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 typedef struct { 1345 PetscInt vote, rank, index; 1346 } Petsc3Int; 1347 1348 /* MaxLoc, but carry a third piece of information around */ 1349 static void MaxLocCarry(void *in_, void *inout_, PetscMPIInt *len_, MPI_Datatype *dtype) 1350 { 1351 Petsc3Int *a = (Petsc3Int *)inout_; 1352 Petsc3Int *b = (Petsc3Int *)in_; 1353 PetscInt i, len = *len_; 1354 for (i = 0; i < len; i++) { 1355 if (a[i].vote < b[i].vote) { 1356 a[i].vote = b[i].vote; 1357 a[i].rank = b[i].rank; 1358 a[i].index = b[i].index; 1359 } else if (a[i].vote <= b[i].vote) { 1360 if (a[i].rank >= b[i].rank) { 1361 a[i].rank = b[i].rank; 1362 a[i].index = b[i].index; 1363 } 1364 } 1365 } 1366 } 1367 1368 /*@C 1369 DMPlexCreatePointSF - Build a point SF from an SF describing a point migration 1370 1371 Input Parameter: 1372 + dm - The source DMPlex object 1373 . migrationSF - The star forest that describes the parallel point remapping 1374 . ownership - Flag causing a vote to determine point ownership 1375 1376 Output Parameter: 1377 - pointSF - The star forest describing the point overlap in the remapped DM 1378 1379 Level: developer 1380 1381 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1382 @*/ 1383 PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF) 1384 { 1385 PetscMPIInt rank, size; 1386 PetscInt p, nroots, nleaves, idx, npointLeaves; 1387 PetscInt *pointLocal; 1388 const PetscInt *leaves; 1389 const PetscSFNode *roots; 1390 PetscSFNode *rootNodes, *leafNodes, *pointRemote; 1391 Vec shifts; 1392 const PetscInt numShifts = 13759; 1393 const PetscScalar *shift = NULL; 1394 const PetscBool shiftDebug = PETSC_FALSE; 1395 PetscBool balance; 1396 PetscErrorCode ierr; 1397 1398 PetscFunctionBegin; 1399 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1400 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 1401 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 1402 ierr = PetscLogEventBegin(DMPLEX_CreatePointSF,dm,0,0,0);CHKERRQ(ierr); 1403 1404 ierr = DMPlexGetPartitionBalance(dm, &balance);CHKERRQ(ierr); 1405 ierr = PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);CHKERRQ(ierr); 1406 ierr = PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);CHKERRQ(ierr); 1407 if (ownership) { 1408 MPI_Op op; 1409 MPI_Datatype datatype; 1410 Petsc3Int *rootVote = NULL, *leafVote = NULL; 1411 /* If balancing, we compute a random cyclic shift of the rank for each remote point. That way, the max will evenly distribute among ranks. */ 1412 if (balance) { 1413 PetscRandom r; 1414 1415 ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 1416 ierr = PetscRandomSetInterval(r, 0, 2467*size);CHKERRQ(ierr); 1417 ierr = VecCreate(PETSC_COMM_SELF, &shifts);CHKERRQ(ierr); 1418 ierr = VecSetSizes(shifts, numShifts, numShifts);CHKERRQ(ierr); 1419 ierr = VecSetType(shifts, VECSTANDARD);CHKERRQ(ierr); 1420 ierr = VecSetRandom(shifts, r);CHKERRQ(ierr); 1421 ierr = PetscRandomDestroy(&r);CHKERRQ(ierr); 1422 ierr = VecGetArrayRead(shifts, &shift);CHKERRQ(ierr); 1423 } 1424 1425 ierr = PetscMalloc1(nroots, &rootVote);CHKERRQ(ierr); 1426 ierr = PetscMalloc1(nleaves, &leafVote);CHKERRQ(ierr); 1427 /* Point ownership vote: Process with highest rank owns shared points */ 1428 for (p = 0; p < nleaves; ++p) { 1429 if (shiftDebug) { 1430 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); 1431 } 1432 /* Either put in a bid or we know we own it */ 1433 leafVote[p].vote = (rank + (shift ? (PetscInt) PetscRealPart(shift[roots[p].index%numShifts]) : 0))%size; 1434 leafVote[p].rank = rank; 1435 leafVote[p].index = p; 1436 } 1437 for (p = 0; p < nroots; p++) { 1438 /* Root must not participate in the reduction, flag so that MAXLOC does not use */ 1439 rootVote[p].vote = -3; 1440 rootVote[p].rank = -3; 1441 rootVote[p].index = -3; 1442 } 1443 ierr = MPI_Type_contiguous(3, MPIU_INT, &datatype);CHKERRQ(ierr); 1444 ierr = MPI_Type_commit(&datatype);CHKERRQ(ierr); 1445 ierr = MPI_Op_create(&MaxLocCarry, 1, &op);CHKERRQ(ierr); 1446 ierr = PetscSFReduceBegin(migrationSF, datatype, leafVote, rootVote, op);CHKERRQ(ierr); 1447 ierr = PetscSFReduceEnd(migrationSF, datatype, leafVote, rootVote, op);CHKERRQ(ierr); 1448 ierr = MPI_Op_free(&op);CHKERRQ(ierr); 1449 ierr = MPI_Type_free(&datatype);CHKERRQ(ierr); 1450 for (p = 0; p < nroots; p++) { 1451 rootNodes[p].rank = rootVote[p].rank; 1452 rootNodes[p].index = rootVote[p].index; 1453 } 1454 ierr = PetscFree(leafVote);CHKERRQ(ierr); 1455 ierr = PetscFree(rootVote);CHKERRQ(ierr); 1456 } else { 1457 for (p = 0; p < nroots; p++) { 1458 rootNodes[p].index = -1; 1459 rootNodes[p].rank = rank; 1460 } 1461 for (p = 0; p < nleaves; p++) { 1462 /* Write new local id into old location */ 1463 if (roots[p].rank == rank) { 1464 rootNodes[roots[p].index].index = leaves ? leaves[p] : p; 1465 } 1466 } 1467 } 1468 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1469 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1470 1471 for (npointLeaves = 0, p = 0; p < nleaves; p++) { 1472 if (leafNodes[p].rank != rank) npointLeaves++; 1473 } 1474 ierr = PetscMalloc1(npointLeaves, &pointLocal);CHKERRQ(ierr); 1475 ierr = PetscMalloc1(npointLeaves, &pointRemote);CHKERRQ(ierr); 1476 for (idx = 0, p = 0; p < nleaves; p++) { 1477 if (leafNodes[p].rank != rank) { 1478 pointLocal[idx] = p; 1479 pointRemote[idx] = leafNodes[p]; 1480 idx++; 1481 } 1482 } 1483 if (shift) { 1484 ierr = VecRestoreArrayRead(shifts, &shift);CHKERRQ(ierr); 1485 ierr = VecDestroy(&shifts);CHKERRQ(ierr); 1486 } 1487 if (shiftDebug) {ierr = PetscSynchronizedFlush(PetscObjectComm((PetscObject) dm), PETSC_STDOUT);CHKERRQ(ierr);} 1488 ierr = PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);CHKERRQ(ierr); 1489 ierr = PetscSFSetFromOptions(*pointSF);CHKERRQ(ierr); 1490 ierr = PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1491 ierr = PetscFree2(rootNodes, leafNodes);CHKERRQ(ierr); 1492 ierr = PetscLogEventEnd(DMPLEX_CreatePointSF,dm,0,0,0);CHKERRQ(ierr); 1493 PetscFunctionReturn(0); 1494 } 1495 1496 /*@C 1497 DMPlexMigrate - Migrates internal DM data over the supplied star forest 1498 1499 Collective on dm 1500 1501 Input Parameter: 1502 + dm - The source DMPlex object 1503 . sf - The star forest communication context describing the migration pattern 1504 1505 Output Parameter: 1506 - targetDM - The target DMPlex object 1507 1508 Level: intermediate 1509 1510 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1511 @*/ 1512 PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM) 1513 { 1514 MPI_Comm comm; 1515 PetscInt dim, cdim, nroots; 1516 PetscSF sfPoint; 1517 ISLocalToGlobalMapping ltogMigration; 1518 ISLocalToGlobalMapping ltogOriginal = NULL; 1519 PetscBool flg; 1520 PetscErrorCode ierr; 1521 1522 PetscFunctionBegin; 1523 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1524 ierr = PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1525 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 1526 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1527 ierr = DMSetDimension(targetDM, dim);CHKERRQ(ierr); 1528 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 1529 ierr = DMSetCoordinateDim(targetDM, cdim);CHKERRQ(ierr); 1530 1531 /* Check for a one-to-all distribution pattern */ 1532 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1533 ierr = PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 1534 if (nroots >= 0) { 1535 IS isOriginal; 1536 PetscInt n, size, nleaves; 1537 PetscInt *numbering_orig, *numbering_new; 1538 1539 /* Get the original point numbering */ 1540 ierr = DMPlexCreatePointNumbering(dm, &isOriginal);CHKERRQ(ierr); 1541 ierr = ISLocalToGlobalMappingCreateIS(isOriginal, <ogOriginal);CHKERRQ(ierr); 1542 ierr = ISLocalToGlobalMappingGetSize(ltogOriginal, &size);CHKERRQ(ierr); 1543 ierr = ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1544 /* Convert to positive global numbers */ 1545 for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);} 1546 /* Derive the new local-to-global mapping from the old one */ 1547 ierr = PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1548 ierr = PetscMalloc1(nleaves, &numbering_new);CHKERRQ(ierr); 1549 ierr = PetscSFBcastBegin(sf, MPIU_INT, numbering_orig, numbering_new);CHKERRQ(ierr); 1550 ierr = PetscSFBcastEnd(sf, MPIU_INT, numbering_orig, numbering_new);CHKERRQ(ierr); 1551 ierr = ISLocalToGlobalMappingCreate(comm, 1, nleaves, numbering_new, PETSC_OWN_POINTER, <ogMigration);CHKERRQ(ierr); 1552 ierr = ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1553 ierr = ISDestroy(&isOriginal);CHKERRQ(ierr); 1554 } else { 1555 /* One-to-all distribution pattern: We can derive LToG from SF */ 1556 ierr = ISLocalToGlobalMappingCreateSF(sf, 0, <ogMigration);CHKERRQ(ierr); 1557 } 1558 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1559 if (flg) { 1560 ierr = PetscPrintf(comm, "Point renumbering for DM migration:\n");CHKERRQ(ierr); 1561 ierr = ISLocalToGlobalMappingView(ltogMigration, NULL);CHKERRQ(ierr); 1562 } 1563 /* Migrate DM data to target DM */ 1564 ierr = DMPlexDistributeCones(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1565 ierr = DMPlexDistributeLabels(dm, sf, targetDM);CHKERRQ(ierr); 1566 ierr = DMPlexDistributeCoordinates(dm, sf, targetDM);CHKERRQ(ierr); 1567 ierr = DMPlexDistributeSetupHybrid(dm, sf, ltogMigration, targetDM);CHKERRQ(ierr); 1568 ierr = DMPlexDistributeSetupTree(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1569 ierr = ISLocalToGlobalMappingDestroy(<ogOriginal);CHKERRQ(ierr); 1570 ierr = ISLocalToGlobalMappingDestroy(<ogMigration);CHKERRQ(ierr); 1571 ierr = PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1572 PetscFunctionReturn(0); 1573 } 1574 1575 /*@C 1576 DMPlexDistribute - Distributes the mesh and any associated sections. 1577 1578 Collective on dm 1579 1580 Input Parameter: 1581 + dm - The original DMPlex object 1582 - overlap - The overlap of partitions, 0 is the default 1583 1584 Output Parameter: 1585 + sf - The PetscSF used for point distribution, or NULL if not needed 1586 - dmParallel - The distributed DMPlex object 1587 1588 Note: If the mesh was not distributed, the output dmParallel will be NULL. 1589 1590 The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function 1591 representation on the mesh. 1592 1593 Level: intermediate 1594 1595 .seealso: DMPlexCreate(), DMSetAdjacency() 1596 @*/ 1597 PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel) 1598 { 1599 MPI_Comm comm; 1600 PetscPartitioner partitioner; 1601 IS cellPart; 1602 PetscSection cellPartSection; 1603 DM dmCoord; 1604 DMLabel lblPartition, lblMigration; 1605 PetscSF sfMigration, sfStratified, sfPoint; 1606 PetscBool flg, balance; 1607 PetscMPIInt rank, size; 1608 PetscErrorCode ierr; 1609 1610 PetscFunctionBegin; 1611 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1612 PetscValidLogicalCollectiveInt(dm, overlap, 2); 1613 if (sf) PetscValidPointer(sf,3); 1614 PetscValidPointer(dmParallel,4); 1615 1616 if (sf) *sf = NULL; 1617 *dmParallel = NULL; 1618 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1619 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1620 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1621 if (size == 1) PetscFunctionReturn(0); 1622 1623 ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1624 /* Create cell partition */ 1625 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1626 ierr = PetscSectionCreate(comm, &cellPartSection);CHKERRQ(ierr); 1627 ierr = DMPlexGetPartitioner(dm, &partitioner);CHKERRQ(ierr); 1628 ierr = PetscPartitionerPartition(partitioner, dm, cellPartSection, &cellPart);CHKERRQ(ierr); 1629 ierr = PetscLogEventBegin(DMPLEX_PartSelf,dm,0,0,0);CHKERRQ(ierr); 1630 { 1631 /* Convert partition to DMLabel */ 1632 IS is; 1633 PetscHSetI ht; 1634 const PetscInt *points; 1635 PetscInt *iranks; 1636 PetscInt pStart, pEnd, proc, npoints, poff = 0, nranks; 1637 1638 ierr = DMLabelCreate(PETSC_COMM_SELF, "Point Partition", &lblPartition);CHKERRQ(ierr); 1639 /* Preallocate strata */ 1640 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1641 ierr = PetscSectionGetChart(cellPartSection, &pStart, &pEnd);CHKERRQ(ierr); 1642 for (proc = pStart; proc < pEnd; proc++) { 1643 ierr = PetscSectionGetDof(cellPartSection, proc, &npoints);CHKERRQ(ierr); 1644 if (npoints) {ierr = PetscHSetIAdd(ht, proc);CHKERRQ(ierr);} 1645 } 1646 ierr = PetscHSetIGetSize(ht, &nranks);CHKERRQ(ierr); 1647 ierr = PetscMalloc1(nranks, &iranks);CHKERRQ(ierr); 1648 ierr = PetscHSetIGetElems(ht, &poff, iranks);CHKERRQ(ierr); 1649 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1650 ierr = DMLabelAddStrata(lblPartition, nranks, iranks);CHKERRQ(ierr); 1651 ierr = PetscFree(iranks);CHKERRQ(ierr); 1652 /* Inline DMPlexPartitionLabelClosure() */ 1653 ierr = ISGetIndices(cellPart, &points);CHKERRQ(ierr); 1654 ierr = PetscSectionGetChart(cellPartSection, &pStart, &pEnd);CHKERRQ(ierr); 1655 for (proc = pStart; proc < pEnd; proc++) { 1656 ierr = PetscSectionGetDof(cellPartSection, proc, &npoints);CHKERRQ(ierr); 1657 if (!npoints) continue; 1658 ierr = PetscSectionGetOffset(cellPartSection, proc, &poff);CHKERRQ(ierr); 1659 ierr = DMPlexClosurePoints_Private(dm, npoints, points+poff, &is);CHKERRQ(ierr); 1660 ierr = DMLabelSetStratumIS(lblPartition, proc, is);CHKERRQ(ierr); 1661 ierr = ISDestroy(&is);CHKERRQ(ierr); 1662 } 1663 ierr = ISRestoreIndices(cellPart, &points);CHKERRQ(ierr); 1664 } 1665 ierr = PetscLogEventEnd(DMPLEX_PartSelf,dm,0,0,0);CHKERRQ(ierr); 1666 1667 ierr = DMLabelCreate(PETSC_COMM_SELF, "Point migration", &lblMigration);CHKERRQ(ierr); 1668 ierr = DMPlexPartitionLabelInvert(dm, lblPartition, NULL, lblMigration);CHKERRQ(ierr); 1669 ierr = DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);CHKERRQ(ierr); 1670 ierr = DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);CHKERRQ(ierr); 1671 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1672 sfMigration = sfStratified; 1673 ierr = PetscSFSetUp(sfMigration);CHKERRQ(ierr); 1674 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1675 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1676 if (flg) { 1677 ierr = DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1678 ierr = PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1679 } 1680 1681 /* Create non-overlapping parallel DM and migrate internal data */ 1682 ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr); 1683 ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr); 1684 ierr = DMPlexMigrate(dm, sfMigration, *dmParallel);CHKERRQ(ierr); 1685 1686 /* Build the point SF without overlap */ 1687 ierr = DMPlexGetPartitionBalance(dm, &balance);CHKERRQ(ierr); 1688 ierr = DMPlexSetPartitionBalance(*dmParallel, balance);CHKERRQ(ierr); 1689 ierr = DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);CHKERRQ(ierr); 1690 ierr = DMSetPointSF(*dmParallel, sfPoint);CHKERRQ(ierr); 1691 ierr = DMGetCoordinateDM(*dmParallel, &dmCoord);CHKERRQ(ierr); 1692 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1693 if (flg) {ierr = PetscSFView(sfPoint, NULL);CHKERRQ(ierr);} 1694 1695 if (overlap > 0) { 1696 DM dmOverlap; 1697 PetscInt nroots, nleaves, noldleaves, l; 1698 const PetscInt *oldLeaves; 1699 PetscSFNode *newRemote, *permRemote; 1700 const PetscSFNode *oldRemote; 1701 PetscSF sfOverlap, sfOverlapPoint; 1702 1703 /* Add the partition overlap to the distributed DM */ 1704 ierr = DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);CHKERRQ(ierr); 1705 ierr = DMDestroy(dmParallel);CHKERRQ(ierr); 1706 *dmParallel = dmOverlap; 1707 if (flg) { 1708 ierr = PetscPrintf(comm, "Overlap Migration SF:\n");CHKERRQ(ierr); 1709 ierr = PetscSFView(sfOverlap, NULL);CHKERRQ(ierr); 1710 } 1711 1712 /* Re-map the migration SF to establish the full migration pattern */ 1713 ierr = PetscSFGetGraph(sfMigration, &nroots, &noldleaves, &oldLeaves, &oldRemote);CHKERRQ(ierr); 1714 ierr = PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1715 ierr = PetscMalloc1(nleaves, &newRemote);CHKERRQ(ierr); 1716 /* oldRemote: original root point mapping to original leaf point 1717 newRemote: original leaf point mapping to overlapped leaf point */ 1718 if (oldLeaves) { 1719 /* After stratification, the migration remotes may not be in root (canonical) order, so we reorder using the leaf numbering */ 1720 ierr = PetscMalloc1(noldleaves, &permRemote);CHKERRQ(ierr); 1721 for (l = 0; l < noldleaves; ++l) permRemote[oldLeaves[l]] = oldRemote[l]; 1722 oldRemote = permRemote; 1723 } 1724 ierr = PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1725 ierr = PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1726 if (oldLeaves) {ierr = PetscFree(oldRemote);CHKERRQ(ierr);} 1727 ierr = PetscSFCreate(comm, &sfOverlapPoint);CHKERRQ(ierr); 1728 ierr = PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1729 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1730 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1731 sfMigration = sfOverlapPoint; 1732 } 1733 /* Cleanup Partition */ 1734 ierr = DMLabelDestroy(&lblPartition);CHKERRQ(ierr); 1735 ierr = DMLabelDestroy(&lblMigration);CHKERRQ(ierr); 1736 ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr); 1737 ierr = ISDestroy(&cellPart);CHKERRQ(ierr); 1738 /* Copy BC */ 1739 ierr = DMCopyBoundary(dm, *dmParallel);CHKERRQ(ierr); 1740 /* Create sfNatural */ 1741 if (dm->useNatural) { 1742 PetscSection section; 1743 1744 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1745 ierr = DMPlexCreateGlobalToNaturalSF(*dmParallel, section, sfMigration, &(*dmParallel)->sfNatural);CHKERRQ(ierr); 1746 ierr = DMSetUseNatural(*dmParallel, PETSC_TRUE);CHKERRQ(ierr); 1747 } 1748 /* Cleanup */ 1749 if (sf) {*sf = sfMigration;} 1750 else {ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr);} 1751 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1752 ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1753 PetscFunctionReturn(0); 1754 } 1755 1756 /*@C 1757 DMPlexDistributeOverlap - Add partition overlap to a distributed non-overlapping DM. 1758 1759 Collective on dm 1760 1761 Input Parameter: 1762 + dm - The non-overlapping distrbuted DMPlex object 1763 - overlap - The overlap of partitions 1764 1765 Output Parameter: 1766 + sf - The PetscSF used for point distribution 1767 - dmOverlap - The overlapping distributed DMPlex object, or NULL 1768 1769 Note: If the mesh was not distributed, the return value is NULL. 1770 1771 The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function 1772 representation on the mesh. 1773 1774 Level: intermediate 1775 1776 .seealso: DMPlexCreate(), DMSetAdjacency() 1777 @*/ 1778 PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap) 1779 { 1780 MPI_Comm comm; 1781 PetscMPIInt size, rank; 1782 PetscSection rootSection, leafSection; 1783 IS rootrank, leafrank; 1784 DM dmCoord; 1785 DMLabel lblOverlap; 1786 PetscSF sfOverlap, sfStratified, sfPoint; 1787 PetscErrorCode ierr; 1788 1789 PetscFunctionBegin; 1790 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1791 if (sf) PetscValidPointer(sf, 3); 1792 PetscValidPointer(dmOverlap, 4); 1793 1794 if (sf) *sf = NULL; 1795 *dmOverlap = NULL; 1796 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1797 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1798 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1799 if (size == 1) PetscFunctionReturn(0); 1800 1801 ierr = PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1802 /* Compute point overlap with neighbouring processes on the distributed DM */ 1803 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1804 ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr); 1805 ierr = PetscSectionCreate(comm, &leafSection);CHKERRQ(ierr); 1806 ierr = DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);CHKERRQ(ierr); 1807 ierr = DMPlexCreateOverlap(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);CHKERRQ(ierr); 1808 /* Convert overlap label to stratified migration SF */ 1809 ierr = DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);CHKERRQ(ierr); 1810 ierr = DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);CHKERRQ(ierr); 1811 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1812 sfOverlap = sfStratified; 1813 ierr = PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");CHKERRQ(ierr); 1814 ierr = PetscSFSetFromOptions(sfOverlap);CHKERRQ(ierr); 1815 1816 ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr); 1817 ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr); 1818 ierr = ISDestroy(&rootrank);CHKERRQ(ierr); 1819 ierr = ISDestroy(&leafrank);CHKERRQ(ierr); 1820 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1821 1822 /* Build the overlapping DM */ 1823 ierr = DMPlexCreate(comm, dmOverlap);CHKERRQ(ierr); 1824 ierr = PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");CHKERRQ(ierr); 1825 ierr = DMPlexMigrate(dm, sfOverlap, *dmOverlap);CHKERRQ(ierr); 1826 /* Build the new point SF */ 1827 ierr = DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1828 ierr = DMSetPointSF(*dmOverlap, sfPoint);CHKERRQ(ierr); 1829 ierr = DMGetCoordinateDM(*dmOverlap, &dmCoord);CHKERRQ(ierr); 1830 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1831 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1832 /* Cleanup overlap partition */ 1833 ierr = DMLabelDestroy(&lblOverlap);CHKERRQ(ierr); 1834 if (sf) *sf = sfOverlap; 1835 else {ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr);} 1836 ierr = PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1837 PetscFunctionReturn(0); 1838 } 1839 1840 /*@C 1841 DMPlexGetGatherDM - Get a copy of the DMPlex that gathers all points on the 1842 root process of the original's communicator. 1843 1844 Collective on dm 1845 1846 Input Parameters: 1847 . dm - the original DMPlex object 1848 1849 Output Parameters: 1850 + sf - the PetscSF used for point distribution (optional) 1851 - gatherMesh - the gathered DM object, or NULL 1852 1853 Level: intermediate 1854 1855 .seealso: DMPlexDistribute(), DMPlexGetRedundantDM() 1856 @*/ 1857 PetscErrorCode DMPlexGetGatherDM(DM dm, PetscSF *sf, DM *gatherMesh) 1858 { 1859 MPI_Comm comm; 1860 PetscMPIInt size; 1861 PetscPartitioner oldPart, gatherPart; 1862 PetscErrorCode ierr; 1863 1864 PetscFunctionBegin; 1865 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1866 PetscValidPointer(gatherMesh,2); 1867 *gatherMesh = NULL; 1868 if (sf) *sf = NULL; 1869 comm = PetscObjectComm((PetscObject)dm); 1870 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1871 if (size == 1) PetscFunctionReturn(0); 1872 ierr = DMPlexGetPartitioner(dm,&oldPart);CHKERRQ(ierr); 1873 ierr = PetscObjectReference((PetscObject)oldPart);CHKERRQ(ierr); 1874 ierr = PetscPartitionerCreate(comm,&gatherPart);CHKERRQ(ierr); 1875 ierr = PetscPartitionerSetType(gatherPart,PETSCPARTITIONERGATHER);CHKERRQ(ierr); 1876 ierr = DMPlexSetPartitioner(dm,gatherPart);CHKERRQ(ierr); 1877 ierr = DMPlexDistribute(dm,0,sf,gatherMesh);CHKERRQ(ierr); 1878 1879 ierr = DMPlexSetPartitioner(dm,oldPart);CHKERRQ(ierr); 1880 ierr = PetscPartitionerDestroy(&gatherPart);CHKERRQ(ierr); 1881 ierr = PetscPartitionerDestroy(&oldPart);CHKERRQ(ierr); 1882 PetscFunctionReturn(0); 1883 } 1884 1885 /*@C 1886 DMPlexGetRedundantDM - Get a copy of the DMPlex that is completely copied on each process. 1887 1888 Collective on dm 1889 1890 Input Parameters: 1891 . dm - the original DMPlex object 1892 1893 Output Parameters: 1894 + sf - the PetscSF used for point distribution (optional) 1895 - redundantMesh - the redundant DM object, or NULL 1896 1897 Level: intermediate 1898 1899 .seealso: DMPlexDistribute(), DMPlexGetGatherDM() 1900 @*/ 1901 PetscErrorCode DMPlexGetRedundantDM(DM dm, PetscSF *sf, DM *redundantMesh) 1902 { 1903 MPI_Comm comm; 1904 PetscMPIInt size, rank; 1905 PetscInt pStart, pEnd, p; 1906 PetscInt numPoints = -1; 1907 PetscSF migrationSF, sfPoint, gatherSF; 1908 DM gatherDM, dmCoord; 1909 PetscSFNode *points; 1910 PetscErrorCode ierr; 1911 1912 PetscFunctionBegin; 1913 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1914 PetscValidPointer(redundantMesh,2); 1915 *redundantMesh = NULL; 1916 comm = PetscObjectComm((PetscObject)dm); 1917 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1918 if (size == 1) { 1919 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 1920 *redundantMesh = dm; 1921 if (sf) *sf = NULL; 1922 PetscFunctionReturn(0); 1923 } 1924 ierr = DMPlexGetGatherDM(dm,&gatherSF,&gatherDM);CHKERRQ(ierr); 1925 if (!gatherDM) PetscFunctionReturn(0); 1926 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1927 ierr = DMPlexGetChart(gatherDM,&pStart,&pEnd);CHKERRQ(ierr); 1928 numPoints = pEnd - pStart; 1929 ierr = MPI_Bcast(&numPoints,1,MPIU_INT,0,comm);CHKERRQ(ierr); 1930 ierr = PetscMalloc1(numPoints,&points);CHKERRQ(ierr); 1931 ierr = PetscSFCreate(comm,&migrationSF);CHKERRQ(ierr); 1932 for (p = 0; p < numPoints; p++) { 1933 points[p].index = p; 1934 points[p].rank = 0; 1935 } 1936 ierr = PetscSFSetGraph(migrationSF,pEnd-pStart,numPoints,NULL,PETSC_OWN_POINTER,points,PETSC_OWN_POINTER);CHKERRQ(ierr); 1937 ierr = DMPlexCreate(comm, redundantMesh);CHKERRQ(ierr); 1938 ierr = PetscObjectSetName((PetscObject) *redundantMesh, "Redundant Mesh");CHKERRQ(ierr); 1939 ierr = DMPlexMigrate(gatherDM, migrationSF, *redundantMesh);CHKERRQ(ierr); 1940 ierr = DMPlexCreatePointSF(*redundantMesh, migrationSF, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1941 ierr = DMSetPointSF(*redundantMesh, sfPoint);CHKERRQ(ierr); 1942 ierr = DMGetCoordinateDM(*redundantMesh, &dmCoord);CHKERRQ(ierr); 1943 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1944 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1945 if (sf) { 1946 PetscSF tsf; 1947 1948 ierr = PetscSFCompose(gatherSF,migrationSF,&tsf);CHKERRQ(ierr); 1949 ierr = DMPlexStratifyMigrationSF(dm, tsf, sf);CHKERRQ(ierr); 1950 ierr = PetscSFDestroy(&tsf);CHKERRQ(ierr); 1951 } 1952 ierr = PetscSFDestroy(&migrationSF);CHKERRQ(ierr); 1953 ierr = PetscSFDestroy(&gatherSF);CHKERRQ(ierr); 1954 ierr = DMDestroy(&gatherDM);CHKERRQ(ierr); 1955 PetscFunctionReturn(0); 1956 } 1957