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 Parameter: 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; 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 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 = DMPlexPartitionLabelClosure(dm, ovAdjByRank);CHKERRQ(ierr); 542 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-overlap_view", &flg);CHKERRQ(ierr); 543 if (flg) { 544 PetscViewer viewer; 545 ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)dm), &viewer);CHKERRQ(ierr); 546 ierr = DMLabelView(ovAdjByRank, viewer);CHKERRQ(ierr); 547 } 548 /* Invert sender to receiver label */ 549 ierr = DMLabelCreate(PETSC_COMM_SELF, "Overlap label", ovLabel);CHKERRQ(ierr); 550 ierr = DMPlexPartitionLabelInvert(dm, ovAdjByRank, NULL, *ovLabel);CHKERRQ(ierr); 551 /* Add owned points, except for shared local points */ 552 for (p = pStart; p < pEnd; ++p) {ierr = DMLabelSetValue(*ovLabel, p, rank);CHKERRQ(ierr);} 553 for (l = 0; l < nleaves; ++l) { 554 ierr = DMLabelClearValue(*ovLabel, local[l], rank);CHKERRQ(ierr); 555 ierr = DMLabelSetValue(*ovLabel, remote[l].index, remote[l].rank);CHKERRQ(ierr); 556 } 557 /* Clean up */ 558 ierr = DMLabelDestroy(&ovAdjByRank);CHKERRQ(ierr); 559 PetscFunctionReturn(0); 560 } 561 562 /*@C 563 DMPlexCreateOverlapMigrationSF - Create an SF describing the new mesh distribution to make the overlap described by the input SF 564 565 Collective on dm 566 567 Input Parameters: 568 + dm - The DM 569 - overlapSF - The SF mapping ghost points in overlap to owner points on other processes 570 571 Output Parameters: 572 . migrationSF - An SF that maps original points in old locations to points in new locations 573 574 Level: developer 575 576 .seealso: DMPlexCreateOverlap(), DMPlexDistribute() 577 @*/ 578 PetscErrorCode DMPlexCreateOverlapMigrationSF(DM dm, PetscSF overlapSF, PetscSF *migrationSF) 579 { 580 MPI_Comm comm; 581 PetscMPIInt rank, size; 582 PetscInt d, dim, p, pStart, pEnd, nroots, nleaves, newLeaves, point, numSharedPoints; 583 PetscInt *pointDepths, *remoteDepths, *ilocal; 584 PetscInt *depthRecv, *depthShift, *depthIdx; 585 PetscSFNode *iremote; 586 PetscSF pointSF; 587 const PetscInt *sharedLocal; 588 const PetscSFNode *overlapRemote, *sharedRemote; 589 PetscErrorCode ierr; 590 591 PetscFunctionBegin; 592 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 593 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 594 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 595 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 596 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 597 598 /* Before building the migration SF we need to know the new stratum offsets */ 599 ierr = PetscSFGetGraph(overlapSF, &nroots, &nleaves, NULL, &overlapRemote);CHKERRQ(ierr); 600 ierr = PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);CHKERRQ(ierr); 601 for (d=0; d<dim+1; d++) { 602 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 603 for (p=pStart; p<pEnd; p++) pointDepths[p] = d; 604 } 605 for (p=0; p<nleaves; p++) remoteDepths[p] = -1; 606 ierr = PetscSFBcastBegin(overlapSF, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 607 ierr = PetscSFBcastEnd(overlapSF, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 608 609 /* Count recevied points in each stratum and compute the internal strata shift */ 610 ierr = PetscMalloc3(dim+1, &depthRecv, dim+1, &depthShift, dim+1, &depthIdx);CHKERRQ(ierr); 611 for (d=0; d<dim+1; d++) depthRecv[d]=0; 612 for (p=0; p<nleaves; p++) depthRecv[remoteDepths[p]]++; 613 depthShift[dim] = 0; 614 for (d=0; d<dim; d++) depthShift[d] = depthRecv[dim]; 615 for (d=1; d<dim; d++) depthShift[d] += depthRecv[0]; 616 for (d=dim-2; d>0; d--) depthShift[d] += depthRecv[d+1]; 617 for (d=0; d<dim+1; d++) { 618 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 619 depthIdx[d] = pStart + depthShift[d]; 620 } 621 622 /* Form the overlap SF build an SF that describes the full overlap migration SF */ 623 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 624 newLeaves = pEnd - pStart + nleaves; 625 ierr = PetscMalloc1(newLeaves, &ilocal);CHKERRQ(ierr); 626 ierr = PetscMalloc1(newLeaves, &iremote);CHKERRQ(ierr); 627 /* First map local points to themselves */ 628 for (d=0; d<dim+1; d++) { 629 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 630 for (p=pStart; p<pEnd; p++) { 631 point = p + depthShift[d]; 632 ilocal[point] = point; 633 iremote[point].index = p; 634 iremote[point].rank = rank; 635 depthIdx[d]++; 636 } 637 } 638 639 /* Add in the remote roots for currently shared points */ 640 ierr = DMGetPointSF(dm, &pointSF);CHKERRQ(ierr); 641 ierr = PetscSFGetGraph(pointSF, NULL, &numSharedPoints, &sharedLocal, &sharedRemote);CHKERRQ(ierr); 642 for (d=0; d<dim+1; d++) { 643 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 644 for (p=0; p<numSharedPoints; p++) { 645 if (pStart <= sharedLocal[p] && sharedLocal[p] < pEnd) { 646 point = sharedLocal[p] + depthShift[d]; 647 iremote[point].index = sharedRemote[p].index; 648 iremote[point].rank = sharedRemote[p].rank; 649 } 650 } 651 } 652 653 /* Now add the incoming overlap points */ 654 for (p=0; p<nleaves; p++) { 655 point = depthIdx[remoteDepths[p]]; 656 ilocal[point] = point; 657 iremote[point].index = overlapRemote[p].index; 658 iremote[point].rank = overlapRemote[p].rank; 659 depthIdx[remoteDepths[p]]++; 660 } 661 ierr = PetscFree2(pointDepths,remoteDepths);CHKERRQ(ierr); 662 663 ierr = PetscSFCreate(comm, migrationSF);CHKERRQ(ierr); 664 ierr = PetscObjectSetName((PetscObject) *migrationSF, "Overlap Migration SF");CHKERRQ(ierr); 665 ierr = PetscSFSetFromOptions(*migrationSF);CHKERRQ(ierr); 666 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 667 ierr = PetscSFSetGraph(*migrationSF, pEnd-pStart, newLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);CHKERRQ(ierr); 668 669 ierr = PetscFree3(depthRecv, depthShift, depthIdx);CHKERRQ(ierr); 670 PetscFunctionReturn(0); 671 } 672 673 /*@ 674 DMPlexStratifyMigrationSF - Rearrange the leaves of a migration sf for stratification. 675 676 Input Parameter: 677 + dm - The DM 678 - sf - A star forest with non-ordered leaves, usually defining a DM point migration 679 680 Output Parameter: 681 . migrationSF - A star forest with added leaf indirection that ensures the resulting DM is stratified 682 683 Level: developer 684 685 .seealso: DMPlexPartitionLabelCreateSF(), DMPlexDistribute(), DMPlexDistributeOverlap() 686 @*/ 687 PetscErrorCode DMPlexStratifyMigrationSF(DM dm, PetscSF sf, PetscSF *migrationSF) 688 { 689 MPI_Comm comm; 690 PetscMPIInt rank, size; 691 PetscInt d, ldepth, depth, p, pStart, pEnd, nroots, nleaves; 692 PetscInt *pointDepths, *remoteDepths, *ilocal; 693 PetscInt *depthRecv, *depthShift, *depthIdx; 694 PetscInt hybEnd[4]; 695 const PetscSFNode *iremote; 696 PetscErrorCode ierr; 697 698 PetscFunctionBegin; 699 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 700 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 701 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 702 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 703 ierr = DMPlexGetDepth(dm, &ldepth);CHKERRQ(ierr); 704 ierr = MPIU_Allreduce(&ldepth, &depth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 705 if ((ldepth >= 0) && (depth != ldepth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", ldepth, depth); 706 ierr = PetscLogEventBegin(DMPLEX_PartStratSF,dm,0,0,0);CHKERRQ(ierr); 707 708 /* Before building the migration SF we need to know the new stratum offsets */ 709 ierr = PetscSFGetGraph(sf, &nroots, &nleaves, NULL, &iremote);CHKERRQ(ierr); 710 ierr = PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);CHKERRQ(ierr); 711 ierr = DMPlexGetHybridBounds(dm,&hybEnd[depth],&hybEnd[PetscMax(depth-1,0)],&hybEnd[1],&hybEnd[0]);CHKERRQ(ierr); 712 for (d = 0; d < depth+1; ++d) { 713 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 714 for (p = pStart; p < pEnd; ++p) { 715 if (hybEnd[d] >= 0 && p >= hybEnd[d]) { /* put in a separate value for hybrid points */ 716 pointDepths[p] = 2 * d; 717 } else { 718 pointDepths[p] = 2 * d + 1; 719 } 720 } 721 } 722 for (p = 0; p < nleaves; ++p) remoteDepths[p] = -1; 723 ierr = PetscSFBcastBegin(sf, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 724 ierr = PetscSFBcastEnd(sf, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 725 /* Count received points in each stratum and compute the internal strata shift */ 726 ierr = PetscMalloc3(2*(depth+1), &depthRecv, 2*(depth+1), &depthShift, 2*(depth+1), &depthIdx);CHKERRQ(ierr); 727 for (d = 0; d < 2*(depth+1); ++d) depthRecv[d] = 0; 728 for (p = 0; p < nleaves; ++p) depthRecv[remoteDepths[p]]++; 729 depthShift[2*depth+1] = 0; 730 for (d = 0; d < 2*depth+1; ++d) depthShift[d] = depthRecv[2 * depth + 1]; 731 for (d = 0; d < 2*depth; ++d) depthShift[d] += depthRecv[2 * depth]; 732 depthShift[0] += depthRecv[1]; 733 for (d = 2; d < 2*depth; ++d) depthShift[d] += depthRecv[1]; 734 for (d = 2; d < 2*depth; ++d) depthShift[d] += depthRecv[0]; 735 for (d = 2 * depth-1; d > 2; --d) { 736 PetscInt e; 737 738 for (e = d -1; e > 1; --e) depthShift[e] += depthRecv[d]; 739 } 740 for (d = 0; d < 2*(depth+1); ++d) {depthIdx[d] = 0;} 741 /* Derive a new local permutation based on stratified indices */ 742 ierr = PetscMalloc1(nleaves, &ilocal);CHKERRQ(ierr); 743 for (p = 0; p < nleaves; ++p) { 744 const PetscInt dep = remoteDepths[p]; 745 746 ilocal[p] = depthShift[dep] + depthIdx[dep]; 747 depthIdx[dep]++; 748 } 749 ierr = PetscSFCreate(comm, migrationSF);CHKERRQ(ierr); 750 ierr = PetscObjectSetName((PetscObject) *migrationSF, "Migration SF");CHKERRQ(ierr); 751 ierr = PetscSFSetGraph(*migrationSF, nroots, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_COPY_VALUES);CHKERRQ(ierr); 752 ierr = PetscFree2(pointDepths,remoteDepths);CHKERRQ(ierr); 753 ierr = PetscFree3(depthRecv, depthShift, depthIdx);CHKERRQ(ierr); 754 ierr = PetscLogEventEnd(DMPLEX_PartStratSF,dm,0,0,0);CHKERRQ(ierr); 755 PetscFunctionReturn(0); 756 } 757 758 /*@ 759 DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 760 761 Collective on dm 762 763 Input Parameters: 764 + dm - The DMPlex object 765 . pointSF - The PetscSF describing the communication pattern 766 . originalSection - The PetscSection for existing data layout 767 - originalVec - The existing data in a local vector 768 769 Output Parameters: 770 + newSection - The PetscSF describing the new data layout 771 - newVec - The new data in a local vector 772 773 Level: developer 774 775 .seealso: DMPlexDistribute(), DMPlexDistributeFieldIS(), DMPlexDistributeData() 776 @*/ 777 PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec) 778 { 779 PetscSF fieldSF; 780 PetscInt *remoteOffsets, fieldSize; 781 PetscScalar *originalValues, *newValues; 782 PetscErrorCode ierr; 783 784 PetscFunctionBegin; 785 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 786 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 787 788 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 789 ierr = VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);CHKERRQ(ierr); 790 ierr = VecSetType(newVec,dm->vectype);CHKERRQ(ierr); 791 792 ierr = VecGetArray(originalVec, &originalValues);CHKERRQ(ierr); 793 ierr = VecGetArray(newVec, &newValues);CHKERRQ(ierr); 794 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 795 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 796 ierr = PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); 797 ierr = PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); 798 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 799 ierr = VecRestoreArray(newVec, &newValues);CHKERRQ(ierr); 800 ierr = VecRestoreArray(originalVec, &originalValues);CHKERRQ(ierr); 801 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 802 PetscFunctionReturn(0); 803 } 804 805 /*@ 806 DMPlexDistributeFieldIS - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 807 808 Collective on dm 809 810 Input Parameters: 811 + dm - The DMPlex object 812 . pointSF - The PetscSF describing the communication pattern 813 . originalSection - The PetscSection for existing data layout 814 - originalIS - The existing data 815 816 Output Parameters: 817 + newSection - The PetscSF describing the new data layout 818 - newIS - The new data 819 820 Level: developer 821 822 .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexDistributeData() 823 @*/ 824 PetscErrorCode DMPlexDistributeFieldIS(DM dm, PetscSF pointSF, PetscSection originalSection, IS originalIS, PetscSection newSection, IS *newIS) 825 { 826 PetscSF fieldSF; 827 PetscInt *newValues, *remoteOffsets, fieldSize; 828 const PetscInt *originalValues; 829 PetscErrorCode ierr; 830 831 PetscFunctionBegin; 832 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 833 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 834 835 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 836 ierr = PetscMalloc1(fieldSize, &newValues);CHKERRQ(ierr); 837 838 ierr = ISGetIndices(originalIS, &originalValues);CHKERRQ(ierr); 839 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 840 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 841 ierr = PetscSFBcastBegin(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);CHKERRQ(ierr); 842 ierr = PetscSFBcastEnd(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);CHKERRQ(ierr); 843 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 844 ierr = ISRestoreIndices(originalIS, &originalValues);CHKERRQ(ierr); 845 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) pointSF), fieldSize, newValues, PETSC_OWN_POINTER, newIS);CHKERRQ(ierr); 846 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 847 PetscFunctionReturn(0); 848 } 849 850 /*@ 851 DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 852 853 Collective on dm 854 855 Input Parameters: 856 + dm - The DMPlex object 857 . pointSF - The PetscSF describing the communication pattern 858 . originalSection - The PetscSection for existing data layout 859 . datatype - The type of data 860 - originalData - The existing data 861 862 Output Parameters: 863 + newSection - The PetscSection describing the new data layout 864 - newData - The new data 865 866 Level: developer 867 868 .seealso: DMPlexDistribute(), DMPlexDistributeField() 869 @*/ 870 PetscErrorCode DMPlexDistributeData(DM dm, PetscSF pointSF, PetscSection originalSection, MPI_Datatype datatype, void *originalData, PetscSection newSection, void **newData) 871 { 872 PetscSF fieldSF; 873 PetscInt *remoteOffsets, fieldSize; 874 PetscMPIInt dataSize; 875 PetscErrorCode ierr; 876 877 PetscFunctionBegin; 878 ierr = PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 879 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 880 881 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 882 ierr = MPI_Type_size(datatype, &dataSize);CHKERRQ(ierr); 883 ierr = PetscMalloc(fieldSize * dataSize, newData);CHKERRQ(ierr); 884 885 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 886 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 887 ierr = PetscSFBcastBegin(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr); 888 ierr = PetscSFBcastEnd(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr); 889 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 890 ierr = PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 891 PetscFunctionReturn(0); 892 } 893 894 static PetscErrorCode DMPlexDistributeCones(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel) 895 { 896 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 897 MPI_Comm comm; 898 PetscSF coneSF; 899 PetscSection originalConeSection, newConeSection; 900 PetscInt *remoteOffsets, *cones, *globCones, *newCones, newConesSize; 901 PetscBool flg; 902 PetscErrorCode ierr; 903 904 PetscFunctionBegin; 905 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 906 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 5); 907 ierr = PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 908 /* Distribute cone section */ 909 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 910 ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr); 911 ierr = DMPlexGetConeSection(dmParallel, &newConeSection);CHKERRQ(ierr); 912 ierr = PetscSFDistributeSection(migrationSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr); 913 ierr = DMSetUp(dmParallel);CHKERRQ(ierr); 914 { 915 PetscInt pStart, pEnd, p; 916 917 ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr); 918 for (p = pStart; p < pEnd; ++p) { 919 PetscInt coneSize; 920 ierr = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr); 921 pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize); 922 } 923 } 924 /* Communicate and renumber cones */ 925 ierr = PetscSFCreateSectionSF(migrationSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr); 926 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 927 ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); 928 if (original) { 929 PetscInt numCones; 930 931 ierr = PetscSectionGetStorageSize(originalConeSection,&numCones);CHKERRQ(ierr); 932 ierr = PetscMalloc1(numCones,&globCones);CHKERRQ(ierr); 933 ierr = ISLocalToGlobalMappingApplyBlock(original, numCones, cones, globCones);CHKERRQ(ierr); 934 } else { 935 globCones = cones; 936 } 937 ierr = DMPlexGetCones(dmParallel, &newCones);CHKERRQ(ierr); 938 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, globCones, newCones);CHKERRQ(ierr); 939 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, globCones, newCones);CHKERRQ(ierr); 940 if (original) { 941 ierr = PetscFree(globCones);CHKERRQ(ierr); 942 } 943 ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr); 944 ierr = ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);CHKERRQ(ierr); 945 #if defined(PETSC_USE_DEBUG) 946 { 947 PetscInt p; 948 PetscBool valid = PETSC_TRUE; 949 for (p = 0; p < newConesSize; ++p) { 950 if (newCones[p] < 0) {valid = PETSC_FALSE; ierr = PetscPrintf(PETSC_COMM_SELF, "[%d] Point %D not in overlap SF\n", PetscGlobalRank,p);CHKERRQ(ierr);} 951 } 952 if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map"); 953 } 954 #endif 955 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr); 956 if (flg) { 957 ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr); 958 ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 959 ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr); 960 ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 961 ierr = PetscSFView(coneSF, NULL);CHKERRQ(ierr); 962 } 963 ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr); 964 ierr = DMPlexGetConeOrientations(dmParallel, &newCones);CHKERRQ(ierr); 965 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 966 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 967 ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr); 968 ierr = PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 969 /* Create supports and stratify DMPlex */ 970 { 971 PetscInt pStart, pEnd; 972 973 ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 974 ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr); 975 } 976 ierr = DMPlexSymmetrize(dmParallel);CHKERRQ(ierr); 977 ierr = DMPlexStratify(dmParallel);CHKERRQ(ierr); 978 { 979 PetscBool useCone, useClosure, useAnchors; 980 981 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 982 ierr = DMSetBasicAdjacency(dmParallel, useCone, useClosure);CHKERRQ(ierr); 983 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 984 ierr = DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);CHKERRQ(ierr); 985 } 986 PetscFunctionReturn(0); 987 } 988 989 static PetscErrorCode DMPlexDistributeCoordinates(DM dm, PetscSF migrationSF, DM dmParallel) 990 { 991 MPI_Comm comm; 992 PetscSection originalCoordSection, newCoordSection; 993 Vec originalCoordinates, newCoordinates; 994 PetscInt bs; 995 PetscBool isper; 996 const char *name; 997 const PetscReal *maxCell, *L; 998 const DMBoundaryType *bd; 999 PetscErrorCode ierr; 1000 1001 PetscFunctionBegin; 1002 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1003 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1004 1005 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1006 ierr = DMGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr); 1007 ierr = DMGetCoordinateSection(dmParallel, &newCoordSection);CHKERRQ(ierr); 1008 ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr); 1009 if (originalCoordinates) { 1010 ierr = VecCreate(PETSC_COMM_SELF, &newCoordinates);CHKERRQ(ierr); 1011 ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr); 1012 ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr); 1013 1014 ierr = DMPlexDistributeField(dm, migrationSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr); 1015 ierr = DMSetCoordinatesLocal(dmParallel, newCoordinates);CHKERRQ(ierr); 1016 ierr = VecGetBlockSize(originalCoordinates, &bs);CHKERRQ(ierr); 1017 ierr = VecSetBlockSize(newCoordinates, bs);CHKERRQ(ierr); 1018 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 1019 } 1020 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 1021 ierr = DMSetPeriodicity(dmParallel, isper, maxCell, L, bd);CHKERRQ(ierr); 1022 PetscFunctionReturn(0); 1023 } 1024 1025 static PetscErrorCode DMPlexDistributeLabels(DM dm, PetscSF migrationSF, DM dmParallel) 1026 { 1027 DM_Plex *mesh = (DM_Plex*) dm->data; 1028 MPI_Comm comm; 1029 DMLabel depthLabel; 1030 PetscMPIInt rank; 1031 PetscInt depth, d, numLabels, numLocalLabels, l; 1032 PetscBool hasLabels = PETSC_FALSE, lsendDepth, sendDepth; 1033 PetscObjectState depthState = -1; 1034 PetscErrorCode ierr; 1035 1036 PetscFunctionBegin; 1037 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1038 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1039 1040 ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1041 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1042 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1043 1044 /* If the user has changed the depth label, communicate it instead */ 1045 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1046 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1047 if (depthLabel) {ierr = PetscObjectStateGet((PetscObject) depthLabel, &depthState);CHKERRQ(ierr);} 1048 lsendDepth = mesh->depthState != depthState ? PETSC_TRUE : PETSC_FALSE; 1049 ierr = MPIU_Allreduce(&lsendDepth, &sendDepth, 1, MPIU_BOOL, MPI_LOR, comm);CHKERRQ(ierr); 1050 if (sendDepth) { 1051 ierr = DMRemoveLabel(dmParallel, "depth", &depthLabel);CHKERRQ(ierr); 1052 ierr = DMLabelDestroy(&depthLabel);CHKERRQ(ierr); 1053 } 1054 /* Everyone must have either the same number of labels, or none */ 1055 ierr = DMGetNumLabels(dm, &numLocalLabels);CHKERRQ(ierr); 1056 numLabels = numLocalLabels; 1057 ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1058 if (numLabels == numLocalLabels) hasLabels = PETSC_TRUE; 1059 for (l = numLabels-1; l >= 0; --l) { 1060 DMLabel label = NULL, labelNew = NULL; 1061 PetscBool isDepth, lisOutput = PETSC_TRUE, isOutput; 1062 const char *name = NULL; 1063 1064 if (hasLabels) { 1065 ierr = DMGetLabelByNum(dm, l, &label);CHKERRQ(ierr); 1066 /* Skip "depth" because it is recreated */ 1067 ierr = PetscObjectGetName((PetscObject) label, &name);CHKERRQ(ierr); 1068 ierr = PetscStrcmp(name, "depth", &isDepth);CHKERRQ(ierr); 1069 } 1070 ierr = MPI_Bcast(&isDepth, 1, MPIU_BOOL, 0, comm);CHKERRQ(ierr); 1071 if (isDepth && !sendDepth) continue; 1072 ierr = DMLabelDistribute(label, migrationSF, &labelNew);CHKERRQ(ierr); 1073 if (isDepth) { 1074 /* Put in any missing strata which can occur if users are managing the depth label themselves */ 1075 PetscInt gdepth; 1076 1077 ierr = MPIU_Allreduce(&depth, &gdepth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 1078 if ((depth >= 0) && (gdepth != depth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", depth, gdepth); 1079 for (d = 0; d <= gdepth; ++d) { 1080 PetscBool has; 1081 1082 ierr = DMLabelHasStratum(labelNew, d, &has);CHKERRQ(ierr); 1083 if (!has) {ierr = DMLabelAddStratum(labelNew, d);CHKERRQ(ierr);} 1084 } 1085 } 1086 ierr = DMAddLabel(dmParallel, labelNew);CHKERRQ(ierr); 1087 /* Put the output flag in the new label */ 1088 if (hasLabels) {ierr = DMGetLabelOutput(dm, name, &lisOutput);CHKERRQ(ierr);} 1089 ierr = MPIU_Allreduce(&lisOutput, &isOutput, 1, MPIU_BOOL, MPI_LAND, comm);CHKERRQ(ierr); 1090 ierr = PetscObjectGetName((PetscObject) labelNew, &name);CHKERRQ(ierr); 1091 ierr = DMSetLabelOutput(dmParallel, name, isOutput);CHKERRQ(ierr); 1092 } 1093 ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1094 PetscFunctionReturn(0); 1095 } 1096 1097 static PetscErrorCode DMPlexDistributeSetupHybrid(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel) 1098 { 1099 DM_Plex *mesh = (DM_Plex*) dm->data; 1100 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1101 PetscBool *isHybrid, *isHybridParallel; 1102 PetscInt dim, depth, d; 1103 PetscInt pStart, pEnd, pStartP, pEndP; 1104 PetscErrorCode ierr; 1105 1106 PetscFunctionBegin; 1107 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1108 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1109 1110 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1111 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1112 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1113 ierr = DMPlexGetChart(dmParallel,&pStartP,&pEndP);CHKERRQ(ierr); 1114 ierr = PetscCalloc2(pEnd-pStart,&isHybrid,pEndP-pStartP,&isHybridParallel);CHKERRQ(ierr); 1115 for (d = 0; d <= depth; d++) { 1116 PetscInt hybridMax = (depth == 1 && d == 1) ? mesh->hybridPointMax[dim] : mesh->hybridPointMax[d]; 1117 1118 if (hybridMax >= 0) { 1119 PetscInt sStart, sEnd, p; 1120 1121 ierr = DMPlexGetDepthStratum(dm,d,&sStart,&sEnd);CHKERRQ(ierr); 1122 for (p = hybridMax; p < sEnd; p++) isHybrid[p-pStart] = PETSC_TRUE; 1123 } 1124 } 1125 ierr = PetscSFBcastBegin(migrationSF,MPIU_BOOL,isHybrid,isHybridParallel);CHKERRQ(ierr); 1126 ierr = PetscSFBcastEnd(migrationSF,MPIU_BOOL,isHybrid,isHybridParallel);CHKERRQ(ierr); 1127 for (d = 0; d <= dim; d++) pmesh->hybridPointMax[d] = -1; 1128 for (d = 0; d <= depth; d++) { 1129 PetscInt sStart, sEnd, p, dd; 1130 1131 ierr = DMPlexGetDepthStratum(dmParallel,d,&sStart,&sEnd);CHKERRQ(ierr); 1132 dd = (depth == 1 && d == 1) ? dim : d; 1133 for (p = sStart; p < sEnd; p++) { 1134 if (isHybridParallel[p-pStartP]) { 1135 pmesh->hybridPointMax[dd] = p; 1136 break; 1137 } 1138 } 1139 } 1140 ierr = PetscFree2(isHybrid,isHybridParallel);CHKERRQ(ierr); 1141 PetscFunctionReturn(0); 1142 } 1143 1144 static PetscErrorCode DMPlexDistributeSetupTree(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel) 1145 { 1146 DM_Plex *mesh = (DM_Plex*) dm->data; 1147 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1148 MPI_Comm comm; 1149 DM refTree; 1150 PetscSection origParentSection, newParentSection; 1151 PetscInt *origParents, *origChildIDs; 1152 PetscBool flg; 1153 PetscErrorCode ierr; 1154 1155 PetscFunctionBegin; 1156 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1157 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 5); 1158 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1159 1160 /* Set up tree */ 1161 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 1162 ierr = DMPlexSetReferenceTree(dmParallel,refTree);CHKERRQ(ierr); 1163 ierr = DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);CHKERRQ(ierr); 1164 if (origParentSection) { 1165 PetscInt pStart, pEnd; 1166 PetscInt *newParents, *newChildIDs, *globParents; 1167 PetscInt *remoteOffsetsParents, newParentSize; 1168 PetscSF parentSF; 1169 1170 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1171 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dmParallel),&newParentSection);CHKERRQ(ierr); 1172 ierr = PetscSectionSetChart(newParentSection,pStart,pEnd);CHKERRQ(ierr); 1173 ierr = PetscSFDistributeSection(migrationSF, origParentSection, &remoteOffsetsParents, newParentSection);CHKERRQ(ierr); 1174 ierr = PetscSFCreateSectionSF(migrationSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);CHKERRQ(ierr); 1175 ierr = PetscFree(remoteOffsetsParents);CHKERRQ(ierr); 1176 ierr = PetscSectionGetStorageSize(newParentSection,&newParentSize);CHKERRQ(ierr); 1177 ierr = PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);CHKERRQ(ierr); 1178 if (original) { 1179 PetscInt numParents; 1180 1181 ierr = PetscSectionGetStorageSize(origParentSection,&numParents);CHKERRQ(ierr); 1182 ierr = PetscMalloc1(numParents,&globParents);CHKERRQ(ierr); 1183 ierr = ISLocalToGlobalMappingApplyBlock(original, numParents, origParents, globParents);CHKERRQ(ierr); 1184 } 1185 else { 1186 globParents = origParents; 1187 } 1188 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, globParents, newParents);CHKERRQ(ierr); 1189 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, globParents, newParents);CHKERRQ(ierr); 1190 if (original) { 1191 ierr = PetscFree(globParents);CHKERRQ(ierr); 1192 } 1193 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1194 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1195 ierr = ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);CHKERRQ(ierr); 1196 #if defined(PETSC_USE_DEBUG) 1197 { 1198 PetscInt p; 1199 PetscBool valid = PETSC_TRUE; 1200 for (p = 0; p < newParentSize; ++p) { 1201 if (newParents[p] < 0) {valid = PETSC_FALSE; ierr = PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);CHKERRQ(ierr);} 1202 } 1203 if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map"); 1204 } 1205 #endif 1206 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-parents_view", &flg);CHKERRQ(ierr); 1207 if (flg) { 1208 ierr = PetscPrintf(comm, "Serial Parent Section: \n");CHKERRQ(ierr); 1209 ierr = PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1210 ierr = PetscPrintf(comm, "Parallel Parent Section: \n");CHKERRQ(ierr); 1211 ierr = PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1212 ierr = PetscSFView(parentSF, NULL);CHKERRQ(ierr); 1213 } 1214 ierr = DMPlexSetTree(dmParallel,newParentSection,newParents,newChildIDs);CHKERRQ(ierr); 1215 ierr = PetscSectionDestroy(&newParentSection);CHKERRQ(ierr); 1216 ierr = PetscFree2(newParents,newChildIDs);CHKERRQ(ierr); 1217 ierr = PetscSFDestroy(&parentSF);CHKERRQ(ierr); 1218 } 1219 pmesh->useAnchors = mesh->useAnchors; 1220 PetscFunctionReturn(0); 1221 } 1222 1223 PETSC_UNUSED static PetscErrorCode DMPlexDistributeSF(DM dm, PetscSF migrationSF, DM dmParallel) 1224 { 1225 PetscMPIInt rank, size; 1226 MPI_Comm comm; 1227 PetscErrorCode ierr; 1228 1229 PetscFunctionBegin; 1230 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1231 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1232 1233 /* Create point SF for parallel mesh */ 1234 ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1235 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1236 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1237 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1238 { 1239 const PetscInt *leaves; 1240 PetscSFNode *remotePoints, *rowners, *lowners; 1241 PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints; 1242 PetscInt pStart, pEnd; 1243 1244 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1245 ierr = PetscSFGetGraph(migrationSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr); 1246 ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr); 1247 for (p=0; p<numRoots; p++) { 1248 rowners[p].rank = -1; 1249 rowners[p].index = -1; 1250 } 1251 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1252 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1253 for (p = 0; p < numLeaves; ++p) { 1254 if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */ 1255 lowners[p].rank = rank; 1256 lowners[p].index = leaves ? leaves[p] : p; 1257 } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */ 1258 lowners[p].rank = -2; 1259 lowners[p].index = -2; 1260 } 1261 } 1262 for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */ 1263 rowners[p].rank = -3; 1264 rowners[p].index = -3; 1265 } 1266 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1267 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1268 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1269 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1270 for (p = 0; p < numLeaves; ++p) { 1271 if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed"); 1272 if (lowners[p].rank != rank) ++numGhostPoints; 1273 } 1274 ierr = PetscMalloc1(numGhostPoints, &ghostPoints);CHKERRQ(ierr); 1275 ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr); 1276 for (p = 0, gp = 0; p < numLeaves; ++p) { 1277 if (lowners[p].rank != rank) { 1278 ghostPoints[gp] = leaves ? leaves[p] : p; 1279 remotePoints[gp].rank = lowners[p].rank; 1280 remotePoints[gp].index = lowners[p].index; 1281 ++gp; 1282 } 1283 } 1284 ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr); 1285 ierr = PetscSFSetGraph((dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 1286 ierr = PetscSFSetFromOptions((dmParallel)->sf);CHKERRQ(ierr); 1287 } 1288 { 1289 PetscBool useCone, useClosure, useAnchors; 1290 1291 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 1292 ierr = DMSetBasicAdjacency(dmParallel, useCone, useClosure);CHKERRQ(ierr); 1293 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 1294 ierr = DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);CHKERRQ(ierr); 1295 } 1296 ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1297 PetscFunctionReturn(0); 1298 } 1299 1300 /*@ 1301 DMPlexSetPartitionBalance - Should distribution of the DM attempt to balance the shared point partition? 1302 1303 Input Parameters: 1304 + dm - The DMPlex object 1305 - flg - Balance the partition? 1306 1307 Level: intermediate 1308 1309 .seealso: DMPlexDistribute(), DMPlexGetPartitionBalance() 1310 @*/ 1311 PetscErrorCode DMPlexSetPartitionBalance(DM dm, PetscBool flg) 1312 { 1313 DM_Plex *mesh = (DM_Plex *)dm->data; 1314 1315 PetscFunctionBegin; 1316 mesh->partitionBalance = flg; 1317 PetscFunctionReturn(0); 1318 } 1319 1320 /*@ 1321 DMPlexGetPartitionBalance - Does distribution of the DM attempt to balance the shared point partition? 1322 1323 Input Parameter: 1324 . dm - The DMPlex object 1325 1326 Output Parameter: 1327 . flg - Balance the partition? 1328 1329 Level: intermediate 1330 1331 .seealso: DMPlexDistribute(), DMPlexSetPartitionBalance() 1332 @*/ 1333 PetscErrorCode DMPlexGetPartitionBalance(DM dm, PetscBool *flg) 1334 { 1335 DM_Plex *mesh = (DM_Plex *)dm->data; 1336 1337 PetscFunctionBegin; 1338 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1339 PetscValidBoolPointer(flg, 2); 1340 *flg = mesh->partitionBalance; 1341 PetscFunctionReturn(0); 1342 } 1343 1344 /*@C 1345 DMPlexCreatePointSF - Build a point SF from an SF describing a point migration 1346 1347 Input Parameter: 1348 + dm - The source DMPlex object 1349 . migrationSF - The star forest that describes the parallel point remapping 1350 . ownership - Flag causing a vote to determine point ownership 1351 1352 Output Parameter: 1353 - pointSF - The star forest describing the point overlap in the remapped DM 1354 1355 Level: developer 1356 1357 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1358 @*/ 1359 PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF) 1360 { 1361 PetscMPIInt rank, size; 1362 PetscInt p, nroots, nleaves, idx, npointLeaves; 1363 PetscInt *pointLocal; 1364 const PetscInt *leaves; 1365 const PetscSFNode *roots; 1366 PetscSFNode *rootNodes, *leafNodes, *pointRemote; 1367 Vec shifts; 1368 const PetscInt numShifts = 13759; 1369 const PetscScalar *shift = NULL; 1370 const PetscBool shiftDebug = PETSC_FALSE; 1371 PetscBool balance; 1372 PetscErrorCode ierr; 1373 1374 PetscFunctionBegin; 1375 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1376 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 1377 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 1378 ierr = PetscLogEventBegin(DMPLEX_CreatePointSF,dm,0,0,0);CHKERRQ(ierr); 1379 1380 ierr = DMPlexGetPartitionBalance(dm, &balance);CHKERRQ(ierr); 1381 ierr = PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);CHKERRQ(ierr); 1382 ierr = PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);CHKERRQ(ierr); 1383 if (ownership) { 1384 /* If balancing, we compute a random cyclic shift of the rank for each remote point. That way, the max will evenly distribute among ranks. */ 1385 if (balance) { 1386 PetscRandom r; 1387 1388 ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 1389 ierr = PetscRandomSetInterval(r, 0, 2467*size);CHKERRQ(ierr); 1390 ierr = VecCreate(PETSC_COMM_SELF, &shifts);CHKERRQ(ierr); 1391 ierr = VecSetSizes(shifts, numShifts, numShifts);CHKERRQ(ierr); 1392 ierr = VecSetType(shifts, VECSTANDARD);CHKERRQ(ierr); 1393 ierr = VecSetRandom(shifts, r);CHKERRQ(ierr); 1394 ierr = PetscRandomDestroy(&r);CHKERRQ(ierr); 1395 ierr = VecGetArrayRead(shifts, &shift);CHKERRQ(ierr); 1396 } 1397 1398 /* Point ownership vote: Process with highest rank owns shared points */ 1399 for (p = 0; p < nleaves; ++p) { 1400 if (shiftDebug) { 1401 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); 1402 } 1403 /* Either put in a bid or we know we own it */ 1404 leafNodes[p].rank = (rank + (shift ? (PetscInt) PetscRealPart(shift[roots[p].index%numShifts]) : 0))%size; 1405 leafNodes[p].index = p; 1406 } 1407 for (p = 0; p < nroots; p++) { 1408 /* Root must not participate in the reduction, flag so that MAXLOC does not use */ 1409 rootNodes[p].rank = -3; 1410 rootNodes[p].index = -3; 1411 } 1412 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);CHKERRQ(ierr); 1413 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);CHKERRQ(ierr); 1414 if (balance) { 1415 /* We've voted, now we need to get the rank. When we're balancing the partition, the "rank" in rootNotes is not 1416 * the rank but rather (rank + random)%size. So we do another reduction, voting the same way, but sending the 1417 * rank instead of the index. */ 1418 PetscSFNode *rootRanks = NULL; 1419 ierr = PetscMalloc1(nroots, &rootRanks);CHKERRQ(ierr); 1420 for (p = 0; p < nroots; p++) { 1421 rootRanks[p].rank = -3; 1422 rootRanks[p].index = -3; 1423 } 1424 for (p = 0; p < nleaves; p++) leafNodes[p].index = rank; 1425 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, leafNodes, rootRanks, MPI_MAXLOC);CHKERRQ(ierr); 1426 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, leafNodes, rootRanks, MPI_MAXLOC);CHKERRQ(ierr); 1427 for (p = 0; p < nroots; p++) rootNodes[p].rank = rootRanks[p].index; 1428 ierr = PetscFree(rootRanks);CHKERRQ(ierr); 1429 } 1430 } else { 1431 for (p = 0; p < nroots; p++) { 1432 rootNodes[p].index = -1; 1433 rootNodes[p].rank = rank; 1434 }; 1435 for (p = 0; p < nleaves; p++) { 1436 /* Write new local id into old location */ 1437 if (roots[p].rank == rank) { 1438 rootNodes[roots[p].index].index = leaves ? leaves[p] : p; 1439 } 1440 } 1441 } 1442 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1443 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1444 1445 for (npointLeaves = 0, p = 0; p < nleaves; p++) { 1446 if (leafNodes[p].rank != rank) npointLeaves++; 1447 } 1448 ierr = PetscMalloc1(npointLeaves, &pointLocal);CHKERRQ(ierr); 1449 ierr = PetscMalloc1(npointLeaves, &pointRemote);CHKERRQ(ierr); 1450 for (idx = 0, p = 0; p < nleaves; p++) { 1451 if (leafNodes[p].rank != rank) { 1452 pointLocal[idx] = p; 1453 pointRemote[idx] = leafNodes[p]; 1454 idx++; 1455 } 1456 } 1457 if (shift) { 1458 ierr = VecRestoreArrayRead(shifts, &shift);CHKERRQ(ierr); 1459 ierr = VecDestroy(&shifts);CHKERRQ(ierr); 1460 } 1461 if (shiftDebug) {ierr = PetscSynchronizedFlush(PetscObjectComm((PetscObject) dm), PETSC_STDOUT);CHKERRQ(ierr);} 1462 ierr = PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);CHKERRQ(ierr); 1463 ierr = PetscSFSetFromOptions(*pointSF);CHKERRQ(ierr); 1464 ierr = PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1465 ierr = PetscFree2(rootNodes, leafNodes);CHKERRQ(ierr); 1466 ierr = PetscLogEventEnd(DMPLEX_CreatePointSF,dm,0,0,0);CHKERRQ(ierr); 1467 PetscFunctionReturn(0); 1468 } 1469 1470 /*@C 1471 DMPlexMigrate - Migrates internal DM data over the supplied star forest 1472 1473 Collective on dm 1474 1475 Input Parameter: 1476 + dm - The source DMPlex object 1477 . sf - The star forest communication context describing the migration pattern 1478 1479 Output Parameter: 1480 - targetDM - The target DMPlex object 1481 1482 Level: intermediate 1483 1484 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1485 @*/ 1486 PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM) 1487 { 1488 MPI_Comm comm; 1489 PetscInt dim, cdim, nroots; 1490 PetscSF sfPoint; 1491 ISLocalToGlobalMapping ltogMigration; 1492 ISLocalToGlobalMapping ltogOriginal = NULL; 1493 PetscBool flg; 1494 PetscErrorCode ierr; 1495 1496 PetscFunctionBegin; 1497 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1498 ierr = PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1499 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 1500 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1501 ierr = DMSetDimension(targetDM, dim);CHKERRQ(ierr); 1502 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 1503 ierr = DMSetCoordinateDim(targetDM, cdim);CHKERRQ(ierr); 1504 1505 /* Check for a one-to-all distribution pattern */ 1506 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1507 ierr = PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 1508 if (nroots >= 0) { 1509 IS isOriginal; 1510 PetscInt n, size, nleaves; 1511 PetscInt *numbering_orig, *numbering_new; 1512 1513 /* Get the original point numbering */ 1514 ierr = DMPlexCreatePointNumbering(dm, &isOriginal);CHKERRQ(ierr); 1515 ierr = ISLocalToGlobalMappingCreateIS(isOriginal, <ogOriginal);CHKERRQ(ierr); 1516 ierr = ISLocalToGlobalMappingGetSize(ltogOriginal, &size);CHKERRQ(ierr); 1517 ierr = ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1518 /* Convert to positive global numbers */ 1519 for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);} 1520 /* Derive the new local-to-global mapping from the old one */ 1521 ierr = PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1522 ierr = PetscMalloc1(nleaves, &numbering_new);CHKERRQ(ierr); 1523 ierr = PetscSFBcastBegin(sf, MPIU_INT, numbering_orig, numbering_new);CHKERRQ(ierr); 1524 ierr = PetscSFBcastEnd(sf, MPIU_INT, numbering_orig, numbering_new);CHKERRQ(ierr); 1525 ierr = ISLocalToGlobalMappingCreate(comm, 1, nleaves, numbering_new, PETSC_OWN_POINTER, <ogMigration);CHKERRQ(ierr); 1526 ierr = ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1527 ierr = ISDestroy(&isOriginal);CHKERRQ(ierr); 1528 } else { 1529 /* One-to-all distribution pattern: We can derive LToG from SF */ 1530 ierr = ISLocalToGlobalMappingCreateSF(sf, 0, <ogMigration);CHKERRQ(ierr); 1531 } 1532 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1533 if (flg) { 1534 ierr = PetscPrintf(comm, "Point renumbering for DM migration:\n");CHKERRQ(ierr); 1535 ierr = ISLocalToGlobalMappingView(ltogMigration, NULL);CHKERRQ(ierr); 1536 } 1537 /* Migrate DM data to target DM */ 1538 ierr = DMPlexDistributeCones(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1539 ierr = DMPlexDistributeLabels(dm, sf, targetDM);CHKERRQ(ierr); 1540 ierr = DMPlexDistributeCoordinates(dm, sf, targetDM);CHKERRQ(ierr); 1541 ierr = DMPlexDistributeSetupHybrid(dm, sf, ltogMigration, targetDM);CHKERRQ(ierr); 1542 ierr = DMPlexDistributeSetupTree(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1543 ierr = ISLocalToGlobalMappingDestroy(<ogOriginal);CHKERRQ(ierr); 1544 ierr = ISLocalToGlobalMappingDestroy(<ogMigration);CHKERRQ(ierr); 1545 ierr = PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1546 PetscFunctionReturn(0); 1547 } 1548 1549 /*@C 1550 DMPlexDistribute - Distributes the mesh and any associated sections. 1551 1552 Collective on dm 1553 1554 Input Parameter: 1555 + dm - The original DMPlex object 1556 - overlap - The overlap of partitions, 0 is the default 1557 1558 Output Parameter: 1559 + sf - The PetscSF used for point distribution, or NULL if not needed 1560 - dmParallel - The distributed DMPlex object 1561 1562 Note: If the mesh was not distributed, the output dmParallel will be NULL. 1563 1564 The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function 1565 representation on the mesh. 1566 1567 Level: intermediate 1568 1569 .seealso: DMPlexCreate(), DMSetAdjacency() 1570 @*/ 1571 PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel) 1572 { 1573 MPI_Comm comm; 1574 PetscPartitioner partitioner; 1575 IS cellPart; 1576 PetscSection cellPartSection; 1577 DM dmCoord; 1578 DMLabel lblPartition, lblMigration; 1579 PetscSF sfMigration, sfStratified, sfPoint; 1580 PetscBool flg, balance; 1581 PetscMPIInt rank, size; 1582 PetscErrorCode ierr; 1583 1584 PetscFunctionBegin; 1585 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1586 PetscValidLogicalCollectiveInt(dm, overlap, 2); 1587 if (sf) PetscValidPointer(sf,3); 1588 PetscValidPointer(dmParallel,4); 1589 1590 if (sf) *sf = NULL; 1591 *dmParallel = NULL; 1592 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1593 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1594 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1595 if (size == 1) PetscFunctionReturn(0); 1596 1597 ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1598 /* Create cell partition */ 1599 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1600 ierr = PetscSectionCreate(comm, &cellPartSection);CHKERRQ(ierr); 1601 ierr = DMPlexGetPartitioner(dm, &partitioner);CHKERRQ(ierr); 1602 ierr = PetscPartitionerPartition(partitioner, dm, cellPartSection, &cellPart);CHKERRQ(ierr); 1603 ierr = PetscLogEventBegin(DMPLEX_PartSelf,dm,0,0,0);CHKERRQ(ierr); 1604 { 1605 /* Convert partition to DMLabel */ 1606 IS is; 1607 PetscHSetI ht; 1608 const PetscInt *points; 1609 PetscInt *iranks; 1610 PetscInt pStart, pEnd, proc, npoints, poff = 0, nranks; 1611 1612 ierr = DMLabelCreate(PETSC_COMM_SELF, "Point Partition", &lblPartition);CHKERRQ(ierr); 1613 /* Preallocate strata */ 1614 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1615 ierr = PetscSectionGetChart(cellPartSection, &pStart, &pEnd);CHKERRQ(ierr); 1616 for (proc = pStart; proc < pEnd; proc++) { 1617 ierr = PetscSectionGetDof(cellPartSection, proc, &npoints);CHKERRQ(ierr); 1618 if (npoints) {ierr = PetscHSetIAdd(ht, proc);CHKERRQ(ierr);} 1619 } 1620 ierr = PetscHSetIGetSize(ht, &nranks);CHKERRQ(ierr); 1621 ierr = PetscMalloc1(nranks, &iranks);CHKERRQ(ierr); 1622 ierr = PetscHSetIGetElems(ht, &poff, iranks);CHKERRQ(ierr); 1623 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1624 ierr = DMLabelAddStrata(lblPartition, nranks, iranks);CHKERRQ(ierr); 1625 ierr = PetscFree(iranks);CHKERRQ(ierr); 1626 /* Inline DMPlexPartitionLabelClosure() */ 1627 ierr = ISGetIndices(cellPart, &points);CHKERRQ(ierr); 1628 ierr = PetscSectionGetChart(cellPartSection, &pStart, &pEnd);CHKERRQ(ierr); 1629 for (proc = pStart; proc < pEnd; proc++) { 1630 ierr = PetscSectionGetDof(cellPartSection, proc, &npoints);CHKERRQ(ierr); 1631 if (!npoints) continue; 1632 ierr = PetscSectionGetOffset(cellPartSection, proc, &poff);CHKERRQ(ierr); 1633 ierr = DMPlexClosurePoints_Private(dm, npoints, points+poff, &is);CHKERRQ(ierr); 1634 ierr = DMLabelSetStratumIS(lblPartition, proc, is);CHKERRQ(ierr); 1635 ierr = ISDestroy(&is);CHKERRQ(ierr); 1636 } 1637 ierr = ISRestoreIndices(cellPart, &points);CHKERRQ(ierr); 1638 } 1639 ierr = PetscLogEventEnd(DMPLEX_PartSelf,dm,0,0,0);CHKERRQ(ierr); 1640 1641 ierr = DMLabelCreate(PETSC_COMM_SELF, "Point migration", &lblMigration);CHKERRQ(ierr); 1642 ierr = DMPlexPartitionLabelInvert(dm, lblPartition, NULL, lblMigration);CHKERRQ(ierr); 1643 ierr = DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);CHKERRQ(ierr); 1644 ierr = DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);CHKERRQ(ierr); 1645 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1646 sfMigration = sfStratified; 1647 ierr = PetscSFSetUp(sfMigration);CHKERRQ(ierr); 1648 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1649 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1650 if (flg) { 1651 ierr = DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1652 ierr = PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1653 } 1654 1655 /* Create non-overlapping parallel DM and migrate internal data */ 1656 ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr); 1657 ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr); 1658 ierr = DMPlexMigrate(dm, sfMigration, *dmParallel);CHKERRQ(ierr); 1659 1660 /* Build the point SF without overlap */ 1661 ierr = DMPlexGetPartitionBalance(dm, &balance);CHKERRQ(ierr); 1662 ierr = DMPlexSetPartitionBalance(*dmParallel, balance);CHKERRQ(ierr); 1663 ierr = DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);CHKERRQ(ierr); 1664 ierr = DMSetPointSF(*dmParallel, sfPoint);CHKERRQ(ierr); 1665 ierr = DMGetCoordinateDM(*dmParallel, &dmCoord);CHKERRQ(ierr); 1666 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1667 if (flg) {ierr = PetscSFView(sfPoint, NULL);CHKERRQ(ierr);} 1668 1669 if (overlap > 0) { 1670 DM dmOverlap; 1671 PetscInt nroots, nleaves, noldleaves, l; 1672 const PetscInt *oldLeaves; 1673 PetscSFNode *newRemote, *permRemote; 1674 const PetscSFNode *oldRemote; 1675 PetscSF sfOverlap, sfOverlapPoint; 1676 1677 /* Add the partition overlap to the distributed DM */ 1678 ierr = DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);CHKERRQ(ierr); 1679 ierr = DMDestroy(dmParallel);CHKERRQ(ierr); 1680 *dmParallel = dmOverlap; 1681 if (flg) { 1682 ierr = PetscPrintf(comm, "Overlap Migration SF:\n");CHKERRQ(ierr); 1683 ierr = PetscSFView(sfOverlap, NULL);CHKERRQ(ierr); 1684 } 1685 1686 /* Re-map the migration SF to establish the full migration pattern */ 1687 ierr = PetscSFGetGraph(sfMigration, &nroots, &noldleaves, &oldLeaves, &oldRemote);CHKERRQ(ierr); 1688 ierr = PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1689 ierr = PetscMalloc1(nleaves, &newRemote);CHKERRQ(ierr); 1690 /* oldRemote: original root point mapping to original leaf point 1691 newRemote: original leaf point mapping to overlapped leaf point */ 1692 if (oldLeaves) { 1693 /* After stratification, the migration remotes may not be in root (canonical) order, so we reorder using the leaf numbering */ 1694 ierr = PetscMalloc1(noldleaves, &permRemote);CHKERRQ(ierr); 1695 for (l = 0; l < noldleaves; ++l) permRemote[oldLeaves[l]] = oldRemote[l]; 1696 oldRemote = permRemote; 1697 } 1698 ierr = PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1699 ierr = PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1700 if (oldLeaves) {ierr = PetscFree(oldRemote);CHKERRQ(ierr);} 1701 ierr = PetscSFCreate(comm, &sfOverlapPoint);CHKERRQ(ierr); 1702 ierr = PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1703 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1704 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1705 sfMigration = sfOverlapPoint; 1706 } 1707 /* Cleanup Partition */ 1708 ierr = DMLabelDestroy(&lblPartition);CHKERRQ(ierr); 1709 ierr = DMLabelDestroy(&lblMigration);CHKERRQ(ierr); 1710 ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr); 1711 ierr = ISDestroy(&cellPart);CHKERRQ(ierr); 1712 /* Copy BC */ 1713 ierr = DMCopyBoundary(dm, *dmParallel);CHKERRQ(ierr); 1714 /* Create sfNatural */ 1715 if (dm->useNatural) { 1716 PetscSection section; 1717 1718 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1719 ierr = DMPlexCreateGlobalToNaturalSF(*dmParallel, section, sfMigration, &(*dmParallel)->sfNatural);CHKERRQ(ierr); 1720 ierr = DMSetUseNatural(*dmParallel, PETSC_TRUE);CHKERRQ(ierr); 1721 } 1722 /* Cleanup */ 1723 if (sf) {*sf = sfMigration;} 1724 else {ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr);} 1725 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1726 ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1727 PetscFunctionReturn(0); 1728 } 1729 1730 /*@C 1731 DMPlexDistributeOverlap - Add partition overlap to a distributed non-overlapping DM. 1732 1733 Collective on dm 1734 1735 Input Parameter: 1736 + dm - The non-overlapping distrbuted DMPlex object 1737 - overlap - The overlap of partitions 1738 1739 Output Parameter: 1740 + sf - The PetscSF used for point distribution 1741 - dmOverlap - The overlapping distributed DMPlex object, or NULL 1742 1743 Note: If the mesh was not distributed, the return value is NULL. 1744 1745 The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function 1746 representation on the mesh. 1747 1748 Level: intermediate 1749 1750 .seealso: DMPlexCreate(), DMSetAdjacency() 1751 @*/ 1752 PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap) 1753 { 1754 MPI_Comm comm; 1755 PetscMPIInt size, rank; 1756 PetscSection rootSection, leafSection; 1757 IS rootrank, leafrank; 1758 DM dmCoord; 1759 DMLabel lblOverlap; 1760 PetscSF sfOverlap, sfStratified, sfPoint; 1761 PetscErrorCode ierr; 1762 1763 PetscFunctionBegin; 1764 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1765 if (sf) PetscValidPointer(sf, 3); 1766 PetscValidPointer(dmOverlap, 4); 1767 1768 if (sf) *sf = NULL; 1769 *dmOverlap = NULL; 1770 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1771 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1772 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1773 if (size == 1) PetscFunctionReturn(0); 1774 1775 ierr = PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1776 /* Compute point overlap with neighbouring processes on the distributed DM */ 1777 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1778 ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr); 1779 ierr = PetscSectionCreate(comm, &leafSection);CHKERRQ(ierr); 1780 ierr = DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);CHKERRQ(ierr); 1781 ierr = DMPlexCreateOverlap(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);CHKERRQ(ierr); 1782 /* Convert overlap label to stratified migration SF */ 1783 ierr = DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);CHKERRQ(ierr); 1784 ierr = DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);CHKERRQ(ierr); 1785 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1786 sfOverlap = sfStratified; 1787 ierr = PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");CHKERRQ(ierr); 1788 ierr = PetscSFSetFromOptions(sfOverlap);CHKERRQ(ierr); 1789 1790 ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr); 1791 ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr); 1792 ierr = ISDestroy(&rootrank);CHKERRQ(ierr); 1793 ierr = ISDestroy(&leafrank);CHKERRQ(ierr); 1794 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1795 1796 /* Build the overlapping DM */ 1797 ierr = DMPlexCreate(comm, dmOverlap);CHKERRQ(ierr); 1798 ierr = PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");CHKERRQ(ierr); 1799 ierr = DMPlexMigrate(dm, sfOverlap, *dmOverlap);CHKERRQ(ierr); 1800 /* Build the new point SF */ 1801 ierr = DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1802 ierr = DMSetPointSF(*dmOverlap, sfPoint);CHKERRQ(ierr); 1803 ierr = DMGetCoordinateDM(*dmOverlap, &dmCoord);CHKERRQ(ierr); 1804 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1805 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1806 /* Cleanup overlap partition */ 1807 ierr = DMLabelDestroy(&lblOverlap);CHKERRQ(ierr); 1808 if (sf) *sf = sfOverlap; 1809 else {ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr);} 1810 ierr = PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1811 PetscFunctionReturn(0); 1812 } 1813 1814 /*@C 1815 DMPlexGetGatherDM - Get a copy of the DMPlex that gathers all points on the 1816 root process of the original's communicator. 1817 1818 Collective on dm 1819 1820 Input Parameters: 1821 . dm - the original DMPlex object 1822 1823 Output Parameters: 1824 + sf - the PetscSF used for point distribution (optional) 1825 - gatherMesh - the gathered DM object, or NULL 1826 1827 Level: intermediate 1828 1829 .seealso: DMPlexDistribute(), DMPlexGetRedundantDM() 1830 @*/ 1831 PetscErrorCode DMPlexGetGatherDM(DM dm, PetscSF *sf, DM *gatherMesh) 1832 { 1833 MPI_Comm comm; 1834 PetscMPIInt size; 1835 PetscPartitioner oldPart, gatherPart; 1836 PetscErrorCode ierr; 1837 1838 PetscFunctionBegin; 1839 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1840 PetscValidPointer(gatherMesh,2); 1841 *gatherMesh = NULL; 1842 if (sf) *sf = NULL; 1843 comm = PetscObjectComm((PetscObject)dm); 1844 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1845 if (size == 1) PetscFunctionReturn(0); 1846 ierr = DMPlexGetPartitioner(dm,&oldPart);CHKERRQ(ierr); 1847 ierr = PetscObjectReference((PetscObject)oldPart);CHKERRQ(ierr); 1848 ierr = PetscPartitionerCreate(comm,&gatherPart);CHKERRQ(ierr); 1849 ierr = PetscPartitionerSetType(gatherPart,PETSCPARTITIONERGATHER);CHKERRQ(ierr); 1850 ierr = DMPlexSetPartitioner(dm,gatherPart);CHKERRQ(ierr); 1851 ierr = DMPlexDistribute(dm,0,sf,gatherMesh);CHKERRQ(ierr); 1852 1853 ierr = DMPlexSetPartitioner(dm,oldPart);CHKERRQ(ierr); 1854 ierr = PetscPartitionerDestroy(&gatherPart);CHKERRQ(ierr); 1855 ierr = PetscPartitionerDestroy(&oldPart);CHKERRQ(ierr); 1856 PetscFunctionReturn(0); 1857 } 1858 1859 /*@C 1860 DMPlexGetRedundantDM - Get a copy of the DMPlex that is completely copied on each process. 1861 1862 Collective on dm 1863 1864 Input Parameters: 1865 . dm - the original DMPlex object 1866 1867 Output Parameters: 1868 + sf - the PetscSF used for point distribution (optional) 1869 - redundantMesh - the redundant DM object, or NULL 1870 1871 Level: intermediate 1872 1873 .seealso: DMPlexDistribute(), DMPlexGetGatherDM() 1874 @*/ 1875 PetscErrorCode DMPlexGetRedundantDM(DM dm, PetscSF *sf, DM *redundantMesh) 1876 { 1877 MPI_Comm comm; 1878 PetscMPIInt size, rank; 1879 PetscInt pStart, pEnd, p; 1880 PetscInt numPoints = -1; 1881 PetscSF migrationSF, sfPoint, gatherSF; 1882 DM gatherDM, dmCoord; 1883 PetscSFNode *points; 1884 PetscErrorCode ierr; 1885 1886 PetscFunctionBegin; 1887 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1888 PetscValidPointer(redundantMesh,2); 1889 *redundantMesh = NULL; 1890 comm = PetscObjectComm((PetscObject)dm); 1891 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1892 if (size == 1) { 1893 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 1894 *redundantMesh = dm; 1895 if (sf) *sf = NULL; 1896 PetscFunctionReturn(0); 1897 } 1898 ierr = DMPlexGetGatherDM(dm,&gatherSF,&gatherDM);CHKERRQ(ierr); 1899 if (!gatherDM) PetscFunctionReturn(0); 1900 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1901 ierr = DMPlexGetChart(gatherDM,&pStart,&pEnd);CHKERRQ(ierr); 1902 numPoints = pEnd - pStart; 1903 ierr = MPI_Bcast(&numPoints,1,MPIU_INT,0,comm);CHKERRQ(ierr); 1904 ierr = PetscMalloc1(numPoints,&points);CHKERRQ(ierr); 1905 ierr = PetscSFCreate(comm,&migrationSF);CHKERRQ(ierr); 1906 for (p = 0; p < numPoints; p++) { 1907 points[p].index = p; 1908 points[p].rank = 0; 1909 } 1910 ierr = PetscSFSetGraph(migrationSF,pEnd-pStart,numPoints,NULL,PETSC_OWN_POINTER,points,PETSC_OWN_POINTER);CHKERRQ(ierr); 1911 ierr = DMPlexCreate(comm, redundantMesh);CHKERRQ(ierr); 1912 ierr = PetscObjectSetName((PetscObject) *redundantMesh, "Redundant Mesh");CHKERRQ(ierr); 1913 ierr = DMPlexMigrate(gatherDM, migrationSF, *redundantMesh);CHKERRQ(ierr); 1914 ierr = DMPlexCreatePointSF(*redundantMesh, migrationSF, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1915 ierr = DMSetPointSF(*redundantMesh, sfPoint);CHKERRQ(ierr); 1916 ierr = DMGetCoordinateDM(*redundantMesh, &dmCoord);CHKERRQ(ierr); 1917 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1918 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1919 if (sf) { 1920 PetscSF tsf; 1921 1922 ierr = PetscSFCompose(gatherSF,migrationSF,&tsf);CHKERRQ(ierr); 1923 ierr = DMPlexStratifyMigrationSF(dm, tsf, sf);CHKERRQ(ierr); 1924 ierr = PetscSFDestroy(&tsf);CHKERRQ(ierr); 1925 } 1926 ierr = PetscSFDestroy(&migrationSF);CHKERRQ(ierr); 1927 ierr = PetscSFDestroy(&gatherSF);CHKERRQ(ierr); 1928 ierr = DMDestroy(&gatherDM);CHKERRQ(ierr); 1929 PetscFunctionReturn(0); 1930 } 1931