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. If not `NULL`, it should be allocated by `PetscMalloc1()` and will be owned by `mat` thereafter. 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 If `garray` is `NULL`, `B` will be compacted to use local indices. In this sense, `B`'s sparsity pattern (nonzerostate) will be changed. If `B` is a device matrix, we need to somehow also update 3496 `B`'s copy on device. We do so by increasing `B`'s nonzerostate. In use of `B` on device, device matrix types should detect this change (ref. internal routines `MatSeqAIJCUSPARSECopyToGPU()` or 3497 `MatAssemblyEnd_SeqAIJKokkos()`) and will just destroy and then recreate the device copy of `B`. It is not optimal, but is easy to implement and less hacky. To avoid this overhead, try to compute `garray` 3498 yourself, see algorithms in the private function `MatSetUpMultiply_MPIAIJ()`. 3499 3500 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MATSEQAIJ`, `MatCreateMPIAIJWithSplitArrays()` 3501 @*/ 3502 PetscErrorCode MatCreateMPIAIJWithSeqAIJ(MPI_Comm comm, PetscInt M, PetscInt N, Mat A, Mat B, PetscInt *garray, Mat *mat) 3503 { 3504 PetscInt m, n; 3505 MatType mpi_mat_type; 3506 3507 PetscFunctionBegin; 3508 PetscCall(MatCreate(comm, mat)); 3509 PetscCall(MatGetSize(A, &m, &n)); 3510 PetscCheck(m == B->rmap->N, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Am %" PetscInt_FMT " != Bm %" PetscInt_FMT, m, B->rmap->N); 3511 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); 3512 3513 PetscCall(MatSetSizes(*mat, m, n, M, N)); 3514 /* Determine the type of MPI matrix that should be created from the type of matrix A, which holds the "diagonal" portion. */ 3515 PetscCall(MatGetMPIMatType_Private(A, &mpi_mat_type)); 3516 PetscCall(MatSetType(*mat, mpi_mat_type)); 3517 3518 PetscCall(MatSetBlockSizes(*mat, A->rmap->bs, A->cmap->bs)); 3519 3520 PetscCall(PetscLayoutSetUp((*mat)->rmap)); 3521 PetscCall(PetscLayoutSetUp((*mat)->cmap)); 3522 if (!garray) { 3523 const PetscScalar *ba; 3524 3525 B->nonzerostate++; 3526 PetscCall(MatSeqAIJGetArrayRead(B, &ba)); /* Since we will destroy B's device copy, we need to make sure the host copy is up to date */ 3527 PetscCall(MatSeqAIJRestoreArrayRead(B, &ba)); 3528 } 3529 PetscCall(MatSetMPIAIJWithSplitSeqAIJ(*mat, A, B, garray)); 3530 PetscFunctionReturn(PETSC_SUCCESS); 3531 } 3532 3533 /* 3534 MatSetMPIAIJWithSplitSeqAIJ - Set the diag and offdiag matrices of a `MATMPIAIJ` matrix. 3535 It is similar to `MatCreateMPIAIJWithSplitArrays()`. This routine allows passing in 3536 B with local indices and the correct size, along with the accompanying 3537 garray, hence skipping compactification 3538 3539 Collective 3540 3541 Input Parameters: 3542 + mat - the MATMPIAIJ matrix, which should have its type and layout set, but should not have its diag, offdiag matrices set 3543 . A - the diag matrix using local col ids 3544 . 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 3545 - garray - either `NULL` or the global index of `B` columns 3546 3547 Output Parameter: 3548 . mat - the updated `MATMPIAIJ` matrix 3549 3550 Level: advanced 3551 3552 Notes: 3553 See `MatCreateAIJ()` for the definition of "diagonal" and "off-diagonal" portion of the matrix. 3554 3555 `A` and `B` become part of output mat. The user cannot use `A` and `B` anymore. 3556 3557 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MATSEQAIJ`, `MatCreateMPIAIJWithSplitArrays()` 3558 */ 3559 PETSC_INTERN PetscErrorCode MatSetMPIAIJWithSplitSeqAIJ(Mat mat, Mat A, Mat B, PetscInt *garray) 3560 { 3561 PetscFunctionBegin; 3562 Mat_MPIAIJ *mpiaij = (Mat_MPIAIJ *)mat->data; 3563 PetscInt m, n, M, N, Am, An, Bm, Bn; 3564 3565 PetscCall(MatGetSize(mat, &M, &N)); 3566 PetscCall(MatGetLocalSize(mat, &m, &n)); 3567 PetscCall(MatGetLocalSize(A, &Am, &An)); 3568 PetscCall(MatGetLocalSize(B, &Bm, &Bn)); 3569 3570 PetscCheck(m == Am && m == Bm, PETSC_COMM_SELF, PETSC_ERR_PLIB, "local number of rows do not match"); 3571 PetscCheck(n == An, PETSC_COMM_SELF, PETSC_ERR_PLIB, "local number of columns do not match"); 3572 PetscCheck(!mpiaij->A && !mpiaij->B, PETSC_COMM_SELF, PETSC_ERR_PLIB, "A, B of the MPIAIJ matrix are not empty"); 3573 mpiaij->A = A; 3574 mpiaij->B = B; 3575 mpiaij->garray = garray; 3576 3577 mat->preallocated = PETSC_TRUE; 3578 mat->nooffprocentries = PETSC_TRUE; /* See MatAssemblyBegin_MPIAIJ. In effect, making MatAssemblyBegin a nop */ 3579 3580 PetscCall(MatSetOption(mat, MAT_NO_OFF_PROC_ENTRIES, PETSC_TRUE)); 3581 PetscCall(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY)); 3582 /* MatAssemblyEnd is critical here. It sets mat->offloadmask according to A and B's, and 3583 also gets mpiaij->B compacted (if garray is NULL), with its col ids and size reduced 3584 */ 3585 PetscCall(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY)); 3586 PetscCall(MatSetOption(mat, MAT_NO_OFF_PROC_ENTRIES, PETSC_FALSE)); 3587 PetscCall(MatSetOption(mat, MAT_NEW_NONZERO_LOCATION_ERR, PETSC_TRUE)); 3588 PetscFunctionReturn(PETSC_SUCCESS); 3589 } 3590 3591 extern PetscErrorCode MatCreateSubMatrices_MPIAIJ_SingleIS_Local(Mat, PetscInt, const IS[], const IS[], MatReuse, PetscBool, Mat *); 3592 3593 PetscErrorCode MatCreateSubMatrix_MPIAIJ_SameRowDist(Mat mat, IS isrow, IS iscol, IS iscol_local, MatReuse call, Mat *newmat) 3594 { 3595 PetscInt i, m, n, rstart, row, rend, nz, j, bs, cbs; 3596 PetscInt *ii, *jj, nlocal, *dlens, *olens, dlen, olen, jend, mglobal; 3597 Mat_MPIAIJ *a = (Mat_MPIAIJ *)mat->data; 3598 Mat M, Msub, B = a->B; 3599 MatScalar *aa; 3600 Mat_SeqAIJ *aij; 3601 PetscInt *garray = a->garray, *colsub, Ncols; 3602 PetscInt count, Bn = B->cmap->N, cstart = mat->cmap->rstart, cend = mat->cmap->rend; 3603 IS iscol_sub, iscmap; 3604 const PetscInt *is_idx, *cmap; 3605 PetscBool allcolumns = PETSC_FALSE; 3606 MPI_Comm comm; 3607 3608 PetscFunctionBegin; 3609 PetscCall(PetscObjectGetComm((PetscObject)mat, &comm)); 3610 if (call == MAT_REUSE_MATRIX) { 3611 PetscCall(PetscObjectQuery((PetscObject)*newmat, "SubIScol", (PetscObject *)&iscol_sub)); 3612 PetscCheck(iscol_sub, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "SubIScol passed in was not used before, cannot reuse"); 3613 PetscCall(ISGetLocalSize(iscol_sub, &count)); 3614 3615 PetscCall(PetscObjectQuery((PetscObject)*newmat, "Subcmap", (PetscObject *)&iscmap)); 3616 PetscCheck(iscmap, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Subcmap passed in was not used before, cannot reuse"); 3617 3618 PetscCall(PetscObjectQuery((PetscObject)*newmat, "SubMatrix", (PetscObject *)&Msub)); 3619 PetscCheck(Msub, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Submatrix passed in was not used before, cannot reuse"); 3620 3621 PetscCall(MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat, 1, &isrow, &iscol_sub, MAT_REUSE_MATRIX, PETSC_FALSE, &Msub)); 3622 3623 } else { /* call == MAT_INITIAL_MATRIX) */ 3624 PetscBool flg; 3625 3626 PetscCall(ISGetLocalSize(iscol, &n)); 3627 PetscCall(ISGetSize(iscol, &Ncols)); 3628 3629 /* (1) iscol -> nonscalable iscol_local */ 3630 /* Check for special case: each processor gets entire matrix columns */ 3631 PetscCall(ISIdentity(iscol_local, &flg)); 3632 if (flg && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3633 PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &allcolumns, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)mat))); 3634 if (allcolumns) { 3635 iscol_sub = iscol_local; 3636 PetscCall(PetscObjectReference((PetscObject)iscol_local)); 3637 PetscCall(ISCreateStride(PETSC_COMM_SELF, n, 0, 1, &iscmap)); 3638 3639 } else { 3640 /* (2) iscol_local -> iscol_sub and iscmap. Implementation below requires iscol_local be sorted, it can have duplicate indices */ 3641 PetscInt *idx, *cmap1, k; 3642 PetscCall(PetscMalloc1(Ncols, &idx)); 3643 PetscCall(PetscMalloc1(Ncols, &cmap1)); 3644 PetscCall(ISGetIndices(iscol_local, &is_idx)); 3645 count = 0; 3646 k = 0; 3647 for (i = 0; i < Ncols; i++) { 3648 j = is_idx[i]; 3649 if (j >= cstart && j < cend) { 3650 /* diagonal part of mat */ 3651 idx[count] = j; 3652 cmap1[count++] = i; /* column index in submat */ 3653 } else if (Bn) { 3654 /* off-diagonal part of mat */ 3655 if (j == garray[k]) { 3656 idx[count] = j; 3657 cmap1[count++] = i; /* column index in submat */ 3658 } else if (j > garray[k]) { 3659 while (j > garray[k] && k < Bn - 1) k++; 3660 if (j == garray[k]) { 3661 idx[count] = j; 3662 cmap1[count++] = i; /* column index in submat */ 3663 } 3664 } 3665 } 3666 } 3667 PetscCall(ISRestoreIndices(iscol_local, &is_idx)); 3668 3669 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, count, idx, PETSC_OWN_POINTER, &iscol_sub)); 3670 PetscCall(ISGetBlockSize(iscol, &cbs)); 3671 PetscCall(ISSetBlockSize(iscol_sub, cbs)); 3672 3673 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)iscol_local), count, cmap1, PETSC_OWN_POINTER, &iscmap)); 3674 } 3675 3676 /* (3) Create sequential Msub */ 3677 PetscCall(MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat, 1, &isrow, &iscol_sub, MAT_INITIAL_MATRIX, allcolumns, &Msub)); 3678 } 3679 3680 PetscCall(ISGetLocalSize(iscol_sub, &count)); 3681 aij = (Mat_SeqAIJ *)Msub->data; 3682 ii = aij->i; 3683 PetscCall(ISGetIndices(iscmap, &cmap)); 3684 3685 /* 3686 m - number of local rows 3687 Ncols - number of columns (same on all processors) 3688 rstart - first row in new global matrix generated 3689 */ 3690 PetscCall(MatGetSize(Msub, &m, NULL)); 3691 3692 if (call == MAT_INITIAL_MATRIX) { 3693 /* (4) Create parallel newmat */ 3694 PetscMPIInt rank, size; 3695 PetscInt csize; 3696 3697 PetscCallMPI(MPI_Comm_size(comm, &size)); 3698 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 3699 3700 /* 3701 Determine the number of non-zeros in the diagonal and off-diagonal 3702 portions of the matrix in order to do correct preallocation 3703 */ 3704 3705 /* first get start and end of "diagonal" columns */ 3706 PetscCall(ISGetLocalSize(iscol, &csize)); 3707 if (csize == PETSC_DECIDE) { 3708 PetscCall(ISGetSize(isrow, &mglobal)); 3709 if (mglobal == Ncols) { /* square matrix */ 3710 nlocal = m; 3711 } else { 3712 nlocal = Ncols / size + ((Ncols % size) > rank); 3713 } 3714 } else { 3715 nlocal = csize; 3716 } 3717 PetscCallMPI(MPI_Scan(&nlocal, &rend, 1, MPIU_INT, MPI_SUM, comm)); 3718 rstart = rend - nlocal; 3719 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); 3720 3721 /* next, compute all the lengths */ 3722 jj = aij->j; 3723 PetscCall(PetscMalloc1(2 * m + 1, &dlens)); 3724 olens = dlens + m; 3725 for (i = 0; i < m; i++) { 3726 jend = ii[i + 1] - ii[i]; 3727 olen = 0; 3728 dlen = 0; 3729 for (j = 0; j < jend; j++) { 3730 if (cmap[*jj] < rstart || cmap[*jj] >= rend) olen++; 3731 else dlen++; 3732 jj++; 3733 } 3734 olens[i] = olen; 3735 dlens[i] = dlen; 3736 } 3737 3738 PetscCall(ISGetBlockSize(isrow, &bs)); 3739 PetscCall(ISGetBlockSize(iscol, &cbs)); 3740 3741 PetscCall(MatCreate(comm, &M)); 3742 PetscCall(MatSetSizes(M, m, nlocal, PETSC_DECIDE, Ncols)); 3743 PetscCall(MatSetBlockSizes(M, bs, cbs)); 3744 PetscCall(MatSetType(M, ((PetscObject)mat)->type_name)); 3745 PetscCall(MatMPIAIJSetPreallocation(M, 0, dlens, 0, olens)); 3746 PetscCall(PetscFree(dlens)); 3747 3748 } else { /* call == MAT_REUSE_MATRIX */ 3749 M = *newmat; 3750 PetscCall(MatGetLocalSize(M, &i, NULL)); 3751 PetscCheck(i == m, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Previous matrix must be same size/layout as request"); 3752 PetscCall(MatZeroEntries(M)); 3753 /* 3754 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3755 rather than the slower MatSetValues(). 3756 */ 3757 M->was_assembled = PETSC_TRUE; 3758 M->assembled = PETSC_FALSE; 3759 } 3760 3761 /* (5) Set values of Msub to *newmat */ 3762 PetscCall(PetscMalloc1(count, &colsub)); 3763 PetscCall(MatGetOwnershipRange(M, &rstart, NULL)); 3764 3765 jj = aij->j; 3766 PetscCall(MatSeqAIJGetArrayRead(Msub, (const PetscScalar **)&aa)); 3767 for (i = 0; i < m; i++) { 3768 row = rstart + i; 3769 nz = ii[i + 1] - ii[i]; 3770 for (j = 0; j < nz; j++) colsub[j] = cmap[jj[j]]; 3771 PetscCall(MatSetValues_MPIAIJ(M, 1, &row, nz, colsub, aa, INSERT_VALUES)); 3772 jj += nz; 3773 aa += nz; 3774 } 3775 PetscCall(MatSeqAIJRestoreArrayRead(Msub, (const PetscScalar **)&aa)); 3776 PetscCall(ISRestoreIndices(iscmap, &cmap)); 3777 3778 PetscCall(MatAssemblyBegin(M, MAT_FINAL_ASSEMBLY)); 3779 PetscCall(MatAssemblyEnd(M, MAT_FINAL_ASSEMBLY)); 3780 3781 PetscCall(PetscFree(colsub)); 3782 3783 /* save Msub, iscol_sub and iscmap used in processor for next request */ 3784 if (call == MAT_INITIAL_MATRIX) { 3785 *newmat = M; 3786 PetscCall(PetscObjectCompose((PetscObject)*newmat, "SubMatrix", (PetscObject)Msub)); 3787 PetscCall(MatDestroy(&Msub)); 3788 3789 PetscCall(PetscObjectCompose((PetscObject)*newmat, "SubIScol", (PetscObject)iscol_sub)); 3790 PetscCall(ISDestroy(&iscol_sub)); 3791 3792 PetscCall(PetscObjectCompose((PetscObject)*newmat, "Subcmap", (PetscObject)iscmap)); 3793 PetscCall(ISDestroy(&iscmap)); 3794 3795 if (iscol_local) { 3796 PetscCall(PetscObjectCompose((PetscObject)*newmat, "ISAllGather", (PetscObject)iscol_local)); 3797 PetscCall(ISDestroy(&iscol_local)); 3798 } 3799 } 3800 PetscFunctionReturn(PETSC_SUCCESS); 3801 } 3802 3803 /* 3804 Not great since it makes two copies of the submatrix, first an SeqAIJ 3805 in local and then by concatenating the local matrices the end result. 3806 Writing it directly would be much like MatCreateSubMatrices_MPIAIJ() 3807 3808 This requires a sequential iscol with all indices. 3809 */ 3810 PetscErrorCode MatCreateSubMatrix_MPIAIJ_nonscalable(Mat mat, IS isrow, IS iscol, PetscInt csize, MatReuse call, Mat *newmat) 3811 { 3812 PetscMPIInt rank, size; 3813 PetscInt i, m, n, rstart, row, rend, nz, *cwork, j, bs, cbs; 3814 PetscInt *ii, *jj, nlocal, *dlens, *olens, dlen, olen, jend, mglobal; 3815 Mat M, Mreuse; 3816 MatScalar *aa, *vwork; 3817 MPI_Comm comm; 3818 Mat_SeqAIJ *aij; 3819 PetscBool colflag, allcolumns = PETSC_FALSE; 3820 3821 PetscFunctionBegin; 3822 PetscCall(PetscObjectGetComm((PetscObject)mat, &comm)); 3823 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 3824 PetscCallMPI(MPI_Comm_size(comm, &size)); 3825 3826 /* Check for special case: each processor gets entire matrix columns */ 3827 PetscCall(ISIdentity(iscol, &colflag)); 3828 PetscCall(ISGetLocalSize(iscol, &n)); 3829 if (colflag && n == mat->cmap->N) allcolumns = PETSC_TRUE; 3830 PetscCallMPI(MPIU_Allreduce(MPI_IN_PLACE, &allcolumns, 1, MPIU_BOOL, MPI_LAND, PetscObjectComm((PetscObject)mat))); 3831 3832 if (call == MAT_REUSE_MATRIX) { 3833 PetscCall(PetscObjectQuery((PetscObject)*newmat, "SubMatrix", (PetscObject *)&Mreuse)); 3834 PetscCheck(Mreuse, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Submatrix passed in was not used before, cannot reuse"); 3835 PetscCall(MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat, 1, &isrow, &iscol, MAT_REUSE_MATRIX, allcolumns, &Mreuse)); 3836 } else { 3837 PetscCall(MatCreateSubMatrices_MPIAIJ_SingleIS_Local(mat, 1, &isrow, &iscol, MAT_INITIAL_MATRIX, allcolumns, &Mreuse)); 3838 } 3839 3840 /* 3841 m - number of local rows 3842 n - number of columns (same on all processors) 3843 rstart - first row in new global matrix generated 3844 */ 3845 PetscCall(MatGetSize(Mreuse, &m, &n)); 3846 PetscCall(MatGetBlockSizes(Mreuse, &bs, &cbs)); 3847 if (call == MAT_INITIAL_MATRIX) { 3848 aij = (Mat_SeqAIJ *)Mreuse->data; 3849 ii = aij->i; 3850 jj = aij->j; 3851 3852 /* 3853 Determine the number of non-zeros in the diagonal and off-diagonal 3854 portions of the matrix in order to do correct preallocation 3855 */ 3856 3857 /* first get start and end of "diagonal" columns */ 3858 if (csize == PETSC_DECIDE) { 3859 PetscCall(ISGetSize(isrow, &mglobal)); 3860 if (mglobal == n) { /* square matrix */ 3861 nlocal = m; 3862 } else { 3863 nlocal = n / size + ((n % size) > rank); 3864 } 3865 } else { 3866 nlocal = csize; 3867 } 3868 PetscCallMPI(MPI_Scan(&nlocal, &rend, 1, MPIU_INT, MPI_SUM, comm)); 3869 rstart = rend - nlocal; 3870 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); 3871 3872 /* next, compute all the lengths */ 3873 PetscCall(PetscMalloc1(2 * m + 1, &dlens)); 3874 olens = dlens + m; 3875 for (i = 0; i < m; i++) { 3876 jend = ii[i + 1] - ii[i]; 3877 olen = 0; 3878 dlen = 0; 3879 for (j = 0; j < jend; j++) { 3880 if (*jj < rstart || *jj >= rend) olen++; 3881 else dlen++; 3882 jj++; 3883 } 3884 olens[i] = olen; 3885 dlens[i] = dlen; 3886 } 3887 PetscCall(MatCreate(comm, &M)); 3888 PetscCall(MatSetSizes(M, m, nlocal, PETSC_DECIDE, n)); 3889 PetscCall(MatSetBlockSizes(M, bs, cbs)); 3890 PetscCall(MatSetType(M, ((PetscObject)mat)->type_name)); 3891 PetscCall(MatMPIAIJSetPreallocation(M, 0, dlens, 0, olens)); 3892 PetscCall(PetscFree(dlens)); 3893 } else { 3894 PetscInt ml, nl; 3895 3896 M = *newmat; 3897 PetscCall(MatGetLocalSize(M, &ml, &nl)); 3898 PetscCheck(ml == m, PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Previous matrix must be same size/layout as request"); 3899 PetscCall(MatZeroEntries(M)); 3900 /* 3901 The next two lines are needed so we may call MatSetValues_MPIAIJ() below directly, 3902 rather than the slower MatSetValues(). 3903 */ 3904 M->was_assembled = PETSC_TRUE; 3905 M->assembled = PETSC_FALSE; 3906 } 3907 PetscCall(MatGetOwnershipRange(M, &rstart, &rend)); 3908 aij = (Mat_SeqAIJ *)Mreuse->data; 3909 ii = aij->i; 3910 jj = aij->j; 3911 3912 /* trigger copy to CPU if needed */ 3913 PetscCall(MatSeqAIJGetArrayRead(Mreuse, (const PetscScalar **)&aa)); 3914 for (i = 0; i < m; i++) { 3915 row = rstart + i; 3916 nz = ii[i + 1] - ii[i]; 3917 cwork = jj; 3918 jj = PetscSafePointerPlusOffset(jj, nz); 3919 vwork = aa; 3920 aa = PetscSafePointerPlusOffset(aa, nz); 3921 PetscCall(MatSetValues_MPIAIJ(M, 1, &row, nz, cwork, vwork, INSERT_VALUES)); 3922 } 3923 PetscCall(MatSeqAIJRestoreArrayRead(Mreuse, (const PetscScalar **)&aa)); 3924 3925 PetscCall(MatAssemblyBegin(M, MAT_FINAL_ASSEMBLY)); 3926 PetscCall(MatAssemblyEnd(M, MAT_FINAL_ASSEMBLY)); 3927 *newmat = M; 3928 3929 /* save submatrix used in processor for next request */ 3930 if (call == MAT_INITIAL_MATRIX) { 3931 PetscCall(PetscObjectCompose((PetscObject)M, "SubMatrix", (PetscObject)Mreuse)); 3932 PetscCall(MatDestroy(&Mreuse)); 3933 } 3934 PetscFunctionReturn(PETSC_SUCCESS); 3935 } 3936 3937 static PetscErrorCode MatMPIAIJSetPreallocationCSR_MPIAIJ(Mat B, const PetscInt Ii[], const PetscInt J[], const PetscScalar v[]) 3938 { 3939 PetscInt m, cstart, cend, j, nnz, i, d, *ld; 3940 PetscInt *d_nnz, *o_nnz, nnz_max = 0, rstart, ii, irstart; 3941 const PetscInt *JJ; 3942 PetscBool nooffprocentries; 3943 Mat_MPIAIJ *Aij = (Mat_MPIAIJ *)B->data; 3944 3945 PetscFunctionBegin; 3946 PetscCall(PetscLayoutSetUp(B->rmap)); 3947 PetscCall(PetscLayoutSetUp(B->cmap)); 3948 m = B->rmap->n; 3949 cstart = B->cmap->rstart; 3950 cend = B->cmap->rend; 3951 rstart = B->rmap->rstart; 3952 irstart = Ii[0]; 3953 3954 PetscCall(PetscCalloc2(m, &d_nnz, m, &o_nnz)); 3955 3956 if (PetscDefined(USE_DEBUG)) { 3957 for (i = 0; i < m; i++) { 3958 nnz = Ii[i + 1] - Ii[i]; 3959 JJ = PetscSafePointerPlusOffset(J, Ii[i] - irstart); 3960 PetscCheck(nnz >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Local row %" PetscInt_FMT " has a negative %" PetscInt_FMT " number of columns", i, nnz); 3961 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]); 3962 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); 3963 } 3964 } 3965 3966 for (i = 0; i < m; i++) { 3967 nnz = Ii[i + 1] - Ii[i]; 3968 JJ = PetscSafePointerPlusOffset(J, Ii[i] - irstart); 3969 nnz_max = PetscMax(nnz_max, nnz); 3970 d = 0; 3971 for (j = 0; j < nnz; j++) { 3972 if (cstart <= JJ[j] && JJ[j] < cend) d++; 3973 } 3974 d_nnz[i] = d; 3975 o_nnz[i] = nnz - d; 3976 } 3977 PetscCall(MatMPIAIJSetPreallocation(B, 0, d_nnz, 0, o_nnz)); 3978 PetscCall(PetscFree2(d_nnz, o_nnz)); 3979 3980 for (i = 0; i < m; i++) { 3981 ii = i + rstart; 3982 PetscCall(MatSetValues_MPIAIJ(B, 1, &ii, Ii[i + 1] - Ii[i], PetscSafePointerPlusOffset(J, Ii[i] - irstart), PetscSafePointerPlusOffset(v, Ii[i] - irstart), INSERT_VALUES)); 3983 } 3984 nooffprocentries = B->nooffprocentries; 3985 B->nooffprocentries = PETSC_TRUE; 3986 PetscCall(MatAssemblyBegin(B, MAT_FINAL_ASSEMBLY)); 3987 PetscCall(MatAssemblyEnd(B, MAT_FINAL_ASSEMBLY)); 3988 B->nooffprocentries = nooffprocentries; 3989 3990 /* count number of entries below block diagonal */ 3991 PetscCall(PetscFree(Aij->ld)); 3992 PetscCall(PetscCalloc1(m, &ld)); 3993 Aij->ld = ld; 3994 for (i = 0; i < m; i++) { 3995 nnz = Ii[i + 1] - Ii[i]; 3996 j = 0; 3997 while (j < nnz && J[j] < cstart) j++; 3998 ld[i] = j; 3999 if (J) J += nnz; 4000 } 4001 4002 PetscCall(MatSetOption(B, MAT_NEW_NONZERO_LOCATION_ERR, PETSC_TRUE)); 4003 PetscFunctionReturn(PETSC_SUCCESS); 4004 } 4005 4006 /*@ 4007 MatMPIAIJSetPreallocationCSR - Allocates memory for a sparse parallel matrix in `MATAIJ` format 4008 (the default parallel PETSc format). 4009 4010 Collective 4011 4012 Input Parameters: 4013 + B - the matrix 4014 . i - the indices into `j` for the start of each local row (indices start with zero) 4015 . j - the column indices for each local row (indices start with zero) 4016 - v - optional values in the matrix 4017 4018 Level: developer 4019 4020 Notes: 4021 The `i`, `j`, and `v` arrays ARE copied by this routine into the internal format used by PETSc; 4022 thus you CANNOT change the matrix entries by changing the values of `v` after you have 4023 called this routine. Use `MatCreateMPIAIJWithSplitArrays()` to avoid needing to copy the arrays. 4024 4025 The `i` and `j` indices are 0 based, and `i` indices are indices corresponding to the local `j` array. 4026 4027 A convenience routine for this functionality is `MatCreateMPIAIJWithArrays()`. 4028 4029 You can update the matrix with new numerical values using `MatUpdateMPIAIJWithArrays()` after this call if the column indices in `j` are sorted. 4030 4031 If you do **not** use `MatUpdateMPIAIJWithArrays()`, the column indices in `j` do not need to be sorted. If you will use 4032 `MatUpdateMPIAIJWithArrays()`, the column indices **must** be sorted. 4033 4034 The format which is used for the sparse matrix input, is equivalent to a 4035 row-major ordering.. i.e for the following matrix, the input data expected is 4036 as shown 4037 .vb 4038 1 0 0 4039 2 0 3 P0 4040 ------- 4041 4 5 6 P1 4042 4043 Process0 [P0] rows_owned=[0,1] 4044 i = {0,1,3} [size = nrow+1 = 2+1] 4045 j = {0,0,2} [size = 3] 4046 v = {1,2,3} [size = 3] 4047 4048 Process1 [P1] rows_owned=[2] 4049 i = {0,3} [size = nrow+1 = 1+1] 4050 j = {0,1,2} [size = 3] 4051 v = {4,5,6} [size = 3] 4052 .ve 4053 4054 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatCreateAIJ()`, 4055 `MatCreateSeqAIJWithArrays()`, `MatCreateMPIAIJWithSplitArrays()`, `MatCreateMPIAIJWithArrays()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4056 @*/ 4057 PetscErrorCode MatMPIAIJSetPreallocationCSR(Mat B, const PetscInt i[], const PetscInt j[], const PetscScalar v[]) 4058 { 4059 PetscFunctionBegin; 4060 PetscTryMethod(B, "MatMPIAIJSetPreallocationCSR_C", (Mat, const PetscInt[], const PetscInt[], const PetscScalar[]), (B, i, j, v)); 4061 PetscFunctionReturn(PETSC_SUCCESS); 4062 } 4063 4064 /*@ 4065 MatMPIAIJSetPreallocation - Preallocates memory for a sparse parallel matrix in `MATMPIAIJ` format 4066 (the default parallel PETSc format). For good matrix assembly performance 4067 the user should preallocate the matrix storage by setting the parameters 4068 `d_nz` (or `d_nnz`) and `o_nz` (or `o_nnz`). 4069 4070 Collective 4071 4072 Input Parameters: 4073 + B - the matrix 4074 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4075 (same value is used for all local rows) 4076 . d_nnz - array containing the number of nonzeros in the various rows of the 4077 DIAGONAL portion of the local submatrix (possibly different for each row) 4078 or `NULL` (`PETSC_NULL_INTEGER` in Fortran), if `d_nz` is used to specify the nonzero structure. 4079 The size of this array is equal to the number of local rows, i.e 'm'. 4080 For matrices that will be factored, you must leave room for (and set) 4081 the diagonal entry even if it is zero. 4082 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4083 submatrix (same value is used for all local rows). 4084 - o_nnz - array containing the number of nonzeros in the various rows of the 4085 OFF-DIAGONAL portion of the local submatrix (possibly different for 4086 each row) or `NULL` (`PETSC_NULL_INTEGER` in Fortran), if `o_nz` is used to specify the nonzero 4087 structure. The size of this array is equal to the number 4088 of local rows, i.e 'm'. 4089 4090 Example Usage: 4091 Consider the following 8x8 matrix with 34 non-zero values, that is 4092 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4093 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4094 as follows 4095 4096 .vb 4097 1 2 0 | 0 3 0 | 0 4 4098 Proc0 0 5 6 | 7 0 0 | 8 0 4099 9 0 10 | 11 0 0 | 12 0 4100 ------------------------------------- 4101 13 0 14 | 15 16 17 | 0 0 4102 Proc1 0 18 0 | 19 20 21 | 0 0 4103 0 0 0 | 22 23 0 | 24 0 4104 ------------------------------------- 4105 Proc2 25 26 27 | 0 0 28 | 29 0 4106 30 0 0 | 31 32 33 | 0 34 4107 .ve 4108 4109 This can be represented as a collection of submatrices as 4110 .vb 4111 A B C 4112 D E F 4113 G H I 4114 .ve 4115 4116 Where the submatrices A,B,C are owned by proc0, D,E,F are 4117 owned by proc1, G,H,I are owned by proc2. 4118 4119 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4120 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4121 The 'M','N' parameters are 8,8, and have the same values on all procs. 4122 4123 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4124 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4125 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4126 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4127 part as `MATSEQAIJ` matrices. For example, proc1 will store [E] as a `MATSEQAIJ` 4128 matrix, and [DF] as another `MATSEQAIJ` matrix. 4129 4130 When `d_nz`, `o_nz` parameters are specified, `d_nz` storage elements are 4131 allocated for every row of the local DIAGONAL submatrix, and `o_nz` 4132 storage locations are allocated for every row of the OFF-DIAGONAL submatrix. 4133 One way to choose `d_nz` and `o_nz` is to use the maximum number of nonzeros over 4134 the local rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4135 In this case, the values of `d_nz`, `o_nz` are 4136 .vb 4137 proc0 dnz = 2, o_nz = 2 4138 proc1 dnz = 3, o_nz = 2 4139 proc2 dnz = 1, o_nz = 4 4140 .ve 4141 We are allocating `m`*(`d_nz`+`o_nz`) storage locations for every proc. This 4142 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4143 for proc3. i.e we are using 12+15+10=37 storage locations to store 4144 34 values. 4145 4146 When `d_nnz`, `o_nnz` parameters are specified, the storage is specified 4147 for every row, corresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4148 In the above case the values for `d_nnz`, `o_nnz` are 4149 .vb 4150 proc0 d_nnz = [2,2,2] and o_nnz = [2,2,2] 4151 proc1 d_nnz = [3,3,2] and o_nnz = [2,1,1] 4152 proc2 d_nnz = [1,1] and o_nnz = [4,4] 4153 .ve 4154 Here the space allocated is sum of all the above values i.e 34, and 4155 hence pre-allocation is perfect. 4156 4157 Level: intermediate 4158 4159 Notes: 4160 If the *_nnz parameter is given then the *_nz parameter is ignored 4161 4162 The `MATAIJ` format, also called compressed row storage (CSR), is compatible with standard Fortran 4163 storage. The stored row and column indices begin with zero. 4164 See [Sparse Matrices](sec_matsparse) for details. 4165 4166 The parallel matrix is partitioned such that the first m0 rows belong to 4167 process 0, the next m1 rows belong to process 1, the next m2 rows belong 4168 to process 2 etc.. where m0,m1,m2... are the input parameter 'm'. 4169 4170 The DIAGONAL portion of the local submatrix of a processor can be defined 4171 as the submatrix which is obtained by extraction the part corresponding to 4172 the rows r1-r2 and columns c1-c2 of the global matrix, where r1 is the 4173 first row that belongs to the processor, r2 is the last row belonging to 4174 the this processor, and c1-c2 is range of indices of the local part of a 4175 vector suitable for applying the matrix to. This is an mxn matrix. In the 4176 common case of a square matrix, the row and column ranges are the same and 4177 the DIAGONAL part is also square. The remaining portion of the local 4178 submatrix (mxN) constitute the OFF-DIAGONAL portion. 4179 4180 If `o_nnz` and `d_nnz` are specified, then `o_nz` and `d_nz` are ignored. 4181 4182 You can call `MatGetInfo()` to get information on how effective the preallocation was; 4183 for example the fields mallocs,nz_allocated,nz_used,nz_unneeded; 4184 You can also run with the option `-info` and look for messages with the string 4185 malloc in them to see if additional memory allocation was needed. 4186 4187 .seealso: [](ch_matrices), `Mat`, [Sparse Matrices](sec_matsparse), `MATMPIAIJ`, `MATAIJ`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatCreateAIJ()`, `MatMPIAIJSetPreallocationCSR()`, 4188 `MatGetInfo()`, `PetscSplitOwnership()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4189 @*/ 4190 PetscErrorCode MatMPIAIJSetPreallocation(Mat B, PetscInt d_nz, const PetscInt d_nnz[], PetscInt o_nz, const PetscInt o_nnz[]) 4191 { 4192 PetscFunctionBegin; 4193 PetscValidHeaderSpecific(B, MAT_CLASSID, 1); 4194 PetscValidType(B, 1); 4195 PetscTryMethod(B, "MatMPIAIJSetPreallocation_C", (Mat, PetscInt, const PetscInt[], PetscInt, const PetscInt[]), (B, d_nz, d_nnz, o_nz, o_nnz)); 4196 PetscFunctionReturn(PETSC_SUCCESS); 4197 } 4198 4199 /*@ 4200 MatCreateMPIAIJWithArrays - creates a `MATMPIAIJ` matrix using arrays that contain in standard 4201 CSR format for the local rows. 4202 4203 Collective 4204 4205 Input Parameters: 4206 + comm - MPI communicator 4207 . m - number of local rows (Cannot be `PETSC_DECIDE`) 4208 . n - This value should be the same as the local size used in creating the 4209 x vector for the matrix-vector product $ y = Ax$. (or `PETSC_DECIDE` to have 4210 calculated if `N` is given) For square matrices n is almost always `m`. 4211 . M - number of global rows (or `PETSC_DETERMINE` to have calculated if `m` is given) 4212 . N - number of global columns (or `PETSC_DETERMINE` to have calculated if `n` is given) 4213 . 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 4214 . j - global column indices 4215 - a - optional matrix values 4216 4217 Output Parameter: 4218 . mat - the matrix 4219 4220 Level: intermediate 4221 4222 Notes: 4223 The `i`, `j`, and `a` arrays ARE copied by this routine into the internal format used by PETSc; 4224 thus you CANNOT change the matrix entries by changing the values of `a[]` after you have 4225 called this routine. Use `MatCreateMPIAIJWithSplitArrays()` to avoid needing to copy the arrays. 4226 4227 The `i` and `j` indices are 0 based, and `i` indices are indices corresponding to the local `j` array. 4228 4229 Once you have created the matrix you can update it with new numerical values using `MatUpdateMPIAIJWithArray()` 4230 4231 If you do **not** use `MatUpdateMPIAIJWithArray()`, the column indices in `j` do not need to be sorted. If you will use 4232 `MatUpdateMPIAIJWithArrays()`, the column indices **must** be sorted. 4233 4234 The format which is used for the sparse matrix input, is equivalent to a 4235 row-major ordering, i.e., for the following matrix, the input data expected is 4236 as shown 4237 .vb 4238 1 0 0 4239 2 0 3 P0 4240 ------- 4241 4 5 6 P1 4242 4243 Process0 [P0] rows_owned=[0,1] 4244 i = {0,1,3} [size = nrow+1 = 2+1] 4245 j = {0,0,2} [size = 3] 4246 v = {1,2,3} [size = 3] 4247 4248 Process1 [P1] rows_owned=[2] 4249 i = {0,3} [size = nrow+1 = 1+1] 4250 j = {0,1,2} [size = 3] 4251 v = {4,5,6} [size = 3] 4252 .ve 4253 4254 .seealso: [](ch_matrices), `Mat`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 4255 `MATMPIAIJ`, `MatCreateAIJ()`, `MatCreateMPIAIJWithSplitArrays()`, `MatUpdateMPIAIJWithArray()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4256 @*/ 4257 PetscErrorCode MatCreateMPIAIJWithArrays(MPI_Comm comm, PetscInt m, PetscInt n, PetscInt M, PetscInt N, const PetscInt i[], const PetscInt j[], const PetscScalar a[], Mat *mat) 4258 { 4259 PetscFunctionBegin; 4260 PetscCheck(!i || !i[0], PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "i (row indices) must start with 0"); 4261 PetscCheck(m >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4262 PetscCall(MatCreate(comm, mat)); 4263 PetscCall(MatSetSizes(*mat, m, n, M, N)); 4264 /* PetscCall(MatSetBlockSizes(M,bs,cbs)); */ 4265 PetscCall(MatSetType(*mat, MATMPIAIJ)); 4266 PetscCall(MatMPIAIJSetPreallocationCSR(*mat, i, j, a)); 4267 PetscFunctionReturn(PETSC_SUCCESS); 4268 } 4269 4270 /*@ 4271 MatUpdateMPIAIJWithArrays - updates a `MATMPIAIJ` matrix using arrays that contain in standard 4272 CSR format for the local rows. Only the numerical values are updated the other arrays must be identical to what was passed 4273 from `MatCreateMPIAIJWithArrays()` 4274 4275 Deprecated: Use `MatUpdateMPIAIJWithArray()` 4276 4277 Collective 4278 4279 Input Parameters: 4280 + mat - the matrix 4281 . m - number of local rows (Cannot be `PETSC_DECIDE`) 4282 . n - This value should be the same as the local size used in creating the 4283 x vector for the matrix-vector product y = Ax. (or `PETSC_DECIDE` to have 4284 calculated if N is given) For square matrices n is almost always m. 4285 . M - number of global rows (or `PETSC_DETERMINE` to have calculated if m is given) 4286 . N - number of global columns (or `PETSC_DETERMINE` to have calculated if n is given) 4287 . Ii - row indices; that is Ii[0] = 0, Ii[row] = Ii[row-1] + number of elements in that row of the matrix 4288 . J - column indices 4289 - v - matrix values 4290 4291 Level: deprecated 4292 4293 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 4294 `MatCreateAIJ()`, `MatCreateMPIAIJWithSplitArrays()`, `MatUpdateMPIAIJWithArray()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4295 @*/ 4296 PetscErrorCode MatUpdateMPIAIJWithArrays(Mat mat, PetscInt m, PetscInt n, PetscInt M, PetscInt N, const PetscInt Ii[], const PetscInt J[], const PetscScalar v[]) 4297 { 4298 PetscInt nnz, i; 4299 PetscBool nooffprocentries; 4300 Mat_MPIAIJ *Aij = (Mat_MPIAIJ *)mat->data; 4301 Mat_SeqAIJ *Ad = (Mat_SeqAIJ *)Aij->A->data; 4302 PetscScalar *ad, *ao; 4303 PetscInt ldi, Iii, md; 4304 const PetscInt *Adi = Ad->i; 4305 PetscInt *ld = Aij->ld; 4306 4307 PetscFunctionBegin; 4308 PetscCheck(Ii[0] == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "i (row indices) must start with 0"); 4309 PetscCheck(m >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "local number of rows (m) cannot be PETSC_DECIDE, or negative"); 4310 PetscCheck(m == mat->rmap->n, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Local number of rows cannot change from call to MatUpdateMPIAIJWithArrays()"); 4311 PetscCheck(n == mat->cmap->n, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Local number of columns cannot change from call to MatUpdateMPIAIJWithArrays()"); 4312 4313 PetscCall(MatSeqAIJGetArrayWrite(Aij->A, &ad)); 4314 PetscCall(MatSeqAIJGetArrayWrite(Aij->B, &ao)); 4315 4316 for (i = 0; i < m; i++) { 4317 if (PetscDefined(USE_DEBUG)) { 4318 for (PetscInt j = Ii[i] + 1; j < Ii[i + 1]; ++j) { 4319 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); 4320 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); 4321 } 4322 } 4323 nnz = Ii[i + 1] - Ii[i]; 4324 Iii = Ii[i]; 4325 ldi = ld[i]; 4326 md = Adi[i + 1] - Adi[i]; 4327 PetscCall(PetscArraycpy(ao, v + Iii, ldi)); 4328 PetscCall(PetscArraycpy(ad, v + Iii + ldi, md)); 4329 PetscCall(PetscArraycpy(ao + ldi, v + Iii + ldi + md, nnz - ldi - md)); 4330 ad += md; 4331 ao += nnz - md; 4332 } 4333 nooffprocentries = mat->nooffprocentries; 4334 mat->nooffprocentries = PETSC_TRUE; 4335 PetscCall(MatSeqAIJRestoreArrayWrite(Aij->A, &ad)); 4336 PetscCall(MatSeqAIJRestoreArrayWrite(Aij->B, &ao)); 4337 PetscCall(PetscObjectStateIncrease((PetscObject)Aij->A)); 4338 PetscCall(PetscObjectStateIncrease((PetscObject)Aij->B)); 4339 PetscCall(PetscObjectStateIncrease((PetscObject)mat)); 4340 PetscCall(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY)); 4341 PetscCall(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY)); 4342 mat->nooffprocentries = nooffprocentries; 4343 PetscFunctionReturn(PETSC_SUCCESS); 4344 } 4345 4346 /*@ 4347 MatUpdateMPIAIJWithArray - updates an `MATMPIAIJ` matrix using an array that contains the nonzero values 4348 4349 Collective 4350 4351 Input Parameters: 4352 + mat - the matrix 4353 - v - matrix values, stored by row 4354 4355 Level: intermediate 4356 4357 Notes: 4358 The matrix must have been obtained with `MatCreateMPIAIJWithArrays()` or `MatMPIAIJSetPreallocationCSR()` 4359 4360 The column indices in the call to `MatCreateMPIAIJWithArrays()` or `MatMPIAIJSetPreallocationCSR()` must have been sorted for this call to work correctly 4361 4362 .seealso: [](ch_matrices), `Mat`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 4363 `MATMPIAIJ`, `MatCreateAIJ()`, `MatCreateMPIAIJWithSplitArrays()`, `MatUpdateMPIAIJWithArrays()`, `MatSetPreallocationCOO()`, `MatSetValuesCOO()` 4364 @*/ 4365 PetscErrorCode MatUpdateMPIAIJWithArray(Mat mat, const PetscScalar v[]) 4366 { 4367 PetscInt nnz, i, m; 4368 PetscBool nooffprocentries; 4369 Mat_MPIAIJ *Aij = (Mat_MPIAIJ *)mat->data; 4370 Mat_SeqAIJ *Ad = (Mat_SeqAIJ *)Aij->A->data; 4371 Mat_SeqAIJ *Ao = (Mat_SeqAIJ *)Aij->B->data; 4372 PetscScalar *ad, *ao; 4373 const PetscInt *Adi = Ad->i, *Adj = Ao->i; 4374 PetscInt ldi, Iii, md; 4375 PetscInt *ld = Aij->ld; 4376 4377 PetscFunctionBegin; 4378 m = mat->rmap->n; 4379 4380 PetscCall(MatSeqAIJGetArrayWrite(Aij->A, &ad)); 4381 PetscCall(MatSeqAIJGetArrayWrite(Aij->B, &ao)); 4382 Iii = 0; 4383 for (i = 0; i < m; i++) { 4384 nnz = Adi[i + 1] - Adi[i] + Adj[i + 1] - Adj[i]; 4385 ldi = ld[i]; 4386 md = Adi[i + 1] - Adi[i]; 4387 PetscCall(PetscArraycpy(ad, v + Iii + ldi, md)); 4388 ad += md; 4389 if (ao) { 4390 PetscCall(PetscArraycpy(ao, v + Iii, ldi)); 4391 PetscCall(PetscArraycpy(ao + ldi, v + Iii + ldi + md, nnz - ldi - md)); 4392 ao += nnz - md; 4393 } 4394 Iii += nnz; 4395 } 4396 nooffprocentries = mat->nooffprocentries; 4397 mat->nooffprocentries = PETSC_TRUE; 4398 PetscCall(MatSeqAIJRestoreArrayWrite(Aij->A, &ad)); 4399 PetscCall(MatSeqAIJRestoreArrayWrite(Aij->B, &ao)); 4400 PetscCall(PetscObjectStateIncrease((PetscObject)Aij->A)); 4401 PetscCall(PetscObjectStateIncrease((PetscObject)Aij->B)); 4402 PetscCall(PetscObjectStateIncrease((PetscObject)mat)); 4403 PetscCall(MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY)); 4404 PetscCall(MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY)); 4405 mat->nooffprocentries = nooffprocentries; 4406 PetscFunctionReturn(PETSC_SUCCESS); 4407 } 4408 4409 /*@ 4410 MatCreateAIJ - Creates a sparse parallel matrix in `MATAIJ` format 4411 (the default parallel PETSc format). For good matrix assembly performance 4412 the user should preallocate the matrix storage by setting the parameters 4413 `d_nz` (or `d_nnz`) and `o_nz` (or `o_nnz`). 4414 4415 Collective 4416 4417 Input Parameters: 4418 + comm - MPI communicator 4419 . m - number of local rows (or `PETSC_DECIDE` to have calculated if M is given) 4420 This value should be the same as the local size used in creating the 4421 y vector for the matrix-vector product y = Ax. 4422 . n - This value should be the same as the local size used in creating the 4423 x vector for the matrix-vector product y = Ax. (or `PETSC_DECIDE` to have 4424 calculated if N is given) For square matrices n is almost always m. 4425 . M - number of global rows (or `PETSC_DETERMINE` to have calculated if m is given) 4426 . N - number of global columns (or `PETSC_DETERMINE` to have calculated if n is given) 4427 . d_nz - number of nonzeros per row in DIAGONAL portion of local submatrix 4428 (same value is used for all local rows) 4429 . d_nnz - array containing the number of nonzeros in the various rows of the 4430 DIAGONAL portion of the local submatrix (possibly different for each row) 4431 or `NULL`, if `d_nz` is used to specify the nonzero structure. 4432 The size of this array is equal to the number of local rows, i.e 'm'. 4433 . o_nz - number of nonzeros per row in the OFF-DIAGONAL portion of local 4434 submatrix (same value is used for all local rows). 4435 - o_nnz - array containing the number of nonzeros in the various rows of the 4436 OFF-DIAGONAL portion of the local submatrix (possibly different for 4437 each row) or `NULL`, if `o_nz` is used to specify the nonzero 4438 structure. The size of this array is equal to the number 4439 of local rows, i.e 'm'. 4440 4441 Output Parameter: 4442 . A - the matrix 4443 4444 Options Database Keys: 4445 + -mat_no_inode - Do not use inodes 4446 . -mat_inode_limit <limit> - Sets inode limit (max limit=5) 4447 - -matmult_vecscatter_view <viewer> - View the vecscatter (i.e., communication pattern) used in `MatMult()` of sparse parallel matrices. 4448 See viewer types in manual of `MatView()`. Of them, ascii_matlab, draw or binary cause the `VecScatter` 4449 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. 4450 4451 Level: intermediate 4452 4453 Notes: 4454 It is recommended that one use `MatCreateFromOptions()` or the `MatCreate()`, `MatSetType()` and/or `MatSetFromOptions()`, 4455 MatXXXXSetPreallocation() paradigm instead of this routine directly. 4456 [MatXXXXSetPreallocation() is, for example, `MatSeqAIJSetPreallocation()`] 4457 4458 If the *_nnz parameter is given then the *_nz parameter is ignored 4459 4460 The `m`,`n`,`M`,`N` parameters specify the size of the matrix, and its partitioning across 4461 processors, while `d_nz`,`d_nnz`,`o_nz`,`o_nnz` parameters specify the approximate 4462 storage requirements for this matrix. 4463 4464 If `PETSC_DECIDE` or `PETSC_DETERMINE` is used for a particular argument on one 4465 processor than it must be used on all processors that share the object for 4466 that argument. 4467 4468 If `m` and `n` are not `PETSC_DECIDE`, then the values determine the `PetscLayout` of the matrix and the ranges returned by 4469 `MatGetOwnershipRange()`, `MatGetOwnershipRanges()`, `MatGetOwnershipRangeColumn()`, and `MatGetOwnershipRangesColumn()`. 4470 4471 The user MUST specify either the local or global matrix dimensions 4472 (possibly both). 4473 4474 The parallel matrix is partitioned across processors such that the 4475 first `m0` rows belong to process 0, the next `m1` rows belong to 4476 process 1, the next `m2` rows belong to process 2, etc., where 4477 `m0`, `m1`, `m2`... are the input parameter `m` on each MPI process. I.e., each MPI process stores 4478 values corresponding to [m x N] submatrix. 4479 4480 The columns are logically partitioned with the n0 columns belonging 4481 to 0th partition, the next n1 columns belonging to the next 4482 partition etc.. where n0,n1,n2... are the input parameter 'n'. 4483 4484 The DIAGONAL portion of the local submatrix on any given processor 4485 is the submatrix corresponding to the rows and columns m,n 4486 corresponding to the given processor. i.e diagonal matrix on 4487 process 0 is [m0 x n0], diagonal matrix on process 1 is [m1 x n1] 4488 etc. The remaining portion of the local submatrix [m x (N-n)] 4489 constitute the OFF-DIAGONAL portion. The example below better 4490 illustrates this concept. The two matrices, the DIAGONAL portion and 4491 the OFF-DIAGONAL portion are each stored as `MATSEQAIJ` matrices. 4492 4493 For a square global matrix we define each processor's diagonal portion 4494 to be its local rows and the corresponding columns (a square submatrix); 4495 each processor's off-diagonal portion encompasses the remainder of the 4496 local matrix (a rectangular submatrix). 4497 4498 If `o_nnz`, `d_nnz` are specified, then `o_nz`, and `d_nz` are ignored. 4499 4500 When calling this routine with a single process communicator, a matrix of 4501 type `MATSEQAIJ` is returned. If a matrix of type `MATMPIAIJ` is desired for this 4502 type of communicator, use the construction mechanism 4503 .vb 4504 MatCreate(..., &A); 4505 MatSetType(A, MATMPIAIJ); 4506 MatSetSizes(A, m, n, M, N); 4507 MatMPIAIJSetPreallocation(A, ...); 4508 .ve 4509 4510 By default, this format uses inodes (identical nodes) when possible. 4511 We search for consecutive rows with the same nonzero structure, thereby 4512 reusing matrix information to achieve increased efficiency. 4513 4514 Example Usage: 4515 Consider the following 8x8 matrix with 34 non-zero values, that is 4516 assembled across 3 processors. Lets assume that proc0 owns 3 rows, 4517 proc1 owns 3 rows, proc2 owns 2 rows. This division can be shown 4518 as follows 4519 4520 .vb 4521 1 2 0 | 0 3 0 | 0 4 4522 Proc0 0 5 6 | 7 0 0 | 8 0 4523 9 0 10 | 11 0 0 | 12 0 4524 ------------------------------------- 4525 13 0 14 | 15 16 17 | 0 0 4526 Proc1 0 18 0 | 19 20 21 | 0 0 4527 0 0 0 | 22 23 0 | 24 0 4528 ------------------------------------- 4529 Proc2 25 26 27 | 0 0 28 | 29 0 4530 30 0 0 | 31 32 33 | 0 34 4531 .ve 4532 4533 This can be represented as a collection of submatrices as 4534 4535 .vb 4536 A B C 4537 D E F 4538 G H I 4539 .ve 4540 4541 Where the submatrices A,B,C are owned by proc0, D,E,F are 4542 owned by proc1, G,H,I are owned by proc2. 4543 4544 The 'm' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4545 The 'n' parameters for proc0,proc1,proc2 are 3,3,2 respectively. 4546 The 'M','N' parameters are 8,8, and have the same values on all procs. 4547 4548 The DIAGONAL submatrices corresponding to proc0,proc1,proc2 are 4549 submatrices [A], [E], [I] respectively. The OFF-DIAGONAL submatrices 4550 corresponding to proc0,proc1,proc2 are [BC], [DF], [GH] respectively. 4551 Internally, each processor stores the DIAGONAL part, and the OFF-DIAGONAL 4552 part as `MATSEQAIJ` matrices. For example, proc1 will store [E] as a `MATSEQAIJ` 4553 matrix, and [DF] as another SeqAIJ matrix. 4554 4555 When `d_nz`, `o_nz` parameters are specified, `d_nz` storage elements are 4556 allocated for every row of the local DIAGONAL submatrix, and `o_nz` 4557 storage locations are allocated for every row of the OFF-DIAGONAL submatrix. 4558 One way to choose `d_nz` and `o_nz` is to use the maximum number of nonzeros over 4559 the local rows for each of the local DIAGONAL, and the OFF-DIAGONAL submatrices. 4560 In this case, the values of `d_nz`,`o_nz` are 4561 .vb 4562 proc0 dnz = 2, o_nz = 2 4563 proc1 dnz = 3, o_nz = 2 4564 proc2 dnz = 1, o_nz = 4 4565 .ve 4566 We are allocating m*(`d_nz`+`o_nz`) storage locations for every proc. This 4567 translates to 3*(2+2)=12 for proc0, 3*(3+2)=15 for proc1, 2*(1+4)=10 4568 for proc3. i.e we are using 12+15+10=37 storage locations to store 4569 34 values. 4570 4571 When `d_nnz`, `o_nnz` parameters are specified, the storage is specified 4572 for every row, corresponding to both DIAGONAL and OFF-DIAGONAL submatrices. 4573 In the above case the values for d_nnz,o_nnz are 4574 .vb 4575 proc0 d_nnz = [2,2,2] and o_nnz = [2,2,2] 4576 proc1 d_nnz = [3,3,2] and o_nnz = [2,1,1] 4577 proc2 d_nnz = [1,1] and o_nnz = [4,4] 4578 .ve 4579 Here the space allocated is sum of all the above values i.e 34, and 4580 hence pre-allocation is perfect. 4581 4582 .seealso: [](ch_matrices), `Mat`, [Sparse Matrix Creation](sec_matsparse), `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 4583 `MATMPIAIJ`, `MatCreateMPIAIJWithArrays()`, `MatGetOwnershipRange()`, `MatGetOwnershipRanges()`, `MatGetOwnershipRangeColumn()`, 4584 `MatGetOwnershipRangesColumn()`, `PetscLayout` 4585 @*/ 4586 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) 4587 { 4588 PetscMPIInt size; 4589 4590 PetscFunctionBegin; 4591 PetscCall(MatCreate(comm, A)); 4592 PetscCall(MatSetSizes(*A, m, n, M, N)); 4593 PetscCallMPI(MPI_Comm_size(comm, &size)); 4594 if (size > 1) { 4595 PetscCall(MatSetType(*A, MATMPIAIJ)); 4596 PetscCall(MatMPIAIJSetPreallocation(*A, d_nz, d_nnz, o_nz, o_nnz)); 4597 } else { 4598 PetscCall(MatSetType(*A, MATSEQAIJ)); 4599 PetscCall(MatSeqAIJSetPreallocation(*A, d_nz, d_nnz)); 4600 } 4601 PetscFunctionReturn(PETSC_SUCCESS); 4602 } 4603 4604 /*@C 4605 MatMPIAIJGetSeqAIJ - Returns the local pieces of this distributed matrix 4606 4607 Not Collective 4608 4609 Input Parameter: 4610 . A - The `MATMPIAIJ` matrix 4611 4612 Output Parameters: 4613 + Ad - The local diagonal block as a `MATSEQAIJ` matrix 4614 . Ao - The local off-diagonal block as a `MATSEQAIJ` matrix 4615 - colmap - An array mapping local column numbers of `Ao` to global column numbers of the parallel matrix 4616 4617 Level: intermediate 4618 4619 Note: 4620 The rows in `Ad` and `Ao` are in [0, Nr), where Nr is the number of local rows on this process. The columns 4621 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 4622 the number of nonzero columns in the local off-diagonal piece of the matrix `A`. The array colmap maps these 4623 local column numbers to global column numbers in the original matrix. 4624 4625 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatMPIAIJGetLocalMat()`, `MatMPIAIJGetLocalMatCondensed()`, `MatCreateAIJ()`, `MATSEQAIJ` 4626 @*/ 4627 PetscErrorCode MatMPIAIJGetSeqAIJ(Mat A, Mat *Ad, Mat *Ao, const PetscInt *colmap[]) 4628 { 4629 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 4630 PetscBool flg; 4631 4632 PetscFunctionBegin; 4633 PetscCall(PetscStrbeginswith(((PetscObject)A)->type_name, MATMPIAIJ, &flg)); 4634 PetscCheck(flg, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "This function requires a MATMPIAIJ matrix as input"); 4635 if (Ad) *Ad = a->A; 4636 if (Ao) *Ao = a->B; 4637 if (colmap) *colmap = a->garray; 4638 PetscFunctionReturn(PETSC_SUCCESS); 4639 } 4640 4641 PetscErrorCode MatCreateMPIMatConcatenateSeqMat_MPIAIJ(MPI_Comm comm, Mat inmat, PetscInt n, MatReuse scall, Mat *outmat) 4642 { 4643 PetscInt m, N, i, rstart, nnz, Ii; 4644 PetscInt *indx; 4645 PetscScalar *values; 4646 MatType rootType; 4647 4648 PetscFunctionBegin; 4649 PetscCall(MatGetSize(inmat, &m, &N)); 4650 if (scall == MAT_INITIAL_MATRIX) { /* symbolic phase */ 4651 PetscInt *dnz, *onz, sum, bs, cbs; 4652 4653 if (n == PETSC_DECIDE) PetscCall(PetscSplitOwnership(comm, &n, &N)); 4654 /* Check sum(n) = N */ 4655 PetscCallMPI(MPIU_Allreduce(&n, &sum, 1, MPIU_INT, MPI_SUM, comm)); 4656 PetscCheck(sum == N, PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Sum of local columns %" PetscInt_FMT " != global columns %" PetscInt_FMT, sum, N); 4657 4658 PetscCallMPI(MPI_Scan(&m, &rstart, 1, MPIU_INT, MPI_SUM, comm)); 4659 rstart -= m; 4660 4661 MatPreallocateBegin(comm, m, n, dnz, onz); 4662 for (i = 0; i < m; i++) { 4663 PetscCall(MatGetRow_SeqAIJ(inmat, i, &nnz, &indx, NULL)); 4664 PetscCall(MatPreallocateSet(i + rstart, nnz, indx, dnz, onz)); 4665 PetscCall(MatRestoreRow_SeqAIJ(inmat, i, &nnz, &indx, NULL)); 4666 } 4667 4668 PetscCall(MatCreate(comm, outmat)); 4669 PetscCall(MatSetSizes(*outmat, m, n, PETSC_DETERMINE, PETSC_DETERMINE)); 4670 PetscCall(MatGetBlockSizes(inmat, &bs, &cbs)); 4671 PetscCall(MatSetBlockSizes(*outmat, bs, cbs)); 4672 PetscCall(MatGetRootType_Private(inmat, &rootType)); 4673 PetscCall(MatSetType(*outmat, rootType)); 4674 PetscCall(MatSeqAIJSetPreallocation(*outmat, 0, dnz)); 4675 PetscCall(MatMPIAIJSetPreallocation(*outmat, 0, dnz, 0, onz)); 4676 MatPreallocateEnd(dnz, onz); 4677 PetscCall(MatSetOption(*outmat, MAT_NO_OFF_PROC_ENTRIES, PETSC_TRUE)); 4678 } 4679 4680 /* numeric phase */ 4681 PetscCall(MatGetOwnershipRange(*outmat, &rstart, NULL)); 4682 for (i = 0; i < m; i++) { 4683 PetscCall(MatGetRow_SeqAIJ(inmat, i, &nnz, &indx, &values)); 4684 Ii = i + rstart; 4685 PetscCall(MatSetValues(*outmat, 1, &Ii, nnz, indx, values, INSERT_VALUES)); 4686 PetscCall(MatRestoreRow_SeqAIJ(inmat, i, &nnz, &indx, &values)); 4687 } 4688 PetscCall(MatAssemblyBegin(*outmat, MAT_FINAL_ASSEMBLY)); 4689 PetscCall(MatAssemblyEnd(*outmat, MAT_FINAL_ASSEMBLY)); 4690 PetscFunctionReturn(PETSC_SUCCESS); 4691 } 4692 4693 static PetscErrorCode MatDestroy_MPIAIJ_SeqsToMPI(void **data) 4694 { 4695 Mat_Merge_SeqsToMPI *merge = (Mat_Merge_SeqsToMPI *)*data; 4696 4697 PetscFunctionBegin; 4698 if (!merge) PetscFunctionReturn(PETSC_SUCCESS); 4699 PetscCall(PetscFree(merge->id_r)); 4700 PetscCall(PetscFree(merge->len_s)); 4701 PetscCall(PetscFree(merge->len_r)); 4702 PetscCall(PetscFree(merge->bi)); 4703 PetscCall(PetscFree(merge->bj)); 4704 PetscCall(PetscFree(merge->buf_ri[0])); 4705 PetscCall(PetscFree(merge->buf_ri)); 4706 PetscCall(PetscFree(merge->buf_rj[0])); 4707 PetscCall(PetscFree(merge->buf_rj)); 4708 PetscCall(PetscFree(merge->coi)); 4709 PetscCall(PetscFree(merge->coj)); 4710 PetscCall(PetscFree(merge->owners_co)); 4711 PetscCall(PetscLayoutDestroy(&merge->rowmap)); 4712 PetscCall(PetscFree(merge)); 4713 PetscFunctionReturn(PETSC_SUCCESS); 4714 } 4715 4716 #include <../src/mat/utils/freespace.h> 4717 #include <petscbt.h> 4718 4719 PetscErrorCode MatCreateMPIAIJSumSeqAIJNumeric(Mat seqmat, Mat mpimat) 4720 { 4721 MPI_Comm comm; 4722 Mat_SeqAIJ *a = (Mat_SeqAIJ *)seqmat->data; 4723 PetscMPIInt size, rank, taga, *len_s; 4724 PetscInt N = mpimat->cmap->N, i, j, *owners, *ai = a->i, *aj, m; 4725 PetscMPIInt proc, k; 4726 PetscInt **buf_ri, **buf_rj; 4727 PetscInt anzi, *bj_i, *bi, *bj, arow, bnzi, nextaj; 4728 PetscInt nrows, **buf_ri_k, **nextrow, **nextai; 4729 MPI_Request *s_waits, *r_waits; 4730 MPI_Status *status; 4731 const MatScalar *aa, *a_a; 4732 MatScalar **abuf_r, *ba_i; 4733 Mat_Merge_SeqsToMPI *merge; 4734 PetscContainer container; 4735 4736 PetscFunctionBegin; 4737 PetscCall(PetscObjectGetComm((PetscObject)mpimat, &comm)); 4738 PetscCall(PetscLogEventBegin(MAT_Seqstompinum, seqmat, 0, 0, 0)); 4739 4740 PetscCallMPI(MPI_Comm_size(comm, &size)); 4741 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 4742 4743 PetscCall(PetscObjectQuery((PetscObject)mpimat, "MatMergeSeqsToMPI", (PetscObject *)&container)); 4744 PetscCheck(container, PetscObjectComm((PetscObject)mpimat), PETSC_ERR_PLIB, "Mat not created from MatCreateMPIAIJSumSeqAIJSymbolic"); 4745 PetscCall(PetscContainerGetPointer(container, (void **)&merge)); 4746 PetscCall(MatSeqAIJGetArrayRead(seqmat, &a_a)); 4747 aa = a_a; 4748 4749 bi = merge->bi; 4750 bj = merge->bj; 4751 buf_ri = merge->buf_ri; 4752 buf_rj = merge->buf_rj; 4753 4754 PetscCall(PetscMalloc1(size, &status)); 4755 owners = merge->rowmap->range; 4756 len_s = merge->len_s; 4757 4758 /* send and recv matrix values */ 4759 PetscCall(PetscObjectGetNewTag((PetscObject)mpimat, &taga)); 4760 PetscCall(PetscPostIrecvScalar(comm, taga, merge->nrecv, merge->id_r, merge->len_r, &abuf_r, &r_waits)); 4761 4762 PetscCall(PetscMalloc1(merge->nsend + 1, &s_waits)); 4763 for (proc = 0, k = 0; proc < size; proc++) { 4764 if (!len_s[proc]) continue; 4765 i = owners[proc]; 4766 PetscCallMPI(MPIU_Isend(aa + ai[i], len_s[proc], MPIU_MATSCALAR, proc, taga, comm, s_waits + k)); 4767 k++; 4768 } 4769 4770 if (merge->nrecv) PetscCallMPI(MPI_Waitall(merge->nrecv, r_waits, status)); 4771 if (merge->nsend) PetscCallMPI(MPI_Waitall(merge->nsend, s_waits, status)); 4772 PetscCall(PetscFree(status)); 4773 4774 PetscCall(PetscFree(s_waits)); 4775 PetscCall(PetscFree(r_waits)); 4776 4777 /* insert mat values of mpimat */ 4778 PetscCall(PetscMalloc1(N, &ba_i)); 4779 PetscCall(PetscMalloc3(merge->nrecv, &buf_ri_k, merge->nrecv, &nextrow, merge->nrecv, &nextai)); 4780 4781 for (k = 0; k < merge->nrecv; k++) { 4782 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4783 nrows = *buf_ri_k[k]; 4784 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4785 nextai[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recved i-structure */ 4786 } 4787 4788 /* set values of ba */ 4789 m = merge->rowmap->n; 4790 for (i = 0; i < m; i++) { 4791 arow = owners[rank] + i; 4792 bj_i = bj + bi[i]; /* col indices of the i-th row of mpimat */ 4793 bnzi = bi[i + 1] - bi[i]; 4794 PetscCall(PetscArrayzero(ba_i, bnzi)); 4795 4796 /* add local non-zero vals of this proc's seqmat into ba */ 4797 anzi = ai[arow + 1] - ai[arow]; 4798 aj = a->j + ai[arow]; 4799 aa = a_a + ai[arow]; 4800 nextaj = 0; 4801 for (j = 0; nextaj < anzi; j++) { 4802 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4803 ba_i[j] += aa[nextaj++]; 4804 } 4805 } 4806 4807 /* add received vals into ba */ 4808 for (k = 0; k < merge->nrecv; k++) { /* k-th received message */ 4809 /* i-th row */ 4810 if (i == *nextrow[k]) { 4811 anzi = *(nextai[k] + 1) - *nextai[k]; 4812 aj = buf_rj[k] + *nextai[k]; 4813 aa = abuf_r[k] + *nextai[k]; 4814 nextaj = 0; 4815 for (j = 0; nextaj < anzi; j++) { 4816 if (*(bj_i + j) == aj[nextaj]) { /* bcol == acol */ 4817 ba_i[j] += aa[nextaj++]; 4818 } 4819 } 4820 nextrow[k]++; 4821 nextai[k]++; 4822 } 4823 } 4824 PetscCall(MatSetValues(mpimat, 1, &arow, bnzi, bj_i, ba_i, INSERT_VALUES)); 4825 } 4826 PetscCall(MatSeqAIJRestoreArrayRead(seqmat, &a_a)); 4827 PetscCall(MatAssemblyBegin(mpimat, MAT_FINAL_ASSEMBLY)); 4828 PetscCall(MatAssemblyEnd(mpimat, MAT_FINAL_ASSEMBLY)); 4829 4830 PetscCall(PetscFree(abuf_r[0])); 4831 PetscCall(PetscFree(abuf_r)); 4832 PetscCall(PetscFree(ba_i)); 4833 PetscCall(PetscFree3(buf_ri_k, nextrow, nextai)); 4834 PetscCall(PetscLogEventEnd(MAT_Seqstompinum, seqmat, 0, 0, 0)); 4835 PetscFunctionReturn(PETSC_SUCCESS); 4836 } 4837 4838 PetscErrorCode MatCreateMPIAIJSumSeqAIJSymbolic(MPI_Comm comm, Mat seqmat, PetscInt m, PetscInt n, Mat *mpimat) 4839 { 4840 Mat B_mpi; 4841 Mat_SeqAIJ *a = (Mat_SeqAIJ *)seqmat->data; 4842 PetscMPIInt size, rank, tagi, tagj, *len_s, *len_si, *len_ri; 4843 PetscInt **buf_rj, **buf_ri, **buf_ri_k; 4844 PetscInt M = seqmat->rmap->n, N = seqmat->cmap->n, i, *owners, *ai = a->i, *aj = a->j; 4845 PetscInt len, *dnz, *onz, bs, cbs; 4846 PetscInt k, anzi, *bi, *bj, *lnk, nlnk, arow, bnzi; 4847 PetscInt nrows, *buf_s, *buf_si, *buf_si_i, **nextrow, **nextai; 4848 MPI_Request *si_waits, *sj_waits, *ri_waits, *rj_waits; 4849 MPI_Status *status; 4850 PetscFreeSpaceList free_space = NULL, current_space = NULL; 4851 PetscBT lnkbt; 4852 Mat_Merge_SeqsToMPI *merge; 4853 PetscContainer container; 4854 4855 PetscFunctionBegin; 4856 PetscCall(PetscLogEventBegin(MAT_Seqstompisym, seqmat, 0, 0, 0)); 4857 4858 /* make sure it is a PETSc comm */ 4859 PetscCall(PetscCommDuplicate(comm, &comm, NULL)); 4860 PetscCallMPI(MPI_Comm_size(comm, &size)); 4861 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 4862 4863 PetscCall(PetscNew(&merge)); 4864 PetscCall(PetscMalloc1(size, &status)); 4865 4866 /* determine row ownership */ 4867 PetscCall(PetscLayoutCreate(comm, &merge->rowmap)); 4868 PetscCall(PetscLayoutSetLocalSize(merge->rowmap, m)); 4869 PetscCall(PetscLayoutSetSize(merge->rowmap, M)); 4870 PetscCall(PetscLayoutSetBlockSize(merge->rowmap, 1)); 4871 PetscCall(PetscLayoutSetUp(merge->rowmap)); 4872 PetscCall(PetscMalloc1(size, &len_si)); 4873 PetscCall(PetscMalloc1(size, &merge->len_s)); 4874 4875 m = merge->rowmap->n; 4876 owners = merge->rowmap->range; 4877 4878 /* determine the number of messages to send, their lengths */ 4879 len_s = merge->len_s; 4880 4881 len = 0; /* length of buf_si[] */ 4882 merge->nsend = 0; 4883 for (PetscMPIInt proc = 0; proc < size; proc++) { 4884 len_si[proc] = 0; 4885 if (proc == rank) { 4886 len_s[proc] = 0; 4887 } else { 4888 PetscCall(PetscMPIIntCast(owners[proc + 1] - owners[proc] + 1, &len_si[proc])); 4889 PetscCall(PetscMPIIntCast(ai[owners[proc + 1]] - ai[owners[proc]], &len_s[proc])); /* num of rows to be sent to [proc] */ 4890 } 4891 if (len_s[proc]) { 4892 merge->nsend++; 4893 nrows = 0; 4894 for (i = owners[proc]; i < owners[proc + 1]; i++) { 4895 if (ai[i + 1] > ai[i]) nrows++; 4896 } 4897 PetscCall(PetscMPIIntCast(2 * (nrows + 1), &len_si[proc])); 4898 len += len_si[proc]; 4899 } 4900 } 4901 4902 /* determine the number and length of messages to receive for ij-structure */ 4903 PetscCall(PetscGatherNumberOfMessages(comm, NULL, len_s, &merge->nrecv)); 4904 PetscCall(PetscGatherMessageLengths2(comm, merge->nsend, merge->nrecv, len_s, len_si, &merge->id_r, &merge->len_r, &len_ri)); 4905 4906 /* post the Irecv of j-structure */ 4907 PetscCall(PetscCommGetNewTag(comm, &tagj)); 4908 PetscCall(PetscPostIrecvInt(comm, tagj, merge->nrecv, merge->id_r, merge->len_r, &buf_rj, &rj_waits)); 4909 4910 /* post the Isend of j-structure */ 4911 PetscCall(PetscMalloc2(merge->nsend, &si_waits, merge->nsend, &sj_waits)); 4912 4913 for (PetscMPIInt proc = 0, k = 0; proc < size; proc++) { 4914 if (!len_s[proc]) continue; 4915 i = owners[proc]; 4916 PetscCallMPI(MPIU_Isend(aj + ai[i], len_s[proc], MPIU_INT, proc, tagj, comm, sj_waits + k)); 4917 k++; 4918 } 4919 4920 /* receives and sends of j-structure are complete */ 4921 if (merge->nrecv) PetscCallMPI(MPI_Waitall(merge->nrecv, rj_waits, status)); 4922 if (merge->nsend) PetscCallMPI(MPI_Waitall(merge->nsend, sj_waits, status)); 4923 4924 /* send and recv i-structure */ 4925 PetscCall(PetscCommGetNewTag(comm, &tagi)); 4926 PetscCall(PetscPostIrecvInt(comm, tagi, merge->nrecv, merge->id_r, len_ri, &buf_ri, &ri_waits)); 4927 4928 PetscCall(PetscMalloc1(len + 1, &buf_s)); 4929 buf_si = buf_s; /* points to the beginning of k-th msg to be sent */ 4930 for (PetscMPIInt proc = 0, k = 0; proc < size; proc++) { 4931 if (!len_s[proc]) continue; 4932 /* form outgoing message for i-structure: 4933 buf_si[0]: nrows to be sent 4934 [1:nrows]: row index (global) 4935 [nrows+1:2*nrows+1]: i-structure index 4936 */ 4937 nrows = len_si[proc] / 2 - 1; 4938 buf_si_i = buf_si + nrows + 1; 4939 buf_si[0] = nrows; 4940 buf_si_i[0] = 0; 4941 nrows = 0; 4942 for (i = owners[proc]; i < owners[proc + 1]; i++) { 4943 anzi = ai[i + 1] - ai[i]; 4944 if (anzi) { 4945 buf_si_i[nrows + 1] = buf_si_i[nrows] + anzi; /* i-structure */ 4946 buf_si[nrows + 1] = i - owners[proc]; /* local row index */ 4947 nrows++; 4948 } 4949 } 4950 PetscCallMPI(MPIU_Isend(buf_si, len_si[proc], MPIU_INT, proc, tagi, comm, si_waits + k)); 4951 k++; 4952 buf_si += len_si[proc]; 4953 } 4954 4955 if (merge->nrecv) PetscCallMPI(MPI_Waitall(merge->nrecv, ri_waits, status)); 4956 if (merge->nsend) PetscCallMPI(MPI_Waitall(merge->nsend, si_waits, status)); 4957 4958 PetscCall(PetscInfo(seqmat, "nsend: %d, nrecv: %d\n", merge->nsend, merge->nrecv)); 4959 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])); 4960 4961 PetscCall(PetscFree(len_si)); 4962 PetscCall(PetscFree(len_ri)); 4963 PetscCall(PetscFree(rj_waits)); 4964 PetscCall(PetscFree2(si_waits, sj_waits)); 4965 PetscCall(PetscFree(ri_waits)); 4966 PetscCall(PetscFree(buf_s)); 4967 PetscCall(PetscFree(status)); 4968 4969 /* compute a local seq matrix in each processor */ 4970 /* allocate bi array and free space for accumulating nonzero column info */ 4971 PetscCall(PetscMalloc1(m + 1, &bi)); 4972 bi[0] = 0; 4973 4974 /* create and initialize a linked list */ 4975 nlnk = N + 1; 4976 PetscCall(PetscLLCreate(N, N, nlnk, lnk, lnkbt)); 4977 4978 /* initial FreeSpace size is 2*(num of local nnz(seqmat)) */ 4979 len = ai[owners[rank + 1]] - ai[owners[rank]]; 4980 PetscCall(PetscFreeSpaceGet(PetscIntMultTruncate(2, len) + 1, &free_space)); 4981 4982 current_space = free_space; 4983 4984 /* determine symbolic info for each local row */ 4985 PetscCall(PetscMalloc3(merge->nrecv, &buf_ri_k, merge->nrecv, &nextrow, merge->nrecv, &nextai)); 4986 4987 for (k = 0; k < merge->nrecv; k++) { 4988 buf_ri_k[k] = buf_ri[k]; /* beginning of k-th recved i-structure */ 4989 nrows = *buf_ri_k[k]; 4990 nextrow[k] = buf_ri_k[k] + 1; /* next row number of k-th recved i-structure */ 4991 nextai[k] = buf_ri_k[k] + (nrows + 1); /* points to the next i-structure of k-th recved i-structure */ 4992 } 4993 4994 MatPreallocateBegin(comm, m, n, dnz, onz); 4995 len = 0; 4996 for (i = 0; i < m; i++) { 4997 bnzi = 0; 4998 /* add local non-zero cols of this proc's seqmat into lnk */ 4999 arow = owners[rank] + i; 5000 anzi = ai[arow + 1] - ai[arow]; 5001 aj = a->j + ai[arow]; 5002 PetscCall(PetscLLAddSorted(anzi, aj, N, &nlnk, lnk, lnkbt)); 5003 bnzi += nlnk; 5004 /* add received col data into lnk */ 5005 for (k = 0; k < merge->nrecv; k++) { /* k-th received message */ 5006 if (i == *nextrow[k]) { /* i-th row */ 5007 anzi = *(nextai[k] + 1) - *nextai[k]; 5008 aj = buf_rj[k] + *nextai[k]; 5009 PetscCall(PetscLLAddSorted(anzi, aj, N, &nlnk, lnk, lnkbt)); 5010 bnzi += nlnk; 5011 nextrow[k]++; 5012 nextai[k]++; 5013 } 5014 } 5015 if (len < bnzi) len = bnzi; /* =max(bnzi) */ 5016 5017 /* if free space is not available, make more free space */ 5018 if (current_space->local_remaining < bnzi) PetscCall(PetscFreeSpaceGet(PetscIntSumTruncate(bnzi, current_space->total_array_size), ¤t_space)); 5019 /* copy data into free space, then initialize lnk */ 5020 PetscCall(PetscLLClean(N, N, bnzi, lnk, current_space->array, lnkbt)); 5021 PetscCall(MatPreallocateSet(i + owners[rank], bnzi, current_space->array, dnz, onz)); 5022 5023 current_space->array += bnzi; 5024 current_space->local_used += bnzi; 5025 current_space->local_remaining -= bnzi; 5026 5027 bi[i + 1] = bi[i] + bnzi; 5028 } 5029 5030 PetscCall(PetscFree3(buf_ri_k, nextrow, nextai)); 5031 5032 PetscCall(PetscMalloc1(bi[m] + 1, &bj)); 5033 PetscCall(PetscFreeSpaceContiguous(&free_space, bj)); 5034 PetscCall(PetscLLDestroy(lnk, lnkbt)); 5035 5036 /* create symbolic parallel matrix B_mpi */ 5037 PetscCall(MatGetBlockSizes(seqmat, &bs, &cbs)); 5038 PetscCall(MatCreate(comm, &B_mpi)); 5039 if (n == PETSC_DECIDE) { 5040 PetscCall(MatSetSizes(B_mpi, m, n, PETSC_DETERMINE, N)); 5041 } else { 5042 PetscCall(MatSetSizes(B_mpi, m, n, PETSC_DETERMINE, PETSC_DETERMINE)); 5043 } 5044 PetscCall(MatSetBlockSizes(B_mpi, bs, cbs)); 5045 PetscCall(MatSetType(B_mpi, MATMPIAIJ)); 5046 PetscCall(MatMPIAIJSetPreallocation(B_mpi, 0, dnz, 0, onz)); 5047 MatPreallocateEnd(dnz, onz); 5048 PetscCall(MatSetOption(B_mpi, MAT_NEW_NONZERO_ALLOCATION_ERR, PETSC_FALSE)); 5049 5050 /* B_mpi is not ready for use - assembly will be done by MatCreateMPIAIJSumSeqAIJNumeric() */ 5051 B_mpi->assembled = PETSC_FALSE; 5052 merge->bi = bi; 5053 merge->bj = bj; 5054 merge->buf_ri = buf_ri; 5055 merge->buf_rj = buf_rj; 5056 merge->coi = NULL; 5057 merge->coj = NULL; 5058 merge->owners_co = NULL; 5059 5060 PetscCall(PetscCommDestroy(&comm)); 5061 5062 /* attach the supporting struct to B_mpi for reuse */ 5063 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container)); 5064 PetscCall(PetscContainerSetPointer(container, merge)); 5065 PetscCall(PetscContainerSetCtxDestroy(container, MatDestroy_MPIAIJ_SeqsToMPI)); 5066 PetscCall(PetscObjectCompose((PetscObject)B_mpi, "MatMergeSeqsToMPI", (PetscObject)container)); 5067 PetscCall(PetscContainerDestroy(&container)); 5068 *mpimat = B_mpi; 5069 5070 PetscCall(PetscLogEventEnd(MAT_Seqstompisym, seqmat, 0, 0, 0)); 5071 PetscFunctionReturn(PETSC_SUCCESS); 5072 } 5073 5074 /*@ 5075 MatCreateMPIAIJSumSeqAIJ - Creates a `MATMPIAIJ` matrix by adding sequential 5076 matrices from each processor 5077 5078 Collective 5079 5080 Input Parameters: 5081 + comm - the communicators the parallel matrix will live on 5082 . seqmat - the input sequential matrices 5083 . m - number of local rows (or `PETSC_DECIDE`) 5084 . n - number of local columns (or `PETSC_DECIDE`) 5085 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5086 5087 Output Parameter: 5088 . mpimat - the parallel matrix generated 5089 5090 Level: advanced 5091 5092 Note: 5093 The dimensions of the sequential matrix in each processor MUST be the same. 5094 The input seqmat is included into the container "Mat_Merge_SeqsToMPI", and will be 5095 destroyed when `mpimat` is destroyed. Call `PetscObjectQuery()` to access `seqmat`. 5096 5097 .seealso: [](ch_matrices), `Mat`, `MatCreateAIJ()` 5098 @*/ 5099 PetscErrorCode MatCreateMPIAIJSumSeqAIJ(MPI_Comm comm, Mat seqmat, PetscInt m, PetscInt n, MatReuse scall, Mat *mpimat) 5100 { 5101 PetscMPIInt size; 5102 5103 PetscFunctionBegin; 5104 PetscCallMPI(MPI_Comm_size(comm, &size)); 5105 if (size == 1) { 5106 PetscCall(PetscLogEventBegin(MAT_Seqstompi, seqmat, 0, 0, 0)); 5107 if (scall == MAT_INITIAL_MATRIX) { 5108 PetscCall(MatDuplicate(seqmat, MAT_COPY_VALUES, mpimat)); 5109 } else { 5110 PetscCall(MatCopy(seqmat, *mpimat, SAME_NONZERO_PATTERN)); 5111 } 5112 PetscCall(PetscLogEventEnd(MAT_Seqstompi, seqmat, 0, 0, 0)); 5113 PetscFunctionReturn(PETSC_SUCCESS); 5114 } 5115 PetscCall(PetscLogEventBegin(MAT_Seqstompi, seqmat, 0, 0, 0)); 5116 if (scall == MAT_INITIAL_MATRIX) PetscCall(MatCreateMPIAIJSumSeqAIJSymbolic(comm, seqmat, m, n, mpimat)); 5117 PetscCall(MatCreateMPIAIJSumSeqAIJNumeric(seqmat, *mpimat)); 5118 PetscCall(PetscLogEventEnd(MAT_Seqstompi, seqmat, 0, 0, 0)); 5119 PetscFunctionReturn(PETSC_SUCCESS); 5120 } 5121 5122 /*@ 5123 MatAIJGetLocalMat - Creates a `MATSEQAIJ` from a `MATAIJ` matrix. 5124 5125 Not Collective 5126 5127 Input Parameter: 5128 . A - the matrix 5129 5130 Output Parameter: 5131 . A_loc - the local sequential matrix generated 5132 5133 Level: developer 5134 5135 Notes: 5136 The matrix is created by taking `A`'s local rows and putting them into a sequential matrix 5137 with `mlocal` rows and `n` columns. Where `mlocal` is obtained with `MatGetLocalSize()` and 5138 `n` is the global column count obtained with `MatGetSize()` 5139 5140 In other words combines the two parts of a parallel `MATMPIAIJ` matrix on each process to a single matrix. 5141 5142 For parallel matrices this creates an entirely new matrix. If the matrix is sequential it merely increases the reference count. 5143 5144 Destroy the matrix with `MatDestroy()` 5145 5146 .seealso: [](ch_matrices), `Mat`, `MatMPIAIJGetLocalMat()` 5147 @*/ 5148 PetscErrorCode MatAIJGetLocalMat(Mat A, Mat *A_loc) 5149 { 5150 PetscBool mpi; 5151 5152 PetscFunctionBegin; 5153 PetscCall(PetscObjectTypeCompare((PetscObject)A, MATMPIAIJ, &mpi)); 5154 if (mpi) { 5155 PetscCall(MatMPIAIJGetLocalMat(A, MAT_INITIAL_MATRIX, A_loc)); 5156 } else { 5157 *A_loc = A; 5158 PetscCall(PetscObjectReference((PetscObject)*A_loc)); 5159 } 5160 PetscFunctionReturn(PETSC_SUCCESS); 5161 } 5162 5163 /*@ 5164 MatMPIAIJGetLocalMat - Creates a `MATSEQAIJ` from a `MATMPIAIJ` matrix. 5165 5166 Not Collective 5167 5168 Input Parameters: 5169 + A - the matrix 5170 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5171 5172 Output Parameter: 5173 . A_loc - the local sequential matrix generated 5174 5175 Level: developer 5176 5177 Notes: 5178 The matrix is created by taking all `A`'s local rows and putting them into a sequential 5179 matrix with `mlocal` rows and `n` columns.`mlocal` is the row count obtained with 5180 `MatGetLocalSize()` and `n` is the global column count obtained with `MatGetSize()`. 5181 5182 In other words combines the two parts of a parallel `MATMPIAIJ` matrix on each process to a single matrix. 5183 5184 When `A` is sequential and `MAT_INITIAL_MATRIX` is requested, the matrix returned is the diagonal part of `A` (which contains the entire matrix), 5185 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 5186 then `MatCopy`(Adiag,*`A_loc`,`SAME_NONZERO_PATTERN`) is called to fill `A_loc`. Thus one can preallocate the appropriate sequential matrix `A_loc` 5187 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. 5188 5189 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatGetOwnershipRange()`, `MatMPIAIJGetLocalMatCondensed()`, `MatMPIAIJGetLocalMatMerge()` 5190 @*/ 5191 PetscErrorCode MatMPIAIJGetLocalMat(Mat A, MatReuse scall, Mat *A_loc) 5192 { 5193 Mat_MPIAIJ *mpimat = (Mat_MPIAIJ *)A->data; 5194 Mat_SeqAIJ *mat, *a, *b; 5195 PetscInt *ai, *aj, *bi, *bj, *cmap = mpimat->garray; 5196 const PetscScalar *aa, *ba, *aav, *bav; 5197 PetscScalar *ca, *cam; 5198 PetscMPIInt size; 5199 PetscInt am = A->rmap->n, i, j, k, cstart = A->cmap->rstart; 5200 PetscInt *ci, *cj, col, ncols_d, ncols_o, jo; 5201 PetscBool match; 5202 5203 PetscFunctionBegin; 5204 PetscCall(PetscStrbeginswith(((PetscObject)A)->type_name, MATMPIAIJ, &match)); 5205 PetscCheck(match, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Requires MATMPIAIJ matrix as input"); 5206 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)A), &size)); 5207 if (size == 1) { 5208 if (scall == MAT_INITIAL_MATRIX) { 5209 PetscCall(PetscObjectReference((PetscObject)mpimat->A)); 5210 *A_loc = mpimat->A; 5211 } else if (scall == MAT_REUSE_MATRIX) { 5212 PetscCall(MatCopy(mpimat->A, *A_loc, SAME_NONZERO_PATTERN)); 5213 } 5214 PetscFunctionReturn(PETSC_SUCCESS); 5215 } 5216 5217 PetscCall(PetscLogEventBegin(MAT_Getlocalmat, A, 0, 0, 0)); 5218 a = (Mat_SeqAIJ *)mpimat->A->data; 5219 b = (Mat_SeqAIJ *)mpimat->B->data; 5220 ai = a->i; 5221 aj = a->j; 5222 bi = b->i; 5223 bj = b->j; 5224 PetscCall(MatSeqAIJGetArrayRead(mpimat->A, &aav)); 5225 PetscCall(MatSeqAIJGetArrayRead(mpimat->B, &bav)); 5226 aa = aav; 5227 ba = bav; 5228 if (scall == MAT_INITIAL_MATRIX) { 5229 PetscCall(PetscMalloc1(1 + am, &ci)); 5230 ci[0] = 0; 5231 for (i = 0; i < am; i++) ci[i + 1] = ci[i] + (ai[i + 1] - ai[i]) + (bi[i + 1] - bi[i]); 5232 PetscCall(PetscMalloc1(1 + ci[am], &cj)); 5233 PetscCall(PetscMalloc1(1 + ci[am], &ca)); 5234 k = 0; 5235 for (i = 0; i < am; i++) { 5236 ncols_o = bi[i + 1] - bi[i]; 5237 ncols_d = ai[i + 1] - ai[i]; 5238 /* off-diagonal portion of A */ 5239 for (jo = 0; jo < ncols_o; jo++) { 5240 col = cmap[*bj]; 5241 if (col >= cstart) break; 5242 cj[k] = col; 5243 bj++; 5244 ca[k++] = *ba++; 5245 } 5246 /* diagonal portion of A */ 5247 for (j = 0; j < ncols_d; j++) { 5248 cj[k] = cstart + *aj++; 5249 ca[k++] = *aa++; 5250 } 5251 /* off-diagonal portion of A */ 5252 for (j = jo; j < ncols_o; j++) { 5253 cj[k] = cmap[*bj++]; 5254 ca[k++] = *ba++; 5255 } 5256 } 5257 /* put together the new matrix */ 5258 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, am, A->cmap->N, ci, cj, ca, A_loc)); 5259 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5260 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5261 mat = (Mat_SeqAIJ *)(*A_loc)->data; 5262 mat->free_a = PETSC_TRUE; 5263 mat->free_ij = PETSC_TRUE; 5264 mat->nonew = 0; 5265 } else if (scall == MAT_REUSE_MATRIX) { 5266 mat = (Mat_SeqAIJ *)(*A_loc)->data; 5267 ci = mat->i; 5268 cj = mat->j; 5269 PetscCall(MatSeqAIJGetArrayWrite(*A_loc, &cam)); 5270 for (i = 0; i < am; i++) { 5271 /* off-diagonal portion of A */ 5272 ncols_o = bi[i + 1] - bi[i]; 5273 for (jo = 0; jo < ncols_o; jo++) { 5274 col = cmap[*bj]; 5275 if (col >= cstart) break; 5276 *cam++ = *ba++; 5277 bj++; 5278 } 5279 /* diagonal portion of A */ 5280 ncols_d = ai[i + 1] - ai[i]; 5281 for (j = 0; j < ncols_d; j++) *cam++ = *aa++; 5282 /* off-diagonal portion of A */ 5283 for (j = jo; j < ncols_o; j++) { 5284 *cam++ = *ba++; 5285 bj++; 5286 } 5287 } 5288 PetscCall(MatSeqAIJRestoreArrayWrite(*A_loc, &cam)); 5289 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid MatReuse %d", (int)scall); 5290 PetscCall(MatSeqAIJRestoreArrayRead(mpimat->A, &aav)); 5291 PetscCall(MatSeqAIJRestoreArrayRead(mpimat->B, &bav)); 5292 PetscCall(PetscLogEventEnd(MAT_Getlocalmat, A, 0, 0, 0)); 5293 PetscFunctionReturn(PETSC_SUCCESS); 5294 } 5295 5296 /*@ 5297 MatMPIAIJGetLocalMatMerge - Creates a `MATSEQAIJ` from a `MATMPIAIJ` matrix by taking all its local rows and putting them into a sequential matrix with 5298 mlocal rows and n columns. Where n is the sum of the number of columns of the diagonal and off-diagonal part 5299 5300 Not Collective 5301 5302 Input Parameters: 5303 + A - the matrix 5304 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5305 5306 Output Parameters: 5307 + glob - sequential `IS` with global indices associated with the columns of the local sequential matrix generated (can be `NULL`) 5308 - A_loc - the local sequential matrix generated 5309 5310 Level: developer 5311 5312 Note: 5313 This is different from `MatMPIAIJGetLocalMat()` since the first columns in the returning matrix are those associated with the diagonal 5314 part, then those associated with the off-diagonal part (in its local ordering) 5315 5316 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatGetOwnershipRange()`, `MatMPIAIJGetLocalMat()`, `MatMPIAIJGetLocalMatCondensed()` 5317 @*/ 5318 PetscErrorCode MatMPIAIJGetLocalMatMerge(Mat A, MatReuse scall, IS *glob, Mat *A_loc) 5319 { 5320 Mat Ao, Ad; 5321 const PetscInt *cmap; 5322 PetscMPIInt size; 5323 PetscErrorCode (*f)(Mat, MatReuse, IS *, Mat *); 5324 5325 PetscFunctionBegin; 5326 PetscCall(MatMPIAIJGetSeqAIJ(A, &Ad, &Ao, &cmap)); 5327 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)A), &size)); 5328 if (size == 1) { 5329 if (scall == MAT_INITIAL_MATRIX) { 5330 PetscCall(PetscObjectReference((PetscObject)Ad)); 5331 *A_loc = Ad; 5332 } else if (scall == MAT_REUSE_MATRIX) { 5333 PetscCall(MatCopy(Ad, *A_loc, SAME_NONZERO_PATTERN)); 5334 } 5335 if (glob) PetscCall(ISCreateStride(PetscObjectComm((PetscObject)Ad), Ad->cmap->n, Ad->cmap->rstart, 1, glob)); 5336 PetscFunctionReturn(PETSC_SUCCESS); 5337 } 5338 PetscCall(PetscObjectQueryFunction((PetscObject)A, "MatMPIAIJGetLocalMatMerge_C", &f)); 5339 PetscCall(PetscLogEventBegin(MAT_Getlocalmat, A, 0, 0, 0)); 5340 if (f) { 5341 PetscCall((*f)(A, scall, glob, A_loc)); 5342 } else { 5343 Mat_SeqAIJ *a = (Mat_SeqAIJ *)Ad->data; 5344 Mat_SeqAIJ *b = (Mat_SeqAIJ *)Ao->data; 5345 Mat_SeqAIJ *c; 5346 PetscInt *ai = a->i, *aj = a->j; 5347 PetscInt *bi = b->i, *bj = b->j; 5348 PetscInt *ci, *cj; 5349 const PetscScalar *aa, *ba; 5350 PetscScalar *ca; 5351 PetscInt i, j, am, dn, on; 5352 5353 PetscCall(MatGetLocalSize(Ad, &am, &dn)); 5354 PetscCall(MatGetLocalSize(Ao, NULL, &on)); 5355 PetscCall(MatSeqAIJGetArrayRead(Ad, &aa)); 5356 PetscCall(MatSeqAIJGetArrayRead(Ao, &ba)); 5357 if (scall == MAT_INITIAL_MATRIX) { 5358 PetscInt k; 5359 PetscCall(PetscMalloc1(1 + am, &ci)); 5360 PetscCall(PetscMalloc1(ai[am] + bi[am], &cj)); 5361 PetscCall(PetscMalloc1(ai[am] + bi[am], &ca)); 5362 ci[0] = 0; 5363 for (i = 0, k = 0; i < am; i++) { 5364 const PetscInt ncols_o = bi[i + 1] - bi[i]; 5365 const PetscInt ncols_d = ai[i + 1] - ai[i]; 5366 ci[i + 1] = ci[i] + ncols_o + ncols_d; 5367 /* diagonal portion of A */ 5368 for (j = 0; j < ncols_d; j++, k++) { 5369 cj[k] = *aj++; 5370 ca[k] = *aa++; 5371 } 5372 /* off-diagonal portion of A */ 5373 for (j = 0; j < ncols_o; j++, k++) { 5374 cj[k] = dn + *bj++; 5375 ca[k] = *ba++; 5376 } 5377 } 5378 /* put together the new matrix */ 5379 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, am, dn + on, ci, cj, ca, A_loc)); 5380 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 5381 /* Since these are PETSc arrays, change flags to free them as necessary. */ 5382 c = (Mat_SeqAIJ *)(*A_loc)->data; 5383 c->free_a = PETSC_TRUE; 5384 c->free_ij = PETSC_TRUE; 5385 c->nonew = 0; 5386 PetscCall(MatSetType(*A_loc, ((PetscObject)Ad)->type_name)); 5387 } else if (scall == MAT_REUSE_MATRIX) { 5388 PetscCall(MatSeqAIJGetArrayWrite(*A_loc, &ca)); 5389 for (i = 0; i < am; i++) { 5390 const PetscInt ncols_d = ai[i + 1] - ai[i]; 5391 const PetscInt ncols_o = bi[i + 1] - bi[i]; 5392 /* diagonal portion of A */ 5393 for (j = 0; j < ncols_d; j++) *ca++ = *aa++; 5394 /* off-diagonal portion of A */ 5395 for (j = 0; j < ncols_o; j++) *ca++ = *ba++; 5396 } 5397 PetscCall(MatSeqAIJRestoreArrayWrite(*A_loc, &ca)); 5398 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Invalid MatReuse %d", (int)scall); 5399 PetscCall(MatSeqAIJRestoreArrayRead(Ad, &aa)); 5400 PetscCall(MatSeqAIJRestoreArrayRead(Ao, &aa)); 5401 if (glob) { 5402 PetscInt cst, *gidx; 5403 5404 PetscCall(MatGetOwnershipRangeColumn(A, &cst, NULL)); 5405 PetscCall(PetscMalloc1(dn + on, &gidx)); 5406 for (i = 0; i < dn; i++) gidx[i] = cst + i; 5407 for (i = 0; i < on; i++) gidx[i + dn] = cmap[i]; 5408 PetscCall(ISCreateGeneral(PetscObjectComm((PetscObject)Ad), dn + on, gidx, PETSC_OWN_POINTER, glob)); 5409 } 5410 } 5411 PetscCall(PetscLogEventEnd(MAT_Getlocalmat, A, 0, 0, 0)); 5412 PetscFunctionReturn(PETSC_SUCCESS); 5413 } 5414 5415 /*@C 5416 MatMPIAIJGetLocalMatCondensed - Creates a `MATSEQAIJ` matrix from an `MATMPIAIJ` matrix by taking all its local rows and NON-ZERO columns 5417 5418 Not Collective 5419 5420 Input Parameters: 5421 + A - the matrix 5422 . scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5423 . row - index set of rows to extract (or `NULL`) 5424 - col - index set of columns to extract (or `NULL`) 5425 5426 Output Parameter: 5427 . A_loc - the local sequential matrix generated 5428 5429 Level: developer 5430 5431 .seealso: [](ch_matrices), `Mat`, `MATMPIAIJ`, `MatGetOwnershipRange()`, `MatMPIAIJGetLocalMat()` 5432 @*/ 5433 PetscErrorCode MatMPIAIJGetLocalMatCondensed(Mat A, MatReuse scall, IS *row, IS *col, Mat *A_loc) 5434 { 5435 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 5436 PetscInt i, start, end, ncols, nzA, nzB, *cmap, imark, *idx; 5437 IS isrowa, iscola; 5438 Mat *aloc; 5439 PetscBool match; 5440 5441 PetscFunctionBegin; 5442 PetscCall(PetscObjectTypeCompare((PetscObject)A, MATMPIAIJ, &match)); 5443 PetscCheck(match, PetscObjectComm((PetscObject)A), PETSC_ERR_SUP, "Requires MATMPIAIJ matrix as input"); 5444 PetscCall(PetscLogEventBegin(MAT_Getlocalmatcondensed, A, 0, 0, 0)); 5445 if (!row) { 5446 start = A->rmap->rstart; 5447 end = A->rmap->rend; 5448 PetscCall(ISCreateStride(PETSC_COMM_SELF, end - start, start, 1, &isrowa)); 5449 } else { 5450 isrowa = *row; 5451 } 5452 if (!col) { 5453 start = A->cmap->rstart; 5454 cmap = a->garray; 5455 nzA = a->A->cmap->n; 5456 nzB = a->B->cmap->n; 5457 PetscCall(PetscMalloc1(nzA + nzB, &idx)); 5458 ncols = 0; 5459 for (i = 0; i < nzB; i++) { 5460 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5461 else break; 5462 } 5463 imark = i; 5464 for (i = 0; i < nzA; i++) idx[ncols++] = start + i; 5465 for (i = imark; i < nzB; i++) idx[ncols++] = cmap[i]; 5466 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, ncols, idx, PETSC_OWN_POINTER, &iscola)); 5467 } else { 5468 iscola = *col; 5469 } 5470 if (scall != MAT_INITIAL_MATRIX) { 5471 PetscCall(PetscMalloc1(1, &aloc)); 5472 aloc[0] = *A_loc; 5473 } 5474 PetscCall(MatCreateSubMatrices(A, 1, &isrowa, &iscola, scall, &aloc)); 5475 if (!col) { /* attach global id of condensed columns */ 5476 PetscCall(PetscObjectCompose((PetscObject)aloc[0], "_petsc_GetLocalMatCondensed_iscol", (PetscObject)iscola)); 5477 } 5478 *A_loc = aloc[0]; 5479 PetscCall(PetscFree(aloc)); 5480 if (!row) PetscCall(ISDestroy(&isrowa)); 5481 if (!col) PetscCall(ISDestroy(&iscola)); 5482 PetscCall(PetscLogEventEnd(MAT_Getlocalmatcondensed, A, 0, 0, 0)); 5483 PetscFunctionReturn(PETSC_SUCCESS); 5484 } 5485 5486 /* 5487 * Create a sequential AIJ matrix based on row indices. a whole column is extracted once a row is matched. 5488 * Row could be local or remote.The routine is designed to be scalable in memory so that nothing is based 5489 * on a global size. 5490 * */ 5491 static PetscErrorCode MatCreateSeqSubMatrixWithRows_Private(Mat P, IS rows, Mat *P_oth) 5492 { 5493 Mat_MPIAIJ *p = (Mat_MPIAIJ *)P->data; 5494 Mat_SeqAIJ *pd = (Mat_SeqAIJ *)p->A->data, *po = (Mat_SeqAIJ *)p->B->data, *p_oth; 5495 PetscInt plocalsize, nrows, *ilocal, *oilocal, i, lidx, *nrcols, *nlcols, ncol; 5496 PetscMPIInt owner; 5497 PetscSFNode *iremote, *oiremote; 5498 const PetscInt *lrowindices; 5499 PetscSF sf, osf; 5500 PetscInt pcstart, *roffsets, *loffsets, *pnnz, j; 5501 PetscInt ontotalcols, dntotalcols, ntotalcols, nout; 5502 MPI_Comm comm; 5503 ISLocalToGlobalMapping mapping; 5504 const PetscScalar *pd_a, *po_a; 5505 5506 PetscFunctionBegin; 5507 PetscCall(PetscObjectGetComm((PetscObject)P, &comm)); 5508 /* plocalsize is the number of roots 5509 * nrows is the number of leaves 5510 * */ 5511 PetscCall(MatGetLocalSize(P, &plocalsize, NULL)); 5512 PetscCall(ISGetLocalSize(rows, &nrows)); 5513 PetscCall(PetscCalloc1(nrows, &iremote)); 5514 PetscCall(ISGetIndices(rows, &lrowindices)); 5515 for (i = 0; i < nrows; i++) { 5516 /* Find a remote index and an owner for a row 5517 * The row could be local or remote 5518 * */ 5519 owner = 0; 5520 lidx = 0; 5521 PetscCall(PetscLayoutFindOwnerIndex(P->rmap, lrowindices[i], &owner, &lidx)); 5522 iremote[i].index = lidx; 5523 iremote[i].rank = owner; 5524 } 5525 /* Create SF to communicate how many nonzero columns for each row */ 5526 PetscCall(PetscSFCreate(comm, &sf)); 5527 /* SF will figure out the number of nonzero columns for each row, and their 5528 * offsets 5529 * */ 5530 PetscCall(PetscSFSetGraph(sf, plocalsize, nrows, NULL, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER)); 5531 PetscCall(PetscSFSetFromOptions(sf)); 5532 PetscCall(PetscSFSetUp(sf)); 5533 5534 PetscCall(PetscCalloc1(2 * (plocalsize + 1), &roffsets)); 5535 PetscCall(PetscCalloc1(2 * plocalsize, &nrcols)); 5536 PetscCall(PetscCalloc1(nrows, &pnnz)); 5537 roffsets[0] = 0; 5538 roffsets[1] = 0; 5539 for (i = 0; i < plocalsize; i++) { 5540 /* diagonal */ 5541 nrcols[i * 2 + 0] = pd->i[i + 1] - pd->i[i]; 5542 /* off-diagonal */ 5543 nrcols[i * 2 + 1] = po->i[i + 1] - po->i[i]; 5544 /* compute offsets so that we relative location for each row */ 5545 roffsets[(i + 1) * 2 + 0] = roffsets[i * 2 + 0] + nrcols[i * 2 + 0]; 5546 roffsets[(i + 1) * 2 + 1] = roffsets[i * 2 + 1] + nrcols[i * 2 + 1]; 5547 } 5548 PetscCall(PetscCalloc1(2 * nrows, &nlcols)); 5549 PetscCall(PetscCalloc1(2 * nrows, &loffsets)); 5550 /* 'r' means root, and 'l' means leaf */ 5551 PetscCall(PetscSFBcastBegin(sf, MPIU_2INT, nrcols, nlcols, MPI_REPLACE)); 5552 PetscCall(PetscSFBcastBegin(sf, MPIU_2INT, roffsets, loffsets, MPI_REPLACE)); 5553 PetscCall(PetscSFBcastEnd(sf, MPIU_2INT, nrcols, nlcols, MPI_REPLACE)); 5554 PetscCall(PetscSFBcastEnd(sf, MPIU_2INT, roffsets, loffsets, MPI_REPLACE)); 5555 PetscCall(PetscSFDestroy(&sf)); 5556 PetscCall(PetscFree(roffsets)); 5557 PetscCall(PetscFree(nrcols)); 5558 dntotalcols = 0; 5559 ontotalcols = 0; 5560 ncol = 0; 5561 for (i = 0; i < nrows; i++) { 5562 pnnz[i] = nlcols[i * 2 + 0] + nlcols[i * 2 + 1]; 5563 ncol = PetscMax(pnnz[i], ncol); 5564 /* diagonal */ 5565 dntotalcols += nlcols[i * 2 + 0]; 5566 /* off-diagonal */ 5567 ontotalcols += nlcols[i * 2 + 1]; 5568 } 5569 /* We do not need to figure the right number of columns 5570 * since all the calculations will be done by going through the raw data 5571 * */ 5572 PetscCall(MatCreateSeqAIJ(PETSC_COMM_SELF, nrows, ncol, 0, pnnz, P_oth)); 5573 PetscCall(MatSetUp(*P_oth)); 5574 PetscCall(PetscFree(pnnz)); 5575 p_oth = (Mat_SeqAIJ *)(*P_oth)->data; 5576 /* diagonal */ 5577 PetscCall(PetscCalloc1(dntotalcols, &iremote)); 5578 /* off-diagonal */ 5579 PetscCall(PetscCalloc1(ontotalcols, &oiremote)); 5580 /* diagonal */ 5581 PetscCall(PetscCalloc1(dntotalcols, &ilocal)); 5582 /* off-diagonal */ 5583 PetscCall(PetscCalloc1(ontotalcols, &oilocal)); 5584 dntotalcols = 0; 5585 ontotalcols = 0; 5586 ntotalcols = 0; 5587 for (i = 0; i < nrows; i++) { 5588 owner = 0; 5589 PetscCall(PetscLayoutFindOwnerIndex(P->rmap, lrowindices[i], &owner, NULL)); 5590 /* Set iremote for diag matrix */ 5591 for (j = 0; j < nlcols[i * 2 + 0]; j++) { 5592 iremote[dntotalcols].index = loffsets[i * 2 + 0] + j; 5593 iremote[dntotalcols].rank = owner; 5594 /* P_oth is seqAIJ so that ilocal need to point to the first part of memory */ 5595 ilocal[dntotalcols++] = ntotalcols++; 5596 } 5597 /* off-diagonal */ 5598 for (j = 0; j < nlcols[i * 2 + 1]; j++) { 5599 oiremote[ontotalcols].index = loffsets[i * 2 + 1] + j; 5600 oiremote[ontotalcols].rank = owner; 5601 oilocal[ontotalcols++] = ntotalcols++; 5602 } 5603 } 5604 PetscCall(ISRestoreIndices(rows, &lrowindices)); 5605 PetscCall(PetscFree(loffsets)); 5606 PetscCall(PetscFree(nlcols)); 5607 PetscCall(PetscSFCreate(comm, &sf)); 5608 /* P serves as roots and P_oth is leaves 5609 * Diag matrix 5610 * */ 5611 PetscCall(PetscSFSetGraph(sf, pd->i[plocalsize], dntotalcols, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER)); 5612 PetscCall(PetscSFSetFromOptions(sf)); 5613 PetscCall(PetscSFSetUp(sf)); 5614 5615 PetscCall(PetscSFCreate(comm, &osf)); 5616 /* off-diagonal */ 5617 PetscCall(PetscSFSetGraph(osf, po->i[plocalsize], ontotalcols, oilocal, PETSC_OWN_POINTER, oiremote, PETSC_OWN_POINTER)); 5618 PetscCall(PetscSFSetFromOptions(osf)); 5619 PetscCall(PetscSFSetUp(osf)); 5620 PetscCall(MatSeqAIJGetArrayRead(p->A, &pd_a)); 5621 PetscCall(MatSeqAIJGetArrayRead(p->B, &po_a)); 5622 /* operate on the matrix internal data to save memory */ 5623 PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, pd_a, p_oth->a, MPI_REPLACE)); 5624 PetscCall(PetscSFBcastBegin(osf, MPIU_SCALAR, po_a, p_oth->a, MPI_REPLACE)); 5625 PetscCall(MatGetOwnershipRangeColumn(P, &pcstart, NULL)); 5626 /* Convert to global indices for diag matrix */ 5627 for (i = 0; i < pd->i[plocalsize]; i++) pd->j[i] += pcstart; 5628 PetscCall(PetscSFBcastBegin(sf, MPIU_INT, pd->j, p_oth->j, MPI_REPLACE)); 5629 /* We want P_oth store global indices */ 5630 PetscCall(ISLocalToGlobalMappingCreate(comm, 1, p->B->cmap->n, p->garray, PETSC_COPY_VALUES, &mapping)); 5631 /* Use memory scalable approach */ 5632 PetscCall(ISLocalToGlobalMappingSetType(mapping, ISLOCALTOGLOBALMAPPINGHASH)); 5633 PetscCall(ISLocalToGlobalMappingApply(mapping, po->i[plocalsize], po->j, po->j)); 5634 PetscCall(PetscSFBcastBegin(osf, MPIU_INT, po->j, p_oth->j, MPI_REPLACE)); 5635 PetscCall(PetscSFBcastEnd(sf, MPIU_INT, pd->j, p_oth->j, MPI_REPLACE)); 5636 /* Convert back to local indices */ 5637 for (i = 0; i < pd->i[plocalsize]; i++) pd->j[i] -= pcstart; 5638 PetscCall(PetscSFBcastEnd(osf, MPIU_INT, po->j, p_oth->j, MPI_REPLACE)); 5639 nout = 0; 5640 PetscCall(ISGlobalToLocalMappingApply(mapping, IS_GTOLM_DROP, po->i[plocalsize], po->j, &nout, po->j)); 5641 PetscCheck(nout == po->i[plocalsize], comm, PETSC_ERR_ARG_INCOMP, "n %" PetscInt_FMT " does not equal to nout %" PetscInt_FMT " ", po->i[plocalsize], nout); 5642 PetscCall(ISLocalToGlobalMappingDestroy(&mapping)); 5643 /* Exchange values */ 5644 PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, pd_a, p_oth->a, MPI_REPLACE)); 5645 PetscCall(PetscSFBcastEnd(osf, MPIU_SCALAR, po_a, p_oth->a, MPI_REPLACE)); 5646 PetscCall(MatSeqAIJRestoreArrayRead(p->A, &pd_a)); 5647 PetscCall(MatSeqAIJRestoreArrayRead(p->B, &po_a)); 5648 /* Stop PETSc from shrinking memory */ 5649 for (i = 0; i < nrows; i++) p_oth->ilen[i] = p_oth->imax[i]; 5650 PetscCall(MatAssemblyBegin(*P_oth, MAT_FINAL_ASSEMBLY)); 5651 PetscCall(MatAssemblyEnd(*P_oth, MAT_FINAL_ASSEMBLY)); 5652 /* Attach PetscSF objects to P_oth so that we can reuse it later */ 5653 PetscCall(PetscObjectCompose((PetscObject)*P_oth, "diagsf", (PetscObject)sf)); 5654 PetscCall(PetscObjectCompose((PetscObject)*P_oth, "offdiagsf", (PetscObject)osf)); 5655 PetscCall(PetscSFDestroy(&sf)); 5656 PetscCall(PetscSFDestroy(&osf)); 5657 PetscFunctionReturn(PETSC_SUCCESS); 5658 } 5659 5660 /* 5661 * Creates a SeqAIJ matrix by taking rows of B that equal to nonzero columns of local A 5662 * This supports MPIAIJ and MAIJ 5663 * */ 5664 PetscErrorCode MatGetBrowsOfAcols_MPIXAIJ(Mat A, Mat P, PetscInt dof, MatReuse reuse, Mat *P_oth) 5665 { 5666 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data, *p = (Mat_MPIAIJ *)P->data; 5667 Mat_SeqAIJ *p_oth; 5668 IS rows, map; 5669 PetscHMapI hamp; 5670 PetscInt i, htsize, *rowindices, off, *mapping, key, count; 5671 MPI_Comm comm; 5672 PetscSF sf, osf; 5673 PetscBool has; 5674 5675 PetscFunctionBegin; 5676 PetscCall(PetscObjectGetComm((PetscObject)A, &comm)); 5677 PetscCall(PetscLogEventBegin(MAT_GetBrowsOfAocols, A, P, 0, 0)); 5678 /* If it is the first time, create an index set of off-diag nonzero columns of A, 5679 * and then create a submatrix (that often is an overlapping matrix) 5680 * */ 5681 if (reuse == MAT_INITIAL_MATRIX) { 5682 /* Use a hash table to figure out unique keys */ 5683 PetscCall(PetscHMapICreateWithSize(a->B->cmap->n, &hamp)); 5684 PetscCall(PetscCalloc1(a->B->cmap->n, &mapping)); 5685 count = 0; 5686 /* Assume that a->g is sorted, otherwise the following does not make sense */ 5687 for (i = 0; i < a->B->cmap->n; i++) { 5688 key = a->garray[i] / dof; 5689 PetscCall(PetscHMapIHas(hamp, key, &has)); 5690 if (!has) { 5691 mapping[i] = count; 5692 PetscCall(PetscHMapISet(hamp, key, count++)); 5693 } else { 5694 /* Current 'i' has the same value the previous step */ 5695 mapping[i] = count - 1; 5696 } 5697 } 5698 PetscCall(ISCreateGeneral(comm, a->B->cmap->n, mapping, PETSC_OWN_POINTER, &map)); 5699 PetscCall(PetscHMapIGetSize(hamp, &htsize)); 5700 PetscCheck(htsize == count, comm, PETSC_ERR_ARG_INCOMP, " Size of hash map %" PetscInt_FMT " is inconsistent with count %" PetscInt_FMT, htsize, count); 5701 PetscCall(PetscCalloc1(htsize, &rowindices)); 5702 off = 0; 5703 PetscCall(PetscHMapIGetKeys(hamp, &off, rowindices)); 5704 PetscCall(PetscHMapIDestroy(&hamp)); 5705 PetscCall(PetscSortInt(htsize, rowindices)); 5706 PetscCall(ISCreateGeneral(comm, htsize, rowindices, PETSC_OWN_POINTER, &rows)); 5707 /* In case, the matrix was already created but users want to recreate the matrix */ 5708 PetscCall(MatDestroy(P_oth)); 5709 PetscCall(MatCreateSeqSubMatrixWithRows_Private(P, rows, P_oth)); 5710 PetscCall(PetscObjectCompose((PetscObject)*P_oth, "aoffdiagtopothmapping", (PetscObject)map)); 5711 PetscCall(ISDestroy(&map)); 5712 PetscCall(ISDestroy(&rows)); 5713 } else if (reuse == MAT_REUSE_MATRIX) { 5714 /* If matrix was already created, we simply update values using SF objects 5715 * that as attached to the matrix earlier. 5716 */ 5717 const PetscScalar *pd_a, *po_a; 5718 5719 PetscCall(PetscObjectQuery((PetscObject)*P_oth, "diagsf", (PetscObject *)&sf)); 5720 PetscCall(PetscObjectQuery((PetscObject)*P_oth, "offdiagsf", (PetscObject *)&osf)); 5721 PetscCheck(sf && osf, comm, PETSC_ERR_ARG_NULL, "Matrix is not initialized yet"); 5722 p_oth = (Mat_SeqAIJ *)(*P_oth)->data; 5723 /* Update values in place */ 5724 PetscCall(MatSeqAIJGetArrayRead(p->A, &pd_a)); 5725 PetscCall(MatSeqAIJGetArrayRead(p->B, &po_a)); 5726 PetscCall(PetscSFBcastBegin(sf, MPIU_SCALAR, pd_a, p_oth->a, MPI_REPLACE)); 5727 PetscCall(PetscSFBcastBegin(osf, MPIU_SCALAR, po_a, p_oth->a, MPI_REPLACE)); 5728 PetscCall(PetscSFBcastEnd(sf, MPIU_SCALAR, pd_a, p_oth->a, MPI_REPLACE)); 5729 PetscCall(PetscSFBcastEnd(osf, MPIU_SCALAR, po_a, p_oth->a, MPI_REPLACE)); 5730 PetscCall(MatSeqAIJRestoreArrayRead(p->A, &pd_a)); 5731 PetscCall(MatSeqAIJRestoreArrayRead(p->B, &po_a)); 5732 } else SETERRQ(comm, PETSC_ERR_ARG_UNKNOWN_TYPE, "Unknown reuse type"); 5733 PetscCall(PetscLogEventEnd(MAT_GetBrowsOfAocols, A, P, 0, 0)); 5734 PetscFunctionReturn(PETSC_SUCCESS); 5735 } 5736 5737 /*@C 5738 MatGetBrowsOfAcols - Returns `IS` that contain rows of `B` that equal to nonzero columns of local `A` 5739 5740 Collective 5741 5742 Input Parameters: 5743 + A - the first matrix in `MATMPIAIJ` format 5744 . B - the second matrix in `MATMPIAIJ` format 5745 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5746 5747 Output Parameters: 5748 + rowb - On input index sets of rows of B to extract (or `NULL`), modified on output 5749 . colb - On input index sets of columns of B to extract (or `NULL`), modified on output 5750 - B_seq - the sequential matrix generated 5751 5752 Level: developer 5753 5754 .seealso: `Mat`, `MATMPIAIJ`, `IS`, `MatReuse` 5755 @*/ 5756 PetscErrorCode MatGetBrowsOfAcols(Mat A, Mat B, MatReuse scall, IS *rowb, IS *colb, Mat *B_seq) 5757 { 5758 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 5759 PetscInt *idx, i, start, ncols, nzA, nzB, *cmap, imark; 5760 IS isrowb, iscolb; 5761 Mat *bseq = NULL; 5762 5763 PetscFunctionBegin; 5764 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 ")", 5765 A->cmap->rstart, A->cmap->rend, B->rmap->rstart, B->rmap->rend); 5766 PetscCall(PetscLogEventBegin(MAT_GetBrowsOfAcols, A, B, 0, 0)); 5767 5768 if (scall == MAT_INITIAL_MATRIX) { 5769 start = A->cmap->rstart; 5770 cmap = a->garray; 5771 nzA = a->A->cmap->n; 5772 nzB = a->B->cmap->n; 5773 PetscCall(PetscMalloc1(nzA + nzB, &idx)); 5774 ncols = 0; 5775 for (i = 0; i < nzB; i++) { /* row < local row index */ 5776 if (cmap[i] < start) idx[ncols++] = cmap[i]; 5777 else break; 5778 } 5779 imark = i; 5780 for (i = 0; i < nzA; i++) idx[ncols++] = start + i; /* local rows */ 5781 for (i = imark; i < nzB; i++) idx[ncols++] = cmap[i]; /* row > local row index */ 5782 PetscCall(ISCreateGeneral(PETSC_COMM_SELF, ncols, idx, PETSC_OWN_POINTER, &isrowb)); 5783 PetscCall(ISCreateStride(PETSC_COMM_SELF, B->cmap->N, 0, 1, &iscolb)); 5784 } else { 5785 PetscCheck(rowb && colb, PETSC_COMM_SELF, PETSC_ERR_SUP, "IS rowb and colb must be provided for MAT_REUSE_MATRIX"); 5786 isrowb = *rowb; 5787 iscolb = *colb; 5788 PetscCall(PetscMalloc1(1, &bseq)); 5789 bseq[0] = *B_seq; 5790 } 5791 PetscCall(MatCreateSubMatrices(B, 1, &isrowb, &iscolb, scall, &bseq)); 5792 *B_seq = bseq[0]; 5793 PetscCall(PetscFree(bseq)); 5794 if (!rowb) { 5795 PetscCall(ISDestroy(&isrowb)); 5796 } else { 5797 *rowb = isrowb; 5798 } 5799 if (!colb) { 5800 PetscCall(ISDestroy(&iscolb)); 5801 } else { 5802 *colb = iscolb; 5803 } 5804 PetscCall(PetscLogEventEnd(MAT_GetBrowsOfAcols, A, B, 0, 0)); 5805 PetscFunctionReturn(PETSC_SUCCESS); 5806 } 5807 5808 /* 5809 MatGetBrowsOfAoCols_MPIAIJ - Creates a `MATSEQAIJ` matrix by taking rows of B that equal to nonzero columns 5810 of the OFF-DIAGONAL portion of local A 5811 5812 Collective 5813 5814 Input Parameters: 5815 + A,B - the matrices in `MATMPIAIJ` format 5816 - scall - either `MAT_INITIAL_MATRIX` or `MAT_REUSE_MATRIX` 5817 5818 Output Parameter: 5819 + startsj_s - starting point in B's sending j-arrays, saved for MAT_REUSE (or NULL) 5820 . startsj_r - starting point in B's receiving j-arrays, saved for MAT_REUSE (or NULL) 5821 . bufa_ptr - array for sending matrix values, saved for MAT_REUSE (or NULL) 5822 - B_oth - the sequential matrix generated with size aBn=a->B->cmap->n by B->cmap->N 5823 5824 Developer Note: 5825 This directly accesses information inside the VecScatter associated with the matrix-vector product 5826 for this matrix. This is not desirable.. 5827 5828 Level: developer 5829 5830 */ 5831 5832 PetscErrorCode MatGetBrowsOfAoCols_MPIAIJ(Mat A, Mat B, MatReuse scall, PetscInt **startsj_s, PetscInt **startsj_r, MatScalar **bufa_ptr, Mat *B_oth) 5833 { 5834 Mat_MPIAIJ *a = (Mat_MPIAIJ *)A->data; 5835 VecScatter ctx; 5836 MPI_Comm comm; 5837 const PetscMPIInt *rprocs, *sprocs; 5838 PetscMPIInt nrecvs, nsends; 5839 const PetscInt *srow, *rstarts, *sstarts; 5840 PetscInt *rowlen, *bufj, *bufJ, ncols = 0, aBn = a->B->cmap->n, row, *b_othi, *b_othj, *rvalues = NULL, *svalues = NULL, *cols, sbs, rbs; 5841 PetscInt i, j, k = 0, l, ll, nrows, *rstartsj = NULL, *sstartsj, len; 5842 PetscScalar *b_otha, *bufa, *bufA, *vals = NULL; 5843 MPI_Request *reqs = NULL, *rwaits = NULL, *swaits = NULL; 5844 PetscMPIInt size, tag, rank, nreqs; 5845 5846 PetscFunctionBegin; 5847 PetscCall(PetscObjectGetComm((PetscObject)A, &comm)); 5848 PetscCallMPI(MPI_Comm_size(comm, &size)); 5849 5850 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 ")", 5851 A->cmap->rstart, A->cmap->rend, B->rmap->rstart, B->rmap->rend); 5852 PetscCall(PetscLogEventBegin(MAT_GetBrowsOfAocols, A, B, 0, 0)); 5853 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 5854 5855 if (size == 1) { 5856 startsj_s = NULL; 5857 bufa_ptr = NULL; 5858 *B_oth = NULL; 5859 PetscFunctionReturn(PETSC_SUCCESS); 5860 } 5861 5862 ctx = a->Mvctx; 5863 tag = ((PetscObject)ctx)->tag; 5864 5865 PetscCall(VecScatterGetRemote_Private(ctx, PETSC_TRUE /*send*/, &nsends, &sstarts, &srow, &sprocs, &sbs)); 5866 /* rprocs[] must be ordered so that indices received from them are ordered in rvalues[], which is key to algorithms used in this subroutine */ 5867 PetscCall(VecScatterGetRemoteOrdered_Private(ctx, PETSC_FALSE /*recv*/, &nrecvs, &rstarts, NULL /*indices not needed*/, &rprocs, &rbs)); 5868 PetscCall(PetscMPIIntCast(nsends + nrecvs, &nreqs)); 5869 PetscCall(PetscMalloc1(nreqs, &reqs)); 5870 rwaits = reqs; 5871 swaits = PetscSafePointerPlusOffset(reqs, nrecvs); 5872 5873 if (!startsj_s || !bufa_ptr) scall = MAT_INITIAL_MATRIX; 5874 if (scall == MAT_INITIAL_MATRIX) { 5875 /* i-array */ 5876 /* post receives */ 5877 if (nrecvs) PetscCall(PetscMalloc1(rbs * (rstarts[nrecvs] - rstarts[0]), &rvalues)); /* rstarts can be NULL when nrecvs=0 */ 5878 for (i = 0; i < nrecvs; i++) { 5879 rowlen = rvalues + rstarts[i] * rbs; 5880 nrows = (rstarts[i + 1] - rstarts[i]) * rbs; /* num of indices to be received */ 5881 PetscCallMPI(MPIU_Irecv(rowlen, nrows, MPIU_INT, rprocs[i], tag, comm, rwaits + i)); 5882 } 5883 5884 /* pack the outgoing message */ 5885 PetscCall(PetscMalloc2(nsends + 1, &sstartsj, nrecvs + 1, &rstartsj)); 5886 5887 sstartsj[0] = 0; 5888 rstartsj[0] = 0; 5889 len = 0; /* total length of j or a array to be sent */ 5890 if (nsends) { 5891 k = sstarts[0]; /* ATTENTION: sstarts[0] and rstarts[0] are not necessarily zero */ 5892 PetscCall(PetscMalloc1(sbs * (sstarts[nsends] - sstarts[0]), &svalues)); 5893 } 5894 for (i = 0; i < nsends; i++) { 5895 rowlen = svalues + (sstarts[i] - sstarts[0]) * sbs; 5896 nrows = sstarts[i + 1] - sstarts[i]; /* num of block rows */ 5897 for (j = 0; j < nrows; j++) { 5898 row = srow[k] + B->rmap->range[rank]; /* global row idx */ 5899 for (l = 0; l < sbs; l++) { 5900 PetscCall(MatGetRow_MPIAIJ(B, row + l, &ncols, NULL, NULL)); /* rowlength */ 5901 5902 rowlen[j * sbs + l] = ncols; 5903 5904 len += ncols; 5905 PetscCall(MatRestoreRow_MPIAIJ(B, row + l, &ncols, NULL, NULL)); 5906 } 5907 k++; 5908 } 5909 PetscCallMPI(MPIU_Isend(rowlen, nrows * sbs, MPIU_INT, sprocs[i], tag, comm, swaits + i)); 5910 5911 sstartsj[i + 1] = len; /* starting point of (i+1)-th outgoing msg in bufj and bufa */ 5912 } 5913 /* recvs and sends of i-array are completed */ 5914 if (nreqs) PetscCallMPI(MPI_Waitall(nreqs, reqs, MPI_STATUSES_IGNORE)); 5915 PetscCall(PetscFree(svalues)); 5916 5917 /* allocate buffers for sending j and a arrays */ 5918 PetscCall(PetscMalloc1(len + 1, &bufj)); 5919 PetscCall(PetscMalloc1(len + 1, &bufa)); 5920 5921 /* create i-array of B_oth */ 5922 PetscCall(PetscMalloc1(aBn + 2, &b_othi)); 5923 5924 b_othi[0] = 0; 5925 len = 0; /* total length of j or a array to be received */ 5926 k = 0; 5927 for (i = 0; i < nrecvs; i++) { 5928 rowlen = rvalues + (rstarts[i] - rstarts[0]) * rbs; 5929 nrows = (rstarts[i + 1] - rstarts[i]) * rbs; /* num of rows to be received */ 5930 for (j = 0; j < nrows; j++) { 5931 b_othi[k + 1] = b_othi[k] + rowlen[j]; 5932 PetscCall(PetscIntSumError(rowlen[j], len, &len)); 5933 k++; 5934 } 5935 rstartsj[i + 1] = len; /* starting point of (i+1)-th incoming msg in bufj and bufa */ 5936 } 5937 PetscCall(PetscFree(rvalues)); 5938 5939 /* allocate space for j and a arrays of B_oth */ 5940 PetscCall(PetscMalloc1(b_othi[aBn] + 1, &b_othj)); 5941 PetscCall(PetscMalloc1(b_othi[aBn] + 1, &b_otha)); 5942 5943 /* j-array */ 5944 /* post receives of j-array */ 5945 for (i = 0; i < nrecvs; i++) { 5946 nrows = rstartsj[i + 1] - rstartsj[i]; /* length of the msg received */ 5947 PetscCallMPI(MPIU_Irecv(b_othj + rstartsj[i], nrows, MPIU_INT, rprocs[i], tag, comm, rwaits + i)); 5948 } 5949 5950 /* pack the outgoing message j-array */ 5951 if (nsends) k = sstarts[0]; 5952 for (i = 0; i < nsends; i++) { 5953 nrows = sstarts[i + 1] - sstarts[i]; /* num of block rows */ 5954 bufJ = bufj + sstartsj[i]; 5955 for (j = 0; j < nrows; j++) { 5956 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5957 for (ll = 0; ll < sbs; ll++) { 5958 PetscCall(MatGetRow_MPIAIJ(B, row + ll, &ncols, &cols, NULL)); 5959 for (l = 0; l < ncols; l++) *bufJ++ = cols[l]; 5960 PetscCall(MatRestoreRow_MPIAIJ(B, row + ll, &ncols, &cols, NULL)); 5961 } 5962 } 5963 PetscCallMPI(MPIU_Isend(bufj + sstartsj[i], sstartsj[i + 1] - sstartsj[i], MPIU_INT, sprocs[i], tag, comm, swaits + i)); 5964 } 5965 5966 /* recvs and sends of j-array are completed */ 5967 if (nreqs) PetscCallMPI(MPI_Waitall(nreqs, reqs, MPI_STATUSES_IGNORE)); 5968 } else if (scall == MAT_REUSE_MATRIX) { 5969 sstartsj = *startsj_s; 5970 rstartsj = *startsj_r; 5971 bufa = *bufa_ptr; 5972 PetscCall(MatSeqAIJGetArrayWrite(*B_oth, &b_otha)); 5973 } else SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Matrix P does not possess an object container"); 5974 5975 /* a-array */ 5976 /* post receives of a-array */ 5977 for (i = 0; i < nrecvs; i++) { 5978 nrows = rstartsj[i + 1] - rstartsj[i]; /* length of the msg received */ 5979 PetscCallMPI(MPIU_Irecv(b_otha + rstartsj[i], nrows, MPIU_SCALAR, rprocs[i], tag, comm, rwaits + i)); 5980 } 5981 5982 /* pack the outgoing message a-array */ 5983 if (nsends) k = sstarts[0]; 5984 for (i = 0; i < nsends; i++) { 5985 nrows = sstarts[i + 1] - sstarts[i]; /* num of block rows */ 5986 bufA = bufa + sstartsj[i]; 5987 for (j = 0; j < nrows; j++) { 5988 row = srow[k++] + B->rmap->range[rank]; /* global row idx */ 5989 for (ll = 0; ll < sbs; ll++) { 5990 PetscCall(MatGetRow_MPIAIJ(B, row + ll, &ncols, NULL, &vals)); 5991 for (l = 0; l < ncols; l++) *bufA++ = vals[l]; 5992 PetscCall(MatRestoreRow_MPIAIJ(B, row + ll, &ncols, NULL, &vals)); 5993 } 5994 } 5995 PetscCallMPI(MPIU_Isend(bufa + sstartsj[i], sstartsj[i + 1] - sstartsj[i], MPIU_SCALAR, sprocs[i], tag, comm, swaits + i)); 5996 } 5997 /* recvs and sends of a-array are completed */ 5998 if (nreqs) PetscCallMPI(MPI_Waitall(nreqs, reqs, MPI_STATUSES_IGNORE)); 5999 PetscCall(PetscFree(reqs)); 6000 6001 if (scall == MAT_INITIAL_MATRIX) { 6002 Mat_SeqAIJ *b_oth; 6003 6004 /* put together the new matrix */ 6005 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, aBn, B->cmap->N, b_othi, b_othj, b_otha, B_oth)); 6006 6007 /* MatCreateSeqAIJWithArrays flags matrix so PETSc doesn't free the user's arrays. */ 6008 /* Since these are PETSc arrays, change flags to free them as necessary. */ 6009 b_oth = (Mat_SeqAIJ *)(*B_oth)->data; 6010 b_oth->free_a = PETSC_TRUE; 6011 b_oth->free_ij = PETSC_TRUE; 6012 b_oth->nonew = 0; 6013 6014 PetscCall(PetscFree(bufj)); 6015 if (!startsj_s || !bufa_ptr) { 6016 PetscCall(PetscFree2(sstartsj, rstartsj)); 6017 PetscCall(PetscFree(bufa_ptr)); 6018 } else { 6019 *startsj_s = sstartsj; 6020 *startsj_r = rstartsj; 6021 *bufa_ptr = bufa; 6022 } 6023 } else if (scall == MAT_REUSE_MATRIX) { 6024 PetscCall(MatSeqAIJRestoreArrayWrite(*B_oth, &b_otha)); 6025 } 6026 6027 PetscCall(VecScatterRestoreRemote_Private(ctx, PETSC_TRUE, &nsends, &sstarts, &srow, &sprocs, &sbs)); 6028 PetscCall(VecScatterRestoreRemoteOrdered_Private(ctx, PETSC_FALSE, &nrecvs, &rstarts, NULL, &rprocs, &rbs)); 6029 PetscCall(PetscLogEventEnd(MAT_GetBrowsOfAocols, A, B, 0, 0)); 6030 PetscFunctionReturn(PETSC_SUCCESS); 6031 } 6032 6033 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCRL(Mat, MatType, MatReuse, Mat *); 6034 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJPERM(Mat, MatType, MatReuse, Mat *); 6035 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJSELL(Mat, MatType, MatReuse, Mat *); 6036 #if defined(PETSC_HAVE_MKL_SPARSE) 6037 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJMKL(Mat, MatType, MatReuse, Mat *); 6038 #endif 6039 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIBAIJ(Mat, MatType, MatReuse, Mat *); 6040 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISBAIJ(Mat, MatType, MatReuse, Mat *); 6041 #if defined(PETSC_HAVE_ELEMENTAL) 6042 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_Elemental(Mat, MatType, MatReuse, Mat *); 6043 #endif 6044 #if defined(PETSC_HAVE_SCALAPACK) 6045 PETSC_INTERN PetscErrorCode MatConvert_AIJ_ScaLAPACK(Mat, MatType, MatReuse, Mat *); 6046 #endif 6047 #if defined(PETSC_HAVE_HYPRE) 6048 PETSC_INTERN PetscErrorCode MatConvert_AIJ_HYPRE(Mat, MatType, MatReuse, Mat *); 6049 #endif 6050 #if defined(PETSC_HAVE_CUDA) 6051 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJCUSPARSE(Mat, MatType, MatReuse, Mat *); 6052 #endif 6053 #if defined(PETSC_HAVE_HIP) 6054 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJHIPSPARSE(Mat, MatType, MatReuse, Mat *); 6055 #endif 6056 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 6057 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPIAIJKokkos(Mat, MatType, MatReuse, Mat *); 6058 #endif 6059 PETSC_INTERN PetscErrorCode MatConvert_MPIAIJ_MPISELL(Mat, MatType, MatReuse, Mat *); 6060 PETSC_INTERN PetscErrorCode MatConvert_XAIJ_IS(Mat, MatType, MatReuse, Mat *); 6061 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_IS_XAIJ(Mat); 6062 6063 /* 6064 Computes (B'*A')' since computing B*A directly is untenable 6065 6066 n p p 6067 [ ] [ ] [ ] 6068 m [ A ] * n [ B ] = m [ C ] 6069 [ ] [ ] [ ] 6070 6071 */ 6072 static PetscErrorCode MatMatMultNumeric_MPIDense_MPIAIJ(Mat A, Mat B, Mat C) 6073 { 6074 Mat At, Bt, Ct; 6075 6076 PetscFunctionBegin; 6077 PetscCall(MatTranspose(A, MAT_INITIAL_MATRIX, &At)); 6078 PetscCall(MatTranspose(B, MAT_INITIAL_MATRIX, &Bt)); 6079 PetscCall(MatMatMult(Bt, At, MAT_INITIAL_MATRIX, PETSC_CURRENT, &Ct)); 6080 PetscCall(MatDestroy(&At)); 6081 PetscCall(MatDestroy(&Bt)); 6082 PetscCall(MatTransposeSetPrecursor(Ct, C)); 6083 PetscCall(MatTranspose(Ct, MAT_REUSE_MATRIX, &C)); 6084 PetscCall(MatDestroy(&Ct)); 6085 PetscFunctionReturn(PETSC_SUCCESS); 6086 } 6087 6088 static PetscErrorCode MatMatMultSymbolic_MPIDense_MPIAIJ(Mat A, Mat B, PetscReal fill, Mat C) 6089 { 6090 PetscBool cisdense; 6091 6092 PetscFunctionBegin; 6093 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); 6094 PetscCall(MatSetSizes(C, A->rmap->n, B->cmap->n, A->rmap->N, B->cmap->N)); 6095 PetscCall(MatSetBlockSizesFromMats(C, A, B)); 6096 PetscCall(PetscObjectTypeCompareAny((PetscObject)C, &cisdense, MATMPIDENSE, MATMPIDENSECUDA, MATMPIDENSEHIP, "")); 6097 if (!cisdense) PetscCall(MatSetType(C, ((PetscObject)A)->type_name)); 6098 PetscCall(MatSetUp(C)); 6099 6100 C->ops->matmultnumeric = MatMatMultNumeric_MPIDense_MPIAIJ; 6101 PetscFunctionReturn(PETSC_SUCCESS); 6102 } 6103 6104 static PetscErrorCode MatProductSetFromOptions_MPIDense_MPIAIJ_AB(Mat C) 6105 { 6106 Mat_Product *product = C->product; 6107 Mat A = product->A, B = product->B; 6108 6109 PetscFunctionBegin; 6110 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 ")", 6111 A->cmap->rstart, A->cmap->rend, B->rmap->rstart, B->rmap->rend); 6112 C->ops->matmultsymbolic = MatMatMultSymbolic_MPIDense_MPIAIJ; 6113 C->ops->productsymbolic = MatProductSymbolic_AB; 6114 PetscFunctionReturn(PETSC_SUCCESS); 6115 } 6116 6117 PETSC_INTERN PetscErrorCode MatProductSetFromOptions_MPIDense_MPIAIJ(Mat C) 6118 { 6119 Mat_Product *product = C->product; 6120 6121 PetscFunctionBegin; 6122 if (product->type == MATPRODUCT_AB) PetscCall(MatProductSetFromOptions_MPIDense_MPIAIJ_AB(C)); 6123 PetscFunctionReturn(PETSC_SUCCESS); 6124 } 6125 6126 /* 6127 Merge two sets of sorted nonzeros and return a CSR for the merged (sequential) matrix 6128 6129 Input Parameters: 6130 6131 j1,rowBegin1,rowEnd1,jmap1: describe the first set of nonzeros (Set1) 6132 j2,rowBegin2,rowEnd2,jmap2: describe the second set of nonzeros (Set2) 6133 6134 mat: both sets' nonzeros are on m rows, where m is the number of local rows of the matrix mat 6135 6136 For Set1, j1[] contains column indices of the nonzeros. 6137 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 6138 respectively (note rowEnd1[k] is not necessarily equal to rwoBegin1[k+1]). Indices in this range of j1[] are sorted, 6139 but might have repeats. jmap1[t+1] - jmap1[t] is the number of repeats for the t-th unique nonzero in Set1. 6140 6141 Similar for Set2. 6142 6143 This routine merges the two sets of nonzeros row by row and removes repeats. 6144 6145 Output Parameters: (memory is allocated by the caller) 6146 6147 i[],j[]: the CSR of the merged matrix, which has m rows. 6148 imap1[]: the k-th unique nonzero in Set1 (k=0,1,...) corresponds to imap1[k]-th unique nonzero in the merged matrix. 6149 imap2[]: similar to imap1[], but for Set2. 6150 Note we order nonzeros row-by-row and from left to right. 6151 */ 6152 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[]) 6153 { 6154 PetscInt r, m; /* Row index of mat */ 6155 PetscCount t, t1, t2, b1, e1, b2, e2; 6156 6157 PetscFunctionBegin; 6158 PetscCall(MatGetLocalSize(mat, &m, NULL)); 6159 t1 = t2 = t = 0; /* Count unique nonzeros of in Set1, Set1 and the merged respectively */ 6160 i[0] = 0; 6161 for (r = 0; r < m; r++) { /* Do row by row merging */ 6162 b1 = rowBegin1[r]; 6163 e1 = rowEnd1[r]; 6164 b2 = rowBegin2[r]; 6165 e2 = rowEnd2[r]; 6166 while (b1 < e1 && b2 < e2) { 6167 if (j1[b1] == j2[b2]) { /* Same column index and hence same nonzero */ 6168 j[t] = j1[b1]; 6169 imap1[t1] = t; 6170 imap2[t2] = t; 6171 b1 += jmap1[t1 + 1] - jmap1[t1]; /* Jump to next unique local nonzero */ 6172 b2 += jmap2[t2 + 1] - jmap2[t2]; /* Jump to next unique remote nonzero */ 6173 t1++; 6174 t2++; 6175 t++; 6176 } else if (j1[b1] < j2[b2]) { 6177 j[t] = j1[b1]; 6178 imap1[t1] = t; 6179 b1 += jmap1[t1 + 1] - jmap1[t1]; 6180 t1++; 6181 t++; 6182 } else { 6183 j[t] = j2[b2]; 6184 imap2[t2] = t; 6185 b2 += jmap2[t2 + 1] - jmap2[t2]; 6186 t2++; 6187 t++; 6188 } 6189 } 6190 /* Merge the remaining in either j1[] or j2[] */ 6191 while (b1 < e1) { 6192 j[t] = j1[b1]; 6193 imap1[t1] = t; 6194 b1 += jmap1[t1 + 1] - jmap1[t1]; 6195 t1++; 6196 t++; 6197 } 6198 while (b2 < e2) { 6199 j[t] = j2[b2]; 6200 imap2[t2] = t; 6201 b2 += jmap2[t2 + 1] - jmap2[t2]; 6202 t2++; 6203 t++; 6204 } 6205 PetscCall(PetscIntCast(t, i + r + 1)); 6206 } 6207 PetscFunctionReturn(PETSC_SUCCESS); 6208 } 6209 6210 /* 6211 Split nonzeros in a block of local rows into two subsets: those in the diagonal block and those in the off-diagonal block 6212 6213 Input Parameters: 6214 mat: an MPI matrix that provides row and column layout information for splitting. Let's say its number of local rows is m. 6215 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[] 6216 respectively, along with a permutation array perm[]. Length of the i[],j[],perm[] arrays is n. 6217 6218 i[] is already sorted, but within a row, j[] is not sorted and might have repeats. 6219 i[] might contain negative indices at the beginning, which means the corresponding entries should be ignored in the splitting. 6220 6221 Output Parameters: 6222 j[],perm[]: the routine needs to sort j[] within each row along with perm[]. 6223 rowBegin[],rowMid[],rowEnd[]: of length m, and the memory is preallocated and zeroed by the caller. 6224 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, 6225 and [rowMid[r],rowEnd[r]) point to begin/end entries of row r of the off-diagonal block. 6226 6227 Aperm[],Ajmap[],Atot,Annz: Arrays are allocated by this routine. 6228 Atot: number of entries belonging to the diagonal block. 6229 Annz: number of unique nonzeros belonging to the diagonal block. 6230 Aperm[Atot] stores values from perm[] for entries belonging to the diagonal block. Length of Aperm[] is Atot, though it may also count 6231 repeats (i.e., same 'i,j' pair). 6232 Ajmap[Annz+1] stores the number of repeats of each unique entry belonging to the diagonal block. More precisely, Ajmap[t+1] - Ajmap[t] 6233 is the number of repeats for the t-th unique entry in the diagonal block. Ajmap[0] is always 0. 6234 6235 Atot: number of entries belonging to the diagonal block 6236 Annz: number of unique nonzeros belonging to the diagonal block. 6237 6238 Bperm[], Bjmap[], Btot, Bnnz are similar but for the off-diagonal block. 6239 6240 Aperm[],Bperm[],Ajmap[] and Bjmap[] are allocated separately by this routine with PetscMalloc1(). 6241 */ 6242 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_) 6243 { 6244 PetscInt cstart, cend, rstart, rend, row, col; 6245 PetscCount Atot = 0, Btot = 0; /* Total number of nonzeros in the diagonal and off-diagonal blocks */ 6246 PetscCount Annz = 0, Bnnz = 0; /* Number of unique nonzeros in the diagonal and off-diagonal blocks */ 6247 PetscCount k, m, p, q, r, s, mid; 6248 PetscCount *Aperm, *Bperm, *Ajmap, *Bjmap; 6249 6250 PetscFunctionBegin; 6251 PetscCall(PetscLayoutGetRange(mat->rmap, &rstart, &rend)); 6252 PetscCall(PetscLayoutGetRange(mat->cmap, &cstart, &cend)); 6253 m = rend - rstart; 6254 6255 /* Skip negative rows */ 6256 for (k = 0; k < n; k++) 6257 if (i[k] >= 0) break; 6258 6259 /* Process [k,n): sort and partition each local row into diag and offdiag portions, 6260 fill rowBegin[], rowMid[], rowEnd[], and count Atot, Btot, Annz, Bnnz. 6261 */ 6262 while (k < n) { 6263 row = i[k]; 6264 /* Entries in [k,s) are in one row. Shift diagonal block col indices so that diag is ahead of offdiag after sorting the row */ 6265 for (s = k; s < n; s++) 6266 if (i[s] != row) break; 6267 6268 /* Shift diag columns to range of [-PETSC_INT_MAX, -1] */ 6269 for (p = k; p < s; p++) { 6270 if (j[p] >= cstart && j[p] < cend) j[p] -= PETSC_INT_MAX; 6271 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]); 6272 } 6273 PetscCall(PetscSortIntWithCountArray(s - k, j + k, perm + k)); 6274 PetscCall(PetscSortedIntUpperBound(j, k, s, -1, &mid)); /* Separate [k,s) into [k,mid) for diag and [mid,s) for offdiag */ 6275 rowBegin[row - rstart] = k; 6276 rowMid[row - rstart] = mid; 6277 rowEnd[row - rstart] = s; 6278 6279 /* Count nonzeros of this diag/offdiag row, which might have repeats */ 6280 Atot += mid - k; 6281 Btot += s - mid; 6282 6283 /* Count unique nonzeros of this diag row */ 6284 for (p = k; p < mid;) { 6285 col = j[p]; 6286 do { 6287 j[p] += PETSC_INT_MAX; /* Revert the modified diagonal indices */ 6288 p++; 6289 } while (p < mid && j[p] == col); 6290 Annz++; 6291 } 6292 6293 /* Count unique nonzeros of this offdiag row */ 6294 for (p = mid; p < s;) { 6295 col = j[p]; 6296 do { 6297 p++; 6298 } while (p < s && j[p] == col); 6299 Bnnz++; 6300 } 6301 k = s; 6302 } 6303 6304 /* Allocation according to Atot, Btot, Annz, Bnnz */ 6305 PetscCall(PetscMalloc1(Atot, &Aperm)); 6306 PetscCall(PetscMalloc1(Btot, &Bperm)); 6307 PetscCall(PetscMalloc1(Annz + 1, &Ajmap)); 6308 PetscCall(PetscMalloc1(Bnnz + 1, &Bjmap)); 6309 6310 /* Re-scan indices and copy diag/offdiag permutation indices to Aperm, Bperm and also fill Ajmap and Bjmap */ 6311 Ajmap[0] = Bjmap[0] = Atot = Btot = Annz = Bnnz = 0; 6312 for (r = 0; r < m; r++) { 6313 k = rowBegin[r]; 6314 mid = rowMid[r]; 6315 s = rowEnd[r]; 6316 PetscCall(PetscArraycpy(PetscSafePointerPlusOffset(Aperm, Atot), PetscSafePointerPlusOffset(perm, k), mid - k)); 6317 PetscCall(PetscArraycpy(PetscSafePointerPlusOffset(Bperm, Btot), PetscSafePointerPlusOffset(perm, mid), s - mid)); 6318 Atot += mid - k; 6319 Btot += s - mid; 6320 6321 /* Scan column indices in this row and find out how many repeats each unique nonzero has */ 6322 for (p = k; p < mid;) { 6323 col = j[p]; 6324 q = p; 6325 do { 6326 p++; 6327 } while (p < mid && j[p] == col); 6328 Ajmap[Annz + 1] = Ajmap[Annz] + (p - q); 6329 Annz++; 6330 } 6331 6332 for (p = mid; p < s;) { 6333 col = j[p]; 6334 q = p; 6335 do { 6336 p++; 6337 } while (p < s && j[p] == col); 6338 Bjmap[Bnnz + 1] = Bjmap[Bnnz] + (p - q); 6339 Bnnz++; 6340 } 6341 } 6342 /* Output */ 6343 *Aperm_ = Aperm; 6344 *Annz_ = Annz; 6345 *Atot_ = Atot; 6346 *Ajmap_ = Ajmap; 6347 *Bperm_ = Bperm; 6348 *Bnnz_ = Bnnz; 6349 *Btot_ = Btot; 6350 *Bjmap_ = Bjmap; 6351 PetscFunctionReturn(PETSC_SUCCESS); 6352 } 6353 6354 /* 6355 Expand the jmap[] array to make a new one in view of nonzeros in the merged matrix 6356 6357 Input Parameters: 6358 nnz1: number of unique nonzeros in a set that was used to produce imap[], jmap[] 6359 nnz: number of unique nonzeros in the merged matrix 6360 imap[nnz1]: i-th nonzero in the set is the imap[i]-th nonzero in the merged matrix 6361 jmap[nnz1+1]: i-th nonzero in the set has jmap[i+1] - jmap[i] repeats in the set 6362 6363 Output Parameter: (memory is allocated by the caller) 6364 jmap_new[nnz+1]: i-th nonzero in the merged matrix has jmap_new[i+1] - jmap_new[i] repeats in the set 6365 6366 Example: 6367 nnz1 = 4 6368 nnz = 6 6369 imap = [1,3,4,5] 6370 jmap = [0,3,5,6,7] 6371 then, 6372 jmap_new = [0,0,3,3,5,6,7] 6373 */ 6374 static PetscErrorCode ExpandJmap_Internal(PetscCount nnz1, PetscCount nnz, const PetscCount imap[], const PetscCount jmap[], PetscCount jmap_new[]) 6375 { 6376 PetscCount k, p; 6377 6378 PetscFunctionBegin; 6379 jmap_new[0] = 0; 6380 p = nnz; /* p loops over jmap_new[] backwards */ 6381 for (k = nnz1 - 1; k >= 0; k--) { /* k loops over imap[] */ 6382 for (; p > imap[k]; p--) jmap_new[p] = jmap[k + 1]; 6383 } 6384 for (; p >= 0; p--) jmap_new[p] = jmap[0]; 6385 PetscFunctionReturn(PETSC_SUCCESS); 6386 } 6387 6388 static PetscErrorCode MatCOOStructDestroy_MPIAIJ(void **data) 6389 { 6390 MatCOOStruct_MPIAIJ *coo = (MatCOOStruct_MPIAIJ *)*data; 6391 6392 PetscFunctionBegin; 6393 PetscCall(PetscSFDestroy(&coo->sf)); 6394 PetscCall(PetscFree(coo->Aperm1)); 6395 PetscCall(PetscFree(coo->Bperm1)); 6396 PetscCall(PetscFree(coo->Ajmap1)); 6397 PetscCall(PetscFree(coo->Bjmap1)); 6398 PetscCall(PetscFree(coo->Aimap2)); 6399 PetscCall(PetscFree(coo->Bimap2)); 6400 PetscCall(PetscFree(coo->Aperm2)); 6401 PetscCall(PetscFree(coo->Bperm2)); 6402 PetscCall(PetscFree(coo->Ajmap2)); 6403 PetscCall(PetscFree(coo->Bjmap2)); 6404 PetscCall(PetscFree(coo->Cperm1)); 6405 PetscCall(PetscFree2(coo->sendbuf, coo->recvbuf)); 6406 PetscCall(PetscFree(coo)); 6407 PetscFunctionReturn(PETSC_SUCCESS); 6408 } 6409 6410 PetscErrorCode MatSetPreallocationCOO_MPIAIJ(Mat mat, PetscCount coo_n, PetscInt coo_i[], PetscInt coo_j[]) 6411 { 6412 MPI_Comm comm; 6413 PetscMPIInt rank, size; 6414 PetscInt m, n, M, N, rstart, rend, cstart, cend; /* Sizes, indices of row/col, therefore with type PetscInt */ 6415 PetscCount k, p, q, rem; /* Loop variables over coo arrays */ 6416 Mat_MPIAIJ *mpiaij = (Mat_MPIAIJ *)mat->data; 6417 PetscContainer container; 6418 MatCOOStruct_MPIAIJ *coo; 6419 6420 PetscFunctionBegin; 6421 PetscCall(PetscFree(mpiaij->garray)); 6422 PetscCall(VecDestroy(&mpiaij->lvec)); 6423 #if defined(PETSC_USE_CTABLE) 6424 PetscCall(PetscHMapIDestroy(&mpiaij->colmap)); 6425 #else 6426 PetscCall(PetscFree(mpiaij->colmap)); 6427 #endif 6428 PetscCall(VecScatterDestroy(&mpiaij->Mvctx)); 6429 mat->assembled = PETSC_FALSE; 6430 mat->was_assembled = PETSC_FALSE; 6431 6432 PetscCall(PetscObjectGetComm((PetscObject)mat, &comm)); 6433 PetscCallMPI(MPI_Comm_size(comm, &size)); 6434 PetscCallMPI(MPI_Comm_rank(comm, &rank)); 6435 PetscCall(PetscLayoutSetUp(mat->rmap)); 6436 PetscCall(PetscLayoutSetUp(mat->cmap)); 6437 PetscCall(PetscLayoutGetRange(mat->rmap, &rstart, &rend)); 6438 PetscCall(PetscLayoutGetRange(mat->cmap, &cstart, &cend)); 6439 PetscCall(MatGetLocalSize(mat, &m, &n)); 6440 PetscCall(MatGetSize(mat, &M, &N)); 6441 6442 /* Sort (i,j) by row along with a permutation array, so that the to-be-ignored */ 6443 /* entries come first, then local rows, then remote rows. */ 6444 PetscCount n1 = coo_n, *perm1; 6445 PetscInt *i1 = coo_i, *j1 = coo_j; 6446 6447 PetscCall(PetscMalloc1(n1, &perm1)); 6448 for (k = 0; k < n1; k++) perm1[k] = k; 6449 6450 /* Manipulate indices so that entries with negative row or col indices will have smallest 6451 row indices, local entries will have greater but negative row indices, and remote entries 6452 will have positive row indices. 6453 */ 6454 for (k = 0; k < n1; k++) { 6455 if (i1[k] < 0 || j1[k] < 0) i1[k] = PETSC_INT_MIN; /* e.g., -2^31, minimal to move them ahead */ 6456 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] */ 6457 else { 6458 PetscCheck(!mat->nooffprocentries, PETSC_COMM_SELF, PETSC_ERR_USER_INPUT, "MAT_NO_OFF_PROC_ENTRIES is set but insert to remote rows"); 6459 if (mpiaij->donotstash) i1[k] = PETSC_INT_MIN; /* Ignore offproc entries as if they had negative indices */ 6460 } 6461 } 6462 6463 /* Sort by row; after that, [0,k) have ignored entries, [k,rem) have local rows and [rem,n1) have remote rows */ 6464 PetscCall(PetscSortIntWithIntCountArrayPair(n1, i1, j1, perm1)); 6465 6466 /* Advance k to the first entry we need to take care of */ 6467 for (k = 0; k < n1; k++) 6468 if (i1[k] > PETSC_INT_MIN) break; 6469 PetscCount i1start = k; 6470 6471 PetscCall(PetscSortedIntUpperBound(i1, k, n1, rend - 1 - PETSC_INT_MAX, &rem)); /* rem is upper bound of the last local row */ 6472 for (; k < rem; k++) i1[k] += PETSC_INT_MAX; /* Revert row indices of local rows*/ 6473 6474 /* Send remote rows to their owner */ 6475 /* Find which rows should be sent to which remote ranks*/ 6476 PetscInt nsend = 0; /* Number of MPI ranks to send data to */ 6477 PetscMPIInt *sendto; /* [nsend], storing remote ranks */ 6478 PetscInt *nentries; /* [nsend], storing number of entries sent to remote ranks; Assume PetscInt is big enough for this count, and error if not */ 6479 const PetscInt *ranges; 6480 PetscInt maxNsend = size >= 128 ? 128 : size; /* Assume max 128 neighbors; realloc when needed */ 6481 6482 PetscCall(PetscLayoutGetRanges(mat->rmap, &ranges)); 6483 PetscCall(PetscMalloc2(maxNsend, &sendto, maxNsend, &nentries)); 6484 for (k = rem; k < n1;) { 6485 PetscMPIInt owner; 6486 PetscInt firstRow, lastRow; 6487 6488 /* Locate a row range */ 6489 firstRow = i1[k]; /* first row of this owner */ 6490 PetscCall(PetscLayoutFindOwner(mat->rmap, firstRow, &owner)); 6491 lastRow = ranges[owner + 1] - 1; /* last row of this owner */ 6492 6493 /* Find the first index 'p' in [k,n) with i[p] belonging to next owner */ 6494 PetscCall(PetscSortedIntUpperBound(i1, k, n1, lastRow, &p)); 6495 6496 /* All entries in [k,p) belong to this remote owner */ 6497 if (nsend >= maxNsend) { /* Double the remote ranks arrays if not long enough */ 6498 PetscMPIInt *sendto2; 6499 PetscInt *nentries2; 6500 PetscInt maxNsend2 = (maxNsend <= size / 2) ? maxNsend * 2 : size; 6501 6502 PetscCall(PetscMalloc2(maxNsend2, &sendto2, maxNsend2, &nentries2)); 6503 PetscCall(PetscArraycpy(sendto2, sendto, maxNsend)); 6504 PetscCall(PetscArraycpy(nentries2, nentries2, maxNsend + 1)); 6505 PetscCall(PetscFree2(sendto, nentries2)); 6506 sendto = sendto2; 6507 nentries = nentries2; 6508 maxNsend = maxNsend2; 6509 } 6510 sendto[nsend] = owner; 6511 PetscCall(PetscIntCast(p - k, &nentries[nsend])); 6512 nsend++; 6513 k = p; 6514 } 6515 6516 /* Build 1st SF to know offsets on remote to send data */ 6517 PetscSF sf1; 6518 PetscInt nroots = 1, nroots2 = 0; 6519 PetscInt nleaves = nsend, nleaves2 = 0; 6520 PetscInt *offsets; 6521 PetscSFNode *iremote; 6522 6523 PetscCall(PetscSFCreate(comm, &sf1)); 6524 PetscCall(PetscMalloc1(nsend, &iremote)); 6525 PetscCall(PetscMalloc1(nsend, &offsets)); 6526 for (k = 0; k < nsend; k++) { 6527 iremote[k].rank = sendto[k]; 6528 iremote[k].index = 0; 6529 nleaves2 += nentries[k]; 6530 PetscCheck(nleaves2 >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of SF leaves is too large for PetscInt"); 6531 } 6532 PetscCall(PetscSFSetGraph(sf1, nroots, nleaves, NULL, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER)); 6533 PetscCall(PetscSFFetchAndOpWithMemTypeBegin(sf1, MPIU_INT, PETSC_MEMTYPE_HOST, &nroots2 /*rootdata*/, PETSC_MEMTYPE_HOST, nentries /*leafdata*/, PETSC_MEMTYPE_HOST, offsets /*leafupdate*/, MPI_SUM)); 6534 PetscCall(PetscSFFetchAndOpEnd(sf1, MPIU_INT, &nroots2, nentries, offsets, MPI_SUM)); /* Would nroots2 overflow, we check offsets[] below */ 6535 PetscCall(PetscSFDestroy(&sf1)); 6536 PetscAssert(nleaves2 == n1 - rem, PETSC_COMM_SELF, PETSC_ERR_PLIB, "nleaves2 %" PetscInt_FMT " != number of remote entries %" PetscCount_FMT, nleaves2, n1 - rem); 6537 6538 /* Build 2nd SF to send remote COOs to their owner */ 6539 PetscSF sf2; 6540 nroots = nroots2; 6541 nleaves = nleaves2; 6542 PetscCall(PetscSFCreate(comm, &sf2)); 6543 PetscCall(PetscSFSetFromOptions(sf2)); 6544 PetscCall(PetscMalloc1(nleaves, &iremote)); 6545 p = 0; 6546 for (k = 0; k < nsend; k++) { 6547 PetscCheck(offsets[k] >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Number of SF roots is too large for PetscInt"); 6548 for (q = 0; q < nentries[k]; q++, p++) { 6549 iremote[p].rank = sendto[k]; 6550 PetscCall(PetscIntCast(offsets[k] + q, &iremote[p].index)); 6551 } 6552 } 6553 PetscCall(PetscSFSetGraph(sf2, nroots, nleaves, NULL, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER)); 6554 6555 /* Send the remote COOs to their owner */ 6556 PetscInt n2 = nroots, *i2, *j2; /* Buffers for received COOs from other ranks, along with a permutation array */ 6557 PetscCount *perm2; /* Though PetscInt is enough for remote entries, we use PetscCount here as we want to reuse MatSplitEntries_Internal() */ 6558 PetscCall(PetscMalloc3(n2, &i2, n2, &j2, n2, &perm2)); 6559 PetscAssert(rem == 0 || i1 != NULL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cannot add nonzero offset to null"); 6560 PetscAssert(rem == 0 || j1 != NULL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cannot add nonzero offset to null"); 6561 PetscInt *i1prem = PetscSafePointerPlusOffset(i1, rem); 6562 PetscInt *j1prem = PetscSafePointerPlusOffset(j1, rem); 6563 PetscCall(PetscSFReduceWithMemTypeBegin(sf2, MPIU_INT, PETSC_MEMTYPE_HOST, i1prem, PETSC_MEMTYPE_HOST, i2, MPI_REPLACE)); 6564 PetscCall(PetscSFReduceEnd(sf2, MPIU_INT, i1prem, i2, MPI_REPLACE)); 6565 PetscCall(PetscSFReduceWithMemTypeBegin(sf2, MPIU_INT, PETSC_MEMTYPE_HOST, j1prem, PETSC_MEMTYPE_HOST, j2, MPI_REPLACE)); 6566 PetscCall(PetscSFReduceEnd(sf2, MPIU_INT, j1prem, j2, MPI_REPLACE)); 6567 6568 PetscCall(PetscFree(offsets)); 6569 PetscCall(PetscFree2(sendto, nentries)); 6570 6571 /* Sort received COOs by row along with the permutation array */ 6572 for (k = 0; k < n2; k++) perm2[k] = k; 6573 PetscCall(PetscSortIntWithIntCountArrayPair(n2, i2, j2, perm2)); 6574 6575 /* sf2 only sends contiguous leafdata to contiguous rootdata. We record the permutation which will be used to fill leafdata */ 6576 PetscCount *Cperm1; 6577 PetscAssert(rem == 0 || perm1 != NULL, PETSC_COMM_SELF, PETSC_ERR_PLIB, "Cannot add nonzero offset to null"); 6578 PetscCount *perm1prem = PetscSafePointerPlusOffset(perm1, rem); 6579 PetscCall(PetscMalloc1(nleaves, &Cperm1)); 6580 PetscCall(PetscArraycpy(Cperm1, perm1prem, nleaves)); 6581 6582 /* Support for HYPRE matrices, kind of a hack. 6583 Swap min column with diagonal so that diagonal values will go first */ 6584 PetscBool hypre; 6585 PetscCall(PetscStrcmp("_internal_COO_mat_for_hypre", ((PetscObject)mat)->name, &hypre)); 6586 if (hypre) { 6587 PetscInt *minj; 6588 PetscBT hasdiag; 6589 6590 PetscCall(PetscBTCreate(m, &hasdiag)); 6591 PetscCall(PetscMalloc1(m, &minj)); 6592 for (k = 0; k < m; k++) minj[k] = PETSC_INT_MAX; 6593 for (k = i1start; k < rem; k++) { 6594 if (j1[k] < cstart || j1[k] >= cend) continue; 6595 const PetscInt rindex = i1[k] - rstart; 6596 if ((j1[k] - cstart) == rindex) PetscCall(PetscBTSet(hasdiag, rindex)); 6597 minj[rindex] = PetscMin(minj[rindex], j1[k]); 6598 } 6599 for (k = 0; k < n2; k++) { 6600 if (j2[k] < cstart || j2[k] >= cend) continue; 6601 const PetscInt rindex = i2[k] - rstart; 6602 if ((j2[k] - cstart) == rindex) PetscCall(PetscBTSet(hasdiag, rindex)); 6603 minj[rindex] = PetscMin(minj[rindex], j2[k]); 6604 } 6605 for (k = i1start; k < rem; k++) { 6606 const PetscInt rindex = i1[k] - rstart; 6607 if (j1[k] < cstart || j1[k] >= cend || !PetscBTLookup(hasdiag, rindex)) continue; 6608 if (j1[k] == minj[rindex]) j1[k] = i1[k] + (cstart - rstart); 6609 else if ((j1[k] - cstart) == rindex) j1[k] = minj[rindex]; 6610 } 6611 for (k = 0; k < n2; k++) { 6612 const PetscInt rindex = i2[k] - rstart; 6613 if (j2[k] < cstart || j2[k] >= cend || !PetscBTLookup(hasdiag, rindex)) continue; 6614 if (j2[k] == minj[rindex]) j2[k] = i2[k] + (cstart - rstart); 6615 else if ((j2[k] - cstart) == rindex) j2[k] = minj[rindex]; 6616 } 6617 PetscCall(PetscBTDestroy(&hasdiag)); 6618 PetscCall(PetscFree(minj)); 6619 } 6620 6621 /* Split local COOs and received COOs into diag/offdiag portions */ 6622 PetscCount *rowBegin1, *rowMid1, *rowEnd1; 6623 PetscCount *Ajmap1, *Aperm1, *Bjmap1, *Bperm1; 6624 PetscCount Annz1, Bnnz1, Atot1, Btot1; 6625 PetscCount *rowBegin2, *rowMid2, *rowEnd2; 6626 PetscCount *Ajmap2, *Aperm2, *Bjmap2, *Bperm2; 6627 PetscCount Annz2, Bnnz2, Atot2, Btot2; 6628 6629 PetscCall(PetscCalloc3(m, &rowBegin1, m, &rowMid1, m, &rowEnd1)); 6630 PetscCall(PetscCalloc3(m, &rowBegin2, m, &rowMid2, m, &rowEnd2)); 6631 PetscCall(MatSplitEntries_Internal(mat, rem, i1, j1, perm1, rowBegin1, rowMid1, rowEnd1, &Atot1, &Aperm1, &Annz1, &Ajmap1, &Btot1, &Bperm1, &Bnnz1, &Bjmap1)); 6632 PetscCall(MatSplitEntries_Internal(mat, n2, i2, j2, perm2, rowBegin2, rowMid2, rowEnd2, &Atot2, &Aperm2, &Annz2, &Ajmap2, &Btot2, &Bperm2, &Bnnz2, &Bjmap2)); 6633 6634 /* Merge local COOs with received COOs: diag with diag, offdiag with offdiag */ 6635 PetscInt *Ai, *Bi; 6636 PetscInt *Aj, *Bj; 6637 6638 PetscCall(PetscMalloc1(m + 1, &Ai)); 6639 PetscCall(PetscMalloc1(m + 1, &Bi)); 6640 PetscCall(PetscMalloc1(Annz1 + Annz2, &Aj)); /* Since local and remote entries might have dups, we might allocate excess memory */ 6641 PetscCall(PetscMalloc1(Bnnz1 + Bnnz2, &Bj)); 6642 6643 PetscCount *Aimap1, *Bimap1, *Aimap2, *Bimap2; 6644 PetscCall(PetscMalloc1(Annz1, &Aimap1)); 6645 PetscCall(PetscMalloc1(Bnnz1, &Bimap1)); 6646 PetscCall(PetscMalloc1(Annz2, &Aimap2)); 6647 PetscCall(PetscMalloc1(Bnnz2, &Bimap2)); 6648 6649 PetscCall(MatMergeEntries_Internal(mat, j1, j2, rowBegin1, rowMid1, rowBegin2, rowMid2, Ajmap1, Ajmap2, Aimap1, Aimap2, Ai, Aj)); 6650 PetscCall(MatMergeEntries_Internal(mat, j1, j2, rowMid1, rowEnd1, rowMid2, rowEnd2, Bjmap1, Bjmap2, Bimap1, Bimap2, Bi, Bj)); 6651 6652 /* Expand Ajmap1/Bjmap1 to make them based off nonzeros in A/B, since we */ 6653 /* expect nonzeros in A/B most likely have local contributing entries */ 6654 PetscInt Annz = Ai[m]; 6655 PetscInt Bnnz = Bi[m]; 6656 PetscCount *Ajmap1_new, *Bjmap1_new; 6657 6658 PetscCall(PetscMalloc1(Annz + 1, &Ajmap1_new)); 6659 PetscCall(PetscMalloc1(Bnnz + 1, &Bjmap1_new)); 6660 6661 PetscCall(ExpandJmap_Internal(Annz1, Annz, Aimap1, Ajmap1, Ajmap1_new)); 6662 PetscCall(ExpandJmap_Internal(Bnnz1, Bnnz, Bimap1, Bjmap1, Bjmap1_new)); 6663 6664 PetscCall(PetscFree(Aimap1)); 6665 PetscCall(PetscFree(Ajmap1)); 6666 PetscCall(PetscFree(Bimap1)); 6667 PetscCall(PetscFree(Bjmap1)); 6668 PetscCall(PetscFree3(rowBegin1, rowMid1, rowEnd1)); 6669 PetscCall(PetscFree3(rowBegin2, rowMid2, rowEnd2)); 6670 PetscCall(PetscFree(perm1)); 6671 PetscCall(PetscFree3(i2, j2, perm2)); 6672 6673 Ajmap1 = Ajmap1_new; 6674 Bjmap1 = Bjmap1_new; 6675 6676 /* Reallocate Aj, Bj once we know actual numbers of unique nonzeros in A and B */ 6677 if (Annz < Annz1 + Annz2) { 6678 PetscInt *Aj_new; 6679 PetscCall(PetscMalloc1(Annz, &Aj_new)); 6680 PetscCall(PetscArraycpy(Aj_new, Aj, Annz)); 6681 PetscCall(PetscFree(Aj)); 6682 Aj = Aj_new; 6683 } 6684 6685 if (Bnnz < Bnnz1 + Bnnz2) { 6686 PetscInt *Bj_new; 6687 PetscCall(PetscMalloc1(Bnnz, &Bj_new)); 6688 PetscCall(PetscArraycpy(Bj_new, Bj, Bnnz)); 6689 PetscCall(PetscFree(Bj)); 6690 Bj = Bj_new; 6691 } 6692 6693 /* Create new submatrices for on-process and off-process coupling */ 6694 PetscScalar *Aa, *Ba; 6695 MatType rtype; 6696 Mat_SeqAIJ *a, *b; 6697 PetscObjectState state; 6698 PetscCall(PetscCalloc1(Annz, &Aa)); /* Zero matrix on device */ 6699 PetscCall(PetscCalloc1(Bnnz, &Ba)); 6700 /* make Aj[] local, i.e, based off the start column of the diagonal portion */ 6701 if (cstart) { 6702 for (k = 0; k < Annz; k++) Aj[k] -= cstart; 6703 } 6704 6705 PetscCall(MatGetRootType_Private(mat, &rtype)); 6706 6707 MatSeqXAIJGetOptions_Private(mpiaij->A); 6708 PetscCall(MatDestroy(&mpiaij->A)); 6709 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, m, n, Ai, Aj, Aa, &mpiaij->A)); 6710 PetscCall(MatSetBlockSizesFromMats(mpiaij->A, mat, mat)); 6711 MatSeqXAIJRestoreOptions_Private(mpiaij->A); 6712 6713 MatSeqXAIJGetOptions_Private(mpiaij->B); 6714 PetscCall(MatDestroy(&mpiaij->B)); 6715 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, m, mat->cmap->N, Bi, Bj, Ba, &mpiaij->B)); 6716 PetscCall(MatSetBlockSizesFromMats(mpiaij->B, mat, mat)); 6717 MatSeqXAIJRestoreOptions_Private(mpiaij->B); 6718 6719 PetscCall(MatSetUpMultiply_MPIAIJ(mat)); 6720 mat->was_assembled = PETSC_TRUE; // was_assembled in effect means the Mvctx is built; doing so avoids redundant MatSetUpMultiply_MPIAIJ 6721 state = mpiaij->A->nonzerostate + mpiaij->B->nonzerostate; 6722 PetscCallMPI(MPIU_Allreduce(&state, &mat->nonzerostate, 1, MPIU_INT64, MPI_SUM, PetscObjectComm((PetscObject)mat))); 6723 6724 a = (Mat_SeqAIJ *)mpiaij->A->data; 6725 b = (Mat_SeqAIJ *)mpiaij->B->data; 6726 a->free_a = PETSC_TRUE; 6727 a->free_ij = PETSC_TRUE; 6728 b->free_a = PETSC_TRUE; 6729 b->free_ij = PETSC_TRUE; 6730 a->maxnz = a->nz; 6731 b->maxnz = b->nz; 6732 6733 /* conversion must happen AFTER multiply setup */ 6734 PetscCall(MatConvert(mpiaij->A, rtype, MAT_INPLACE_MATRIX, &mpiaij->A)); 6735 PetscCall(MatConvert(mpiaij->B, rtype, MAT_INPLACE_MATRIX, &mpiaij->B)); 6736 PetscCall(VecDestroy(&mpiaij->lvec)); 6737 PetscCall(MatCreateVecs(mpiaij->B, &mpiaij->lvec, NULL)); 6738 6739 // Put the COO struct in a container and then attach that to the matrix 6740 PetscCall(PetscMalloc1(1, &coo)); 6741 coo->n = coo_n; 6742 coo->sf = sf2; 6743 coo->sendlen = nleaves; 6744 coo->recvlen = nroots; 6745 coo->Annz = Annz; 6746 coo->Bnnz = Bnnz; 6747 coo->Annz2 = Annz2; 6748 coo->Bnnz2 = Bnnz2; 6749 coo->Atot1 = Atot1; 6750 coo->Atot2 = Atot2; 6751 coo->Btot1 = Btot1; 6752 coo->Btot2 = Btot2; 6753 coo->Ajmap1 = Ajmap1; 6754 coo->Aperm1 = Aperm1; 6755 coo->Bjmap1 = Bjmap1; 6756 coo->Bperm1 = Bperm1; 6757 coo->Aimap2 = Aimap2; 6758 coo->Ajmap2 = Ajmap2; 6759 coo->Aperm2 = Aperm2; 6760 coo->Bimap2 = Bimap2; 6761 coo->Bjmap2 = Bjmap2; 6762 coo->Bperm2 = Bperm2; 6763 coo->Cperm1 = Cperm1; 6764 // Allocate in preallocation. If not used, it has zero cost on host 6765 PetscCall(PetscMalloc2(coo->sendlen, &coo->sendbuf, coo->recvlen, &coo->recvbuf)); 6766 PetscCall(PetscContainerCreate(PETSC_COMM_SELF, &container)); 6767 PetscCall(PetscContainerSetPointer(container, coo)); 6768 PetscCall(PetscContainerSetCtxDestroy(container, MatCOOStructDestroy_MPIAIJ)); 6769 PetscCall(PetscObjectCompose((PetscObject)mat, "__PETSc_MatCOOStruct_Host", (PetscObject)container)); 6770 PetscCall(PetscContainerDestroy(&container)); 6771 PetscFunctionReturn(PETSC_SUCCESS); 6772 } 6773 6774 static PetscErrorCode MatSetValuesCOO_MPIAIJ(Mat mat, const PetscScalar v[], InsertMode imode) 6775 { 6776 Mat_MPIAIJ *mpiaij = (Mat_MPIAIJ *)mat->data; 6777 Mat A = mpiaij->A, B = mpiaij->B; 6778 PetscScalar *Aa, *Ba; 6779 PetscScalar *sendbuf, *recvbuf; 6780 const PetscCount *Ajmap1, *Ajmap2, *Aimap2; 6781 const PetscCount *Bjmap1, *Bjmap2, *Bimap2; 6782 const PetscCount *Aperm1, *Aperm2, *Bperm1, *Bperm2; 6783 const PetscCount *Cperm1; 6784 PetscContainer container; 6785 MatCOOStruct_MPIAIJ *coo; 6786 6787 PetscFunctionBegin; 6788 PetscCall(PetscObjectQuery((PetscObject)mat, "__PETSc_MatCOOStruct_Host", (PetscObject *)&container)); 6789 PetscCheck(container, PetscObjectComm((PetscObject)mat), PETSC_ERR_PLIB, "Not found MatCOOStruct on this matrix"); 6790 PetscCall(PetscContainerGetPointer(container, (void **)&coo)); 6791 sendbuf = coo->sendbuf; 6792 recvbuf = coo->recvbuf; 6793 Ajmap1 = coo->Ajmap1; 6794 Ajmap2 = coo->Ajmap2; 6795 Aimap2 = coo->Aimap2; 6796 Bjmap1 = coo->Bjmap1; 6797 Bjmap2 = coo->Bjmap2; 6798 Bimap2 = coo->Bimap2; 6799 Aperm1 = coo->Aperm1; 6800 Aperm2 = coo->Aperm2; 6801 Bperm1 = coo->Bperm1; 6802 Bperm2 = coo->Bperm2; 6803 Cperm1 = coo->Cperm1; 6804 6805 PetscCall(MatSeqAIJGetArray(A, &Aa)); /* Might read and write matrix values */ 6806 PetscCall(MatSeqAIJGetArray(B, &Ba)); 6807 6808 /* Pack entries to be sent to remote */ 6809 for (PetscCount i = 0; i < coo->sendlen; i++) sendbuf[i] = v[Cperm1[i]]; 6810 6811 /* Send remote entries to their owner and overlap the communication with local computation */ 6812 PetscCall(PetscSFReduceWithMemTypeBegin(coo->sf, MPIU_SCALAR, PETSC_MEMTYPE_HOST, sendbuf, PETSC_MEMTYPE_HOST, recvbuf, MPI_REPLACE)); 6813 /* Add local entries to A and B */ 6814 for (PetscCount i = 0; i < coo->Annz; i++) { /* All nonzeros in A are either zero'ed or added with a value (i.e., initialized) */ 6815 PetscScalar sum = 0.0; /* Do partial summation first to improve numerical stability */ 6816 for (PetscCount k = Ajmap1[i]; k < Ajmap1[i + 1]; k++) sum += v[Aperm1[k]]; 6817 Aa[i] = (imode == INSERT_VALUES ? 0.0 : Aa[i]) + sum; 6818 } 6819 for (PetscCount i = 0; i < coo->Bnnz; i++) { 6820 PetscScalar sum = 0.0; 6821 for (PetscCount k = Bjmap1[i]; k < Bjmap1[i + 1]; k++) sum += v[Bperm1[k]]; 6822 Ba[i] = (imode == INSERT_VALUES ? 0.0 : Ba[i]) + sum; 6823 } 6824 PetscCall(PetscSFReduceEnd(coo->sf, MPIU_SCALAR, sendbuf, recvbuf, MPI_REPLACE)); 6825 6826 /* Add received remote entries to A and B */ 6827 for (PetscCount i = 0; i < coo->Annz2; i++) { 6828 for (PetscCount k = Ajmap2[i]; k < Ajmap2[i + 1]; k++) Aa[Aimap2[i]] += recvbuf[Aperm2[k]]; 6829 } 6830 for (PetscCount i = 0; i < coo->Bnnz2; i++) { 6831 for (PetscCount k = Bjmap2[i]; k < Bjmap2[i + 1]; k++) Ba[Bimap2[i]] += recvbuf[Bperm2[k]]; 6832 } 6833 PetscCall(MatSeqAIJRestoreArray(A, &Aa)); 6834 PetscCall(MatSeqAIJRestoreArray(B, &Ba)); 6835 PetscFunctionReturn(PETSC_SUCCESS); 6836 } 6837 6838 /*MC 6839 MATMPIAIJ - MATMPIAIJ = "mpiaij" - A matrix type to be used for parallel sparse matrices. 6840 6841 Options Database Keys: 6842 . -mat_type mpiaij - sets the matrix type to `MATMPIAIJ` during a call to `MatSetFromOptions()` 6843 6844 Level: beginner 6845 6846 Notes: 6847 `MatSetValues()` may be called for this matrix type with a `NULL` argument for the numerical values, 6848 in this case the values associated with the rows and columns one passes in are set to zero 6849 in the matrix 6850 6851 `MatSetOptions`(,`MAT_STRUCTURE_ONLY`,`PETSC_TRUE`) may be called for this matrix type. In this no 6852 space is allocated for the nonzero entries and any entries passed with `MatSetValues()` are ignored 6853 6854 .seealso: [](ch_matrices), `Mat`, `MATSEQAIJ`, `MATAIJ`, `MatCreateAIJ()` 6855 M*/ 6856 PETSC_EXTERN PetscErrorCode MatCreate_MPIAIJ(Mat B) 6857 { 6858 Mat_MPIAIJ *b; 6859 PetscMPIInt size; 6860 6861 PetscFunctionBegin; 6862 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)B), &size)); 6863 6864 PetscCall(PetscNew(&b)); 6865 B->data = (void *)b; 6866 B->ops[0] = MatOps_Values; 6867 B->assembled = PETSC_FALSE; 6868 B->insertmode = NOT_SET_VALUES; 6869 b->size = size; 6870 6871 PetscCallMPI(MPI_Comm_rank(PetscObjectComm((PetscObject)B), &b->rank)); 6872 6873 /* build cache for off array entries formed */ 6874 PetscCall(MatStashCreate_Private(PetscObjectComm((PetscObject)B), 1, &B->stash)); 6875 6876 b->donotstash = PETSC_FALSE; 6877 b->colmap = NULL; 6878 b->garray = NULL; 6879 b->roworiented = PETSC_TRUE; 6880 6881 /* stuff used for matrix vector multiply */ 6882 b->lvec = NULL; 6883 b->Mvctx = NULL; 6884 6885 /* stuff for MatGetRow() */ 6886 b->rowindices = NULL; 6887 b->rowvalues = NULL; 6888 b->getrowactive = PETSC_FALSE; 6889 6890 /* flexible pointer used in CUSPARSE classes */ 6891 b->spptr = NULL; 6892 6893 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatMPIAIJSetUseScalableIncreaseOverlap_C", MatMPIAIJSetUseScalableIncreaseOverlap_MPIAIJ)); 6894 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatStoreValues_C", MatStoreValues_MPIAIJ)); 6895 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatRetrieveValues_C", MatRetrieveValues_MPIAIJ)); 6896 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatIsTranspose_C", MatIsTranspose_MPIAIJ)); 6897 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatMPIAIJSetPreallocation_C", MatMPIAIJSetPreallocation_MPIAIJ)); 6898 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatResetPreallocation_C", MatResetPreallocation_MPIAIJ)); 6899 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatResetHash_C", MatResetHash_MPIAIJ)); 6900 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatMPIAIJSetPreallocationCSR_C", MatMPIAIJSetPreallocationCSR_MPIAIJ)); 6901 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatDiagonalScaleLocal_C", MatDiagonalScaleLocal_MPIAIJ)); 6902 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijperm_C", MatConvert_MPIAIJ_MPIAIJPERM)); 6903 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijsell_C", MatConvert_MPIAIJ_MPIAIJSELL)); 6904 #if defined(PETSC_HAVE_CUDA) 6905 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijcusparse_C", MatConvert_MPIAIJ_MPIAIJCUSPARSE)); 6906 #endif 6907 #if defined(PETSC_HAVE_HIP) 6908 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijhipsparse_C", MatConvert_MPIAIJ_MPIAIJHIPSPARSE)); 6909 #endif 6910 #if defined(PETSC_HAVE_KOKKOS_KERNELS) 6911 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijkokkos_C", MatConvert_MPIAIJ_MPIAIJKokkos)); 6912 #endif 6913 #if defined(PETSC_HAVE_MKL_SPARSE) 6914 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijmkl_C", MatConvert_MPIAIJ_MPIAIJMKL)); 6915 #endif 6916 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpiaijcrl_C", MatConvert_MPIAIJ_MPIAIJCRL)); 6917 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpibaij_C", MatConvert_MPIAIJ_MPIBAIJ)); 6918 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpisbaij_C", MatConvert_MPIAIJ_MPISBAIJ)); 6919 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpidense_C", MatConvert_MPIAIJ_MPIDense)); 6920 #if defined(PETSC_HAVE_ELEMENTAL) 6921 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_elemental_C", MatConvert_MPIAIJ_Elemental)); 6922 #endif 6923 #if defined(PETSC_HAVE_SCALAPACK) 6924 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_scalapack_C", MatConvert_AIJ_ScaLAPACK)); 6925 #endif 6926 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_is_C", MatConvert_XAIJ_IS)); 6927 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_mpisell_C", MatConvert_MPIAIJ_MPISELL)); 6928 #if defined(PETSC_HAVE_HYPRE) 6929 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatConvert_mpiaij_hypre_C", MatConvert_AIJ_HYPRE)); 6930 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatProductSetFromOptions_transpose_mpiaij_mpiaij_C", MatProductSetFromOptions_Transpose_AIJ_AIJ)); 6931 #endif 6932 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatProductSetFromOptions_is_mpiaij_C", MatProductSetFromOptions_IS_XAIJ)); 6933 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatProductSetFromOptions_mpiaij_mpiaij_C", MatProductSetFromOptions_MPIAIJ)); 6934 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatSetPreallocationCOO_C", MatSetPreallocationCOO_MPIAIJ)); 6935 PetscCall(PetscObjectComposeFunction((PetscObject)B, "MatSetValuesCOO_C", MatSetValuesCOO_MPIAIJ)); 6936 PetscCall(PetscObjectChangeTypeName((PetscObject)B, MATMPIAIJ)); 6937 PetscFunctionReturn(PETSC_SUCCESS); 6938 } 6939 6940 /*@ 6941 MatCreateMPIAIJWithSplitArrays - creates a `MATMPIAIJ` matrix using arrays that contain the "diagonal" 6942 and "off-diagonal" part of the matrix in CSR format. 6943 6944 Collective 6945 6946 Input Parameters: 6947 + comm - MPI communicator 6948 . m - number of local rows (Cannot be `PETSC_DECIDE`) 6949 . n - This value should be the same as the local size used in creating the 6950 x vector for the matrix-vector product $y = Ax$. (or `PETSC_DECIDE` to have 6951 calculated if `N` is given) For square matrices `n` is almost always `m`. 6952 . M - number of global rows (or `PETSC_DETERMINE` to have calculated if `m` is given) 6953 . N - number of global columns (or `PETSC_DETERMINE` to have calculated if `n` is given) 6954 . 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 6955 . j - column indices, which must be local, i.e., based off the start column of the diagonal portion 6956 . a - matrix values 6957 . 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 6958 . oj - column indices, which must be global, representing global columns in the `MATMPIAIJ` matrix 6959 - oa - matrix values 6960 6961 Output Parameter: 6962 . mat - the matrix 6963 6964 Level: advanced 6965 6966 Notes: 6967 The `i`, `j`, and `a` arrays ARE NOT copied by this routine into the internal format used by PETSc (even in Fortran). The user 6968 must free the arrays once the matrix has been destroyed and not before. 6969 6970 The `i` and `j` indices are 0 based 6971 6972 See `MatCreateAIJ()` for the definition of "diagonal" and "off-diagonal" portion of the matrix 6973 6974 This sets local rows and cannot be used to set off-processor values. 6975 6976 Use of this routine is discouraged because it is inflexible and cumbersome to use. It is extremely rare that a 6977 legacy application natively assembles into exactly this split format. The code to do so is nontrivial and does 6978 not easily support in-place reassembly. It is recommended to use MatSetValues() (or a variant thereof) because 6979 the resulting assembly is easier to implement, will work with any matrix format, and the user does not have to 6980 keep track of the underlying array. Use `MatSetOption`(A,`MAT_NO_OFF_PROC_ENTRIES`,`PETSC_TRUE`) to disable all 6981 communication if it is known that only local entries will be set. 6982 6983 .seealso: [](ch_matrices), `Mat`, `MatCreate()`, `MatCreateSeqAIJ()`, `MatSetValues()`, `MatMPIAIJSetPreallocation()`, `MatMPIAIJSetPreallocationCSR()`, 6984 `MATMPIAIJ`, `MatCreateAIJ()`, `MatCreateMPIAIJWithArrays()` 6985 @*/ 6986 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) 6987 { 6988 Mat_MPIAIJ *maij; 6989 6990 PetscFunctionBegin; 6991 PetscCheck(m >= 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "local number of rows (m) cannot be PETSC_DECIDE, or negative"); 6992 PetscCheck(i[0] == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "i (row indices) must start with 0"); 6993 PetscCheck(oi[0] == 0, PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "oi (row indices) must start with 0"); 6994 PetscCall(MatCreate(comm, mat)); 6995 PetscCall(MatSetSizes(*mat, m, n, M, N)); 6996 PetscCall(MatSetType(*mat, MATMPIAIJ)); 6997 maij = (Mat_MPIAIJ *)(*mat)->data; 6998 6999 (*mat)->preallocated = PETSC_TRUE; 7000 7001 PetscCall(PetscLayoutSetUp((*mat)->rmap)); 7002 PetscCall(PetscLayoutSetUp((*mat)->cmap)); 7003 7004 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, m, n, i, j, a, &maij->A)); 7005 PetscCall(MatCreateSeqAIJWithArrays(PETSC_COMM_SELF, m, (*mat)->cmap->N, oi, oj, oa, &maij->B)); 7006 7007 PetscCall(MatSetOption(*mat, MAT_NO_OFF_PROC_ENTRIES, PETSC_TRUE)); 7008 PetscCall(MatAssemblyBegin(*mat, MAT_FINAL_ASSEMBLY)); 7009 PetscCall(MatAssemblyEnd(*mat, MAT_FINAL_ASSEMBLY)); 7010 PetscCall(MatSetOption(*mat, MAT_NO_OFF_PROC_ENTRIES, PETSC_FALSE)); 7011 PetscCall(MatSetOption(*mat, MAT_NEW_NONZERO_LOCATION_ERR, PETSC_TRUE)); 7012 PetscFunctionReturn(PETSC_SUCCESS); 7013 } 7014 7015 typedef struct { 7016 Mat *mp; /* intermediate products */ 7017 PetscBool *mptmp; /* is the intermediate product temporary ? */ 7018 PetscInt cp; /* number of intermediate products */ 7019 7020 /* support for MatGetBrowsOfAoCols_MPIAIJ for P_oth */ 7021 PetscInt *startsj_s, *startsj_r; 7022 PetscScalar *bufa; 7023 Mat P_oth; 7024 7025 /* may take advantage of merging product->B */ 7026 Mat Bloc; /* B-local by merging diag and off-diag */ 7027 7028 /* cusparse does not have support to split between symbolic and numeric phases. 7029 When api_user is true, we don't need to update the numerical values 7030 of the temporary storage */ 7031 PetscBool reusesym; 7032 7033 /* support for COO values insertion */ 7034 PetscScalar *coo_v, *coo_w; /* store on-process and off-process COO scalars, and used as MPI recv/send buffers respectively */ 7035 PetscInt **own; /* own[i] points to address of on-process COO indices for Mat mp[i] */ 7036 PetscInt **off; /* off[i] points to address of off-process COO indices for Mat mp[i] */ 7037 PetscBool hasoffproc; /* if true, have off-process values insertion (i.e. AtB or PtAP) */ 7038 PetscSF sf; /* used for non-local values insertion and memory malloc */ 7039 PetscMemType mtype; 7040 7041 /* customization */ 7042 PetscBool abmerge; 7043 PetscBool P_oth_bind; 7044 } MatMatMPIAIJBACKEND; 7045 7046 static PetscErrorCode MatDestroy_MatMatMPIAIJBACKEND(void *data) 7047 { 7048 MatMatMPIAIJBACKEND *mmdata = (MatMatMPIAIJBACKEND *)data; 7049 PetscInt i; 7050 7051 PetscFunctionBegin; 7052 PetscCall(PetscFree2(mmdata->startsj_s, mmdata->startsj_r)); 7053 PetscCall(PetscFree(mmdata->bufa)); 7054 PetscCall(PetscSFFree(mmdata->sf, mmdata->mtype, mmdata->coo_v)); 7055 PetscCall(PetscSFFree(mmdata->sf, mmdata->mtype, mmdata->coo_w)); 7056 PetscCall(MatDestroy(&mmdata->P_oth)); 7057 PetscCall(MatDestroy(&mmdata->Bloc)); 7058 PetscCall(PetscSFDestroy(&mmdata->sf)); 7059 for (i = 0; i < mmdata->cp; i++) PetscCall(MatDestroy(&mmdata->mp[i])); 7060 PetscCall(PetscFree2(mmdata->mp, mmdata->mptmp)); 7061 PetscCall(PetscFree(mmdata->own[0])); 7062 PetscCall(PetscFree(mmdata->own)); 7063 PetscCall(PetscFree(mmdata->off[0])); 7064 PetscCall(PetscFree(mmdata->off)); 7065 PetscCall(PetscFree(mmdata)); 7066 PetscFunctionReturn(PETSC_SUCCESS); 7067 } 7068 7069 /* Copy selected n entries with indices in idx[] of A to v[]. 7070 If idx is NULL, copy the whole data array of A to v[] 7071 */ 7072 static PetscErrorCode MatSeqAIJCopySubArray(Mat A, PetscInt n, const PetscInt idx[], PetscScalar v[]) 7073 { 7074 PetscErrorCode (*f)(Mat, PetscInt, const PetscInt[], PetscScalar[]); 7075 7076 PetscFunctionBegin; 7077 PetscCall(PetscObjectQueryFunction((PetscObject)A, "MatSeqAIJCopySubArray_C", &f)); 7078 if (f) { 7079 PetscCall((*f)(A, n, idx, v)); 7080 } else { 7081 const PetscScalar *vv; 7082 7083 PetscCall(MatSeqAIJGetArrayRead(A, &vv)); 7084 if (n && idx) { 7085 PetscScalar *w = v; 7086 const PetscInt *oi = idx; 7087 PetscInt j; 7088 7089 for (j = 0; j < n; j++) *w++ = vv[*oi++]; 7090 } else { 7091 PetscCall(PetscArraycpy(v, vv, n)); 7092 } 7093 PetscCall(MatSeqAIJRestoreArrayRead(A, &vv)); 7094 } 7095 PetscFunctionReturn(PETSC_SUCCESS); 7096 } 7097 7098 static PetscErrorCode MatProductNumeric_MPIAIJBACKEND(Mat C) 7099 { 7100 MatMatMPIAIJBACKEND *mmdata; 7101 PetscInt i, n_d, n_o; 7102 7103 PetscFunctionBegin; 7104 MatCheckProduct(C, 1); 7105 PetscCheck(C->product->data, PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Product data empty"); 7106 mmdata = (MatMatMPIAIJBACKEND *)C->product->data; 7107 if (!mmdata->reusesym) { /* update temporary matrices */ 7108 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)); 7109 if (mmdata->Bloc) PetscCall(MatMPIAIJGetLocalMatMerge(C->product->B, MAT_REUSE_MATRIX, NULL, &mmdata->Bloc)); 7110 } 7111 mmdata->reusesym = PETSC_FALSE; 7112 7113 for (i = 0; i < mmdata->cp; i++) { 7114 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]); 7115 PetscCall((*mmdata->mp[i]->ops->productnumeric)(mmdata->mp[i])); 7116 } 7117 for (i = 0, n_d = 0, n_o = 0; i < mmdata->cp; i++) { 7118 PetscInt noff; 7119 7120 PetscCall(PetscIntCast(mmdata->off[i + 1] - mmdata->off[i], &noff)); 7121 if (mmdata->mptmp[i]) continue; 7122 if (noff) { 7123 PetscInt nown; 7124 7125 PetscCall(PetscIntCast(mmdata->own[i + 1] - mmdata->own[i], &nown)); 7126 PetscCall(MatSeqAIJCopySubArray(mmdata->mp[i], noff, mmdata->off[i], mmdata->coo_w + n_o)); 7127 PetscCall(MatSeqAIJCopySubArray(mmdata->mp[i], nown, mmdata->own[i], mmdata->coo_v + n_d)); 7128 n_o += noff; 7129 n_d += nown; 7130 } else { 7131 Mat_SeqAIJ *mm = (Mat_SeqAIJ *)mmdata->mp[i]->data; 7132 7133 PetscCall(MatSeqAIJCopySubArray(mmdata->mp[i], mm->nz, NULL, mmdata->coo_v + n_d)); 7134 n_d += mm->nz; 7135 } 7136 } 7137 if (mmdata->hasoffproc) { /* offprocess insertion */ 7138 PetscCall(PetscSFGatherBegin(mmdata->sf, MPIU_SCALAR, mmdata->coo_w, mmdata->coo_v + n_d)); 7139 PetscCall(PetscSFGatherEnd(mmdata->sf, MPIU_SCALAR, mmdata->coo_w, mmdata->coo_v + n_d)); 7140 } 7141 PetscCall(MatSetValuesCOO(C, mmdata->coo_v, INSERT_VALUES)); 7142 PetscFunctionReturn(PETSC_SUCCESS); 7143 } 7144 7145 /* Support for Pt * A, A * P, or Pt * A * P */ 7146 #define MAX_NUMBER_INTERMEDIATE 4 7147 PetscErrorCode MatProductSymbolic_MPIAIJBACKEND(Mat C) 7148 { 7149 Mat_Product *product = C->product; 7150 Mat A, P, mp[MAX_NUMBER_INTERMEDIATE]; /* A, P and a series of intermediate matrices */ 7151 Mat_MPIAIJ *a, *p; 7152 MatMatMPIAIJBACKEND *mmdata; 7153 ISLocalToGlobalMapping P_oth_l2g = NULL; 7154 IS glob = NULL; 7155 const char *prefix; 7156 char pprefix[256]; 7157 const PetscInt *globidx, *P_oth_idx; 7158 PetscInt i, j, cp, m, n, M, N, *coo_i, *coo_j; 7159 PetscCount ncoo, ncoo_d, ncoo_o, ncoo_oown; 7160 PetscInt cmapt[MAX_NUMBER_INTERMEDIATE], rmapt[MAX_NUMBER_INTERMEDIATE]; /* col/row map type for each Mat in mp[]. */ 7161 /* type-0: consecutive, start from 0; type-1: consecutive with */ 7162 /* a base offset; type-2: sparse with a local to global map table */ 7163 const PetscInt *cmapa[MAX_NUMBER_INTERMEDIATE], *rmapa[MAX_NUMBER_INTERMEDIATE]; /* col/row local to global map array (table) for type-2 map type */ 7164 7165 MatProductType ptype; 7166 PetscBool mptmp[MAX_NUMBER_INTERMEDIATE], hasoffproc = PETSC_FALSE, iscuda, iship, iskokk; 7167 PetscMPIInt size; 7168 7169 PetscFunctionBegin; 7170 MatCheckProduct(C, 1); 7171 PetscCheck(!product->data, PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Product data not empty"); 7172 ptype = product->type; 7173 if (product->A->symmetric == PETSC_BOOL3_TRUE && ptype == MATPRODUCT_AtB) { 7174 ptype = MATPRODUCT_AB; 7175 product->symbolic_used_the_fact_A_is_symmetric = PETSC_TRUE; 7176 } 7177 switch (ptype) { 7178 case MATPRODUCT_AB: 7179 A = product->A; 7180 P = product->B; 7181 m = A->rmap->n; 7182 n = P->cmap->n; 7183 M = A->rmap->N; 7184 N = P->cmap->N; 7185 hasoffproc = PETSC_FALSE; /* will not scatter mat product values to other processes */ 7186 break; 7187 case MATPRODUCT_AtB: 7188 P = product->A; 7189 A = product->B; 7190 m = P->cmap->n; 7191 n = A->cmap->n; 7192 M = P->cmap->N; 7193 N = A->cmap->N; 7194 hasoffproc = PETSC_TRUE; 7195 break; 7196 case MATPRODUCT_PtAP: 7197 A = product->A; 7198 P = product->B; 7199 m = P->cmap->n; 7200 n = P->cmap->n; 7201 M = P->cmap->N; 7202 N = P->cmap->N; 7203 hasoffproc = PETSC_TRUE; 7204 break; 7205 default: 7206 SETERRQ(PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Not for product type %s", MatProductTypes[ptype]); 7207 } 7208 PetscCallMPI(MPI_Comm_size(PetscObjectComm((PetscObject)C), &size)); 7209 if (size == 1) hasoffproc = PETSC_FALSE; 7210 7211 /* defaults */ 7212 for (i = 0; i < MAX_NUMBER_INTERMEDIATE; i++) { 7213 mp[i] = NULL; 7214 mptmp[i] = PETSC_FALSE; 7215 rmapt[i] = -1; 7216 cmapt[i] = -1; 7217 rmapa[i] = NULL; 7218 cmapa[i] = NULL; 7219 } 7220 7221 /* customization */ 7222 PetscCall(PetscNew(&mmdata)); 7223 mmdata->reusesym = product->api_user; 7224 if (ptype == MATPRODUCT_AB) { 7225 if (product->api_user) { 7226 PetscOptionsBegin(PetscObjectComm((PetscObject)C), ((PetscObject)C)->prefix, "MatMatMult", "Mat"); 7227 PetscCall(PetscOptionsBool("-matmatmult_backend_mergeB", "Merge product->B local matrices", "MatMatMult", mmdata->abmerge, &mmdata->abmerge, NULL)); 7228 PetscCall(PetscOptionsBool("-matmatmult_backend_pothbind", "Bind P_oth to CPU", "MatBindToCPU", mmdata->P_oth_bind, &mmdata->P_oth_bind, NULL)); 7229 PetscOptionsEnd(); 7230 } else { 7231 PetscOptionsBegin(PetscObjectComm((PetscObject)C), ((PetscObject)C)->prefix, "MatProduct_AB", "Mat"); 7232 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_mergeB", "Merge product->B local matrices", "MatMatMult", mmdata->abmerge, &mmdata->abmerge, NULL)); 7233 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_pothbind", "Bind P_oth to CPU", "MatBindToCPU", mmdata->P_oth_bind, &mmdata->P_oth_bind, NULL)); 7234 PetscOptionsEnd(); 7235 } 7236 } else if (ptype == MATPRODUCT_PtAP) { 7237 if (product->api_user) { 7238 PetscOptionsBegin(PetscObjectComm((PetscObject)C), ((PetscObject)C)->prefix, "MatPtAP", "Mat"); 7239 PetscCall(PetscOptionsBool("-matptap_backend_pothbind", "Bind P_oth to CPU", "MatBindToCPU", mmdata->P_oth_bind, &mmdata->P_oth_bind, NULL)); 7240 PetscOptionsEnd(); 7241 } else { 7242 PetscOptionsBegin(PetscObjectComm((PetscObject)C), ((PetscObject)C)->prefix, "MatProduct_PtAP", "Mat"); 7243 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_pothbind", "Bind P_oth to CPU", "MatBindToCPU", mmdata->P_oth_bind, &mmdata->P_oth_bind, NULL)); 7244 PetscOptionsEnd(); 7245 } 7246 } 7247 a = (Mat_MPIAIJ *)A->data; 7248 p = (Mat_MPIAIJ *)P->data; 7249 PetscCall(MatSetSizes(C, m, n, M, N)); 7250 PetscCall(PetscLayoutSetUp(C->rmap)); 7251 PetscCall(PetscLayoutSetUp(C->cmap)); 7252 PetscCall(MatSetType(C, ((PetscObject)A)->type_name)); 7253 PetscCall(MatGetOptionsPrefix(C, &prefix)); 7254 7255 cp = 0; 7256 switch (ptype) { 7257 case MATPRODUCT_AB: /* A * P */ 7258 PetscCall(MatGetBrowsOfAoCols_MPIAIJ(A, P, MAT_INITIAL_MATRIX, &mmdata->startsj_s, &mmdata->startsj_r, &mmdata->bufa, &mmdata->P_oth)); 7259 7260 /* A_diag * P_local (merged or not) */ 7261 if (mmdata->abmerge) { /* P's diagonal and off-diag blocks are merged to one matrix, then multiplied by A_diag */ 7262 /* P is product->B */ 7263 PetscCall(MatMPIAIJGetLocalMatMerge(P, MAT_INITIAL_MATRIX, &glob, &mmdata->Bloc)); 7264 PetscCall(MatProductCreate(a->A, mmdata->Bloc, NULL, &mp[cp])); 7265 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7266 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7267 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7268 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7269 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7270 mp[cp]->product->api_user = product->api_user; 7271 PetscCall(MatProductSetFromOptions(mp[cp])); 7272 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7273 PetscCall(ISGetIndices(glob, &globidx)); 7274 rmapt[cp] = 1; 7275 cmapt[cp] = 2; 7276 cmapa[cp] = globidx; 7277 mptmp[cp] = PETSC_FALSE; 7278 cp++; 7279 } else { /* A_diag * P_diag and A_diag * P_off */ 7280 PetscCall(MatProductCreate(a->A, p->A, NULL, &mp[cp])); 7281 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7282 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7283 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7284 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7285 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7286 mp[cp]->product->api_user = product->api_user; 7287 PetscCall(MatProductSetFromOptions(mp[cp])); 7288 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7289 rmapt[cp] = 1; 7290 cmapt[cp] = 1; 7291 mptmp[cp] = PETSC_FALSE; 7292 cp++; 7293 PetscCall(MatProductCreate(a->A, p->B, NULL, &mp[cp])); 7294 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7295 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7296 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7297 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7298 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7299 mp[cp]->product->api_user = product->api_user; 7300 PetscCall(MatProductSetFromOptions(mp[cp])); 7301 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7302 rmapt[cp] = 1; 7303 cmapt[cp] = 2; 7304 cmapa[cp] = p->garray; 7305 mptmp[cp] = PETSC_FALSE; 7306 cp++; 7307 } 7308 7309 /* A_off * P_other */ 7310 if (mmdata->P_oth) { 7311 PetscCall(MatSeqAIJCompactOutExtraColumns_SeqAIJ(mmdata->P_oth, &P_oth_l2g)); /* make P_oth use local col ids */ 7312 PetscCall(ISLocalToGlobalMappingGetIndices(P_oth_l2g, &P_oth_idx)); 7313 PetscCall(MatSetType(mmdata->P_oth, ((PetscObject)a->B)->type_name)); 7314 PetscCall(MatBindToCPU(mmdata->P_oth, mmdata->P_oth_bind)); 7315 PetscCall(MatProductCreate(a->B, mmdata->P_oth, NULL, &mp[cp])); 7316 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7317 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7318 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7319 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7320 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7321 mp[cp]->product->api_user = product->api_user; 7322 PetscCall(MatProductSetFromOptions(mp[cp])); 7323 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7324 rmapt[cp] = 1; 7325 cmapt[cp] = 2; 7326 cmapa[cp] = P_oth_idx; 7327 mptmp[cp] = PETSC_FALSE; 7328 cp++; 7329 } 7330 break; 7331 7332 case MATPRODUCT_AtB: /* (P^t * A): P_diag * A_loc + P_off * A_loc */ 7333 /* A is product->B */ 7334 PetscCall(MatMPIAIJGetLocalMatMerge(A, MAT_INITIAL_MATRIX, &glob, &mmdata->Bloc)); 7335 if (A == P) { /* when A==P, we can take advantage of the already merged mmdata->Bloc */ 7336 PetscCall(MatProductCreate(mmdata->Bloc, mmdata->Bloc, NULL, &mp[cp])); 7337 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AtB)); 7338 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7339 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7340 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7341 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7342 mp[cp]->product->api_user = product->api_user; 7343 PetscCall(MatProductSetFromOptions(mp[cp])); 7344 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7345 PetscCall(ISGetIndices(glob, &globidx)); 7346 rmapt[cp] = 2; 7347 rmapa[cp] = globidx; 7348 cmapt[cp] = 2; 7349 cmapa[cp] = globidx; 7350 mptmp[cp] = PETSC_FALSE; 7351 cp++; 7352 } else { 7353 PetscCall(MatProductCreate(p->A, mmdata->Bloc, NULL, &mp[cp])); 7354 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AtB)); 7355 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7356 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7357 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7358 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7359 mp[cp]->product->api_user = product->api_user; 7360 PetscCall(MatProductSetFromOptions(mp[cp])); 7361 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7362 PetscCall(ISGetIndices(glob, &globidx)); 7363 rmapt[cp] = 1; 7364 cmapt[cp] = 2; 7365 cmapa[cp] = globidx; 7366 mptmp[cp] = PETSC_FALSE; 7367 cp++; 7368 PetscCall(MatProductCreate(p->B, mmdata->Bloc, NULL, &mp[cp])); 7369 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AtB)); 7370 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7371 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7372 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7373 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7374 mp[cp]->product->api_user = product->api_user; 7375 PetscCall(MatProductSetFromOptions(mp[cp])); 7376 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7377 rmapt[cp] = 2; 7378 rmapa[cp] = p->garray; 7379 cmapt[cp] = 2; 7380 cmapa[cp] = globidx; 7381 mptmp[cp] = PETSC_FALSE; 7382 cp++; 7383 } 7384 break; 7385 case MATPRODUCT_PtAP: 7386 PetscCall(MatGetBrowsOfAoCols_MPIAIJ(A, P, MAT_INITIAL_MATRIX, &mmdata->startsj_s, &mmdata->startsj_r, &mmdata->bufa, &mmdata->P_oth)); 7387 /* P is product->B */ 7388 PetscCall(MatMPIAIJGetLocalMatMerge(P, MAT_INITIAL_MATRIX, &glob, &mmdata->Bloc)); 7389 PetscCall(MatProductCreate(a->A, mmdata->Bloc, NULL, &mp[cp])); 7390 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_PtAP)); 7391 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7392 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7393 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7394 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7395 mp[cp]->product->api_user = product->api_user; 7396 PetscCall(MatProductSetFromOptions(mp[cp])); 7397 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7398 PetscCall(ISGetIndices(glob, &globidx)); 7399 rmapt[cp] = 2; 7400 rmapa[cp] = globidx; 7401 cmapt[cp] = 2; 7402 cmapa[cp] = globidx; 7403 mptmp[cp] = PETSC_FALSE; 7404 cp++; 7405 if (mmdata->P_oth) { 7406 PetscCall(MatSeqAIJCompactOutExtraColumns_SeqAIJ(mmdata->P_oth, &P_oth_l2g)); 7407 PetscCall(ISLocalToGlobalMappingGetIndices(P_oth_l2g, &P_oth_idx)); 7408 PetscCall(MatSetType(mmdata->P_oth, ((PetscObject)a->B)->type_name)); 7409 PetscCall(MatBindToCPU(mmdata->P_oth, mmdata->P_oth_bind)); 7410 PetscCall(MatProductCreate(a->B, mmdata->P_oth, NULL, &mp[cp])); 7411 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AB)); 7412 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7413 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7414 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7415 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7416 mp[cp]->product->api_user = product->api_user; 7417 PetscCall(MatProductSetFromOptions(mp[cp])); 7418 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7419 mptmp[cp] = PETSC_TRUE; 7420 cp++; 7421 PetscCall(MatProductCreate(mmdata->Bloc, mp[1], NULL, &mp[cp])); 7422 PetscCall(MatProductSetType(mp[cp], MATPRODUCT_AtB)); 7423 PetscCall(MatProductSetFill(mp[cp], product->fill)); 7424 PetscCall(PetscSNPrintf(pprefix, sizeof(pprefix), "backend_p%" PetscInt_FMT "_", cp)); 7425 PetscCall(MatSetOptionsPrefix(mp[cp], prefix)); 7426 PetscCall(MatAppendOptionsPrefix(mp[cp], pprefix)); 7427 mp[cp]->product->api_user = product->api_user; 7428 PetscCall(MatProductSetFromOptions(mp[cp])); 7429 PetscCall((*mp[cp]->ops->productsymbolic)(mp[cp])); 7430 rmapt[cp] = 2; 7431 rmapa[cp] = globidx; 7432 cmapt[cp] = 2; 7433 cmapa[cp] = P_oth_idx; 7434 mptmp[cp] = PETSC_FALSE; 7435 cp++; 7436 } 7437 break; 7438 default: 7439 SETERRQ(PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Not for product type %s", MatProductTypes[ptype]); 7440 } 7441 /* sanity check */ 7442 if (size > 1) 7443 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); 7444 7445 PetscCall(PetscMalloc2(cp, &mmdata->mp, cp, &mmdata->mptmp)); 7446 for (i = 0; i < cp; i++) { 7447 mmdata->mp[i] = mp[i]; 7448 mmdata->mptmp[i] = mptmp[i]; 7449 } 7450 mmdata->cp = cp; 7451 C->product->data = mmdata; 7452 C->product->destroy = MatDestroy_MatMatMPIAIJBACKEND; 7453 C->ops->productnumeric = MatProductNumeric_MPIAIJBACKEND; 7454 7455 /* memory type */ 7456 mmdata->mtype = PETSC_MEMTYPE_HOST; 7457 PetscCall(PetscObjectTypeCompareAny((PetscObject)C, &iscuda, MATSEQAIJCUSPARSE, MATMPIAIJCUSPARSE, "")); 7458 PetscCall(PetscObjectTypeCompareAny((PetscObject)C, &iship, MATSEQAIJHIPSPARSE, MATMPIAIJHIPSPARSE, "")); 7459 PetscCall(PetscObjectTypeCompareAny((PetscObject)C, &iskokk, MATSEQAIJKOKKOS, MATMPIAIJKOKKOS, "")); 7460 if (iscuda) mmdata->mtype = PETSC_MEMTYPE_CUDA; 7461 else if (iship) mmdata->mtype = PETSC_MEMTYPE_HIP; 7462 else if (iskokk) mmdata->mtype = PETSC_MEMTYPE_KOKKOS; 7463 7464 /* prepare coo coordinates for values insertion */ 7465 7466 /* count total nonzeros of those intermediate seqaij Mats 7467 ncoo_d: # of nonzeros of matrices that do not have offproc entries 7468 ncoo_o: # of nonzeros (of matrices that might have offproc entries) that will be inserted to remote procs 7469 ncoo_oown: # of nonzeros (of matrices that might have offproc entries) that will be inserted locally 7470 */ 7471 for (cp = 0, ncoo_d = 0, ncoo_o = 0, ncoo_oown = 0; cp < mmdata->cp; cp++) { 7472 Mat_SeqAIJ *mm = (Mat_SeqAIJ *)mp[cp]->data; 7473 if (mptmp[cp]) continue; 7474 if (rmapt[cp] == 2 && hasoffproc) { /* the rows need to be scatter to all processes (might include self) */ 7475 const PetscInt *rmap = rmapa[cp]; 7476 const PetscInt mr = mp[cp]->rmap->n; 7477 const PetscInt rs = C->rmap->rstart; 7478 const PetscInt re = C->rmap->rend; 7479 const PetscInt *ii = mm->i; 7480 for (i = 0; i < mr; i++) { 7481 const PetscInt gr = rmap[i]; 7482 const PetscInt nz = ii[i + 1] - ii[i]; 7483 if (gr < rs || gr >= re) ncoo_o += nz; /* this row is offproc */ 7484 else ncoo_oown += nz; /* this row is local */ 7485 } 7486 } else ncoo_d += mm->nz; 7487 } 7488 7489 /* 7490 ncoo: total number of nonzeros (including those inserted by remote procs) belonging to this proc 7491 7492 ncoo = ncoo_d + ncoo_oown + ncoo2, which ncoo2 is number of nonzeros inserted to me by other procs. 7493 7494 off[0] points to a big index array, which is shared by off[1,2,...]. Similarly, for own[0]. 7495 7496 off[p]: points to the segment for matrix mp[p], storing location of nonzeros that mp[p] will insert to others 7497 own[p]: points to the segment for matrix mp[p], storing location of nonzeros that mp[p] will insert locally 7498 so, off[p+1]-off[p] is the number of nonzeros that mp[p] will send to others. 7499 7500 coo_i/j/v[]: [ncoo] row/col/val of nonzeros belonging to this proc. 7501 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. 7502 */ 7503 PetscCall(PetscCalloc1(mmdata->cp + 1, &mmdata->off)); /* +1 to make a csr-like data structure */ 7504 PetscCall(PetscCalloc1(mmdata->cp + 1, &mmdata->own)); 7505 7506 /* gather (i,j) of nonzeros inserted by remote procs */ 7507 if (hasoffproc) { 7508 PetscSF msf; 7509 PetscInt ncoo2, *coo_i2, *coo_j2; 7510 7511 PetscCall(PetscMalloc1(ncoo_o, &mmdata->off[0])); 7512 PetscCall(PetscMalloc1(ncoo_oown, &mmdata->own[0])); 7513 PetscCall(PetscMalloc2(ncoo_o, &coo_i, ncoo_o, &coo_j)); /* to collect (i,j) of entries to be sent to others */ 7514 7515 for (cp = 0, ncoo_o = 0; cp < mmdata->cp; cp++) { 7516 Mat_SeqAIJ *mm = (Mat_SeqAIJ *)mp[cp]->data; 7517 PetscInt *idxoff = mmdata->off[cp]; 7518 PetscInt *idxown = mmdata->own[cp]; 7519 if (!mptmp[cp] && rmapt[cp] == 2) { /* row map is sparse */ 7520 const PetscInt *rmap = rmapa[cp]; 7521 const PetscInt *cmap = cmapa[cp]; 7522 const PetscInt *ii = mm->i; 7523 PetscInt *coi = coo_i + ncoo_o; 7524 PetscInt *coj = coo_j + ncoo_o; 7525 const PetscInt mr = mp[cp]->rmap->n; 7526 const PetscInt rs = C->rmap->rstart; 7527 const PetscInt re = C->rmap->rend; 7528 const PetscInt cs = C->cmap->rstart; 7529 for (i = 0; i < mr; i++) { 7530 const PetscInt *jj = mm->j + ii[i]; 7531 const PetscInt gr = rmap[i]; 7532 const PetscInt nz = ii[i + 1] - ii[i]; 7533 if (gr < rs || gr >= re) { /* this is an offproc row */ 7534 for (j = ii[i]; j < ii[i + 1]; j++) { 7535 *coi++ = gr; 7536 *idxoff++ = j; 7537 } 7538 if (!cmapt[cp]) { /* already global */ 7539 for (j = 0; j < nz; j++) *coj++ = jj[j]; 7540 } else if (cmapt[cp] == 1) { /* local to global for owned columns of C */ 7541 for (j = 0; j < nz; j++) *coj++ = jj[j] + cs; 7542 } else { /* offdiag */ 7543 for (j = 0; j < nz; j++) *coj++ = cmap[jj[j]]; 7544 } 7545 ncoo_o += nz; 7546 } else { /* this is a local row */ 7547 for (j = ii[i]; j < ii[i + 1]; j++) *idxown++ = j; 7548 } 7549 } 7550 } 7551 mmdata->off[cp + 1] = idxoff; 7552 mmdata->own[cp + 1] = idxown; 7553 } 7554 7555 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)C), &mmdata->sf)); 7556 PetscInt incoo_o; 7557 PetscCall(PetscIntCast(ncoo_o, &incoo_o)); 7558 PetscCall(PetscSFSetGraphLayout(mmdata->sf, C->rmap, incoo_o /*nleaves*/, NULL /*ilocal*/, PETSC_OWN_POINTER, coo_i)); 7559 PetscCall(PetscSFGetMultiSF(mmdata->sf, &msf)); 7560 PetscCall(PetscSFGetGraph(msf, &ncoo2 /*nroots*/, NULL, NULL, NULL)); 7561 ncoo = ncoo_d + ncoo_oown + ncoo2; 7562 PetscCall(PetscMalloc2(ncoo, &coo_i2, ncoo, &coo_j2)); 7563 PetscCall(PetscSFGatherBegin(mmdata->sf, MPIU_INT, coo_i, coo_i2 + ncoo_d + ncoo_oown)); /* put (i,j) of remote nonzeros at back */ 7564 PetscCall(PetscSFGatherEnd(mmdata->sf, MPIU_INT, coo_i, coo_i2 + ncoo_d + ncoo_oown)); 7565 PetscCall(PetscSFGatherBegin(mmdata->sf, MPIU_INT, coo_j, coo_j2 + ncoo_d + ncoo_oown)); 7566 PetscCall(PetscSFGatherEnd(mmdata->sf, MPIU_INT, coo_j, coo_j2 + ncoo_d + ncoo_oown)); 7567 PetscCall(PetscFree2(coo_i, coo_j)); 7568 /* allocate MPI send buffer to collect nonzero values to be sent to remote procs */ 7569 PetscCall(PetscSFMalloc(mmdata->sf, mmdata->mtype, ncoo_o * sizeof(PetscScalar), (void **)&mmdata->coo_w)); 7570 coo_i = coo_i2; 7571 coo_j = coo_j2; 7572 } else { /* no offproc values insertion */ 7573 ncoo = ncoo_d; 7574 PetscCall(PetscMalloc2(ncoo, &coo_i, ncoo, &coo_j)); 7575 7576 PetscCall(PetscSFCreate(PetscObjectComm((PetscObject)C), &mmdata->sf)); 7577 PetscCall(PetscSFSetGraph(mmdata->sf, 0, 0, NULL, PETSC_OWN_POINTER, NULL, PETSC_OWN_POINTER)); 7578 PetscCall(PetscSFSetUp(mmdata->sf)); 7579 } 7580 mmdata->hasoffproc = hasoffproc; 7581 7582 /* gather (i,j) of nonzeros inserted locally */ 7583 for (cp = 0, ncoo_d = 0; cp < mmdata->cp; cp++) { 7584 Mat_SeqAIJ *mm = (Mat_SeqAIJ *)mp[cp]->data; 7585 PetscInt *coi = coo_i + ncoo_d; 7586 PetscInt *coj = coo_j + ncoo_d; 7587 const PetscInt *jj = mm->j; 7588 const PetscInt *ii = mm->i; 7589 const PetscInt *cmap = cmapa[cp]; 7590 const PetscInt *rmap = rmapa[cp]; 7591 const PetscInt mr = mp[cp]->rmap->n; 7592 const PetscInt rs = C->rmap->rstart; 7593 const PetscInt re = C->rmap->rend; 7594 const PetscInt cs = C->cmap->rstart; 7595 7596 if (mptmp[cp]) continue; 7597 if (rmapt[cp] == 1) { /* consecutive rows */ 7598 /* fill coo_i */ 7599 for (i = 0; i < mr; i++) { 7600 const PetscInt gr = i + rs; 7601 for (j = ii[i]; j < ii[i + 1]; j++) coi[j] = gr; 7602 } 7603 /* fill coo_j */ 7604 if (!cmapt[cp]) { /* type-0, already global */ 7605 PetscCall(PetscArraycpy(coj, jj, mm->nz)); 7606 } else if (cmapt[cp] == 1) { /* type-1, local to global for consecutive columns of C */ 7607 for (j = 0; j < mm->nz; j++) coj[j] = jj[j] + cs; /* lid + col start */ 7608 } else { /* type-2, local to global for sparse columns */ 7609 for (j = 0; j < mm->nz; j++) coj[j] = cmap[jj[j]]; 7610 } 7611 ncoo_d += mm->nz; 7612 } else if (rmapt[cp] == 2) { /* sparse rows */ 7613 for (i = 0; i < mr; i++) { 7614 const PetscInt *jj = mm->j + ii[i]; 7615 const PetscInt gr = rmap[i]; 7616 const PetscInt nz = ii[i + 1] - ii[i]; 7617 if (gr >= rs && gr < re) { /* local rows */ 7618 for (j = ii[i]; j < ii[i + 1]; j++) *coi++ = gr; 7619 if (!cmapt[cp]) { /* type-0, already global */ 7620 for (j = 0; j < nz; j++) *coj++ = jj[j]; 7621 } else if (cmapt[cp] == 1) { /* local to global for owned columns of C */ 7622 for (j = 0; j < nz; j++) *coj++ = jj[j] + cs; 7623 } else { /* type-2, local to global for sparse columns */ 7624 for (j = 0; j < nz; j++) *coj++ = cmap[jj[j]]; 7625 } 7626 ncoo_d += nz; 7627 } 7628 } 7629 } 7630 } 7631 if (glob) PetscCall(ISRestoreIndices(glob, &globidx)); 7632 PetscCall(ISDestroy(&glob)); 7633 if (P_oth_l2g) PetscCall(ISLocalToGlobalMappingRestoreIndices(P_oth_l2g, &P_oth_idx)); 7634 PetscCall(ISLocalToGlobalMappingDestroy(&P_oth_l2g)); 7635 /* allocate an array to store all nonzeros (inserted locally or remotely) belonging to this proc */ 7636 PetscCall(PetscSFMalloc(mmdata->sf, mmdata->mtype, ncoo * sizeof(PetscScalar), (void **)&mmdata->coo_v)); 7637 7638 /* set block sizes */ 7639 A = product->A; 7640 P = product->B; 7641 switch (ptype) { 7642 case MATPRODUCT_PtAP: 7643 PetscCall(MatSetBlockSizes(C, P->cmap->bs, P->cmap->bs)); 7644 break; 7645 case MATPRODUCT_RARt: 7646 PetscCall(MatSetBlockSizes(C, P->rmap->bs, P->rmap->bs)); 7647 break; 7648 case MATPRODUCT_ABC: 7649 PetscCall(MatSetBlockSizesFromMats(C, A, product->C)); 7650 break; 7651 case MATPRODUCT_AB: 7652 PetscCall(MatSetBlockSizesFromMats(C, A, P)); 7653 break; 7654 case MATPRODUCT_AtB: 7655 PetscCall(MatSetBlockSizes(C, A->cmap->bs, P->cmap->bs)); 7656 break; 7657 case MATPRODUCT_ABt: 7658 PetscCall(MatSetBlockSizes(C, A->rmap->bs, P->rmap->bs)); 7659 break; 7660 default: 7661 SETERRQ(PetscObjectComm((PetscObject)C), PETSC_ERR_PLIB, "Not for ProductType %s", MatProductTypes[ptype]); 7662 } 7663 7664 /* preallocate with COO data */ 7665 PetscCall(MatSetPreallocationCOO(C, ncoo, coo_i, coo_j)); 7666 PetscCall(PetscFree2(coo_i, coo_j)); 7667 PetscFunctionReturn(PETSC_SUCCESS); 7668 } 7669 7670 PetscErrorCode MatProductSetFromOptions_MPIAIJBACKEND(Mat mat) 7671 { 7672 Mat_Product *product = mat->product; 7673 #if defined(PETSC_HAVE_DEVICE) 7674 PetscBool match = PETSC_FALSE; 7675 PetscBool usecpu = PETSC_FALSE; 7676 #else 7677 PetscBool match = PETSC_TRUE; 7678 #endif 7679 7680 PetscFunctionBegin; 7681 MatCheckProduct(mat, 1); 7682 #if defined(PETSC_HAVE_DEVICE) 7683 if (!product->A->boundtocpu && !product->B->boundtocpu) PetscCall(PetscObjectTypeCompare((PetscObject)product->B, ((PetscObject)product->A)->type_name, &match)); 7684 if (match) { /* we can always fallback to the CPU if requested */ 7685 switch (product->type) { 7686 case MATPRODUCT_AB: 7687 if (product->api_user) { 7688 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatMatMult", "Mat"); 7689 PetscCall(PetscOptionsBool("-matmatmult_backend_cpu", "Use CPU code", "MatMatMult", usecpu, &usecpu, NULL)); 7690 PetscOptionsEnd(); 7691 } else { 7692 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatProduct_AB", "Mat"); 7693 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_cpu", "Use CPU code", "MatMatMult", usecpu, &usecpu, NULL)); 7694 PetscOptionsEnd(); 7695 } 7696 break; 7697 case MATPRODUCT_AtB: 7698 if (product->api_user) { 7699 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatTransposeMatMult", "Mat"); 7700 PetscCall(PetscOptionsBool("-mattransposematmult_backend_cpu", "Use CPU code", "MatTransposeMatMult", usecpu, &usecpu, NULL)); 7701 PetscOptionsEnd(); 7702 } else { 7703 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatProduct_AtB", "Mat"); 7704 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_cpu", "Use CPU code", "MatTransposeMatMult", usecpu, &usecpu, NULL)); 7705 PetscOptionsEnd(); 7706 } 7707 break; 7708 case MATPRODUCT_PtAP: 7709 if (product->api_user) { 7710 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatPtAP", "Mat"); 7711 PetscCall(PetscOptionsBool("-matptap_backend_cpu", "Use CPU code", "MatPtAP", usecpu, &usecpu, NULL)); 7712 PetscOptionsEnd(); 7713 } else { 7714 PetscOptionsBegin(PetscObjectComm((PetscObject)mat), ((PetscObject)mat)->prefix, "MatProduct_PtAP", "Mat"); 7715 PetscCall(PetscOptionsBool("-mat_product_algorithm_backend_cpu", "Use CPU code", "MatPtAP", usecpu, &usecpu, NULL)); 7716 PetscOptionsEnd(); 7717 } 7718 break; 7719 default: 7720 break; 7721 } 7722 match = (PetscBool)!usecpu; 7723 } 7724 #endif 7725 if (match) { 7726 switch (product->type) { 7727 case MATPRODUCT_AB: 7728 case MATPRODUCT_AtB: 7729 case MATPRODUCT_PtAP: 7730 mat->ops->productsymbolic = MatProductSymbolic_MPIAIJBACKEND; 7731 break; 7732 default: 7733 break; 7734 } 7735 } 7736 /* fallback to MPIAIJ ops */ 7737 if (!mat->ops->productsymbolic) PetscCall(MatProductSetFromOptions_MPIAIJ(mat)); 7738 PetscFunctionReturn(PETSC_SUCCESS); 7739 } 7740 7741 /* 7742 Produces a set of block column indices of the matrix row, one for each block represented in the original row 7743 7744 n - the number of block indices in cc[] 7745 cc - the block indices (must be large enough to contain the indices) 7746 */ 7747 static inline PetscErrorCode MatCollapseRow(Mat Amat, PetscInt row, PetscInt bs, PetscInt *n, PetscInt *cc) 7748 { 7749 PetscInt cnt = -1, nidx, j; 7750 const PetscInt *idx; 7751 7752 PetscFunctionBegin; 7753 PetscCall(MatGetRow(Amat, row, &nidx, &idx, NULL)); 7754 if (nidx) { 7755 cnt = 0; 7756 cc[cnt] = idx[0] / bs; 7757 for (j = 1; j < nidx; j++) { 7758 if (cc[cnt] < idx[j] / bs) cc[++cnt] = idx[j] / bs; 7759 } 7760 } 7761 PetscCall(MatRestoreRow(Amat, row, &nidx, &idx, NULL)); 7762 *n = cnt + 1; 7763 PetscFunctionReturn(PETSC_SUCCESS); 7764 } 7765 7766 /* 7767 Produces a set of block column indices of the matrix block row, one for each block represented in the original set of rows 7768 7769 ncollapsed - the number of block indices 7770 collapsed - the block indices (must be large enough to contain the indices) 7771 */ 7772 static inline PetscErrorCode MatCollapseRows(Mat Amat, PetscInt start, PetscInt bs, PetscInt *w0, PetscInt *w1, PetscInt *w2, PetscInt *ncollapsed, PetscInt **collapsed) 7773 { 7774 PetscInt i, nprev, *cprev = w0, ncur = 0, *ccur = w1, *merged = w2, *cprevtmp; 7775 7776 PetscFunctionBegin; 7777 PetscCall(MatCollapseRow(Amat, start, bs, &nprev, cprev)); 7778 for (i = start + 1; i < start + bs; i++) { 7779 PetscCall(MatCollapseRow(Amat, i, bs, &ncur, ccur)); 7780 PetscCall(PetscMergeIntArray(nprev, cprev, ncur, ccur, &nprev, &merged)); 7781 cprevtmp = cprev; 7782 cprev = merged; 7783 merged = cprevtmp; 7784 } 7785 *ncollapsed = nprev; 7786 if (collapsed) *collapsed = cprev; 7787 PetscFunctionReturn(PETSC_SUCCESS); 7788 } 7789 7790 /* 7791 MatCreateGraph_Simple_AIJ - create simple scalar matrix (graph) from potentially blocked matrix 7792 7793 Input Parameter: 7794 . Amat - matrix 7795 - symmetrize - make the result symmetric 7796 + scale - scale with diagonal 7797 7798 Output Parameter: 7799 . a_Gmat - output scalar graph >= 0 7800 7801 */ 7802 PETSC_INTERN PetscErrorCode MatCreateGraph_Simple_AIJ(Mat Amat, PetscBool symmetrize, PetscBool scale, PetscReal filter, PetscInt index_size, PetscInt index[], Mat *a_Gmat) 7803 { 7804 PetscInt Istart, Iend, Ii, jj, kk, ncols, nloc, NN, MM, bs; 7805 MPI_Comm comm; 7806 Mat Gmat; 7807 PetscBool ismpiaij, isseqaij; 7808 Mat a, b, c; 7809 MatType jtype; 7810 7811 PetscFunctionBegin; 7812 PetscCall(PetscObjectGetComm((PetscObject)Amat, &comm)); 7813 PetscCall(MatGetOwnershipRange(Amat, &Istart, &Iend)); 7814 PetscCall(MatGetSize(Amat, &MM, &NN)); 7815 PetscCall(MatGetBlockSize(Amat, &bs)); 7816 nloc = (Iend - Istart) / bs; 7817 7818 PetscCall(PetscObjectBaseTypeCompare((PetscObject)Amat, MATSEQAIJ, &isseqaij)); 7819 PetscCall(PetscObjectBaseTypeCompare((PetscObject)Amat, MATMPIAIJ, &ismpiaij)); 7820 PetscCheck(isseqaij || ismpiaij, comm, PETSC_ERR_USER, "Require (MPI)AIJ matrix type"); 7821 7822 /* TODO GPU: these calls are potentially expensive if matrices are large and we want to use the GPU */ 7823 /* A solution consists in providing a new API, MatAIJGetCollapsedAIJ, and each class can provide a fast 7824 implementation */ 7825 if (bs > 1) { 7826 PetscCall(MatGetType(Amat, &jtype)); 7827 PetscCall(MatCreate(comm, &Gmat)); 7828 PetscCall(MatSetType(Gmat, jtype)); 7829 PetscCall(MatSetSizes(Gmat, nloc, nloc, PETSC_DETERMINE, PETSC_DETERMINE)); 7830 PetscCall(MatSetBlockSizes(Gmat, 1, 1)); 7831 if (isseqaij || ((Mat_MPIAIJ *)Amat->data)->garray) { 7832 PetscInt *d_nnz, *o_nnz; 7833 MatScalar *aa, val, *AA; 7834 PetscInt *aj, *ai, *AJ, nc, nmax = 0; 7835 7836 if (isseqaij) { 7837 a = Amat; 7838 b = NULL; 7839 } else { 7840 Mat_MPIAIJ *d = (Mat_MPIAIJ *)Amat->data; 7841 a = d->A; 7842 b = d->B; 7843 } 7844 PetscCall(PetscInfo(Amat, "New bs>1 Graph. nloc=%" PetscInt_FMT "\n", nloc)); 7845 PetscCall(PetscMalloc2(nloc, &d_nnz, (isseqaij ? 0 : nloc), &o_nnz)); 7846 for (c = a, kk = 0; c && kk < 2; c = b, kk++) { 7847 PetscInt *nnz = (c == a) ? d_nnz : o_nnz; 7848 const PetscInt *cols1, *cols2; 7849 7850 for (PetscInt brow = 0, nc1, nc2, ok = 1; brow < nloc * bs; brow += bs) { // block rows 7851 PetscCall(MatGetRow(c, brow, &nc2, &cols2, NULL)); 7852 nnz[brow / bs] = nc2 / bs; 7853 if (nc2 % bs) ok = 0; 7854 if (nnz[brow / bs] > nmax) nmax = nnz[brow / bs]; 7855 for (PetscInt ii = 1; ii < bs; ii++) { // check for non-dense blocks 7856 PetscCall(MatGetRow(c, brow + ii, &nc1, &cols1, NULL)); 7857 if (nc1 != nc2) ok = 0; 7858 else { 7859 for (PetscInt jj = 0; jj < nc1 && ok == 1; jj++) { 7860 if (cols1[jj] != cols2[jj]) ok = 0; 7861 if (cols1[jj] % bs != jj % bs) ok = 0; 7862 } 7863 } 7864 PetscCall(MatRestoreRow(c, brow + ii, &nc1, &cols1, NULL)); 7865 } 7866 PetscCall(MatRestoreRow(c, brow, &nc2, &cols2, NULL)); 7867 if (!ok) { 7868 PetscCall(PetscFree2(d_nnz, o_nnz)); 7869 PetscCall(PetscInfo(Amat, "Found sparse blocks - revert to slow method\n")); 7870 goto old_bs; 7871 } 7872 } 7873 } 7874 PetscCall(MatSeqAIJSetPreallocation(Gmat, 0, d_nnz)); 7875 PetscCall(MatMPIAIJSetPreallocation(Gmat, 0, d_nnz, 0, o_nnz)); 7876 PetscCall(PetscFree2(d_nnz, o_nnz)); 7877 PetscCall(PetscMalloc2(nmax, &AA, nmax, &AJ)); 7878 // diag 7879 for (PetscInt brow = 0, n, grow; brow < nloc * bs; brow += bs) { // block rows 7880 Mat_SeqAIJ *aseq = (Mat_SeqAIJ *)a->data; 7881 7882 ai = aseq->i; 7883 n = ai[brow + 1] - ai[brow]; 7884 aj = aseq->j + ai[brow]; 7885 for (PetscInt k = 0; k < n; k += bs) { // block columns 7886 AJ[k / bs] = aj[k] / bs + Istart / bs; // diag starts at (Istart,Istart) 7887 val = 0; 7888 if (index_size == 0) { 7889 for (PetscInt ii = 0; ii < bs; ii++) { // rows in block 7890 aa = aseq->a + ai[brow + ii] + k; 7891 for (PetscInt jj = 0; jj < bs; jj++) { // columns in block 7892 val += PetscAbs(PetscRealPart(aa[jj])); // a sort of norm 7893 } 7894 } 7895 } else { // use (index,index) value if provided 7896 for (PetscInt iii = 0; iii < index_size; iii++) { // rows in block 7897 PetscInt ii = index[iii]; 7898 aa = aseq->a + ai[brow + ii] + k; 7899 for (PetscInt jjj = 0; jjj < index_size; jjj++) { // columns in block 7900 PetscInt jj = index[jjj]; 7901 val += PetscAbs(PetscRealPart(aa[jj])); 7902 } 7903 } 7904 } 7905 PetscAssert(k / bs < nmax, comm, PETSC_ERR_USER, "k / bs (%" PetscInt_FMT ") >= nmax (%" PetscInt_FMT ")", k / bs, nmax); 7906 AA[k / bs] = val; 7907 } 7908 grow = Istart / bs + brow / bs; 7909 PetscCall(MatSetValues(Gmat, 1, &grow, n / bs, AJ, AA, ADD_VALUES)); 7910 } 7911 // off-diag 7912 if (ismpiaij) { 7913 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)Amat->data; 7914 const PetscScalar *vals; 7915 const PetscInt *cols, *garray = aij->garray; 7916 7917 PetscCheck(garray, PETSC_COMM_SELF, PETSC_ERR_USER, "No garray ?"); 7918 for (PetscInt brow = 0, grow; brow < nloc * bs; brow += bs) { // block rows 7919 PetscCall(MatGetRow(b, brow, &ncols, &cols, NULL)); 7920 for (PetscInt k = 0, cidx = 0; k < ncols; k += bs, cidx++) { 7921 PetscAssert(k / bs < nmax, comm, PETSC_ERR_USER, "k / bs >= nmax"); 7922 AA[k / bs] = 0; 7923 AJ[cidx] = garray[cols[k]] / bs; 7924 } 7925 nc = ncols / bs; 7926 PetscCall(MatRestoreRow(b, brow, &ncols, &cols, NULL)); 7927 if (index_size == 0) { 7928 for (PetscInt ii = 0; ii < bs; ii++) { // rows in block 7929 PetscCall(MatGetRow(b, brow + ii, &ncols, &cols, &vals)); 7930 for (PetscInt k = 0; k < ncols; k += bs) { 7931 for (PetscInt jj = 0; jj < bs; jj++) { // cols in block 7932 PetscAssert(k / bs < nmax, comm, PETSC_ERR_USER, "k / bs (%" PetscInt_FMT ") >= nmax (%" PetscInt_FMT ")", k / bs, nmax); 7933 AA[k / bs] += PetscAbs(PetscRealPart(vals[k + jj])); 7934 } 7935 } 7936 PetscCall(MatRestoreRow(b, brow + ii, &ncols, &cols, &vals)); 7937 } 7938 } else { // use (index,index) value if provided 7939 for (PetscInt iii = 0; iii < index_size; iii++) { // rows in block 7940 PetscInt ii = index[iii]; 7941 PetscCall(MatGetRow(b, brow + ii, &ncols, &cols, &vals)); 7942 for (PetscInt k = 0; k < ncols; k += bs) { 7943 for (PetscInt jjj = 0; jjj < index_size; jjj++) { // cols in block 7944 PetscInt jj = index[jjj]; 7945 AA[k / bs] += PetscAbs(PetscRealPart(vals[k + jj])); 7946 } 7947 } 7948 PetscCall(MatRestoreRow(b, brow + ii, &ncols, &cols, &vals)); 7949 } 7950 } 7951 grow = Istart / bs + brow / bs; 7952 PetscCall(MatSetValues(Gmat, 1, &grow, nc, AJ, AA, ADD_VALUES)); 7953 } 7954 } 7955 PetscCall(MatAssemblyBegin(Gmat, MAT_FINAL_ASSEMBLY)); 7956 PetscCall(MatAssemblyEnd(Gmat, MAT_FINAL_ASSEMBLY)); 7957 PetscCall(PetscFree2(AA, AJ)); 7958 } else { 7959 const PetscScalar *vals; 7960 const PetscInt *idx; 7961 PetscInt *d_nnz, *o_nnz, *w0, *w1, *w2; 7962 old_bs: 7963 /* 7964 Determine the preallocation needed for the scalar matrix derived from the vector matrix. 7965 */ 7966 PetscCall(PetscInfo(Amat, "OLD bs>1 CreateGraph\n")); 7967 PetscCall(PetscMalloc2(nloc, &d_nnz, (isseqaij ? 0 : nloc), &o_nnz)); 7968 if (isseqaij) { 7969 PetscInt max_d_nnz; 7970 7971 /* 7972 Determine exact preallocation count for (sequential) scalar matrix 7973 */ 7974 PetscCall(MatSeqAIJGetMaxRowNonzeros(Amat, &max_d_nnz)); 7975 max_d_nnz = PetscMin(nloc, bs * max_d_nnz); 7976 PetscCall(PetscMalloc3(max_d_nnz, &w0, max_d_nnz, &w1, max_d_nnz, &w2)); 7977 for (Ii = 0, jj = 0; Ii < Iend; Ii += bs, jj++) PetscCall(MatCollapseRows(Amat, Ii, bs, w0, w1, w2, &d_nnz[jj], NULL)); 7978 PetscCall(PetscFree3(w0, w1, w2)); 7979 } else if (ismpiaij) { 7980 Mat Daij, Oaij; 7981 const PetscInt *garray; 7982 PetscInt max_d_nnz; 7983 7984 PetscCall(MatMPIAIJGetSeqAIJ(Amat, &Daij, &Oaij, &garray)); 7985 /* 7986 Determine exact preallocation count for diagonal block portion of scalar matrix 7987 */ 7988 PetscCall(MatSeqAIJGetMaxRowNonzeros(Daij, &max_d_nnz)); 7989 max_d_nnz = PetscMin(nloc, bs * max_d_nnz); 7990 PetscCall(PetscMalloc3(max_d_nnz, &w0, max_d_nnz, &w1, max_d_nnz, &w2)); 7991 for (Ii = 0, jj = 0; Ii < Iend - Istart; Ii += bs, jj++) PetscCall(MatCollapseRows(Daij, Ii, bs, w0, w1, w2, &d_nnz[jj], NULL)); 7992 PetscCall(PetscFree3(w0, w1, w2)); 7993 /* 7994 Over estimate (usually grossly over), preallocation count for off-diagonal portion of scalar matrix 7995 */ 7996 for (Ii = 0, jj = 0; Ii < Iend - Istart; Ii += bs, jj++) { 7997 o_nnz[jj] = 0; 7998 for (kk = 0; kk < bs; kk++) { /* rows that get collapsed to a single row */ 7999 PetscCall(MatGetRow(Oaij, Ii + kk, &ncols, NULL, NULL)); 8000 o_nnz[jj] += ncols; 8001 PetscCall(MatRestoreRow(Oaij, Ii + kk, &ncols, NULL, NULL)); 8002 } 8003 if (o_nnz[jj] > (NN / bs - nloc)) o_nnz[jj] = NN / bs - nloc; 8004 } 8005 } else SETERRQ(comm, PETSC_ERR_USER, "Require AIJ matrix type"); 8006 /* get scalar copy (norms) of matrix */ 8007 PetscCall(MatSeqAIJSetPreallocation(Gmat, 0, d_nnz)); 8008 PetscCall(MatMPIAIJSetPreallocation(Gmat, 0, d_nnz, 0, o_nnz)); 8009 PetscCall(PetscFree2(d_nnz, o_nnz)); 8010 for (Ii = Istart; Ii < Iend; Ii++) { 8011 PetscInt dest_row = Ii / bs; 8012 8013 PetscCall(MatGetRow(Amat, Ii, &ncols, &idx, &vals)); 8014 for (jj = 0; jj < ncols; jj++) { 8015 PetscInt dest_col = idx[jj] / bs; 8016 PetscScalar sv = PetscAbs(PetscRealPart(vals[jj])); 8017 8018 PetscCall(MatSetValues(Gmat, 1, &dest_row, 1, &dest_col, &sv, ADD_VALUES)); 8019 } 8020 PetscCall(MatRestoreRow(Amat, Ii, &ncols, &idx, &vals)); 8021 } 8022 PetscCall(MatAssemblyBegin(Gmat, MAT_FINAL_ASSEMBLY)); 8023 PetscCall(MatAssemblyEnd(Gmat, MAT_FINAL_ASSEMBLY)); 8024 } 8025 } else { 8026 if (symmetrize || filter >= 0 || scale) PetscCall(MatDuplicate(Amat, MAT_COPY_VALUES, &Gmat)); 8027 else { 8028 Gmat = Amat; 8029 PetscCall(PetscObjectReference((PetscObject)Gmat)); 8030 } 8031 if (isseqaij) { 8032 a = Gmat; 8033 b = NULL; 8034 } else { 8035 Mat_MPIAIJ *d = (Mat_MPIAIJ *)Gmat->data; 8036 a = d->A; 8037 b = d->B; 8038 } 8039 if (filter >= 0 || scale) { 8040 /* take absolute value of each entry */ 8041 for (c = a, kk = 0; c && kk < 2; c = b, kk++) { 8042 MatInfo info; 8043 PetscScalar *avals; 8044 8045 PetscCall(MatGetInfo(c, MAT_LOCAL, &info)); 8046 PetscCall(MatSeqAIJGetArray(c, &avals)); 8047 for (int jj = 0; jj < info.nz_used; jj++) avals[jj] = PetscAbsScalar(avals[jj]); 8048 PetscCall(MatSeqAIJRestoreArray(c, &avals)); 8049 } 8050 } 8051 } 8052 if (symmetrize) { 8053 PetscBool isset, issym; 8054 8055 PetscCall(MatIsSymmetricKnown(Amat, &isset, &issym)); 8056 if (!isset || !issym) { 8057 Mat matTrans; 8058 8059 PetscCall(MatTranspose(Gmat, MAT_INITIAL_MATRIX, &matTrans)); 8060 PetscCall(MatAXPY(Gmat, 1.0, matTrans, Gmat->structurally_symmetric == PETSC_BOOL3_TRUE ? SAME_NONZERO_PATTERN : DIFFERENT_NONZERO_PATTERN)); 8061 PetscCall(MatDestroy(&matTrans)); 8062 } 8063 PetscCall(MatSetOption(Gmat, MAT_SYMMETRIC, PETSC_TRUE)); 8064 } else if (Amat != Gmat) PetscCall(MatPropagateSymmetryOptions(Amat, Gmat)); 8065 if (scale) { 8066 /* scale c for all diagonal values = 1 or -1 */ 8067 Vec diag; 8068 8069 PetscCall(MatCreateVecs(Gmat, &diag, NULL)); 8070 PetscCall(MatGetDiagonal(Gmat, diag)); 8071 PetscCall(VecReciprocal(diag)); 8072 PetscCall(VecSqrtAbs(diag)); 8073 PetscCall(MatDiagonalScale(Gmat, diag, diag)); 8074 PetscCall(VecDestroy(&diag)); 8075 } 8076 PetscCall(MatViewFromOptions(Gmat, NULL, "-mat_graph_view")); 8077 if (filter >= 0) { 8078 PetscCall(MatFilter(Gmat, filter, PETSC_TRUE, PETSC_TRUE)); 8079 PetscCall(MatViewFromOptions(Gmat, NULL, "-mat_filter_graph_view")); 8080 } 8081 *a_Gmat = Gmat; 8082 PetscFunctionReturn(PETSC_SUCCESS); 8083 } 8084 8085 /* 8086 Special version for direct calls from Fortran 8087 */ 8088 8089 /* Change these macros so can be used in void function */ 8090 /* Identical to PetscCallVoid, except it assigns to *_ierr */ 8091 #undef PetscCall 8092 #define PetscCall(...) \ 8093 do { \ 8094 PetscErrorCode ierr_msv_mpiaij = __VA_ARGS__; \ 8095 if (PetscUnlikely(ierr_msv_mpiaij)) { \ 8096 *_ierr = PetscError(PETSC_COMM_SELF, __LINE__, PETSC_FUNCTION_NAME, __FILE__, ierr_msv_mpiaij, PETSC_ERROR_REPEAT, " "); \ 8097 return; \ 8098 } \ 8099 } while (0) 8100 8101 #undef SETERRQ 8102 #define SETERRQ(comm, ierr, ...) \ 8103 do { \ 8104 *_ierr = PetscError(comm, __LINE__, PETSC_FUNCTION_NAME, __FILE__, ierr, PETSC_ERROR_INITIAL, __VA_ARGS__); \ 8105 return; \ 8106 } while (0) 8107 8108 #if defined(PETSC_HAVE_FORTRAN_CAPS) 8109 #define matsetvaluesmpiaij_ MATSETVALUESMPIAIJ 8110 #elif !defined(PETSC_HAVE_FORTRAN_UNDERSCORE) 8111 #define matsetvaluesmpiaij_ matsetvaluesmpiaij 8112 #else 8113 #endif 8114 PETSC_EXTERN void matsetvaluesmpiaij_(Mat *mmat, PetscInt *mm, const PetscInt im[], PetscInt *mn, const PetscInt in[], const PetscScalar v[], InsertMode *maddv, PetscErrorCode *_ierr) 8115 { 8116 Mat mat = *mmat; 8117 PetscInt m = *mm, n = *mn; 8118 InsertMode addv = *maddv; 8119 Mat_MPIAIJ *aij = (Mat_MPIAIJ *)mat->data; 8120 PetscScalar value; 8121 8122 MatCheckPreallocated(mat, 1); 8123 if (mat->insertmode == NOT_SET_VALUES) mat->insertmode = addv; 8124 else PetscCheck(mat->insertmode == addv, PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Cannot mix add values and insert values"); 8125 { 8126 PetscInt i, j, rstart = mat->rmap->rstart, rend = mat->rmap->rend; 8127 PetscInt cstart = mat->cmap->rstart, cend = mat->cmap->rend, row, col; 8128 PetscBool roworiented = aij->roworiented; 8129 8130 /* Some Variables required in the macro */ 8131 Mat A = aij->A; 8132 Mat_SeqAIJ *a = (Mat_SeqAIJ *)A->data; 8133 PetscInt *aimax = a->imax, *ai = a->i, *ailen = a->ilen, *aj = a->j; 8134 MatScalar *aa; 8135 PetscBool ignorezeroentries = ((a->ignorezeroentries && (addv == ADD_VALUES)) ? PETSC_TRUE : PETSC_FALSE); 8136 Mat B = aij->B; 8137 Mat_SeqAIJ *b = (Mat_SeqAIJ *)B->data; 8138 PetscInt *bimax = b->imax, *bi = b->i, *bilen = b->ilen, *bj = b->j, bm = aij->B->rmap->n, am = aij->A->rmap->n; 8139 MatScalar *ba; 8140 /* This variable below is only for the PETSC_HAVE_VIENNACL or PETSC_HAVE_CUDA cases, but we define it in all cases because we 8141 * cannot use "#if defined" inside a macro. */ 8142 PETSC_UNUSED PetscBool inserted = PETSC_FALSE; 8143 8144 PetscInt *rp1, *rp2, ii, nrow1, nrow2, _i, rmax1, rmax2, N, low1, high1, low2, high2, t, lastcol1, lastcol2; 8145 PetscInt nonew = a->nonew; 8146 MatScalar *ap1, *ap2; 8147 8148 PetscFunctionBegin; 8149 PetscCall(MatSeqAIJGetArray(A, &aa)); 8150 PetscCall(MatSeqAIJGetArray(B, &ba)); 8151 for (i = 0; i < m; i++) { 8152 if (im[i] < 0) continue; 8153 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); 8154 if (im[i] >= rstart && im[i] < rend) { 8155 row = im[i] - rstart; 8156 lastcol1 = -1; 8157 rp1 = aj + ai[row]; 8158 ap1 = aa + ai[row]; 8159 rmax1 = aimax[row]; 8160 nrow1 = ailen[row]; 8161 low1 = 0; 8162 high1 = nrow1; 8163 lastcol2 = -1; 8164 rp2 = bj + bi[row]; 8165 ap2 = ba + bi[row]; 8166 rmax2 = bimax[row]; 8167 nrow2 = bilen[row]; 8168 low2 = 0; 8169 high2 = nrow2; 8170 8171 for (j = 0; j < n; j++) { 8172 if (roworiented) value = v[i * n + j]; 8173 else value = v[i + j * m]; 8174 if (ignorezeroentries && value == 0.0 && (addv == ADD_VALUES) && im[i] != in[j]) continue; 8175 if (in[j] >= cstart && in[j] < cend) { 8176 col = in[j] - cstart; 8177 MatSetValues_SeqAIJ_A_Private(row, col, value, addv, im[i], in[j]); 8178 } else if (in[j] < 0) continue; 8179 else if (PetscUnlikelyDebug(in[j] >= mat->cmap->N)) { 8180 SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Column too large: col %" PetscInt_FMT " max %" PetscInt_FMT, in[j], mat->cmap->N - 1); 8181 } else { 8182 if (mat->was_assembled) { 8183 if (!aij->colmap) PetscCall(MatCreateColmap_MPIAIJ_Private(mat)); 8184 #if defined(PETSC_USE_CTABLE) 8185 PetscCall(PetscHMapIGetWithDefault(aij->colmap, in[j] + 1, 0, &col)); 8186 col--; 8187 #else 8188 col = aij->colmap[in[j]] - 1; 8189 #endif 8190 if (col < 0 && !((Mat_SeqAIJ *)aij->A->data)->nonew) { 8191 PetscCall(MatDisAssemble_MPIAIJ(mat, PETSC_FALSE)); 8192 col = in[j]; 8193 /* Reinitialize the variables required by MatSetValues_SeqAIJ_B_Private() */ 8194 B = aij->B; 8195 b = (Mat_SeqAIJ *)B->data; 8196 bimax = b->imax; 8197 bi = b->i; 8198 bilen = b->ilen; 8199 bj = b->j; 8200 rp2 = bj + bi[row]; 8201 ap2 = ba + bi[row]; 8202 rmax2 = bimax[row]; 8203 nrow2 = bilen[row]; 8204 low2 = 0; 8205 high2 = nrow2; 8206 bm = aij->B->rmap->n; 8207 ba = b->a; 8208 inserted = PETSC_FALSE; 8209 } 8210 } else col = in[j]; 8211 MatSetValues_SeqAIJ_B_Private(row, col, value, addv, im[i], in[j]); 8212 } 8213 } 8214 } else if (!aij->donotstash) { 8215 if (roworiented) { 8216 PetscCall(MatStashValuesRow_Private(&mat->stash, im[i], n, in, v + i * n, (PetscBool)(ignorezeroentries && (addv == ADD_VALUES)))); 8217 } else { 8218 PetscCall(MatStashValuesCol_Private(&mat->stash, im[i], n, in, v + i, m, (PetscBool)(ignorezeroentries && (addv == ADD_VALUES)))); 8219 } 8220 } 8221 } 8222 PetscCall(MatSeqAIJRestoreArray(A, &aa)); 8223 PetscCall(MatSeqAIJRestoreArray(B, &ba)); 8224 } 8225 PetscFunctionReturnVoid(); 8226 } 8227 8228 /* Undefining these here since they were redefined from their original definition above! No 8229 * other PETSc functions should be defined past this point, as it is impossible to recover the 8230 * original definitions */ 8231 #undef PetscCall 8232 #undef SETERRQ 8233