306 PetscErrorCode MatMPIAIJGetLocalMatMerge(Mat A, MatReuse scall, IS *glob, Mat *A_loc) 5307 { 5308 Mat Ao, Ad; 5309 const PetscInt *cmap; 5310 PetscMPIInt size; 5311 PetscErrorCode (*f)(Mat, MatReuse, IS *, Mat *); 5312 5313 PetscFunctionBegin; 5314 PetscCall(MatMPIAIJGetSeqAIJ(A, &Ad, &Ao, &cmap)); 5315 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)A), &size)); 5316 if (size == 1) { 5317 if (scall == MAT_INITIAL_MATRIX) { 5318 PetscCall(PetscObjectReference((PetscObject)Ad)); 5319 *A_loc = Ad; 5320 } else if (scall == MAT_REUSE_MATRIX) { 5321 PetscCall(MatCopy(Ad, *A_loc, SAME_NONZERO_PATTERN)); 5322 } 5323 if (glob) PetscCall(ISCreateStride(PetscObjectComm((PetscObject)Ad), Ad->cmap->n, Ad->cmap->rstart, 1, glob)); 5324 PetscFunctionReturn(PETSC_SUCCESS); 5325 } 5326 PetscCall(PetscObjectQueryFunction((PetscObject)A, "MatMPIAIJGetLocalMatMerge_C", &f)); 5327 PetscCall(PetscLogEventBegin(MAT_Getlocalmat, A, 0, 0, 0)); 5328 if (f) { 5329 PetscCall((*f)(A, scall, glob, A_loc)); 5330 } else { 5331 Mat_SeqAIJ *a = (Mat_SeqAIJ *)Ad->data; 5332 Mat_SeqAIJ *b = (Mat_SeqAIJ *)Ao->data; 5333 Mat_SeqAIJ *c; 5334 PetscInt *ai = a->i, *aj = a->j; 5335 PetscInt *bi = b->i, *bj = b->j; 5336 PetscInt *ci, *cj; 5337 const PetscScalar *aa, *ba; 5338 PetscScalar *ca; 5339 PetscInt i, j, am, dn, on; 5340 5341 PetscCall(MatGetLocalSize(Ad, &am, &dn)); 5342 PetscCall(MatGetLocalSize(Ao, NULL, &on)); 5343 PetscCall(MatSeqAIJGetArrayRead(Ad, &aa)); 5344 PetscCall(MatSeqAIJGetArrayRead(Ao, &ba)); 5345 if (scall == MAT_INITIAL_MATRIX) { 5346 PetscInt k; 5347 PetscCall(PetscMalloc1(1 + am, &ci)); 5348 PetscCall(PetscMalloc1(ai[am] + bi[am], &cj)); 5349 PetscCall(PetscMalloc1(ai[am] + bi[am], &ca)); 5350 ci[0] = 0; 5351 for (i = 0, k = 0; i < am; i++) { 5352 const PetscInt ncols_o = bi[i + 1] - bi[i]; 5353 const PetscInt ncols_d = ai[i + 1] - ai[i]; 5354 ci[i + 1] = ci[i] + ncols_o + ncols_d; 5355 /* diagonal portion of A */ 5356 for (j = 0; j < ncols_d; j++, k++) { 5357 cj[k] = *aj++; 5358 ca[k] = *aa++; 5359 } 5360 /* off-diagonal portion of A */ 5361 for (j = 0; j < ncols_o; j++, k++) { 5362 cj[k] = dn + *bj++; 5363 ca[k] = *ba++; 5364 } 5365 } 5366 /* put together the new matrix */ 5367 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, am, dn + on, ci, cj, ca, A_loc)); 5368 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5369 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5370 c = (Mat_SeqAIJ *)(*A_loc)->data; 5371 c->free_a = PETSC_TRUE; 5372 c->free_ij = PETSC_TRUE; 5373 c->nonew = 0; 5374 PetscCall(MatSetType(*A_loc, ((PetscObject)Ad)->type_name)); 5375 } else if (scall == MAT_REUSE_MATRIX) { 5376 PetscCall(MatSeqAIJGetArrayWrite(*A_loc, &ca)); 5377 for (i = 0; i < am; i++) { 5378 const PetscInt ncols_d = ai[i + 1] - ai[i]; 5379 const PetscInt ncols_o = bi[i + 1] - bi[i]; 5380 /* diagonal portion of A */ 5381 for (j = 0; j < ncols_d; j++) *ca++ = *aa++; 5382 /* off-diagonal portion of A */ 5383 for (j = 0; j < ncols_o; j++) *ca++ = *ba++; 5384 } 5385 PetscCall(MatSeqAIJRestoreArrayWrite(*A_loc, &ca)); 5386 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid MatReuse %d", (int)scall); 5387 PetscCall(MatSeqAIJRestoreArrayRead(Ad, &aa)); 5388 PetscCall(MatSeqAIJRestoreArrayRead(Ao, &aa)); 5389 if (glob) { 5390 PetscInt cst, *gidx; 5391 5392 PetscCall(MatGetOwnershipRangeColumn(A, &cst, NULL)); 5393 PetscCall(PetscMalloc1(dn + on, &gidx)); 5394 for (i = 0; i < dn; i++) gidx[i] = cst + i; 5395 for (i = 0; i < on; i++) gidx[i + dn] = cmap[i]; 5396 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)Ad), dn + on, gidx, PETSC_OWN_POINTER, glob)); 5397 } 5398 } 5399 PetscCall(PetscLogEventEnd(MAT_Getlocalmat, A, 0, 0, 0)); 5400 PetscFunctionReturn(PETSC_SUCCESS); 5401 } 5402 5403 /*@C 5404 MatMPIAIJGetLocalMatCondensed - Creates a `MATSEQAIJ` matrix from an `MATMPIAIJ` matrix by taking all its local rows and NON-ZERO columns 5405 5406 Not Collective 5407 5408 Input Parameters: 5409 + A - the matrix 5410 . scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5411 . row - index set of rows to extract (or `NULL`) 5412 - col - index set of columns to extract (or `NULL`) 5413 5414 Output Parameter: 5415 . A_loc - the local sequential matrix generated 5416 5417 Level: developer 5418 5419 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatGetOwnershipRange()`, `MatMPIAIJGetLocalMat()` 5420 @*/ 5421 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A, MatReuse scall, IS *row, IS *col, Mat *A_loc) 5422 { 5423 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 5424 PetscInt i, start, end, ncols, nzA, nzB, *cmap, imark, *idx; 5425 IS isrowa, iscola; 5426 Mat *aloc; 5427 PetscBool match; 5428 5429 PetscFunctionBegin; 5430 PetscCall(PetscObjectTypeCompare((PetscObject)A, MATMPIAIJ, &match)); 5431 PetscCheck(match, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Requires MATMPIAIJ matrix as input"); 5432 PetscCall(PetscLogEventBegin(MAT_Getlocalmatcondensed, A, 0, 0, 0)); 5433 if (!row) { 5434 start = A->rmap->rstart; 5435 end = A->rmap->rend; 5436 PetscCall(ISCreateStride(PETSC_COMM_SELF, end - start, start, 1, &isrowa)); 5437 } else { 5438 isrowa = *row; 5439 } 5440 if (!col) { 5441 start = A->cmap->rstart; 5442 cmap = a->garray; 5443 nzA = a->A->cmap->n; 5444 nzB = a->B->cmap->n; 5445 PetscCall(PetscMalloc1(nzA + nzB, &idx)); 5446 ncols = 0; 5447 for (i = 0; i < nzB; i++) { 5448 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5449 else break; 5450 } 5451 imark = i; 5452 for (i = 0; i < nzA; i++) idx[ncols++] = start + i; 5453 for (i = imark; i < nzB; i++) idx[ncols++] = cmap[i]; 5454 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, ncols, idx, PETSC_OWN_POINTER, &iscola)); 5455 } else { 5456 iscola = *col; 5457 } 5458 if (scall != MAT_INITIAL_MATRIX) { 5459 PetscCall(PetscMalloc1(1, &aloc)); 5460 aloc[0] = *A_loc; 5461 } 5462 PetscCall(MatCreateSubMatrices(A, 1, &isrowa, &iscola, scall, &aloc)); 5463 if (!col) { /* attach global id of condensed columns */ 5464 PetscCall(PetscObjectCompose((PetscObject)aloc[0], "_petsc_GetLocalMatCondensed_iscol", (PetscObject)iscola)); 5465 } 5466 *A_loc = aloc[0]; 5467 PetscCall(PetscFree(aloc)); 5468 if (!row) PetscCall(ISDestroy(&isrowa)); 5469 if (!col) PetscCall(ISDestroy(&iscola)); 5470 PetscCall(PetscLogEventEnd(MAT_Getlocalmatcondensed, A, 0, 0, 0)); 5471 PetscFunctionReturn(PETSC_SUCCESS); 5472 } 5473 5474 /* 5475 * Create a sequential AIJ matrix based on row indices. a whole column is extracted once a row is matched. 5476 * Row could be local or remote.The routine is designed to be scalable in memory so that nothing is based 5477 * on a global size. 5478 * */ 5479 static PetscErrorCode MatCreateSeqSubMatrixWithRows_Private(Mat P, IS rows, Mat *P_oth) 5480 { 5481 Mat_MPIAIJ *p = (Mat_MPIAIJ *)P->data; 5482 Mat_SeqAIJ *pd = (Mat_SeqAIJ *)p->A->data, *po = (Mat_SeqAIJ *)p->B->data, *p_oth; 5483 PetscInt plocalsize, nrows, *ilocal, *oilocal, i, lidx, *nrcols, *nlcols, ncol; 5484 PetscMPIInt owner; 5485 PetscSFNode *iremote, *oiremote; 5486 const PetscInt *lrowindices; 5487 PetscSF sf, osf; 5488 PetscInt pcstart, *roffsets, *loffsets, *pnnz, j; 5489 PetscInt ontotalcols, dntotalcols, ntotalcols, nout; 5490 MPI_Comm comm; 5491 ISLocalToGlobalMapping mapping; 5492 const PetscScalar *pd_a, *po_a; 5493 5494 PetscFunctionBegin; 5495 PetscCall(PetscObjectGetComm((PetscObject)P, &comm)); 5496 /* plocalsize is the number of roots 5497 * nrows is the number of leaves 5498 * */ 5499 PetscCall(MatGetLocalSize(P, &plocalsize, NULL)); 5500 PetscCall(ISGetLocalSize(rows, &nrows)); 5501 PetscCall(PetscCalloc1(nrows, &iremote)); 5502 PetscCall(ISGetIndices(rows, &lrowindices)); 5503 for (i = 0; i < nrows; i++) { 5504 /* Find a remote index and an owner for a row 5505 * The row could be local or remote 5506 * */ 5507 owner = 0; 5508 lidx = 0; 5509 PetscCall(PetscLayoutFindOwnerIndex(P->rmap, lrowindices[i], &owner, &lidx)); 5510 iremote[i].index = lidx; 5511 iremote[i].rank = owner; 5512 } 5513 /* Create SF to communicate how many nonzero columns for each row */ 5514 PetscCall(PetscSFCreate(comm, &sf)); 5515 /* SF will figure out the number of nonzero columns for each row, and their 5516 * offsets 5517 * */ 5518 PetscCall(PetscSFSetGraph(sf, plocalsize, nrows, NULL, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER)); 5519 PetscCall(PetscSFSetFromOptions(sf)); 5520 PetscCall(PetscSFSetUp(sf)); 5521 5522 PetscCall(PetscCalloc1(2 * (plocalsize + 1), &roffsets)); 5523 PetscCall(PetscCalloc1(2 * plocalsize, &nrcols)); 5524 PetscCall(PetscCalloc1(nrows, &pnnz)); 5525 roffsets[0] = 0; 5526 roffsets[1] = 0; 5527 for (i = 0; i < plocalsize; i++) { 5528 /* diagonal */ 5529 nrcols[i * 2 + 0] = pd->i[i + 1] - pd->i[i]; 5530 /* off-diagonal */ 5531 nrcols[i * 2 + 1] = po->i[i + 1] - po->i[i]; 5532 /* compute offsets so that we relative location for each row */ 5533 roffsets[(i + 1) * 2 + 0] = roffsets[i * 2 + 0] + nrcols[i * 2 + 0]; 5534 roffsets[(i + 1) * 2 + 1] = roffsets[i * 2 + 1] + nrcols[i * 2 + 1]; 5535 } 5536 PetscCall(PetscCalloc1(2 * nrows, &nlcols)); 5537 PetscCall(PetscCalloc1(2 * nrows, &loffsets)); 5538 /* 'r' means root, and 'l' means leaf */ 5539 PetscCall(PetscSFBcastBegin(sf, MPIU_2INT, nrcols, nlcols, MPI_REPLACE)); 5540 PetscCall(PetscSFBcastBegin(sf, MPIU_2INT, roffsets, loffsets, MPI_REPLACE)); 5541 PetscCall(PetscSFBcastEnd(sf, MPIU_2INT, nrcols, nlcols, MPI_REPLACE)); 5542 PetscCall(PetscSFBcastEnd(sf, MPIU_2INT, roffsets, loffsets, MPI_REPLACE)); 5543 PetscCall(PetscSFDestroy(&sf)); 5544 PetscCall(PetscFree(roffsets)); 5545 PetscCall(PetscFree(nrcols)); 5546 dntotalcols = 0; 5547 ontotalcols = 0; 5548 ncol = 0; 5549 for (i = 0; i < nrows; i++) { 5550 pnnz[i] = nlcols[i * 2 + 0] + nlcols[i * 2 + 1]; 5551 ncol = PetscMax(pnnz[i], ncol); 5552 /* diagonal */ 5553 dntotalcols += nlcols[i * 2 + 0]; 5554 /* off-diagonal */ 5555 ontotalcols += nlcols[i * 2 + 1]; 5556 } 5557 /* We do not need to figure the right number of columns 5558 * since all the calculations will be done by going through the raw data 5559 * */ 5560 PetscCall(MatCreateSeqAIJ(PETSC_COMM_SELF, nrows, ncol, 0, pnnz, P_oth)); 5561 PetscCall(MatSetUp(*P_oth)); 5562 PetscCall(PetscFree(pnnz)); 5563 p_oth = (Mat_SeqAIJ *)(*P_oth)->data; 5564 /* diagonal */ 5565 PetscCall(PetscCalloc1(dntotalcols, &iremote)); 5566 /* off-diagonal */ 5567 PetscCall(PetscCalloc1(ontotalcols, &oiremote)); 5568 /* diagonal */ 5569 PetscCall(PetscCalloc1(dntotalcols, &ilocal)); 5570 /* off-diagonal */ 5571 PetscCall(PetscCalloc1(ontotalcols, &oilocal)); 5572 dntotalcols = 0; 5573 ontotalcols = 0; 5574 ntotalcols = 0; 5575 for (i = 0; i < nrows; i++) { 5576 owner = 0; 5577 PetscCall(PetscLayoutFindOwnerIndex(P->rmap, lrowindices[i], &owner, NULL)); 5578 /* Set iremote for diag matrix */ 5579 for (j = 0; j < nlcols[i * 2 + 0]; j++) { 5580 iremote[dntotalcols].index = loffsets[i * 2 + 0] + j; 5581 iremote[dntotalcols].rank = owner; 5582 /* P_oth is seqAIJ so that ilocal need to point to the first part of memory */ 5583 ilocal[dntotalcols++] = ntotalcols++; 5584 } 5585 /* off-diagonal */ 5586 for (j = 0; j < nlcols[i * 2 + 1]; j++) { 5587 oiremote[ontotalcols].index = loffsets[i * 2 + 1] + j; 5588 oiremote[ontotalcols].rank = owner; 5589 oilocal[ontotalcols++] = ntotalcols++; 5590 } 5591 } 5592 PetscCall(ISRestoreIndices(rows, &lrowindices)); 5593 PetscCall(PetscFree(loffsets)); 5594 PetscCall(PetscFree(nlcols)); 5595 PetscCall(PetscSFCreate(comm, &sf)); 5596 /* P serves as roots and P_oth is leaves 5597 * Diag matrix 5598 * */ 5599 PetscCall(PetscSFSetGraph(sf, pd->i[plocalsize], dntotalcols, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER)); 5600 PetscCall(PetscSFSetFromOptions(sf)); 5601 PetscCall(PetscSFSetUp(sf)); 5602 5603 PetscCall(PetscSFCreate(comm, &osf)); 5604 /* off-diagonal */ 5605 PetscCall(PetscSFSetGraph(osf, po->i[plocalsize], ontotalcols, oilocal, PETSC_OWN_POINTER, oiremote, PETSC_OWN_POINTER)); 5606 PetscCall(PetscSFSetFromOptions(osf)); 5607 PetscCall(PetscSFSetUp(osf)); 5608 PetscCall(MatSeqAIJGetArrayRead(p->A, &pd_a)); 5609 PetscCall(MatSeqAIJGetArrayRead(p->B, &po_a)); 5610 /* operate on the matrix internal data to save memory */ 5611 PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, pd_a, p_oth->a, MPI_REPLACE)); 5612 PetscCall(PetscSFBcastBegin(osf, MPIU_SCALAR, po_a, p_oth->a, MPI_REPLACE)); 5613 PetscCall(MatGetOwnershipRangeColumn(P, &pcstart, NULL)); 5614 /* Convert to global indices for diag matrix */ 5615 for (i = 0; i < pd->i[plocalsize]; i++) pd->j[i] += pcstart; 5616 PetscCall(PetscSFBcastBegin(sf, MPIU_INT, pd->j, p_oth->j, MPI_REPLACE)); 5617 /* We want P_oth store global indices */ 5618 PetscCall(ISLocalToGlobalMappingCreate(comm, 1, p->B->cmap->n, p->garray, PETSC_COPY_VALUES, &mapping)); 5619 /* Use memory scalable approach */ 5620 PetscCall(ISLocalToGlobalMappingSetType(mapping, ISLOCALTOGLOBALMAPPINGHASH)); 5621 PetscCall(ISLocalToGlobalMappingApply(mapping, po->i[plocalsize], po->j, po->j)); 5622 PetscCall(PetscSFBcastBegin(osf, MPIU_INT, po->j, p_oth->j, MPI_REPLACE)); 5623 PetscCall(PetscSFBcastEnd(sf, MPIU_INT, pd->j, p_oth->j, MPI_REPLACE)); 5624 /* Convert back to local indices */ 5625 for (i = 0; i < pd->i[plocalsize]; i++) pd->j[i] -= pcstart; 5626 PetscCall(PetscSFBcastEnd(osf, MPIU_INT, po->j, p_oth->j, MPI_REPLACE)); 5627 nout = 0; 5628 PetscCall(ISGlobalToLocalMappingApply(mapping, IS_GTOLM_DROP, po->i[plocalsize], po->j, &nout, po->j)); 5629 PetscCheck(nout == po->i[plocalsize], comm, PETSC_ERR_ARG_INCOMP, "n %" PetscInt_FMT " does not equal to nout %" PetscInt_FMT " ", po->i[plocalsize], nout); 5630 PetscCall(ISLocalToGlobalMappingDestroy(&mapping)); 5631 /* Exchange values */ 5632 PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, pd_a, p_oth->a, MPI_REPLACE)); 5633 PetscCall(PetscSFBcastEnd(osf, MPIU_SCALAR, po_a, p_oth->a, MPI_REPLACE)); 5634 PetscCall(MatSeqAIJRestoreArrayRead(p->A, &pd_a)); 5635 PetscCall(MatSeqAIJRestoreArrayRead(p->B, &po_a)); 5636 /* Stop PETSc from shrinking memory */ 5637 for (i = 0; i < nrows; i++) p_oth->ilen[i] = p_oth->imax[i]; 5638 PetscCall(MatAssemblyBegin(*P_oth, MAT_FINAL_ASSEMBLY)); 5639 PetscCall(MatAssemblyEnd(*P_oth, MAT_FINAL_ASSEMBLY)); 5640 /* Attach PetscSF objects to P_oth so that we can reuse it later */ 5641 PetscCall(PetscObjectCompose((PetscObject)*P_oth, "diagsf", (PetscObject)sf)); 5642 PetscCall(PetscObjectCompose((PetscObject)*P_oth, "offdiagsf", (PetscObject)osf)); 5643 PetscCall(PetscSFDestroy(&sf)); 5644 PetscCall(PetscSFDestroy(&osf)); 5645 PetscFunctionReturn(PETSC_SUCCESS); 5646 } 5647 5648 /* 5649 * Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 5650 * This supports MPIAIJ and MAIJ 5651 * */ 5652 PetscErrorCode MatGetBrowsOfAcols_MPIXAIJ(Mat A, Mat P, PetscInt dof, MatReuse reuse, Mat *P_oth) 5653 { 5654 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data, *p = (Mat_MPIAIJ *)P->data; 5655 Mat_SeqAIJ *p_oth; 5656 IS rows, map; 5657 PetscHMapI hamp; 5658 PetscInt i, htsize, *rowindices, off, *mapping, key, count; 5659 MPI_Comm comm; 5660 PetscSF sf, osf; 5661 PetscBool has; 5662 5663 PetscFunctionBegin; 5664 PetscCall(PetscObjectGetComm((PetscObject)A, &comm)); 5665 PetscCall(PetscLogEventBegin(MAT_GetBrowsOfAocols, A, P, 0, 0)); 5666 /* If it is the first time, create an index set of off-diag nonzero columns of A, 5667 * and then create a submatrix (that often is an overlapping matrix) 5668 * */ 5669 if (reuse == MAT_INITIAL_MATRIX) { 5670 /* Use a hash table to figure out unique keys */ 5671 PetscCall(PetscHMapICreateWithSize(a->B->cmap->n, &hamp)); 5672 PetscCall(PetscCalloc1(a->B->cmap->n, &mapping)); 5673 count = 0; 5674 /* Assume that a->g is sorted, otherwise the following does not make sense */ 5675 for (i = 0; i < a->B->cmap->n; i++) { 5676 key = a->garray[i] / dof; 5677 PetscCall(PetscHMapIHas(hamp, key, &has)); 5678 if (!has) { 5679 mapping[i] = count; 5680 PetscCall(PetscHMapISet(hamp, key, count++)); 5681 } else { 5682 /* Current 'i' has the same value the previous step */ 5683 mapping[i] = count - 1; 5684 } 5685 } 5686 PetscCall(ISCreateGeneral(comm, a->B->cmap->n, mapping, PETSC_OWN_POINTER, &map)); 5687 PetscCall(PetscHMapIGetSize(hamp, &htsize)); 5688 PetscCheck(htsize == count, comm, PETSC_ERR_ARG_INCOMP, " Size of hash map %" PetscInt_FMT " is inconsistent with count %" PetscInt_FMT, htsize, count); 5689 PetscCall(PetscCalloc1(htsize, &rowindices)); 5690 off = 0; 5691 PetscCall(PetscHMapIGetKeys(hamp, &off, rowindices)); 5692 PetscCall(PetscHMapIDestroy(&hamp)); 5693 PetscCall(PetscSortInt(htsize, rowindices)); 5694 PetscCall(ISCreateGeneral(comm, htsize, rowindices, PETSC_OWN_POINTER, &rows)); 5695 /* In case, the matrix was already created but users want to recreate the matrix */ 5696 PetscCall(MatDestroy(P_oth)); 5697 PetscCall(MatCreateSeqSubMatrixWithRows_Private(P, rows, P_oth)); 5698 PetscCall(PetscObjectCompose((PetscObject)*P_oth, "aoffdiagtopothmapping", (PetscObject)map)); 5699 PetscCall(ISDestroy(&map)); 5700 PetscCall(ISDestroy(&rows)); 5701 } else if (reuse == MAT_REUSE_MATRIX) { 5702 /* If matrix was already created, we simply update values using SF objects 5703 * that as attached to the matrix earlier. 5704 */ 5705 const PetscScalar *pd_a, *po_a; 5706 5707 PetscCall(PetscObjectQuery((PetscObject)*P_oth, "diagsf", (PetscObject *)&sf)); 5708 PetscCall(PetscObjectQuery((PetscObject)*P_oth, "offdiagsf", (PetscObject *)&osf)); 5709 PetscCheck(sf && osf, comm, PETSC_ERR_ARG_NULL, "Matrix is not initialized yet"); 5710 p_oth = (Mat_SeqAIJ *)(*P_oth)->data; 5711 /* Update values in place */ 5712 PetscCall(MatSeqAIJGetArrayRead(p->A, &pd_a)); 5713 PetscCall(MatSeqAIJGetArrayRead(p->B, &po_a)); 5714 PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, pd_a, p_oth->a, MPI_REPLACE)); 5715 PetscCall(PetscSFBcastBegin(osf, MPIU_SCALAR, po_a, p_oth->a, MPI_REPLACE)); 5716 PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, pd_a, p_oth->a, MPI_REPLACE)); 5717 PetscCall(PetscSFBcastEnd(osf, MPIU_SCALAR, po_a, p_oth->a, MPI_REPLACE)); 5718 PetscCall(MatSeqAIJRestoreArrayRead(p->A, &pd_a)); 5719 PetscCall(MatSeqAIJRestoreArrayRead(p->B, &po_a)); 5720 } else SETERRQ(comm, PETSC_ERR_ARG_UNKNOWN_TYPE, "Unknown reuse type"); 5721 PetscCall(PetscLogEventEnd(MAT_GetBrowsOfAocols, A, P, 0, 0)); 5722 PetscFunctionReturn(PETSC_SUCCESS); 5723 } 5724 5725 /*@C 5726 MatGetBrowsOfAcols - Returns `IS` that contain rows of `B` that equal to nonzero columns of local `A` 5727 5728 Collective 5729 5730 Input Parameters: 5731 + A - the first matrix in `MATMPIAIJ` format 5732 . B - the second matrix in `MATMPIAIJ` format 5733 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5734 5735 Output Parameters: 5736 + rowb - On input index sets of rows of B to extract (or `NULL`), modified on output 5737 . colb - On input index sets of columns of B to extract (or `NULL`), modified on output 5738 - B_seq - the sequential matrix generated 5739 5740 Level: developer 5741 5742 .seealso: `Mat`, `MATMPIAIJ`, `IS`, `MatReuse` 5743 @*/ 5744 PetscErrorCode MatGetBrowsOfAcols(Mat A, Mat B, MatReuse scall, IS *rowb, IS *colb, Mat *B_seq) 5745 { 5746 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 5747 PetscInt *idx, i, start, ncols, nzA, nzB, *cmap, imark; 5748 IS isrowb, iscolb; 5749 Mat *bseq = NULL; 5750 5751 PetscFunctionBegin; 5752 PetscCheck(A->cmap->rstart == B->rmap->rstart && A->cmap->rend == B->rmap->rend, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Matrix local dimensions are incompatible, (%" PetscInt_FMT ", %" PetscInt_FMT ") != (%" PetscInt_FMT ",%" PetscInt_FMT ")", 5753 A->cmap->rstart, A->cmap->rend, B->rmap->rstart, B->rmap->rend); 5754 PetscCall(PetscLogEventBegin(MAT_GetBrowsOfAcols, A, B, 0, 0)); 5755 5756 if (scall == MAT_INITIAL_MATRIX) { 5757 start = A->cmap->rstart; 5758 cmap = a->garray; 5759 nzA = a->A->cmap->n; 5760 nzB = a->B->cmap->n; 5761 PetscCall(PetscMalloc1(nzA + nzB, &idx)); 5762 ncols = 0; 5763 for (i = 0; i < nzB; i++) { /* row < local row index */ 5764 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5765 else break; 5766 } 5767 imark = i; 5768 for (i = 0; i < nzA; i++) idx[ncols++] = start + i; /* local rows */ 5769 for (i = imark; i < nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5770 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, ncols, idx, PETSC_OWN_POINTER, &isrowb)); 5771 PetscCall(ISCreateStride(PETSC_COMM_SELF, B->cmap->N, 0, 1, &iscolb)); 5772 } else { 5773 PetscCheck(rowb && colb, PETSC_COMM_SELF, PETSC_ERR_SUP, "IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5774 isrowb = *rowb; 5775 iscolb = *colb; 5776 PetscCall(PetscMalloc1(1, &bseq)); 5777 bseq[0] = *B_seq; 5778 } 5779 PetscCall(MatCreateSubMatrices(B, 1, &isrowb, &iscolb, scall, &bseq)); 5780 *B_seq = bseq[0]; 5781 PetscCall(PetscFree(bseq)); 5782 if (!rowb) { 5783 PetscCall(ISDestroy(&isrowb)); 5784 } else { 5785 *rowb = isrowb; 5786 } 5787 if (!colb) { 5788 PetscCall(ISDestroy(&iscolb)); 5789 } else { 5790 *colb = iscolb; 5791 } 5792 PetscCall(PetscLogEventEnd(MAT_GetBrowsOfAcols, A, B, 0, 0)); 5793 PetscFunctionReturn(PETSC_SUCCESS); 5794 } 5795 5796 /* 5797 MatGetBrowsOfAoCols_MPIAIJ - Creates a `MATSEQAIJ` matrix by taking rows of B that equal to nonzero columns 5798 of the OFF-DIAGONAL portion of local A 5799 5800 Collective 5801 5802 Input Parameters: 5803 + A,B - the matrices in `MATMPIAIJ` format 5804 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5805 5806 Output Parameter: 5807 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5808 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5809 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5810 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5811 5812 Developer Note: 5813 This directly accesses information inside the VecScatter associated with the matrix-vector product 5814 for this matrix. This is not desirable.. 5815 5816 Level: developer 5817 5818 */ 5819 5820 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A, Mat B, MatReuse scall, PetscInt **startsj_s, PetscInt **startsj_r, MatScalar **bufa_ptr, Mat *B_oth) 5821 { 5822 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 5823 VecScatter ctx; 5824 MPI_Comm comm; 5825 const PetscMPIInt *rprocs, *sprocs; 5826 PetscMPIInt nrecvs, nsends; 5827 const PetscInt *srow, *rstarts, *sstarts; 5828 PetscInt *rowlen, *bufj, *bufJ, ncols = 0, aBn = a->B->cmap->n, row, *b_othi, *b_othj, *rvalues = NULL, *svalues = NULL, *cols, sbs, rbs; 5829 PetscInt i, j, k = 0, l, ll, nrows, *rstartsj = NULL, *sstartsj, len; 5830 PetscScalar *b_otha, *bufa, *bufA, *vals = NULL; 5831 MPI_Request *reqs = NULL, *rwaits = NULL, *swaits = NULL; 5832 PetscMPIInt size, tag, rank, nreqs; 5833 5834 PetscFunctionBegin; 5835 PetscCall(PetscObjectGetComm((PetscObject)A, &comm)); 5836 PetscCallMPI(MPI_Comm_size(comm, &size)); 5837 5838 PetscCheck(A->cmap->rstart == B->rmap->rstart && A->cmap->rend == B->rmap->rend, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Matrix local dimensions are incompatible, (%" PetscInt_FMT ", %" PetscInt_FMT ") != (%" PetscInt_FMT ",%" PetscInt_FMT ")", 5839 A->cmap->rstart, A->cmap->rend, B->rmap->rstart, B->rmap->rend); 5840 PetscCall(PetscLogEventBegin(MAT_GetBrowsOfAocols, A, B, 0, 0)); 5841 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5842 5843 if (size == 1) { 5844 startsj_s = NULL; 5845 bufa_ptr = NULL; 5846 *B_oth = NULL; 5847 PetscFunctionReturn(PETSC_SUCCESS); 5848 } 5849 5850 ctx = a->Mvctx; 5851 tag = ((PetscObject)ctx)->tag; 5852 5853 PetscCall(VecScatterGetRemote_Private(ctx, PETSC_TRUE /*send*/, &nsends, &sstarts, &srow, &sprocs, &sbs)); 5854 /* rprocs[] must be ordered so that indices received from them are ordered in rvalues[], which is key to algorithms used in this subroutine */ 5855 PetscCall(VecScatterGetRemoteOrdered_Private(ctx, PETSC_FALSE /*recv*/, &nrecvs, &rstarts, NULL /*indices not needed*/, &rprocs, &rbs)); 5856 PetscCall(PetscMPIIntCast(nsends + nrecvs, &nreqs)); 5857 PetscCall(PetscMalloc1(nreqs, &reqs)); 5858 rwaits = reqs; 5859 swaits = PetscSafePointerPlusOffset(reqs, nrecvs); 5860 5861 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5862 if (scall == MAT_INITIAL_MATRIX) { 5863 /* i-array */ 5864 /* post receives */ 5865 if (nrecvs) PetscCall(PetscMalloc1(rbs * (rstarts[nrecvs] - rstarts[0]), &rvalues)); /* rstarts can be NULL when nrecvs=0 */ 5866 for (i = 0; i < nrecvs; i++) { 5867 rowlen = rvalues + rstarts[i] * rbs; 5868 nrows = (rstarts[i + 1] - rstarts[i]) * rbs; /* num of indices to be received */ 5869 PetscCallMPI(MPIU_Irecv(rowlen, nrows, MPIU_INT, rprocs[i], tag, comm, rwaits + i)); 5870 } 5871 5872 /* pack the outgoing message */ 5873 PetscCall(PetscMalloc2(nsends + 1, &sstartsj, nrecvs + 1, &rstartsj)); 5874 5875 sstartsj[0] = 0; 5876 rstartsj[0] = 0; 5877 len = 0; /* total length of j or a array to be sent */ 5878 if (nsends) { 5879 k = sstarts[0]; /* ATTENTION: sstarts[0] and rstarts[0] are not necessarily zero */ 5880 PetscCall(PetscMalloc1(sbs * (sstarts[nsends] - sstarts[0]), &svalues)); 5881 } 5882 for (i = 0; i < nsends; i++) { 5883 rowlen = svalues + (sstarts[i] - sstarts[0]) * sbs; 5884 nrows = sstarts[i + 1] - sstarts[i]; /* num of block rows */ 5885 for (j = 0; j < nrows; j++) { 5886 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5887 for (l = 0; l < sbs; l++) { 5888 PetscCall(MatGetRow_MPIAIJ(B, row + l, &ncols, NULL, NULL)); /* rowlength */ 5889 5890 rowlen[j * sbs + l] = ncols; 5891 5892 len += ncols; 5893 PetscCall(MatRestoreRow_MPIAIJ(B, row + l, &ncols, NULL, NULL)); 5894 } 5895 k++; 5896 } 5897 PetscCallMPI(MPIU_Isend(rowlen, nrows * sbs, MPIU_INT, sprocs[i], tag, comm, swaits + i)); 5898 5899 sstartsj[i + 1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5900 } 5901 /* recvs and sends of i-array are completed */ 5902 if (nreqs) PetscCallMPI(MPI_Waitall(nreqs, reqs, MPI_STATUSES_IGNORE)); 5903 PetscCall(PetscFree(svalues)); 5904 5905 /* allocate buffers for sending j and a arrays */ 5906 PetscCall(PetscMalloc1(len + 1, &bufj)); 5907 PetscCall(PetscMalloc1(len + 1, &bufa)); 5908 5909 /* create i-array of B_oth */ 5910 PetscCall(PetscMalloc1(aBn + 2, &b_othi)); 5911 5912 b_othi[0] = 0; 5913 len = 0; /* total length of j or a array to be received */ 5914 k = 0; 5915 for (i = 0; i < nrecvs; i++) { 5916 rowlen = rvalues + (rstarts[i] - rstarts[0]) * rbs; 5917 nrows = (rstarts[i + 1] - rstarts[i]) * rbs; /* num of rows to be received */ 5918 for (j = 0; j < nrows; j++) { 5919 b_othi[k + 1] = b_othi[k] + rowlen[j]; 5920 PetscCall(PetscIntSumError(rowlen[j], len, &len)); 5921 k++; 5922 } 5923 rstartsj[i + 1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5924 } 5925 PetscCall(PetscFree(rvalues)); 5926 5927 /* allocate space for j and a arrays of B_oth */ 5928 PetscCall(PetscMalloc1(b_othi[aBn] + 1, &b_othj)); 5929 PetscCall(PetscMalloc1(b_othi[aBn] + 1, &b_otha)); 5930 5931 /* j-array */ 5932 /* post receives of j-array */ 5933 for (i = 0; i < nrecvs; i++) { 5934 nrows = rstartsj[i + 1] - rstartsj[i]; /* length of the msg received */ 5935 PetscCallMPI(MPIU_Irecv(b_othj + rstartsj[i], nrows, MPIU_INT, rprocs[i], tag, comm, rwaits + i)); 5936 } 5937 5938 /* pack the outgoing message j-array */ 5939 if (nsends) k = sstarts[0]; 5940 for (i = 0; i < nsends; i++) { 5941 nrows = sstarts[i + 1] - sstarts[i]; /* num of block rows */ 5942 bufJ = bufj + sstartsj[i]; 5943 for (j = 0; j < nrows; j++) { 5944 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5945 for (ll = 0; ll < sbs; ll++) { 5946 PetscCall(MatGetRow_MPIAIJ(B, row + ll, &ncols, &cols, NULL)); 5947 for (l = 0; l < ncols; l++) *bufJ++ = cols[l]; 5948 PetscCall(MatRestoreRow_MPIAIJ(B, row + ll, &ncols, &cols, NULL)); 5949 } 5950 } 5951 PetscCallMPI(MPIU_Isend(bufj + sstartsj[i], sstartsj[i + 1] - sstartsj[i], MPIU_INT, sprocs[i], tag, comm, swaits + i)); 5952 } 5953 5954 /* recvs and sends of j-array are completed */ 5955 if (nreqs) PetscCallMPI(MPI_Waitall(nreqs, reqs, MPI_STATUSES_IGNORE)); 5956 } else if (scall == MAT_REUSE_MATRIX) { 5957 sstartsj = *startsj_s; 5958 rstartsj = *startsj_r; 5959 bufa = *bufa_ptr; 5960 PetscCall(MatSeqAIJGetArrayWrite(*B_oth, &b_otha)); 5961 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not possess an object container"); 5962 5963 /* a-array */ 5964 /* post receives of a-array */ 5965 for (i = 0; i < nrecvs; i++) { 5966 nrows = rstartsj[i + 1] - rstartsj[i]; /* length of the msg received */ 5967 PetscCallMPI(MPIU_Irecv(b_otha + rstartsj[i], nrows, MPIU_SCALAR, rprocs[i], tag, comm, rwaits + i)); 5968 } 5969 5970 /* pack the outgoing message a-array */ 5971 if (nsends) k = sstarts[0]; 5972 for (i = 0; i < nsends; i++) { 5973 nrows = sstarts[i + 1] - sstarts[i]; /* num of block rows */ 5974 bufA = bufa + sstartsj[i]; 5975 for (j = 0; j < nrows; j++) { 5976 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5977 for (ll = 0; ll < sbs; ll++) { 5978 PetscCall(MatGetRow_MPIAIJ(B, row + ll, &ncols, NULL, &vals)); 5979 for (l = 0; l < ncols; l++) *bufA++ = vals[l]; 5980 PetscCall(MatRestoreRow_MPIAIJ(B, row + ll, &ncols, NULL, &vals)); 5981 } 5982 } 5983 PetscCallMPI(MPIU_Isend(bufa + sstartsj[i], sstartsj[i + 1] - sstartsj[i], MPIU_SCALAR, sprocs[i], tag, comm, swaits + i)); 5984 } 5985 /* recvs and sends of a-array are completed */ 5986 if (nreqs) PetscCallMPI(MPI_Waitall(nreqs, reqs, MPI_STATUSES_IGNORE)); 5987 PetscCall(PetscFree(reqs)); 5988 5989 if (scall == MAT_INITIAL_MATRIX) { 5990 Mat_SeqAIJ *b_oth; 5991 5992 /* put together the new matrix */ 5993 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, aBn, B->cmap->N, b_othi, b_othj, b_otha, B_oth)); 5994 5995 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5996 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5997 b_oth = (Mat_SeqAIJ *)(*B_oth)->data; 5998 b_oth->free_a = PETSC_TRUE; 5999 b_oth->free_ij = PETSC_TRUE; 6000 b_oth->nonew = 0; 6001 6002 PetscCall(PetscFree(bufj)); 6003 if (!startsj_s || !bufa_ptr) { 6004 PetscCall(PetscFree2(sstartsj, rstartsj)); 6005 PetscCall(PetscFree(bufa_ptr)); 6006 } else { 6007 *startsj_s = sstartsj; 6008 *startsj_r = rstartsj; 6009 *bufa_ptr = bufa; 6010 } 6011 } else if (scall == MAT_REUSE_MATRIX) { 6012 PetscCall(MatSeqAIJRestoreArrayWrite(*B_oth, &b_otha)); 6013 } 6014 6015 PetscCall(VecScatterRestoreRemote_Private(ctx, PETSC_TRUE, &nsends, &sstarts, &srow, &sprocs, &sbs)); 6016 PetscCall(VecScatterRestoreRemoteOrdered_Private(ctx, PETSC_FALSE, &nrecvs, &rstarts, NULL, &rprocs, &rbs)); 6017 PetscCall(PetscLogEventEnd(MAT_GetBrowsOfAocols, A, B, 0, 0)); 6018 PetscFunctionReturn(PETSC_SUCCESS); 6019 } 6020 6021 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat, MatType, MatReuse, Mat *); 6022 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat, MatType, MatReuse, Mat *); 6023 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJSELL(Mat, MatType, MatReuse, Mat *); 6024 #if defined(PETSC_HAVE_MKL_SPARSE) 6025 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJMKL(Mat, MatType, MatReuse, Mat *); 6026 #endif 6027 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIBAIJ(Mat, MatType, MatReuse, Mat *); 6028 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat, MatType, MatReuse, Mat *); 6029 #if defined(PETSC_HAVE_ELEMENTAL) 6030 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat, MatType, MatReuse, Mat *); 6031 #endif 6032 #if defined(PETSC_HAVE_SCALAPACK) 6033 PETSC_INTERN PetscErrorCode MatConvert_AIJ_ScaLAPACK(Mat, MatType, MatReuse, Mat *); 6034 #endif 6035 #if defined(PETSC_HAVE_HYPRE) 6036 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat, MatType, MatReuse, Mat *); 6037 #endif 6038 #if defined(PETSC_HAVE_CUDA) 6039 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCUSPARSE(Mat, MatType, MatReuse, Mat *); 6040 #endif 6041 #if defined(PETSC_HAVE_HIP) 6042 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJHIPSPARSE(Mat, MatType, MatReuse, Mat *); 6043 #endif 6044 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 6045 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJKokkos(Mat, MatType, MatReuse, Mat *); 6046 #endif 6047 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISELL(Mat, MatType, MatReuse, Mat *); 6048 PETSC_INTERN PetscErrorCode MatConvert_XAIJ_IS(Mat, MatType, MatReuse, Mat *); 6049 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_IS_XAIJ(Mat); 6050 6051 /* 6052 Computes (B'*A')' since computing B*A directly is untenable 6053 6054 n p p 6055 [ ] [ ] [ ] 6056 m [ A ] * n [ B ] = m [ C ] 6057 [ ] [ ] [ ] 6058 6059 */ 6060 static PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A, Mat B, Mat C) 6061 { 6062 Mat At, Bt, Ct; 6063 6064 PetscFunctionBegin; 6065 PetscCall(MatTranspose(A, MAT_INITIAL_MATRIX, &At)); 6066 PetscCall(MatTranspose(B, MAT_INITIAL_MATRIX, &Bt)); 6067 PetscCall(MatMatMult(Bt, At, MAT_INITIAL_MATRIX, PETSC_CURRENT, &Ct)); 6068 PetscCall(MatDestroy(&At)); 6069 PetscCall(MatDestroy(&Bt)); 6070 PetscCall(MatTransposeSetPrecursor(Ct, C)); 6071 PetscCall(MatTranspose(Ct, MAT_REUSE_MATRIX, &C)); 6072 PetscCall(MatDestroy(&Ct)); 6073 PetscFunctionReturn(PETSC_SUCCESS); 6074 } 6075 6076 static PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A, Mat B, PetscReal fill, Mat C) 6077 { 6078 PetscBool cisdense; 6079 6080 PetscFunctionBegin; 6081 PetscCheck(A->cmap->n == B->rmap->n, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "A->cmap->n %" PetscInt_FMT " != B->rmap->n %" PetscInt_FMT, A->cmap->n, B->rmap->n); 6082 PetscCall(MatSetSizes(C, A->rmap->n, B->cmap->n, A->rmap->N, B->cmap->N)); 6083 PetscCall(MatSetBlockSizesFromMats(C, A, B)); 6084 PetscCall(PetscObjectTypeCompareAny((PetscObject)C, &cisdense, MATMPIDENSE, MATMPIDENSECUDA, MATMPIDENSEHIP, "")); 6085 if (!cisdense) PetscCall(MatSetType(C, ((PetscObject)A)->type_name)); 6086 PetscCall(MatSetUp(C)); 6087 6088 C->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 6089 PetscFunctionReturn(PETSC_SUCCESS); 6090 } 6091 6092 static PetscErrorCode MatProductSetFromOptions_MPIDense_MPIAIJ_AB(Mat C) 6093 { 6094 Mat_Product *product = C->product; 6095 Mat A = product->A, B = product->B; 6096 6097 PetscFunctionBegin; 6098 PetscCheck(A->cmap->rstart == B->rmap->rstart && A->cmap->rend == B->rmap->rend, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Matrix local dimensions are incompatible, (%" PetscInt_FMT ", %" PetscInt_FMT ") != (%" PetscInt_FMT ",%" PetscInt_FMT ")", 6099 A->cmap->rstart, A->cmap->rend, B->rmap->rstart, B->rmap->rend); 6100 C->ops->matmultsymbolic = MatMatMultSymbolic_MPIDense_MPIAIJ; 6101 C->ops->productsymbolic = MatProductSymbolic_AB; 6102 PetscFunctionReturn(PETSC_SUCCESS); 6103 } 6104 6105 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_MPIDense_MPIAIJ(Mat C) 6106 { 6107 Mat_Product *product = C->product; 6108 6109 PetscFunctionBegin; 6110 if (product->type == MATPRODUCT_AB) PetscCall(MatProductSetFromOptions_MPIDense_MPIAIJ_AB(C)); 6111 PetscFunctionReturn(PETSC_SUCCESS); 6112 } 6113 6114 /* 6115 Merge two sets of sorted nonzeros and return a CSR for the merged (sequential) matrix 6116 6117 Input Parameters: 6118 6119 j1,rowBegin1,rowEnd1,jmap1: describe the first set of nonzeros (Set1) 6120 j2,rowBegin2,rowEnd2,jmap2: describe the second set of nonzeros (Set2) 6121 6122 mat: both sets' nonzeros are on m rows, where m is the number of local rows of the matrix mat 6123 6124 For Set1, j1[] contains column indices of the nonzeros. 6125 For the k-th row (0<=k<m), [rowBegin1[k],rowEnd1[k]) index into j1[] and point to the begin/end nonzero in row k 6126 respectively (note rowEnd1[k] is not necessarily equal to rwoBegin1[k+1]). Indices in this range of j1[] are sorted, 6127 but might have repeats. jmap1[t+1] - jmap1[t] is the number of repeats for the t-th unique nonzero in Set1. 6128 6129 Similar for Set2. 6130 6131 This routine merges the two sets of nonzeros row by row and removes repeats. 6132 6133 Output Parameters: (memory is allocated by the caller) 6134 6135 i[],j[]: the CSR of the merged matrix, which has m rows. 6136 imap1[]: the k-th unique nonzero in Set1 (k=0,1,...) corresponds to imap1[k]-th unique nonzero in the merged matrix. 6137 imap2[]: similar to imap1[], but for Set2. 6138 Note we order nonzeros row-by-row and from left to right. 6139 */ 6140 static PetscErrorCode MatMergeEntries_Internal(Mat mat, const PetscInt j1[], const PetscInt j2[], const PetscCount rowBegin1[], const PetscCount rowEnd1[], const PetscCount rowBegin2[], const PetscCount rowEnd2[], const PetscCount jmap1[], const PetscCount jmap2[], PetscCount imap1[], PetscCount imap2[], PetscInt i[], PetscInt j[]) 6141 { 6142 PetscInt r, m; /* Row index of mat */ 6143 PetscCount t, t1, t2, b1, e1, b2, e2; 6144 6145 PetscFunctionBegin; 6146 PetscCall(MatGetLocalSize(mat, &m, NULL)); 6147 t1 = t2 = t = 0; /* Count unique nonzeros of in Set1, Set1 and the merged respectively */ 6148 i[0] = 0; 6149 for (r = 0; r < m; r++) { /* Do row by row merging */ 6150 b1 = rowBegin1[r]; 6151 e1 = rowEnd1[r]; 6152 b2 = rowBegin2[r]; 6153 e2 = rowEnd2[r]; 6154 while (b1 < e1 && b2 < e2) { 6155 if (j1[b1] == j2[b2]) { /* Same column index and hence same nonzero */ 6156 j[t] = j1[b1]; 6157 imap1[t1] = t; 6158 imap2[t2] = t; 6159 b1 += jmap1[t1 + 1] - jmap1[t1]; /* Jump to next unique local nonzero */ 6160 b2 += jmap2[t2 + 1] - jmap2[t2]; /* Jump to next unique remote nonzero */ 6161 t1++; 6162 t2++; 6163 t++; 6164 } else if (j1[b1] < j2[b2]) { 6165 j[t] = j1[b1]; 6166 imap1[t1] = t; 6167 b1 += jmap1[t1 + 1] - jmap1[t1]; 6168 t1++; 6169 t++; 6170 } else { 6171 j[t] = j2[b2]; 6172 imap2[t2] = t; 6173 b2 += jmap2[t2 + 1] - jmap2[t2]; 6174 t2++; 6175 t++; 6176 } 6177 } 6178 /* Merge the remaining in either j1[] or j2[] */ 6179 while (b1 < e1) { 6180 j[t] = j1[b1]; 6181 imap1[t1] = t; 6182 b1 += jmap1[t1 + 1] - jmap1[t1]; 6183 t1++; 6184 t++; 6185 } 6186 while (b2 < e2) { 6187 j[t] = j2[b2]; 6188 imap2[t2] = t; 6189 b2 += jmap2[t2 + 1] - jmap2[t2]; 6190 t2++; 6191 t++; 6192 } 6193 PetscCall(PetscIntCast(t, i + r + 1)); 6194 } 6195 PetscFunctionReturn(PETSC_SUCCESS); 6196 } 6197 6198 /* 6199 Split nonzeros in a block of local rows into two subsets: those in the diagonal block and those in the off-diagonal block 6200 6201 Input Parameters: 6202 mat: an MPI matrix that provides row and column layout information for splitting. Let's say its number of local rows is m. 6203 n,i[],j[],perm[]: there are n input entries, belonging to m rows. Row/col indices of the entries are stored in i[] and j[] 6204 respectively, along with a permutation array perm[]. Length of the i[],j[],perm[] arrays is n. 6205 6206 i[] is already sorted, but within a row, j[] is not sorted and might have repeats. 6207 i[] might contain negative indices at the beginning, which means the corresponding entries should be ignored in the splitting. 6208 6209 Output Parameters: 6210 j[],perm[]: the routine needs to sort j[] within each row along with perm[]. 6211 rowBegin[],rowMid[],rowEnd[]: of length m, and the memory is preallocated and zeroed by the caller. 6212 They contain indices pointing to j[]. For 0<=r<m, [rowBegin[r],rowMid[r]) point to begin/end entries of row r of the diagonal block, 6213 and [rowMid[r],rowEnd[r]) point to begin/end entries of row r of the off-diagonal block. 6214 6215 Aperm[],Ajmap[],Atot,Annz: Arrays are allocated by this routine. 6216 Atot: number of entries belonging to the diagonal block. 6217 Annz: number of unique nonzeros belonging to the diagonal block. 6218 Aperm[Atot] stores values from perm[] for entries belonging to the diagonal block. Length of Aperm[] is Atot, though it may also count 6219 repeats (i.e., same 'i,j' pair). 6220 Ajmap[Annz+1] stores the number of repeats of each unique entry belonging to the diagonal block. More precisely, Ajmap[t+1] - Ajmap[t] 6221 is the number of repeats for the t-th unique entry in the diagonal block. Ajmap[0] is always 0. 6222 6223 Atot: number of entries belonging to the diagonal block 6224 Annz: number of unique nonzeros belonging to the diagonal block. 6225 6226 Bperm[], Bjmap[], Btot, Bnnz are similar but for the off-diagonal block. 6227 6228 Aperm[],Bperm[],Ajmap[] and Bjmap[] are allocated separately by this routine with PetscMalloc1(). 6229 */ 6230 static PetscErrorCode MatSplitEntries_Internal(Mat mat, PetscCount n, const PetscInt i[], PetscInt j[], PetscCount perm[], PetscCount rowBegin[], PetscCount rowMid[], PetscCount rowEnd[], PetscCount *Atot_, PetscCount **Aperm_, PetscCount *Annz_, PetscCount **Ajmap_, PetscCount *Btot_, PetscCount **Bperm_, PetscCount *Bnnz_, PetscCount **Bjmap_) 6231 { 6232 PetscInt cstart, cend, rstart, rend, row, col; 6233 PetscCount Atot = 0, Btot = 0; /* Total number of nonzeros in the diagonal and off-diagonal blocks */ 6234 PetscCount Annz = 0, Bnnz = 0; /* Number of unique nonzeros in the diagonal and off-diagonal blocks */ 6235 PetscCount k, m, p, q, r, s, mid; 6236 PetscCount *Aperm, *Bperm, *Ajmap, *Bjmap; 6237 6238 PetscFunctionBegin; 6239 PetscCall(PetscLayoutGetRange(mat->rmap, &rstart, &rend)); 6240 PetscCall(PetscLayoutGetRange(mat->cmap, &cstart, &cend)); 6241 m = rend - rstart; 6242 6243 /* Skip negative rows */ 6244 for (k = 0; k < n; k++) 6245 if (i[k] >= 0) break; 6246 6247 /* Process [k,n): sort and partition each local row into diag and offdiag portions, 6248 fill rowBegin[], rowMid[], rowEnd[], and count Atot, Btot, Annz, Bnnz. 6249 */ 6250 while (k < n) { 6251 row = i[k]; 6252 /* Entries in [k,s) are in one row. Shift diagonal block col indices so that diag is ahead of offdiag after sorting the row */ 6253 for (s = k; s < n; s++) 6254 if (i[s] != row) break; 6255 6256 /* Shift diag columns to range of [-PETSC_INT_MAX, -1] */ 6257 for (p = k; p < s; p++) { 6258 if (j[p] >= cstart && j[p] < cend) j[p] -= PETSC_INT_MAX; 6259 else PetscAssert((j[p] >= 0) && (j[p] <= mat->cmap->N), PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Column index %" PetscInt_FMT " is out of range", j[p]); 6260 } 6261 PetscCall(PetscSortIntWithCountArray(s - k, j + k, perm + k)); 6262 PetscCall(PetscSortedIntUpperBound(j, k, s, -1, &mid)); /* Separate [k,s) into [k,mid) for diag and [mid,s) for offdiag */ 6263 rowBegin[row - rstart] = k; 6264 rowMid[row - rstart] = mid; 6265 rowEnd[row - rstart] = s; 6266 6267 /* Count nonzeros of this diag/offdiag row, which might have repeats */ 6268 Atot += mid - k; 6269 Btot += s - mid; 6270 6271 /* Count unique nonzeros of this diag row */ 6272 for (p = k; p < mid;) { 6273 col = j[p]; 6274 do { 6275 j[p] += PETSC_INT_MAX; /* Revert the modified diagonal indices */ 6276 p++; 6277 } while (p < mid && j[p] == col); 6278 Annz++; 6279 } 6280 6281 /* Count unique nonzeros of this offdiag row */ 6282 for (p = mid; p < s;) { 6283 col = j[p]; 6284 do { 6285 p++; 6286 } while (p < s && j[p] == col); 6287 Bnnz++; 6288 } 6289 k = s; 6290 } 6291 6292 /* Allocation according to Atot, Btot, Annz, Bnnz */ 6293 PetscCall(PetscMalloc1(Atot, &Aperm)); 6294 PetscCall(PetscMalloc1(Btot, &Bperm)); 6295 PetscCall(PetscMalloc1(Annz + 1, &Ajmap)); 6296 PetscCall(PetscMalloc1(Bnnz + 1, &Bjmap)); 6297 6298 /* Re-scan indices and copy diag/offdiag permutation indices to Aperm, Bperm and also fill Ajmap and Bjmap */ 6299 Ajmap[0] = Bjmap[0] = Atot = Btot = Annz = Bnnz = 0; 6300 for (r = 0; r < m; r++) { 6301 k = rowBegin[r]; 6302 mid = rowMid[r]; 6303 s = rowEnd[r]; 6304 PetscCall(PetscArraycpy(PetscSafePointerPlusOffset(Aperm, Atot), PetscSafePointerPlusOffset(perm, k), mid - k)); 6305 PetscCall(PetscArraycpy(PetscSafePointerPlusOffset(Bperm, Btot), PetscSafePointerPlusOffset(perm, mid), s - mid)); 6306 Atot += mid - k; 6307 Btot += s - mid; 6308 6309 /* Scan column indices in this row and find out how many repeats each unique nonzero has */ 6310 for (p = k; p < mid;) { 6311 col = j[p]; 6312 q = p; 6313 do { 6314 p++; 6315 } while (p < mid && j[p] == col); 6316 Ajmap[Annz + 1] = Ajmap[Annz] + (p - q); 6317 Annz++; 6318 } 6319 6320 for (p = mid; p < s;) { 6321 col = j[p]; 6322 q = p; 6323 do { 6324 p++; 6325 } while (p < s && j[p] == col); 6326 Bjmap[Bnnz + 1] = Bjmap[Bnnz] + (p - q); 6327 Bnnz++; 6328 } 6329 } 6330 /* Output */ 6331 *Aperm_ = Aperm; 6332 *Annz_ = Annz; 6333 *Atot_ = Atot; 6334 *Ajmap_ = Ajmap; 6335 *Bperm_ = Bperm; 6336 *Bnnz_ = Bnnz; 6337 *Btot_ = Btot; 6338 *Bjmap_ = Bjmap; 6339 PetscFunctionReturn(PETSC_SUCCESS); 6340 } 6341 6342 /* 6343 Expand the jmap[] array to make a new one in view of nonzeros in the merged matrix 6344 6345 Input Parameters: 6346 nnz1: number of unique nonzeros in a set that was used to produce imap[], jmap[] 6347 nnz: number of unique nonzeros in the merged matrix 6348 imap[nnz1]: i-th nonzero in the set is the imap[i]-th nonzero in the merged matrix 6349 jmap[nnz1+1]: i-th nonzero in the set has jmap[i+1] - jmap[i] repeats in the set 6350 6351 Output Parameter: (memory is allocated by the caller) 6352 jmap_new[nnz+1]: i-th nonzero in the merged matrix has jmap_new[i+1] - jmap_new[i] repeats in the set 6353 6354 Example: 6355 nnz1 = 4 6356 nnz = 6 6357 imap = [1,3,4,5] 6358 jmap = [0,3,5,6,7] 6359 then, 6360 jmap_new = [0,0,3,3,5,6,7] 6361 */ 6362 static PetscErrorCode ExpandJmap_Internal(PetscCount nnz1, PetscCount nnz, const PetscCount imap[], const PetscCount jmap[], PetscCount jmap_new[]) 6363 { 6364 PetscCount k, p; 6365 6366 PetscFunctionBegin; 6367 jmap_new[0] = 0; 6368 p = nnz; /* p loops over jmap_new[] backwards */ 6369 for (k = nnz1 - 1; k >= 0; k--) { /* k loops over imap[] */ 6370 for (; p > imap[k]; p--) jmap_new[p] = jmap[k + 1]; 6371 } 6372 for (; p >= 0; p--) jmap_new[p] = jmap[0]; 6373 PetscFunctionReturn(PETSC_SUCCESS); 6374 } 6375 6376 static PetscErrorCode MatCOOStructDestroy_MPIAIJ(void **data) 6377 { 6378 MatCOOStruct_MPIAIJ *coo = (MatCOOStruct_MPIAIJ *)*data; 6379 6380 PetscFunctionBegin; 6381 PetscCall(PetscSFDestroy(&coo->sf)); 6382 PetscCall(PetscFree(coo->Aperm1)); 6383 PetscCall(PetscFree(coo->Bperm1)); 6384 PetscCall(PetscFree(coo->Ajmap1)); 6385 PetscCall(PetscFree(coo->Bjmap1)); 6386 PetscCall(PetscFree(coo->Aimap2)); 6387 PetscCall(PetscFree(coo->Bimap2)); 6388 PetscCall(PetscFree(coo->Aperm2)); 6389 PetscCall(PetscFree(coo->Bperm2)); 6390 PetscCall(PetscFree(coo->Ajmap2)); 6391 PetscCall(PetscFree(coo->Bjmap2)); 6392 PetscCall(PetscFree(coo->Cperm1)); 6393 PetscCall(PetscFree2(coo->sendbuf, coo->recvbuf)); 6394 PetscCall(PetscFree(coo)); 6395 PetscFunctionReturn(PETSC_SUCCESS); 6396 } 6397 6398 PetscErrorCode MatSetPreallocationCOO_MPIAIJ(Mat mat, PetscCount coo_n, PetscInt coo_i[], PetscInt coo_j[]) 6399 { 6400 MPI_Comm comm; 6401 PetscMPIInt rank, size; 6402 PetscInt m, n, M, N, rstart, rend, cstart, cend; /* Sizes, indices of row/col, therefore with type PetscInt */ 6403 PetscCount k, p, q, rem; /* Loop variables over coo arrays */ 6404 Mat_MPIAIJ *mpiaij = (Mat_MPIAIJ *)mat->data; 6405 PetscContainer container; 6406 MatCOOStruct_MPIAIJ *coo; 6407 6408 PetscFunctionBegin; 6409 PetscCall(PetscFree(mpiaij->garray)); 6410 PetscCall(VecDestroy(&mpiaij->lvec)); 6411 #if defined(PETSC_USE_CTABLE) 6412 PetscCall(PetscHMapIDestroy(&mpiaij->colmap)); 6413 #else 6414 PetscCall(PetscFree(mpiaij->colmap)); 6415 #endif 6416 PetscCall(VecScatterDestroy(&mpiaij->Mvctx)); 6417 mat->assembled = PETSC_FALSE; 6418 mat->was_assembled = PETSC_FALSE; 6419 6420 PetscCall(PetscObjectGetComm((PetscObject)mat, &comm)); 6421 PetscCallMPI(MPI_Comm_size(comm, &size)); 6422 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 6423 PetscCall(PetscLayoutSetUp(mat->rmap)); 6424 PetscCall(PetscLayoutSetUp(mat->cmap)); 6425 PetscCall(PetscLayoutGetRange(mat->rmap, &rstart, &rend)); 6426 PetscCall(PetscLayoutGetRange(mat->cmap, &cstart, &cend)); 6427 PetscCall(MatGetLocalSize(mat, &m, &n)); 6428 PetscCall(MatGetSize(mat, &M, &N)); 6429 6430 /* Sort (i,j) by row along with a permutation array, so that the to-be-ignored */ 6431 /* entries come first, then local rows, then remote rows. */ 6432 PetscCount n1 = coo_n, *perm1; 6433 PetscInt *i1 = coo_i, *j1 = coo_j; 6434 6435 PetscCall(PetscMalloc1(n1, &perm1)); 6436 for (k = 0; k < n1; k++) perm1[k] = k; 6437 6438 /* Manipulate indices so that entries with negative row or col indices will have smallest 6439 row indices, local entries will have greater but negative row indices, and remote entries 6440 will have positive row indices. 6441 */ 6442 for (k = 0; k < n1; k++) { 6443 if (i1[k] < 0 || j1[k] < 0) i1[k] = PETSC_INT_MIN; /* e.g., -2^31, minimal to move them ahead */ 6444 else if (i1[k] >= rstart && i1[k] < rend) i1[k] -= PETSC_INT_MAX; /* e.g., minus 2^31-1 to shift local rows to range of [-PETSC_INT_MAX, -1] */ 6445 else { 6446 PetscCheck(!mat->nooffprocentries, PETSC_COMM_SELF, PETSC_ERR_USER_INPUT, "MAT_NO_OFF_PROC_ENTRIES is set but insert to remote rows"); 6447 if (mpiaij->donotstash) i1[k] = PETSC_INT_MIN; /* Ignore offproc entries as if they had negative indices */ 6448 } 6449 } 6450 6451 /* Sort by row; after that, [0,k) have ignored entries, [k,rem) have local rows and [rem,n1) have remote rows */ 6452 PetscCall(PetscSortIntWithIntCountArrayPair(n1, i1, j1, perm1)); 6453 6454 /* Advance k to the first entry we need to take care of */ 6455 for (k = 0; k < n1; k++) 6456 if (i1[k] > PETSC_INT_MIN) break; 6457 PetscCount i1start = k; 6458 6459 PetscCall(PetscSortedIntUpperBound(i1, k, n1, rend - 1 - PETSC_INT_MAX, &rem)); /* rem is upper bound of the last local row */ 6460 for (; k < rem; k++) i1[k] += PETSC_INT_MAX; /* Revert row indices of local rows*/ 6461 6462 /* Send remote rows to their owner */ 6463 /* Find which rows should be sent to which remote ranks*/ 6464 PetscInt nsend = 0; /* Number of MPI ranks to send data to */ 6465 PetscMPIInt *sendto; /* [nsend], storing remote ranks */ 6466 PetscInt *nentries; /* [nsend], storing number of entries sent to remote ranks; Assume PetscInt is big enough for this count, and error if not */ 6467 const PetscInt *ranges; 6468 PetscInt maxNsend = size >= 128 ? 128 : size; /* Assume max 128 neighbors; realloc when needed */ 6469 6470 PetscCall(PetscLayoutGetRanges(mat->rmap, &ranges)); 6471 PetscCall(PetscMalloc2(maxNsend, &sendto, maxNsend, &nentries)); 6472 for (k = rem; k < n1;) { 6473 PetscMPIInt owner; 6474 PetscInt firstRow, lastRow; 6475 6476 /* Locate a row range */ 6477 firstRow = i1[k]; /* first row of this owner */ 6478 PetscCall(PetscLayoutFindOwner(mat->rmap, firstRow, &owner)); 6479 lastRow = ranges[owner + 1] - 1; /* last row of this owner */ 6480 6481 /* Find the first index 'p' in [k,n) with i[p] belonging to next owner */ 6482 PetscCall(PetscSortedIntUpperBound(i1, k, n1, lastRow, &p)); 6483 6484 /* All entries in [k,p) belong to this remote owner */ 6485 if (nsend >= maxNsend) { /* Double the remote ranks arrays if not long enough */ 6486 PetscMPIInt *sendto2; 6487 PetscInt *nentries2; 6488 PetscInt maxNsend2 = (maxNsend <= size / 2) ? maxNsend * 2 : size; 6489 6490 PetscCall(PetscMalloc2(maxNsend2, &sendto2, maxNsend2, &nentries2)); 6491 PetscCall(PetscArraycpy(sendto2, sendto, maxNsend)); 6492 PetscCall(PetscArraycpy(nentries2, nentries2, maxNsend + 1)); 6493 PetscCall(PetscFree2(sendto, nentries2)); 6494 sendto = sendto2; 6495 nentries = nentries2; 6496 maxNsend = maxNsend2; 6497 } 6498 sendto[nsend] = owner; 6499 PetscCall(PetscIntCast(p - k, &nentries[nsend])); 6500 nsend++; 6501 k = p; 6502 } 6503 6504 /* Build 1st SF to know offsets on remote to send data */ 6505 PetscSF sf1; 6506 PetscInt nroots = 1, nroots2 = 0; 6507 PetscInt nleaves = nsend, nleaves2 = 0; 6508 PetscInt *offsets; 6509 PetscSFNode *iremote; 6510 6511 PetscCall(PetscSFCreate(comm, &sf1)); 6512 PetscCall(PetscMalloc1(nsend, &iremote)); 6513 PetscCall(PetscMalloc1(nsend, &offsets)); 6514 for (k = 0; k < nsend; k++) { 6515 iremote[k].rank = sendto[k]; 6516 iremote[k].index = 0; 6517 nleaves2 += nentries[k]; 6518 PetscCheck(nleaves2 >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of SF leaves is too large for PetscInt"); 6519 } 6520 PetscCall(PetscSFSetGraph(sf1, nroots, nleaves, NULL, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER)); 6521 PetscCall(PetscSFFetchAndOpWithMemTypeBegin(sf1, MPIU_INT, PETSC_MEMTYPE_HOST, &nroots2 /*rootdata*/, PETSC_MEMTYPE_HOST, nentries /*leafdata*/, PETSC_MEMTYPE_HOST, offsets /*leafupdate*/, MPI_SUM)); 6522 PetscCall(PetscSFFetchAndOpEnd(sf1, MPIU_INT, &nroots2, nentries, offsets, MPI_SUM)); /* Would nroots2 overflow, we check offsets[] below */ 6523 PetscCall(PetscSFDestroy(&sf1)); 6524 PetscAssert(nleaves2 == n1 - rem, PETSC_COMM_SELF, PETSC_ERR_PLIB, "nleaves2 %" PetscInt_FMT " != number of remote entries %" PetscCount_FMT, nleaves2, n1 - rem); 6525 6526 /* Build 2nd SF to send remote COOs to their owner */ 6527 PetscSF sf2; 6528 nroots = nroots2; 6529 nleaves = nleaves2; 6530 PetscCall(PetscSFCreate(comm, &sf2)); 6531 PetscCall(PetscSFSetFromOptions(sf2)); 6532 PetscCall(PetscMalloc1(nleaves, &iremote)); 6533 p = 0; 6534 for (k = 0; k < nsend; k++) { 6535 PetscCheck(offsets[k] >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of SF roots is too large for PetscInt"); 6536 for (q = 0; q < nentries[k]; q++, p++) { 6537 iremote[p].rank = sendto[k]; 6538 PetscCall(PetscIntCast(offsets[k] + q, &iremote[p].index)); 6539 } 6540 } 6541 PetscCall(PetscSFSetGraph(sf2, nroots, nleaves, NULL, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER)); 6542 6543 /* Send the remote COOs to their owner */ 6544 PetscInt n2 = nroots, *i2, *j2; /* Buffers for received COOs from other ranks, along with a permutation array */ 6545 PetscCount *perm2; /* Though PetscInt is enough for remote entries, we use PetscCount here as we want to reuse MatSplitEntries_Internal() */ 6546 PetscCall(PetscMalloc3(n2, &i2, n2, &j2, n2, &perm2)); 6547 PetscAssert(rem == 0 || i1 != NULL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cannot add nonzero offset to null"); 6548 PetscAssert(rem == 0 || j1 != NULL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cannot add nonzero offset to null"); 6549 PetscInt *i1prem = PetscSafePointerPlusOffset(i1, rem); 6550 PetscInt *j1prem = PetscSafePointerPlusOffset(j1, rem); 6551 PetscCall(PetscSFReduceWithMemTypeBegin(sf2, MPIU_INT, PETSC_MEMTYPE_HOST, i1prem, PETSC_MEMTYPE_HOST, i2, MPI_REPLACE)); 6552 PetscCall(PetscSFReduceEnd(sf2, MPIU_INT, i1prem, i2, MPI_REPLACE)); 6553 PetscCall(PetscSFReduceWithMemTypeBegin(sf2, MPIU_INT, PETSC_MEMTYPE_HOST, j1prem, PETSC_MEMTYPE_HOST, j2, MPI_REPLACE)); 6554 PetscCall(PetscSFReduceEnd(sf2, MPIU_INT, j1prem, j2, MPI_REPLACE)); 6555 6556 PetscCall(PetscFree(offsets)); 6557 PetscCall(PetscFree2(sendto, nentries)); 6558 6559 /* Sort received COOs by row along with the permutation array */ 6560 for (k = 0; k < n2; k++) perm2[k] = k; 6561 PetscCall(PetscSortIntWithIntCountArrayPair(n2, i2, j2, perm2)); 6562 6563 /* sf2 only sends contiguous leafdata to contiguous rootdata. We record the permutation which will be used to fill leafdata */ 6564 PetscCount *Cperm1; 6565 PetscAssert(rem == 0 || perm1 != NULL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cannot add nonzero offset to null"); 6566 PetscCount *perm1prem = PetscSafePointerPlusOffset(perm1, rem); 6567 PetscCall(PetscMalloc1(nleaves, &Cperm1)); 6568 PetscCall(PetscArraycpy(Cperm1, perm1prem, nleaves)); 6569 6570 /* Support for HYPRE matrices, kind of a hack. 6571 Swap min column with diagonal so that diagonal values will go first */ 6572 PetscBool hypre; 6573 PetscCall(PetscStrcmp("_internal_COO_mat_for_hypre", ((PetscObject)mat)->name, &hypre)); 6574 if (hypre) { 6575 PetscInt *minj; 6576 PetscBT hasdiag; 6577 6578 PetscCall(PetscBTCreate(m, &hasdiag)); 6579 PetscCall(PetscMalloc1(m, &minj)); 6580 for (k = 0; k < m; k++) minj[k] = PETSC_INT_MAX; 6581 for (k = i1start; k < rem; k++) { 6582 if (j1[k] < cstart || j1[k] >= cend) continue; 6583 const PetscInt rindex = i1[k] - rstart; 6584 if ((j1[k] - cstart) == rindex) PetscCall(PetscBTSet(hasdiag, rindex)); 6585 minj[rindex] = PetscMin(minj[rindex], j1[k]); 6586 } 6587 for (k = 0; k < n2; k++) { 6588 if (j2[k] < cstart || j2[k] >= cend) continue; 6589 const PetscInt rindex = i2[k] - rstart; 6590 if ((j2[k] - cstart) == rindex) PetscCall(PetscBTSet(hasdiag, rindex)); 6591 minj[rindex] = PetscMin(minj[rindex], j2[k]); 6592 } 6593 for (k = i1start; k < rem; k++) { 6594 const PetscInt rindex = i1[k] - rstart; 6595 if (j1[k] < cstart || j1[k] >= cend || !PetscBTLookup(hasdiag, rindex)) continue; 6596 if (j1[k] == minj[rindex]) j1[k] = i1[k] + (cstart - rstart); 6597 else if ((j1[k] - cstart) == rindex) j1[k] = minj[rindex]; 6598 } 6599 for (k = 0; k < n2; k++) { 6600 const PetscInt rindex = i2[k] - rstart; 6601 if (j2[k] < cstart || j2[k] >= cend || !PetscBTLookup(hasdiag, rindex)) continue; 6602 if (j2[k] == minj[rindex]) j2[k] = i2[k] + (cstart - rstart); 6603 else if ((j2[k] - cstart) == rindex) j2[k] = minj[rindex]; 6604 } 6605 PetscCall(PetscBTDestroy(&hasdiag)); 6606 PetscCall(PetscFree(minj)); 6607 } 6608 6609 /* Split local COOs and received COOs into diag/offdiag portions */ 6610 PetscCount *rowBegin1, *rowMid1, *rowEnd1; 6611 PetscCount *Ajmap1, *Aperm1, *Bjmap1, *Bperm1; 6612 PetscCount Annz1, Bnnz1, Atot1, Btot1; 6613 PetscCount *rowBegin2, *rowMid2, *rowEnd2; 6614 PetscCount *Ajmap2, *Aperm2, *Bjmap2, *Bperm2; 6615 PetscCount Annz2, Bnnz2, Atot2, Btot2; 6616 6617 PetscCall(PetscCalloc3(m, &rowBegin1, m, &rowMid1, m, &rowEnd1)); 6618 PetscCall(PetscCalloc3(m, &rowBegin2, m, &rowMid2, m, &rowEnd2)); 6619 PetscCall(MatSplitEntries_Internal(mat, rem, i1, j1, perm1, rowBegin1, rowMid1, rowEnd1, &Atot1, &Aperm1, &Annz1, &Ajmap1, &Btot1, &Bperm1, &Bnnz1, &Bjmap1)); 6620 PetscCall(MatSplitEntries_Internal(mat, n2, i2, j2, perm2, rowBegin2, rowMid2, rowEnd2, &Atot2, &Aperm2, &Annz2, &Ajmap2, &Btot2, &Bperm2, &Bnnz2, &Bjmap2)); 6621 6622 /* Merge local COOs with received COOs: diag with diag, offdiag with offdiag */ 6623 PetscInt *Ai, *Bi; 6624 PetscInt *Aj, *Bj; 6625 6626 PetscCall(PetscMalloc1(m + 1, &Ai)); 6627 PetscCall(PetscMalloc1(m + 1, &Bi)); 6628 PetscCall(PetscMalloc1(Annz1 + Annz2, &Aj)); /* Since local and remote entries might have dups, we might allocate excess memory */ 6629 PetscCall(PetscMalloc1(Bnnz1 + Bnnz2, &Bj)); 6630 6631 PetscCount *Aimap1, *Bimap1, *Aimap2, *Bimap2; 6632 PetscCall(PetscMalloc1(Annz1, &Aimap1)); 6633 PetscCall(PetscMalloc1(Bnnz1, &Bimap1)); 6634 PetscCall(PetscMalloc1(Annz2, &Aimap2)); 6635 PetscCall(PetscMalloc1(Bnnz2, &Bimap2)); 6636 6637 PetscCall(MatMergeEntries_Internal(mat, j1, j2, rowBegin1, rowMid1, rowBegin2, rowMid2, Ajmap1, Ajmap2, Aimap1, Aimap2, Ai, Aj)); 6638 PetscCall(MatMergeEntries_Internal(mat, j1, j2, rowMid1, rowEnd1, rowMid2, rowEnd2, Bjmap1, Bjmap2, Bimap1, Bimap2, Bi, Bj)); 6639 6640 /* Expand Ajmap1/Bjmap1 to make them based off nonzeros in A/B, since we */ 6641 /* expect nonzeros in A/B most likely have local contributing entries */ 6642 PetscInt Annz = Ai[m]; 6643 PetscInt Bnnz = Bi[m]; 6644 PetscCount *Ajmap1_new, *Bjmap1_new; 6645 6646 PetscCall(PetscMalloc1(Annz + 1, &Ajmap1_new)); 6647 PetscCall(PetscMalloc1(Bnnz + 1, &Bjmap1_new)); 6648 6649 PetscCall(ExpandJmap_Internal(Annz1, Annz, Aimap1, Ajmap1, Ajmap1_new)); 6650 PetscCall(ExpandJmap_Internal(Bnnz1, Bnnz, Bimap1, Bjmap1, Bjmap1_new)); 6651 6652 PetscCall(PetscFree(Aimap1)); 6653 PetscCall(PetscFree(Ajmap1)); 6654 PetscCall(PetscFree(Bimap1)); 6655 PetscCall(PetscFree(Bjmap1)); 6656 PetscCall(PetscFree3(rowBegin1, rowMid1, rowEnd1)); 6657 PetscCall(PetscFree3(rowBegin2, rowMid2, rowEnd2)); 6658 PetscCall(PetscFree(perm1)); 6659 PetscCall(PetscFree3(i2, j2, perm2)); 6660 6661 Ajmap1 = Ajmap1_new; 6662 Bjmap1 = Bjmap1_new; 6663 6664 /* Reallocate Aj, Bj once we know actual numbers of unique nonzeros in A and B */ 6665 if (Annz < Annz1 + Annz2) { 6666 PetscInt *Aj_new; 6667 PetscCall(PetscMalloc1(Annz, &Aj_new)); 6668 PetscCall(PetscArraycpy(Aj_new, Aj, Annz)); 6669 PetscCall(PetscFree(Aj)); 6670 Aj = Aj_new; 6671 } 6672 6673 if (Bnnz < Bnnz1 + Bnnz2) { 6674 PetscInt *Bj_new; 6675 PetscCall(PetscMalloc1(Bnnz, &Bj_new)); 6676 PetscCall(PetscArraycpy(Bj_new, Bj, Bnnz)); 6677 PetscCall(PetscFree(Bj)); 6678 Bj = Bj_new; 6679 } 6680 6681 /* Create new submatrices for on-process and off-process coupling */ 6682 PetscScalar *Aa, *Ba; 6683 MatType rtype; 6684 Mat_SeqAIJ *a, *b; 6685 PetscObjectState state; 6686 PetscCall(PetscCalloc1(Annz, &Aa)); /* Zero matrix on device */ 6687 PetscCall(PetscCalloc1(Bnnz, &Ba)); 6688 /* make Aj[] local, i.e, based off the start column of the diagonal portion */ 6689 if (cstart) { 6690 for (k = 0; k < Annz; k++) Aj[k] -= cstart; 6691 } 6692 6693 PetscCall(MatGetRootType_Private(mat, &rtype)); 6694 6695 MatSeqXAIJGetOptions_Private(mpiaij->A); 6696 PetscCall(MatDestroy(&mpiaij->A)); 6697 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, m, n, Ai, Aj, Aa, &mpiaij->A)); 6698 PetscCall(MatSetBlockSizesFromMats(mpiaij->A, mat, mat)); 6699 MatSeqXAIJRestoreOptions_Private(mpiaij->A); 6700 6701 MatSeqXAIJGetOptions_Private(mpiaij->B); 6702 PetscCall(MatDestroy(&mpiaij->B)); 6703 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, m, mat->cmap->N, Bi, Bj, Ba, &mpiaij->B)); 6704 PetscCall(MatSetBlockSizesFromMats(mpiaij->B, mat, mat)); 6705 MatSeqXAIJRestoreOptions_Private(mpiaij->B); 6706 6707 PetscCall(MatSetUpMultiply_MPIAIJ(mat)); 6708 mat->was_assembled = PETSC_TRUE; // was_assembled in effect means the Mvctx is built; doing so avoids redundant MatSetUpMultiply_MPIAIJ 6709 state = mpiaij->A->nonzerostate + mpiaij->B->nonzerostate; 6710 PetscCallMPI(MPIU_Allreduce(&state, &mat->nonzerostate, 1, MPIU_INT64, MPI_SUM, PetscObjectComm((PetscObject)mat))); 6711 6712 a = (Mat_SeqAIJ *)mpiaij->A->data; 6713 b = (Mat_SeqAIJ *)mpiaij->B->data; 6714 a->free_a = PETSC_TRUE; 6715 a->free_ij = PETSC_TRUE; 6716 b->free_a = PETSC_TRUE; 6717 b->free_ij = PETSC_TRUE; 6718 a->maxnz = a->nz; 6719 b->maxnz = b->nz; 6720 6721 /* conversion must happen AFTER multiply setup */ 6722 PetscCall(MatConvert(mpiaij->A, rtype, MAT_INPLACE_MATRIX, &mpiaij->A)); 6723 PetscCall(MatConvert(mpiaij->B, rtype, MAT_INPLACE_MATRIX, &mpiaij->B)); 6724 PetscCall(VecDestroy(&mpiaij->lvec)); 6725 PetscCall(MatCreateVecs(mpiaij->B, &mpiaij->lvec, NULL)); 6726 6727 // Put the COO struct in a container and then attach that to the matrix 6728 PetscCall(PetscMalloc1(1, &coo)); 6729 coo->n = coo_n; 6730 coo->sf = sf2; 6731 coo->sendlen = nleaves; 6732 coo->recvlen = nroots; 6733 coo->Annz = Annz; 6734 coo->Bnnz = Bnnz; 6735 coo->Annz2 = Annz2; 6736 coo->Bnnz2 = Bnnz2; 6737 coo->Atot1 = Atot1; 6738 coo->Atot2 = Atot2; 6739 coo->Btot1 = Btot1; 6740 coo->Btot2 = Btot2; 6741 coo->Ajmap1 = Ajmap1; 6742 coo->Aperm1 = Aperm1; 6743 coo->Bjmap1 = Bjmap1; 6744 coo->Bperm1 = Bperm1; 6745 coo->Aimap2 = Aimap2; 6746 coo->Ajmap2 = Ajmap2; 6747 coo->Aperm2 = Aperm2; 6748 coo->Bimap2 = Bimap2; 6749 coo->Bjmap2 = Bjmap2; 6750 coo->Bperm2 = Bperm2; 6751 coo->Cperm1 = Cperm1; 6752 // Allocate in preallocation. If not used, it has zero cost on host 6753 PetscCall(PetscMalloc2(coo->sendlen, &coo->sendbuf, coo->recvlen, &coo->recvbuf)); 6754 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container)); 6755 PetscCall(PetscContainerSetPointer(container, coo)); 6756 PetscCall(PetscContainerSetCtxDestroy(container, MatCOOStructDestroy_MPIAIJ)); 6757 PetscCall(PetscObjectCompose((PetscObject)mat, "__PETSc_MatCOOStruct_Host", (PetscObject)container)); 6758 PetscCall(PetscContainerDestroy(&container)); 6759 PetscFunctionReturn(PETSC_SUCCESS); 6760 } 6761 6762 static PetscErrorCode MatSetValuesCOO_MPIAIJ(Mat mat, const PetscScalar v[], InsertMode imode) 6763 { 6764 Mat_MPIAIJ *mpiaij = (Mat_MPIAIJ *)mat->data; 6765 Mat A = mpiaij->A, B = mpiaij->B; 6766 PetscScalar *Aa, *Ba; 6767 PetscScalar *sendbuf, *recvbuf; 6768 const PetscCount *Ajmap1, *Ajmap2, *Aimap2; 6769 const PetscCount *Bjmap1, *Bjmap2, *Bimap2; 6770 const PetscCount *Aperm1, *Aperm2, *Bperm1, *Bperm2; 6771 const PetscCount *Cperm1; 6772 PetscContainer container; 6773 MatCOOStruct_MPIAIJ *coo; 6774 6775 PetscFunctionBegin; 6776 PetscCall(PetscObjectQuery((PetscObject)mat, "__PETSc_MatCOOStruct_Host", (PetscObject *)&container)); 6777 PetscCheck(container, PetscObjectComm((PetscObject)mat), PETSC_ERR_PLIB, "Not found MatCOOStruct on this matrix"); 6778 PetscCall(PetscContainerGetPointer(container, (void **)&coo)); 6779 sendbuf = coo->sendbuf; 6780 recvbuf = coo->recvbuf; 6781 Ajmap1 = coo->Ajmap1; 6782 Ajmap2 = coo->Ajmap2; 6783 Aimap2 = coo->Aimap2; 6784 Bjmap1 = coo->Bjmap1; 6785 Bjmap2 = coo->Bjmap2; 6786 Bimap2 = coo->Bimap2; 6787 Aperm1 = coo->Aperm1; 6788 Aperm2 = coo->Aperm2; 6789 Bperm1 = coo->Bperm1; 6790 Bperm2 = coo->Bperm2; 6791 Cperm1 = coo->Cperm1; 6792 6793 PetscCall(MatSeqAIJGetArray(A, &Aa)); /* Might read and write matrix values */ 6794 PetscCall(MatSeqAIJGetArray(B, &Ba)); 6795 6796 /* Pack entries to be sent to remote */ 6797 for (PetscCount i = 0; i < coo->sendlen; i++) sendbuf[i] = v[Cperm1[i]]; 6798 6799 /* Send remote entries to their owner and overlap the communication with local computation */ 6800 PetscCall(PetscSFReduceWithMemTypeBegin(coo->sf, MPIU_SCALAR, PETSC_MEMTYPE_HOST, sendbuf, PETSC_MEMTYPE_HOST, recvbuf, MPI_REPLACE)); 6801 /* Add local entries to A and B */ 6802 for (PetscCount i = 0; i < coo->Annz; i++) { /* All nonzeros in A are either zero'ed or added with a value (i.e., initialized) */ 6803 PetscScalar sum = 0.0; /* Do partial summation first to improve numerical stability */ 6804 for (PetscCount k = Ajmap1[i]; k < Ajmap1[i + 1]; k++) sum += v[Aperm1[k]]; 6805 Aa[i] = (imode == INSERT_VALUES ? 0.0 : Aa[i]) + sum; 6806 } 6807 for (PetscCount i = 0; i < coo->Bnnz; i++) { 6808 PetscScalar sum = 0.0; 6809 for (PetscCount k = Bjmap1[i]; k < Bjmap1[i + 1]; k++) sum += v[Bperm1[k]]; 6810 Ba[i] = (imode == INSERT_VALUES ? 0.0 : Ba[i]) + sum; 6811 } 6812 PetscCall(PetscSFReduceEnd(coo->sf, MPIU_SCALAR, sendbuf, recvbuf, MPI_REPLACE)); 6813 6814 /* Add received remote entries to A and B */ 6815 for (PetscCount i = 0; i < coo->Annz2; i++) { 6816 for (PetscCount k = Ajmap2[i]; k < Ajmap2[i + 1]; k++) Aa[Aimap2[i]] += recvbuf[Aperm2[k]]; 6817 } 6818 for (PetscCount i = 0; i < coo->Bnnz2; i++) { 6819 for (PetscCount k = Bjmap2[i]; k < Bjmap2[i + 1]; k++) Ba[Bimap2[i]] += recvbuf[Bperm2[k]]; 6820 } 6821 PetscCall(MatSeqAIJRestoreArray(A, &Aa)); 6822 PetscCall(MatSeqAIJRestoreArray(B, &Ba)); 6823 PetscFunctionReturn(PETSC_SUCCESS); 6824 } 6825 6826 /*MC 6827 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 6828 6829 Options Database Keys: 6830 . -mat_type mpiaij - sets the matrix type to `MATMPIAIJ` during a call to `MatSetFromOptions()` 6831 6832 Level: beginner 6833 6834 Notes: 6835 `MatSetValues()` may be called for this matrix type with a `NULL` argument for the numerical values, 6836 in this case the values associated with the rows and columns one passes in are set to zero 6837 in the matrix 6838 6839 `MatSetOptions`(,`MAT_STRUCTURE_ONLY`,`PETSC_TRUE`) may be called for this matrix type. In this no 6840 space is allocated for the nonzero entries and any entries passed with `MatSetValues()` are ignored 6841 6842 .seealso: [](ch_matrices), `Mat`, `MATSEQAIJ`, `MATAIJ`, `MatCreateAIJ()` 6843 M*/ 6844 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 6845 { 6846 Mat_MPIAIJ *b; 6847 PetscMPIInt size; 6848 6849 PetscFunctionBegin; 6850 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)B), &size)); 6851 6852 PetscCall(PetscNew(&b)); 6853 B->data = (void *)b; 6854 B->ops[0] = MatOps_Values; 6855 B->assembled = PETSC_FALSE; 6856 B->insertmode = NOT_SET_VALUES; 6857 b->size = size; 6858 6859 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)B), &b->rank)); 6860 6861 /* build cache for off array entries formed */ 6862 PetscCall(MatStashCreate_Private(PetscObjectComm((PetscObject)B), 1, &B->stash)); 6863 6864 b->donotstash = PETSC_FALSE; 6865 b->colmap = NULL; 6866 b->garray = NULL; 6867 b->roworiented = PETSC_TRUE; 6868 6869 /* stuff used for matrix vector multiply */ 6870 b->lvec = NULL; 6871 b->Mvctx = NULL; 6872 6873 /* stuff for MatGetRow() */ 6874 b->rowindices = NULL; 6875 b->rowvalues = NULL; 6876 b->getrowactive = PETSC_FALSE; 6877 6878 /* flexible pointer used in CUSPARSE classes */ 6879 b->spptr = NULL; 6880 6881 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatMPIAIJSetUseScalableIncreaseOverlap_C", MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ)); 6882 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatStoreValues_C", MatStoreValues_MPIAIJ)); 6883 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatRetrieveValues_C", MatRetrieveValues_MPIAIJ)); 6884 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatIsTranspose_C", MatIsTranspose_MPIAIJ)); 6885 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatMPIAIJSetPreallocation_C", MatMPIAIJSetPreallocation_MPIAIJ)); 6886 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatResetPreallocation_C", MatResetPreallocation_MPIAIJ)); 6887 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatResetHash_C", MatResetHash_MPIAIJ)); 6888 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatMPIAIJSetPreallocationCSR_C", MatMPIAIJSetPreallocationCSR_MPIAIJ)); 6889 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatDiagonalScaleLocal_C", MatDiagonalScaleLocal_MPIAIJ)); 6890 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijperm_C", MatConvert_MPIAIJ_MPIAIJPERM)); 6891 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijsell_C", MatConvert_MPIAIJ_MPIAIJSELL)); 6892 #if defined(PETSC_HAVE_CUDA) 6893 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijcusparse_C", MatConvert_MPIAIJ_MPIAIJCUSPARSE)); 6894 #endif 6895 #if defined(PETSC_HAVE_HIP) 6896 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijhipsparse_C", MatConvert_MPIAIJ_MPIAIJHIPSPARSE)); 6897 #endif 6898 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 6899 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijkokkos_C", MatConvert_MPIAIJ_MPIAIJKokkos)); 6900 #endif 6901 #if defined(PETSC_HAVE_MKL_SPARSE) 6902 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijmkl_C", MatConvert_MPIAIJ_MPIAIJMKL)); 6903 #endif 6904 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijcrl_C", MatConvert_MPIAIJ_MPIAIJCRL)); 6905 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpibaij_C", MatConvert_MPIAIJ_MPIBAIJ)); 6906 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpisbaij_C", MatConvert_MPIAIJ_MPISBAIJ)); 6907 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpidense_C", MatConvert_MPIAIJ_MPIDense)); 6908 #if defined(PETSC_HAVE_ELEMENTAL) 6909 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_elemental_C", MatConvert_MPIAIJ_Elemental)); 6910 #endif 6911 #if defined(PETSC_HAVE_SCALAPACK) 6912 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_scalapack_C", MatConvert_AIJ_ScaLAPACK)); 6913 #endif 6914 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_is_C", MatConvert_XAIJ_IS)); 6915 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpisell_C", MatConvert_MPIAIJ_MPISELL)); 6916 #if defined(PETSC_HAVE_HYPRE) 6917 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_hypre_C", MatConvert_AIJ_HYPRE)); 6918 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatProductSetFromOptions_transpose_mpiaij_mpiaij_C", MatProductSetFromOptions_Transpose_AIJ_AIJ)); 6919 #endif 6920 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatProductSetFromOptions_is_mpiaij_C", MatProductSetFromOptions_IS_XAIJ)); 6921 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatProductSetFromOptions_mpiaij_mpiaij_C", MatProductSetFromOptions_MPIAIJ)); 6922 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatSetPreallocationCOO_C", MatSetPreallocationCOO_MPIAIJ)); 6923 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatSetValuesCOO_C", MatSetValuesCOO_MPIAIJ)); 6924 PetscCall(PetscObjectChangeTypeName((PetscObject)B, MATMPIAIJ)); 6925 PetscFunctionReturn(PETSC_SUCCESS); 6926 } 6927 6928 /*@ 6929 MatCreateMPIAIJWithSplitArrays - creates a `MATMPIAIJ` matrix using arrays that contain the "diagonal" 6930 and "off-diagonal" part of the matrix in CSR format. 6931 6932 Collective 6933 6934 Input Parameters: 6935 + comm - MPI communicator 6936 . m - number of local rows (Cannot be `PETSC_DECIDE`) 6937 . n - This value should be the same as the local size used in creating the 6938 x vector for the matrix-vector product $y = Ax$. (or `PETSC_DECIDE` to have 6939 calculated if `N` is given) For square matrices `n` is almost always `m`. 6940 . M - number of global rows (or `PETSC_DETERMINE` to have calculated if `m` is given) 6941 . N - number of global columns (or `PETSC_DETERMINE` to have calculated if `n` is given) 6942 . i - row indices for "diagonal" portion of matrix; that is i[0] = 0, i[row] = i[row-1] + number of elements in that row of the matrix 6943 . j - column indices, which must be local, i.e., based off the start column of the diagonal portion 6944 . a - matrix values 6945 . oi - row indices for "off-diagonal" portion of matrix; that is oi[0] = 0, oi[row] = oi[row-1] + number of elements in that row of the matrix 6946 . oj - column indices, which must be global, representing global columns in the `MATMPIAIJ` matrix 6947 - oa - matrix values 6948 6949 Output Parameter: 6950 . mat - the matrix 6951 6952 Level: advanced 6953 6954 Notes: 6955 The `i`, `j`, and `a` arrays ARE NOT copied by this routine into the internal format used by PETSc (even in Fortran). The user 6956 must free the arrays once the matrix has been destroyed and not before. 6957 6958 The `i` and `j` indices are 0 based 6959 6960 See `MatCreateAIJ()` for the definition of "diagonal" and "off-diagonal" portion of the matrix 6961 6962 This sets local rows and cannot be used to set off-processor values. 6963 6964 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 6965 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 6966 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 6967 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 6968 keep track of the underlying array. Use `MatSetOption`(A,`MAT_NO_OFF_PROC_ENTRIES`,`PETSC_TRUE`) to disable all 6969 communication if it is known that only local entries will be set. 6970 6971 .seealso: [](ch_matrices), `Mat`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 6972 `MATMPIAIJ`, `MatCreateAIJ()`, `MatCreateMPIAIJWithArrays()` 6973 @*/ 6974 PetscErrorCode MatCreateMPIAIJWithSplitArrays(MPI_Comm comm, PetscInt m, PetscInt n, PetscInt M, PetscInt N, PetscInt i[], PetscInt j[], PetscScalar a[], PetscInt oi[], PetscInt oj[], PetscScalar oa[], Mat *mat) 6975 { 6976 Mat_MPIAIJ *maij; 6977 6978 PetscFunctionBegin; 6979 PetscCheck(m >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "local number of rows (m) cannot be PETSC_DECIDE, or negative"); 6980 PetscCheck(i[0] == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "i (row indices) must start with 0"); 6981 PetscCheck(oi[0] == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "oi (row indices) must start with 0"); 6982 PetscCall(MatCreate(comm, mat)); 6983 PetscCall(MatSetSizes(*mat, m, n, M, N)); 6984 PetscCall(MatSetType(*mat, MATMPIAIJ)); 6985 maij = (Mat_MPIAIJ *)(*mat)->data; 6986 6987 (*mat)->preallocated = PETSC_TRUE; 6988 6989 PetscCall(PetscLayoutSetUp((*mat)->rmap)); 6990 PetscCall(PetscLayoutSetUp((*mat)->cmap)); 6991 6992 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, m, n, i, j, a, &maij->A)); 6993 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, m, (*mat)->cmap->N, oi, oj, oa, &maij->B)); 6994 6995 PetscCall(MatSetOption(*mat, MAT_NO_OFF_PROC_ENTRIES, PETSC_TRUE)); 6996 PetscCall(MatAssemblyBegin(*mat, MAT_FINAL_ASSEMBLY)); 6997 PetscCall(MatAssemblyEnd(*mat, MAT_FINAL_ASSEMBLY)); 6998 PetscCall(MatSetOption(*mat, MAT_NO_OFF_PROC_ENTRIES, PETSC_FALSE)); 6999 PetscCall(MatSetOption(*mat, MAT_NEW_NONZERO_LOCATION_ERR, PETSC_TRUE)); 7000 PetscFunctionReturn(PETSC_SUCCESS); 7001 } 7002 7003 typedef struct { 7004 Mat *mp; /* intermediate products */ 7005 PetscBool *mptmp; /* is the intermediate product temporary ? */ 7006 PetscInt cp; /* number of intermediate products */ 7007 7008 /* support for MatGetBrowsOfAoCols_MPIAIJ for P_oth */ 7009 PetscInt *startsj_s, *startsj_r; 7010 PetscScalar *bufa; 7011 Mat P_oth; 7012 7013 /* may take advantage of merging product->B */ 7014 Mat Bloc; /* B-local by merging diag and off-diag */ 7015 7016 /* cusparse does not have support to split between symbolic and numeric phases. 7017 When api_user is true, we don't need to update the numerical values 7018 of the temporary storage */ 7019 PetscBool reusesym; 7020 7021 /* support for COO values insertion */ 7022 PetscScalar *coo_v, *coo_w; /* store on-process and off-process COO scalars, and used as MPI recv/send buffers respectively */ 7023 PetscInt **own; /* own[i] points to address of on-process COO indices for Mat mp[i] */ 7024 PetscInt **off; /* off[i] points to address of off-process COO indices for Mat mp[i] */ 7025 PetscBool hasoffproc; /* if true, have off-process values insertion (i.e. AtB or PtAP) */ 7026 PetscSF sf; /* used for non-local values insertion and memory malloc */ 7027 PetscMemType mtype; 7028 7029 /* customization */ 7030 PetscBool abmerge; 7031 PetscBool P_oth_bind; 7032 } MatMatMPIAIJBACKEND; 7033 7034 static PetscErrorCode MatDestroy_MatMatMPIAIJBACKEND(void *data) 7035 { 7036 MatMatMPIAIJBACKEND *mmdata = (MatMatMPIAIJBACKEND *)data; 7037 PetscInt i; 7038 7039 PetscFunctionBegin; 7040 PetscCall(PetscFree2(mmdata->startsj_s, mmdata->startsj_r)); 7041 PetscCall(PetscFree(mmdata->bufa)); 7042 PetscCall(PetscSFFree(mmdata->sf, mmdata->mtype, mmdata->coo_v)); 7043 PetscCall(PetscSFFree(mmdata->sf, mmdata->mtype, mmdata->coo_w)); 7044 PetscCall(MatDestroy(&mmdata->P_oth)); 7045 PetscCall(MatDestroy(&mmdata->Bloc)); 7046 PetscCall(PetscSFDestroy(&mmdata->sf)); 7047 for (i = 0; i < mmdata->cp; i++) PetscCall(MatDestroy(&mmdata->mp[i])); 7048 PetscCall(PetscFree2(mmdata->mp, mmdata->mptmp)); 7049 PetscCall(PetscFree(mmdata->own[0])); 7050 PetscCall(PetscFree(mmdata->own)); 7051 PetscCall(PetscFree(mmdata->off[0])); 7052 PetscCall(PetscFree(mmdata->off)); 7053 PetscCall(PetscFree(mmdata)); 7054 PetscFunctionReturn(PETSC_SUCCESS); 7055 } 7056 7057 /* Copy selected n entries with indices in idx[] of A to v[]. 7058 If idx is NULL, copy the whole data array of A to v[] 7059 */ 7060 static PetscErrorCode MatSeqAIJCopySubArray(Mat A, PetscInt n, const PetscInt idx[], PetscScalar v[]) 7061 { 7062 PetscErrorCode (*f)(Mat, PetscInt, const PetscInt[], PetscScalar[]); 7063 7064 PetscFunctionBegin; 7065 PetscCall(PetscObjectQueryFunction((PetscObject)A, "MatSeqAIJCopySubArray_C", &f)); 7066 if (f) { 7067 PetscCall((*f)(A, n, idx, v)); 7068 } else { 7069 const PetscScalar *vv; 7070 7071 PetscCall(MatSeqAIJGetArrayRead(A, &vv)); 7072 if (n && idx) { 7073 PetscScalar *w = v; 7074 const PetscInt *oi = idx; 7075 PetscInt j; 7076 7077 for (j = 0; j < n; j++) *w++ = vv[*oi++]; 7078 } else { 7079 PetscCall(PetscArraycpy(v, vv, n)); 7080 } 7081 PetscCall(MatSeqAIJRestoreArrayRead(A, &vv)); 7082 } 7083 PetscFunctionReturn(PETSC_SUCCESS); 7084 } 7085 7086 static PetscErrorCode MatProductNumeric_MPIAIJBACKEND(Mat C) 7087 { 7088 MatMatMPIAIJBACKEND *mmdata; 7089 PetscInt i, n_d, n_o; 7090 7091 PetscFunctionBegin; 7092 MatCheckProduct(C, 1); 7093 PetscCheck(C->product->data, PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Product data empty"); 7094 mmdata = (MatMatMPIAIJBACKEND *)C->product->data; 7095 if (!mmdata->reusesym) { /* update temporary matrices */ 7096 if (mmdata->P_oth) PetscCall(MatGetBrowsOfAoCols_MPIAIJ(C->product->A, C->product->B, MAT_REUSE_MATRIX, &mmdata->startsj_s, &mmdata->startsj_r, &mmdata->bufa, &mmdata->P_oth)); 7097 if (mmdata->Bloc) PetscCall(MatMPIAIJGetLocalMatMerge(C->product->B, MAT_REUSE_MATRIX, NULL, &mmdata->Bloc)); 7098 } 7099 mmdata->reusesym = PETSC_FALSE; 7100 7101 for (i = 0; i < mmdata->cp; i++) { 7102 PetscCheck(mmdata->mp[i]->ops->productnumeric, PetscObjectComm((PetscObject)mmdata->mp[i]), PETSC_ERR_PLIB, "Missing numeric op for %s", MatProductTypes[mmdata->mp[i]->product->type]); 7103 PetscCall((*mmdata->mp[i]->ops->productnumeric)(mmdata->mp[i])); 7104 } 7105 for (i = 0, n_d = 0, n_o = 0; i < mmdata->cp; i++) { 7106 PetscInt noff; 7107 7108 PetscCall(PetscIntCast(mmdata->off[i + 1] - mmdata->off[i], &noff)); 7109 if (mmdata->mptmp[i]) continue; 7110 if (noff) { 7111 PetscInt nown; 7112 7113 PetscCall(PetscIntCast(mmdata->own[i + 1] - mmdata->own[i], &nown)); 7114 PetscCall(MatSeqAIJCopySubArray(mmdata->mp[i], noff, mmdata->off[i], mmdata->coo_w + n_o)); 7115 PetscCall(MatSeqAIJCopySubArray(mmdata->mp[i], nown, mmdata->own[i], mmdata->coo_v + n_d)); 7116 n_o += noff; 7117 n_d += nown; 7118 } else { 7119 Mat_SeqAIJ *mm = (Mat_SeqAIJ *)mmdata->mp[i]->data; 7120 7121 PetscCall(MatSeqAIJCopySubArray(mmdata->mp[i], mm->nz, NULL, mmdata->coo_v + n_d)); 7122 n_d += mm->nz; 7123 } 7124 } 7125 if (mmdata->hasoffproc) { /* offprocess insertion */ 7126 PetscCall(PetscSFGatherBegin(mmdata->sf, MPIU_SCALAR, mmdata->coo_w, mmdata->coo_v + n_d)); 7127 PetscCall(PetscSFGatherEnd(mmdata->sf, MPIU_SCALAR, mmdata->coo_w, mmdata->coo_v + n_d)); 7128 } 7129 PetscCall(MatSetValuesCOO(C, mmdata->coo_v, INSERT_VALUES)); 7130 PetscFunctionReturn(PETSC_SUCCESS); 7131 } 7132 7133 /* Support for Pt * A, A * P, or Pt * A * P */ 7134 #define MAX_NUMBER_INTERMEDIATE 4 7135 PetscErrorCode MatProductSymbolic_MPIAIJBACKEND(Mat C) 7136 { 7137 Mat_Product *product = C->product; 7138 Mat A, P, mp[MAX_NUMBER_INTERMEDIATE]; /* A, P and a series of intermediate matrices */ 7139 Mat_MPIAIJ *a, *p; 7140 MatMatMPIAIJBACKEND *mmdata; 7141 ISLocalToGlobalMapping P_oth_l2g = NULL; 7142 IS glob = NULL; 7143 const char *prefix; 7144 char pprefix[256]; 7145 const PetscInt *globidx, *P_oth_idx; 7146 PetscInt i, j, cp, m, n, M, N, *coo_i, *coo_j; 7147 PetscCount ncoo, ncoo_d, ncoo_o, ncoo_oown; 7148 PetscInt cmapt[MAX_NUMBER_INTERMEDIATE], rmapt[MAX_NUMBER_INTERMEDIATE]; /* col/row map type for each Mat in mp[]. */ 7149 /* type-0: consecutive, start from 0; type-1: consecutive with */ 7150 /* a base offset; type-2: sparse with a local to global map table */ 7151 const PetscInt *cmapa[MAX_NUMBER_INTERMEDIATE], *rmapa[MAX_NUMBER_INTERMEDIATE]; /* col/row local to global map array (table) for type-2 map type */ 7152 7153 MatProductType ptype; 7154 PetscBool mptmp[MAX_NUMBER_INTERMEDIATE], hasoffproc = PETSC_FALSE, iscuda, iship, iskokk; 7155 PetscMPIInt size; 7156 7157 PetscFunctionBegin; 7158 MatCheckProduct(C, 1); 7159 PetscCheck(!product->data, PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Product data not empty"); 7160 ptype = product->type; 7161 if (product->A->symmetric == PETSC_BOOL3_TRUE && ptype == MATPRODUCT_AtB) { 7162 ptype = MATPRODUCT_AB; 7163 product->symbolic_used_the_fact_A_is_symmetric = PETSC_TRUE; 7164 } 7165 switch (ptype) { 7166 case MATPRODUCT_AB: 7167 A = product->A; 7168 P = product->B; 7169 m = A->rmap->n; 7170 n = P->cmap->n; 7171 M = A->rmap->N; 7172 N = P->cmap->N; 7173 hasoffproc = PETSC_FALSE; /* will not scatter mat product values to other processes */ 7174 break; 7175 case MATPRODUCT_AtB: 7176 P = product->A; 7177 A = product->B; 7178 m = P->cmap->n; 7179 n = A->cmap->n; 7180 M = P->cmap->N; 7181 N = A->cmap->N; 7182 hasoffproc = PETSC_TRUE; 7183 break; 7184 case MATPRODUCT_PtAP: 7185 A = product->A; 7186 P = product->B; 7187 m = P->cmap->n; 7188 n = P->cmap->n; 7189 M = P->cmap->N; 7190 N = P->cmap->N; 7191 hasoffproc = PETSC_TRUE; 7192 break; 7193 default: 7194 SETERRQ(PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Not for product type %s", MatProductTypes[ptype]); 7195 } 7196 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)C), &size)); 7197 if (size == 1) hasoffproc = PETSC_FALSE; 7198 7199 /* defaults */ 7200 for (i = 0; i < MAX_NUMBER_INTERMEDIATE; i++) { 7201 mp[i] = NULL; 7202 mptmp[i] = PETSC_FALSE; 7203 rmapt[i] = -1; 7204 cmapt[i] = -1; 7205 rmapa[i] = NULL; 7206 cmapa[i] = NULL; 7207 } 7208 7209 /* customization */ 7210 PetscCall(PetscNew(&mmdata)); 7211 mmdata->reusesym = product->api_user; 7212 if (ptype == MATPRODUCT_AB) { 7213 if (product->api_user) { 7214 PetscOptionsBegin(PetscObjectComm((PetscObject)C), ((PetscObject)C)->prefix, "MatMatMult", "Mat"); 7215 PetscCall(PetscOptionsBool("-matmatmult_backend_mergeB", "Merge product->B local matrices", "MatMatMult", mmdata->abmerge, &mmdata->abmerge, NULL)); 7216 PetscCall(PetscOptionsBool("-matmatmult_backend_pothbind", "Bind P_oth to CPU", "MatBindToCPU", mmdata->P_oth_bind, &mmdata->P_oth_bind, NULL)); 7217 PetscOptionsEnd(); 7218 } else { 7219 PetscOptionsBegin(PetscObjectComm((PetscObject)C), ((PetscObject)C)->prefix, "MatProduct_AB", "Mat"); 7220 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_mergeB", "Merge product->B local matrices", "MatMatMult", mmdata->abmerge, &mmdata->abmerge, NULL)); 7221 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_pothbind", "Bind P_oth to CPU", "MatBindToCPU", mmdata->P_oth_bind, &mmdata->P_oth_bind, NULL)); 7222 PetscOptionsEnd(); 7223 } 7224 } else if (ptype == MATPRODUCT_PtAP) { 7225 if (product->api_user) { 7226 PetscOptionsBegin(PetscObjectComm((PetscObject)C), ((PetscObject)C)->prefix, "MatPtAP", "Mat"); 7227 PetscCall(PetscOptionsBool("-matptap_backend_pothbind", "Bind P_oth to CPU", "MatBindToCPU", mmdata->P_oth_bind, &mmdata->P_oth_bind, NULL)); 7228 PetscOptionsEnd(); 7229 } else { 7230 PetscOptionsBegin(PetscObjectComm((PetscObject)C), ((PetscObject)C)->prefix, "MatProduct_PtAP", "Mat"); 7231 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_pothbind", "Bind P_oth to CPU", "MatBindToCPU", mmdata->P_oth_bind, &mmdata->P_oth_bind, NULL)); 7232 PetscOptionsEnd(); 7233 } 7234 } 7235 a = (Mat_MPIAIJ *)A->data; 7236 p = (Mat_MPIAIJ *)P->data; 7237 PetscCall(MatSetSizes(C, m, n, M, N)); 7238 PetscCall(PetscLayoutSetUp(C->rmap)); 7239 PetscCall(PetscLayoutSetUp(C->cmap)); 7240 PetscCall(MatSetType(C, ((PetscObject)A)->type_name)); 7241 PetscCall(MatGetOptionsPrefix(C, &prefix)); 7242 7243 cp = 0; 7244 switch (ptype) { 7245 case MATPRODUCT_AB: /* A * P */ 7246 PetscCall(MatGetBrowsOfAoCols_MPIAIJ(A, P, MAT_INITIAL_MATRIX, &mmdata->startsj_s, &mmdata->startsj_r, &mmdata->bufa, &mmdata->P_oth)); 7247 7248 /* A_diag * P_local (merged or not) */ 7249 if (mmdata->abmerge) { /* P's diagonal and off-diag blocks are merged to one matrix, then multiplied by A_diag */ 7250 /* P is product->B */ 7251 PetscCall(MatMPIAIJGetLocalMatMerge(P, MAT_INITIAL_MATRIX, &glob, &mmdata->Bloc)); 7252 PetscCall(MatProductCreate(a->A, mmdata->Bloc, NULL, &mp[cp])); 7253 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7254 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7255 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7256 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7257 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7258 mp[cp]->product->api_user = product->api_user; 7259 PetscCall(MatProductSetFromOptions(mp[cp])); 7260 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7261 PetscCall(ISGetIndices(glob, &globidx)); 7262 rmapt[cp] = 1; 7263 cmapt[cp] = 2; 7264 cmapa[cp] = globidx; 7265 mptmp[cp] = PETSC_FALSE; 7266 cp++; 7267 } else { /* A_diag * P_diag and A_diag * P_off */ 7268 PetscCall(MatProductCreate(a->A, p->A, NULL, &mp[cp])); 7269 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7270 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7271 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7272 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7273 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7274 mp[cp]->product->api_user = product->api_user; 7275 PetscCall(MatProductSetFromOptions(mp[cp])); 7276 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7277 rmapt[cp] = 1; 7278 cmapt[cp] = 1; 7279 mptmp[cp] = PETSC_FALSE; 7280 cp++; 7281 PetscCall(MatProductCreate(a->A, p->B, NULL, &mp[cp])); 7282 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7283 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7284 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7285 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7286 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7287 mp[cp]->product->api_user = product->api_user; 7288 PetscCall(MatProductSetFromOptions(mp[cp])); 7289 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7290 rmapt[cp] = 1; 7291 cmapt[cp] = 2; 7292 cmapa[cp] = p->garray; 7293 mptmp[cp] = PETSC_FALSE; 7294 cp++; 7295 } 7296 7297 /* A_off * P_other */ 7298 if (mmdata->P_oth) { 7299 PetscCall(MatSeqAIJCompactOutExtraColumns_SeqAIJ(mmdata->P_oth, &P_oth_l2g)); /* make P_oth use local col ids */ 7300 PetscCall(ISLocalToGlobalMappingGetIndices(P_oth_l2g, &P_oth_idx)); 7301 PetscCall(MatSetType(mmdata->P_oth, ((PetscObject)a->B)->type_name)); 7302 PetscCall(MatBindToCPU(mmdata->P_oth, mmdata->P_oth_bind)); 7303 PetscCall(MatProductCreate(a->B, mmdata->P_oth, NULL, &mp[cp])); 7304 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7305 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7306 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7307 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7308 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7309 mp[cp]->product->api_user = product->api_user; 7310 PetscCall(MatProductSetFromOptions(mp[cp])); 7311 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7312 rmapt[cp] = 1; 7313 cmapt[cp] = 2; 7314 cmapa[cp] = P_oth_idx; 7315 mptmp[cp] = PETSC_FALSE; 7316 cp++; 7317 } 7318 break; 7319 7320 case MATPRODUCT_AtB: /* (P^t * A): P_diag * A_loc + P_off * A_loc */ 7321 /* A is product->B */ 7322 PetscCall(MatMPIAIJGetLocalMatMerge(A, MAT_INITIAL_MATRIX, &glob, &mmdata->Bloc)); 7323 if (A == P) { /* when A==P, we can take advantage of the already merged mmdata->Bloc */ 7324 PetscCall(MatProductCreate(mmdata->Bloc, mmdata->Bloc, NULL, &mp[cp])); 7325 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AtB)); 7326 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7327 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7328 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7329 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7330 mp[cp]->product->api_user = product->api_user; 7331 PetscCall(MatProductSetFromOptions(mp[cp])); 7332 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7333 PetscCall(ISGetIndices(glob, &globidx)); 7334 rmapt[cp] = 2; 7335 rmapa[cp] = globidx; 7336 cmapt[cp] = 2; 7337 cmapa[cp] = globidx; 7338 mptmp[cp] = PETSC_FALSE; 7339 cp++; 7340 } else { 7341 PetscCall(MatProductCreate(p->A, mmdata->Bloc, NULL, &mp[cp])); 7342 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AtB)); 7343 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7344 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7345 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7346 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7347 mp[cp]->product->api_user = product->api_user; 7348 PetscCall(MatProductSetFromOptions(mp[cp])); 7349 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7350 PetscCall(ISGetIndices(glob, &globidx)); 7351 rmapt[cp] = 1; 7352 cmapt[cp] = 2; 7353 cmapa[cp] = globidx; 7354 mptmp[cp] = PETSC_FALSE; 7355 cp++; 7356 PetscCall(MatProductCreate(p->B, mmdata->Bloc, NULL, &mp[cp])); 7357 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AtB)); 7358 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7359 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7360 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7361 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7362 mp[cp]->product->api_user = product->api_user; 7363 PetscCall(MatProductSetFromOptions(mp[cp])); 7364 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7365 rmapt[cp] = 2; 7366 rmapa[cp] = p->garray; 7367 cmapt[cp] = 2; 7368 cmapa[cp] = globidx; 7369 mptmp[cp] = PETSC_FALSE; 7370 cp++; 7371 } 7372 break; 7373 case MATPRODUCT_PtAP: 7374 PetscCall(MatGetBrowsOfAoCols_MPIAIJ(A, P, MAT_INITIAL_MATRIX, &mmdata->startsj_s, &mmdata->startsj_r, &mmdata->bufa, &mmdata->P_oth)); 7375 /* P is product->B */ 7376 PetscCall(MatMPIAIJGetLocalMatMerge(P, MAT_INITIAL_MATRIX, &glob, &mmdata->Bloc)); 7377 PetscCall(MatProductCreate(a->A, mmdata->Bloc, NULL, &mp[cp])); 7378 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_PtAP)); 7379 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7380 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7381 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7382 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7383 mp[cp]->product->api_user = product->api_user; 7384 PetscCall(MatProductSetFromOptions(mp[cp])); 7385 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7386 PetscCall(ISGetIndices(glob, &globidx)); 7387 rmapt[cp] = 2; 7388 rmapa[cp] = globidx; 7389 cmapt[cp] = 2; 7390 cmapa[cp] = globidx; 7391 mptmp[cp] = PETSC_FALSE; 7392 cp++; 7393 if (mmdata->P_oth) { 7394 PetscCall(MatSeqAIJCompactOutExtraColumns_SeqAIJ(mmdata->P_oth, &P_oth_l2g)); 7395 PetscCall(ISLocalToGlobalMappingGetIndices(P_oth_l2g, &P_oth_idx)); 7396 PetscCall(MatSetType(mmdata->P_oth, ((PetscObject)a->B)->type_name)); 7397 PetscCall(MatBindToCPU(mmdata->P_oth, mmdata->P_oth_bind)); 7398 PetscCall(MatProductCreate(a->B, mmdata->P_oth, NULL, &mp[cp])); 7399 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7400 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7401 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7402 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7403 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7404 mp[cp]->product->api_user = product->api_user; 7405 PetscCall(MatProductSetFromOptions(mp[cp])); 7406 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7407 mptmp[cp] = PETSC_TRUE; 7408 cp++; 7409 PetscCall(MatProductCreate(mmdata->Bloc, mp[1], NULL, &mp[cp])); 7410 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AtB)); 7411 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7412 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7413 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7414 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7415 mp[cp]->product->api_user = product->api_user; 7416 PetscCall(MatProductSetFromOptions(mp[cp])); 7417 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7418 rmapt[cp] = 2; 7419 rmapa[cp] = globidx; 7420 cmapt[cp] = 2; 7421 cmapa[cp] = P_oth_idx; 7422 mptmp[cp] = PETSC_FALSE; 7423 cp++; 7424 } 7425 break; 7426 default: 7427 SETERRQ(PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Not for product type %s", MatProductTypes[ptype]); 7428 } 7429 /* sanity check */ 7430 if (size > 1) 7431 for (i = 0; i < cp; i++) PetscCheck(rmapt[i] != 2 || hasoffproc, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Unexpected offproc map type for product %" PetscInt_FMT, i); 7432 7433 PetscCall(PetscMalloc2(cp, &mmdata->mp, cp, &mmdata->mptmp)); 7434 for (i = 0; i < cp; i++) { 7435 mmdata->mp[i] = mp[i]; 7436 mmdata->mptmp[i] = mptmp[i]; 7437 } 7438 mmdata->cp = cp; 7439 C->product->data = mmdata; 7440 C->product->destroy = MatDestroy_MatMatMPIAIJBACKEND; 7441 C->ops->productnumeric = MatProductNumeric_MPIAIJBACKEND; 7442 7443 /* memory type */ 7444 mmdata->mtype = PETSC_MEMTYPE_HOST; 7445 PetscCall(PetscObjectTypeCompareAny((PetscObject)C, &iscuda, MATSEQAIJCUSPARSE, MATMPIAIJCUSPARSE, "")); 7446 PetscCall(PetscObjectTypeCompareAny((PetscObject)C, &iship, MATSEQAIJHIPSPARSE, MATMPIAIJHIPSPARSE, "")); 7447 PetscCall(PetscObjectTypeCompareAny((PetscObject)C, &iskokk, MATSEQAIJKOKKOS, MATMPIAIJKOKKOS, "")); 7448 if (iscuda) mmdata->mtype = PETSC_MEMTYPE_CUDA; 7449 else if (iship) mmdata->mtype = PETSC_MEMTYPE_HIP; 7450 else if (iskokk) mmdata->mtype = PETSC_MEMTYPE_KOKKOS; 7451 7452 /* prepare coo coordinates for values insertion */ 7453 7454 /* count total nonzeros of those intermediate seqaij Mats 7455 ncoo_d: # of nonzeros of matrices that do not have offproc entries 7456 ncoo_o: # of nonzeros (of matrices that might have offproc entries) that will be inserted to remote procs 7457 ncoo_oown: # of nonzeros (of matrices that might have offproc entries) that will be inserted locally 7458 */ 7459 for (cp = 0, ncoo_d = 0, ncoo_o = 0, ncoo_oown = 0; cp < mmdata->cp; cp++) { 7460 Mat_SeqAIJ *mm = (Mat_SeqAIJ *)mp[cp]->data; 7461 if (mptmp[cp]) continue; 7462 if (rmapt[cp] == 2 && hasoffproc) { /* the rows need to be scatter to all processes (might include self) */ 7463 const PetscInt *rmap = rmapa[cp]; 7464 const PetscInt mr = mp[cp]->rmap->n; 7465 const PetscInt rs = C->rmap->rstart; 7466 const PetscInt re = C->rmap->rend; 7467 const PetscInt *ii = mm->i; 7468 for (i = 0; i < mr; i++) { 7469 const PetscInt gr = rmap[i]; 7470 const PetscInt nz = ii[i + 1] - ii[i]; 7471 if (gr < rs || gr >= re) ncoo_o += nz; /* this row is offproc */ 7472 else ncoo_oown += nz; /* this row is local */ 7473 } 7474 } else ncoo_d += mm->nz; 7475 } 7476 7477 /* 7478 ncoo: total number of nonzeros (including those inserted by remote procs) belonging to this proc 7479 7480 ncoo = ncoo_d + ncoo_oown + ncoo2, which ncoo2 is number of nonzeros inserted to me by other procs. 7481 7482 off[0] points to a big index array, which is shared by off[1,2,...]. Similarly, for own[0]. 7483 7484 off[p]: points to the segment for matrix mp[p], storing location of nonzeros that mp[p] will insert to others 7485 own[p]: points to the segment for matrix mp[p], storing location of nonzeros that mp[p] will insert locally 7486 so, off[p+1]-off[p] is the number of nonzeros that mp[p] will send to others. 7487 7488 coo_i/j/v[]: [ncoo] row/col/val of nonzeros belonging to this proc. 7489 Ex. coo_i[]: the beginning part (of size ncoo_d + ncoo_oown) stores i of local nonzeros, and the remaining part stores i of nonzeros I will receive. 7490 */ 7491 PetscCall(PetscCalloc1(mmdata->cp + 1, &mmdata->off)); /* +1 to make a csr-like data structure */ 7492 PetscCall(PetscCalloc1(mmdata->cp + 1, &mmdata->own)); 7493 7494 /* gather (i,j) of nonzeros inserted by remote procs */ 7495 if (hasoffproc) { 7496 PetscSF msf; 7497 PetscInt ncoo2, *coo_i2, *coo_j2; 7498 7499 PetscCall(PetscMalloc1(ncoo_o, &mmdata->off[0])); 7500 PetscCall(PetscMalloc1(ncoo_oown, &mmdata->own[0])); 7501 PetscCall(PetscMalloc2(ncoo_o, &coo_i, ncoo_o, &coo_j)); /* to collect (i,j) of entries to be sent to others */ 7502 7503 for (cp = 0, ncoo_o = 0; cp < mmdata->cp; cp++) { 7504 Mat_SeqAIJ *mm = (Mat_SeqAIJ *)mp[cp]->data; 7505 PetscInt *idxoff = mmdata->off[cp]; 7506 PetscInt *idxown = mmdata->own[cp]; 7507 if (!mptmp[cp] && rmapt[cp] == 2) { /* row map is sparse */ 7508 const PetscInt *rmap = rmapa[cp]; 7509 const PetscInt *cmap = cmapa[cp]; 7510 const PetscInt *ii = mm->i; 7511 PetscInt *coi = coo_i + ncoo_o; 7512 PetscInt *coj = coo_j + ncoo_o; 7513 const PetscInt mr = mp[cp]->rmap->n; 7514 const PetscInt rs = C->rmap->rstart; 7515 const PetscInt re = C->rmap->rend; 7516 const PetscInt cs = C->cmap->rstart; 7517 for (i = 0; i < mr; i++) { 7518 const PetscInt *jj = mm->j + ii[i]; 7519 const PetscInt gr = rmap[i]; 7520 const PetscInt nz = ii[i + 1] - ii[i]; 7521 if (gr < rs || gr >= re) { /* this is an offproc row */ 7522 for (j = ii[i]; j < ii[i + 1]; j++) { 7523 *coi++ = gr; 7524 *idxoff++ = j; 7525 } 7526 if (!cmapt[cp]) { /* already global */ 7527 for (j = 0; j < nz; j++) *coj++ = jj[j]; 7528 } else if (cmapt[cp] == 1) { /* local to global for owned columns of C */ 7529 for (j = 0; j < nz; j++) *coj++ = jj[j] + cs; 7530 } else { /* offdiag */ 7531 for (j = 0; j < nz; j++) *coj++ = cmap[jj[j]]; 7532 } 7533 ncoo_o += nz; 7534 } else { /* this is a local row */ 7535 for (j = ii[i]; j < ii[i + 1]; j++) *idxown++ = j; 7536 } 7537 } 7538 } 7539 mmdata->off[cp + 1] = idxoff; 7540 mmdata->own[cp + 1] = idxown; 7541 } 7542 7543 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)C), &mmdata->sf)); 7544 PetscInt incoo_o; 7545 PetscCall(PetscIntCast(ncoo_o, &incoo_o)); 7546 PetscCall(PetscSFSetGraphLayout(mmdata->sf, C->rmap, incoo_o /*nleaves*/, NULL /*ilocal*/, PETSC_OWN_POINTER, coo_i)); 7547 PetscCall(PetscSFGetMultiSF(mmdata->sf, &msf)); 7548 PetscCall(PetscSFGetGraph(msf, &ncoo2 /*nroots*/, NULL, NULL, NULL)); 7549 ncoo = ncoo_d + ncoo_oown + ncoo2; 7550 PetscCall(PetscMalloc2(ncoo, &coo_i2, ncoo, &coo_j2)); 7551 PetscCall(PetscSFGatherBegin(mmdata->sf, MPIU_INT, coo_i, coo_i2 + ncoo_d + ncoo_oown)); /* put (i,j) of remote nonzeros at back */ 7552 PetscCall(PetscSFGatherEnd(mmdata->sf, MPIU_INT, coo_i, coo_i2 + ncoo_d + ncoo_oown)); 7553 PetscCall(PetscSFGatherBegin(mmdata->sf, MPIU_INT, coo_j, coo_j2 + ncoo_d + ncoo_oown)); 7554 PetscCall(PetscSFGatherEnd(mmdata->sf, MPIU_INT, coo_j, coo_j2 + ncoo_d + ncoo_oown)); 7555 PetscCall(PetscFree2(coo_i, coo_j)); 7556 /* allocate MPI send buffer to collect nonzero values to be sent to remote procs */ 7557 PetscCall(PetscSFMalloc(mmdata->sf, mmdata->mtype, ncoo_o * sizeof(PetscScalar), (void **)&mmdata->coo_w)); 7558 coo_i = coo_i2; 7559 coo_j = coo_j2; 7560 } else { /* no offproc values insertion */ 7561 ncoo = ncoo_d; 7562 PetscCall(PetscMalloc2(ncoo, &coo_i, ncoo, &coo_j)); 7563 7564 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)C), &mmdata->sf)); 7565 PetscCall(PetscSFSetGraph(mmdata->sf, 0, 0, NULL, PETSC_OWN_POINTER, NULL, PETSC_OWN_POINTER)); 7566 PetscCall(PetscSFSetUp(mmdata->sf)); 7567 } 7568 mmdata->hasoffproc = hasoffproc; 7569 7570 /* gather (i,j) of nonzeros inserted locally */ 7571 for (cp = 0, ncoo_d = 0; cp < mmdata->cp; cp++) { 7572 Mat_SeqAIJ *mm = (Mat_SeqAIJ *)mp[cp]->data; 7573 PetscInt *coi = coo_i + ncoo_d; 7574 PetscInt *coj = coo_j + ncoo_d; 7575 const PetscInt *jj = mm->j; 7576 const PetscInt *ii = mm->i; 7577 const PetscInt *cmap = cmapa[cp]; 7578 const PetscInt *rmap = rmapa[cp]; 7579 const PetscInt mr = mp[cp]->rmap->n; 7580 const PetscInt rs = C->rmap->rstart; 7581 const PetscInt re = C->rmap->rend; 7582 const PetscInt cs = C->cmap->rstart; 7583 7584 if (mptmp[cp]) continue; 7585 if (rmapt[cp] == 1) { /* consecutive rows */ 7586 /* fill coo_i */ 7587 for (i = 0; i < mr; i++) { 7588 const PetscInt gr = i + rs; 7589 for (j = ii[i]; j < ii[i + 1]; j++) coi[j] = gr; 7590 } 7591 /* fill coo_j */ 7592 if (!cmapt[cp]) { /* type-0, already global */ 7593 PetscCall(PetscArraycpy(coj, jj, mm->nz)); 7594 } else if (cmapt[cp] == 1) { /* type-1, local to global for consecutive columns of C */ 7595 for (j = 0; j < mm->nz; j++) coj[j] = jj[j] + cs; /* lid + col start */ 7596 } else { /* type-2, local to global for sparse columns */ 7597 for (j = 0; j < mm->nz; j++) coj[j] = cmap[jj[j]]; 7598 } 7599 ncoo_d += mm->nz; 7600 } else if (rmapt[cp] == 2) { /* sparse rows */ 7601 for (i = 0; i < mr; i++) { 7602 const PetscInt *jj = mm->j + ii[i]; 7603 const PetscInt gr = rmap[i]; 7604 const PetscInt nz = ii[i + 1] - ii[i]; 7605 if (gr >= rs && gr < re) { /* local rows */ 7606 for (j = ii[i]; j < ii[i + 1]; j++) *coi++ = gr; 7607 if (!cmapt[cp]) { /* type-0, already global */ 7608 for (j = 0; j < nz; j++) *coj++ = jj[j]; 7609 } else if (cmapt[cp] == 1) { /* local to global for owned columns of C */ 7610 for (j = 0; j < nz; j++) *coj++ = jj[j] + cs; 7611 } else { /* type-2, local to global for sparse columns */ 7612 for (j = 0; j < nz; j++) *coj++ = cmap[jj[j]]; 7613 } 7614 ncoo_d += nz; 7615 } 7616 } 7617 } 7618 } 7619 if (glob) PetscCall(ISRestoreIndices(glob, &globidx)); 7620 PetscCall(ISDestroy(&glob)); 7621 if (P_oth_l2g) PetscCall(ISLocalToGlobalMappingRestoreIndices(P_oth_l2g, &P_oth_idx)); 7622 PetscCall(ISLocalToGlobalMappingDestroy(&P_oth_l2g)); 7623 /* allocate an array to store all nonzeros (inserted locally or remotely) belonging to this proc */ 7624 PetscCall(PetscSFMalloc(mmdata->sf, mmdata->mtype, ncoo * sizeof(PetscScalar), (void **)&mmdata->coo_v)); 7625 7626 /* set block sizes */ 7627 A = product->A; 7628 P = product->B; 7629 switch (ptype) { 7630 case MATPRODUCT_PtAP: 7631 PetscCall(MatSetBlockSizes(C, P->cmap->bs, P->cmap->bs)); 7632 break; 7633 case MATPRODUCT_RARt: 7634 PetscCall(MatSetBlockSizes(C, P->rmap->bs, P->rmap->bs)); 7635 break; 7636 case MATPRODUCT_ABC: 7637 PetscCall(MatSetBlockSizesFromMats(C, A, product->C)); 7638 break; 7639 case MATPRODUCT_AB: 7640 PetscCall(MatSetBlockSizesFromMats(C, A, P)); 7641 break; 7642 case MATPRODUCT_AtB: 7643 PetscCall(MatSetBlockSizes(C, A->cmap->bs, P->cmap->bs)); 7644 break; 7645 case MATPRODUCT_ABt: 7646 PetscCall(MatSetBlockSizes(C, A->rmap->bs, P->rmap->bs)); 7647 break; 7648 default: 7649 SETERRQ(PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Not for ProductType %s", MatProductTypes[ptype]); 7650 } 7651 7652 /* preallocate with COO data */ 7653 PetscCall(MatSetPreallocationCOO(C, ncoo, coo_i, coo_j)); 7654 PetscCall(PetscFree2(coo_i, coo_j)); 7655 PetscFunctionReturn(PETSC_SUCCESS); 7656 } 7657 7658 PetscErrorCode MatProductSetFromOptions_MPIAIJBACKEND(Mat mat) 7659 { 7660 Mat_Product *product = mat->product; 7661 #if defined(PETSC_HAVE_DEVICE) 7662 PetscBool match = PETSC_FALSE; 7663 PetscBool usecpu = PETSC_FALSE; 7664 #else 7665 PetscBool match = PETSC_TRUE; 7666 #endif 7667 7668 PetscFunctionBegin; 7669 MatCheckProduct(mat, 1); 7670 #if defined(PETSC_HAVE_DEVICE) 7671 if (!product->A->boundtocpu && !product->B->boundtocpu) PetscCall(PetscObjectTypeCompare((PetscObject)product->B, ((PetscObject)product->A)->type_name, &match)); 7672 if (match) { /* we can always fallback to the CPU if requested */ 7673 switch (product->type) { 7674 case MATPRODUCT_AB: 7675 if (product->api_user) { 7676 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatMatMult", "Mat"); 7677 PetscCall(PetscOptionsBool("-matmatmult_backend_cpu", "Use CPU code", "MatMatMult", usecpu, &usecpu, NULL)); 7678 PetscOptionsEnd(); 7679 } else { 7680 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatProduct_AB", "Mat"); 7681 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_cpu", "Use CPU code", "MatMatMult", usecpu, &usecpu, NULL)); 7682 PetscOptionsEnd(); 7683 } 7684 break; 7685 case MATPRODUCT_AtB: 7686 if (product->api_user) { 7687 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatTransposeMatMult", "Mat"); 7688 PetscCall(PetscOptionsBool("-mattransposematmult_backend_cpu", "Use CPU code", "MatTransposeMatMult", usecpu, &usecpu, NULL)); 7689 PetscOptionsEnd(); 7690 } else { 7691 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatProduct_AtB", "Mat"); 7692 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_cpu", "Use CPU code", "MatTransposeMatMult", usecpu, &usecpu, NULL)); 7693 PetscOptionsEnd(); 7694 } 7695 break; 7696 case MATPRODUCT_PtAP: 7697 if (product->api_user) { 7698 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatPtAP", "Mat"); 7699 PetscCall(PetscOptionsBool("-matptap_backend_cpu", "Use CPU code", "MatPtAP", usecpu, &usecpu, NULL)); 7700 PetscOptionsEnd(); 7701 } else { 7702 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatProduct_PtAP", "Mat"); 7703 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_cpu", "Use CPU code", "MatPtAP", usecpu, &usecpu, NULL)); 7704 PetscOptionsEnd(); 7705 } 7706 break; 7707 default: 7708 break; 7709 } 7710 match = (PetscBool)!usecpu; 7711 } 7712 #endif 7713 if (match) { 7714 switch (product->type) { 7715 case MATPRODUCT_AB: 7716 case MATPRODUCT_AtB: 7717 case MATPRODUCT_PtAP: 7718 mat->ops->productsymbolic = MatProductSymbolic_MPIAIJBACKEND; 7719 break; 7720 default: 7721 break; 7722 } 7723 } 7724 /* fallback to MPIAIJ ops */ 7725 if (!mat->ops->productsymbolic) PetscCall(MatProductSetFromOptions_MPIAIJ(mat)); 7726 PetscFunctionReturn(PETSC_SUCCESS); 7727 } 7728 7729 /* 7730 Produces a set of block column indices of the matrix row, one for each block represented in the original row 7731 7732 n - the number of block indices in cc[] 7733 cc - the block indices (must be large enough to contain the indices) 7734 */ 7735 static inline PetscErrorCode MatCollapseRow(Mat Amat, PetscInt row, PetscInt bs, PetscInt *n, PetscInt *cc) 7736 { 7737 PetscInt cnt = -1, nidx, j; 7738 const PetscInt *idx; 7739 7740 PetscFunctionBegin; 7741 PetscCall(MatGetRow(Amat, row, &nidx, &idx, NULL)); 7742 if (nidx) { 7743 cnt = 0; 7744 cc[cnt] = idx[0] / bs; 7745 for (j = 1; j < nidx; j++) { 7746 if (cc[cnt] < idx[j] / bs) cc[++cnt] = idx[j] / bs; 7747 } 7748 } 7749 PetscCall(MatRestoreRow(Amat, row, &nidx, &idx, NULL)); 7750 *n = cnt + 1; 7751 PetscFunctionReturn(PETSC_SUCCESS); 7752 } 7753 7754 /* 7755 Produces a set of block column indices of the matrix block row, one for each block represented in the original set of rows 7756 7757 ncollapsed - the number of block indices 7758 collapsed - the block indices (must be large enough to contain the indices) 7759 */ 7760 static inline PetscErrorCode MatCollapseRows(Mat Amat, PetscInt start, PetscInt bs, PetscInt *w0, PetscInt *w1, PetscInt *w2, PetscInt *ncollapsed, PetscInt **collapsed) 7761 { 7762 PetscInt i, nprev, *cprev = w0, ncur = 0, *ccur = w1, *merged = w2, *cprevtmp; 7763 7764 PetscFunctionBegin; 7765 PetscCall(MatCollapseRow(Amat, start, bs, &nprev, cprev)); 7766 for (i = start + 1; i < start + bs; i++) { 7767 PetscCall(MatCollapseRow(Amat, i, bs, &ncur, ccur)); 7768 PetscCall(PetscMergeIntArray(nprev, cprev, ncur, ccur, &nprev, &merged)); 7769 cprevtmp = cprev; 7770 cprev = merged; 7771 merged = cprevtmp; 7772 } 7773 *ncollapsed = nprev; 7774 if (collapsed) *collapsed = cprev; 7775 PetscFunctionReturn(PETSC_SUCCESS); 7776 } 7777 7778 /* 7779 MatCreateGraph_Simple_AIJ - create simple scalar matrix (graph) from potentially blocked matrix 7780 7781 Input Parameter: 7782 . Amat - matrix 7783 - symmetrize - make the result symmetric 7784 + scale - scale with diagonal 7785 7786 Output Parameter: 7787 . a_Gmat - output scalar graph >= 0 7788 7789 */ 7790 PETSC_INTERN PetscErrorCode MatCreateGraph_Simple_AIJ(Mat Amat, PetscBool symmetrize, PetscBool scale, PetscReal filter, PetscInt index_size, PetscInt index[], Mat *a_Gmat) 7791 { 7792 PetscInt Istart, Iend, Ii, jj, kk, ncols, nloc, NN, MM, bs; 7793 MPI_Comm comm; 7794 Mat Gmat; 7795 PetscBool ismpiaij, isseqaij; 7796 Mat a, b, c; 7797 MatType jtype; 7798 7799 PetscFunctionBegin; 7800 PetscCall(PetscObjectGetComm((PetscObject)Amat, &comm)); 7801 PetscCall(MatGetOwnershipRange(Amat, &Istart, &Iend)); 7802 PetscCall(MatGetSize(Amat, &MM, &NN)); 7803 PetscCall(MatGetBlockSize(Amat, &bs)); 7804 nloc = (Iend - Istart) / bs; 7805 7806 PetscCall(PetscObjectBaseTypeCompare((PetscObject)Amat, MATSEQAIJ, &isseqaij)); 7807 PetscCall(PetscObjectBaseTypeCompare((PetscObject)Amat, MATMPIAIJ, &ismpiaij)); 7808 PetscCheck(isseqaij || ismpiaij, comm, PETSC_ERR_USER, "Require (MPI)AIJ matrix type"); 7809 7810 /* TODO GPU: these calls are potentially expensive if matrices are large and we want to use the GPU */ 7811 /* A solution consists in providing a new API, MatAIJGetCollapsedAIJ, and each class can provide a fast 7812 implementation */ 7813 if (bs > 1) { 7814 PetscCall(MatGetType(Amat, &jtype)); 7815 PetscCall(MatCreate(comm, &Gmat)); 7816 PetscCall(MatSetType(Gmat, jtype)); 7817 PetscCall(MatSetSizes(Gmat, nloc, nloc, PETSC_DETERMINE, PETSC_DETERMINE)); 7818 PetscCall(MatSetBlockSizes(Gmat, 1, 1)); 7819 if (isseqaij || ((Mat_MPIAIJ *)Amat->data)->garray) { 7820 PetscInt *d_nnz, *o_nnz; 7821 MatScalar *aa, val, *AA; 7822 PetscInt *aj, *ai, *AJ, nc, nmax = 0; 7823 7824 if (isseqaij) { 7825 a = Amat; 7826 b = NULL; 7827 } else { 7828 Mat_MPIAIJ *d = (Mat_MPIAIJ *)Amat->data; 7829 a = d->A; 7830 b = d->B; 7831 } 7832 PetscCall(PetscInfo(Amat, "New bs>1 Graph. nloc=%" PetscInt_FMT "\n", nloc)); 7833 PetscCall(PetscMalloc2(nloc, &d_nnz, (isseqaij ? 0 : nloc), &o_nnz)); 7834 for (c = a, kk = 0; c && kk < 2; c = b, kk++) { 7835 PetscInt *nnz = (c == a) ? d_nnz : o_nnz; 7836 const PetscInt *cols1, *cols2; 7837 7838 for (PetscInt brow = 0, nc1, nc2, ok = 1; brow < nloc * bs; brow += bs) { // block rows 7839 PetscCall(MatGetRow(c, brow, &nc2, &cols2, NULL)); 7840 nnz[brow / bs] = nc2 / bs; 7841 if (nc2 % bs) ok = 0; 7842 if (nnz[brow / bs] > nmax) nmax = nnz[brow / bs]; 7843 for (PetscInt ii = 1; ii < bs; ii++) { // check for non-dense blocks 7844 PetscCall(MatGetRow(c, brow + ii, &nc1, &cols1, NULL)); 7845 if (nc1 != nc2) ok = 0; 7846 else { 7847 for (PetscInt jj = 0; jj < nc1 && ok == 1; jj++) { 7848 if (cols1[jj] != cols2[jj]) ok = 0; 7849 if (cols1[jj] % bs != jj % bs) ok = 0; 7850 } 7851 } 7852 PetscCall(MatRestoreRow(c, brow + ii, &nc1, &cols1, NULL)); 7853 } 7854 PetscCall(MatRestoreRow(c, brow, &nc2, &cols2, NULL)); 7855 if (!ok) { 7856 PetscCall(PetscFree2(d_nnz, o_nnz)); 7857 PetscCall(PetscInfo(Amat, "Found sparse blocks - revert to slow method\n")); 7858 goto old_bs; 7859 } 7860 } 7861 } 7862 PetscCall(MatSeqAIJSetPreallocation(Gmat, 0, d_nnz)); 7863 PetscCall(MatMPIAIJSetPreallocation(Gmat, 0, d_nnz, 0, o_nnz)); 7864 PetscCall(PetscFree2(d_nnz, o_nnz)); 7865 PetscCall(PetscMalloc2(nmax, &AA, nmax, &AJ)); 7866 // diag 7867 for (PetscInt brow = 0, n, grow; brow < nloc * bs; brow += bs) { // block rows 7868 Mat_SeqAIJ *aseq = (Mat_SeqAIJ *)a->data; 7869 7870 ai = aseq->i; 7871 n = ai[brow + 1] - ai[brow]; 7872 aj = aseq->j + ai[brow]; 7873 for (PetscInt k = 0; k < n; k += bs) { // block columns 7874 AJ[k / bs] = aj[k] / bs + Istart / bs; // diag starts at (Istart,Istart) 7875 val = 0; 7876 if (index_size == 0) { 7877 for (PetscInt ii = 0; ii < bs; ii++) { // rows in block 7878 aa = aseq->a + ai[brow + ii] + k; 7879 for (PetscInt jj = 0; jj < bs; jj++) { // columns in block 7880 val += PetscAbs(PetscRealPart(aa[jj])); // a sort of norm 7881 } 7882 } 7883 } else { // use (index,index) value if provided 7884 for (PetscInt iii = 0; iii < index_size; iii++) { // rows in block 7885 PetscInt ii = index[iii]; 7886 aa = aseq->a + ai[brow + ii] + k; 7887 for (PetscInt jjj = 0; jjj < index_size; jjj++) { // columns in block 7888 PetscInt jj = index[jjj]; 7889 val += PetscAbs(PetscRealPart(aa[jj])); 7890 } 7891 } 7892 } 7893 PetscAssert(k / bs < nmax, comm, PETSC_ERR_USER, "k / bs (%" PetscInt_FMT ") >= nmax (%" PetscInt_FMT ")", k / bs, nmax); 7894 AA[k / bs] = val; 7895 } 7896 grow = Istart / bs + brow / bs; 7897 PetscCall(MatSetValues(Gmat, 1, &grow, n / bs, AJ, AA, ADD_VALUES)); 7898 } 7899 // off-diag 7900 if (ismpiaij) { 7901 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)Amat->data; 7902 const PetscScalar *vals; 7903 const PetscInt *cols, *garray = aij->garray; 7904 7905 PetscCheck(garray, PETSC_COMM_SELF, PETSC_ERR_USER, "No garray ?"); 7906 for (PetscInt brow = 0, grow; brow < nloc * bs; brow += bs) { // block rows 7907 PetscCall(MatGetRow(b, brow, &ncols, &cols, NULL)); 7908 for (PetscInt k = 0, cidx = 0; k < ncols; k += bs, cidx++) { 7909 PetscAssert(k / bs < nmax, comm, PETSC_ERR_USER, "k / bs >= nmax"); 7910 AA[k / bs] = 0; 7911 AJ[cidx] = garray[cols[k]] / bs; 7912 } 7913 nc = ncols / bs; 7914 PetscCall(MatRestoreRow(b, brow, &ncols, &cols, NULL)); 7915 if (index_size == 0) { 7916 for (PetscInt ii = 0; ii < bs; ii++) { // rows in block 7917 PetscCall(MatGetRow(b, brow + ii, &ncols, &cols, &vals)); 7918 for (PetscInt k = 0; k < ncols; k += bs) { 7919 for (PetscInt jj = 0; jj < bs; jj++) { // cols in block 7920 PetscAssert(k / bs < nmax, comm, PETSC_ERR_USER, "k / bs (%" PetscInt_FMT ") >= nmax (%" PetscInt_FMT ")", k / bs, nmax); 7921 AA[k / bs] += PetscAbs(PetscRealPart(vals[k + jj])); 7922 } 7923 } 7924 PetscCall(MatRestoreRow(b, brow + ii, &ncols, &cols, &vals)); 7925 } 7926 } else { // use (index,index) value if provided 7927 for (PetscInt iii = 0; iii < index_size; iii++) { // rows in block 7928 PetscInt ii = index[iii]; 7929 PetscCall(MatGetRow(b, brow + ii, &ncols, &cols, &vals)); 7930 for (PetscInt k = 0; k < ncols; k += bs) { 7931 for (PetscInt jjj = 0; jjj < index_size; jjj++) { // cols in block 7932 PetscInt jj = index[jjj]; 7933 AA[k / bs] += PetscAbs(PetscRealPart(vals[k + jj])); 7934 } 7935 } 7936 PetscCall(MatRestoreRow(b, brow + ii, &ncols, &cols, &vals)); 7937 } 7938 } 7939 grow = Istart / bs + brow / bs; 7940 PetscCall(MatSetValues(Gmat, 1, &grow, nc, AJ, AA, ADD_VALUES)); 7941 } 7942 } 7943 PetscCall(MatAssemblyBegin(Gmat, MAT_FINAL_ASSEMBLY)); 7944 PetscCall(MatAssemblyEnd(Gmat, MAT_FINAL_ASSEMBLY)); 7945 PetscCall(PetscFree2(AA, AJ)); 7946 } else { 7947 const PetscScalar *vals; 7948 const PetscInt *idx; 7949 PetscInt *d_nnz, *o_nnz, *w0, *w1, *w2; 7950 old_bs: 7951 /* 7952 Determine the preallocation needed for the scalar matrix derived from the vector matrix. 7953 */ 7954 PetscCall(PetscInfo(Amat, "OLD bs>1 CreateGraph\n")); 7955 PetscCall(PetscMalloc2(nloc, &d_nnz, (isseqaij ? 0 : nloc), &o_nnz)); 7956 if (isseqaij) { 7957 PetscInt max_d_nnz; 7958 7959 /* 7960 Determine exact preallocation count for (sequential) scalar matrix 7961 */ 7962 PetscCall(MatSeqAIJGetMaxRowNonzeros(Amat, &max_d_nnz)); 7963 max_d_nnz = PetscMin(nloc, bs * max_d_nnz); 7964 PetscCall(PetscMalloc3(max_d_nnz, &w0, max_d_nnz, &w1, max_d_nnz, &w2)); 7965 for (Ii = 0, jj = 0; Ii < Iend; Ii += bs, jj++) PetscCall(MatCollapseRows(Amat, Ii, bs, w0, w1, w2, &d_nnz[jj], NULL)); 7966 PetscCall(PetscFree3(w0, w1, w2)); 7967 } else if (ismpiaij) { 7968 Mat Daij, Oaij; 7969 const PetscInt *garray; 7970 PetscInt max_d_nnz; 7971 7972 PetscCall(MatMPIAIJGetSeqAIJ(Amat, &Daij, &Oaij, &garray)); 7973 /* 7974 Determine exact preallocation count for diagonal block portion of scalar matrix 7975 */ 7976 PetscCall(MatSeqAIJGetMaxRowNonzeros(Daij, &max_d_nnz)); 7977 max_d_nnz = PetscMin(nloc, bs * max_d_nnz); 7978 PetscCall(PetscMalloc3(max_d_nnz, &w0, max_d_nnz, &w1, max_d_nnz, &w2)); 7979 for (Ii = 0, jj = 0; Ii < Iend - Istart; Ii += bs, jj++) PetscCall(MatCollapseRows(Daij, Ii, bs, w0, w1, w2, &d_nnz[jj], NULL)); 7980 PetscCall(PetscFree3(w0, w1, w2)); 7981 /* 7982 Over estimate (usually grossly over), preallocation count for off-diagonal portion of scalar matrix 7983 */ 7984 for (Ii = 0, jj = 0; Ii < Iend - Istart; Ii += bs, jj++) { 7985 o_nnz[jj] = 0; 7986 for (kk = 0; kk < bs; kk++) { /* rows that get collapsed to a single row */ 7987 PetscCall(MatGetRow(Oaij, Ii + kk, &ncols, NULL, NULL)); 7988 o_nnz[jj] += ncols; 7989 PetscCall(MatRestoreRow(Oaij, Ii + kk, &ncols, NULL, NULL)); 7990 } 7991 if (o_nnz[jj] > (NN / bs - nloc)) o_nnz[jj] = NN / bs - nloc; 7992 } 7993 } else SETERRQ(comm, PETSC_ERR_USER, "Require AIJ matrix type"); 7994 /* get scalar copy (norms) of matrix */ 7995 PetscCall(MatSeqAIJSetPreallocation(Gmat, 0, d_nnz)); 7996 PetscCall(MatMPIAIJSetPreallocation(Gmat, 0, d_nnz, 0, o_nnz)); 7997 PetscCall(PetscFree2(d_nnz, o_nnz)); 7998 for (Ii = Istart; Ii < Iend; Ii++) { 7999 PetscInt dest_row = Ii / bs; 8000 8001 PetscCall(MatGetRow(Amat, Ii, &ncols, &idx, &vals)); 8002 for (jj = 0; jj < ncols; jj++) { 8003 PetscInt dest_col = idx[jj] / bs; 8004 PetscScalar sv = PetscAbs(PetscRealPart(vals[jj])); 8005 8006 PetscCall(MatSetValues(Gmat, 1, &dest_row, 1, &dest_col, &sv, ADD_VALUES)); 8007 } 8008 PetscCall(MatRestoreRow(Amat, Ii, &ncols, &idx, &vals)); 8009 } 8010 PetscCall(MatAssemblyBegin(Gmat, MAT_FINAL_ASSEMBLY)); 8011 PetscCall(MatAssemblyEnd(Gmat, MAT_FINAL_ASSEMBLY)); 8012 } 8013 } else { 8014 if (symmetrize || filter >= 0 || scale) PetscCall(MatDuplicate(Amat, MAT_COPY_VALUES, &Gmat)); 8015 else { 8016 Gmat = Amat; 8017 PetscCall(PetscObjectReference((PetscObject)Gmat)); 8018 } 8019 if (isseqaij) { 8020 a = Gmat; 8021 b = NULL; 8022 } else { 8023 Mat_MPIAIJ *d = (Mat_MPIAIJ *)Gmat->data; 8024 a = d->A; 8025 b = d->B; 8026 } 8027 if (filter >= 0 || scale) { 8028 /* take absolute value of each entry */ 8029 for (c = a, kk = 0; c && kk < 2; c = b, kk++) { 8030 MatInfo info; 8031 PetscScalar *avals; 8032 8033 PetscCall(MatGetInfo(c, MAT_LOCAL, &info)); 8034 PetscCall(MatSeqAIJGetArray(c, &avals)); 8035 for (int jj = 0; jj < info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]); 8036 PetscCall(MatSeqAIJRestoreArray(c, &avals)); 8037 } 8038 } 8039 } 8040 if (symmetrize) { 8041 PetscBool isset, issym; 8042 8043 PetscCall(MatIsSymmetricKnown(Amat, &isset, &issym)); 8044 if (!isset || !issym) { 8045 Mat matTrans; 8046 8047 PetscCall(MatTranspose(Gmat, MAT_INITIAL_MATRIX, &matTrans)); 8048 PetscCall(MatAXPY(Gmat, 1.0, matTrans, Gmat->structurally_symmetric == PETSC_BOOL3_TRUE ? SAME_NONZERO_PATTERN : DIFFERENT_NONZERO_PATTERN)); 8049 PetscCall(MatDestroy(&matTrans)); 8050 } 8051 PetscCall(MatSetOption(Gmat, MAT_SYMMETRIC, PETSC_TRUE)); 8052 } else if (Amat != Gmat) PetscCall(MatPropagateSymmetryOptions(Amat, Gmat)); 8053 if (scale) { 8054 /* scale c for all diagonal values = 1 or -1 */ 8055 Vec diag; 8056 8057 PetscCall(MatCreateVecs(Gmat, &diag, NULL)); 8058 PetscCall(MatGetDiagonal(Gmat, diag)); 8059 PetscCall(VecReciprocal(diag)); 8060 PetscCall(VecSqrtAbs(diag)); 8061 PetscCall(MatDiagonalScale(Gmat, diag, diag)); 8062 PetscCall(VecDestroy(&diag)); 8063 } 8064 PetscCall(MatViewFromOptions(Gmat, NULL, "-mat_graph_view")); 8065 if (filter >= 0) { 8066 PetscCall(MatFilter(Gmat, filter, PETSC_TRUE, PETSC_TRUE)); 8067 PetscCall(MatViewFromOptions(Gmat, NULL, "-mat_filter_graph_view")); 8068 } 8069 *a_Gmat = Gmat; 8070 PetscFunctionReturn(PETSC_SUCCESS); 8071 } 8072 8073 /* 8074 Special version for direct calls from Fortran 8075 */ 8076 8077 /* Change these macros so can be used in void function */ 8078 /* Identical to PetscCallVoid, except it assigns to *_ierr */ 8079 #undef PetscCall 8080 #define PetscCall(...) \ 8081 do { \ 8082 PetscErrorCode ierr_msv_mpiaij = __VA_ARGS__; \ 8083 if (PetscUnlikely(ierr_msv_mpiaij)) { \ 8084 *_ierr = PetscError(PETSC_COMM_SELF, __LINE__, PETSC_FUNCTION_NAME, __FILE__, ierr_msv_mpiaij, PETSC_ERROR_REPEAT, " "); \ 8085 return; \ 8086 } \ 8087 } while (0) 8088 8089 #undef SETERRQ 8090 #define SETERRQ(comm, ierr, ...) \ 8091 do { \ 8092 *_ierr = PetscError(comm, __LINE__, PETSC_FUNCTION_NAME, __FILE__, ierr, PETSC_ERROR_INITIAL, __VA_ARGS__); \ 8093 return; \ 8094 } while (0) 8095 8096 #if defined(PETSC_HAVE_FORTRAN_CAPS) 8097 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 8098 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 8099 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 8100 #else 8101 #endif 8102 PETSC_EXTERN void matsetvaluesmpiaij_(Mat *mmat, PetscInt *mm, const PetscInt im[], PetscInt *mn, const PetscInt in[], const PetscScalar v[], InsertMode *maddv, PetscErrorCode *_ierr) 8103 { 8104 Mat mat = *mmat; 8105 PetscInt m = *mm, n = *mn; 8106 InsertMode addv = *maddv; 8107 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 8108 PetscScalar value; 8109 8110 MatCheckPreallocated(mat, 1); 8111 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 8112 else PetscCheck(mat->insertmode == addv, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Cannot mix add values and insert values"); 8113 { 8114 PetscInt i, j, rstart = mat->rmap->rstart, rend = mat->rmap->rend; 8115 PetscInt cstart = mat->cmap->rstart, cend = mat->cmap->rend, row, col; 8116 PetscBool roworiented = aij->roworiented; 8117 8118 /* Some Variables required in the macro */ 8119 Mat A = aij->A; 8120 Mat_SeqAIJ *a = (Mat_SeqAIJ *)A->data; 8121 PetscInt *aimax = a->imax, *ai = a->i, *ailen = a->ilen, *aj = a->j; 8122 MatScalar *aa; 8123 PetscBool ignorezeroentries = ((a->ignorezeroentries && (addv == ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 8124 Mat B = aij->B; 8125 Mat_SeqAIJ *b = (Mat_SeqAIJ *)B->data; 8126 PetscInt *bimax = b->imax, *bi = b->i, *bilen = b->ilen, *bj = b->j, bm = aij->B->rmap->n, am = aij->A->rmap->n; 8127 MatScalar *ba; 8128 /* This variable below is only for the PETSC_HAVE_VIENNACL or PETSC_HAVE_CUDA cases, but we define it in all cases because we 8129 * cannot use "#if defined" inside a macro. */ 8130 PETSC_UNUSED PetscBool inserted = PETSC_FALSE; 8131 8132 PetscInt *rp1, *rp2, ii, nrow1, nrow2, _i, rmax1, rmax2, N, low1, high1, low2, high2, t, lastcol1, lastcol2; 8133 PetscInt nonew = a->nonew; 8134 MatScalar *ap1, *ap2; 8135 8136 PetscFunctionBegin; 8137 PetscCall(MatSeqAIJGetArray(A, &aa)); 8138 PetscCall(MatSeqAIJGetArray(B, &ba)); 8139 for (i = 0; i < m; i++) { 8140 if (im[i] < 0) continue; 8141 PetscCheck(im[i] < mat->rmap->N, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Row too large: row %" PetscInt_FMT " max %" PetscInt_FMT, im[i], mat->rmap->N - 1); 8142 if (im[i] >= rstart && im[i] < rend) { 8143 row = im[i] - rstart; 8144 lastcol1 = -1; 8145 rp1 = aj + ai[row]; 8146 ap1 = aa + ai[row]; 8147 rmax1 = aimax[row]; 8148 nrow1 = ailen[row]; 8149 low1 = 0; 8150 high1 = nrow1; 8151 lastcol2 = -1; 8152 rp2 = bj + bi[row]; 8153 ap2 = ba + bi[row]; 8154 rmax2 = bimax[row]; 8155 nrow2 = bilen[row]; 8156 low2 = 0; 8157 high2 = nrow2; 8158 8159 for (j = 0; j < n; j++) { 8160 if (roworiented) value = v[i * n + j]; 8161 else value = v[i + j * m]; 8162 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && im[i] != in[j]) continue; 8163 if (in[j] >= cstart && in[j] < cend) { 8164 col = in[j] - cstart; 8165 MatSetValues_SeqAIJ_A_Private(row, col, value, addv, im[i], in[j]); 8166 } else if (in[j] < 0) continue; 8167 else if (PetscUnlikelyDebug(in[j] >= mat->cmap->N)) { 8168 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Column too large: col %" PetscInt_FMT " max %" PetscInt_FMT, in[j], mat->cmap->N - 1); 8169 } else { 8170 if (mat->was_assembled) { 8171 if (!aij->colmap) PetscCall(MatCreateColmap_MPIAIJ_Private(mat)); 8172 #if defined(PETSC_USE_CTABLE) 8173 PetscCall(PetscHMapIGetWithDefault(aij->colmap, in[j] + 1, 0, &col)); 8174 col--; 8175 #else 8176 col = aij->colmap[in[j]] - 1; 8177 #endif 8178 if (col < 0 && !((Mat_SeqAIJ *)aij->A->data)->nonew) { 8179 PetscCall(MatDisAssemble_MPIAIJ(mat, PETSC_FALSE)); 8180 col = in[j]; 8181 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 8182 B = aij->B; 8183 b = (Mat_SeqAIJ *)B->data; 8184 bimax = b->imax; 8185 bi = b->i; 8186 bilen = b->ilen; 8187 bj = b->j; 8188 rp2 = bj + bi[row]; 8189 ap2 = ba + bi[row]; 8190 rmax2 = bimax[row]; 8191 nrow2 = bilen[row]; 8192 low2 = 0; 8193 high2 = nrow2; 8194 bm = aij->B->rmap->n; 8195 ba = b->a; 8196 inserted = PETSC_FALSE; 8197 } 8198 } else col = in[j]; 8199 MatSetValues_SeqAIJ_B_Private(row, col, value, addv, im[i], in[j]); 8200 } 8201 } 8202 } else if (!aij->donotstash) { 8203 if (roworiented) { 8204 PetscCall(MatStashValuesRow_Private(&mat->stash, im[i], n, in, v + i * n, (PetscBool)(ignorezeroentries && (addv == ADD_VALUES)))); 8205 } else { 8206 PetscCall(MatStashValuesCol_Private(&mat->stash, im[i], n, in, v + i, m, (PetscBool)(ignorezeroentries && (addv == ADD_VALUES)))); 8207 } 8208 } 8209 } 8210 PetscCall(MatSeqAIJRestoreArray(A, &aa)); 8211 PetscCall(MatSeqAIJRestoreArray(B, &ba)); 8212 } 8213 PetscFunctionReturnVoid(); 8214 } 8215 8216 /* Undefining these here since they were redefined from their original definition above! No 8217 * other PETSc functions should be defined past this point, as it is impossible to recover the 8218 * original definitions */ 8219 #undef PetscCall 8220 #undef SETERRQ 8221