1 #include <petsc/private/pcpatchimpl.h> /*I "petscpc.h" I*/ 2 #include <petsc/private/dmpleximpl.h> /* For DMPlexComputeJacobian_Patch_Internal() */ 3 #include <petscsf.h> 4 #include <petscbt.h> 5 #include <petscds.h> 6 7 PetscLogEvent PC_Patch_CreatePatches, PC_Patch_ComputeOp, PC_Patch_Solve, PC_Patch_Scatter, PC_Patch_Apply, PC_Patch_Prealloc; 8 9 PETSC_STATIC_INLINE PetscErrorCode ObjectView(PetscObject obj, PetscViewer viewer, PetscViewerFormat format) 10 { 11 PetscErrorCode ierr; 12 13 ierr = PetscViewerPushFormat(viewer, format);CHKERRQ(ierr); 14 ierr = PetscObjectView(obj, viewer);CHKERRQ(ierr); 15 ierr = PetscViewerPopFormat(viewer);CHKERRQ(ierr); 16 return(0); 17 } 18 19 static PetscErrorCode PCPatchConstruct_Star(void *vpatch, DM dm, PetscInt point, PetscHashI ht) 20 { 21 PetscInt starSize; 22 PetscInt *star = NULL, si; 23 PetscErrorCode ierr; 24 25 PetscFunctionBegin; 26 PetscHashIClear(ht); 27 /* To start with, add the point we care about */ 28 PetscHashIAdd(ht, point, 0); 29 /* Loop over all the points that this point connects to */ 30 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 31 for (si = 0; si < starSize*2; si += 2) {PetscHashIAdd(ht, star[si], 0);} 32 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 33 PetscFunctionReturn(0); 34 } 35 36 static PetscErrorCode PCPatchConstruct_Vanka(void *vpatch, DM dm, PetscInt point, PetscHashI ht) 37 { 38 PC_PATCH *patch = (PC_PATCH *) vpatch; 39 PetscInt starSize; 40 PetscInt *star = NULL; 41 PetscBool shouldIgnore = PETSC_FALSE; 42 PetscInt cStart, cEnd, iStart, iEnd, si; 43 PetscErrorCode ierr; 44 45 PetscFunctionBegin; 46 PetscHashIClear(ht); 47 /* To start with, add the point we care about */ 48 PetscHashIAdd(ht, point, 0); 49 /* Should we ignore any points of a certain dimension? */ 50 if (patch->vankadim >= 0) { 51 shouldIgnore = PETSC_TRUE; 52 ierr = DMPlexGetDepthStratum(dm, patch->vankadim, &iStart, &iEnd);CHKERRQ(ierr); 53 } 54 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 55 /* Loop over all the cells that this point connects to */ 56 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 57 for (si = 0; si < starSize*2; si += 2) { 58 const PetscInt cell = star[si]; 59 PetscInt closureSize; 60 PetscInt *closure = NULL, ci; 61 62 if (cell < cStart || cell >= cEnd) continue; 63 /* now loop over all entities in the closure of that cell */ 64 ierr = DMPlexGetTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 65 for (ci = 0; ci < closureSize*2; ci += 2) { 66 const PetscInt newpoint = closure[ci]; 67 68 /* We've been told to ignore entities of this type.*/ 69 if (shouldIgnore && newpoint >= iStart && newpoint < iEnd) continue; 70 PetscHashIAdd(ht, newpoint, 0); 71 } 72 ierr = DMPlexRestoreTransitiveClosure(dm, cell, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 73 } 74 ierr = DMPlexRestoreTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 75 PetscFunctionReturn(0); 76 } 77 78 /* The user's already set the patches in patch->userIS. Build the hash tables */ 79 static PetscErrorCode PCPatchConstruct_User(void *vpatch, DM dm, PetscInt point, PetscHashI ht) 80 { 81 PC_PATCH *patch = (PC_PATCH *) vpatch; 82 IS patchis = patch->userIS[point]; 83 PetscInt n; 84 const PetscInt *patchdata; 85 PetscInt pStart, pEnd, i; 86 PetscErrorCode ierr; 87 88 PetscFunctionBegin; 89 PetscHashIClear(ht); 90 ierr = DMPlexGetChart(dm, &pStart, &pEnd); 91 ierr = ISGetLocalSize(patchis, &n);CHKERRQ(ierr); 92 ierr = ISGetIndices(patchis, &patchdata);CHKERRQ(ierr); 93 for (i = 0; i < n; ++i) { 94 const PetscInt ownedpoint = patchdata[i]; 95 96 if (ownedpoint < pStart || ownedpoint >= pEnd) { 97 SETERRQ3(PetscObjectComm((PetscObject) dm), PETSC_ERR_ARG_OUTOFRANGE, "Mesh point %D was not in [%D, %D)", ownedpoint, pStart, pEnd); 98 } 99 PetscHashIAdd(ht, ownedpoint, 0); 100 } 101 ierr = ISRestoreIndices(patchis, &patchdata);CHKERRQ(ierr); 102 PetscFunctionReturn(0); 103 } 104 105 static PetscErrorCode PCPatchCreateDefaultSF_Private(PC pc, PetscInt n, const PetscSF *sf, const PetscInt *bs) 106 { 107 PC_PATCH *patch = (PC_PATCH *) pc->data; 108 PetscInt i; 109 PetscErrorCode ierr; 110 111 PetscFunctionBegin; 112 if (n == 1 && bs[0] == 1) { 113 patch->defaultSF = sf[0]; 114 ierr = PetscObjectReference((PetscObject) patch->defaultSF);CHKERRQ(ierr); 115 } else { 116 PetscInt allRoots = 0, allLeaves = 0; 117 PetscInt leafOffset = 0; 118 PetscInt *ilocal = NULL; 119 PetscSFNode *iremote = NULL; 120 PetscInt *remoteOffsets = NULL; 121 PetscInt index = 0; 122 PetscHashI rankToIndex; 123 PetscInt numRanks = 0; 124 PetscSFNode *remote = NULL; 125 PetscSF rankSF; 126 PetscInt *ranks = NULL; 127 PetscInt *offsets = NULL; 128 MPI_Datatype contig; 129 PetscHashI ranksUniq; 130 131 /* First figure out how many dofs there are in the concatenated numbering. 132 * allRoots: number of owned global dofs; 133 * allLeaves: number of visible dofs (global + ghosted). 134 */ 135 for (i = 0; i < n; ++i) { 136 PetscInt nroots, nleaves; 137 138 ierr = PetscSFGetGraph(sf[i], &nroots, &nleaves, NULL, NULL);CHKERRQ(ierr); 139 allRoots += nroots * bs[i]; 140 allLeaves += nleaves * bs[i]; 141 } 142 ierr = PetscMalloc1(allLeaves, &ilocal);CHKERRQ(ierr); 143 ierr = PetscMalloc1(allLeaves, &iremote);CHKERRQ(ierr); 144 /* Now build an SF that just contains process connectivity. */ 145 PetscHashICreate(ranksUniq); 146 for (i = 0; i < n; ++i) { 147 const PetscMPIInt *ranks = NULL; 148 PetscInt nranks, j; 149 150 ierr = PetscSFSetUp(sf[i]);CHKERRQ(ierr); 151 ierr = PetscSFGetRanks(sf[i], &nranks, &ranks, NULL, NULL, NULL);CHKERRQ(ierr); 152 /* These are all the ranks who communicate with me. */ 153 for (j = 0; j < nranks; ++j) { 154 PetscHashIAdd(ranksUniq, (PetscInt) ranks[j], 0); 155 } 156 } 157 PetscHashISize(ranksUniq, numRanks); 158 ierr = PetscMalloc1(numRanks, &remote);CHKERRQ(ierr); 159 ierr = PetscMalloc1(numRanks, &ranks);CHKERRQ(ierr); 160 PetscHashIGetKeys(ranksUniq, &index, ranks); 161 162 PetscHashICreate(rankToIndex); 163 for (i = 0; i < numRanks; ++i) { 164 remote[i].rank = ranks[i]; 165 remote[i].index = 0; 166 PetscHashIAdd(rankToIndex, ranks[i], i); 167 } 168 ierr = PetscFree(ranks);CHKERRQ(ierr); 169 PetscHashIDestroy(ranksUniq); 170 ierr = PetscSFCreate(PetscObjectComm((PetscObject) pc), &rankSF);CHKERRQ(ierr); 171 ierr = PetscSFSetGraph(rankSF, 1, numRanks, NULL, PETSC_OWN_POINTER, remote, PETSC_OWN_POINTER);CHKERRQ(ierr); 172 ierr = PetscSFSetUp(rankSF);CHKERRQ(ierr); 173 /* OK, use it to communicate the root offset on the remote 174 * processes for each subspace. */ 175 ierr = PetscMalloc1(n, &offsets);CHKERRQ(ierr); 176 ierr = PetscMalloc1(n*numRanks, &remoteOffsets);CHKERRQ(ierr); 177 178 offsets[0] = 0; 179 for (i = 1; i < n; ++i) { 180 PetscInt nroots; 181 182 ierr = PetscSFGetGraph(sf[i-1], &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 183 offsets[i] = offsets[i-1] + nroots*bs[i-1]; 184 } 185 /* Offsets are the offsets on the current process of the 186 * global dof numbering for the subspaces. */ 187 ierr = MPI_Type_contiguous(n, MPIU_INT, &contig);CHKERRQ(ierr); 188 ierr = MPI_Type_commit(&contig);CHKERRQ(ierr); 189 190 ierr = PetscSFBcastBegin(rankSF, contig, offsets, remoteOffsets);CHKERRQ(ierr); 191 ierr = PetscSFBcastEnd(rankSF, contig, offsets, remoteOffsets);CHKERRQ(ierr); 192 ierr = MPI_Type_free(&contig);CHKERRQ(ierr); 193 ierr = PetscFree(offsets);CHKERRQ(ierr); 194 ierr = PetscSFDestroy(&rankSF);CHKERRQ(ierr); 195 /* Now remoteOffsets contains the offsets on the remote 196 * processes who communicate with me. So now we can 197 * concatenate the list of SFs into a single one. */ 198 index = 0; 199 for (i = 0; i < n; ++i) { 200 const PetscSFNode *remote = NULL; 201 const PetscInt *local = NULL; 202 PetscInt nroots, nleaves, j; 203 204 ierr = PetscSFGetGraph(sf[i], &nroots, &nleaves, &local, &remote);CHKERRQ(ierr); 205 for (j = 0; j < nleaves; ++j) { 206 PetscInt rank = remote[j].rank; 207 PetscInt idx, rootOffset, k; 208 209 PetscHashIMap(rankToIndex, rank, idx); 210 if (idx == -1) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Didn't find rank, huh?"); 211 /* Offset on given rank for ith subspace */ 212 rootOffset = remoteOffsets[n*idx + i]; 213 for (k = 0; k < bs[i]; ++k) { 214 ilocal[index] = (local ? local[j] : j)*bs[i] + k + leafOffset; 215 iremote[index].rank = remote[j].rank; 216 iremote[index].index = remote[j].index*bs[i] + k + rootOffset; 217 ++index; 218 } 219 } 220 leafOffset += nleaves * bs[i]; 221 } 222 PetscHashIDestroy(rankToIndex); 223 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 224 ierr = PetscSFCreate(PetscObjectComm((PetscObject)pc), &patch->defaultSF);CHKERRQ(ierr); 225 ierr = PetscSFSetGraph(patch->defaultSF, allRoots, allLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);CHKERRQ(ierr); 226 } 227 PetscFunctionReturn(0); 228 } 229 230 /* TODO: Docs */ 231 PetscErrorCode PCPatchSetIgnoreDim(PC pc, PetscInt dim) 232 { 233 PC_PATCH *patch = (PC_PATCH *) pc->data; 234 PetscFunctionBegin; 235 patch->ignoredim = dim; 236 PetscFunctionReturn(0); 237 } 238 239 /* TODO: Docs */ 240 PetscErrorCode PCPatchGetIgnoreDim(PC pc, PetscInt *dim) 241 { 242 PC_PATCH *patch = (PC_PATCH *) pc->data; 243 PetscFunctionBegin; 244 *dim = patch->ignoredim; 245 PetscFunctionReturn(0); 246 } 247 248 /* TODO: Docs */ 249 PetscErrorCode PCPatchSetSaveOperators(PC pc, PetscBool flg) 250 { 251 PC_PATCH *patch = (PC_PATCH *) pc->data; 252 PetscFunctionBegin; 253 patch->save_operators = flg; 254 PetscFunctionReturn(0); 255 } 256 257 /* TODO: Docs */ 258 PetscErrorCode PCPatchGetSaveOperators(PC pc, PetscBool *flg) 259 { 260 PC_PATCH *patch = (PC_PATCH *) pc->data; 261 PetscFunctionBegin; 262 *flg = patch->save_operators; 263 PetscFunctionReturn(0); 264 } 265 266 /* TODO: Docs */ 267 PetscErrorCode PCPatchSetPartitionOfUnity(PC pc, PetscBool flg) 268 { 269 PC_PATCH *patch = (PC_PATCH *) pc->data; 270 PetscFunctionBegin; 271 patch->partition_of_unity = flg; 272 PetscFunctionReturn(0); 273 } 274 275 /* TODO: Docs */ 276 PetscErrorCode PCPatchGetPartitionOfUnity(PC pc, PetscBool *flg) 277 { 278 PC_PATCH *patch = (PC_PATCH *) pc->data; 279 PetscFunctionBegin; 280 *flg = patch->partition_of_unity; 281 PetscFunctionReturn(0); 282 } 283 284 /* TODO: Docs */ 285 PetscErrorCode PCPatchSetSubMatType(PC pc, MatType sub_mat_type) 286 { 287 PC_PATCH *patch = (PC_PATCH *) pc->data; 288 PetscErrorCode ierr; 289 290 PetscFunctionBegin; 291 if (patch->sub_mat_type) {ierr = PetscFree(patch->sub_mat_type);CHKERRQ(ierr);} 292 ierr = PetscStrallocpy(sub_mat_type, (char **) &patch->sub_mat_type);CHKERRQ(ierr); 293 PetscFunctionReturn(0); 294 } 295 296 /* TODO: Docs */ 297 PetscErrorCode PCPatchGetSubMatType(PC pc, MatType *sub_mat_type) 298 { 299 PC_PATCH *patch = (PC_PATCH *) pc->data; 300 PetscFunctionBegin; 301 *sub_mat_type = patch->sub_mat_type; 302 PetscFunctionReturn(0); 303 } 304 305 /* TODO: Docs */ 306 PetscErrorCode PCPatchSetCellNumbering(PC pc, PetscSection cellNumbering) 307 { 308 PC_PATCH *patch = (PC_PATCH *) pc->data; 309 PetscErrorCode ierr; 310 311 PetscFunctionBegin; 312 patch->cellNumbering = cellNumbering; 313 ierr = PetscObjectReference((PetscObject) cellNumbering);CHKERRQ(ierr); 314 PetscFunctionReturn(0); 315 } 316 317 /* TODO: Docs */ 318 PetscErrorCode PCPatchGetCellNumbering(PC pc, PetscSection *cellNumbering) 319 { 320 PC_PATCH *patch = (PC_PATCH *) pc->data; 321 PetscFunctionBegin; 322 *cellNumbering = patch->cellNumbering; 323 PetscFunctionReturn(0); 324 } 325 326 /* TODO: Docs */ 327 PetscErrorCode PCPatchSetConstructType(PC pc, PCPatchConstructType ctype, PetscErrorCode (*func)(PC, PetscInt *, IS **, IS *, void *), void *ctx) 328 { 329 PC_PATCH *patch = (PC_PATCH *) pc->data; 330 331 PetscFunctionBegin; 332 patch->ctype = ctype; 333 switch (ctype) { 334 case PC_PATCH_STAR: 335 patch->patchconstructop = PCPatchConstruct_Star; 336 break; 337 case PC_PATCH_VANKA: 338 patch->patchconstructop = PCPatchConstruct_Vanka; 339 break; 340 case PC_PATCH_USER: 341 case PC_PATCH_PYTHON: 342 patch->user_patches = PETSC_TRUE; 343 patch->patchconstructop = PCPatchConstruct_User; 344 if (func) { 345 patch->userpatchconstructionop = func; 346 patch->userpatchconstructctx = ctx; 347 } 348 break; 349 default: 350 SETERRQ1(PetscObjectComm((PetscObject) pc), PETSC_ERR_USER, "Unknown patch construction type %D", (PetscInt) patch->ctype); 351 } 352 PetscFunctionReturn(0); 353 } 354 355 /* TODO: Docs */ 356 PetscErrorCode PCPatchGetConstructType(PC pc, PCPatchConstructType *ctype, PetscErrorCode (**func)(PC, PetscInt *, IS **, IS *, void *), void **ctx) 357 { 358 PC_PATCH *patch = (PC_PATCH *) pc->data; 359 360 PetscFunctionBegin; 361 *ctype = patch->ctype; 362 switch (patch->ctype) { 363 case PC_PATCH_STAR: 364 case PC_PATCH_VANKA: 365 break; 366 case PC_PATCH_USER: 367 case PC_PATCH_PYTHON: 368 *func = patch->userpatchconstructionop; 369 *ctx = patch->userpatchconstructctx; 370 break; 371 default: 372 SETERRQ1(PetscObjectComm((PetscObject) pc), PETSC_ERR_USER, "Unknown patch construction type %D", (PetscInt) patch->ctype); 373 } 374 PetscFunctionReturn(0); 375 } 376 377 /* TODO: Docs */ 378 PetscErrorCode PCPatchSetDiscretisationInfo(PC pc, PetscInt nsubspaces, DM *dms, PetscInt *bs, PetscInt *nodesPerCell, const PetscInt **cellNodeMap, 379 const PetscInt *subspaceOffsets, PetscInt numGhostBcs, const PetscInt *ghostBcNodes, PetscInt numGlobalBcs, const PetscInt *globalBcNodes) 380 { 381 PC_PATCH *patch = (PC_PATCH *) pc->data; 382 DM dm; 383 PetscSF *sfs; 384 PetscInt cStart, cEnd, i, j; 385 PetscErrorCode ierr; 386 387 PetscFunctionBegin; 388 ierr = PCGetDM(pc, &dm);CHKERRQ(ierr); 389 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 390 ierr = PetscMalloc1(nsubspaces, &sfs);CHKERRQ(ierr); 391 ierr = PetscMalloc1(nsubspaces, &patch->dofSection);CHKERRQ(ierr); 392 ierr = PetscMalloc1(nsubspaces, &patch->bs);CHKERRQ(ierr); 393 ierr = PetscMalloc1(nsubspaces, &patch->nodesPerCell);CHKERRQ(ierr); 394 ierr = PetscMalloc1(nsubspaces, &patch->cellNodeMap);CHKERRQ(ierr); 395 ierr = PetscMalloc1(nsubspaces+1, &patch->subspaceOffsets);CHKERRQ(ierr); 396 397 patch->nsubspaces = nsubspaces; 398 patch->totalDofsPerCell = 0; 399 for (i = 0; i < nsubspaces; ++i) { 400 ierr = DMGetDefaultSection(dms[i], &patch->dofSection[i]);CHKERRQ(ierr); 401 ierr = PetscObjectReference((PetscObject) patch->dofSection[i]);CHKERRQ(ierr); 402 ierr = DMGetDefaultSF(dms[i], &sfs[i]);CHKERRQ(ierr); 403 patch->bs[i] = bs[i]; 404 patch->nodesPerCell[i] = nodesPerCell[i]; 405 patch->totalDofsPerCell += nodesPerCell[i]*bs[i]; 406 ierr = PetscMalloc1((cEnd-cStart)*nodesPerCell[i]*bs[i], &patch->cellNodeMap[i]);CHKERRQ(ierr); 407 for (j = 0; j < (cEnd-cStart)*nodesPerCell[i]*bs[i]; ++j) patch->cellNodeMap[i][j] = cellNodeMap[i][j]; 408 patch->subspaceOffsets[i] = subspaceOffsets[i]; 409 } 410 ierr = PCPatchCreateDefaultSF_Private(pc, nsubspaces, sfs, patch->bs);CHKERRQ(ierr); 411 ierr = PetscFree(sfs);CHKERRQ(ierr); 412 413 patch->subspaceOffsets[nsubspaces] = subspaceOffsets[nsubspaces]; 414 ierr = ISCreateGeneral(PETSC_COMM_SELF, numGhostBcs, ghostBcNodes, PETSC_COPY_VALUES, &patch->ghostBcNodes);CHKERRQ(ierr); 415 ierr = ISCreateGeneral(PETSC_COMM_SELF, numGlobalBcs, globalBcNodes, PETSC_COPY_VALUES, &patch->globalBcNodes);CHKERRQ(ierr); 416 PetscFunctionReturn(0); 417 } 418 419 /* TODO: Docs */ 420 PetscErrorCode PCPatchSetDiscretisationInfoCombined(PC pc, DM dm, PetscInt *nodesPerCell, const PetscInt **cellNodeMap, PetscInt numGhostBcs, const PetscInt *ghostBcNodes, PetscInt numGlobalBcs, const PetscInt *globalBcNodes) 421 { 422 PC_PATCH *patch = (PC_PATCH *) pc->data; 423 PetscInt cStart, cEnd, i, j; 424 PetscErrorCode ierr; 425 426 PetscFunctionBegin; 427 patch->combined = PETSC_TRUE; 428 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 429 ierr = DMGetNumFields(dm, &patch->nsubspaces);CHKERRQ(ierr); 430 ierr = PetscCalloc1(patch->nsubspaces, &patch->dofSection);CHKERRQ(ierr); 431 ierr = PetscMalloc1(patch->nsubspaces, &patch->bs);CHKERRQ(ierr); 432 ierr = PetscMalloc1(patch->nsubspaces, &patch->nodesPerCell);CHKERRQ(ierr); 433 ierr = PetscMalloc1(patch->nsubspaces, &patch->cellNodeMap);CHKERRQ(ierr); 434 ierr = PetscCalloc1(patch->nsubspaces+1, &patch->subspaceOffsets);CHKERRQ(ierr); 435 ierr = DMGetDefaultSection(dm, &patch->dofSection[0]);CHKERRQ(ierr); 436 ierr = PetscObjectReference((PetscObject) patch->dofSection[0]);CHKERRQ(ierr); 437 ierr = PetscSectionGetStorageSize(patch->dofSection[0], &patch->subspaceOffsets[patch->nsubspaces]);CHKERRQ(ierr); 438 patch->totalDofsPerCell = 0; 439 for (i = 0; i < patch->nsubspaces; ++i) { 440 patch->bs[i] = 1; 441 patch->nodesPerCell[i] = nodesPerCell[i]; 442 patch->totalDofsPerCell += nodesPerCell[i]; 443 ierr = PetscMalloc1((cEnd-cStart)*nodesPerCell[i], &patch->cellNodeMap[i]);CHKERRQ(ierr); 444 for (j = 0; j < (cEnd-cStart)*nodesPerCell[i]; ++j) patch->cellNodeMap[i][j] = cellNodeMap[i][j]; 445 } 446 ierr = DMGetDefaultSF(dm, &patch->defaultSF);CHKERRQ(ierr); 447 ierr = PetscObjectReference((PetscObject) patch->defaultSF);CHKERRQ(ierr); 448 ierr = ISCreateGeneral(PETSC_COMM_SELF, numGhostBcs, ghostBcNodes, PETSC_COPY_VALUES, &patch->ghostBcNodes);CHKERRQ(ierr); 449 ierr = ISCreateGeneral(PETSC_COMM_SELF, numGlobalBcs, globalBcNodes, PETSC_COPY_VALUES, &patch->globalBcNodes);CHKERRQ(ierr); 450 PetscFunctionReturn(0); 451 } 452 453 /*@C 454 455 PCPatchSetComputeOperator - Set the callback used to compute patch matrices 456 457 Input Parameters: 458 + pc - The PC 459 . func - The callback 460 - ctx - The user context 461 462 Level: advanced 463 464 Note: 465 The callback has signature: 466 + usercomputeop(pc, point, mat, cellIS, n, u, ctx) 467 + pc - The PC 468 + point - The point 469 + mat - The patch matrix 470 + cellIS - An array of the cell numbers 471 + n - The size of g2l 472 + g2l - The global to local dof translation table 473 + ctx - The user context 474 and can assume that the matrix entries have been set to zero before the call. 475 476 .seealso: PCPatchGetComputeOperator(), PCPatchSetDiscretisationInfo() 477 @*/ 478 PetscErrorCode PCPatchSetComputeOperator(PC pc, PetscErrorCode (*func)(PC, PetscInt, Mat, IS, PetscInt, const PetscInt *, void *), void *ctx) 479 { 480 PC_PATCH *patch = (PC_PATCH *) pc->data; 481 482 PetscFunctionBegin; 483 patch->usercomputeop = func; 484 patch->usercomputectx = ctx; 485 PetscFunctionReturn(0); 486 } 487 488 /* On entry, ht contains the topological entities whose dofs we are responsible for solving for; 489 on exit, cht contains all the topological entities we need to compute their residuals. 490 In full generality this should incorporate knowledge of the sparsity pattern of the matrix; 491 here we assume a standard FE sparsity pattern.*/ 492 /* TODO: Use DMPlexGetAdjacency() */ 493 /* TODO: Look at temp buffer management for GetClosure() */ 494 static PetscErrorCode PCPatchCompleteCellPatch(PC pc, PetscHashI ht, PetscHashI cht) 495 { 496 DM dm; 497 PetscHashIIter hi; 498 PetscInt point; 499 PetscInt *star = NULL, *closure = NULL; 500 PetscInt ignoredim, iStart = 0, iEnd = -1, starSize, closureSize, si, ci; 501 PetscErrorCode ierr; 502 503 PetscFunctionBegin; 504 ierr = PCGetDM(pc, &dm);CHKERRQ(ierr); 505 ierr = PCPatchGetIgnoreDim(pc, &ignoredim);CHKERRQ(ierr); 506 if (ignoredim >= 0) {ierr = DMPlexGetDepthStratum(dm, ignoredim, &iStart, &iEnd);CHKERRQ(ierr);} 507 PetscHashIClear(cht); 508 PetscHashIIterBegin(ht, hi); 509 while (!PetscHashIIterAtEnd(ht, hi)) { 510 511 PetscHashIIterGetKey(ht, hi, point); 512 PetscHashIIterNext(ht, hi); 513 514 /* Loop over all the cells that this point connects to */ 515 ierr = DMPlexGetTransitiveClosure(dm, point, PETSC_FALSE, &starSize, &star);CHKERRQ(ierr); 516 for (si = 0; si < starSize*2; si += 2) { 517 const PetscInt ownedpoint = star[si]; 518 /* TODO Check for point in cht before running through closure again */ 519 /* now loop over all entities in the closure of that cell */ 520 ierr = DMPlexGetTransitiveClosure(dm, ownedpoint, PETSC_TRUE, &closureSize, &closure);CHKERRQ(ierr); 521 for (ci = 0; ci < closureSize*2; ci += 2) { 522 const PetscInt seenpoint = closure[ci]; 523 if (ignoredim >= 0 && seenpoint >= iStart && seenpoint < iEnd) continue; 524 PetscHashIAdd(cht, seenpoint, 0); 525 } 526 } 527 } 528 ierr = DMPlexRestoreTransitiveClosure(dm, 0, PETSC_TRUE, NULL, &closure);CHKERRQ(ierr); 529 ierr = DMPlexRestoreTransitiveClosure(dm, 0, PETSC_FALSE, NULL, &star);CHKERRQ(ierr); 530 PetscFunctionReturn(0); 531 } 532 533 static PetscErrorCode PCPatchGetGlobalDofs(PC pc, PetscSection dofSection[], PetscInt f, PetscBool combined, PetscInt p, PetscInt *dof, PetscInt *off) 534 { 535 PetscErrorCode ierr; 536 537 PetscFunctionBegin; 538 if (combined) { 539 if (f < 0) { 540 if (dof) {ierr = PetscSectionGetDof(dofSection[0], p, dof);CHKERRQ(ierr);} 541 if (off) {ierr = PetscSectionGetOffset(dofSection[0], p, off);CHKERRQ(ierr);} 542 } else { 543 if (dof) {ierr = PetscSectionGetFieldDof(dofSection[0], p, f, dof);CHKERRQ(ierr);} 544 if (off) {ierr = PetscSectionGetFieldOffset(dofSection[0], p, f, off);CHKERRQ(ierr);} 545 } 546 } else { 547 if (f < 0) { 548 PC_PATCH *patch = (PC_PATCH *) pc->data; 549 PetscInt fdof, g; 550 551 if (dof) { 552 *dof = 0; 553 for (g = 0; g < patch->nsubspaces; ++g) { 554 ierr = PetscSectionGetDof(dofSection[g], p, &fdof);CHKERRQ(ierr); 555 *dof += fdof; 556 } 557 } 558 if (off) {ierr = PetscSectionGetOffset(dofSection[0], p, off);CHKERRQ(ierr);} 559 } else { 560 if (dof) {ierr = PetscSectionGetDof(dofSection[f], p, dof);CHKERRQ(ierr);} 561 if (off) {ierr = PetscSectionGetOffset(dofSection[f], p, off);CHKERRQ(ierr);} 562 } 563 } 564 PetscFunctionReturn(0); 565 } 566 567 /* Given a hash table with a set of topological entities (pts), compute the degrees of 568 freedom in global concatenated numbering on those entities. 569 For Vanka smoothing, this needs to do something special: ignore dofs of the 570 constraint subspace on entities that aren't the base entity we're building the patch 571 around. */ 572 static PetscErrorCode PCPatchGetPointDofs(PC pc, PetscHashI pts, PetscHashI dofs, PetscInt base, PetscInt exclude_subspace) 573 { 574 PC_PATCH *patch = (PC_PATCH *) pc->data; 575 PetscHashIIter hi; 576 PetscInt ldof, loff; 577 PetscInt k, p; 578 PetscErrorCode ierr; 579 580 PetscFunctionBegin; 581 PetscHashIClear(dofs); 582 for (k = 0; k < patch->nsubspaces; ++k) { 583 PetscInt subspaceOffset = patch->subspaceOffsets[k]; 584 PetscInt bs = patch->bs[k]; 585 PetscInt j, l; 586 587 if (k == exclude_subspace) { 588 /* only get this subspace dofs at the base entity, not any others */ 589 ierr = PCPatchGetGlobalDofs(pc, patch->dofSection, k, patch->combined, base, &ldof, &loff);CHKERRQ(ierr); 590 if (0 == ldof) continue; 591 for (j = loff; j < ldof + loff; ++j) { 592 for (l = 0; l < bs; ++l) { 593 PetscInt dof = bs*j + l + subspaceOffset; 594 PetscHashIAdd(dofs, dof, 0); 595 } 596 } 597 continue; /* skip the other dofs of this subspace */ 598 } 599 600 PetscHashIIterBegin(pts, hi); 601 while (!PetscHashIIterAtEnd(pts, hi)) { 602 PetscHashIIterGetKey(pts, hi, p); 603 PetscHashIIterNext(pts, hi); 604 ierr = PCPatchGetGlobalDofs(pc, patch->dofSection, k, patch->combined, p, &ldof, &loff);CHKERRQ(ierr); 605 if (0 == ldof) continue; 606 for (j = loff; j < ldof + loff; ++j) { 607 for (l = 0; l < bs; ++l) { 608 PetscInt dof = bs*j + l + subspaceOffset; 609 PetscHashIAdd(dofs, dof, 0); 610 } 611 } 612 } 613 } 614 PetscFunctionReturn(0); 615 } 616 617 /* Given two hash tables A and B, compute the keys in B that are not in A, and put them in C */ 618 static PetscErrorCode PCPatchComputeSetDifference_Private(PetscHashI A, PetscHashI B, PetscHashI C) 619 { 620 PetscHashIIter hi; 621 PetscInt key, val; 622 PetscBool flg; 623 624 PetscFunctionBegin; 625 PetscHashIClear(C); 626 PetscHashIIterBegin(B, hi); 627 while (!PetscHashIIterAtEnd(B, hi)) { 628 PetscHashIIterGetKeyVal(B, hi, key, val); 629 PetscHashIIterNext(B, hi); 630 PetscHashIHasKey(A, key, flg); 631 if (!flg) {PetscHashIAdd(C, key, val);} 632 } 633 PetscFunctionReturn(0); 634 } 635 636 /* 637 * PCPatchCreateCellPatches - create patches. 638 * 639 * Input Parameters: 640 * + dm - The DMPlex object defining the mesh 641 * 642 * Output Parameters: 643 * + cellCounts - Section with counts of cells around each vertex 644 * . cells - IS of the cell point indices of cells in each patch 645 * . pointCounts - Section with counts of cells around each vertex 646 * - point - IS of the cell point indices of cells in each patch 647 */ 648 static PetscErrorCode PCPatchCreateCellPatches(PC pc) 649 { 650 PC_PATCH *patch = (PC_PATCH *) pc->data; 651 DMLabel ghost = NULL; 652 DM dm, plex; 653 PetscHashI ht, cht; 654 PetscSection cellCounts, pointCounts; 655 PetscInt *cellsArray, *pointsArray; 656 PetscInt numCells, numPoints; 657 const PetscInt *leaves; 658 PetscInt nleaves, pStart, pEnd, cStart, cEnd, vStart, vEnd, v; 659 PetscBool isFiredrake; 660 PetscErrorCode ierr; 661 662 PetscFunctionBegin; 663 /* Used to keep track of the cells in the patch. */ 664 PetscHashICreate(ht); 665 PetscHashICreate(cht); 666 667 ierr = PCGetDM(pc, &dm);CHKERRQ(ierr); 668 if (!dm) SETERRQ(PetscObjectComm((PetscObject) pc), PETSC_ERR_ARG_WRONGSTATE, "DM not yet set on patch PC\n"); 669 ierr = DMConvert(dm, DMPLEX, &plex);CHKERRQ(ierr); 670 ierr = DMPlexGetChart(plex, &pStart, &pEnd);CHKERRQ(ierr); 671 ierr = DMPlexGetHeightStratum(plex, 0, &cStart, &cEnd);CHKERRQ(ierr); 672 673 if (patch->user_patches) { 674 ierr = patch->userpatchconstructionop(pc, &patch->npatch, &patch->userIS, &patch->iterationSet, patch->userpatchconstructctx);CHKERRQ(ierr); 675 vStart = 0; vEnd = patch->npatch; 676 } else if (patch->codim < 0) { 677 if (patch->dim < 0) {ierr = DMPlexGetDepthStratum(plex, 0, &vStart, &vEnd);CHKERRQ(ierr);} 678 else {ierr = DMPlexGetDepthStratum(plex, patch->dim, &vStart, &vEnd);CHKERRQ(ierr);} 679 } else {ierr = DMPlexGetHeightStratum(plex, patch->codim, &vStart, &vEnd);CHKERRQ(ierr);} 680 patch->npatch = vEnd - vStart; 681 682 /* These labels mark the owned points. We only create patches around points that this process owns. */ 683 ierr = DMHasLabel(dm, "pyop2_ghost", &isFiredrake);CHKERRQ(ierr); 684 if (isFiredrake) { 685 ierr = DMGetLabel(dm, "pyop2_ghost", &ghost);CHKERRQ(ierr); 686 ierr = DMLabelCreateIndex(ghost, pStart, pEnd);CHKERRQ(ierr); 687 } else { 688 PetscSF sf; 689 690 ierr = DMGetPointSF(dm, &sf);CHKERRQ(ierr); 691 ierr = PetscSFGetGraph(sf, NULL, &nleaves, &leaves, NULL);CHKERRQ(ierr); 692 nleaves = PetscMax(nleaves, 0); 693 } 694 695 ierr = PetscSectionCreate(PETSC_COMM_SELF, &patch->cellCounts);CHKERRQ(ierr); 696 ierr = PetscObjectSetName((PetscObject) patch->cellCounts, "Patch Cell Layout");CHKERRQ(ierr); 697 cellCounts = patch->cellCounts; 698 ierr = PetscSectionSetChart(cellCounts, vStart, vEnd);CHKERRQ(ierr); 699 ierr = PetscSectionCreate(PETSC_COMM_SELF, &patch->pointCounts);CHKERRQ(ierr); 700 ierr = PetscObjectSetName((PetscObject) patch->pointCounts, "Patch Point Layout");CHKERRQ(ierr); 701 pointCounts = patch->pointCounts; 702 ierr = PetscSectionSetChart(pointCounts, vStart, vEnd);CHKERRQ(ierr); 703 /* Count cells and points in the patch surrounding each entity */ 704 for (v = vStart; v < vEnd; ++v) { 705 PetscHashIIter hi; 706 PetscInt chtSize, loc = -1; 707 PetscBool flg; 708 709 if (!patch->user_patches) { 710 if (ghost) {ierr = DMLabelHasPoint(ghost, v, &flg);CHKERRQ(ierr);} 711 else {ierr = PetscFindInt(v, nleaves, leaves, &loc); flg = loc >=0 ? PETSC_TRUE : PETSC_FALSE;} 712 /* Not an owned entity, don't make a cell patch. */ 713 if (flg) continue; 714 } 715 716 ierr = patch->patchconstructop((void *) patch, dm, v, ht);CHKERRQ(ierr); 717 ierr = PCPatchCompleteCellPatch(pc, ht, cht);CHKERRQ(ierr); 718 PetscHashISize(cht, chtSize); 719 /* empty patch, continue */ 720 if (chtSize == 0) continue; 721 722 /* safe because size(cht) > 0 from above */ 723 PetscHashIIterBegin(cht, hi); 724 while (!PetscHashIIterAtEnd(cht, hi)) { 725 PetscInt point, pdof; 726 727 PetscHashIIterGetKey(cht, hi, point); 728 ierr = PCPatchGetGlobalDofs(pc, patch->dofSection, -1, patch->combined, point, &pdof, NULL);CHKERRQ(ierr); 729 if (pdof) {ierr = PetscSectionAddDof(pointCounts, v, 1);CHKERRQ(ierr);} 730 if (point >= cStart && point < cEnd) {ierr = PetscSectionAddDof(cellCounts, v, 1);CHKERRQ(ierr);} 731 PetscHashIIterNext(cht, hi); 732 } 733 } 734 if (isFiredrake) {ierr = DMLabelDestroyIndex(ghost);CHKERRQ(ierr);} 735 736 ierr = PetscSectionSetUp(cellCounts);CHKERRQ(ierr); 737 ierr = PetscSectionGetStorageSize(cellCounts, &numCells);CHKERRQ(ierr); 738 ierr = PetscMalloc1(numCells, &cellsArray);CHKERRQ(ierr); 739 ierr = PetscSectionSetUp(pointCounts);CHKERRQ(ierr); 740 ierr = PetscSectionGetStorageSize(pointCounts, &numPoints);CHKERRQ(ierr); 741 ierr = PetscMalloc1(numPoints, &pointsArray);CHKERRQ(ierr); 742 743 /* Now that we know how much space we need, run through again and actually remember the cells. */ 744 for (v = vStart; v < vEnd; v++ ) { 745 PetscHashIIter hi; 746 PetscInt dof, off, cdof, coff, pdof, n = 0, cn = 0; 747 748 ierr = PetscSectionGetDof(pointCounts, v, &dof);CHKERRQ(ierr); 749 ierr = PetscSectionGetOffset(pointCounts, v, &off);CHKERRQ(ierr); 750 ierr = PetscSectionGetDof(cellCounts, v, &cdof);CHKERRQ(ierr); 751 ierr = PetscSectionGetOffset(cellCounts, v, &coff);CHKERRQ(ierr); 752 if (dof <= 0) continue; 753 ierr = patch->patchconstructop((void *) patch, dm, v, ht);CHKERRQ(ierr); 754 ierr = PCPatchCompleteCellPatch(pc, ht, cht);CHKERRQ(ierr); 755 PetscHashIIterBegin(cht, hi); 756 while (!PetscHashIIterAtEnd(cht, hi)) { 757 PetscInt point; 758 759 PetscHashIIterGetKey(cht, hi, point); 760 ierr = PCPatchGetGlobalDofs(pc, patch->dofSection, -1, patch->combined, point, &pdof, NULL);CHKERRQ(ierr); 761 if (pdof) {pointsArray[off + n++] = point;} 762 if (point >= cStart && point < cEnd) {cellsArray[coff + cn++] = point;} 763 PetscHashIIterNext(cht, hi); 764 } 765 if (cn != cdof) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Number of cells in patch %D is %D, but should be %D", v, cn, cdof); 766 if (n != dof) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_SIZ, "Number of points in patch %D is %D, but should be %D", v, n, dof); 767 } 768 PetscHashIDestroy(ht); 769 PetscHashIDestroy(cht); 770 ierr = DMDestroy(&plex);CHKERRQ(ierr); 771 772 ierr = ISCreateGeneral(PETSC_COMM_SELF, numCells, cellsArray, PETSC_OWN_POINTER, &patch->cells);CHKERRQ(ierr); 773 ierr = PetscObjectSetName((PetscObject) patch->cells, "Patch Cells");CHKERRQ(ierr); 774 if (patch->viewCells) { 775 ierr = ObjectView((PetscObject) patch->cellCounts, patch->viewerCells, patch->formatCells);CHKERRQ(ierr); 776 ierr = ObjectView((PetscObject) patch->cells, patch->viewerCells, patch->formatCells);CHKERRQ(ierr); 777 } 778 ierr = ISCreateGeneral(PETSC_COMM_SELF, numPoints, pointsArray, PETSC_OWN_POINTER, &patch->points);CHKERRQ(ierr); 779 ierr = PetscObjectSetName((PetscObject) patch->points, "Patch Points");CHKERRQ(ierr); 780 if (patch->viewPoints) { 781 ierr = ObjectView((PetscObject) patch->pointCounts, patch->viewerPoints, patch->formatPoints);CHKERRQ(ierr); 782 ierr = ObjectView((PetscObject) patch->points, patch->viewerPoints, patch->formatPoints);CHKERRQ(ierr); 783 } 784 PetscFunctionReturn(0); 785 } 786 787 /* 788 * PCPatchCreateCellPatchDiscretisationInfo - Build the dof maps for cell patches 789 * 790 * Input Parameters: 791 * + dm - The DMPlex object defining the mesh 792 * . cellCounts - Section with counts of cells around each vertex 793 * . cells - IS of the cell point indices of cells in each patch 794 * . cellNumbering - Section mapping plex cell points to Firedrake cell indices. 795 * . nodesPerCell - number of nodes per cell. 796 * - cellNodeMap - map from cells to node indices (nodesPerCell * numCells) 797 * 798 * Output Parameters: 799 * + dofs - IS of local dof numbers of each cell in the patch, where local is a patch local numbering 800 * . gtolCounts - Section with counts of dofs per cell patch 801 * - gtol - IS mapping from global dofs to local dofs for each patch. 802 */ 803 static PetscErrorCode PCPatchCreateCellPatchDiscretisationInfo(PC pc) 804 { 805 PC_PATCH *patch = (PC_PATCH *) pc->data; 806 PetscSection cellCounts = patch->cellCounts; 807 PetscSection pointCounts = patch->pointCounts; 808 PetscSection gtolCounts; 809 IS cells = patch->cells; 810 IS points = patch->points; 811 PetscSection cellNumbering = patch->cellNumbering; 812 PetscInt Nf = patch->nsubspaces; 813 PetscInt numCells, numPoints; 814 PetscInt numDofs; 815 PetscInt numGlobalDofs; 816 PetscInt totalDofsPerCell = patch->totalDofsPerCell; 817 PetscInt vStart, vEnd, v; 818 const PetscInt *cellsArray, *pointsArray; 819 PetscInt *newCellsArray = NULL; 820 PetscInt *dofsArray = NULL; 821 PetscInt *offsArray = NULL; 822 PetscInt *asmArray = NULL; 823 PetscInt *globalDofsArray = NULL; 824 PetscInt globalIndex = 0; 825 PetscInt key = 0; 826 PetscInt asmKey = 0; 827 DM dm = NULL; 828 const PetscInt *bcNodes = NULL; 829 PetscHashI ht; 830 PetscHashI globalBcs; 831 PetscInt numBcs; 832 PetscHashI ownedpts, seenpts, owneddofs, seendofs, artificialbcs; 833 PetscInt pStart, pEnd, p; 834 PetscErrorCode ierr; 835 836 PetscFunctionBegin; 837 838 ierr = PCGetDM(pc, &dm); CHKERRQ(ierr); 839 /* dofcounts section is cellcounts section * dofPerCell */ 840 ierr = PetscSectionGetStorageSize(cellCounts, &numCells);CHKERRQ(ierr); 841 ierr = PetscSectionGetStorageSize(patch->pointCounts, &numPoints);CHKERRQ(ierr); 842 numDofs = numCells * totalDofsPerCell; 843 ierr = PetscMalloc1(numDofs, &dofsArray);CHKERRQ(ierr); 844 ierr = PetscMalloc1(numPoints*Nf, &offsArray);CHKERRQ(ierr); 845 ierr = PetscMalloc1(numDofs, &asmArray);CHKERRQ(ierr); 846 ierr = PetscMalloc1(numCells, &newCellsArray);CHKERRQ(ierr); 847 ierr = PetscSectionGetChart(cellCounts, &vStart, &vEnd);CHKERRQ(ierr); 848 ierr = PetscSectionCreate(PETSC_COMM_SELF, &patch->gtolCounts);CHKERRQ(ierr); 849 gtolCounts = patch->gtolCounts; 850 ierr = PetscSectionSetChart(gtolCounts, vStart, vEnd);CHKERRQ(ierr); 851 ierr = PetscObjectSetName((PetscObject) patch->gtolCounts, "Patch Global Index Section");CHKERRQ(ierr); 852 853 /* Outside the patch loop, get the dofs that are globally-enforced Dirichlet 854 conditions */ 855 PetscHashICreate(globalBcs); 856 ierr = ISGetIndices(patch->ghostBcNodes, &bcNodes); CHKERRQ(ierr); 857 ierr = ISGetSize(patch->ghostBcNodes, &numBcs); CHKERRQ(ierr); 858 for ( PetscInt i = 0; i < numBcs; i++ ) { 859 PetscHashIAdd(globalBcs, bcNodes[i], 0); /* these are already in concatenated numbering */ 860 } 861 ierr = ISRestoreIndices(patch->ghostBcNodes, &bcNodes); CHKERRQ(ierr); 862 ierr = ISDestroy(&patch->ghostBcNodes); CHKERRQ(ierr); /* memory optimisation */ 863 864 /* Hash tables for artificial BC construction */ 865 PetscHashICreate(ownedpts); 866 PetscHashICreate(seenpts); 867 PetscHashICreate(owneddofs); 868 PetscHashICreate(seendofs); 869 PetscHashICreate(artificialbcs); 870 871 ierr = ISGetIndices(cells, &cellsArray);CHKERRQ(ierr); 872 ierr = ISGetIndices(points, &pointsArray);CHKERRQ(ierr); 873 PetscHashICreate(ht); 874 for (v = vStart; v < vEnd; ++v) { 875 PetscInt localIndex = 0; 876 PetscInt dof, off, i, j, k, l; 877 878 PetscHashIClear(ht); 879 ierr = PetscSectionGetDof(cellCounts, v, &dof);CHKERRQ(ierr); 880 ierr = PetscSectionGetOffset(cellCounts, v, &off);CHKERRQ(ierr); 881 if (dof <= 0) continue; 882 883 /* Calculate the global numbers of the artificial BC dofs here first */ 884 ierr = patch->patchconstructop((void*)patch, dm, v, ownedpts); CHKERRQ(ierr); 885 ierr = PCPatchCompleteCellPatch(pc, ownedpts, seenpts); CHKERRQ(ierr); 886 ierr = PCPatchGetPointDofs(pc, ownedpts, owneddofs, v, patch->exclude_subspace); CHKERRQ(ierr); 887 ierr = PCPatchGetPointDofs(pc, seenpts, seendofs, v, -1); CHKERRQ(ierr); 888 ierr = PCPatchComputeSetDifference_Private(owneddofs, seendofs, artificialbcs); CHKERRQ(ierr); 889 if (patch->viewPatches) { 890 PetscHashI globalbcdofs; 891 PetscHashIIter hi; 892 PetscHashICreate(globalbcdofs); 893 894 MPI_Comm comm = PetscObjectComm((PetscObject)pc); 895 ierr = PetscSynchronizedPrintf(comm, "Patch %d: owned dofs:\n", v); CHKERRQ(ierr); 896 PetscHashIIterBegin(owneddofs, hi); 897 while (!PetscHashIIterAtEnd(owneddofs, hi)) { 898 PetscInt globalDof; 899 900 PetscHashIIterGetKey(owneddofs, hi, globalDof); 901 PetscHashIIterNext(owneddofs, hi); 902 ierr = PetscSynchronizedPrintf(comm, "%d ", globalDof); CHKERRQ(ierr); 903 } 904 ierr = PetscSynchronizedPrintf(comm, "\n"); CHKERRQ(ierr); 905 ierr = PetscSynchronizedPrintf(comm, "Patch %d: seen dofs:\n", v); CHKERRQ(ierr); 906 PetscHashIIterBegin(seendofs, hi); 907 while (!PetscHashIIterAtEnd(seendofs, hi)) { 908 PetscInt globalDof; 909 PetscBool flg; 910 911 PetscHashIIterGetKey(seendofs, hi, globalDof); 912 PetscHashIIterNext(seendofs, hi); 913 ierr = PetscSynchronizedPrintf(comm, "%d ", globalDof); CHKERRQ(ierr); 914 915 PetscHashIHasKey(globalBcs, globalDof, flg); 916 if (flg) { 917 PetscHashIAdd(globalbcdofs, globalDof, 0); 918 } 919 } 920 ierr = PetscSynchronizedPrintf(comm, "\n"); CHKERRQ(ierr); 921 ierr = PetscSynchronizedPrintf(comm, "Patch %d: global BCs:\n", v); CHKERRQ(ierr); 922 PetscHashISize(globalbcdofs, numBcs); 923 if (numBcs > 0) { 924 PetscHashIIterBegin(globalbcdofs, hi); 925 while (!PetscHashIIterAtEnd(globalbcdofs, hi)) { 926 PetscInt globalDof; 927 PetscHashIIterGetKey(globalbcdofs, hi, globalDof); 928 PetscHashIIterNext(globalbcdofs, hi); 929 ierr = PetscSynchronizedPrintf(comm, "%d ", globalDof); CHKERRQ(ierr); 930 } 931 } 932 ierr = PetscSynchronizedPrintf(comm, "\n"); CHKERRQ(ierr); 933 ierr = PetscSynchronizedPrintf(comm, "Patch %d: artificial BCs:\n", v); CHKERRQ(ierr); 934 PetscHashISize(artificialbcs, numBcs); 935 if (numBcs > 0) { 936 PetscHashIIterBegin(artificialbcs, hi); 937 while (!PetscHashIIterAtEnd(artificialbcs, hi)) { 938 PetscInt globalDof; 939 PetscHashIIterGetKey(artificialbcs, hi, globalDof); 940 PetscHashIIterNext(artificialbcs, hi); 941 ierr = PetscSynchronizedPrintf(comm, "%d ", globalDof); CHKERRQ(ierr); 942 } 943 } 944 ierr = PetscSynchronizedPrintf(comm, "\n\n"); CHKERRQ(ierr); 945 PetscHashIDestroy(globalbcdofs); 946 } 947 for (k = 0; k < patch->nsubspaces; ++k) { 948 const PetscInt *cellNodeMap = patch->cellNodeMap[k]; 949 PetscInt nodesPerCell = patch->nodesPerCell[k]; 950 PetscInt subspaceOffset = patch->subspaceOffsets[k]; 951 PetscInt bs = patch->bs[k]; 952 953 for (i = off; i < off + dof; ++i) { 954 /* Walk over the cells in this patch. */ 955 const PetscInt c = cellsArray[i]; 956 PetscInt cell = c; 957 958 /* TODO Change this to an IS */ 959 if (cellNumbering) { 960 ierr = PetscSectionGetDof(cellNumbering, c, &cell);CHKERRQ(ierr); 961 if (cell <= 0) SETERRQ1(PetscObjectComm((PetscObject) pc), PETSC_ERR_ARG_OUTOFRANGE, "Cell %D doesn't appear in cell numbering map", c); 962 ierr = PetscSectionGetOffset(cellNumbering, c, &cell);CHKERRQ(ierr); 963 } 964 newCellsArray[i] = cell; 965 for (j = 0; j < nodesPerCell; ++j) { 966 /* For each global dof, map it into contiguous local storage. */ 967 const PetscInt globalDof = cellNodeMap[cell*nodesPerCell + j]*bs + subspaceOffset; 968 /* finally, loop over block size */ 969 for (l = 0; l < bs; ++l) { 970 PetscInt localDof, isGlobalBcDof, isArtificialBcDof; 971 972 /* first, check if this is either a globally enforced or locally enforced BC dof */ 973 PetscHashIMap(globalBcs, globalDof + l, isGlobalBcDof); 974 PetscHashIMap(artificialbcs, globalDof + l, isArtificialBcDof); 975 976 /* if it's either, don't ever give it a local dof number */ 977 if (isGlobalBcDof >= 0 || isArtificialBcDof >= 0) { 978 dofsArray[globalIndex++] = -1; /* don't use this in assembly in this patch */ 979 } else { 980 PetscHashIMap(ht, globalDof + l, localDof); 981 if (localDof == -1) { 982 localDof = localIndex++; 983 PetscHashIAdd(ht, globalDof + l, localDof); 984 } 985 if ( globalIndex >= numDofs ) SETERRQ2(PETSC_COMM_WORLD, PETSC_ERR_ARG_OUTOFRANGE, "Found more dofs %D than expected %D", globalIndex+1, numDofs); 986 /* And store. */ 987 dofsArray[globalIndex++] = localDof; 988 } 989 } 990 } 991 } 992 } 993 /* How many local dofs in this patch? */ 994 PetscHashISize(ht, dof); 995 ierr = PetscSectionSetDof(gtolCounts, v, dof);CHKERRQ(ierr); 996 } 997 if (globalIndex != numDofs) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Expected number of dofs (%d) doesn't match found number (%d)", numDofs, globalIndex); 998 ierr = PetscSectionSetUp(gtolCounts);CHKERRQ(ierr); 999 ierr = PetscSectionGetStorageSize(gtolCounts, &numGlobalDofs);CHKERRQ(ierr); 1000 ierr = PetscMalloc1(numGlobalDofs, &globalDofsArray);CHKERRQ(ierr); 1001 1002 /* Now populate the global to local map. This could be merged into the above loop if we were willing to deal with reallocs. */ 1003 for (v = vStart; v < vEnd; ++v) { 1004 PetscHashIIter hi; 1005 PetscInt dof, off, Np, ooff, i, j, k, l; 1006 1007 PetscHashIClear(ht); 1008 ierr = PetscSectionGetDof(cellCounts, v, &dof);CHKERRQ(ierr); 1009 ierr = PetscSectionGetOffset(cellCounts, v, &off);CHKERRQ(ierr); 1010 ierr = PetscSectionGetDof(pointCounts, v, &Np);CHKERRQ(ierr); 1011 ierr = PetscSectionGetOffset(pointCounts, v, &ooff);CHKERRQ(ierr); 1012 if (dof <= 0) continue; 1013 1014 for (k = 0; k < patch->nsubspaces; ++k) { 1015 const PetscInt *cellNodeMap = patch->cellNodeMap[k]; 1016 PetscInt nodesPerCell = patch->nodesPerCell[k]; 1017 PetscInt subspaceOffset = patch->subspaceOffsets[k]; 1018 PetscInt bs = patch->bs[k]; 1019 1020 for (i = off; i < off + dof; ++i) { 1021 /* Reconstruct mapping of global-to-local on this patch. */ 1022 const PetscInt c = cellsArray[i]; 1023 PetscInt cell = c; 1024 1025 if (cellNumbering) {ierr = PetscSectionGetOffset(cellNumbering, c, &cell);CHKERRQ(ierr);} 1026 for (j = 0; j < nodesPerCell; ++j) { 1027 for (l = 0; l < bs; ++l) { 1028 const PetscInt globalDof = cellNodeMap[cell*nodesPerCell + j]*bs + l + subspaceOffset; 1029 const PetscInt localDof = dofsArray[key++]; 1030 1031 if (localDof >= 0) PetscHashIAdd(ht, globalDof, localDof); 1032 } 1033 } 1034 } 1035 1036 /* Shove it in the output data structure. */ 1037 PetscInt goff; 1038 1039 ierr = PetscSectionGetOffset(gtolCounts, v, &goff);CHKERRQ(ierr); 1040 PetscHashIIterBegin(ht, hi); 1041 while (!PetscHashIIterAtEnd(ht, hi)) { 1042 PetscInt globalDof, localDof; 1043 1044 PetscHashIIterGetKeyVal(ht, hi, globalDof, localDof); 1045 if (globalDof >= 0) globalDofsArray[goff + localDof] = globalDof; 1046 PetscHashIIterNext(ht, hi); 1047 } 1048 1049 for (p = 0; p < Np; ++p) { 1050 const PetscInt point = pointsArray[ooff + p]; 1051 PetscInt globalDof, localDof; 1052 1053 ierr = PCPatchGetGlobalDofs(pc, patch->dofSection, k, patch->combined, point, NULL, &globalDof);CHKERRQ(ierr); 1054 PetscHashIMap(ht, globalDof, localDof); 1055 offsArray[(ooff + p)*Nf + k] = localDof; 1056 } 1057 } 1058 1059 PetscHashIDestroy(ownedpts); 1060 PetscHashIDestroy(seenpts); 1061 PetscHashIDestroy(owneddofs); 1062 PetscHashIDestroy(seendofs); 1063 PetscHashIDestroy(artificialbcs); 1064 1065 /* At this point, we have a hash table ht built that maps globalDof -> localDof. 1066 We need to create the dof table laid out cellwise first, then by subspace, 1067 as the assembler assembles cell-wise and we need to stuff the different 1068 contributions of the different function spaces to the right places. So we loop 1069 over cells, then over subspaces. */ 1070 if (patch->nsubspaces > 1) { /* for nsubspaces = 1, data we need is already in dofsArray */ 1071 for (i = off; i < off + dof; ++i) { 1072 const PetscInt c = cellsArray[i]; 1073 PetscInt cell = c; 1074 1075 if (cellNumbering) {ierr = PetscSectionGetOffset(cellNumbering, c, &cell);CHKERRQ(ierr);} 1076 for (k = 0; k < patch->nsubspaces; ++k) { 1077 const PetscInt *cellNodeMap = patch->cellNodeMap[k]; 1078 PetscInt nodesPerCell = patch->nodesPerCell[k]; 1079 PetscInt subspaceOffset = patch->subspaceOffsets[k]; 1080 PetscInt bs = patch->bs[k]; 1081 1082 for (j = 0; j < nodesPerCell; ++j) { 1083 for (l = 0; l < bs; ++l) { 1084 const PetscInt globalDof = cellNodeMap[cell*nodesPerCell + j]*bs + l + subspaceOffset; 1085 PetscInt localDof; 1086 1087 PetscHashIMap(ht, globalDof, localDof); 1088 /* If it's not in the hash table, i.e. is a BC dof, 1089 then the PetscHashIMap above gives -1, which matches 1090 exactly the convention for PETSc's matrix assembly to 1091 ignore the dof. So we don't need to do anything here */ 1092 asmArray[asmKey++] = localDof; 1093 } 1094 } 1095 } 1096 } 1097 } 1098 } 1099 if (1 == patch->nsubspaces) {ierr = PetscMemcpy(asmArray, dofsArray, numDofs * sizeof(PetscInt));CHKERRQ(ierr);} 1100 1101 PetscHashIDestroy(ht); 1102 ierr = ISRestoreIndices(cells, &cellsArray);CHKERRQ(ierr); 1103 ierr = ISRestoreIndices(points, &pointsArray);CHKERRQ(ierr); 1104 ierr = PetscFree(dofsArray);CHKERRQ(ierr); 1105 /* Create placeholder section for map from points to patch dofs */ 1106 ierr = PetscSectionCreate(PETSC_COMM_SELF, &patch->patchSection);CHKERRQ(ierr); 1107 ierr = PetscSectionSetNumFields(patch->patchSection, patch->nsubspaces);CHKERRQ(ierr); 1108 ierr = PetscSectionGetChart(patch->dofSection[0], &pStart, &pEnd);CHKERRQ(ierr); 1109 ierr = PetscSectionSetChart(patch->patchSection, pStart, pEnd);CHKERRQ(ierr); 1110 for (p = pStart; p < pEnd; ++p) { 1111 PetscInt dof, fdof, f; 1112 1113 ierr = PetscSectionGetDof(patch->dofSection[0], p, &dof);CHKERRQ(ierr); 1114 ierr = PetscSectionSetDof(patch->patchSection, p, dof);CHKERRQ(ierr); 1115 for (f = 0; f < patch->nsubspaces; ++f) { 1116 ierr = PetscSectionGetFieldDof(patch->dofSection[0], p, f, &fdof); 1117 if (ierr == 0) { 1118 ierr = PetscSectionSetFieldDof(patch->patchSection, p, f, fdof);CHKERRQ(ierr); 1119 } 1120 else { 1121 /* assume only one field */ 1122 ierr = PetscSectionSetFieldDof(patch->patchSection, p, f, dof);CHKERRQ(ierr); 1123 } 1124 } 1125 } 1126 ierr = PetscSectionSetUp(patch->patchSection);CHKERRQ(ierr); 1127 ierr = PetscSectionSetUseFieldOffsets(patch->patchSection, PETSC_TRUE);CHKERRQ(ierr); 1128 /* Replace cell indices with firedrake-numbered ones. */ 1129 ierr = ISGeneralSetIndices(cells, numCells, (const PetscInt *) newCellsArray, PETSC_OWN_POINTER);CHKERRQ(ierr); 1130 ierr = ISCreateGeneral(PETSC_COMM_SELF, numGlobalDofs, globalDofsArray, PETSC_OWN_POINTER, &patch->gtol);CHKERRQ(ierr); 1131 ierr = PetscObjectSetName((PetscObject) patch->gtol, "Global Indices");CHKERRQ(ierr); 1132 ierr = PetscSectionViewFromOptions(patch->gtolCounts, (PetscObject) pc, "-pc_patch_g2l_view");CHKERRQ(ierr); 1133 ierr = ISViewFromOptions(patch->gtol, (PetscObject) pc, "-pc_patch_g2l_view");CHKERRQ(ierr); 1134 ierr = ISCreateGeneral(PETSC_COMM_SELF, numDofs, asmArray, PETSC_OWN_POINTER, &patch->dofs);CHKERRQ(ierr); 1135 ierr = ISCreateGeneral(PETSC_COMM_SELF, numPoints*Nf, offsArray, PETSC_OWN_POINTER, &patch->offs);CHKERRQ(ierr); 1136 PetscFunctionReturn(0); 1137 } 1138 1139 static PetscErrorCode PCPatchZeroFillMatrix_Private(Mat mat, const PetscInt ncell, const PetscInt ndof, const PetscInt *dof) 1140 { 1141 const PetscScalar *values = NULL; 1142 PetscInt rows, c, i; 1143 PetscErrorCode ierr; 1144 1145 PetscFunctionBegin; 1146 ierr = PetscCalloc1(ndof*ndof, &values);CHKERRQ(ierr); 1147 for (c = 0; c < ncell; ++c) { 1148 const PetscInt *idx = &dof[ndof*c]; 1149 ierr = MatSetValues(mat, ndof, idx, ndof, idx, values, INSERT_VALUES);CHKERRQ(ierr); 1150 } 1151 ierr = MatGetLocalSize(mat, &rows, NULL);CHKERRQ(ierr); 1152 for (i = 0; i < rows; ++i) { 1153 ierr = MatSetValues(mat, 1, &i, 1, &i, values, INSERT_VALUES);CHKERRQ(ierr); 1154 } 1155 ierr = MatAssemblyBegin(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1156 ierr = MatAssemblyEnd(mat, MAT_FINAL_ASSEMBLY);CHKERRQ(ierr); 1157 ierr = PetscFree(values);CHKERRQ(ierr); 1158 PetscFunctionReturn(0); 1159 } 1160 1161 static PetscErrorCode PCPatchCreateMatrix_Private(PC pc, PetscInt point, Mat *mat) 1162 { 1163 PC_PATCH *patch = (PC_PATCH *) pc->data; 1164 Vec x, y; 1165 PetscBool flg; 1166 PetscInt csize, rsize; 1167 const char *prefix = NULL; 1168 PetscErrorCode ierr; 1169 1170 PetscFunctionBegin; 1171 x = patch->patchX[point]; 1172 y = patch->patchY[point]; 1173 ierr = VecGetSize(x, &csize);CHKERRQ(ierr); 1174 ierr = VecGetSize(y, &rsize);CHKERRQ(ierr); 1175 ierr = MatCreate(PETSC_COMM_SELF, mat);CHKERRQ(ierr); 1176 ierr = PCGetOptionsPrefix(pc, &prefix);CHKERRQ(ierr); 1177 ierr = MatSetOptionsPrefix(*mat, prefix);CHKERRQ(ierr); 1178 ierr = MatAppendOptionsPrefix(*mat, "pc_patch_sub_");CHKERRQ(ierr); 1179 if (patch->sub_mat_type) {ierr = MatSetType(*mat, patch->sub_mat_type);CHKERRQ(ierr);} 1180 else if (!patch->sub_mat_type) {ierr = MatSetType(*mat, MATDENSE);CHKERRQ(ierr);} 1181 ierr = MatSetSizes(*mat, rsize, csize, rsize, csize);CHKERRQ(ierr); 1182 ierr = PetscObjectTypeCompare((PetscObject) *mat, MATDENSE, &flg);CHKERRQ(ierr); 1183 if (!flg) {ierr = PetscObjectTypeCompare((PetscObject)*mat, MATSEQDENSE, &flg);CHKERRQ(ierr);} 1184 /* Sparse patch matrices */ 1185 if (!flg) { 1186 PetscBT bt; 1187 PetscInt *dnnz = NULL; 1188 const PetscInt *dofsArray = NULL; 1189 PetscInt pStart, pEnd, ncell, offset, c, i, j; 1190 1191 ierr = ISGetIndices(patch->dofs, &dofsArray);CHKERRQ(ierr); 1192 ierr = PetscSectionGetChart(patch->cellCounts, &pStart, &pEnd);CHKERRQ(ierr); 1193 point += pStart; 1194 if (point >= pEnd) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Operator point %D not in [%D, %D)\n", point, pStart, pEnd);CHKERRQ(ierr); 1195 ierr = PetscSectionGetDof(patch->cellCounts, point, &ncell);CHKERRQ(ierr); 1196 ierr = PetscSectionGetOffset(patch->cellCounts, point, &offset);CHKERRQ(ierr); 1197 ierr = PetscCalloc1(rsize, &dnnz);CHKERRQ(ierr); 1198 ierr = PetscLogEventBegin(PC_Patch_Prealloc, pc, 0, 0, 0);CHKERRQ(ierr); 1199 /* XXX: This uses N^2 bits to store the sparsity pattern on a 1200 * patch. This is probably OK if the patches are not too big, 1201 * but could use quite a bit of memory for planes in 3D. 1202 * Should we switch based on the value of rsize to a 1203 * hash-table (slower, but more memory efficient) approach? */ 1204 ierr = PetscBTCreate(rsize*rsize, &bt);CHKERRQ(ierr); 1205 for (c = 0; c < ncell; ++c) { 1206 const PetscInt *idx = dofsArray + (offset + c)*patch->totalDofsPerCell; 1207 for (i = 0; i < patch->totalDofsPerCell; ++i) { 1208 const PetscInt row = idx[i]; 1209 if (row < 0) continue; 1210 for (j = 0; j < patch->totalDofsPerCell; ++j) { 1211 const PetscInt col = idx[j]; 1212 const PetscInt key = row*rsize + col; 1213 if (col < 0) continue; 1214 if (!PetscBTLookupSet(bt, key)) ++dnnz[row]; 1215 } 1216 } 1217 } 1218 ierr = PetscBTDestroy(&bt);CHKERRQ(ierr); 1219 ierr = MatXAIJSetPreallocation(*mat, 1, dnnz, NULL, NULL, NULL);CHKERRQ(ierr); 1220 ierr = PetscFree(dnnz);CHKERRQ(ierr); 1221 ierr = PCPatchZeroFillMatrix_Private(*mat, ncell, patch->totalDofsPerCell, &dofsArray[offset*patch->totalDofsPerCell]);CHKERRQ(ierr); 1222 ierr = PetscLogEventEnd(PC_Patch_Prealloc, pc, 0, 0, 0);CHKERRQ(ierr); 1223 ierr = ISRestoreIndices(patch->dofs, &dofsArray);CHKERRQ(ierr); 1224 } 1225 ierr = MatSetUp(*mat);CHKERRQ(ierr); 1226 PetscFunctionReturn(0); 1227 } 1228 1229 static PetscErrorCode PCPatchComputeOperator_DMPlex_Private(PC pc, PetscInt patchNum, Mat J, IS cellIS, PetscInt n, const PetscInt *l2p, void *ctx) 1230 { 1231 PC_PATCH *patch = (PC_PATCH *) pc->data; 1232 DM dm; 1233 PetscSection s; 1234 const PetscInt *parray, *oarray; 1235 PetscInt Nf = patch->nsubspaces, Np, poff, p, f; 1236 PetscErrorCode ierr; 1237 1238 PetscFunctionBegin; 1239 ierr = PCGetDM(pc, &dm);CHKERRQ(ierr); 1240 ierr = DMGetDefaultSection(dm, &s);CHKERRQ(ierr); 1241 /* Set offset into patch */ 1242 ierr = PetscSectionGetDof(patch->pointCounts, patchNum, &Np);CHKERRQ(ierr); 1243 ierr = PetscSectionGetOffset(patch->pointCounts, patchNum, &poff);CHKERRQ(ierr); 1244 ierr = ISGetIndices(patch->points, &parray);CHKERRQ(ierr); 1245 ierr = ISGetIndices(patch->offs, &oarray);CHKERRQ(ierr); 1246 for (f = 0; f < Nf; ++f) { 1247 for (p = 0; p < Np; ++p) { 1248 const PetscInt point = parray[poff+p]; 1249 PetscInt dof; 1250 1251 ierr = PetscSectionGetFieldDof(patch->patchSection, point, f, &dof);CHKERRQ(ierr); 1252 ierr = PetscSectionSetFieldOffset(patch->patchSection, point, f, oarray[(poff+p)*Nf+f]);CHKERRQ(ierr); 1253 if (patch->nsubspaces == 1) {ierr = PetscSectionSetOffset(patch->patchSection, point, oarray[(poff+p)*Nf+f]);CHKERRQ(ierr);} 1254 else {ierr = PetscSectionSetOffset(patch->patchSection, point, -1);CHKERRQ(ierr);} 1255 } 1256 } 1257 ierr = ISRestoreIndices(patch->points, &parray);CHKERRQ(ierr); 1258 ierr = ISRestoreIndices(patch->offs, &oarray);CHKERRQ(ierr); 1259 if (patch->viewSection) {ierr = ObjectView((PetscObject) patch->patchSection, patch->viewerSection, patch->formatSection);CHKERRQ(ierr);} 1260 /* TODO Shut off MatViewFromOptions() in MatAssemblyEnd() here */ 1261 ierr = DMPlexComputeJacobian_Patch_Internal(pc->dm, patch->patchSection, patch->patchSection, cellIS, 0.0, 0.0, NULL, NULL, J, J, ctx);CHKERRQ(ierr); 1262 PetscFunctionReturn(0); 1263 } 1264 1265 static PetscErrorCode PCPatchComputeOperator_Private(PC pc, Mat mat, PetscInt point) 1266 { 1267 PC_PATCH *patch = (PC_PATCH *) pc->data; 1268 const PetscInt *dofsArray; 1269 const PetscInt *cellsArray; 1270 PetscInt ncell, offset, pStart, pEnd; 1271 PetscErrorCode ierr; 1272 1273 PetscFunctionBegin; 1274 ierr = PetscLogEventBegin(PC_Patch_ComputeOp, pc, 0, 0, 0);CHKERRQ(ierr); 1275 if (!patch->usercomputeop) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONGSTATE, "Must call PCPatchSetComputeOperator() to set user callback\n"); 1276 ierr = ISGetIndices(patch->dofs, &dofsArray);CHKERRQ(ierr); 1277 ierr = ISGetIndices(patch->cells, &cellsArray);CHKERRQ(ierr); 1278 ierr = PetscSectionGetChart(patch->cellCounts, &pStart, &pEnd);CHKERRQ(ierr); 1279 1280 point += pStart; 1281 if (point >= pEnd) SETERRQ3(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Operator point %D not in [%D, %D)\n", point, pStart, pEnd);CHKERRQ(ierr); 1282 1283 ierr = PetscSectionGetDof(patch->cellCounts, point, &ncell);CHKERRQ(ierr); 1284 ierr = PetscSectionGetOffset(patch->cellCounts, point, &offset);CHKERRQ(ierr); 1285 if (ncell <= 0) { 1286 ierr = PetscLogEventEnd(PC_Patch_ComputeOp, pc, 0, 0, 0);CHKERRQ(ierr); 1287 PetscFunctionReturn(0); 1288 } 1289 PetscStackPush("PCPatch user callback"); 1290 /* Cannot reuse the same IS because the geometry info is being cached in it */ 1291 ierr = ISCreateGeneral(PETSC_COMM_SELF, ncell, cellsArray + offset, PETSC_USE_POINTER, &patch->cellIS);CHKERRQ(ierr); 1292 ierr = patch->usercomputeop(pc, point, mat, patch->cellIS, ncell*patch->totalDofsPerCell, dofsArray + offset*patch->totalDofsPerCell, patch->usercomputectx);CHKERRQ(ierr); 1293 PetscStackPop; 1294 ierr = ISDestroy(&patch->cellIS);CHKERRQ(ierr); 1295 ierr = ISRestoreIndices(patch->dofs, &dofsArray);CHKERRQ(ierr); 1296 ierr = ISRestoreIndices(patch->cells, &cellsArray);CHKERRQ(ierr); 1297 if (patch->viewMatrix) { 1298 char name[PETSC_MAX_PATH_LEN]; 1299 1300 ierr = PetscSNPrintf(name, PETSC_MAX_PATH_LEN-1, "Patch matrix for Point %D", point);CHKERRQ(ierr); 1301 ierr = PetscObjectSetName((PetscObject) mat, name);CHKERRQ(ierr); 1302 ierr = ObjectView((PetscObject) mat, patch->viewerMatrix, patch->formatMatrix);CHKERRQ(ierr); 1303 } 1304 ierr = PetscLogEventEnd(PC_Patch_ComputeOp, pc, 0, 0, 0);CHKERRQ(ierr); 1305 PetscFunctionReturn(0); 1306 } 1307 1308 static PetscErrorCode PCPatch_ScatterLocal_Private(PC pc, PetscInt p, Vec x, Vec y, InsertMode mode, ScatterMode scat) 1309 { 1310 PC_PATCH *patch = (PC_PATCH *) pc->data; 1311 const PetscScalar *xArray = NULL; 1312 PetscScalar *yArray = NULL; 1313 const PetscInt *gtolArray = NULL; 1314 PetscInt dof, offset, lidx; 1315 PetscErrorCode ierr; 1316 1317 PetscFunctionBeginHot; 1318 ierr = PetscLogEventBegin(PC_Patch_Scatter, pc, 0, 0, 0);CHKERRQ(ierr); 1319 ierr = VecGetArrayRead(x, &xArray);CHKERRQ(ierr); 1320 ierr = VecGetArray(y, &yArray);CHKERRQ(ierr); 1321 ierr = PetscSectionGetDof(patch->gtolCounts, p, &dof);CHKERRQ(ierr); 1322 ierr = PetscSectionGetOffset(patch->gtolCounts, p, &offset);CHKERRQ(ierr); 1323 ierr = ISGetIndices(patch->gtol, >olArray);CHKERRQ(ierr); 1324 if (mode == INSERT_VALUES && scat != SCATTER_FORWARD) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Can't insert if not scattering forward\n"); 1325 if (mode == ADD_VALUES && scat != SCATTER_REVERSE) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_INCOMP, "Can't add if not scattering reverse\n"); 1326 for (lidx = 0; lidx < dof; ++lidx) { 1327 const PetscInt gidx = gtolArray[offset+lidx]; 1328 1329 if (mode == INSERT_VALUES) yArray[lidx] = xArray[gidx]; /* Forward */ 1330 else yArray[gidx] += xArray[lidx]; /* Reverse */ 1331 } 1332 ierr = ISRestoreIndices(patch->gtol, >olArray);CHKERRQ(ierr); 1333 ierr = VecRestoreArrayRead(x, &xArray);CHKERRQ(ierr); 1334 ierr = VecRestoreArray(y, &yArray);CHKERRQ(ierr); 1335 ierr = PetscLogEventEnd(PC_Patch_Scatter, pc, 0, 0, 0);CHKERRQ(ierr); 1336 PetscFunctionReturn(0); 1337 } 1338 1339 static PetscErrorCode PCSetUp_PATCH(PC pc) 1340 { 1341 PC_PATCH *patch = (PC_PATCH *) pc->data; 1342 PetscInt i; 1343 const char *prefix; 1344 PetscErrorCode ierr; 1345 1346 PetscFunctionBegin; 1347 if (!pc->setupcalled) { 1348 PetscInt pStart, pEnd, p; 1349 PetscInt localSize; 1350 1351 ierr = PetscLogEventBegin(PC_Patch_CreatePatches, pc, 0, 0, 0);CHKERRQ(ierr); 1352 1353 if (!patch->nsubspaces) { 1354 DM dm; 1355 PetscDS prob; 1356 PetscSection s; 1357 PetscInt cStart, cEnd, c, Nf, f, numGlobalBcs = 0, *globalBcs, *Nb, totNb = 0, **cellDofs; 1358 1359 ierr = PCGetDM(pc, &dm);CHKERRQ(ierr); 1360 if (!dm) SETERRQ(PetscObjectComm((PetscObject) pc), PETSC_ERR_ARG_WRONG, "Must set DM for PCPATCH or call PCPatchSetDiscretisationInfo()"); 1361 ierr = DMGetDefaultSection(dm, &s);CHKERRQ(ierr); 1362 ierr = PetscSectionGetNumFields(s, &Nf);CHKERRQ(ierr); 1363 ierr = PetscSectionGetChart(s, &pStart, &pEnd);CHKERRQ(ierr); 1364 for (p = pStart; p < pEnd; ++p) { 1365 PetscInt cdof; 1366 ierr = PetscSectionGetConstraintDof(s, p, &cdof);CHKERRQ(ierr); 1367 numGlobalBcs += cdof; 1368 } 1369 ierr = DMPlexGetHeightStratum(dm, 0, &cStart, &cEnd);CHKERRQ(ierr); 1370 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 1371 ierr = PetscMalloc3(Nf, &Nb, Nf, &cellDofs, numGlobalBcs, &globalBcs);CHKERRQ(ierr); 1372 for (f = 0; f < Nf; ++f) { 1373 PetscFE fe; 1374 PetscDualSpace sp; 1375 PetscInt cdoff = 0; 1376 1377 ierr = PetscDSGetDiscretization(prob, f, (PetscObject *) &fe);CHKERRQ(ierr); 1378 /* ierr = PetscFEGetNumComponents(fe, &Nc[f]);CHKERRQ(ierr); */ 1379 ierr = PetscFEGetDualSpace(fe, &sp);CHKERRQ(ierr); 1380 ierr = PetscDualSpaceGetDimension(sp, &Nb[f]);CHKERRQ(ierr); 1381 totNb += Nb[f]; 1382 1383 ierr = PetscMalloc1((cEnd-cStart)*Nb[f], &cellDofs[f]);CHKERRQ(ierr); 1384 for (c = cStart; c < cEnd; ++c) { 1385 PetscInt *closure = NULL; 1386 PetscInt clSize = 0, cl; 1387 1388 ierr = DMPlexGetTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure);CHKERRQ(ierr); 1389 for (cl = 0; cl < clSize*2; cl += 2) { 1390 const PetscInt p = closure[cl]; 1391 PetscInt fdof, d, foff; 1392 1393 ierr = PetscSectionGetFieldDof(s, p, f, &fdof);CHKERRQ(ierr); 1394 ierr = PetscSectionGetFieldOffset(s, p, f, &foff);CHKERRQ(ierr); 1395 for (d = 0; d < fdof; ++d, ++cdoff) cellDofs[f][cdoff] = foff + d; 1396 } 1397 ierr = DMPlexRestoreTransitiveClosure(dm, c, PETSC_TRUE, &clSize, &closure);CHKERRQ(ierr); 1398 } 1399 if (cdoff != (cEnd-cStart)*Nb[f]) SETERRQ4(PetscObjectComm((PetscObject) pc), PETSC_ERR_ARG_SIZ, "Total number of cellDofs %D for field %D should be Nc (%D) * cellDof (%D)", cdoff, f, cEnd-cStart, Nb[f]); 1400 } 1401 numGlobalBcs = 0; 1402 for (p = pStart; p < pEnd; ++p) { 1403 const PetscInt *ind; 1404 PetscInt off, cdof, d; 1405 1406 ierr = PetscSectionGetOffset(s, p, &off);CHKERRQ(ierr); 1407 ierr = PetscSectionGetConstraintDof(s, p, &cdof);CHKERRQ(ierr); 1408 ierr = PetscSectionGetConstraintIndices(s, p, &ind);CHKERRQ(ierr); 1409 for (d = 0; d < cdof; ++d) globalBcs[numGlobalBcs++] = off + ind[d]; 1410 } 1411 1412 ierr = PCPatchSetDiscretisationInfoCombined(pc, dm, Nb, (const PetscInt **) cellDofs, numGlobalBcs, globalBcs, numGlobalBcs, globalBcs);CHKERRQ(ierr); 1413 for (f = 0; f < Nf; ++f) { 1414 ierr = PetscFree(cellDofs[f]);CHKERRQ(ierr); 1415 } 1416 ierr = PetscFree3(Nb, cellDofs, globalBcs);CHKERRQ(ierr); 1417 ierr = PCPatchSetComputeOperator(pc, PCPatchComputeOperator_DMPlex_Private, NULL);CHKERRQ(ierr); 1418 } 1419 1420 localSize = patch->subspaceOffsets[patch->nsubspaces]; 1421 ierr = VecCreateSeq(PETSC_COMM_SELF, localSize, &patch->localX);CHKERRQ(ierr); 1422 ierr = VecSetUp(patch->localX);CHKERRQ(ierr); 1423 ierr = VecDuplicate(patch->localX, &patch->localY);CHKERRQ(ierr); 1424 ierr = PCPatchCreateCellPatches(pc);CHKERRQ(ierr); 1425 ierr = PCPatchCreateCellPatchDiscretisationInfo(pc);CHKERRQ(ierr); 1426 1427 /* OK, now build the work vectors */ 1428 ierr = PetscSectionGetChart(patch->gtolCounts, &pStart, &pEnd);CHKERRQ(ierr); 1429 ierr = PetscMalloc1(patch->npatch, &patch->patchX);CHKERRQ(ierr); 1430 ierr = PetscMalloc1(patch->npatch, &patch->patchY);CHKERRQ(ierr); 1431 for (p = pStart; p < pEnd; ++p) { 1432 PetscInt dof; 1433 1434 ierr = PetscSectionGetDof(patch->gtolCounts, p, &dof);CHKERRQ(ierr); 1435 ierr = VecCreateSeq(PETSC_COMM_SELF, dof, &patch->patchX[p-pStart]);CHKERRQ(ierr); 1436 ierr = VecSetUp(patch->patchX[p-pStart]);CHKERRQ(ierr); 1437 ierr = VecCreateSeq(PETSC_COMM_SELF, dof, &patch->patchY[p-pStart]);CHKERRQ(ierr); 1438 ierr = VecSetUp(patch->patchY[p-pStart]);CHKERRQ(ierr); 1439 } 1440 ierr = PetscMalloc1(patch->npatch, &patch->ksp);CHKERRQ(ierr); 1441 ierr = PCGetOptionsPrefix(pc, &prefix);CHKERRQ(ierr); 1442 for (i = 0; i < patch->npatch; ++i) { 1443 PC subpc; 1444 1445 ierr = KSPCreate(PETSC_COMM_SELF, &patch->ksp[i]);CHKERRQ(ierr); 1446 ierr = KSPSetOptionsPrefix(patch->ksp[i], prefix);CHKERRQ(ierr); 1447 ierr = KSPAppendOptionsPrefix(patch->ksp[i], "sub_");CHKERRQ(ierr); 1448 ierr = PetscObjectIncrementTabLevel((PetscObject) patch->ksp[i], (PetscObject) pc, 1);CHKERRQ(ierr); 1449 ierr = KSPGetPC(patch->ksp[i], &subpc);CHKERRQ(ierr); 1450 ierr = PetscObjectIncrementTabLevel((PetscObject) subpc, (PetscObject) pc, 1);CHKERRQ(ierr); 1451 ierr = PetscLogObjectParent((PetscObject) pc, (PetscObject) patch->ksp[i]);CHKERRQ(ierr); 1452 } 1453 if (patch->save_operators) { 1454 ierr = PetscMalloc1(patch->npatch, &patch->mat);CHKERRQ(ierr); 1455 for (i = 0; i < patch->npatch; ++i) { 1456 ierr = PCPatchCreateMatrix_Private(pc, i, &patch->mat[i]);CHKERRQ(ierr); 1457 } 1458 } 1459 ierr = PetscLogEventEnd(PC_Patch_CreatePatches, pc, 0, 0, 0);CHKERRQ(ierr); 1460 1461 /* If desired, calculate weights for dof multiplicity */ 1462 if (patch->partition_of_unity) { 1463 ierr = VecDuplicate(patch->localX, &patch->dof_weights);CHKERRQ(ierr); 1464 for (i = 0; i < patch->npatch; ++i) { 1465 PetscInt dof; 1466 1467 ierr = PetscSectionGetDof(patch->gtolCounts, i+pStart, &dof);CHKERRQ(ierr); 1468 if (dof <= 0) continue; 1469 ierr = VecSet(patch->patchX[i], 1.0);CHKERRQ(ierr); 1470 ierr = PCPatch_ScatterLocal_Private(pc, i+pStart, patch->patchX[i], patch->dof_weights, ADD_VALUES, SCATTER_REVERSE);CHKERRQ(ierr); 1471 } 1472 ierr = VecReciprocal(patch->dof_weights);CHKERRQ(ierr); 1473 } 1474 } 1475 if (patch->save_operators) { 1476 for (i = 0; i < patch->npatch; ++i) { 1477 ierr = MatZeroEntries(patch->mat[i]);CHKERRQ(ierr); 1478 ierr = PCPatchComputeOperator_Private(pc, patch->mat[i], i);CHKERRQ(ierr); 1479 ierr = KSPSetOperators(patch->ksp[i], patch->mat[i], patch->mat[i]);CHKERRQ(ierr); 1480 } 1481 } 1482 if (!pc->setupcalled && patch->optionsSet) for (i = 0; i < patch->npatch; ++i) {ierr = KSPSetFromOptions(patch->ksp[i]);CHKERRQ(ierr);} 1483 PetscFunctionReturn(0); 1484 } 1485 1486 static PetscErrorCode PCApply_PATCH(PC pc, Vec x, Vec y) 1487 { 1488 PC_PATCH *patch = (PC_PATCH *) pc->data; 1489 const PetscScalar *globalX = NULL; 1490 PetscScalar *localX = NULL; 1491 PetscScalar *globalY = NULL; 1492 const PetscInt *bcNodes = NULL; 1493 PetscInt nsweep = patch->symmetrise_sweep ? 2 : 1; 1494 PetscInt start[2] = {0, 0}; 1495 PetscInt end[2] = {-1, -1}; 1496 const PetscInt inc[2] = {1, -1}; 1497 const PetscScalar *localY; 1498 const PetscInt *iterationSet; 1499 PetscInt pStart, numBcs, n, sweep, bc, j; 1500 PetscErrorCode ierr; 1501 1502 PetscFunctionBegin; 1503 ierr = PetscLogEventBegin(PC_Patch_Apply, pc, 0, 0, 0);CHKERRQ(ierr); 1504 ierr = PetscOptionsPushGetViewerOff(PETSC_TRUE);CHKERRQ(ierr); 1505 end[0] = patch->npatch; 1506 start[1] = patch->npatch-1; 1507 if (patch->user_patches) { 1508 ierr = ISGetLocalSize(patch->iterationSet, &end[0]);CHKERRQ(ierr); 1509 start[1] = end[0] - 1; 1510 ierr = ISGetIndices(patch->iterationSet, &iterationSet);CHKERRQ(ierr); 1511 } 1512 /* Scatter from global space into overlapped local spaces */ 1513 ierr = VecGetArrayRead(x, &globalX);CHKERRQ(ierr); 1514 ierr = VecGetArray(patch->localX, &localX);CHKERRQ(ierr); 1515 ierr = PetscSFBcastBegin(patch->defaultSF, MPIU_SCALAR, globalX, localX);CHKERRQ(ierr); 1516 ierr = PetscSFBcastEnd(patch->defaultSF, MPIU_SCALAR, globalX, localX);CHKERRQ(ierr); 1517 ierr = VecRestoreArrayRead(x, &globalX);CHKERRQ(ierr); 1518 ierr = VecRestoreArray(patch->localX, &localX);CHKERRQ(ierr); 1519 1520 ierr = VecSet(patch->localY, 0.0);CHKERRQ(ierr); 1521 ierr = PetscSectionGetChart(patch->gtolCounts, &pStart, NULL);CHKERRQ(ierr); 1522 for (sweep = 0; sweep < nsweep; sweep++) { 1523 for (j = start[sweep]; j*inc[sweep] < end[sweep]*inc[sweep]; j += inc[sweep]) { 1524 PetscInt i = patch->user_patches ? iterationSet[j] : j; 1525 PetscInt start, len; 1526 1527 ierr = PetscSectionGetDof(patch->gtolCounts, i+pStart, &len);CHKERRQ(ierr); 1528 ierr = PetscSectionGetOffset(patch->gtolCounts, i+pStart, &start);CHKERRQ(ierr); 1529 /* TODO: Squash out these guys in the setup as well. */ 1530 if (len <= 0) continue; 1531 /* TODO: Do we need different scatters for X and Y? */ 1532 ierr = PCPatch_ScatterLocal_Private(pc, i+pStart, patch->localX, patch->patchX[i], INSERT_VALUES, SCATTER_FORWARD);CHKERRQ(ierr); 1533 if (!patch->save_operators) { 1534 Mat mat; 1535 1536 ierr = PCPatchCreateMatrix_Private(pc, i, &mat);CHKERRQ(ierr); 1537 /* Populate operator here. */ 1538 ierr = PCPatchComputeOperator_Private(pc, mat, i);CHKERRQ(ierr); 1539 ierr = KSPSetOperators(patch->ksp[i], mat, mat); 1540 /* Drop reference so the KSPSetOperators below will blow it away. */ 1541 ierr = MatDestroy(&mat);CHKERRQ(ierr); 1542 } 1543 ierr = PetscLogEventBegin(PC_Patch_Solve, pc, 0, 0, 0);CHKERRQ(ierr); 1544 ierr = KSPSolve(patch->ksp[i], patch->patchX[i], patch->patchY[i]);CHKERRQ(ierr); 1545 ierr = PetscLogEventEnd(PC_Patch_Solve, pc, 0, 0, 0);CHKERRQ(ierr); 1546 1547 if (!patch->save_operators) { 1548 PC pc; 1549 ierr = KSPSetOperators(patch->ksp[i], NULL, NULL);CHKERRQ(ierr); 1550 ierr = KSPGetPC(patch->ksp[i], &pc);CHKERRQ(ierr); 1551 /* Destroy PC context too, otherwise the factored matrix hangs around. */ 1552 ierr = PCReset(pc);CHKERRQ(ierr); 1553 } 1554 1555 ierr = PCPatch_ScatterLocal_Private(pc, i+pStart, patch->patchY[i], patch->localY, ADD_VALUES, SCATTER_REVERSE);CHKERRQ(ierr); 1556 } 1557 } 1558 if (patch->user_patches) {ierr = ISRestoreIndices(patch->iterationSet, &iterationSet);CHKERRQ(ierr);} 1559 /* XXX: should we do this on the global vector? */ 1560 if (patch->partition_of_unity) { 1561 ierr = VecPointwiseMult(patch->localY, patch->localY, patch->dof_weights);CHKERRQ(ierr); 1562 } 1563 /* Now patch->localY contains the solution of the patch solves, so we need to combine them all. */ 1564 ierr = VecSet(y, 0.0);CHKERRQ(ierr); 1565 ierr = VecGetArray(y, &globalY);CHKERRQ(ierr); 1566 ierr = VecGetArrayRead(patch->localY, &localY);CHKERRQ(ierr); 1567 ierr = PetscSFReduceBegin(patch->defaultSF, MPIU_SCALAR, localY, globalY, MPI_SUM);CHKERRQ(ierr); 1568 ierr = PetscSFReduceEnd(patch->defaultSF, MPIU_SCALAR, localY, globalY, MPI_SUM);CHKERRQ(ierr); 1569 ierr = VecRestoreArrayRead(patch->localY, &localY);CHKERRQ(ierr); 1570 1571 /* Now we need to send the global BC values through */ 1572 ierr = VecGetArrayRead(x, &globalX);CHKERRQ(ierr); 1573 ierr = ISGetSize(patch->globalBcNodes, &numBcs);CHKERRQ(ierr); 1574 ierr = ISGetIndices(patch->globalBcNodes, &bcNodes);CHKERRQ(ierr); 1575 ierr = VecGetLocalSize(x, &n);CHKERRQ(ierr); 1576 for (bc = 0; bc < numBcs; ++bc) { 1577 const PetscInt idx = bcNodes[bc]; 1578 if (idx < n) globalY[idx] = globalX[idx]; 1579 } 1580 1581 ierr = ISRestoreIndices(patch->globalBcNodes, &bcNodes);CHKERRQ(ierr); 1582 ierr = VecRestoreArrayRead(x, &globalX);CHKERRQ(ierr); 1583 ierr = VecRestoreArray(y, &globalY);CHKERRQ(ierr); 1584 1585 ierr = PetscOptionsPopGetViewerOff();CHKERRQ(ierr); 1586 ierr = PetscLogEventEnd(PC_Patch_Apply, pc, 0, 0, 0);CHKERRQ(ierr); 1587 PetscFunctionReturn(0); 1588 } 1589 1590 static PetscErrorCode PCReset_PATCH(PC pc) 1591 { 1592 PC_PATCH *patch = (PC_PATCH *) pc->data; 1593 PetscInt i; 1594 PetscErrorCode ierr; 1595 1596 PetscFunctionBegin; 1597 /* TODO: Get rid of all these ifs */ 1598 ierr = PetscSFDestroy(&patch->defaultSF);CHKERRQ(ierr); 1599 ierr = PetscSectionDestroy(&patch->cellCounts);CHKERRQ(ierr); 1600 ierr = PetscSectionDestroy(&patch->pointCounts);CHKERRQ(ierr); 1601 ierr = PetscSectionDestroy(&patch->cellNumbering);CHKERRQ(ierr); 1602 ierr = PetscSectionDestroy(&patch->gtolCounts);CHKERRQ(ierr); 1603 ierr = ISDestroy(&patch->gtol);CHKERRQ(ierr); 1604 ierr = ISDestroy(&patch->cells);CHKERRQ(ierr); 1605 ierr = ISDestroy(&patch->points);CHKERRQ(ierr); 1606 ierr = ISDestroy(&patch->dofs);CHKERRQ(ierr); 1607 ierr = ISDestroy(&patch->offs);CHKERRQ(ierr); 1608 ierr = PetscSectionDestroy(&patch->patchSection);CHKERRQ(ierr); 1609 ierr = ISDestroy(&patch->ghostBcNodes);CHKERRQ(ierr); 1610 ierr = ISDestroy(&patch->globalBcNodes);CHKERRQ(ierr); 1611 1612 if (patch->dofSection) for (i = 0; i < patch->nsubspaces; i++) {ierr = PetscSectionDestroy(&patch->dofSection[i]);CHKERRQ(ierr);} 1613 ierr = PetscFree(patch->dofSection);CHKERRQ(ierr); 1614 ierr = PetscFree(patch->bs);CHKERRQ(ierr); 1615 ierr = PetscFree(patch->nodesPerCell);CHKERRQ(ierr); 1616 if (patch->cellNodeMap) for (i = 0; i < patch->nsubspaces; i++) {ierr = PetscFree(patch->cellNodeMap[i]);CHKERRQ(ierr);} 1617 ierr = PetscFree(patch->cellNodeMap);CHKERRQ(ierr); 1618 ierr = PetscFree(patch->subspaceOffsets);CHKERRQ(ierr); 1619 1620 if (patch->ksp) { 1621 for (i = 0; i < patch->npatch; ++i) {ierr = KSPReset(patch->ksp[i]);CHKERRQ(ierr);} 1622 } 1623 1624 ierr = VecDestroy(&patch->localX);CHKERRQ(ierr); 1625 ierr = VecDestroy(&patch->localY);CHKERRQ(ierr); 1626 if (patch->patchX) { 1627 for (i = 0; i < patch->npatch; ++i) {ierr = VecDestroy(&patch->patchX[i]);CHKERRQ(ierr);} 1628 ierr = PetscFree(patch->patchX);CHKERRQ(ierr); 1629 } 1630 if (patch->patchY) { 1631 for (i = 0; i < patch->npatch; ++i) {ierr = VecDestroy(&patch->patchY[i]);CHKERRQ(ierr);} 1632 ierr = PetscFree(patch->patchY);CHKERRQ(ierr); 1633 } 1634 ierr = VecDestroy(&patch->dof_weights);CHKERRQ(ierr); 1635 if (patch->patch_dof_weights) { 1636 for (i = 0; i < patch->npatch; ++i) {ierr = VecDestroy(&patch->patch_dof_weights[i]);CHKERRQ(ierr);} 1637 ierr = PetscFree(patch->patch_dof_weights);CHKERRQ(ierr); 1638 } 1639 if (patch->mat) { 1640 for (i = 0; i < patch->npatch; ++i) {ierr = MatDestroy(&patch->mat[i]);CHKERRQ(ierr);} 1641 ierr = PetscFree(patch->mat);CHKERRQ(ierr); 1642 } 1643 ierr = PetscFree(patch->sub_mat_type);CHKERRQ(ierr); 1644 if (patch->userIS) { 1645 for (i = 0; i < patch->npatch; ++i) {ierr = ISDestroy(&patch->userIS[i]);CHKERRQ(ierr);} 1646 ierr = PetscFree(patch->userIS);CHKERRQ(ierr); 1647 } 1648 patch->bs = 0; 1649 patch->cellNodeMap = NULL; 1650 patch->nsubspaces = 0; 1651 ierr = ISDestroy(&patch->iterationSet);CHKERRQ(ierr); 1652 1653 ierr = PetscViewerDestroy(&patch->viewerSection);CHKERRQ(ierr); 1654 PetscFunctionReturn(0); 1655 } 1656 1657 static PetscErrorCode PCDestroy_PATCH(PC pc) 1658 { 1659 PC_PATCH *patch = (PC_PATCH *) pc->data; 1660 PetscInt i; 1661 PetscErrorCode ierr; 1662 1663 PetscFunctionBegin; 1664 ierr = PCReset_PATCH(pc);CHKERRQ(ierr); 1665 if (patch->ksp) { 1666 for (i = 0; i < patch->npatch; ++i) {ierr = KSPDestroy(&patch->ksp[i]);CHKERRQ(ierr);} 1667 ierr = PetscFree(patch->ksp);CHKERRQ(ierr); 1668 } 1669 ierr = PetscFree(pc->data);CHKERRQ(ierr); 1670 PetscFunctionReturn(0); 1671 } 1672 1673 static PetscErrorCode PCSetFromOptions_PATCH(PetscOptionItems *PetscOptionsObject, PC pc) 1674 { 1675 PC_PATCH *patch = (PC_PATCH *) pc->data; 1676 PCPatchConstructType patchConstructionType = PC_PATCH_STAR; 1677 char sub_mat_type[PETSC_MAX_PATH_LEN]; 1678 const char *prefix; 1679 PetscBool flg, dimflg, codimflg; 1680 MPI_Comm comm; 1681 PetscErrorCode ierr; 1682 1683 PetscFunctionBegin; 1684 ierr = PetscObjectGetComm((PetscObject) pc, &comm);CHKERRQ(ierr); 1685 ierr = PetscObjectGetOptionsPrefix((PetscObject) pc, &prefix);CHKERRQ(ierr); 1686 ierr = PetscOptionsHead(PetscOptionsObject, "Vertex-patch Additive Schwarz options");CHKERRQ(ierr); 1687 ierr = PetscOptionsBool("-pc_patch_save_operators", "Store all patch operators for lifetime of PC?", "PCPatchSetSaveOperators", patch->save_operators, &patch->save_operators, &flg);CHKERRQ(ierr); 1688 ierr = PetscOptionsBool("-pc_patch_partition_of_unity", "Weight contributions by dof multiplicity?", "PCPatchSetPartitionOfUnity", patch->partition_of_unity, &patch->partition_of_unity, &flg);CHKERRQ(ierr); 1689 ierr = PetscOptionsInt("-pc_patch_construct_dim", "What dimension of mesh point to construct patches by? (0 = vertices)", "PCPATCH", patch->dim, &patch->dim, &dimflg);CHKERRQ(ierr); 1690 ierr = PetscOptionsInt("-pc_patch_construct_codim", "What co-dimension of mesh point to construct patches by? (0 = cells)", "PCPATCH", patch->codim, &patch->codim, &codimflg);CHKERRQ(ierr); 1691 if (dimflg && codimflg) SETERRQ(comm, PETSC_ERR_ARG_WRONG, "Can only set one of dimension or co-dimension");CHKERRQ(ierr); 1692 ierr = PetscOptionsEnum("-pc_patch_construct_type", "How should the patches be constructed?", "PCPatchSetConstructType", PCPatchConstructTypes, (PetscEnum) patchConstructionType, (PetscEnum *) &patchConstructionType, &flg);CHKERRQ(ierr); 1693 if (flg) {ierr = PCPatchSetConstructType(pc, patchConstructionType, NULL, NULL);CHKERRQ(ierr);} 1694 ierr = PetscOptionsInt("-pc_patch_vanka_dim", "Topological dimension of entities for Vanka to ignore", "PCPATCH", patch->vankadim, &patch->vankadim, &flg);CHKERRQ(ierr); 1695 ierr = PetscOptionsInt("-pc_patch_ignore_dim", "Topological dimension of entities for completion to ignore", "PCPATCH", patch->ignoredim, &patch->ignoredim, &flg);CHKERRQ(ierr); 1696 ierr = PetscOptionsFList("-pc_patch_sub_mat_type", "Matrix type for patch solves", "PCPatchSetSubMatType", MatList, NULL, sub_mat_type, PETSC_MAX_PATH_LEN, &flg);CHKERRQ(ierr); 1697 if (flg) {ierr = PCPatchSetSubMatType(pc, sub_mat_type);CHKERRQ(ierr);} 1698 ierr = PetscOptionsBool("-pc_patch_symmetrise_sweep", "Go start->end, end->start?", "PCPATCH", patch->symmetrise_sweep, &patch->symmetrise_sweep, &flg);CHKERRQ(ierr); 1699 ierr = PetscOptionsInt("-pc_patch_exclude_subspace", "What subspace (if any) to exclude in construction?", "PCPATCH", patch->exclude_subspace, &patch->exclude_subspace, &flg);CHKERRQ(ierr); 1700 1701 ierr = PetscOptionsBool("-pc_patch_patches_view", "Print out information during patch construction", "PCPATCH", patch->viewPatches, &patch->viewPatches, &flg);CHKERRQ(ierr); 1702 ierr = PetscOptionsGetViewer(comm, prefix, "-pc_patch_cells_view", &patch->viewerCells, &patch->formatCells, &patch->viewCells);CHKERRQ(ierr); 1703 ierr = PetscOptionsGetViewer(comm, prefix, "-pc_patch_points_view", &patch->viewerPoints, &patch->formatPoints, &patch->viewPoints);CHKERRQ(ierr); 1704 ierr = PetscOptionsGetViewer(comm, prefix, "-pc_patch_section_view", &patch->viewerSection, &patch->formatSection, &patch->viewSection);CHKERRQ(ierr); 1705 ierr = PetscOptionsGetViewer(comm, prefix, "-pc_patch_mat_view", &patch->viewerMatrix, &patch->formatMatrix, &patch->viewMatrix);CHKERRQ(ierr); 1706 ierr = PetscOptionsTail();CHKERRQ(ierr); 1707 patch->optionsSet = PETSC_TRUE; 1708 PetscFunctionReturn(0); 1709 } 1710 1711 static PetscErrorCode PCSetUpOnBlocks_PATCH(PC pc) 1712 { 1713 PC_PATCH *patch = (PC_PATCH*) pc->data; 1714 KSPConvergedReason reason; 1715 PetscInt i; 1716 PetscErrorCode ierr; 1717 1718 PetscFunctionBegin; 1719 for (i = 0; i < patch->npatch; ++i) { 1720 ierr = KSPSetUp(patch->ksp[i]);CHKERRQ(ierr); 1721 ierr = KSPGetConvergedReason(patch->ksp[i], &reason);CHKERRQ(ierr); 1722 if (reason == KSP_DIVERGED_PCSETUP_FAILED) pc->failedreason = PC_SUBPC_ERROR; 1723 } 1724 PetscFunctionReturn(0); 1725 } 1726 1727 static PetscErrorCode PCView_PATCH(PC pc, PetscViewer viewer) 1728 { 1729 PC_PATCH *patch = (PC_PATCH *) pc->data; 1730 PetscViewer sviewer; 1731 PetscBool isascii; 1732 PetscMPIInt rank; 1733 PetscErrorCode ierr; 1734 1735 PetscFunctionBegin; 1736 /* TODO Redo tabbing with set tbas in new style */ 1737 ierr = PetscObjectTypeCompare((PetscObject) viewer, PETSCVIEWERASCII, &isascii);CHKERRQ(ierr); 1738 if (!isascii) PetscFunctionReturn(0); 1739 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) pc), &rank);CHKERRQ(ierr); 1740 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 1741 ierr = PetscViewerASCIIPrintf(viewer, "Subspace Correction preconditioner with %d patches\n", patch->npatch);CHKERRQ(ierr); 1742 ierr = PetscViewerASCIIPrintf(viewer, "Schwarz type: additive\n");CHKERRQ(ierr); 1743 if (patch->partition_of_unity) {ierr = PetscViewerASCIIPrintf(viewer, "Weighting by partition of unity\n");CHKERRQ(ierr);} 1744 else {ierr = PetscViewerASCIIPrintf(viewer, "Not weighting by partition of unity\n");CHKERRQ(ierr);} 1745 if (patch->symmetrise_sweep) {ierr = PetscViewerASCIIPrintf(viewer, "Symmetrising sweep (start->end, then end->start)\n");CHKERRQ(ierr);} 1746 else {ierr = PetscViewerASCIIPrintf(viewer, "Not symmetrising sweep\n");CHKERRQ(ierr);} 1747 if (!patch->save_operators) {ierr = PetscViewerASCIIPrintf(viewer, "Not saving patch operators (rebuilt every PCApply)\n");CHKERRQ(ierr);} 1748 else {ierr = PetscViewerASCIIPrintf(viewer, "Saving patch operators (rebuilt every PCSetUp)\n");CHKERRQ(ierr);} 1749 if (patch->patchconstructop == PCPatchConstruct_Star) {ierr = PetscViewerASCIIPrintf(viewer, "Patch construction operator: star\n");CHKERRQ(ierr);} 1750 else if (patch->patchconstructop == PCPatchConstruct_Vanka) {ierr = PetscViewerASCIIPrintf(viewer, "Patch construction operator: Vanka\n");CHKERRQ(ierr);} 1751 else if (patch->patchconstructop == PCPatchConstruct_User) {ierr = PetscViewerASCIIPrintf(viewer, "Patch construction operator: user-specified\n");CHKERRQ(ierr);} 1752 else {ierr = PetscViewerASCIIPrintf(viewer, "Patch construction operator: unknown\n");CHKERRQ(ierr);} 1753 ierr = PetscViewerASCIIPrintf(viewer, "KSP on patches (all same):\n");CHKERRQ(ierr); 1754 if (patch->ksp) { 1755 ierr = PetscViewerGetSubViewer(viewer, PETSC_COMM_SELF, &sviewer);CHKERRQ(ierr); 1756 if (!rank) { 1757 ierr = PetscViewerASCIIPushTab(sviewer);CHKERRQ(ierr); 1758 ierr = KSPView(patch->ksp[0], sviewer);CHKERRQ(ierr); 1759 ierr = PetscViewerASCIIPopTab(sviewer);CHKERRQ(ierr); 1760 } 1761 ierr = PetscViewerRestoreSubViewer(viewer, PETSC_COMM_SELF, &sviewer);CHKERRQ(ierr); 1762 } else { 1763 ierr = PetscViewerASCIIPushTab(viewer);CHKERRQ(ierr); 1764 ierr = PetscViewerASCIIPrintf(viewer, "KSP not yet set.\n");CHKERRQ(ierr); 1765 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 1766 } 1767 ierr = PetscViewerASCIIPopTab(viewer);CHKERRQ(ierr); 1768 PetscFunctionReturn(0); 1769 } 1770 1771 /*MC 1772 PCPATCH = "patch" - A PC object that encapsulates flexible definition of blocks for overlapping and non-overlapping 1773 small block additive and multiplicative preconditioners. Block definition is based on topology from 1774 a DM and equation numbering from a PetscSection. 1775 1776 Options Database Keys: 1777 + -pc_patch_cells_view - Views the process local cell numbers for each patch 1778 . -pc_patch_points_view - Views the process local mesh point numbers for each patch 1779 . -pc_patch_g2l_view - Views the map between global dofs and patch local dofs for each patch 1780 . -pc_patch_patches_view - Views the global dofs associated with each patch and its boundary 1781 - -pc_patch_sub_mat_view - Views the matrix associated with each patch 1782 1783 Level: intermediate 1784 1785 .seealso: PCType, PCCreate(), PCSetType() 1786 M*/ 1787 PETSC_EXTERN PetscErrorCode PCCreate_Patch(PC pc) 1788 { 1789 PC_PATCH *patch; 1790 PetscErrorCode ierr; 1791 1792 PetscFunctionBegin; 1793 ierr = PetscNewLog(pc, &patch);CHKERRQ(ierr); 1794 1795 /* Set some defaults */ 1796 patch->combined = PETSC_FALSE; 1797 patch->save_operators = PETSC_TRUE; 1798 patch->partition_of_unity = PETSC_FALSE; 1799 patch->codim = -1; 1800 patch->dim = -1; 1801 patch->exclude_subspace = -1; 1802 patch->vankadim = -1; 1803 patch->ignoredim = -1; 1804 patch->patchconstructop = PCPatchConstruct_Star; 1805 patch->symmetrise_sweep = PETSC_FALSE; 1806 patch->npatch = 0; 1807 patch->userIS = NULL; 1808 patch->optionsSet = PETSC_FALSE; 1809 patch->iterationSet = NULL; 1810 patch->user_patches = PETSC_FALSE; 1811 ierr = PetscStrallocpy(MATDENSE, (char **) &patch->sub_mat_type);CHKERRQ(ierr); 1812 patch->viewPatches = PETSC_FALSE; 1813 patch->viewCells = PETSC_FALSE; 1814 patch->viewPoints = PETSC_FALSE; 1815 patch->viewSection = PETSC_FALSE; 1816 patch->viewMatrix = PETSC_FALSE; 1817 1818 pc->data = (void *) patch; 1819 pc->ops->apply = PCApply_PATCH; 1820 pc->ops->applytranspose = 0; /* PCApplyTranspose_PATCH; */ 1821 pc->ops->setup = PCSetUp_PATCH; 1822 pc->ops->reset = PCReset_PATCH; 1823 pc->ops->destroy = PCDestroy_PATCH; 1824 pc->ops->setfromoptions = PCSetFromOptions_PATCH; 1825 pc->ops->setuponblocks = PCSetUpOnBlocks_PATCH; 1826 pc->ops->view = PCView_PATCH; 1827 pc->ops->applyrichardson = 0; 1828 1829 PetscFunctionReturn(0); 1830 } 1831