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