1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/dmlabelimpl.h> /*I "petscdmlabel.h" I*/ 3 4 /*@C 5 DMPlexSetAdjacencyUser - Define adjacency in the mesh using a user-provided callback 6 7 Input Parameters: 8 + dm - The DM object 9 . user - The user callback, may be NULL (to clear the callback) 10 - ctx - context for callback evaluation, may be NULL 11 12 Level: advanced 13 14 Notes: 15 The caller of DMPlexGetAdjacency may need to arrange that a large enough array is available for the adjacency. 16 17 Any setting here overrides other configuration of DMPlex adjacency determination. 18 19 .seealso: DMSetAdjacency(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexGetAdjacency(), DMPlexGetAdjacencyUser() 20 @*/ 21 PetscErrorCode DMPlexSetAdjacencyUser(DM dm,PetscErrorCode (*user)(DM,PetscInt,PetscInt*,PetscInt[],void*),void *ctx) 22 { 23 DM_Plex *mesh = (DM_Plex *)dm->data; 24 25 PetscFunctionBegin; 26 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 27 mesh->useradjacency = user; 28 mesh->useradjacencyctx = ctx; 29 PetscFunctionReturn(0); 30 } 31 32 /*@C 33 DMPlexGetAdjacencyUser - get the user-defined adjacency callback 34 35 Input Parameter: 36 . dm - The DM object 37 38 Output Parameters: 39 - user - The user callback 40 - ctx - context for callback evaluation 41 42 Level: advanced 43 44 .seealso: DMSetAdjacency(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexGetAdjacency(), DMPlexSetAdjacencyUser() 45 @*/ 46 PetscErrorCode DMPlexGetAdjacencyUser(DM dm, PetscErrorCode (**user)(DM,PetscInt,PetscInt*,PetscInt[],void*), void **ctx) 47 { 48 DM_Plex *mesh = (DM_Plex *)dm->data; 49 50 PetscFunctionBegin; 51 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 52 if (user) *user = mesh->useradjacency; 53 if (ctx) *ctx = mesh->useradjacencyctx; 54 PetscFunctionReturn(0); 55 } 56 57 /*@ 58 DMPlexSetAdjacencyUseAnchors - Define adjacency in the mesh using the point-to-point constraints. 59 60 Input Parameters: 61 + dm - The DM object 62 - useAnchors - Flag to use the constraints. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place. 63 64 Level: intermediate 65 66 .seealso: DMGetAdjacency(), DMSetAdjacency(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors() 67 @*/ 68 PetscErrorCode DMPlexSetAdjacencyUseAnchors(DM dm, PetscBool useAnchors) 69 { 70 DM_Plex *mesh = (DM_Plex *) dm->data; 71 72 PetscFunctionBegin; 73 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 74 mesh->useAnchors = useAnchors; 75 PetscFunctionReturn(0); 76 } 77 78 /*@ 79 DMPlexGetAdjacencyUseAnchors - Query whether adjacency in the mesh uses the point-to-point constraints. 80 81 Input Parameter: 82 . dm - The DM object 83 84 Output Parameter: 85 . useAnchors - Flag to use the closure. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place. 86 87 Level: intermediate 88 89 .seealso: DMPlexSetAdjacencyUseAnchors(), DMSetAdjacency(), DMGetAdjacency(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors() 90 @*/ 91 PetscErrorCode DMPlexGetAdjacencyUseAnchors(DM dm, PetscBool *useAnchors) 92 { 93 DM_Plex *mesh = (DM_Plex *) dm->data; 94 95 PetscFunctionBegin; 96 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 97 PetscValidIntPointer(useAnchors, 2); 98 *useAnchors = mesh->useAnchors; 99 PetscFunctionReturn(0); 100 } 101 102 static PetscErrorCode DMPlexGetAdjacency_Cone_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[]) 103 { 104 const PetscInt *cone = NULL; 105 PetscInt numAdj = 0, maxAdjSize = *adjSize, coneSize, c; 106 PetscErrorCode ierr; 107 108 PetscFunctionBeginHot; 109 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 110 ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr); 111 for (c = 0; c <= coneSize; ++c) { 112 const PetscInt point = !c ? p : cone[c-1]; 113 const PetscInt *support = NULL; 114 PetscInt supportSize, s, q; 115 116 ierr = DMPlexGetSupportSize(dm, point, &supportSize);CHKERRQ(ierr); 117 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 118 for (s = 0; s < supportSize; ++s) { 119 for (q = 0; q < numAdj || ((void)(adj[numAdj++] = support[s]),0); ++q) { 120 if (support[s] == adj[q]) break; 121 } 122 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 123 } 124 } 125 *adjSize = numAdj; 126 PetscFunctionReturn(0); 127 } 128 129 static PetscErrorCode DMPlexGetAdjacency_Support_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[]) 130 { 131 const PetscInt *support = NULL; 132 PetscInt numAdj = 0, maxAdjSize = *adjSize, supportSize, s; 133 PetscErrorCode ierr; 134 135 PetscFunctionBeginHot; 136 ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); 137 ierr = DMPlexGetSupport(dm, p, &support);CHKERRQ(ierr); 138 for (s = 0; s <= supportSize; ++s) { 139 const PetscInt point = !s ? p : support[s-1]; 140 const PetscInt *cone = NULL; 141 PetscInt coneSize, c, q; 142 143 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 144 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 145 for (c = 0; c < coneSize; ++c) { 146 for (q = 0; q < numAdj || ((void)(adj[numAdj++] = cone[c]),0); ++q) { 147 if (cone[c] == adj[q]) break; 148 } 149 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 150 } 151 } 152 *adjSize = numAdj; 153 PetscFunctionReturn(0); 154 } 155 156 static PetscErrorCode DMPlexGetAdjacency_Transitive_Internal(DM dm, PetscInt p, PetscBool useClosure, PetscInt *adjSize, PetscInt adj[]) 157 { 158 PetscInt *star = NULL; 159 PetscInt numAdj = 0, maxAdjSize = *adjSize, starSize, s; 160 PetscErrorCode ierr; 161 162 PetscFunctionBeginHot; 163 ierr = DMPlexGetTransitiveClosure(dm, p, useClosure, &starSize, &star);CHKERRQ(ierr); 164 for (s = 0; s < starSize*2; s += 2) { 165 const PetscInt *closure = NULL; 166 PetscInt closureSize, c, q; 167 168 ierr = DMPlexGetTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);CHKERRQ(ierr); 169 for (c = 0; c < closureSize*2; c += 2) { 170 for (q = 0; q < numAdj || ((void)(adj[numAdj++] = closure[c]),0); ++q) { 171 if (closure[c] == adj[q]) break; 172 } 173 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 174 } 175 ierr = DMPlexRestoreTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);CHKERRQ(ierr); 176 } 177 ierr = DMPlexRestoreTransitiveClosure(dm, p, useClosure, &starSize, &star);CHKERRQ(ierr); 178 *adjSize = numAdj; 179 PetscFunctionReturn(0); 180 } 181 182 PetscErrorCode DMPlexGetAdjacency_Internal(DM dm, PetscInt p, PetscBool useCone, PetscBool useTransitiveClosure, PetscBool useAnchors, PetscInt *adjSize, PetscInt *adj[]) 183 { 184 static PetscInt asiz = 0; 185 PetscInt maxAnchors = 1; 186 PetscInt aStart = -1, aEnd = -1; 187 PetscInt maxAdjSize; 188 PetscSection aSec = NULL; 189 IS aIS = NULL; 190 const PetscInt *anchors; 191 DM_Plex *mesh = (DM_Plex *)dm->data; 192 PetscErrorCode ierr; 193 194 PetscFunctionBeginHot; 195 if (useAnchors) { 196 ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); 197 if (aSec) { 198 ierr = PetscSectionGetMaxDof(aSec,&maxAnchors);CHKERRQ(ierr); 199 maxAnchors = PetscMax(1,maxAnchors); 200 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 201 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 202 } 203 } 204 if (!*adj) { 205 PetscInt depth, coneSeries, supportSeries, maxC, maxS, pStart, pEnd; 206 207 ierr = DMPlexGetChart(dm, &pStart,&pEnd);CHKERRQ(ierr); 208 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 209 ierr = DMPlexGetMaxSizes(dm, &maxC, &maxS);CHKERRQ(ierr); 210 coneSeries = (maxC > 1) ? ((PetscPowInt(maxC,depth+1)-1)/(maxC-1)) : depth+1; 211 supportSeries = (maxS > 1) ? ((PetscPowInt(maxS,depth+1)-1)/(maxS-1)) : depth+1; 212 asiz = PetscMax(PetscPowInt(maxS,depth)*coneSeries,PetscPowInt(maxC,depth)*supportSeries); 213 asiz *= maxAnchors; 214 asiz = PetscMin(asiz,pEnd-pStart); 215 ierr = PetscMalloc1(asiz,adj);CHKERRQ(ierr); 216 } 217 if (*adjSize < 0) *adjSize = asiz; 218 maxAdjSize = *adjSize; 219 if (mesh->useradjacency) { 220 ierr = mesh->useradjacency(dm, p, adjSize, *adj, mesh->useradjacencyctx);CHKERRQ(ierr); 221 } else if (useTransitiveClosure) { 222 ierr = DMPlexGetAdjacency_Transitive_Internal(dm, p, useCone, adjSize, *adj);CHKERRQ(ierr); 223 } else if (useCone) { 224 ierr = DMPlexGetAdjacency_Cone_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); 225 } else { 226 ierr = DMPlexGetAdjacency_Support_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); 227 } 228 if (useAnchors && aSec) { 229 PetscInt origSize = *adjSize; 230 PetscInt numAdj = origSize; 231 PetscInt i = 0, j; 232 PetscInt *orig = *adj; 233 234 while (i < origSize) { 235 PetscInt p = orig[i]; 236 PetscInt aDof = 0; 237 238 if (p >= aStart && p < aEnd) { 239 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 240 } 241 if (aDof) { 242 PetscInt aOff; 243 PetscInt s, q; 244 245 for (j = i + 1; j < numAdj; j++) { 246 orig[j - 1] = orig[j]; 247 } 248 origSize--; 249 numAdj--; 250 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 251 for (s = 0; s < aDof; ++s) { 252 for (q = 0; q < numAdj || ((void)(orig[numAdj++] = anchors[aOff+s]),0); ++q) { 253 if (anchors[aOff+s] == orig[q]) break; 254 } 255 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 256 } 257 } 258 else { 259 i++; 260 } 261 } 262 *adjSize = numAdj; 263 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 264 } 265 PetscFunctionReturn(0); 266 } 267 268 /*@ 269 DMPlexGetAdjacency - Return all points adjacent to the given point 270 271 Input Parameters: 272 + dm - The DM object 273 . p - The point 274 . adjSize - The maximum size of adj if it is non-NULL, or PETSC_DETERMINE 275 - adj - Either NULL so that the array is allocated, or an existing array with size adjSize 276 277 Output Parameters: 278 + adjSize - The number of adjacent points 279 - adj - The adjacent points 280 281 Level: advanced 282 283 Notes: 284 The user must PetscFree the adj array if it was not passed in. 285 286 .seealso: DMSetAdjacency(), DMPlexDistribute(), DMCreateMatrix(), DMPlexPreallocateOperator() 287 @*/ 288 PetscErrorCode DMPlexGetAdjacency(DM dm, PetscInt p, PetscInt *adjSize, PetscInt *adj[]) 289 { 290 PetscBool useCone, useClosure, useAnchors; 291 PetscErrorCode ierr; 292 293 PetscFunctionBeginHot; 294 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 295 PetscValidPointer(adjSize,3); 296 PetscValidPointer(adj,4); 297 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 298 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 299 ierr = DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, adjSize, adj);CHKERRQ(ierr); 300 PetscFunctionReturn(0); 301 } 302 303 /*@ 304 DMPlexCreateTwoSidedProcessSF - Create an SF which just has process connectivity 305 306 Collective on DM 307 308 Input Parameters: 309 + dm - The DM 310 - sfPoint - The PetscSF which encodes point connectivity 311 312 Output Parameters: 313 + processRanks - A list of process neighbors, or NULL 314 - sfProcess - An SF encoding the two-sided process connectivity, or NULL 315 316 Level: developer 317 318 .seealso: PetscSFCreate(), DMPlexCreateProcessSF() 319 @*/ 320 PetscErrorCode DMPlexCreateTwoSidedProcessSF(DM dm, PetscSF sfPoint, PetscSection rootRankSection, IS rootRanks, PetscSection leafRankSection, IS leafRanks, IS *processRanks, PetscSF *sfProcess) 321 { 322 const PetscSFNode *remotePoints; 323 PetscInt *localPointsNew; 324 PetscSFNode *remotePointsNew; 325 const PetscInt *nranks; 326 PetscInt *ranksNew; 327 PetscBT neighbors; 328 PetscInt pStart, pEnd, p, numLeaves, l, numNeighbors, n; 329 PetscMPIInt size, proc, rank; 330 PetscErrorCode ierr; 331 332 PetscFunctionBegin; 333 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 334 PetscValidHeaderSpecific(sfPoint, PETSCSF_CLASSID, 2); 335 if (processRanks) {PetscValidPointer(processRanks, 3);} 336 if (sfProcess) {PetscValidPointer(sfProcess, 4);} 337 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 338 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 339 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, NULL, &remotePoints);CHKERRQ(ierr); 340 ierr = PetscBTCreate(size, &neighbors);CHKERRQ(ierr); 341 ierr = PetscBTMemzero(size, neighbors);CHKERRQ(ierr); 342 /* Compute root-to-leaf process connectivity */ 343 ierr = PetscSectionGetChart(rootRankSection, &pStart, &pEnd);CHKERRQ(ierr); 344 ierr = ISGetIndices(rootRanks, &nranks);CHKERRQ(ierr); 345 for (p = pStart; p < pEnd; ++p) { 346 PetscInt ndof, noff, n; 347 348 ierr = PetscSectionGetDof(rootRankSection, p, &ndof);CHKERRQ(ierr); 349 ierr = PetscSectionGetOffset(rootRankSection, p, &noff);CHKERRQ(ierr); 350 for (n = 0; n < ndof; ++n) {ierr = PetscBTSet(neighbors, nranks[noff+n]);CHKERRQ(ierr);} 351 } 352 ierr = ISRestoreIndices(rootRanks, &nranks);CHKERRQ(ierr); 353 /* Compute leaf-to-neighbor process connectivity */ 354 ierr = PetscSectionGetChart(leafRankSection, &pStart, &pEnd);CHKERRQ(ierr); 355 ierr = ISGetIndices(leafRanks, &nranks);CHKERRQ(ierr); 356 for (p = pStart; p < pEnd; ++p) { 357 PetscInt ndof, noff, n; 358 359 ierr = PetscSectionGetDof(leafRankSection, p, &ndof);CHKERRQ(ierr); 360 ierr = PetscSectionGetOffset(leafRankSection, p, &noff);CHKERRQ(ierr); 361 for (n = 0; n < ndof; ++n) {ierr = PetscBTSet(neighbors, nranks[noff+n]);CHKERRQ(ierr);} 362 } 363 ierr = ISRestoreIndices(leafRanks, &nranks);CHKERRQ(ierr); 364 /* Compute leaf-to-root process connectivity */ 365 for (l = 0; l < numLeaves; ++l) {PetscBTSet(neighbors, remotePoints[l].rank);} 366 /* Calculate edges */ 367 PetscBTClear(neighbors, rank); 368 for(proc = 0, numNeighbors = 0; proc < size; ++proc) {if (PetscBTLookup(neighbors, proc)) ++numNeighbors;} 369 ierr = PetscMalloc1(numNeighbors, &ranksNew);CHKERRQ(ierr); 370 ierr = PetscMalloc1(numNeighbors, &localPointsNew);CHKERRQ(ierr); 371 ierr = PetscMalloc1(numNeighbors, &remotePointsNew);CHKERRQ(ierr); 372 for(proc = 0, n = 0; proc < size; ++proc) { 373 if (PetscBTLookup(neighbors, proc)) { 374 ranksNew[n] = proc; 375 localPointsNew[n] = proc; 376 remotePointsNew[n].index = rank; 377 remotePointsNew[n].rank = proc; 378 ++n; 379 } 380 } 381 ierr = PetscBTDestroy(&neighbors);CHKERRQ(ierr); 382 if (processRanks) {ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), numNeighbors, ranksNew, PETSC_OWN_POINTER, processRanks);CHKERRQ(ierr);} 383 else {ierr = PetscFree(ranksNew);CHKERRQ(ierr);} 384 if (sfProcess) { 385 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfProcess);CHKERRQ(ierr); 386 ierr = PetscObjectSetName((PetscObject) *sfProcess, "Two-Sided Process SF");CHKERRQ(ierr); 387 ierr = PetscSFSetFromOptions(*sfProcess);CHKERRQ(ierr); 388 ierr = PetscSFSetGraph(*sfProcess, size, numNeighbors, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);CHKERRQ(ierr); 389 } 390 PetscFunctionReturn(0); 391 } 392 393 /*@ 394 DMPlexDistributeOwnership - Compute owner information for shared points. This basically gets two-sided for an SF. 395 396 Collective on DM 397 398 Input Parameter: 399 . dm - The DM 400 401 Output Parameters: 402 + rootSection - The number of leaves for a given root point 403 . rootrank - The rank of each edge into the root point 404 . leafSection - The number of processes sharing a given leaf point 405 - leafrank - The rank of each process sharing a leaf point 406 407 Level: developer 408 409 .seealso: DMPlexCreateOverlap() 410 @*/ 411 PetscErrorCode DMPlexDistributeOwnership(DM dm, PetscSection rootSection, IS *rootrank, PetscSection leafSection, IS *leafrank) 412 { 413 MPI_Comm comm; 414 PetscSF sfPoint; 415 const PetscInt *rootdegree; 416 PetscInt *myrank, *remoterank; 417 PetscInt pStart, pEnd, p, nedges; 418 PetscMPIInt rank; 419 PetscErrorCode ierr; 420 421 PetscFunctionBegin; 422 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 423 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 424 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 425 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 426 /* Compute number of leaves for each root */ 427 ierr = PetscObjectSetName((PetscObject) rootSection, "Root Section");CHKERRQ(ierr); 428 ierr = PetscSectionSetChart(rootSection, pStart, pEnd);CHKERRQ(ierr); 429 ierr = PetscSFComputeDegreeBegin(sfPoint, &rootdegree);CHKERRQ(ierr); 430 ierr = PetscSFComputeDegreeEnd(sfPoint, &rootdegree);CHKERRQ(ierr); 431 for (p = pStart; p < pEnd; ++p) {ierr = PetscSectionSetDof(rootSection, p, rootdegree[p-pStart]);CHKERRQ(ierr);} 432 ierr = PetscSectionSetUp(rootSection);CHKERRQ(ierr); 433 /* Gather rank of each leaf to root */ 434 ierr = PetscSectionGetStorageSize(rootSection, &nedges);CHKERRQ(ierr); 435 ierr = PetscMalloc1(pEnd-pStart, &myrank);CHKERRQ(ierr); 436 ierr = PetscMalloc1(nedges, &remoterank);CHKERRQ(ierr); 437 for (p = 0; p < pEnd-pStart; ++p) myrank[p] = rank; 438 ierr = PetscSFGatherBegin(sfPoint, MPIU_INT, myrank, remoterank);CHKERRQ(ierr); 439 ierr = PetscSFGatherEnd(sfPoint, MPIU_INT, myrank, remoterank);CHKERRQ(ierr); 440 ierr = PetscFree(myrank);CHKERRQ(ierr); 441 ierr = ISCreateGeneral(comm, nedges, remoterank, PETSC_OWN_POINTER, rootrank);CHKERRQ(ierr); 442 /* Distribute remote ranks to leaves */ 443 ierr = PetscObjectSetName((PetscObject) leafSection, "Leaf Section");CHKERRQ(ierr); 444 ierr = DMPlexDistributeFieldIS(dm, sfPoint, rootSection, *rootrank, leafSection, leafrank);CHKERRQ(ierr); 445 PetscFunctionReturn(0); 446 } 447 448 /*@C 449 DMPlexCreateOverlap - Compute owner information for shared points. This basically gets two-sided for an SF. 450 451 Collective on DM 452 453 Input Parameters: 454 + dm - The DM 455 . levels - Number of overlap levels 456 . rootSection - The number of leaves for a given root point 457 . rootrank - The rank of each edge into the root point 458 . leafSection - The number of processes sharing a given leaf point 459 - leafrank - The rank of each process sharing a leaf point 460 461 Output Parameters: 462 + ovLabel - DMLabel containing remote overlap contributions as point/rank pairings 463 464 Level: developer 465 466 .seealso: DMPlexDistributeOwnership(), DMPlexDistribute() 467 @*/ 468 PetscErrorCode DMPlexCreateOverlap(DM dm, PetscInt levels, PetscSection rootSection, IS rootrank, PetscSection leafSection, IS leafrank, DMLabel *ovLabel) 469 { 470 MPI_Comm comm; 471 DMLabel ovAdjByRank; /* A DMLabel containing all points adjacent to shared points, separated by rank (value in label) */ 472 PetscSF sfPoint, sfProc; 473 const PetscSFNode *remote; 474 const PetscInt *local; 475 const PetscInt *nrank, *rrank; 476 PetscInt *adj = NULL; 477 PetscInt pStart, pEnd, p, sStart, sEnd, nleaves, l; 478 PetscMPIInt rank, size; 479 PetscBool useCone, useClosure, flg; 480 PetscErrorCode ierr; 481 482 PetscFunctionBegin; 483 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 484 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 485 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 486 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 487 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 488 ierr = PetscSectionGetChart(leafSection, &sStart, &sEnd);CHKERRQ(ierr); 489 ierr = PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);CHKERRQ(ierr); 490 ierr = DMLabelCreate(PETSC_COMM_SELF, "Overlap adjacency", &ovAdjByRank);CHKERRQ(ierr); 491 /* Handle leaves: shared with the root point */ 492 for (l = 0; l < nleaves; ++l) { 493 PetscInt adjSize = PETSC_DETERMINE, a; 494 495 ierr = DMPlexGetAdjacency(dm, local ? local[l] : l, &adjSize, &adj);CHKERRQ(ierr); 496 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remote[l].rank);CHKERRQ(ierr);} 497 } 498 ierr = ISGetIndices(rootrank, &rrank);CHKERRQ(ierr); 499 ierr = ISGetIndices(leafrank, &nrank);CHKERRQ(ierr); 500 /* Handle roots */ 501 for (p = pStart; p < pEnd; ++p) { 502 PetscInt adjSize = PETSC_DETERMINE, neighbors = 0, noff, n, a; 503 504 if ((p >= sStart) && (p < sEnd)) { 505 /* Some leaves share a root with other leaves on different processes */ 506 ierr = PetscSectionGetDof(leafSection, p, &neighbors);CHKERRQ(ierr); 507 if (neighbors) { 508 ierr = PetscSectionGetOffset(leafSection, p, &noff);CHKERRQ(ierr); 509 ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj);CHKERRQ(ierr); 510 for (n = 0; n < neighbors; ++n) { 511 const PetscInt remoteRank = nrank[noff+n]; 512 513 if (remoteRank == rank) continue; 514 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);CHKERRQ(ierr);} 515 } 516 } 517 } 518 /* Roots are shared with leaves */ 519 ierr = PetscSectionGetDof(rootSection, p, &neighbors);CHKERRQ(ierr); 520 if (!neighbors) continue; 521 ierr = PetscSectionGetOffset(rootSection, p, &noff);CHKERRQ(ierr); 522 ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj);CHKERRQ(ierr); 523 for (n = 0; n < neighbors; ++n) { 524 const PetscInt remoteRank = rrank[noff+n]; 525 526 if (remoteRank == rank) continue; 527 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);CHKERRQ(ierr);} 528 } 529 } 530 ierr = PetscFree(adj);CHKERRQ(ierr); 531 ierr = ISRestoreIndices(rootrank, &rrank);CHKERRQ(ierr); 532 ierr = ISRestoreIndices(leafrank, &nrank);CHKERRQ(ierr); 533 /* Add additional overlap levels */ 534 for (l = 1; l < levels; l++) { 535 /* Propagate point donations over SF to capture remote connections */ 536 ierr = DMPlexPartitionLabelPropagate(dm, ovAdjByRank);CHKERRQ(ierr); 537 /* Add next level of point donations to the label */ 538 ierr = DMPlexPartitionLabelAdjacency(dm, ovAdjByRank);CHKERRQ(ierr); 539 } 540 /* We require the closure in the overlap */ 541 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 542 if (useCone || !useClosure) { 543 ierr = DMPlexPartitionLabelClosure(dm, ovAdjByRank);CHKERRQ(ierr); 544 } 545 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-overlap_view", &flg);CHKERRQ(ierr); 546 if (flg) { 547 ierr = DMLabelView(ovAdjByRank, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 548 } 549 /* Make global process SF and invert sender to receiver label */ 550 { 551 /* Build a global process SF */ 552 PetscSFNode *remoteProc; 553 ierr = PetscMalloc1(size, &remoteProc);CHKERRQ(ierr); 554 for (p = 0; p < size; ++p) { 555 remoteProc[p].rank = p; 556 remoteProc[p].index = rank; 557 } 558 ierr = PetscSFCreate(comm, &sfProc);CHKERRQ(ierr); 559 ierr = PetscObjectSetName((PetscObject) sfProc, "Process SF");CHKERRQ(ierr); 560 ierr = PetscSFSetGraph(sfProc, size, size, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);CHKERRQ(ierr); 561 } 562 ierr = DMLabelCreate(PETSC_COMM_SELF, "Overlap label", ovLabel);CHKERRQ(ierr); 563 ierr = DMPlexPartitionLabelInvert(dm, ovAdjByRank, sfProc, *ovLabel);CHKERRQ(ierr); 564 /* Add owned points, except for shared local points */ 565 for (p = pStart; p < pEnd; ++p) {ierr = DMLabelSetValue(*ovLabel, p, rank);CHKERRQ(ierr);} 566 for (l = 0; l < nleaves; ++l) { 567 ierr = DMLabelClearValue(*ovLabel, local[l], rank);CHKERRQ(ierr); 568 ierr = DMLabelSetValue(*ovLabel, remote[l].index, remote[l].rank);CHKERRQ(ierr); 569 } 570 /* Clean up */ 571 ierr = DMLabelDestroy(&ovAdjByRank);CHKERRQ(ierr); 572 ierr = PetscSFDestroy(&sfProc);CHKERRQ(ierr); 573 PetscFunctionReturn(0); 574 } 575 576 /*@C 577 DMPlexCreateOverlapMigrationSF - Create an SF describing the new mesh distribution to make the overlap described by the input SF 578 579 Collective on DM 580 581 Input Parameters: 582 + dm - The DM 583 - overlapSF - The SF mapping ghost points in overlap to owner points on other processes 584 585 Output Parameters: 586 + migrationSF - An SF that maps original points in old locations to points in new locations 587 588 Level: developer 589 590 .seealso: DMPlexCreateOverlap(), DMPlexDistribute() 591 @*/ 592 PetscErrorCode DMPlexCreateOverlapMigrationSF(DM dm, PetscSF overlapSF, PetscSF *migrationSF) 593 { 594 MPI_Comm comm; 595 PetscMPIInt rank, size; 596 PetscInt d, dim, p, pStart, pEnd, nroots, nleaves, newLeaves, point, numSharedPoints; 597 PetscInt *pointDepths, *remoteDepths, *ilocal; 598 PetscInt *depthRecv, *depthShift, *depthIdx; 599 PetscSFNode *iremote; 600 PetscSF pointSF; 601 const PetscInt *sharedLocal; 602 const PetscSFNode *overlapRemote, *sharedRemote; 603 PetscErrorCode ierr; 604 605 PetscFunctionBegin; 606 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 607 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 608 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 609 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 610 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 611 612 /* Before building the migration SF we need to know the new stratum offsets */ 613 ierr = PetscSFGetGraph(overlapSF, &nroots, &nleaves, NULL, &overlapRemote);CHKERRQ(ierr); 614 ierr = PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);CHKERRQ(ierr); 615 for (d=0; d<dim+1; d++) { 616 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 617 for (p=pStart; p<pEnd; p++) pointDepths[p] = d; 618 } 619 for (p=0; p<nleaves; p++) remoteDepths[p] = -1; 620 ierr = PetscSFBcastBegin(overlapSF, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 621 ierr = PetscSFBcastEnd(overlapSF, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 622 623 /* Count recevied points in each stratum and compute the internal strata shift */ 624 ierr = PetscMalloc3(dim+1, &depthRecv, dim+1, &depthShift, dim+1, &depthIdx);CHKERRQ(ierr); 625 for (d=0; d<dim+1; d++) depthRecv[d]=0; 626 for (p=0; p<nleaves; p++) depthRecv[remoteDepths[p]]++; 627 depthShift[dim] = 0; 628 for (d=0; d<dim; d++) depthShift[d] = depthRecv[dim]; 629 for (d=1; d<dim; d++) depthShift[d] += depthRecv[0]; 630 for (d=dim-2; d>0; d--) depthShift[d] += depthRecv[d+1]; 631 for (d=0; d<dim+1; d++) { 632 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 633 depthIdx[d] = pStart + depthShift[d]; 634 } 635 636 /* Form the overlap SF build an SF that describes the full overlap migration SF */ 637 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 638 newLeaves = pEnd - pStart + nleaves; 639 ierr = PetscMalloc1(newLeaves, &ilocal);CHKERRQ(ierr); 640 ierr = PetscMalloc1(newLeaves, &iremote);CHKERRQ(ierr); 641 /* First map local points to themselves */ 642 for (d=0; d<dim+1; d++) { 643 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 644 for (p=pStart; p<pEnd; p++) { 645 point = p + depthShift[d]; 646 ilocal[point] = point; 647 iremote[point].index = p; 648 iremote[point].rank = rank; 649 depthIdx[d]++; 650 } 651 } 652 653 /* Add in the remote roots for currently shared points */ 654 ierr = DMGetPointSF(dm, &pointSF);CHKERRQ(ierr); 655 ierr = PetscSFGetGraph(pointSF, NULL, &numSharedPoints, &sharedLocal, &sharedRemote);CHKERRQ(ierr); 656 for (d=0; d<dim+1; d++) { 657 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 658 for (p=0; p<numSharedPoints; p++) { 659 if (pStart <= sharedLocal[p] && sharedLocal[p] < pEnd) { 660 point = sharedLocal[p] + depthShift[d]; 661 iremote[point].index = sharedRemote[p].index; 662 iremote[point].rank = sharedRemote[p].rank; 663 } 664 } 665 } 666 667 /* Now add the incoming overlap points */ 668 for (p=0; p<nleaves; p++) { 669 point = depthIdx[remoteDepths[p]]; 670 ilocal[point] = point; 671 iremote[point].index = overlapRemote[p].index; 672 iremote[point].rank = overlapRemote[p].rank; 673 depthIdx[remoteDepths[p]]++; 674 } 675 ierr = PetscFree2(pointDepths,remoteDepths);CHKERRQ(ierr); 676 677 ierr = PetscSFCreate(comm, migrationSF);CHKERRQ(ierr); 678 ierr = PetscObjectSetName((PetscObject) *migrationSF, "Overlap Migration SF");CHKERRQ(ierr); 679 ierr = PetscSFSetFromOptions(*migrationSF);CHKERRQ(ierr); 680 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 681 ierr = PetscSFSetGraph(*migrationSF, pEnd-pStart, newLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);CHKERRQ(ierr); 682 683 ierr = PetscFree3(depthRecv, depthShift, depthIdx);CHKERRQ(ierr); 684 PetscFunctionReturn(0); 685 } 686 687 /*@ 688 DMPlexStratifyMigrationSF - Rearrange the leaves of a migration sf for stratification. 689 690 Input Parameter: 691 + dm - The DM 692 - sf - A star forest with non-ordered leaves, usually defining a DM point migration 693 694 Output Parameter: 695 . migrationSF - A star forest with added leaf indirection that ensures the resulting DM is stratified 696 697 Level: developer 698 699 .seealso: DMPlexPartitionLabelCreateSF(), DMPlexDistribute(), DMPlexDistributeOverlap() 700 @*/ 701 PetscErrorCode DMPlexStratifyMigrationSF(DM dm, PetscSF sf, PetscSF *migrationSF) 702 { 703 MPI_Comm comm; 704 PetscMPIInt rank, size; 705 PetscInt d, ldepth, depth, p, pStart, pEnd, nroots, nleaves; 706 PetscInt *pointDepths, *remoteDepths, *ilocal; 707 PetscInt *depthRecv, *depthShift, *depthIdx; 708 PetscInt hybEnd[4]; 709 const PetscSFNode *iremote; 710 PetscErrorCode ierr; 711 712 PetscFunctionBegin; 713 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 714 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 715 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 716 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 717 ierr = DMPlexGetDepth(dm, &ldepth);CHKERRQ(ierr); 718 ierr = MPIU_Allreduce(&ldepth, &depth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 719 if ((ldepth >= 0) && (depth != ldepth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", ldepth, depth); 720 721 /* Before building the migration SF we need to know the new stratum offsets */ 722 ierr = PetscSFGetGraph(sf, &nroots, &nleaves, NULL, &iremote);CHKERRQ(ierr); 723 ierr = PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);CHKERRQ(ierr); 724 ierr = DMPlexGetHybridBounds(dm,&hybEnd[depth],&hybEnd[depth-1],&hybEnd[1],&hybEnd[0]);CHKERRQ(ierr); 725 for (d = 0; d < depth+1; ++d) { 726 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 727 for (p = pStart; p < pEnd; ++p) { 728 if (hybEnd[d] >= 0 && p >= hybEnd[d]) { /* put in a separate value for hybrid points */ 729 pointDepths[p] = 2 * d; 730 } else { 731 pointDepths[p] = 2 * d + 1; 732 } 733 } 734 } 735 for (p = 0; p < nleaves; ++p) remoteDepths[p] = -1; 736 ierr = PetscSFBcastBegin(sf, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 737 ierr = PetscSFBcastEnd(sf, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 738 /* Count recevied points in each stratum and compute the internal strata shift */ 739 ierr = PetscMalloc3(2*(depth+1), &depthRecv, 2*(depth+1), &depthShift, 2*(depth+1), &depthIdx);CHKERRQ(ierr); 740 for (d = 0; d < 2*(depth+1); ++d) depthRecv[d] = 0; 741 for (p = 0; p < nleaves; ++p) depthRecv[remoteDepths[p]]++; 742 depthShift[2*depth+1] = 0; 743 for (d = 0; d < 2*depth+1; ++d) depthShift[d] = depthRecv[2 * depth + 1]; 744 for (d = 0; d < 2*depth; ++d) depthShift[d] += depthRecv[2 * depth]; 745 depthShift[0] += depthRecv[1]; 746 for (d = 2; d < 2*depth; ++d) depthShift[d] += depthRecv[1]; 747 for (d = 2; d < 2*depth; ++d) depthShift[d] += depthRecv[0]; 748 for (d = 2 * depth-1; d > 2; --d) { 749 PetscInt e; 750 751 for (e = d -1; e > 1; --e) depthShift[e] += depthRecv[d]; 752 } 753 for (d = 0; d < 2*(depth+1); ++d) {depthIdx[d] = 0;} 754 /* Derive a new local permutation based on stratified indices */ 755 ierr = PetscMalloc1(nleaves, &ilocal);CHKERRQ(ierr); 756 for (p = 0; p < nleaves; ++p) { 757 const PetscInt dep = remoteDepths[p]; 758 759 ilocal[p] = depthShift[dep] + depthIdx[dep]; 760 depthIdx[dep]++; 761 } 762 ierr = PetscSFCreate(comm, migrationSF);CHKERRQ(ierr); 763 ierr = PetscObjectSetName((PetscObject) *migrationSF, "Migration SF");CHKERRQ(ierr); 764 ierr = PetscSFSetGraph(*migrationSF, nroots, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_COPY_VALUES);CHKERRQ(ierr); 765 ierr = PetscFree2(pointDepths,remoteDepths);CHKERRQ(ierr); 766 ierr = PetscFree3(depthRecv, depthShift, depthIdx);CHKERRQ(ierr); 767 PetscFunctionReturn(0); 768 } 769 770 /*@ 771 DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 772 773 Collective on DM 774 775 Input Parameters: 776 + dm - The DMPlex object 777 . pointSF - The PetscSF describing the communication pattern 778 . originalSection - The PetscSection for existing data layout 779 - originalVec - The existing data 780 781 Output Parameters: 782 + newSection - The PetscSF describing the new data layout 783 - newVec - The new data 784 785 Level: developer 786 787 .seealso: DMPlexDistribute(), DMPlexDistributeFieldIS(), DMPlexDistributeData() 788 @*/ 789 PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec) 790 { 791 PetscSF fieldSF; 792 PetscInt *remoteOffsets, fieldSize; 793 PetscScalar *originalValues, *newValues; 794 PetscErrorCode ierr; 795 796 PetscFunctionBegin; 797 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 798 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 799 800 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 801 ierr = VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);CHKERRQ(ierr); 802 ierr = VecSetType(newVec,dm->vectype);CHKERRQ(ierr); 803 804 ierr = VecGetArray(originalVec, &originalValues);CHKERRQ(ierr); 805 ierr = VecGetArray(newVec, &newValues);CHKERRQ(ierr); 806 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 807 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 808 ierr = PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); 809 ierr = PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); 810 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 811 ierr = VecRestoreArray(newVec, &newValues);CHKERRQ(ierr); 812 ierr = VecRestoreArray(originalVec, &originalValues);CHKERRQ(ierr); 813 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 814 PetscFunctionReturn(0); 815 } 816 817 /*@ 818 DMPlexDistributeFieldIS - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 819 820 Collective on DM 821 822 Input Parameters: 823 + dm - The DMPlex object 824 . pointSF - The PetscSF describing the communication pattern 825 . originalSection - The PetscSection for existing data layout 826 - originalIS - The existing data 827 828 Output Parameters: 829 + newSection - The PetscSF describing the new data layout 830 - newIS - The new data 831 832 Level: developer 833 834 .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexDistributeData() 835 @*/ 836 PetscErrorCode DMPlexDistributeFieldIS(DM dm, PetscSF pointSF, PetscSection originalSection, IS originalIS, PetscSection newSection, IS *newIS) 837 { 838 PetscSF fieldSF; 839 PetscInt *newValues, *remoteOffsets, fieldSize; 840 const PetscInt *originalValues; 841 PetscErrorCode ierr; 842 843 PetscFunctionBegin; 844 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 845 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 846 847 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 848 ierr = PetscMalloc1(fieldSize, &newValues);CHKERRQ(ierr); 849 850 ierr = ISGetIndices(originalIS, &originalValues);CHKERRQ(ierr); 851 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 852 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 853 ierr = PetscSFBcastBegin(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);CHKERRQ(ierr); 854 ierr = PetscSFBcastEnd(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);CHKERRQ(ierr); 855 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 856 ierr = ISRestoreIndices(originalIS, &originalValues);CHKERRQ(ierr); 857 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) pointSF), fieldSize, newValues, PETSC_OWN_POINTER, newIS);CHKERRQ(ierr); 858 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 859 PetscFunctionReturn(0); 860 } 861 862 /*@ 863 DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 864 865 Collective on DM 866 867 Input Parameters: 868 + dm - The DMPlex object 869 . pointSF - The PetscSF describing the communication pattern 870 . originalSection - The PetscSection for existing data layout 871 . datatype - The type of data 872 - originalData - The existing data 873 874 Output Parameters: 875 + newSection - The PetscSection describing the new data layout 876 - newData - The new data 877 878 Level: developer 879 880 .seealso: DMPlexDistribute(), DMPlexDistributeField() 881 @*/ 882 PetscErrorCode DMPlexDistributeData(DM dm, PetscSF pointSF, PetscSection originalSection, MPI_Datatype datatype, void *originalData, PetscSection newSection, void **newData) 883 { 884 PetscSF fieldSF; 885 PetscInt *remoteOffsets, fieldSize; 886 PetscMPIInt dataSize; 887 PetscErrorCode ierr; 888 889 PetscFunctionBegin; 890 ierr = PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 891 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 892 893 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 894 ierr = MPI_Type_size(datatype, &dataSize);CHKERRQ(ierr); 895 ierr = PetscMalloc(fieldSize * dataSize, newData);CHKERRQ(ierr); 896 897 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 898 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 899 ierr = PetscSFBcastBegin(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr); 900 ierr = PetscSFBcastEnd(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr); 901 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 902 ierr = PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 903 PetscFunctionReturn(0); 904 } 905 906 static PetscErrorCode DMPlexDistributeCones(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel) 907 { 908 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 909 MPI_Comm comm; 910 PetscSF coneSF; 911 PetscSection originalConeSection, newConeSection; 912 PetscInt *remoteOffsets, *cones, *globCones, *newCones, newConesSize; 913 PetscBool flg; 914 PetscErrorCode ierr; 915 916 PetscFunctionBegin; 917 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 918 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 5); 919 920 ierr = PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 921 /* Distribute cone section */ 922 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 923 ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr); 924 ierr = DMPlexGetConeSection(dmParallel, &newConeSection);CHKERRQ(ierr); 925 ierr = PetscSFDistributeSection(migrationSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr); 926 ierr = DMSetUp(dmParallel);CHKERRQ(ierr); 927 { 928 PetscInt pStart, pEnd, p; 929 930 ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr); 931 for (p = pStart; p < pEnd; ++p) { 932 PetscInt coneSize; 933 ierr = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr); 934 pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize); 935 } 936 } 937 /* Communicate and renumber cones */ 938 ierr = PetscSFCreateSectionSF(migrationSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr); 939 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 940 ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); 941 if (original) { 942 PetscInt numCones; 943 944 ierr = PetscSectionGetStorageSize(originalConeSection,&numCones);CHKERRQ(ierr); 945 ierr = PetscMalloc1(numCones,&globCones);CHKERRQ(ierr); 946 ierr = ISLocalToGlobalMappingApplyBlock(original, numCones, cones, globCones);CHKERRQ(ierr); 947 } else { 948 globCones = cones; 949 } 950 ierr = DMPlexGetCones(dmParallel, &newCones);CHKERRQ(ierr); 951 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, globCones, newCones);CHKERRQ(ierr); 952 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, globCones, newCones);CHKERRQ(ierr); 953 if (original) { 954 ierr = PetscFree(globCones);CHKERRQ(ierr); 955 } 956 ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr); 957 ierr = ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);CHKERRQ(ierr); 958 #if defined(PETSC_USE_DEBUG) 959 { 960 PetscInt p; 961 PetscBool valid = PETSC_TRUE; 962 for (p = 0; p < newConesSize; ++p) { 963 if (newCones[p] < 0) {valid = PETSC_FALSE; ierr = PetscPrintf(PETSC_COMM_SELF, "[%d] Point %D not in overlap SF\n", PetscGlobalRank,p);CHKERRQ(ierr);} 964 } 965 if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map"); 966 } 967 #endif 968 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr); 969 if (flg) { 970 ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr); 971 ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 972 ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr); 973 ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 974 ierr = PetscSFView(coneSF, NULL);CHKERRQ(ierr); 975 } 976 ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr); 977 ierr = DMPlexGetConeOrientations(dmParallel, &newCones);CHKERRQ(ierr); 978 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 979 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 980 ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr); 981 ierr = PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 982 /* Create supports and stratify DMPlex */ 983 { 984 PetscInt pStart, pEnd; 985 986 ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 987 ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr); 988 } 989 ierr = DMPlexSymmetrize(dmParallel);CHKERRQ(ierr); 990 ierr = DMPlexStratify(dmParallel);CHKERRQ(ierr); 991 { 992 PetscBool useCone, useClosure, useAnchors; 993 994 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 995 ierr = DMSetBasicAdjacency(dmParallel, useCone, useClosure);CHKERRQ(ierr); 996 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 997 ierr = DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);CHKERRQ(ierr); 998 } 999 PetscFunctionReturn(0); 1000 } 1001 1002 static PetscErrorCode DMPlexDistributeCoordinates(DM dm, PetscSF migrationSF, DM dmParallel) 1003 { 1004 MPI_Comm comm; 1005 PetscSection originalCoordSection, newCoordSection; 1006 Vec originalCoordinates, newCoordinates; 1007 PetscInt bs; 1008 PetscBool isper; 1009 const char *name; 1010 const PetscReal *maxCell, *L; 1011 const DMBoundaryType *bd; 1012 PetscErrorCode ierr; 1013 1014 PetscFunctionBegin; 1015 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1016 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1017 1018 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1019 ierr = DMGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr); 1020 ierr = DMGetCoordinateSection(dmParallel, &newCoordSection);CHKERRQ(ierr); 1021 ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr); 1022 if (originalCoordinates) { 1023 ierr = VecCreate(PETSC_COMM_SELF, &newCoordinates);CHKERRQ(ierr); 1024 ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr); 1025 ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr); 1026 1027 ierr = DMPlexDistributeField(dm, migrationSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr); 1028 ierr = DMSetCoordinatesLocal(dmParallel, newCoordinates);CHKERRQ(ierr); 1029 ierr = VecGetBlockSize(originalCoordinates, &bs);CHKERRQ(ierr); 1030 ierr = VecSetBlockSize(newCoordinates, bs);CHKERRQ(ierr); 1031 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 1032 } 1033 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 1034 ierr = DMSetPeriodicity(dmParallel, isper, maxCell, L, bd);CHKERRQ(ierr); 1035 PetscFunctionReturn(0); 1036 } 1037 1038 /* Here we are assuming that process 0 always has everything */ 1039 static PetscErrorCode DMPlexDistributeLabels(DM dm, PetscSF migrationSF, DM dmParallel) 1040 { 1041 DM_Plex *mesh = (DM_Plex*) dm->data; 1042 MPI_Comm comm; 1043 DMLabel depthLabel; 1044 PetscMPIInt rank; 1045 PetscInt depth, d, numLabels, numLocalLabels, l; 1046 PetscBool hasLabels = PETSC_FALSE, lsendDepth, sendDepth; 1047 PetscObjectState depthState = -1; 1048 PetscErrorCode ierr; 1049 1050 PetscFunctionBegin; 1051 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1052 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1053 1054 ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1055 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1056 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1057 1058 /* If the user has changed the depth label, communicate it instead */ 1059 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1060 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1061 if (depthLabel) {ierr = PetscObjectStateGet((PetscObject) depthLabel, &depthState);CHKERRQ(ierr);} 1062 lsendDepth = mesh->depthState != depthState ? PETSC_TRUE : PETSC_FALSE; 1063 ierr = MPIU_Allreduce(&lsendDepth, &sendDepth, 1, MPIU_BOOL, MPI_LOR, comm);CHKERRQ(ierr); 1064 if (sendDepth) { 1065 ierr = DMRemoveLabel(dmParallel, "depth", &depthLabel);CHKERRQ(ierr); 1066 ierr = DMLabelDestroy(&depthLabel);CHKERRQ(ierr); 1067 } 1068 /* Everyone must have either the same number of labels, or none */ 1069 ierr = DMGetNumLabels(dm, &numLocalLabels);CHKERRQ(ierr); 1070 numLabels = numLocalLabels; 1071 ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1072 if (numLabels == numLocalLabels) hasLabels = PETSC_TRUE; 1073 for (l = numLabels-1; l >= 0; --l) { 1074 DMLabel label = NULL, labelNew = NULL; 1075 PetscBool isDepth, lisOutput = PETSC_TRUE, isOutput; 1076 const char *name = NULL; 1077 1078 if (hasLabels) { 1079 ierr = DMGetLabelByNum(dm, l, &label);CHKERRQ(ierr); 1080 /* Skip "depth" because it is recreated */ 1081 ierr = PetscObjectGetName((PetscObject) label, &name);CHKERRQ(ierr); 1082 ierr = PetscStrcmp(name, "depth", &isDepth);CHKERRQ(ierr); 1083 } 1084 ierr = MPI_Bcast(&isDepth, 1, MPIU_BOOL, 0, comm);CHKERRQ(ierr); 1085 if (isDepth && !sendDepth) continue; 1086 ierr = DMLabelDistribute(label, migrationSF, &labelNew);CHKERRQ(ierr); 1087 if (isDepth) { 1088 /* Put in any missing strata which can occur if users are managing the depth label themselves */ 1089 PetscInt gdepth; 1090 1091 ierr = MPIU_Allreduce(&depth, &gdepth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 1092 if ((depth >= 0) && (gdepth != depth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", depth, gdepth); 1093 for (d = 0; d <= gdepth; ++d) { 1094 PetscBool has; 1095 1096 ierr = DMLabelHasStratum(labelNew, d, &has);CHKERRQ(ierr); 1097 if (!has) {ierr = DMLabelAddStratum(labelNew, d);CHKERRQ(ierr);} 1098 } 1099 } 1100 ierr = DMAddLabel(dmParallel, labelNew);CHKERRQ(ierr); 1101 /* Put the output flag in the new label */ 1102 if (hasLabels) {ierr = DMGetLabelOutput(dm, name, &lisOutput);CHKERRQ(ierr);} 1103 ierr = MPIU_Allreduce(&lisOutput, &isOutput, 1, MPIU_BOOL, MPI_LAND, comm);CHKERRQ(ierr); 1104 ierr = PetscObjectGetName((PetscObject) labelNew, &name);CHKERRQ(ierr); 1105 ierr = DMSetLabelOutput(dmParallel, name, isOutput);CHKERRQ(ierr); 1106 } 1107 ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1108 PetscFunctionReturn(0); 1109 } 1110 1111 static PetscErrorCode DMPlexDistributeSetupHybrid(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel) 1112 { 1113 DM_Plex *mesh = (DM_Plex*) dm->data; 1114 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1115 PetscBool *isHybrid, *isHybridParallel; 1116 PetscInt dim, depth, d; 1117 PetscInt pStart, pEnd, pStartP, pEndP; 1118 PetscErrorCode ierr; 1119 1120 PetscFunctionBegin; 1121 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1122 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1123 1124 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1125 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1126 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1127 ierr = DMPlexGetChart(dmParallel,&pStartP,&pEndP);CHKERRQ(ierr); 1128 ierr = PetscCalloc2(pEnd-pStart,&isHybrid,pEndP-pStartP,&isHybridParallel);CHKERRQ(ierr); 1129 for (d = 0; d <= depth; d++) { 1130 PetscInt hybridMax = (depth == 1 && d == 1) ? mesh->hybridPointMax[dim] : mesh->hybridPointMax[d]; 1131 1132 if (hybridMax >= 0) { 1133 PetscInt sStart, sEnd, p; 1134 1135 ierr = DMPlexGetDepthStratum(dm,d,&sStart,&sEnd);CHKERRQ(ierr); 1136 for (p = hybridMax; p < sEnd; p++) isHybrid[p-pStart] = PETSC_TRUE; 1137 } 1138 } 1139 ierr = PetscSFBcastBegin(migrationSF,MPIU_BOOL,isHybrid,isHybridParallel);CHKERRQ(ierr); 1140 ierr = PetscSFBcastEnd(migrationSF,MPIU_BOOL,isHybrid,isHybridParallel);CHKERRQ(ierr); 1141 for (d = 0; d <= dim; d++) pmesh->hybridPointMax[d] = -1; 1142 for (d = 0; d <= depth; d++) { 1143 PetscInt sStart, sEnd, p, dd; 1144 1145 ierr = DMPlexGetDepthStratum(dmParallel,d,&sStart,&sEnd);CHKERRQ(ierr); 1146 dd = (depth == 1 && d == 1) ? dim : d; 1147 for (p = sStart; p < sEnd; p++) { 1148 if (isHybridParallel[p-pStartP]) { 1149 pmesh->hybridPointMax[dd] = p; 1150 break; 1151 } 1152 } 1153 } 1154 ierr = PetscFree2(isHybrid,isHybridParallel);CHKERRQ(ierr); 1155 PetscFunctionReturn(0); 1156 } 1157 1158 static PetscErrorCode DMPlexDistributeSetupTree(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel) 1159 { 1160 DM_Plex *mesh = (DM_Plex*) dm->data; 1161 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1162 MPI_Comm comm; 1163 DM refTree; 1164 PetscSection origParentSection, newParentSection; 1165 PetscInt *origParents, *origChildIDs; 1166 PetscBool flg; 1167 PetscErrorCode ierr; 1168 1169 PetscFunctionBegin; 1170 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1171 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 5); 1172 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1173 1174 /* Set up tree */ 1175 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 1176 ierr = DMPlexSetReferenceTree(dmParallel,refTree);CHKERRQ(ierr); 1177 ierr = DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);CHKERRQ(ierr); 1178 if (origParentSection) { 1179 PetscInt pStart, pEnd; 1180 PetscInt *newParents, *newChildIDs, *globParents; 1181 PetscInt *remoteOffsetsParents, newParentSize; 1182 PetscSF parentSF; 1183 1184 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1185 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dmParallel),&newParentSection);CHKERRQ(ierr); 1186 ierr = PetscSectionSetChart(newParentSection,pStart,pEnd);CHKERRQ(ierr); 1187 ierr = PetscSFDistributeSection(migrationSF, origParentSection, &remoteOffsetsParents, newParentSection);CHKERRQ(ierr); 1188 ierr = PetscSFCreateSectionSF(migrationSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);CHKERRQ(ierr); 1189 ierr = PetscFree(remoteOffsetsParents);CHKERRQ(ierr); 1190 ierr = PetscSectionGetStorageSize(newParentSection,&newParentSize);CHKERRQ(ierr); 1191 ierr = PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);CHKERRQ(ierr); 1192 if (original) { 1193 PetscInt numParents; 1194 1195 ierr = PetscSectionGetStorageSize(origParentSection,&numParents);CHKERRQ(ierr); 1196 ierr = PetscMalloc1(numParents,&globParents);CHKERRQ(ierr); 1197 ierr = ISLocalToGlobalMappingApplyBlock(original, numParents, origParents, globParents);CHKERRQ(ierr); 1198 } 1199 else { 1200 globParents = origParents; 1201 } 1202 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, globParents, newParents);CHKERRQ(ierr); 1203 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, globParents, newParents);CHKERRQ(ierr); 1204 if (original) { 1205 ierr = PetscFree(globParents);CHKERRQ(ierr); 1206 } 1207 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1208 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1209 ierr = ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);CHKERRQ(ierr); 1210 #if defined(PETSC_USE_DEBUG) 1211 { 1212 PetscInt p; 1213 PetscBool valid = PETSC_TRUE; 1214 for (p = 0; p < newParentSize; ++p) { 1215 if (newParents[p] < 0) {valid = PETSC_FALSE; ierr = PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);CHKERRQ(ierr);} 1216 } 1217 if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map"); 1218 } 1219 #endif 1220 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-parents_view", &flg);CHKERRQ(ierr); 1221 if (flg) { 1222 ierr = PetscPrintf(comm, "Serial Parent Section: \n");CHKERRQ(ierr); 1223 ierr = PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1224 ierr = PetscPrintf(comm, "Parallel Parent Section: \n");CHKERRQ(ierr); 1225 ierr = PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1226 ierr = PetscSFView(parentSF, NULL);CHKERRQ(ierr); 1227 } 1228 ierr = DMPlexSetTree(dmParallel,newParentSection,newParents,newChildIDs);CHKERRQ(ierr); 1229 ierr = PetscSectionDestroy(&newParentSection);CHKERRQ(ierr); 1230 ierr = PetscFree2(newParents,newChildIDs);CHKERRQ(ierr); 1231 ierr = PetscSFDestroy(&parentSF);CHKERRQ(ierr); 1232 } 1233 pmesh->useAnchors = mesh->useAnchors; 1234 PetscFunctionReturn(0); 1235 } 1236 1237 PETSC_UNUSED static PetscErrorCode DMPlexDistributeSF(DM dm, PetscSF migrationSF, DM dmParallel) 1238 { 1239 PetscMPIInt rank, size; 1240 MPI_Comm comm; 1241 PetscErrorCode ierr; 1242 1243 PetscFunctionBegin; 1244 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1245 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1246 1247 /* Create point SF for parallel mesh */ 1248 ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1249 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1250 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1251 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1252 { 1253 const PetscInt *leaves; 1254 PetscSFNode *remotePoints, *rowners, *lowners; 1255 PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints; 1256 PetscInt pStart, pEnd; 1257 1258 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1259 ierr = PetscSFGetGraph(migrationSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr); 1260 ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr); 1261 for (p=0; p<numRoots; p++) { 1262 rowners[p].rank = -1; 1263 rowners[p].index = -1; 1264 } 1265 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1266 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1267 for (p = 0; p < numLeaves; ++p) { 1268 if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */ 1269 lowners[p].rank = rank; 1270 lowners[p].index = leaves ? leaves[p] : p; 1271 } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */ 1272 lowners[p].rank = -2; 1273 lowners[p].index = -2; 1274 } 1275 } 1276 for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */ 1277 rowners[p].rank = -3; 1278 rowners[p].index = -3; 1279 } 1280 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1281 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1282 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1283 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1284 for (p = 0; p < numLeaves; ++p) { 1285 if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed"); 1286 if (lowners[p].rank != rank) ++numGhostPoints; 1287 } 1288 ierr = PetscMalloc1(numGhostPoints, &ghostPoints);CHKERRQ(ierr); 1289 ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr); 1290 for (p = 0, gp = 0; p < numLeaves; ++p) { 1291 if (lowners[p].rank != rank) { 1292 ghostPoints[gp] = leaves ? leaves[p] : p; 1293 remotePoints[gp].rank = lowners[p].rank; 1294 remotePoints[gp].index = lowners[p].index; 1295 ++gp; 1296 } 1297 } 1298 ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr); 1299 ierr = PetscSFSetGraph((dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 1300 ierr = PetscSFSetFromOptions((dmParallel)->sf);CHKERRQ(ierr); 1301 } 1302 { 1303 PetscBool useCone, useClosure, useAnchors; 1304 1305 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 1306 ierr = DMSetBasicAdjacency(dmParallel, useCone, useClosure);CHKERRQ(ierr); 1307 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 1308 ierr = DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);CHKERRQ(ierr); 1309 } 1310 ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1311 PetscFunctionReturn(0); 1312 } 1313 1314 /*@ 1315 DMPlexSetPartitionBalance - Should distribution of the DM attempt to balance the shared point partition? 1316 1317 Input Parameters: 1318 + dm - The DMPlex object 1319 - flg - Balance the partition? 1320 1321 Level: intermediate 1322 1323 .seealso: DMPlexDistribute(), DMPlexGetPartitionBalance() 1324 @*/ 1325 PetscErrorCode DMPlexSetPartitionBalance(DM dm, PetscBool flg) 1326 { 1327 DM_Plex *mesh = (DM_Plex *)dm->data; 1328 1329 PetscFunctionBegin; 1330 mesh->partitionBalance = flg; 1331 PetscFunctionReturn(0); 1332 } 1333 1334 /*@ 1335 DMPlexGetPartitionBalance - Does distribution of the DM attempt to balance the shared point partition? 1336 1337 Input Parameter: 1338 + dm - The DMPlex object 1339 1340 Output Parameter: 1341 + flg - Balance the partition? 1342 1343 Level: intermediate 1344 1345 .seealso: DMPlexDistribute(), DMPlexSetPartitionBalance() 1346 @*/ 1347 PetscErrorCode DMPlexGetPartitionBalance(DM dm, PetscBool *flg) 1348 { 1349 DM_Plex *mesh = (DM_Plex *)dm->data; 1350 1351 PetscFunctionBegin; 1352 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1353 PetscValidIntPointer(flg, 2); 1354 *flg = mesh->partitionBalance; 1355 PetscFunctionReturn(0); 1356 } 1357 1358 /*@C 1359 DMPlexDerivePointSF - Build a point SF from an SF describing a point migration 1360 1361 Input Parameter: 1362 + dm - The source DMPlex object 1363 . migrationSF - The star forest that describes the parallel point remapping 1364 . ownership - Flag causing a vote to determine point ownership 1365 1366 Output Parameter: 1367 - pointSF - The star forest describing the point overlap in the remapped DM 1368 1369 Level: developer 1370 1371 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1372 @*/ 1373 PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF) 1374 { 1375 PetscMPIInt rank, size; 1376 PetscInt p, nroots, nleaves, idx, npointLeaves; 1377 PetscInt *pointLocal; 1378 const PetscInt *leaves; 1379 const PetscSFNode *roots; 1380 PetscSFNode *rootNodes, *leafNodes, *pointRemote; 1381 Vec shifts; 1382 const PetscInt numShifts = 13759; 1383 const PetscScalar *shift = NULL; 1384 const PetscBool shiftDebug = PETSC_FALSE; 1385 PetscBool balance; 1386 PetscErrorCode ierr; 1387 1388 PetscFunctionBegin; 1389 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1390 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 1391 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 1392 1393 ierr = DMPlexGetPartitionBalance(dm, &balance);CHKERRQ(ierr); 1394 ierr = PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);CHKERRQ(ierr); 1395 ierr = PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);CHKERRQ(ierr); 1396 if (ownership) { 1397 /* If balancing, we compute a random cyclic shift of the rank for each remote point. That way, the max will evenly distribute among ranks. */ 1398 if (balance) { 1399 PetscRandom r; 1400 1401 ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 1402 ierr = PetscRandomSetInterval(r, 0, 2467*size);CHKERRQ(ierr); 1403 ierr = VecCreate(PETSC_COMM_SELF, &shifts);CHKERRQ(ierr); 1404 ierr = VecSetSizes(shifts, numShifts, numShifts);CHKERRQ(ierr); 1405 ierr = VecSetType(shifts, VECSTANDARD);CHKERRQ(ierr); 1406 ierr = VecSetRandom(shifts, r);CHKERRQ(ierr); 1407 ierr = PetscRandomDestroy(&r);CHKERRQ(ierr); 1408 ierr = VecGetArrayRead(shifts, &shift);CHKERRQ(ierr); 1409 } 1410 1411 /* Point ownership vote: Process with highest rank owns shared points */ 1412 for (p = 0; p < nleaves; ++p) { 1413 if (shiftDebug) { 1414 ierr = PetscSynchronizedPrintf(PetscObjectComm((PetscObject) dm), "[%d] Point %D RemotePoint %D Shift %D MyRank %D\n", rank, leaves ? leaves[p] : p, roots[p].index, (PetscInt) PetscRealPart(shift[roots[p].index%numShifts]), (rank + (shift ? (PetscInt) PetscRealPart(shift[roots[p].index%numShifts]) : 0))%size);CHKERRQ(ierr); 1415 } 1416 /* Either put in a bid or we know we own it */ 1417 leafNodes[p].rank = (rank + (shift ? (PetscInt) PetscRealPart(shift[roots[p].index%numShifts]) : 0))%size; 1418 leafNodes[p].index = p; 1419 } 1420 for (p = 0; p < nroots; p++) { 1421 /* Root must not participate in the reduction, flag so that MAXLOC does not use */ 1422 rootNodes[p].rank = -3; 1423 rootNodes[p].index = -3; 1424 } 1425 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);CHKERRQ(ierr); 1426 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);CHKERRQ(ierr); 1427 if (balance) { 1428 /* We've voted, now we need to get the rank. When we're balancing the partition, the "rank" in rootNotes is not 1429 * the rank but rather (rank + random)%size. So we do another reduction, voting the same way, but sending the 1430 * rank instead of the index. */ 1431 PetscSFNode *rootRanks = NULL; 1432 ierr = PetscMalloc1(nroots, &rootRanks);CHKERRQ(ierr); 1433 for (p = 0; p < nroots; p++) { 1434 rootRanks[p].rank = -3; 1435 rootRanks[p].index = -3; 1436 } 1437 for (p = 0; p < nleaves; p++) leafNodes[p].index = rank; 1438 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, leafNodes, rootRanks, MPI_MAXLOC);CHKERRQ(ierr); 1439 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, leafNodes, rootRanks, MPI_MAXLOC);CHKERRQ(ierr); 1440 for (p = 0; p < nroots; p++) rootNodes[p].rank = rootRanks[p].index; 1441 ierr = PetscFree(rootRanks);CHKERRQ(ierr); 1442 } 1443 } else { 1444 for (p = 0; p < nroots; p++) { 1445 rootNodes[p].index = -1; 1446 rootNodes[p].rank = rank; 1447 }; 1448 for (p = 0; p < nleaves; p++) { 1449 /* Write new local id into old location */ 1450 if (roots[p].rank == rank) { 1451 rootNodes[roots[p].index].index = leaves ? leaves[p] : p; 1452 } 1453 } 1454 } 1455 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1456 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1457 1458 for (npointLeaves = 0, p = 0; p < nleaves; p++) { 1459 if (leafNodes[p].rank != rank) npointLeaves++; 1460 } 1461 ierr = PetscMalloc1(npointLeaves, &pointLocal);CHKERRQ(ierr); 1462 ierr = PetscMalloc1(npointLeaves, &pointRemote);CHKERRQ(ierr); 1463 for (idx = 0, p = 0; p < nleaves; p++) { 1464 if (leafNodes[p].rank != rank) { 1465 pointLocal[idx] = p; 1466 pointRemote[idx] = leafNodes[p]; 1467 idx++; 1468 } 1469 } 1470 if (shift) { 1471 ierr = VecRestoreArrayRead(shifts, &shift);CHKERRQ(ierr); 1472 ierr = VecDestroy(&shifts);CHKERRQ(ierr); 1473 } 1474 if (shiftDebug) {ierr = PetscSynchronizedFlush(PetscObjectComm((PetscObject) dm), PETSC_STDOUT);CHKERRQ(ierr);} 1475 ierr = PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);CHKERRQ(ierr); 1476 ierr = PetscSFSetFromOptions(*pointSF);CHKERRQ(ierr); 1477 ierr = PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1478 ierr = PetscFree2(rootNodes, leafNodes);CHKERRQ(ierr); 1479 PetscFunctionReturn(0); 1480 } 1481 1482 /*@C 1483 DMPlexMigrate - Migrates internal DM data over the supplied star forest 1484 1485 Collective on DM and PetscSF 1486 1487 Input Parameter: 1488 + dm - The source DMPlex object 1489 . sf - The star forest communication context describing the migration pattern 1490 1491 Output Parameter: 1492 - targetDM - The target DMPlex object 1493 1494 Level: intermediate 1495 1496 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1497 @*/ 1498 PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM) 1499 { 1500 MPI_Comm comm; 1501 PetscInt dim, cdim, nroots; 1502 PetscSF sfPoint; 1503 ISLocalToGlobalMapping ltogMigration; 1504 ISLocalToGlobalMapping ltogOriginal = NULL; 1505 PetscBool flg; 1506 PetscErrorCode ierr; 1507 1508 PetscFunctionBegin; 1509 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1510 ierr = PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1511 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 1512 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1513 ierr = DMSetDimension(targetDM, dim);CHKERRQ(ierr); 1514 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 1515 ierr = DMSetCoordinateDim(targetDM, cdim);CHKERRQ(ierr); 1516 1517 /* Check for a one-to-all distribution pattern */ 1518 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1519 ierr = PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 1520 if (nroots >= 0) { 1521 IS isOriginal; 1522 PetscInt n, size, nleaves; 1523 PetscInt *numbering_orig, *numbering_new; 1524 1525 /* Get the original point numbering */ 1526 ierr = DMPlexCreatePointNumbering(dm, &isOriginal);CHKERRQ(ierr); 1527 ierr = ISLocalToGlobalMappingCreateIS(isOriginal, <ogOriginal);CHKERRQ(ierr); 1528 ierr = ISLocalToGlobalMappingGetSize(ltogOriginal, &size);CHKERRQ(ierr); 1529 ierr = ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1530 /* Convert to positive global numbers */ 1531 for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);} 1532 /* Derive the new local-to-global mapping from the old one */ 1533 ierr = PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1534 ierr = PetscMalloc1(nleaves, &numbering_new);CHKERRQ(ierr); 1535 ierr = PetscSFBcastBegin(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);CHKERRQ(ierr); 1536 ierr = PetscSFBcastEnd(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);CHKERRQ(ierr); 1537 ierr = ISLocalToGlobalMappingCreate(comm, 1, nleaves, (const PetscInt*) numbering_new, PETSC_OWN_POINTER, <ogMigration);CHKERRQ(ierr); 1538 ierr = ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1539 ierr = ISDestroy(&isOriginal);CHKERRQ(ierr); 1540 } else { 1541 /* One-to-all distribution pattern: We can derive LToG from SF */ 1542 ierr = ISLocalToGlobalMappingCreateSF(sf, 0, <ogMigration);CHKERRQ(ierr); 1543 } 1544 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1545 if (flg) { 1546 ierr = PetscPrintf(comm, "Point renumbering for DM migration:\n");CHKERRQ(ierr); 1547 ierr = ISLocalToGlobalMappingView(ltogMigration, NULL);CHKERRQ(ierr); 1548 } 1549 /* Migrate DM data to target DM */ 1550 ierr = DMPlexDistributeCones(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1551 ierr = DMPlexDistributeLabels(dm, sf, targetDM);CHKERRQ(ierr); 1552 ierr = DMPlexDistributeCoordinates(dm, sf, targetDM);CHKERRQ(ierr); 1553 ierr = DMPlexDistributeSetupHybrid(dm, sf, ltogMigration, targetDM);CHKERRQ(ierr); 1554 ierr = DMPlexDistributeSetupTree(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1555 ierr = ISLocalToGlobalMappingDestroy(<ogOriginal);CHKERRQ(ierr); 1556 ierr = ISLocalToGlobalMappingDestroy(<ogMigration);CHKERRQ(ierr); 1557 ierr = PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1558 PetscFunctionReturn(0); 1559 } 1560 1561 /*@C 1562 DMPlexDistribute - Distributes the mesh and any associated sections. 1563 1564 Collective on DM 1565 1566 Input Parameter: 1567 + dm - The original DMPlex object 1568 - overlap - The overlap of partitions, 0 is the default 1569 1570 Output Parameter: 1571 + sf - The PetscSF used for point distribution, or NULL if not needed 1572 - dmParallel - The distributed DMPlex object 1573 1574 Note: If the mesh was not distributed, the output dmParallel will be NULL. 1575 1576 The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function 1577 representation on the mesh. 1578 1579 Level: intermediate 1580 1581 .keywords: mesh, elements 1582 .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMSetAdjacency() 1583 @*/ 1584 PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel) 1585 { 1586 MPI_Comm comm; 1587 PetscPartitioner partitioner; 1588 IS cellPart; 1589 PetscSection cellPartSection; 1590 DM dmCoord; 1591 DMLabel lblPartition, lblMigration; 1592 PetscSF sfProcess, sfMigration, sfStratified, sfPoint; 1593 PetscBool flg, balance; 1594 PetscMPIInt rank, size, p; 1595 PetscErrorCode ierr; 1596 1597 PetscFunctionBegin; 1598 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1599 PetscValidLogicalCollectiveInt(dm, overlap, 2); 1600 if (sf) PetscValidPointer(sf,3); 1601 PetscValidPointer(dmParallel,4); 1602 1603 if (sf) *sf = NULL; 1604 *dmParallel = NULL; 1605 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1606 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1607 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1608 if (size == 1) PetscFunctionReturn(0); 1609 1610 ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1611 /* Create cell partition */ 1612 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1613 ierr = PetscSectionCreate(comm, &cellPartSection);CHKERRQ(ierr); 1614 ierr = DMPlexGetPartitioner(dm, &partitioner);CHKERRQ(ierr); 1615 ierr = PetscPartitionerPartition(partitioner, dm, cellPartSection, &cellPart);CHKERRQ(ierr); 1616 { 1617 /* Convert partition to DMLabel */ 1618 PetscInt proc, pStart, pEnd, npoints, poffset; 1619 const PetscInt *points; 1620 ierr = DMLabelCreate(PETSC_COMM_SELF, "Point Partition", &lblPartition);CHKERRQ(ierr); 1621 ierr = ISGetIndices(cellPart, &points);CHKERRQ(ierr); 1622 ierr = PetscSectionGetChart(cellPartSection, &pStart, &pEnd);CHKERRQ(ierr); 1623 for (proc = pStart; proc < pEnd; proc++) { 1624 ierr = PetscSectionGetDof(cellPartSection, proc, &npoints);CHKERRQ(ierr); 1625 ierr = PetscSectionGetOffset(cellPartSection, proc, &poffset);CHKERRQ(ierr); 1626 for (p = poffset; p < poffset+npoints; p++) { 1627 ierr = DMLabelSetValue(lblPartition, points[p], proc);CHKERRQ(ierr); 1628 } 1629 } 1630 ierr = ISRestoreIndices(cellPart, &points);CHKERRQ(ierr); 1631 } 1632 ierr = DMPlexPartitionLabelClosure(dm, lblPartition);CHKERRQ(ierr); 1633 { 1634 /* Build a global process SF */ 1635 PetscSFNode *remoteProc; 1636 ierr = PetscMalloc1(size, &remoteProc);CHKERRQ(ierr); 1637 for (p = 0; p < size; ++p) { 1638 remoteProc[p].rank = p; 1639 remoteProc[p].index = rank; 1640 } 1641 ierr = PetscSFCreate(comm, &sfProcess);CHKERRQ(ierr); 1642 ierr = PetscObjectSetName((PetscObject) sfProcess, "Process SF");CHKERRQ(ierr); 1643 ierr = PetscSFSetGraph(sfProcess, size, size, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);CHKERRQ(ierr); 1644 } 1645 ierr = DMLabelCreate(PETSC_COMM_SELF, "Point migration", &lblMigration);CHKERRQ(ierr); 1646 ierr = DMPlexPartitionLabelInvert(dm, lblPartition, sfProcess, lblMigration);CHKERRQ(ierr); 1647 ierr = DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);CHKERRQ(ierr); 1648 /* Stratify the SF in case we are migrating an already parallel plex */ 1649 ierr = DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);CHKERRQ(ierr); 1650 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1651 sfMigration = sfStratified; 1652 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1653 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1654 if (flg) { 1655 ierr = DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1656 ierr = PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1657 } 1658 1659 /* Create non-overlapping parallel DM and migrate internal data */ 1660 ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr); 1661 ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr); 1662 ierr = DMPlexMigrate(dm, sfMigration, *dmParallel);CHKERRQ(ierr); 1663 1664 /* Build the point SF without overlap */ 1665 ierr = DMPlexGetPartitionBalance(dm, &balance);CHKERRQ(ierr); 1666 ierr = DMPlexSetPartitionBalance(*dmParallel, balance);CHKERRQ(ierr); 1667 ierr = DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);CHKERRQ(ierr); 1668 ierr = DMSetPointSF(*dmParallel, sfPoint);CHKERRQ(ierr); 1669 ierr = DMGetCoordinateDM(*dmParallel, &dmCoord);CHKERRQ(ierr); 1670 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1671 if (flg) {ierr = PetscSFView(sfPoint, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);} 1672 1673 if (overlap > 0) { 1674 DM dmOverlap; 1675 PetscInt nroots, nleaves; 1676 PetscSFNode *newRemote; 1677 const PetscSFNode *oldRemote; 1678 PetscSF sfOverlap, sfOverlapPoint; 1679 /* Add the partition overlap to the distributed DM */ 1680 ierr = DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);CHKERRQ(ierr); 1681 ierr = DMDestroy(dmParallel);CHKERRQ(ierr); 1682 *dmParallel = dmOverlap; 1683 if (flg) { 1684 ierr = PetscPrintf(comm, "Overlap Migration SF:\n");CHKERRQ(ierr); 1685 ierr = PetscSFView(sfOverlap, NULL);CHKERRQ(ierr); 1686 } 1687 1688 /* Re-map the migration SF to establish the full migration pattern */ 1689 ierr = PetscSFGetGraph(sfMigration, &nroots, NULL, NULL, &oldRemote);CHKERRQ(ierr); 1690 ierr = PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1691 ierr = PetscMalloc1(nleaves, &newRemote);CHKERRQ(ierr); 1692 ierr = PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1693 ierr = PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1694 ierr = PetscSFCreate(comm, &sfOverlapPoint);CHKERRQ(ierr); 1695 ierr = PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1696 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1697 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1698 sfMigration = sfOverlapPoint; 1699 } 1700 /* Cleanup Partition */ 1701 ierr = PetscSFDestroy(&sfProcess);CHKERRQ(ierr); 1702 ierr = DMLabelDestroy(&lblPartition);CHKERRQ(ierr); 1703 ierr = DMLabelDestroy(&lblMigration);CHKERRQ(ierr); 1704 ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr); 1705 ierr = ISDestroy(&cellPart);CHKERRQ(ierr); 1706 /* Copy BC */ 1707 ierr = DMCopyBoundary(dm, *dmParallel);CHKERRQ(ierr); 1708 /* Create sfNatural */ 1709 if (dm->useNatural) { 1710 PetscSection section; 1711 1712 ierr = DMGetSection(dm, §ion);CHKERRQ(ierr); 1713 ierr = DMPlexCreateGlobalToNaturalSF(*dmParallel, section, sfMigration, &(*dmParallel)->sfNatural);CHKERRQ(ierr); 1714 ierr = DMSetUseNatural(*dmParallel, PETSC_TRUE);CHKERRQ(ierr); 1715 } 1716 /* Cleanup */ 1717 if (sf) {*sf = sfMigration;} 1718 else {ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr);} 1719 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1720 ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1721 PetscFunctionReturn(0); 1722 } 1723 1724 /*@C 1725 DMPlexDistributeOverlap - Add partition overlap to a distributed non-overlapping DM. 1726 1727 Collective on DM 1728 1729 Input Parameter: 1730 + dm - The non-overlapping distrbuted DMPlex object 1731 - overlap - The overlap of partitions 1732 1733 Output Parameter: 1734 + sf - The PetscSF used for point distribution 1735 - dmOverlap - The overlapping distributed DMPlex object, or NULL 1736 1737 Note: If the mesh was not distributed, the return value is NULL. 1738 1739 The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function 1740 representation on the mesh. 1741 1742 Level: intermediate 1743 1744 .keywords: mesh, elements 1745 .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMSetAdjacency() 1746 @*/ 1747 PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap) 1748 { 1749 MPI_Comm comm; 1750 PetscMPIInt size, rank; 1751 PetscSection rootSection, leafSection; 1752 IS rootrank, leafrank; 1753 DM dmCoord; 1754 DMLabel lblOverlap; 1755 PetscSF sfOverlap, sfStratified, sfPoint; 1756 PetscErrorCode ierr; 1757 1758 PetscFunctionBegin; 1759 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1760 if (sf) PetscValidPointer(sf, 3); 1761 PetscValidPointer(dmOverlap, 4); 1762 1763 if (sf) *sf = NULL; 1764 *dmOverlap = NULL; 1765 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1766 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1767 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1768 if (size == 1) PetscFunctionReturn(0); 1769 1770 ierr = PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1771 /* Compute point overlap with neighbouring processes on the distributed DM */ 1772 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1773 ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr); 1774 ierr = PetscSectionCreate(comm, &leafSection);CHKERRQ(ierr); 1775 ierr = DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);CHKERRQ(ierr); 1776 ierr = DMPlexCreateOverlap(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);CHKERRQ(ierr); 1777 /* Convert overlap label to stratified migration SF */ 1778 ierr = DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);CHKERRQ(ierr); 1779 ierr = DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);CHKERRQ(ierr); 1780 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1781 sfOverlap = sfStratified; 1782 ierr = PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");CHKERRQ(ierr); 1783 ierr = PetscSFSetFromOptions(sfOverlap);CHKERRQ(ierr); 1784 1785 ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr); 1786 ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr); 1787 ierr = ISDestroy(&rootrank);CHKERRQ(ierr); 1788 ierr = ISDestroy(&leafrank);CHKERRQ(ierr); 1789 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1790 1791 /* Build the overlapping DM */ 1792 ierr = DMPlexCreate(comm, dmOverlap);CHKERRQ(ierr); 1793 ierr = PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");CHKERRQ(ierr); 1794 ierr = DMPlexMigrate(dm, sfOverlap, *dmOverlap);CHKERRQ(ierr); 1795 /* Build the new point SF */ 1796 ierr = DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1797 ierr = DMSetPointSF(*dmOverlap, sfPoint);CHKERRQ(ierr); 1798 ierr = DMGetCoordinateDM(*dmOverlap, &dmCoord);CHKERRQ(ierr); 1799 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1800 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1801 /* Cleanup overlap partition */ 1802 ierr = DMLabelDestroy(&lblOverlap);CHKERRQ(ierr); 1803 if (sf) *sf = sfOverlap; 1804 else {ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr);} 1805 ierr = PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1806 PetscFunctionReturn(0); 1807 } 1808 1809 /*@C 1810 DMPlexGetGatherDM - Get a copy of the DMPlex that gathers all points on the 1811 root process of the original's communicator. 1812 1813 Collective on DM 1814 1815 Input Parameters: 1816 . dm - the original DMPlex object 1817 1818 Output Parameters: 1819 + sf - the PetscSF used for point distribution (optional) 1820 - gatherMesh - the gathered DM object, or NULL 1821 1822 Level: intermediate 1823 1824 .keywords: mesh 1825 .seealso: DMPlexDistribute(), DMPlexGetRedundantDM() 1826 @*/ 1827 PetscErrorCode DMPlexGetGatherDM(DM dm, PetscSF *sf, DM *gatherMesh) 1828 { 1829 MPI_Comm comm; 1830 PetscMPIInt size; 1831 PetscPartitioner oldPart, gatherPart; 1832 PetscErrorCode ierr; 1833 1834 PetscFunctionBegin; 1835 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1836 PetscValidPointer(gatherMesh,2); 1837 *gatherMesh = NULL; 1838 if (sf) *sf = NULL; 1839 comm = PetscObjectComm((PetscObject)dm); 1840 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1841 if (size == 1) PetscFunctionReturn(0); 1842 ierr = DMPlexGetPartitioner(dm,&oldPart);CHKERRQ(ierr); 1843 ierr = PetscObjectReference((PetscObject)oldPart);CHKERRQ(ierr); 1844 ierr = PetscPartitionerCreate(comm,&gatherPart);CHKERRQ(ierr); 1845 ierr = PetscPartitionerSetType(gatherPart,PETSCPARTITIONERGATHER);CHKERRQ(ierr); 1846 ierr = DMPlexSetPartitioner(dm,gatherPart);CHKERRQ(ierr); 1847 ierr = DMPlexDistribute(dm,0,sf,gatherMesh);CHKERRQ(ierr); 1848 1849 ierr = DMPlexSetPartitioner(dm,oldPart);CHKERRQ(ierr); 1850 ierr = PetscPartitionerDestroy(&gatherPart);CHKERRQ(ierr); 1851 ierr = PetscPartitionerDestroy(&oldPart);CHKERRQ(ierr); 1852 PetscFunctionReturn(0); 1853 } 1854 1855 /*@C 1856 DMPlexGetRedundantDM - Get a copy of the DMPlex that is completely copied on each process. 1857 1858 Collective on DM 1859 1860 Input Parameters: 1861 . dm - the original DMPlex object 1862 1863 Output Parameters: 1864 + sf - the PetscSF used for point distribution (optional) 1865 - redundantMesh - the redundant DM object, or NULL 1866 1867 Level: intermediate 1868 1869 .keywords: mesh 1870 .seealso: DMPlexDistribute(), DMPlexGetGatherDM() 1871 @*/ 1872 PetscErrorCode DMPlexGetRedundantDM(DM dm, PetscSF *sf, DM *redundantMesh) 1873 { 1874 MPI_Comm comm; 1875 PetscMPIInt size, rank; 1876 PetscInt pStart, pEnd, p; 1877 PetscInt numPoints = -1; 1878 PetscSF migrationSF, sfPoint, gatherSF; 1879 DM gatherDM, dmCoord; 1880 PetscSFNode *points; 1881 PetscErrorCode ierr; 1882 1883 PetscFunctionBegin; 1884 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1885 PetscValidPointer(redundantMesh,2); 1886 *redundantMesh = NULL; 1887 comm = PetscObjectComm((PetscObject)dm); 1888 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1889 if (size == 1) { 1890 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 1891 *redundantMesh = dm; 1892 if (sf) *sf = NULL; 1893 PetscFunctionReturn(0); 1894 } 1895 ierr = DMPlexGetGatherDM(dm,&gatherSF,&gatherDM);CHKERRQ(ierr); 1896 if (!gatherDM) PetscFunctionReturn(0); 1897 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1898 ierr = DMPlexGetChart(gatherDM,&pStart,&pEnd);CHKERRQ(ierr); 1899 numPoints = pEnd - pStart; 1900 ierr = MPI_Bcast(&numPoints,1,MPIU_INT,0,comm);CHKERRQ(ierr); 1901 ierr = PetscMalloc1(numPoints,&points);CHKERRQ(ierr); 1902 ierr = PetscSFCreate(comm,&migrationSF);CHKERRQ(ierr); 1903 for (p = 0; p < numPoints; p++) { 1904 points[p].index = p; 1905 points[p].rank = 0; 1906 } 1907 ierr = PetscSFSetGraph(migrationSF,pEnd-pStart,numPoints,NULL,PETSC_OWN_POINTER,points,PETSC_OWN_POINTER);CHKERRQ(ierr); 1908 ierr = DMPlexCreate(comm, redundantMesh);CHKERRQ(ierr); 1909 ierr = PetscObjectSetName((PetscObject) *redundantMesh, "Redundant Mesh");CHKERRQ(ierr); 1910 ierr = DMPlexMigrate(gatherDM, migrationSF, *redundantMesh);CHKERRQ(ierr); 1911 ierr = DMPlexCreatePointSF(*redundantMesh, migrationSF, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1912 ierr = DMSetPointSF(*redundantMesh, sfPoint);CHKERRQ(ierr); 1913 ierr = DMGetCoordinateDM(*redundantMesh, &dmCoord);CHKERRQ(ierr); 1914 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1915 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1916 if (sf) { 1917 PetscSF tsf; 1918 1919 ierr = PetscSFCompose(gatherSF,migrationSF,&tsf);CHKERRQ(ierr); 1920 ierr = DMPlexStratifyMigrationSF(dm, tsf, sf);CHKERRQ(ierr); 1921 ierr = PetscSFDestroy(&tsf);CHKERRQ(ierr); 1922 } 1923 ierr = PetscSFDestroy(&migrationSF);CHKERRQ(ierr); 1924 ierr = PetscSFDestroy(&gatherSF);CHKERRQ(ierr); 1925 ierr = DMDestroy(&gatherDM);CHKERRQ(ierr); 1926 PetscFunctionReturn(0); 1927 } 1928