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 depth = PetscMax(depth, -depth); 210 ierr = DMPlexGetMaxSizes(dm, &maxC, &maxS);CHKERRQ(ierr); 211 coneSeries = (maxC > 1) ? ((PetscPowInt(maxC,depth+1)-1)/(maxC-1)) : depth+1; 212 supportSeries = (maxS > 1) ? ((PetscPowInt(maxS,depth+1)-1)/(maxS-1)) : depth+1; 213 asiz = PetscMax(PetscPowInt(maxS,depth)*coneSeries,PetscPowInt(maxC,depth)*supportSeries); 214 asiz *= maxAnchors; 215 asiz = PetscMin(asiz,pEnd-pStart); 216 ierr = PetscMalloc1(asiz,adj);CHKERRQ(ierr); 217 } 218 if (*adjSize < 0) *adjSize = asiz; 219 maxAdjSize = *adjSize; 220 if (mesh->useradjacency) { 221 ierr = (*mesh->useradjacency)(dm, p, adjSize, *adj, mesh->useradjacencyctx);CHKERRQ(ierr); 222 } else if (useTransitiveClosure) { 223 ierr = DMPlexGetAdjacency_Transitive_Internal(dm, p, useCone, adjSize, *adj);CHKERRQ(ierr); 224 } else if (useCone) { 225 ierr = DMPlexGetAdjacency_Cone_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); 226 } else { 227 ierr = DMPlexGetAdjacency_Support_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); 228 } 229 if (useAnchors && aSec) { 230 PetscInt origSize = *adjSize; 231 PetscInt numAdj = origSize; 232 PetscInt i = 0, j; 233 PetscInt *orig = *adj; 234 235 while (i < origSize) { 236 PetscInt p = orig[i]; 237 PetscInt aDof = 0; 238 239 if (p >= aStart && p < aEnd) { 240 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 241 } 242 if (aDof) { 243 PetscInt aOff; 244 PetscInt s, q; 245 246 for (j = i + 1; j < numAdj; j++) { 247 orig[j - 1] = orig[j]; 248 } 249 origSize--; 250 numAdj--; 251 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 252 for (s = 0; s < aDof; ++s) { 253 for (q = 0; q < numAdj || ((void)(orig[numAdj++] = anchors[aOff+s]),0); ++q) { 254 if (anchors[aOff+s] == orig[q]) break; 255 } 256 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 257 } 258 } 259 else { 260 i++; 261 } 262 } 263 *adjSize = numAdj; 264 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 265 } 266 PetscFunctionReturn(0); 267 } 268 269 /*@ 270 DMPlexGetAdjacency - Return all points adjacent to the given point 271 272 Input Parameters: 273 + dm - The DM object 274 . p - The point 275 . adjSize - The maximum size of adj if it is non-NULL, or PETSC_DETERMINE 276 - adj - Either NULL so that the array is allocated, or an existing array with size adjSize 277 278 Output Parameters: 279 + adjSize - The number of adjacent points 280 - adj - The adjacent points 281 282 Level: advanced 283 284 Notes: 285 The user must PetscFree the adj array if it was not passed in. 286 287 .seealso: DMSetAdjacency(), DMPlexDistribute(), DMCreateMatrix(), DMPlexPreallocateOperator() 288 @*/ 289 PetscErrorCode DMPlexGetAdjacency(DM dm, PetscInt p, PetscInt *adjSize, PetscInt *adj[]) 290 { 291 PetscBool useCone, useClosure, useAnchors; 292 PetscErrorCode ierr; 293 294 PetscFunctionBeginHot; 295 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 296 PetscValidPointer(adjSize,3); 297 PetscValidPointer(adj,4); 298 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 299 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 300 ierr = DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, adjSize, adj);CHKERRQ(ierr); 301 PetscFunctionReturn(0); 302 } 303 304 /*@ 305 DMPlexCreateTwoSidedProcessSF - Create an SF which just has process connectivity 306 307 Collective on dm 308 309 Input Parameters: 310 + dm - The DM 311 - sfPoint - The PetscSF which encodes point connectivity 312 313 Output Parameters: 314 + processRanks - A list of process neighbors, or NULL 315 - sfProcess - An SF encoding the two-sided process connectivity, or NULL 316 317 Level: developer 318 319 .seealso: PetscSFCreate(), DMPlexCreateProcessSF() 320 @*/ 321 PetscErrorCode DMPlexCreateTwoSidedProcessSF(DM dm, PetscSF sfPoint, PetscSection rootRankSection, IS rootRanks, PetscSection leafRankSection, IS leafRanks, IS *processRanks, PetscSF *sfProcess) 322 { 323 const PetscSFNode *remotePoints; 324 PetscInt *localPointsNew; 325 PetscSFNode *remotePointsNew; 326 const PetscInt *nranks; 327 PetscInt *ranksNew; 328 PetscBT neighbors; 329 PetscInt pStart, pEnd, p, numLeaves, l, numNeighbors, n; 330 PetscMPIInt size, proc, rank; 331 PetscErrorCode ierr; 332 333 PetscFunctionBegin; 334 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 335 PetscValidHeaderSpecific(sfPoint, PETSCSF_CLASSID, 2); 336 if (processRanks) {PetscValidPointer(processRanks, 3);} 337 if (sfProcess) {PetscValidPointer(sfProcess, 4);} 338 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRMPI(ierr); 339 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 340 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, NULL, &remotePoints);CHKERRQ(ierr); 341 ierr = PetscBTCreate(size, &neighbors);CHKERRQ(ierr); 342 ierr = PetscBTMemzero(size, neighbors);CHKERRQ(ierr); 343 /* Compute root-to-leaf process connectivity */ 344 ierr = PetscSectionGetChart(rootRankSection, &pStart, &pEnd);CHKERRQ(ierr); 345 ierr = ISGetIndices(rootRanks, &nranks);CHKERRQ(ierr); 346 for (p = pStart; p < pEnd; ++p) { 347 PetscInt ndof, noff, n; 348 349 ierr = PetscSectionGetDof(rootRankSection, p, &ndof);CHKERRQ(ierr); 350 ierr = PetscSectionGetOffset(rootRankSection, p, &noff);CHKERRQ(ierr); 351 for (n = 0; n < ndof; ++n) {ierr = PetscBTSet(neighbors, nranks[noff+n]);CHKERRQ(ierr);} 352 } 353 ierr = ISRestoreIndices(rootRanks, &nranks);CHKERRQ(ierr); 354 /* Compute leaf-to-neighbor process connectivity */ 355 ierr = PetscSectionGetChart(leafRankSection, &pStart, &pEnd);CHKERRQ(ierr); 356 ierr = ISGetIndices(leafRanks, &nranks);CHKERRQ(ierr); 357 for (p = pStart; p < pEnd; ++p) { 358 PetscInt ndof, noff, n; 359 360 ierr = PetscSectionGetDof(leafRankSection, p, &ndof);CHKERRQ(ierr); 361 ierr = PetscSectionGetOffset(leafRankSection, p, &noff);CHKERRQ(ierr); 362 for (n = 0; n < ndof; ++n) {ierr = PetscBTSet(neighbors, nranks[noff+n]);CHKERRQ(ierr);} 363 } 364 ierr = ISRestoreIndices(leafRanks, &nranks);CHKERRQ(ierr); 365 /* Compute leaf-to-root process connectivity */ 366 for (l = 0; l < numLeaves; ++l) {PetscBTSet(neighbors, remotePoints[l].rank);} 367 /* Calculate edges */ 368 PetscBTClear(neighbors, rank); 369 for (proc = 0, numNeighbors = 0; proc < size; ++proc) {if (PetscBTLookup(neighbors, proc)) ++numNeighbors;} 370 ierr = PetscMalloc1(numNeighbors, &ranksNew);CHKERRQ(ierr); 371 ierr = PetscMalloc1(numNeighbors, &localPointsNew);CHKERRQ(ierr); 372 ierr = PetscMalloc1(numNeighbors, &remotePointsNew);CHKERRQ(ierr); 373 for (proc = 0, n = 0; proc < size; ++proc) { 374 if (PetscBTLookup(neighbors, proc)) { 375 ranksNew[n] = proc; 376 localPointsNew[n] = proc; 377 remotePointsNew[n].index = rank; 378 remotePointsNew[n].rank = proc; 379 ++n; 380 } 381 } 382 ierr = PetscBTDestroy(&neighbors);CHKERRQ(ierr); 383 if (processRanks) {ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), numNeighbors, ranksNew, PETSC_OWN_POINTER, processRanks);CHKERRQ(ierr);} 384 else {ierr = PetscFree(ranksNew);CHKERRQ(ierr);} 385 if (sfProcess) { 386 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfProcess);CHKERRQ(ierr); 387 ierr = PetscObjectSetName((PetscObject) *sfProcess, "Two-Sided Process SF");CHKERRQ(ierr); 388 ierr = PetscSFSetFromOptions(*sfProcess);CHKERRQ(ierr); 389 ierr = PetscSFSetGraph(*sfProcess, size, numNeighbors, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);CHKERRQ(ierr); 390 } 391 PetscFunctionReturn(0); 392 } 393 394 /*@ 395 DMPlexDistributeOwnership - Compute owner information for shared points. This basically gets two-sided for an SF. 396 397 Collective on dm 398 399 Input Parameter: 400 . dm - The DM 401 402 Output Parameters: 403 + rootSection - The number of leaves for a given root point 404 . rootrank - The rank of each edge into the root point 405 . leafSection - The number of processes sharing a given leaf point 406 - leafrank - The rank of each process sharing a leaf point 407 408 Level: developer 409 410 .seealso: DMPlexCreateOverlapLabel(), DMPlexDistribute(), DMPlexDistributeOverlap() 411 @*/ 412 PetscErrorCode DMPlexDistributeOwnership(DM dm, PetscSection rootSection, IS *rootrank, PetscSection leafSection, IS *leafrank) 413 { 414 MPI_Comm comm; 415 PetscSF sfPoint; 416 const PetscInt *rootdegree; 417 PetscInt *myrank, *remoterank; 418 PetscInt pStart, pEnd, p, nedges; 419 PetscMPIInt rank; 420 PetscErrorCode ierr; 421 422 PetscFunctionBegin; 423 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 424 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 425 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 426 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 427 /* Compute number of leaves for each root */ 428 ierr = PetscObjectSetName((PetscObject) rootSection, "Root Section");CHKERRQ(ierr); 429 ierr = PetscSectionSetChart(rootSection, pStart, pEnd);CHKERRQ(ierr); 430 ierr = PetscSFComputeDegreeBegin(sfPoint, &rootdegree);CHKERRQ(ierr); 431 ierr = PetscSFComputeDegreeEnd(sfPoint, &rootdegree);CHKERRQ(ierr); 432 for (p = pStart; p < pEnd; ++p) {ierr = PetscSectionSetDof(rootSection, p, rootdegree[p-pStart]);CHKERRQ(ierr);} 433 ierr = PetscSectionSetUp(rootSection);CHKERRQ(ierr); 434 /* Gather rank of each leaf to root */ 435 ierr = PetscSectionGetStorageSize(rootSection, &nedges);CHKERRQ(ierr); 436 ierr = PetscMalloc1(pEnd-pStart, &myrank);CHKERRQ(ierr); 437 ierr = PetscMalloc1(nedges, &remoterank);CHKERRQ(ierr); 438 for (p = 0; p < pEnd-pStart; ++p) myrank[p] = rank; 439 ierr = PetscSFGatherBegin(sfPoint, MPIU_INT, myrank, remoterank);CHKERRQ(ierr); 440 ierr = PetscSFGatherEnd(sfPoint, MPIU_INT, myrank, remoterank);CHKERRQ(ierr); 441 ierr = PetscFree(myrank);CHKERRQ(ierr); 442 ierr = ISCreateGeneral(comm, nedges, remoterank, PETSC_OWN_POINTER, rootrank);CHKERRQ(ierr); 443 /* Distribute remote ranks to leaves */ 444 ierr = PetscObjectSetName((PetscObject) leafSection, "Leaf Section");CHKERRQ(ierr); 445 ierr = DMPlexDistributeFieldIS(dm, sfPoint, rootSection, *rootrank, leafSection, leafrank);CHKERRQ(ierr); 446 PetscFunctionReturn(0); 447 } 448 449 /*@C 450 DMPlexCreateOverlapLabel - Compute owner information for shared points. This basically gets two-sided for an SF. 451 452 Collective on dm 453 454 Input Parameters: 455 + dm - The DM 456 . levels - Number of overlap levels 457 . rootSection - The number of leaves for a given root point 458 . rootrank - The rank of each edge into the root point 459 . leafSection - The number of processes sharing a given leaf point 460 - leafrank - The rank of each process sharing a leaf point 461 462 Output Parameter: 463 . ovLabel - DMLabel containing remote overlap contributions as point/rank pairings 464 465 Level: developer 466 467 .seealso: DMPlexDistributeOwnership(), DMPlexDistribute() 468 @*/ 469 PetscErrorCode DMPlexCreateOverlapLabel(DM dm, PetscInt levels, PetscSection rootSection, IS rootrank, PetscSection leafSection, IS leafrank, DMLabel *ovLabel) 470 { 471 MPI_Comm comm; 472 DMLabel ovAdjByRank; /* A DMLabel containing all points adjacent to shared points, separated by rank (value in label) */ 473 PetscSF sfPoint; 474 const PetscSFNode *remote; 475 const PetscInt *local; 476 const PetscInt *nrank, *rrank; 477 PetscInt *adj = NULL; 478 PetscInt pStart, pEnd, p, sStart, sEnd, nleaves, l; 479 PetscMPIInt rank, size; 480 PetscBool flg; 481 PetscErrorCode ierr; 482 483 PetscFunctionBegin; 484 *ovLabel = NULL; 485 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 486 ierr = MPI_Comm_size(comm, &size);CHKERRMPI(ierr); 487 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 488 if (size == 1) PetscFunctionReturn(0); 489 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 490 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 491 if (!levels) { 492 /* Add owned points */ 493 ierr = DMLabelCreate(PETSC_COMM_SELF, "Overlap label", ovLabel);CHKERRQ(ierr); 494 for (p = pStart; p < pEnd; ++p) {ierr = DMLabelSetValue(*ovLabel, p, rank);CHKERRQ(ierr);} 495 PetscFunctionReturn(0); 496 } 497 ierr = PetscSectionGetChart(leafSection, &sStart, &sEnd);CHKERRQ(ierr); 498 ierr = PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);CHKERRQ(ierr); 499 ierr = DMLabelCreate(PETSC_COMM_SELF, "Overlap adjacency", &ovAdjByRank);CHKERRQ(ierr); 500 /* Handle leaves: shared with the root point */ 501 for (l = 0; l < nleaves; ++l) { 502 PetscInt adjSize = PETSC_DETERMINE, a; 503 504 ierr = DMPlexGetAdjacency(dm, local ? local[l] : l, &adjSize, &adj);CHKERRQ(ierr); 505 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remote[l].rank);CHKERRQ(ierr);} 506 } 507 ierr = ISGetIndices(rootrank, &rrank);CHKERRQ(ierr); 508 ierr = ISGetIndices(leafrank, &nrank);CHKERRQ(ierr); 509 /* Handle roots */ 510 for (p = pStart; p < pEnd; ++p) { 511 PetscInt adjSize = PETSC_DETERMINE, neighbors = 0, noff, n, a; 512 513 if ((p >= sStart) && (p < sEnd)) { 514 /* Some leaves share a root with other leaves on different processes */ 515 ierr = PetscSectionGetDof(leafSection, p, &neighbors);CHKERRQ(ierr); 516 if (neighbors) { 517 ierr = PetscSectionGetOffset(leafSection, p, &noff);CHKERRQ(ierr); 518 ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj);CHKERRQ(ierr); 519 for (n = 0; n < neighbors; ++n) { 520 const PetscInt remoteRank = nrank[noff+n]; 521 522 if (remoteRank == rank) continue; 523 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);CHKERRQ(ierr);} 524 } 525 } 526 } 527 /* Roots are shared with leaves */ 528 ierr = PetscSectionGetDof(rootSection, p, &neighbors);CHKERRQ(ierr); 529 if (!neighbors) continue; 530 ierr = PetscSectionGetOffset(rootSection, p, &noff);CHKERRQ(ierr); 531 ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj);CHKERRQ(ierr); 532 for (n = 0; n < neighbors; ++n) { 533 const PetscInt remoteRank = rrank[noff+n]; 534 535 if (remoteRank == rank) continue; 536 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);CHKERRQ(ierr);} 537 } 538 } 539 ierr = PetscFree(adj);CHKERRQ(ierr); 540 ierr = ISRestoreIndices(rootrank, &rrank);CHKERRQ(ierr); 541 ierr = ISRestoreIndices(leafrank, &nrank);CHKERRQ(ierr); 542 /* Add additional overlap levels */ 543 for (l = 1; l < levels; l++) { 544 /* Propagate point donations over SF to capture remote connections */ 545 ierr = DMPlexPartitionLabelPropagate(dm, ovAdjByRank);CHKERRQ(ierr); 546 /* Add next level of point donations to the label */ 547 ierr = DMPlexPartitionLabelAdjacency(dm, ovAdjByRank);CHKERRQ(ierr); 548 } 549 /* We require the closure in the overlap */ 550 ierr = DMPlexPartitionLabelClosure(dm, ovAdjByRank);CHKERRQ(ierr); 551 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-overlap_view", &flg);CHKERRQ(ierr); 552 if (flg) { 553 PetscViewer viewer; 554 ierr = PetscViewerASCIIGetStdout(PetscObjectComm((PetscObject)dm), &viewer);CHKERRQ(ierr); 555 ierr = DMLabelView(ovAdjByRank, viewer);CHKERRQ(ierr); 556 } 557 /* Invert sender to receiver label */ 558 ierr = DMLabelCreate(PETSC_COMM_SELF, "Overlap label", ovLabel);CHKERRQ(ierr); 559 ierr = DMPlexPartitionLabelInvert(dm, ovAdjByRank, NULL, *ovLabel);CHKERRQ(ierr); 560 /* Add owned points, except for shared local points */ 561 for (p = pStart; p < pEnd; ++p) {ierr = DMLabelSetValue(*ovLabel, p, rank);CHKERRQ(ierr);} 562 for (l = 0; l < nleaves; ++l) { 563 ierr = DMLabelClearValue(*ovLabel, local[l], rank);CHKERRQ(ierr); 564 ierr = DMLabelSetValue(*ovLabel, remote[l].index, remote[l].rank);CHKERRQ(ierr); 565 } 566 /* Clean up */ 567 ierr = DMLabelDestroy(&ovAdjByRank);CHKERRQ(ierr); 568 PetscFunctionReturn(0); 569 } 570 571 /*@C 572 DMPlexCreateOverlapMigrationSF - Create an SF describing the new mesh distribution to make the overlap described by the input SF 573 574 Collective on dm 575 576 Input Parameters: 577 + dm - The DM 578 - overlapSF - The SF mapping ghost points in overlap to owner points on other processes 579 580 Output Parameter: 581 . migrationSF - An SF that maps original points in old locations to points in new locations 582 583 Level: developer 584 585 .seealso: DMPlexCreateOverlapLabel(), DMPlexDistributeOverlap(), DMPlexDistribute() 586 @*/ 587 PetscErrorCode DMPlexCreateOverlapMigrationSF(DM dm, PetscSF overlapSF, PetscSF *migrationSF) 588 { 589 MPI_Comm comm; 590 PetscMPIInt rank, size; 591 PetscInt d, dim, p, pStart, pEnd, nroots, nleaves, newLeaves, point, numSharedPoints; 592 PetscInt *pointDepths, *remoteDepths, *ilocal; 593 PetscInt *depthRecv, *depthShift, *depthIdx; 594 PetscSFNode *iremote; 595 PetscSF pointSF; 596 const PetscInt *sharedLocal; 597 const PetscSFNode *overlapRemote, *sharedRemote; 598 PetscErrorCode ierr; 599 600 PetscFunctionBegin; 601 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 602 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 603 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 604 ierr = MPI_Comm_size(comm, &size);CHKERRMPI(ierr); 605 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 606 607 /* Before building the migration SF we need to know the new stratum offsets */ 608 ierr = PetscSFGetGraph(overlapSF, &nroots, &nleaves, NULL, &overlapRemote);CHKERRQ(ierr); 609 ierr = PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);CHKERRQ(ierr); 610 for (d=0; d<dim+1; d++) { 611 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 612 for (p=pStart; p<pEnd; p++) pointDepths[p] = d; 613 } 614 for (p=0; p<nleaves; p++) remoteDepths[p] = -1; 615 ierr = PetscSFBcastBegin(overlapSF, MPIU_INT, pointDepths, remoteDepths,MPI_REPLACE);CHKERRQ(ierr); 616 ierr = PetscSFBcastEnd(overlapSF, MPIU_INT, pointDepths, remoteDepths,MPI_REPLACE);CHKERRQ(ierr); 617 618 /* Count received points in each stratum and compute the internal strata shift */ 619 ierr = PetscMalloc3(dim+1, &depthRecv, dim+1, &depthShift, dim+1, &depthIdx);CHKERRQ(ierr); 620 for (d=0; d<dim+1; d++) depthRecv[d]=0; 621 for (p=0; p<nleaves; p++) depthRecv[remoteDepths[p]]++; 622 depthShift[dim] = 0; 623 for (d=0; d<dim; d++) depthShift[d] = depthRecv[dim]; 624 for (d=1; d<dim; d++) depthShift[d] += depthRecv[0]; 625 for (d=dim-2; d>0; d--) depthShift[d] += depthRecv[d+1]; 626 for (d=0; d<dim+1; d++) { 627 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 628 depthIdx[d] = pStart + depthShift[d]; 629 } 630 631 /* Form the overlap SF build an SF that describes the full overlap migration SF */ 632 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 633 newLeaves = pEnd - pStart + nleaves; 634 ierr = PetscMalloc1(newLeaves, &ilocal);CHKERRQ(ierr); 635 ierr = PetscMalloc1(newLeaves, &iremote);CHKERRQ(ierr); 636 /* First map local points to themselves */ 637 for (d=0; d<dim+1; d++) { 638 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 639 for (p=pStart; p<pEnd; p++) { 640 point = p + depthShift[d]; 641 ilocal[point] = point; 642 iremote[point].index = p; 643 iremote[point].rank = rank; 644 depthIdx[d]++; 645 } 646 } 647 648 /* Add in the remote roots for currently shared points */ 649 ierr = DMGetPointSF(dm, &pointSF);CHKERRQ(ierr); 650 ierr = PetscSFGetGraph(pointSF, NULL, &numSharedPoints, &sharedLocal, &sharedRemote);CHKERRQ(ierr); 651 for (d=0; d<dim+1; d++) { 652 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 653 for (p=0; p<numSharedPoints; p++) { 654 if (pStart <= sharedLocal[p] && sharedLocal[p] < pEnd) { 655 point = sharedLocal[p] + depthShift[d]; 656 iremote[point].index = sharedRemote[p].index; 657 iremote[point].rank = sharedRemote[p].rank; 658 } 659 } 660 } 661 662 /* Now add the incoming overlap points */ 663 for (p=0; p<nleaves; p++) { 664 point = depthIdx[remoteDepths[p]]; 665 ilocal[point] = point; 666 iremote[point].index = overlapRemote[p].index; 667 iremote[point].rank = overlapRemote[p].rank; 668 depthIdx[remoteDepths[p]]++; 669 } 670 ierr = PetscFree2(pointDepths,remoteDepths);CHKERRQ(ierr); 671 672 ierr = PetscSFCreate(comm, migrationSF);CHKERRQ(ierr); 673 ierr = PetscObjectSetName((PetscObject) *migrationSF, "Overlap Migration SF");CHKERRQ(ierr); 674 ierr = PetscSFSetFromOptions(*migrationSF);CHKERRQ(ierr); 675 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 676 ierr = PetscSFSetGraph(*migrationSF, pEnd-pStart, newLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);CHKERRQ(ierr); 677 678 ierr = PetscFree3(depthRecv, depthShift, depthIdx);CHKERRQ(ierr); 679 PetscFunctionReturn(0); 680 } 681 682 /*@ 683 DMPlexStratifyMigrationSF - Rearrange the leaves of a migration sf for stratification. 684 685 Input Parameters: 686 + dm - The DM 687 - sf - A star forest with non-ordered leaves, usually defining a DM point migration 688 689 Output Parameter: 690 . migrationSF - A star forest with added leaf indirection that ensures the resulting DM is stratified 691 692 Note: 693 This lexicographically sorts by (depth, cellType) 694 695 Level: developer 696 697 .seealso: DMPlexPartitionLabelCreateSF(), DMPlexDistribute(), DMPlexDistributeOverlap() 698 @*/ 699 PetscErrorCode DMPlexStratifyMigrationSF(DM dm, PetscSF sf, PetscSF *migrationSF) 700 { 701 MPI_Comm comm; 702 PetscMPIInt rank, size; 703 PetscInt d, ldepth, depth, dim, p, pStart, pEnd, nroots, nleaves; 704 PetscSFNode *pointDepths, *remoteDepths; 705 PetscInt *ilocal; 706 PetscInt *depthRecv, *depthShift, *depthIdx; 707 PetscInt *ctRecv, *ctShift, *ctIdx; 708 const PetscSFNode *iremote; 709 PetscErrorCode ierr; 710 711 PetscFunctionBegin; 712 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 713 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 714 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 715 ierr = MPI_Comm_size(comm, &size);CHKERRMPI(ierr); 716 ierr = DMPlexGetDepth(dm, &ldepth);CHKERRQ(ierr); 717 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 718 ierr = MPIU_Allreduce(&ldepth, &depth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 719 if ((ldepth >= 0) && (depth != ldepth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", ldepth, depth); 720 ierr = PetscLogEventBegin(DMPLEX_PartStratSF,dm,0,0,0);CHKERRQ(ierr); 721 722 /* Before building the migration SF we need to know the new stratum offsets */ 723 ierr = PetscSFGetGraph(sf, &nroots, &nleaves, NULL, &iremote);CHKERRQ(ierr); 724 ierr = PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);CHKERRQ(ierr); 725 for (d = 0; d < depth+1; ++d) { 726 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 727 for (p = pStart; p < pEnd; ++p) { 728 DMPolytopeType ct; 729 730 ierr = DMPlexGetCellType(dm, p, &ct);CHKERRQ(ierr); 731 pointDepths[p].index = d; 732 pointDepths[p].rank = ct; 733 } 734 } 735 for (p = 0; p < nleaves; ++p) {remoteDepths[p].index = -1; remoteDepths[p].rank = -1;} 736 ierr = PetscSFBcastBegin(sf, MPIU_2INT, pointDepths, remoteDepths,MPI_REPLACE);CHKERRQ(ierr); 737 ierr = PetscSFBcastEnd(sf, MPIU_2INT, pointDepths, remoteDepths,MPI_REPLACE);CHKERRQ(ierr); 738 /* Count received points in each stratum and compute the internal strata shift */ 739 ierr = PetscCalloc6(depth+1, &depthRecv, depth+1, &depthShift, depth+1, &depthIdx, DM_NUM_POLYTOPES, &ctRecv, DM_NUM_POLYTOPES, &ctShift, DM_NUM_POLYTOPES, &ctIdx);CHKERRQ(ierr); 740 for (p = 0; p < nleaves; ++p) { 741 if (remoteDepths[p].rank < 0) { 742 ++depthRecv[remoteDepths[p].index]; 743 } else { 744 ++ctRecv[remoteDepths[p].rank]; 745 } 746 } 747 { 748 PetscInt depths[4], dims[4], shift = 0, i, c; 749 750 /* Cells (depth), Vertices (0), Faces (depth-1), Edges (1) 751 Consider DM_POLYTOPE_FV_GHOST and DM_POLYTOPE_INTERIOR_GHOST as cells 752 */ 753 depths[0] = depth; depths[1] = 0; depths[2] = depth-1; depths[3] = 1; 754 dims[0] = dim; dims[1] = 0; dims[2] = dim-1; dims[3] = 1; 755 for (i = 0; i <= depth; ++i) { 756 const PetscInt dep = depths[i]; 757 const PetscInt dim = dims[i]; 758 759 for (c = 0; c < DM_NUM_POLYTOPES; ++c) { 760 if (DMPolytopeTypeGetDim((DMPolytopeType) c) != dim && !(i == 0 && (c == DM_POLYTOPE_FV_GHOST || c == DM_POLYTOPE_INTERIOR_GHOST))) continue; 761 ctShift[c] = shift; 762 shift += ctRecv[c]; 763 } 764 depthShift[dep] = shift; 765 shift += depthRecv[dep]; 766 } 767 for (c = 0; c < DM_NUM_POLYTOPES; ++c) { 768 const PetscInt ctDim = DMPolytopeTypeGetDim((DMPolytopeType) c); 769 770 if ((ctDim < 0 || ctDim > dim) && (c != DM_POLYTOPE_FV_GHOST && c != DM_POLYTOPE_INTERIOR_GHOST)) { 771 ctShift[c] = shift; 772 shift += ctRecv[c]; 773 } 774 } 775 } 776 /* Derive a new local permutation based on stratified indices */ 777 ierr = PetscMalloc1(nleaves, &ilocal);CHKERRQ(ierr); 778 for (p = 0; p < nleaves; ++p) { 779 const PetscInt dep = remoteDepths[p].index; 780 const DMPolytopeType ct = (DMPolytopeType) remoteDepths[p].rank; 781 782 if ((PetscInt) ct < 0) { 783 ilocal[p] = depthShift[dep] + depthIdx[dep]; 784 ++depthIdx[dep]; 785 } else { 786 ilocal[p] = ctShift[ct] + ctIdx[ct]; 787 ++ctIdx[ct]; 788 } 789 } 790 ierr = PetscSFCreate(comm, migrationSF);CHKERRQ(ierr); 791 ierr = PetscObjectSetName((PetscObject) *migrationSF, "Migration SF");CHKERRQ(ierr); 792 ierr = PetscSFSetGraph(*migrationSF, nroots, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_COPY_VALUES);CHKERRQ(ierr); 793 ierr = PetscFree2(pointDepths,remoteDepths);CHKERRQ(ierr); 794 ierr = PetscFree6(depthRecv, depthShift, depthIdx, ctRecv, ctShift, ctIdx);CHKERRQ(ierr); 795 ierr = PetscLogEventEnd(DMPLEX_PartStratSF,dm,0,0,0);CHKERRQ(ierr); 796 PetscFunctionReturn(0); 797 } 798 799 /*@ 800 DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 801 802 Collective on dm 803 804 Input Parameters: 805 + dm - The DMPlex object 806 . pointSF - The PetscSF describing the communication pattern 807 . originalSection - The PetscSection for existing data layout 808 - originalVec - The existing data in a local vector 809 810 Output Parameters: 811 + newSection - The PetscSF describing the new data layout 812 - newVec - The new data in a local vector 813 814 Level: developer 815 816 .seealso: DMPlexDistribute(), DMPlexDistributeFieldIS(), DMPlexDistributeData() 817 @*/ 818 PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec) 819 { 820 PetscSF fieldSF; 821 PetscInt *remoteOffsets, fieldSize; 822 PetscScalar *originalValues, *newValues; 823 PetscErrorCode ierr; 824 825 PetscFunctionBegin; 826 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 827 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 828 829 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 830 ierr = VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);CHKERRQ(ierr); 831 ierr = VecSetType(newVec,dm->vectype);CHKERRQ(ierr); 832 833 ierr = VecGetArray(originalVec, &originalValues);CHKERRQ(ierr); 834 ierr = VecGetArray(newVec, &newValues);CHKERRQ(ierr); 835 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 836 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 837 ierr = PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues,MPI_REPLACE);CHKERRQ(ierr); 838 ierr = PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues,MPI_REPLACE);CHKERRQ(ierr); 839 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 840 ierr = VecRestoreArray(newVec, &newValues);CHKERRQ(ierr); 841 ierr = VecRestoreArray(originalVec, &originalValues);CHKERRQ(ierr); 842 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 843 PetscFunctionReturn(0); 844 } 845 846 /*@ 847 DMPlexDistributeFieldIS - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 848 849 Collective on dm 850 851 Input Parameters: 852 + dm - The DMPlex object 853 . pointSF - The PetscSF describing the communication pattern 854 . originalSection - The PetscSection for existing data layout 855 - originalIS - The existing data 856 857 Output Parameters: 858 + newSection - The PetscSF describing the new data layout 859 - newIS - The new data 860 861 Level: developer 862 863 .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexDistributeData() 864 @*/ 865 PetscErrorCode DMPlexDistributeFieldIS(DM dm, PetscSF pointSF, PetscSection originalSection, IS originalIS, PetscSection newSection, IS *newIS) 866 { 867 PetscSF fieldSF; 868 PetscInt *newValues, *remoteOffsets, fieldSize; 869 const PetscInt *originalValues; 870 PetscErrorCode ierr; 871 872 PetscFunctionBegin; 873 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 874 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 875 876 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 877 ierr = PetscMalloc1(fieldSize, &newValues);CHKERRQ(ierr); 878 879 ierr = ISGetIndices(originalIS, &originalValues);CHKERRQ(ierr); 880 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 881 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 882 ierr = PetscSFBcastBegin(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues,MPI_REPLACE);CHKERRQ(ierr); 883 ierr = PetscSFBcastEnd(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues,MPI_REPLACE);CHKERRQ(ierr); 884 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 885 ierr = ISRestoreIndices(originalIS, &originalValues);CHKERRQ(ierr); 886 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) pointSF), fieldSize, newValues, PETSC_OWN_POINTER, newIS);CHKERRQ(ierr); 887 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 888 PetscFunctionReturn(0); 889 } 890 891 /*@ 892 DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 893 894 Collective on dm 895 896 Input Parameters: 897 + dm - The DMPlex object 898 . pointSF - The PetscSF describing the communication pattern 899 . originalSection - The PetscSection for existing data layout 900 . datatype - The type of data 901 - originalData - The existing data 902 903 Output Parameters: 904 + newSection - The PetscSection describing the new data layout 905 - newData - The new data 906 907 Level: developer 908 909 .seealso: DMPlexDistribute(), DMPlexDistributeField() 910 @*/ 911 PetscErrorCode DMPlexDistributeData(DM dm, PetscSF pointSF, PetscSection originalSection, MPI_Datatype datatype, void *originalData, PetscSection newSection, void **newData) 912 { 913 PetscSF fieldSF; 914 PetscInt *remoteOffsets, fieldSize; 915 PetscMPIInt dataSize; 916 PetscErrorCode ierr; 917 918 PetscFunctionBegin; 919 ierr = PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 920 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 921 922 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 923 ierr = MPI_Type_size(datatype, &dataSize);CHKERRMPI(ierr); 924 ierr = PetscMalloc(fieldSize * dataSize, newData);CHKERRQ(ierr); 925 926 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 927 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 928 ierr = PetscSFBcastBegin(fieldSF, datatype, originalData, *newData,MPI_REPLACE);CHKERRQ(ierr); 929 ierr = PetscSFBcastEnd(fieldSF, datatype, originalData, *newData,MPI_REPLACE);CHKERRQ(ierr); 930 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 931 ierr = PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 932 PetscFunctionReturn(0); 933 } 934 935 static PetscErrorCode DMPlexDistributeCones(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel) 936 { 937 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 938 MPI_Comm comm; 939 PetscSF coneSF; 940 PetscSection originalConeSection, newConeSection; 941 PetscInt *remoteOffsets, *cones, *globCones, *newCones, newConesSize; 942 PetscBool flg; 943 PetscErrorCode ierr; 944 945 PetscFunctionBegin; 946 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 947 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 5); 948 ierr = PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 949 /* Distribute cone section */ 950 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 951 ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr); 952 ierr = DMPlexGetConeSection(dmParallel, &newConeSection);CHKERRQ(ierr); 953 ierr = PetscSFDistributeSection(migrationSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr); 954 ierr = DMSetUp(dmParallel);CHKERRQ(ierr); 955 { 956 PetscInt pStart, pEnd, p; 957 958 ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr); 959 for (p = pStart; p < pEnd; ++p) { 960 PetscInt coneSize; 961 ierr = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr); 962 pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize); 963 } 964 } 965 /* Communicate and renumber cones */ 966 ierr = PetscSFCreateSectionSF(migrationSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr); 967 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 968 ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); 969 if (original) { 970 PetscInt numCones; 971 972 ierr = PetscSectionGetStorageSize(originalConeSection,&numCones);CHKERRQ(ierr); 973 ierr = PetscMalloc1(numCones,&globCones);CHKERRQ(ierr); 974 ierr = ISLocalToGlobalMappingApplyBlock(original, numCones, cones, globCones);CHKERRQ(ierr); 975 } else { 976 globCones = cones; 977 } 978 ierr = DMPlexGetCones(dmParallel, &newCones);CHKERRQ(ierr); 979 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, globCones, newCones,MPI_REPLACE);CHKERRQ(ierr); 980 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, globCones, newCones,MPI_REPLACE);CHKERRQ(ierr); 981 if (original) { 982 ierr = PetscFree(globCones);CHKERRQ(ierr); 983 } 984 ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr); 985 ierr = ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);CHKERRQ(ierr); 986 if (PetscDefined(USE_DEBUG)) { 987 PetscInt p; 988 PetscBool valid = PETSC_TRUE; 989 for (p = 0; p < newConesSize; ++p) { 990 if (newCones[p] < 0) {valid = PETSC_FALSE; ierr = PetscPrintf(PETSC_COMM_SELF, "[%d] Point %D not in overlap SF\n", PetscGlobalRank,p);CHKERRQ(ierr);} 991 } 992 if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map"); 993 } 994 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr); 995 if (flg) { 996 ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr); 997 ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 998 ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr); 999 ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1000 ierr = PetscSFView(coneSF, NULL);CHKERRQ(ierr); 1001 } 1002 ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr); 1003 ierr = DMPlexGetConeOrientations(dmParallel, &newCones);CHKERRQ(ierr); 1004 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones,MPI_REPLACE);CHKERRQ(ierr); 1005 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones,MPI_REPLACE);CHKERRQ(ierr); 1006 ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr); 1007 ierr = PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 1008 /* Create supports and stratify DMPlex */ 1009 { 1010 PetscInt pStart, pEnd; 1011 1012 ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 1013 ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr); 1014 } 1015 ierr = DMPlexSymmetrize(dmParallel);CHKERRQ(ierr); 1016 ierr = DMPlexStratify(dmParallel);CHKERRQ(ierr); 1017 { 1018 PetscBool useCone, useClosure, useAnchors; 1019 1020 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 1021 ierr = DMSetBasicAdjacency(dmParallel, useCone, useClosure);CHKERRQ(ierr); 1022 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 1023 ierr = DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);CHKERRQ(ierr); 1024 } 1025 PetscFunctionReturn(0); 1026 } 1027 1028 static PetscErrorCode DMPlexDistributeCoordinates(DM dm, PetscSF migrationSF, DM dmParallel) 1029 { 1030 MPI_Comm comm; 1031 PetscSection originalCoordSection, newCoordSection; 1032 Vec originalCoordinates, newCoordinates; 1033 PetscInt bs; 1034 PetscBool isper; 1035 const char *name; 1036 const PetscReal *maxCell, *L; 1037 const DMBoundaryType *bd; 1038 PetscErrorCode ierr; 1039 1040 PetscFunctionBegin; 1041 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1042 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1043 1044 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1045 ierr = DMGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr); 1046 ierr = DMGetCoordinateSection(dmParallel, &newCoordSection);CHKERRQ(ierr); 1047 ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr); 1048 if (originalCoordinates) { 1049 ierr = VecCreate(PETSC_COMM_SELF, &newCoordinates);CHKERRQ(ierr); 1050 ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr); 1051 ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr); 1052 1053 ierr = DMPlexDistributeField(dm, migrationSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr); 1054 ierr = DMSetCoordinatesLocal(dmParallel, newCoordinates);CHKERRQ(ierr); 1055 ierr = VecGetBlockSize(originalCoordinates, &bs);CHKERRQ(ierr); 1056 ierr = VecSetBlockSize(newCoordinates, bs);CHKERRQ(ierr); 1057 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 1058 } 1059 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 1060 ierr = DMSetPeriodicity(dmParallel, isper, maxCell, L, bd);CHKERRQ(ierr); 1061 PetscFunctionReturn(0); 1062 } 1063 1064 static PetscErrorCode DMPlexDistributeLabels(DM dm, PetscSF migrationSF, DM dmParallel) 1065 { 1066 DM_Plex *mesh = (DM_Plex*) dm->data; 1067 MPI_Comm comm; 1068 DMLabel depthLabel; 1069 PetscMPIInt rank; 1070 PetscInt depth, d, numLabels, numLocalLabels, l; 1071 PetscBool hasLabels = PETSC_FALSE, lsendDepth, sendDepth; 1072 PetscObjectState depthState = -1; 1073 PetscErrorCode ierr; 1074 1075 PetscFunctionBegin; 1076 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1077 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1078 1079 ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1080 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1081 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 1082 1083 /* If the user has changed the depth label, communicate it instead */ 1084 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1085 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1086 if (depthLabel) {ierr = PetscObjectStateGet((PetscObject) depthLabel, &depthState);CHKERRQ(ierr);} 1087 lsendDepth = mesh->depthState != depthState ? PETSC_TRUE : PETSC_FALSE; 1088 ierr = MPIU_Allreduce(&lsendDepth, &sendDepth, 1, MPIU_BOOL, MPI_LOR, comm);CHKERRQ(ierr); 1089 if (sendDepth) { 1090 ierr = DMPlexGetDepthLabel(dmParallel, &dmParallel->depthLabel);CHKERRQ(ierr); 1091 ierr = DMRemoveLabelBySelf(dmParallel, &dmParallel->depthLabel, PETSC_FALSE);CHKERRQ(ierr); 1092 } 1093 /* Everyone must have either the same number of labels, or none */ 1094 ierr = DMGetNumLabels(dm, &numLocalLabels);CHKERRQ(ierr); 1095 numLabels = numLocalLabels; 1096 ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRMPI(ierr); 1097 if (numLabels == numLocalLabels) hasLabels = PETSC_TRUE; 1098 for (l = 0; l < numLabels; ++l) { 1099 DMLabel label = NULL, labelNew = NULL; 1100 PetscBool isDepth, lisOutput = PETSC_TRUE, isOutput; 1101 const char *name = NULL; 1102 1103 if (hasLabels) { 1104 ierr = DMGetLabelByNum(dm, l, &label);CHKERRQ(ierr); 1105 /* Skip "depth" because it is recreated */ 1106 ierr = PetscObjectGetName((PetscObject) label, &name);CHKERRQ(ierr); 1107 ierr = PetscStrcmp(name, "depth", &isDepth);CHKERRQ(ierr); 1108 } 1109 ierr = MPI_Bcast(&isDepth, 1, MPIU_BOOL, 0, comm);CHKERRMPI(ierr); 1110 if (isDepth && !sendDepth) continue; 1111 ierr = DMLabelDistribute(label, migrationSF, &labelNew);CHKERRQ(ierr); 1112 if (isDepth) { 1113 /* Put in any missing strata which can occur if users are managing the depth label themselves */ 1114 PetscInt gdepth; 1115 1116 ierr = MPIU_Allreduce(&depth, &gdepth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 1117 if ((depth >= 0) && (gdepth != depth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", depth, gdepth); 1118 for (d = 0; d <= gdepth; ++d) { 1119 PetscBool has; 1120 1121 ierr = DMLabelHasStratum(labelNew, d, &has);CHKERRQ(ierr); 1122 if (!has) {ierr = DMLabelAddStratum(labelNew, d);CHKERRQ(ierr);} 1123 } 1124 } 1125 ierr = DMAddLabel(dmParallel, labelNew);CHKERRQ(ierr); 1126 /* Put the output flag in the new label */ 1127 if (hasLabels) {ierr = DMGetLabelOutput(dm, name, &lisOutput);CHKERRQ(ierr);} 1128 ierr = MPIU_Allreduce(&lisOutput, &isOutput, 1, MPIU_BOOL, MPI_LAND, comm);CHKERRQ(ierr); 1129 ierr = PetscObjectGetName((PetscObject) labelNew, &name);CHKERRQ(ierr); 1130 ierr = DMSetLabelOutput(dmParallel, name, isOutput);CHKERRQ(ierr); 1131 ierr = DMLabelDestroy(&labelNew);CHKERRQ(ierr); 1132 } 1133 ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1134 PetscFunctionReturn(0); 1135 } 1136 1137 static PetscErrorCode DMPlexDistributeSetupTree(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel) 1138 { 1139 DM_Plex *mesh = (DM_Plex*) dm->data; 1140 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1141 MPI_Comm comm; 1142 DM refTree; 1143 PetscSection origParentSection, newParentSection; 1144 PetscInt *origParents, *origChildIDs; 1145 PetscBool flg; 1146 PetscErrorCode ierr; 1147 1148 PetscFunctionBegin; 1149 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1150 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 5); 1151 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1152 1153 /* Set up tree */ 1154 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 1155 ierr = DMPlexSetReferenceTree(dmParallel,refTree);CHKERRQ(ierr); 1156 ierr = DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);CHKERRQ(ierr); 1157 if (origParentSection) { 1158 PetscInt pStart, pEnd; 1159 PetscInt *newParents, *newChildIDs, *globParents; 1160 PetscInt *remoteOffsetsParents, newParentSize; 1161 PetscSF parentSF; 1162 1163 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1164 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dmParallel),&newParentSection);CHKERRQ(ierr); 1165 ierr = PetscSectionSetChart(newParentSection,pStart,pEnd);CHKERRQ(ierr); 1166 ierr = PetscSFDistributeSection(migrationSF, origParentSection, &remoteOffsetsParents, newParentSection);CHKERRQ(ierr); 1167 ierr = PetscSFCreateSectionSF(migrationSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);CHKERRQ(ierr); 1168 ierr = PetscFree(remoteOffsetsParents);CHKERRQ(ierr); 1169 ierr = PetscSectionGetStorageSize(newParentSection,&newParentSize);CHKERRQ(ierr); 1170 ierr = PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);CHKERRQ(ierr); 1171 if (original) { 1172 PetscInt numParents; 1173 1174 ierr = PetscSectionGetStorageSize(origParentSection,&numParents);CHKERRQ(ierr); 1175 ierr = PetscMalloc1(numParents,&globParents);CHKERRQ(ierr); 1176 ierr = ISLocalToGlobalMappingApplyBlock(original, numParents, origParents, globParents);CHKERRQ(ierr); 1177 } 1178 else { 1179 globParents = origParents; 1180 } 1181 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, globParents, newParents,MPI_REPLACE);CHKERRQ(ierr); 1182 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, globParents, newParents,MPI_REPLACE);CHKERRQ(ierr); 1183 if (original) { 1184 ierr = PetscFree(globParents);CHKERRQ(ierr); 1185 } 1186 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs,MPI_REPLACE);CHKERRQ(ierr); 1187 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs,MPI_REPLACE);CHKERRQ(ierr); 1188 ierr = ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);CHKERRQ(ierr); 1189 if (PetscDefined(USE_DEBUG)) { 1190 PetscInt p; 1191 PetscBool valid = PETSC_TRUE; 1192 for (p = 0; p < newParentSize; ++p) { 1193 if (newParents[p] < 0) {valid = PETSC_FALSE; ierr = PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);CHKERRQ(ierr);} 1194 } 1195 if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map"); 1196 } 1197 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-parents_view", &flg);CHKERRQ(ierr); 1198 if (flg) { 1199 ierr = PetscPrintf(comm, "Serial Parent Section: \n");CHKERRQ(ierr); 1200 ierr = PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1201 ierr = PetscPrintf(comm, "Parallel Parent Section: \n");CHKERRQ(ierr); 1202 ierr = PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1203 ierr = PetscSFView(parentSF, NULL);CHKERRQ(ierr); 1204 } 1205 ierr = DMPlexSetTree(dmParallel,newParentSection,newParents,newChildIDs);CHKERRQ(ierr); 1206 ierr = PetscSectionDestroy(&newParentSection);CHKERRQ(ierr); 1207 ierr = PetscFree2(newParents,newChildIDs);CHKERRQ(ierr); 1208 ierr = PetscSFDestroy(&parentSF);CHKERRQ(ierr); 1209 } 1210 pmesh->useAnchors = mesh->useAnchors; 1211 PetscFunctionReturn(0); 1212 } 1213 1214 PETSC_UNUSED static PetscErrorCode DMPlexDistributeSF(DM dm, PetscSF migrationSF, DM dmParallel) 1215 { 1216 PetscMPIInt rank, size; 1217 MPI_Comm comm; 1218 PetscErrorCode ierr; 1219 1220 PetscFunctionBegin; 1221 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1222 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1223 1224 /* Create point SF for parallel mesh */ 1225 ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1226 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1227 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 1228 ierr = MPI_Comm_size(comm, &size);CHKERRMPI(ierr); 1229 { 1230 const PetscInt *leaves; 1231 PetscSFNode *remotePoints, *rowners, *lowners; 1232 PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints; 1233 PetscInt pStart, pEnd; 1234 1235 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1236 ierr = PetscSFGetGraph(migrationSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr); 1237 ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr); 1238 for (p=0; p<numRoots; p++) { 1239 rowners[p].rank = -1; 1240 rowners[p].index = -1; 1241 } 1242 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners,MPI_REPLACE);CHKERRQ(ierr); 1243 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners,MPI_REPLACE);CHKERRQ(ierr); 1244 for (p = 0; p < numLeaves; ++p) { 1245 if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */ 1246 lowners[p].rank = rank; 1247 lowners[p].index = leaves ? leaves[p] : p; 1248 } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */ 1249 lowners[p].rank = -2; 1250 lowners[p].index = -2; 1251 } 1252 } 1253 for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */ 1254 rowners[p].rank = -3; 1255 rowners[p].index = -3; 1256 } 1257 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1258 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1259 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners,MPI_REPLACE);CHKERRQ(ierr); 1260 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners,MPI_REPLACE);CHKERRQ(ierr); 1261 for (p = 0; p < numLeaves; ++p) { 1262 if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed"); 1263 if (lowners[p].rank != rank) ++numGhostPoints; 1264 } 1265 ierr = PetscMalloc1(numGhostPoints, &ghostPoints);CHKERRQ(ierr); 1266 ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr); 1267 for (p = 0, gp = 0; p < numLeaves; ++p) { 1268 if (lowners[p].rank != rank) { 1269 ghostPoints[gp] = leaves ? leaves[p] : p; 1270 remotePoints[gp].rank = lowners[p].rank; 1271 remotePoints[gp].index = lowners[p].index; 1272 ++gp; 1273 } 1274 } 1275 ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr); 1276 ierr = PetscSFSetGraph((dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 1277 ierr = PetscSFSetFromOptions((dmParallel)->sf);CHKERRQ(ierr); 1278 } 1279 { 1280 PetscBool useCone, useClosure, useAnchors; 1281 1282 ierr = DMGetBasicAdjacency(dm, &useCone, &useClosure);CHKERRQ(ierr); 1283 ierr = DMSetBasicAdjacency(dmParallel, useCone, useClosure);CHKERRQ(ierr); 1284 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 1285 ierr = DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);CHKERRQ(ierr); 1286 } 1287 ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1288 PetscFunctionReturn(0); 1289 } 1290 1291 /*@ 1292 DMPlexSetPartitionBalance - Should distribution of the DM attempt to balance the shared point partition? 1293 1294 Input Parameters: 1295 + dm - The DMPlex object 1296 - flg - Balance the partition? 1297 1298 Level: intermediate 1299 1300 .seealso: DMPlexDistribute(), DMPlexGetPartitionBalance() 1301 @*/ 1302 PetscErrorCode DMPlexSetPartitionBalance(DM dm, PetscBool flg) 1303 { 1304 DM_Plex *mesh = (DM_Plex *)dm->data; 1305 1306 PetscFunctionBegin; 1307 mesh->partitionBalance = flg; 1308 PetscFunctionReturn(0); 1309 } 1310 1311 /*@ 1312 DMPlexGetPartitionBalance - Does distribution of the DM attempt to balance the shared point partition? 1313 1314 Input Parameter: 1315 . dm - The DMPlex object 1316 1317 Output Parameter: 1318 . flg - Balance the partition? 1319 1320 Level: intermediate 1321 1322 .seealso: DMPlexDistribute(), DMPlexSetPartitionBalance() 1323 @*/ 1324 PetscErrorCode DMPlexGetPartitionBalance(DM dm, PetscBool *flg) 1325 { 1326 DM_Plex *mesh = (DM_Plex *)dm->data; 1327 1328 PetscFunctionBegin; 1329 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1330 PetscValidBoolPointer(flg, 2); 1331 *flg = mesh->partitionBalance; 1332 PetscFunctionReturn(0); 1333 } 1334 1335 typedef struct { 1336 PetscInt vote, rank, index; 1337 } Petsc3Int; 1338 1339 /* MaxLoc, but carry a third piece of information around */ 1340 static void MPIAPI MaxLocCarry(void *in_, void *inout_, PetscMPIInt *len_, MPI_Datatype *dtype) 1341 { 1342 Petsc3Int *a = (Petsc3Int *)inout_; 1343 Petsc3Int *b = (Petsc3Int *)in_; 1344 PetscInt i, len = *len_; 1345 for (i = 0; i < len; i++) { 1346 if (a[i].vote < b[i].vote) { 1347 a[i].vote = b[i].vote; 1348 a[i].rank = b[i].rank; 1349 a[i].index = b[i].index; 1350 } else if (a[i].vote <= b[i].vote) { 1351 if (a[i].rank >= b[i].rank) { 1352 a[i].rank = b[i].rank; 1353 a[i].index = b[i].index; 1354 } 1355 } 1356 } 1357 } 1358 1359 /*@C 1360 DMPlexCreatePointSF - Build a point SF from an SF describing a point migration 1361 1362 Input Parameters: 1363 + dm - The source DMPlex object 1364 . migrationSF - The star forest that describes the parallel point remapping 1365 . ownership - Flag causing a vote to determine point ownership 1366 1367 Output Parameter: 1368 - pointSF - The star forest describing the point overlap in the remapped DM 1369 1370 Notes: 1371 Output pointSF is guaranteed to have the array of local indices (leaves) sorted. 1372 1373 Level: developer 1374 1375 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1376 @*/ 1377 PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF) 1378 { 1379 PetscMPIInt rank, size; 1380 PetscInt p, nroots, nleaves, idx, npointLeaves; 1381 PetscInt *pointLocal; 1382 const PetscInt *leaves; 1383 const PetscSFNode *roots; 1384 PetscSFNode *rootNodes, *leafNodes, *pointRemote; 1385 Vec shifts; 1386 const PetscInt numShifts = 13759; 1387 const PetscScalar *shift = NULL; 1388 const PetscBool shiftDebug = PETSC_FALSE; 1389 PetscBool balance; 1390 PetscErrorCode ierr; 1391 1392 PetscFunctionBegin; 1393 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1394 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRMPI(ierr); 1395 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRMPI(ierr); 1396 ierr = PetscLogEventBegin(DMPLEX_CreatePointSF,dm,0,0,0);CHKERRQ(ierr); 1397 1398 ierr = DMPlexGetPartitionBalance(dm, &balance);CHKERRQ(ierr); 1399 ierr = PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);CHKERRQ(ierr); 1400 ierr = PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);CHKERRQ(ierr); 1401 if (ownership) { 1402 MPI_Op op; 1403 MPI_Datatype datatype; 1404 Petsc3Int *rootVote = NULL, *leafVote = NULL; 1405 /* If balancing, we compute a random cyclic shift of the rank for each remote point. That way, the max will evenly distribute among ranks. */ 1406 if (balance) { 1407 PetscRandom r; 1408 1409 ierr = PetscRandomCreate(PETSC_COMM_SELF, &r);CHKERRQ(ierr); 1410 ierr = PetscRandomSetInterval(r, 0, 2467*size);CHKERRQ(ierr); 1411 ierr = VecCreate(PETSC_COMM_SELF, &shifts);CHKERRQ(ierr); 1412 ierr = VecSetSizes(shifts, numShifts, numShifts);CHKERRQ(ierr); 1413 ierr = VecSetType(shifts, VECSTANDARD);CHKERRQ(ierr); 1414 ierr = VecSetRandom(shifts, r);CHKERRQ(ierr); 1415 ierr = PetscRandomDestroy(&r);CHKERRQ(ierr); 1416 ierr = VecGetArrayRead(shifts, &shift);CHKERRQ(ierr); 1417 } 1418 1419 ierr = PetscMalloc1(nroots, &rootVote);CHKERRQ(ierr); 1420 ierr = PetscMalloc1(nleaves, &leafVote);CHKERRQ(ierr); 1421 /* Point ownership vote: Process with highest rank owns shared points */ 1422 for (p = 0; p < nleaves; ++p) { 1423 if (shiftDebug) { 1424 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); 1425 } 1426 /* Either put in a bid or we know we own it */ 1427 leafVote[p].vote = (rank + (shift ? (PetscInt) PetscRealPart(shift[roots[p].index%numShifts]) : 0))%size; 1428 leafVote[p].rank = rank; 1429 leafVote[p].index = p; 1430 } 1431 for (p = 0; p < nroots; p++) { 1432 /* Root must not participate in the reduction, flag so that MAXLOC does not use */ 1433 rootVote[p].vote = -3; 1434 rootVote[p].rank = -3; 1435 rootVote[p].index = -3; 1436 } 1437 ierr = MPI_Type_contiguous(3, MPIU_INT, &datatype);CHKERRMPI(ierr); 1438 ierr = MPI_Type_commit(&datatype);CHKERRMPI(ierr); 1439 ierr = MPI_Op_create(&MaxLocCarry, 1, &op);CHKERRMPI(ierr); 1440 ierr = PetscSFReduceBegin(migrationSF, datatype, leafVote, rootVote, op);CHKERRQ(ierr); 1441 ierr = PetscSFReduceEnd(migrationSF, datatype, leafVote, rootVote, op);CHKERRQ(ierr); 1442 ierr = MPI_Op_free(&op);CHKERRMPI(ierr); 1443 ierr = MPI_Type_free(&datatype);CHKERRMPI(ierr); 1444 for (p = 0; p < nroots; p++) { 1445 rootNodes[p].rank = rootVote[p].rank; 1446 rootNodes[p].index = rootVote[p].index; 1447 } 1448 ierr = PetscFree(leafVote);CHKERRQ(ierr); 1449 ierr = PetscFree(rootVote);CHKERRQ(ierr); 1450 } else { 1451 for (p = 0; p < nroots; p++) { 1452 rootNodes[p].index = -1; 1453 rootNodes[p].rank = rank; 1454 } 1455 for (p = 0; p < nleaves; p++) { 1456 /* Write new local id into old location */ 1457 if (roots[p].rank == rank) { 1458 rootNodes[roots[p].index].index = leaves ? leaves[p] : p; 1459 } 1460 } 1461 } 1462 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes,MPI_REPLACE);CHKERRQ(ierr); 1463 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes,MPI_REPLACE);CHKERRQ(ierr); 1464 1465 for (npointLeaves = 0, p = 0; p < nleaves; p++) { 1466 if (leafNodes[p].rank != rank) npointLeaves++; 1467 } 1468 ierr = PetscMalloc1(npointLeaves, &pointLocal);CHKERRQ(ierr); 1469 ierr = PetscMalloc1(npointLeaves, &pointRemote);CHKERRQ(ierr); 1470 for (idx = 0, p = 0; p < nleaves; p++) { 1471 if (leafNodes[p].rank != rank) { 1472 /* Note that pointLocal is automatically sorted as it is sublist of 0, ..., nleaves-1 */ 1473 pointLocal[idx] = p; 1474 pointRemote[idx] = leafNodes[p]; 1475 idx++; 1476 } 1477 } 1478 if (shift) { 1479 ierr = VecRestoreArrayRead(shifts, &shift);CHKERRQ(ierr); 1480 ierr = VecDestroy(&shifts);CHKERRQ(ierr); 1481 } 1482 if (shiftDebug) {ierr = PetscSynchronizedFlush(PetscObjectComm((PetscObject) dm), PETSC_STDOUT);CHKERRQ(ierr);} 1483 ierr = PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);CHKERRQ(ierr); 1484 ierr = PetscSFSetFromOptions(*pointSF);CHKERRQ(ierr); 1485 ierr = PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1486 ierr = PetscFree2(rootNodes, leafNodes);CHKERRQ(ierr); 1487 ierr = PetscLogEventEnd(DMPLEX_CreatePointSF,dm,0,0,0);CHKERRQ(ierr); 1488 PetscFunctionReturn(0); 1489 } 1490 1491 /*@C 1492 DMPlexMigrate - Migrates internal DM data over the supplied star forest 1493 1494 Collective on dm 1495 1496 Input Parameters: 1497 + dm - The source DMPlex object 1498 . sf - The star forest communication context describing the migration pattern 1499 1500 Output Parameter: 1501 - targetDM - The target DMPlex object 1502 1503 Level: intermediate 1504 1505 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1506 @*/ 1507 PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM) 1508 { 1509 MPI_Comm comm; 1510 PetscInt dim, cdim, nroots; 1511 PetscSF sfPoint; 1512 ISLocalToGlobalMapping ltogMigration; 1513 ISLocalToGlobalMapping ltogOriginal = NULL; 1514 PetscBool flg; 1515 PetscErrorCode ierr; 1516 1517 PetscFunctionBegin; 1518 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1519 ierr = PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1520 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 1521 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1522 ierr = DMSetDimension(targetDM, dim);CHKERRQ(ierr); 1523 ierr = DMGetCoordinateDim(dm, &cdim);CHKERRQ(ierr); 1524 ierr = DMSetCoordinateDim(targetDM, cdim);CHKERRQ(ierr); 1525 1526 /* Check for a one-to-all distribution pattern */ 1527 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1528 ierr = PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 1529 if (nroots >= 0) { 1530 IS isOriginal; 1531 PetscInt n, size, nleaves; 1532 PetscInt *numbering_orig, *numbering_new; 1533 1534 /* Get the original point numbering */ 1535 ierr = DMPlexCreatePointNumbering(dm, &isOriginal);CHKERRQ(ierr); 1536 ierr = ISLocalToGlobalMappingCreateIS(isOriginal, <ogOriginal);CHKERRQ(ierr); 1537 ierr = ISLocalToGlobalMappingGetSize(ltogOriginal, &size);CHKERRQ(ierr); 1538 ierr = ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1539 /* Convert to positive global numbers */ 1540 for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);} 1541 /* Derive the new local-to-global mapping from the old one */ 1542 ierr = PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1543 ierr = PetscMalloc1(nleaves, &numbering_new);CHKERRQ(ierr); 1544 ierr = PetscSFBcastBegin(sf, MPIU_INT, numbering_orig, numbering_new,MPI_REPLACE);CHKERRQ(ierr); 1545 ierr = PetscSFBcastEnd(sf, MPIU_INT, numbering_orig, numbering_new,MPI_REPLACE);CHKERRQ(ierr); 1546 ierr = ISLocalToGlobalMappingCreate(comm, 1, nleaves, numbering_new, PETSC_OWN_POINTER, <ogMigration);CHKERRQ(ierr); 1547 ierr = ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1548 ierr = ISDestroy(&isOriginal);CHKERRQ(ierr); 1549 } else { 1550 /* One-to-all distribution pattern: We can derive LToG from SF */ 1551 ierr = ISLocalToGlobalMappingCreateSF(sf, 0, <ogMigration);CHKERRQ(ierr); 1552 } 1553 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1554 if (flg) { 1555 ierr = PetscPrintf(comm, "Point renumbering for DM migration:\n");CHKERRQ(ierr); 1556 ierr = ISLocalToGlobalMappingView(ltogMigration, NULL);CHKERRQ(ierr); 1557 } 1558 /* Migrate DM data to target DM */ 1559 ierr = DMPlexDistributeCones(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1560 ierr = DMPlexDistributeLabels(dm, sf, targetDM);CHKERRQ(ierr); 1561 ierr = DMPlexDistributeCoordinates(dm, sf, targetDM);CHKERRQ(ierr); 1562 ierr = DMPlexDistributeSetupTree(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1563 ierr = ISLocalToGlobalMappingDestroy(<ogOriginal);CHKERRQ(ierr); 1564 ierr = ISLocalToGlobalMappingDestroy(<ogMigration);CHKERRQ(ierr); 1565 ierr = PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1566 PetscFunctionReturn(0); 1567 } 1568 1569 /*@C 1570 DMPlexDistribute - Distributes the mesh and any associated sections. 1571 1572 Collective on dm 1573 1574 Input Parameters: 1575 + dm - The original DMPlex object 1576 - overlap - The overlap of partitions, 0 is the default 1577 1578 Output Parameters: 1579 + sf - The PetscSF used for point distribution, or NULL if not needed 1580 - dmParallel - The distributed DMPlex object 1581 1582 Note: If the mesh was not distributed, the output dmParallel will be NULL. 1583 1584 The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function 1585 representation on the mesh. 1586 1587 Level: intermediate 1588 1589 .seealso: DMPlexCreate(), DMSetAdjacency(), DMPlexGetOverlap() 1590 @*/ 1591 PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel) 1592 { 1593 MPI_Comm comm; 1594 PetscPartitioner partitioner; 1595 IS cellPart; 1596 PetscSection cellPartSection; 1597 DM dmCoord; 1598 DMLabel lblPartition, lblMigration; 1599 PetscSF sfMigration, sfStratified, sfPoint; 1600 PetscBool flg, balance; 1601 PetscMPIInt rank, size; 1602 PetscErrorCode ierr; 1603 1604 PetscFunctionBegin; 1605 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1606 PetscValidLogicalCollectiveInt(dm, overlap, 2); 1607 if (sf) PetscValidPointer(sf,3); 1608 PetscValidPointer(dmParallel,4); 1609 1610 if (sf) *sf = NULL; 1611 *dmParallel = NULL; 1612 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1613 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 1614 ierr = MPI_Comm_size(comm, &size);CHKERRMPI(ierr); 1615 if (size == 1) PetscFunctionReturn(0); 1616 1617 ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1618 /* Create cell partition */ 1619 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1620 ierr = PetscSectionCreate(comm, &cellPartSection);CHKERRQ(ierr); 1621 ierr = DMPlexGetPartitioner(dm, &partitioner);CHKERRQ(ierr); 1622 ierr = PetscPartitionerDMPlexPartition(partitioner, dm, NULL, cellPartSection, &cellPart);CHKERRQ(ierr); 1623 ierr = PetscLogEventBegin(DMPLEX_PartSelf,dm,0,0,0);CHKERRQ(ierr); 1624 { 1625 /* Convert partition to DMLabel */ 1626 IS is; 1627 PetscHSetI ht; 1628 const PetscInt *points; 1629 PetscInt *iranks; 1630 PetscInt pStart, pEnd, proc, npoints, poff = 0, nranks; 1631 1632 ierr = DMLabelCreate(PETSC_COMM_SELF, "Point Partition", &lblPartition);CHKERRQ(ierr); 1633 /* Preallocate strata */ 1634 ierr = PetscHSetICreate(&ht);CHKERRQ(ierr); 1635 ierr = PetscSectionGetChart(cellPartSection, &pStart, &pEnd);CHKERRQ(ierr); 1636 for (proc = pStart; proc < pEnd; proc++) { 1637 ierr = PetscSectionGetDof(cellPartSection, proc, &npoints);CHKERRQ(ierr); 1638 if (npoints) {ierr = PetscHSetIAdd(ht, proc);CHKERRQ(ierr);} 1639 } 1640 ierr = PetscHSetIGetSize(ht, &nranks);CHKERRQ(ierr); 1641 ierr = PetscMalloc1(nranks, &iranks);CHKERRQ(ierr); 1642 ierr = PetscHSetIGetElems(ht, &poff, iranks);CHKERRQ(ierr); 1643 ierr = PetscHSetIDestroy(&ht);CHKERRQ(ierr); 1644 ierr = DMLabelAddStrata(lblPartition, nranks, iranks);CHKERRQ(ierr); 1645 ierr = PetscFree(iranks);CHKERRQ(ierr); 1646 /* Inline DMPlexPartitionLabelClosure() */ 1647 ierr = ISGetIndices(cellPart, &points);CHKERRQ(ierr); 1648 ierr = PetscSectionGetChart(cellPartSection, &pStart, &pEnd);CHKERRQ(ierr); 1649 for (proc = pStart; proc < pEnd; proc++) { 1650 ierr = PetscSectionGetDof(cellPartSection, proc, &npoints);CHKERRQ(ierr); 1651 if (!npoints) continue; 1652 ierr = PetscSectionGetOffset(cellPartSection, proc, &poff);CHKERRQ(ierr); 1653 ierr = DMPlexClosurePoints_Private(dm, npoints, points+poff, &is);CHKERRQ(ierr); 1654 ierr = DMLabelSetStratumIS(lblPartition, proc, is);CHKERRQ(ierr); 1655 ierr = ISDestroy(&is);CHKERRQ(ierr); 1656 } 1657 ierr = ISRestoreIndices(cellPart, &points);CHKERRQ(ierr); 1658 } 1659 ierr = PetscLogEventEnd(DMPLEX_PartSelf,dm,0,0,0);CHKERRQ(ierr); 1660 1661 ierr = DMLabelCreate(PETSC_COMM_SELF, "Point migration", &lblMigration);CHKERRQ(ierr); 1662 ierr = DMPlexPartitionLabelInvert(dm, lblPartition, NULL, lblMigration);CHKERRQ(ierr); 1663 ierr = DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);CHKERRQ(ierr); 1664 ierr = DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);CHKERRQ(ierr); 1665 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1666 sfMigration = sfStratified; 1667 ierr = PetscSFSetUp(sfMigration);CHKERRQ(ierr); 1668 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1669 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1670 if (flg) { 1671 ierr = DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1672 ierr = PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_(comm));CHKERRQ(ierr); 1673 } 1674 1675 /* Create non-overlapping parallel DM and migrate internal data */ 1676 ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr); 1677 ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr); 1678 ierr = DMPlexMigrate(dm, sfMigration, *dmParallel);CHKERRQ(ierr); 1679 1680 /* Build the point SF without overlap */ 1681 ierr = DMPlexGetPartitionBalance(dm, &balance);CHKERRQ(ierr); 1682 ierr = DMPlexSetPartitionBalance(*dmParallel, balance);CHKERRQ(ierr); 1683 ierr = DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);CHKERRQ(ierr); 1684 ierr = DMSetPointSF(*dmParallel, sfPoint);CHKERRQ(ierr); 1685 ierr = DMGetCoordinateDM(*dmParallel, &dmCoord);CHKERRQ(ierr); 1686 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1687 if (flg) {ierr = PetscSFView(sfPoint, NULL);CHKERRQ(ierr);} 1688 1689 if (overlap > 0) { 1690 DM dmOverlap; 1691 PetscInt nroots, nleaves, noldleaves, l; 1692 const PetscInt *oldLeaves; 1693 PetscSFNode *newRemote, *permRemote; 1694 const PetscSFNode *oldRemote; 1695 PetscSF sfOverlap, sfOverlapPoint; 1696 1697 /* Add the partition overlap to the distributed DM */ 1698 ierr = DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);CHKERRQ(ierr); 1699 ierr = DMDestroy(dmParallel);CHKERRQ(ierr); 1700 *dmParallel = dmOverlap; 1701 if (flg) { 1702 ierr = PetscPrintf(comm, "Overlap Migration SF:\n");CHKERRQ(ierr); 1703 ierr = PetscSFView(sfOverlap, NULL);CHKERRQ(ierr); 1704 } 1705 1706 /* Re-map the migration SF to establish the full migration pattern */ 1707 ierr = PetscSFGetGraph(sfMigration, &nroots, &noldleaves, &oldLeaves, &oldRemote);CHKERRQ(ierr); 1708 ierr = PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1709 ierr = PetscMalloc1(nleaves, &newRemote);CHKERRQ(ierr); 1710 /* oldRemote: original root point mapping to original leaf point 1711 newRemote: original leaf point mapping to overlapped leaf point */ 1712 if (oldLeaves) { 1713 /* After stratification, the migration remotes may not be in root (canonical) order, so we reorder using the leaf numbering */ 1714 ierr = PetscMalloc1(noldleaves, &permRemote);CHKERRQ(ierr); 1715 for (l = 0; l < noldleaves; ++l) permRemote[oldLeaves[l]] = oldRemote[l]; 1716 oldRemote = permRemote; 1717 } 1718 ierr = PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote,MPI_REPLACE);CHKERRQ(ierr); 1719 ierr = PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote,MPI_REPLACE);CHKERRQ(ierr); 1720 if (oldLeaves) {ierr = PetscFree(oldRemote);CHKERRQ(ierr);} 1721 ierr = PetscSFCreate(comm, &sfOverlapPoint);CHKERRQ(ierr); 1722 ierr = PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1723 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1724 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1725 sfMigration = sfOverlapPoint; 1726 } 1727 /* Cleanup Partition */ 1728 ierr = DMLabelDestroy(&lblPartition);CHKERRQ(ierr); 1729 ierr = DMLabelDestroy(&lblMigration);CHKERRQ(ierr); 1730 ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr); 1731 ierr = ISDestroy(&cellPart);CHKERRQ(ierr); 1732 /* Copy BC */ 1733 ierr = DMCopyBoundary(dm, *dmParallel);CHKERRQ(ierr); 1734 /* Create sfNatural */ 1735 if (dm->useNatural) { 1736 PetscSection section; 1737 1738 ierr = DMGetLocalSection(dm, §ion);CHKERRQ(ierr); 1739 ierr = DMPlexCreateGlobalToNaturalSF(*dmParallel, section, sfMigration, &(*dmParallel)->sfNatural);CHKERRQ(ierr); 1740 ierr = DMSetUseNatural(*dmParallel, PETSC_TRUE);CHKERRQ(ierr); 1741 } 1742 /* Cleanup */ 1743 if (sf) {*sf = sfMigration;} 1744 else {ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr);} 1745 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1746 ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1747 PetscFunctionReturn(0); 1748 } 1749 1750 /*@C 1751 DMPlexDistributeOverlap - Add partition overlap to a distributed non-overlapping DM. 1752 1753 Collective on dm 1754 1755 Input Parameters: 1756 + dm - The non-overlapping distributed DMPlex object 1757 - overlap - The overlap of partitions (the same on all ranks) 1758 1759 Output Parameters: 1760 + sf - The PetscSF used for point distribution 1761 - dmOverlap - The overlapping distributed DMPlex object, or NULL 1762 1763 Notes: 1764 If the mesh was not distributed, the return value is NULL. 1765 1766 The user can control the definition of adjacency for the mesh using DMSetAdjacency(). They should choose the combination appropriate for the function 1767 representation on the mesh. 1768 1769 Level: advanced 1770 1771 .seealso: DMPlexCreate(), DMSetAdjacency(), DMPlexDistribute(), DMPlexCreateOverlapLabel(), DMPlexGetOverlap() 1772 @*/ 1773 PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap) 1774 { 1775 MPI_Comm comm; 1776 PetscMPIInt size, rank; 1777 PetscSection rootSection, leafSection; 1778 IS rootrank, leafrank; 1779 DM dmCoord; 1780 DMLabel lblOverlap; 1781 PetscSF sfOverlap, sfStratified, sfPoint; 1782 PetscErrorCode ierr; 1783 1784 PetscFunctionBegin; 1785 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1786 PetscValidLogicalCollectiveInt(dm, overlap, 2); 1787 if (sf) PetscValidPointer(sf, 3); 1788 PetscValidPointer(dmOverlap, 4); 1789 1790 if (sf) *sf = NULL; 1791 *dmOverlap = NULL; 1792 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1793 ierr = MPI_Comm_size(comm, &size);CHKERRMPI(ierr); 1794 ierr = MPI_Comm_rank(comm, &rank);CHKERRMPI(ierr); 1795 if (size == 1) PetscFunctionReturn(0); 1796 1797 ierr = PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1798 /* Compute point overlap with neighbouring processes on the distributed DM */ 1799 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1800 ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr); 1801 ierr = PetscSectionCreate(comm, &leafSection);CHKERRQ(ierr); 1802 ierr = DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);CHKERRQ(ierr); 1803 ierr = DMPlexCreateOverlapLabel(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);CHKERRQ(ierr); 1804 /* Convert overlap label to stratified migration SF */ 1805 ierr = DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);CHKERRQ(ierr); 1806 ierr = DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);CHKERRQ(ierr); 1807 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1808 sfOverlap = sfStratified; 1809 ierr = PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");CHKERRQ(ierr); 1810 ierr = PetscSFSetFromOptions(sfOverlap);CHKERRQ(ierr); 1811 1812 ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr); 1813 ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr); 1814 ierr = ISDestroy(&rootrank);CHKERRQ(ierr); 1815 ierr = ISDestroy(&leafrank);CHKERRQ(ierr); 1816 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1817 1818 /* Build the overlapping DM */ 1819 ierr = DMPlexCreate(comm, dmOverlap);CHKERRQ(ierr); 1820 ierr = PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");CHKERRQ(ierr); 1821 ierr = DMPlexMigrate(dm, sfOverlap, *dmOverlap);CHKERRQ(ierr); 1822 /* Store the overlap in the new DM */ 1823 ((DM_Plex*)(*dmOverlap)->data)->overlap = overlap + ((DM_Plex*)dm->data)->overlap; 1824 /* Build the new point SF */ 1825 ierr = DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1826 ierr = DMSetPointSF(*dmOverlap, sfPoint);CHKERRQ(ierr); 1827 ierr = DMGetCoordinateDM(*dmOverlap, &dmCoord);CHKERRQ(ierr); 1828 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1829 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1830 /* Cleanup overlap partition */ 1831 ierr = DMLabelDestroy(&lblOverlap);CHKERRQ(ierr); 1832 if (sf) *sf = sfOverlap; 1833 else {ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr);} 1834 ierr = PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1835 PetscFunctionReturn(0); 1836 } 1837 1838 PetscErrorCode DMPlexGetOverlap_Plex(DM dm, PetscInt *overlap) 1839 { 1840 DM_Plex *mesh = (DM_Plex*) dm->data; 1841 1842 PetscFunctionBegin; 1843 *overlap = mesh->overlap; 1844 PetscFunctionReturn(0); 1845 } 1846 1847 /*@ 1848 DMPlexGetOverlap - Get the DMPlex partition overlap. 1849 1850 Not collective 1851 1852 Input Parameter: 1853 . dm - The DM 1854 1855 Output Parameter: 1856 . overlap - The overlap of this DM 1857 1858 Level: intermediate 1859 1860 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap(), DMPlexCreateOverlapLabel() 1861 @*/ 1862 PetscErrorCode DMPlexGetOverlap(DM dm, PetscInt *overlap) 1863 { 1864 PetscErrorCode ierr; 1865 1866 PetscFunctionBegin; 1867 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1868 ierr = PetscUseMethod(dm,"DMPlexGetOverlap_C",(DM,PetscInt*),(dm,overlap));CHKERRQ(ierr); 1869 PetscFunctionReturn(0); 1870 } 1871 1872 1873 /*@C 1874 DMPlexGetGatherDM - Get a copy of the DMPlex that gathers all points on the 1875 root process of the original's communicator. 1876 1877 Collective on dm 1878 1879 Input Parameter: 1880 . dm - the original DMPlex object 1881 1882 Output Parameters: 1883 + sf - the PetscSF used for point distribution (optional) 1884 - gatherMesh - the gathered DM object, or NULL 1885 1886 Level: intermediate 1887 1888 .seealso: DMPlexDistribute(), DMPlexGetRedundantDM() 1889 @*/ 1890 PetscErrorCode DMPlexGetGatherDM(DM dm, PetscSF *sf, DM *gatherMesh) 1891 { 1892 MPI_Comm comm; 1893 PetscMPIInt size; 1894 PetscPartitioner oldPart, gatherPart; 1895 PetscErrorCode ierr; 1896 1897 PetscFunctionBegin; 1898 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1899 PetscValidPointer(gatherMesh,2); 1900 *gatherMesh = NULL; 1901 if (sf) *sf = NULL; 1902 comm = PetscObjectComm((PetscObject)dm); 1903 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 1904 if (size == 1) PetscFunctionReturn(0); 1905 ierr = DMPlexGetPartitioner(dm,&oldPart);CHKERRQ(ierr); 1906 ierr = PetscObjectReference((PetscObject)oldPart);CHKERRQ(ierr); 1907 ierr = PetscPartitionerCreate(comm,&gatherPart);CHKERRQ(ierr); 1908 ierr = PetscPartitionerSetType(gatherPart,PETSCPARTITIONERGATHER);CHKERRQ(ierr); 1909 ierr = DMPlexSetPartitioner(dm,gatherPart);CHKERRQ(ierr); 1910 ierr = DMPlexDistribute(dm,0,sf,gatherMesh);CHKERRQ(ierr); 1911 1912 ierr = DMPlexSetPartitioner(dm,oldPart);CHKERRQ(ierr); 1913 ierr = PetscPartitionerDestroy(&gatherPart);CHKERRQ(ierr); 1914 ierr = PetscPartitionerDestroy(&oldPart);CHKERRQ(ierr); 1915 PetscFunctionReturn(0); 1916 } 1917 1918 /*@C 1919 DMPlexGetRedundantDM - Get a copy of the DMPlex that is completely copied on each process. 1920 1921 Collective on dm 1922 1923 Input Parameter: 1924 . dm - the original DMPlex object 1925 1926 Output Parameters: 1927 + sf - the PetscSF used for point distribution (optional) 1928 - redundantMesh - the redundant DM object, or NULL 1929 1930 Level: intermediate 1931 1932 .seealso: DMPlexDistribute(), DMPlexGetGatherDM() 1933 @*/ 1934 PetscErrorCode DMPlexGetRedundantDM(DM dm, PetscSF *sf, DM *redundantMesh) 1935 { 1936 MPI_Comm comm; 1937 PetscMPIInt size, rank; 1938 PetscInt pStart, pEnd, p; 1939 PetscInt numPoints = -1; 1940 PetscSF migrationSF, sfPoint, gatherSF; 1941 DM gatherDM, dmCoord; 1942 PetscSFNode *points; 1943 PetscErrorCode ierr; 1944 1945 PetscFunctionBegin; 1946 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1947 PetscValidPointer(redundantMesh,2); 1948 *redundantMesh = NULL; 1949 comm = PetscObjectComm((PetscObject)dm); 1950 ierr = MPI_Comm_size(comm,&size);CHKERRMPI(ierr); 1951 if (size == 1) { 1952 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 1953 *redundantMesh = dm; 1954 if (sf) *sf = NULL; 1955 PetscFunctionReturn(0); 1956 } 1957 ierr = DMPlexGetGatherDM(dm,&gatherSF,&gatherDM);CHKERRQ(ierr); 1958 if (!gatherDM) PetscFunctionReturn(0); 1959 ierr = MPI_Comm_rank(comm,&rank);CHKERRMPI(ierr); 1960 ierr = DMPlexGetChart(gatherDM,&pStart,&pEnd);CHKERRQ(ierr); 1961 numPoints = pEnd - pStart; 1962 ierr = MPI_Bcast(&numPoints,1,MPIU_INT,0,comm);CHKERRMPI(ierr); 1963 ierr = PetscMalloc1(numPoints,&points);CHKERRQ(ierr); 1964 ierr = PetscSFCreate(comm,&migrationSF);CHKERRQ(ierr); 1965 for (p = 0; p < numPoints; p++) { 1966 points[p].index = p; 1967 points[p].rank = 0; 1968 } 1969 ierr = PetscSFSetGraph(migrationSF,pEnd-pStart,numPoints,NULL,PETSC_OWN_POINTER,points,PETSC_OWN_POINTER);CHKERRQ(ierr); 1970 ierr = DMPlexCreate(comm, redundantMesh);CHKERRQ(ierr); 1971 ierr = PetscObjectSetName((PetscObject) *redundantMesh, "Redundant Mesh");CHKERRQ(ierr); 1972 ierr = DMPlexMigrate(gatherDM, migrationSF, *redundantMesh);CHKERRQ(ierr); 1973 ierr = DMPlexCreatePointSF(*redundantMesh, migrationSF, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1974 ierr = DMSetPointSF(*redundantMesh, sfPoint);CHKERRQ(ierr); 1975 ierr = DMGetCoordinateDM(*redundantMesh, &dmCoord);CHKERRQ(ierr); 1976 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1977 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1978 if (sf) { 1979 PetscSF tsf; 1980 1981 ierr = PetscSFCompose(gatherSF,migrationSF,&tsf);CHKERRQ(ierr); 1982 ierr = DMPlexStratifyMigrationSF(dm, tsf, sf);CHKERRQ(ierr); 1983 ierr = PetscSFDestroy(&tsf);CHKERRQ(ierr); 1984 } 1985 ierr = PetscSFDestroy(&migrationSF);CHKERRQ(ierr); 1986 ierr = PetscSFDestroy(&gatherSF);CHKERRQ(ierr); 1987 ierr = DMDestroy(&gatherDM);CHKERRQ(ierr); 1988 PetscFunctionReturn(0); 1989 } 1990 1991 /*@ 1992 DMPlexIsDistributed - Find out whether this DM is distributed, i.e. more than one rank owns some points. 1993 1994 Collective 1995 1996 Input Parameter: 1997 . dm - The DM object 1998 1999 Output Parameter: 2000 . distributed - Flag whether the DM is distributed 2001 2002 Level: intermediate 2003 2004 Notes: 2005 This currently finds out whether at least two ranks have any DAG points. 2006 This involves MPI_Allreduce() with one integer. 2007 The result is currently not stashed so every call to this routine involves this global communication. 2008 2009 .seealso: DMPlexDistribute(), DMPlexGetOverlap(), DMPlexIsInterpolated() 2010 @*/ 2011 PetscErrorCode DMPlexIsDistributed(DM dm, PetscBool *distributed) 2012 { 2013 PetscInt pStart, pEnd, count; 2014 MPI_Comm comm; 2015 PetscErrorCode ierr; 2016 2017 PetscFunctionBegin; 2018 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 2019 PetscValidPointer(distributed,2); 2020 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 2021 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 2022 count = !!(pEnd - pStart); 2023 ierr = MPI_Allreduce(MPI_IN_PLACE, &count, 1, MPIU_INT, MPI_SUM, comm);CHKERRMPI(ierr); 2024 *distributed = count > 1 ? PETSC_TRUE : PETSC_FALSE; 2025 PetscFunctionReturn(0); 2026 } 2027