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 DM_Plex *mesh = (DM_Plex*) dm->data; 1080 MPI_Comm comm; 1081 DMLabel depth; 1082 PetscMPIInt rank; 1083 PetscInt numLabels, numLocalLabels, l; 1084 PetscBool hasLabels = PETSC_FALSE, lsendDepth, sendDepth; 1085 PetscObjectState depthState = -1; 1086 PetscErrorCode ierr; 1087 1088 PetscFunctionBegin; 1089 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1090 PetscValidHeaderSpecific(dm, DM_CLASSID, 3); 1091 ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1092 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1093 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1094 1095 /* If the user has changed the depth label, communicate it instead */ 1096 ierr = DMPlexGetDepthLabel(dm, &depth);CHKERRQ(ierr); 1097 if (depth) {ierr = DMLabelGetState(depth, &depthState);CHKERRQ(ierr);} 1098 lsendDepth = mesh->depthState != depthState ? PETSC_TRUE : PETSC_FALSE; 1099 ierr = MPI_Allreduce(&lsendDepth, &sendDepth, 1, MPIU_BOOL, MPI_LOR, comm);CHKERRQ(ierr); 1100 if (sendDepth) { 1101 ierr = DMPlexRemoveLabel(dmParallel, "depth", &depth);CHKERRQ(ierr); 1102 ierr = DMLabelDestroy(&depth);CHKERRQ(ierr); 1103 } 1104 /* Everyone must have either the same number of labels, or none */ 1105 ierr = DMPlexGetNumLabels(dm, &numLocalLabels);CHKERRQ(ierr); 1106 numLabels = numLocalLabels; 1107 ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1108 if (numLabels == numLocalLabels) hasLabels = PETSC_TRUE; 1109 for (l = numLabels-1; l >= 0; --l) { 1110 DMLabel label = NULL, labelNew = NULL; 1111 PetscBool isdepth; 1112 1113 if (hasLabels) { 1114 ierr = DMPlexGetLabelByNum(dm, l, &label);CHKERRQ(ierr); 1115 /* Skip "depth" because it is recreated */ 1116 ierr = PetscStrcmp(label->name, "depth", &isdepth);CHKERRQ(ierr); 1117 } 1118 ierr = MPI_Bcast(&isdepth, 1, MPIU_BOOL, 0, comm);CHKERRQ(ierr); 1119 if (isdepth && !sendDepth) continue; 1120 ierr = DMLabelDistribute(label, migrationSF, &labelNew);CHKERRQ(ierr); 1121 ierr = DMPlexAddLabel(dmParallel, labelNew);CHKERRQ(ierr); 1122 } 1123 ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1124 PetscFunctionReturn(0); 1125 } 1126 1127 #undef __FUNCT__ 1128 #define __FUNCT__ "DMPlexDistributeSetupHybrid" 1129 PetscErrorCode DMPlexDistributeSetupHybrid(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel) 1130 { 1131 DM_Plex *mesh = (DM_Plex*) dm->data; 1132 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1133 MPI_Comm comm; 1134 const PetscInt *gpoints; 1135 PetscInt dim, depth, n, d; 1136 PetscErrorCode ierr; 1137 1138 PetscFunctionBegin; 1139 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1140 PetscValidPointer(dmParallel, 4); 1141 1142 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1143 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1144 1145 /* Setup hybrid structure */ 1146 for (d = 0; d <= dim; ++d) {pmesh->hybridPointMax[d] = mesh->hybridPointMax[d];} 1147 ierr = MPI_Bcast(pmesh->hybridPointMax, dim+1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1148 ierr = ISLocalToGlobalMappingGetSize(renumbering, &n);CHKERRQ(ierr); 1149 ierr = ISLocalToGlobalMappingGetIndices(renumbering, &gpoints);CHKERRQ(ierr); 1150 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1151 for (d = 0; d <= dim; ++d) { 1152 PetscInt pmax = pmesh->hybridPointMax[d], newmax = 0, pEnd, stratum[2], p; 1153 1154 if (pmax < 0) continue; 1155 ierr = DMPlexGetDepthStratum(dm, d > depth ? depth : d, &stratum[0], &stratum[1]);CHKERRQ(ierr); 1156 ierr = DMPlexGetDepthStratum(dmParallel, d, NULL, &pEnd);CHKERRQ(ierr); 1157 ierr = MPI_Bcast(stratum, 2, MPIU_INT, 0, comm);CHKERRQ(ierr); 1158 for (p = 0; p < n; ++p) { 1159 const PetscInt point = gpoints[p]; 1160 1161 if ((point >= stratum[0]) && (point < stratum[1]) && (point >= pmax)) ++newmax; 1162 } 1163 if (newmax > 0) pmesh->hybridPointMax[d] = pEnd - newmax; 1164 else pmesh->hybridPointMax[d] = -1; 1165 } 1166 ierr = ISLocalToGlobalMappingRestoreIndices(renumbering, &gpoints);CHKERRQ(ierr); 1167 PetscFunctionReturn(0); 1168 } 1169 1170 #undef __FUNCT__ 1171 #define __FUNCT__ "DMPlexDistributeSetupTree" 1172 PetscErrorCode DMPlexDistributeSetupTree(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel) 1173 { 1174 DM_Plex *mesh = (DM_Plex*) dm->data; 1175 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1176 MPI_Comm comm; 1177 DM refTree; 1178 PetscSection origParentSection, newParentSection; 1179 PetscInt *origParents, *origChildIDs; 1180 PetscBool flg; 1181 PetscErrorCode ierr; 1182 1183 PetscFunctionBegin; 1184 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1185 PetscValidHeaderSpecific(dm, DM_CLASSID, 4); 1186 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1187 1188 /* Set up tree */ 1189 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 1190 ierr = DMPlexSetReferenceTree(dmParallel,refTree);CHKERRQ(ierr); 1191 ierr = DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);CHKERRQ(ierr); 1192 if (origParentSection) { 1193 PetscInt pStart, pEnd; 1194 PetscInt *newParents, *newChildIDs, *globParents; 1195 PetscInt *remoteOffsetsParents, newParentSize; 1196 PetscSF parentSF; 1197 1198 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1199 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dmParallel),&newParentSection);CHKERRQ(ierr); 1200 ierr = PetscSectionSetChart(newParentSection,pStart,pEnd);CHKERRQ(ierr); 1201 ierr = PetscSFDistributeSection(migrationSF, origParentSection, &remoteOffsetsParents, newParentSection);CHKERRQ(ierr); 1202 ierr = PetscSFCreateSectionSF(migrationSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);CHKERRQ(ierr); 1203 ierr = PetscSectionGetStorageSize(newParentSection,&newParentSize);CHKERRQ(ierr); 1204 ierr = PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);CHKERRQ(ierr); 1205 if (original) { 1206 PetscInt numParents; 1207 1208 ierr = PetscSectionGetStorageSize(origParentSection,&numParents);CHKERRQ(ierr); 1209 ierr = PetscMalloc1(numParents,&globParents);CHKERRQ(ierr); 1210 ierr = ISLocalToGlobalMappingApplyBlock(original, numParents, origParents, globParents);CHKERRQ(ierr); 1211 } 1212 else { 1213 globParents = origParents; 1214 } 1215 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, globParents, newParents);CHKERRQ(ierr); 1216 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, globParents, newParents);CHKERRQ(ierr); 1217 if (original) { 1218 ierr = PetscFree(globParents);CHKERRQ(ierr); 1219 } 1220 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1221 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1222 ierr = ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);CHKERRQ(ierr); 1223 #if PETSC_USE_DEBUG 1224 { 1225 PetscInt p; 1226 PetscBool valid = PETSC_TRUE; 1227 for (p = 0; p < newParentSize; ++p) { 1228 if (newParents[p] < 0) {valid = PETSC_FALSE; ierr = PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);CHKERRQ(ierr);} 1229 } 1230 if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map"); 1231 } 1232 #endif 1233 ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-parents_view", &flg);CHKERRQ(ierr); 1234 if (flg) { 1235 ierr = PetscPrintf(comm, "Serial Parent Section: \n");CHKERRQ(ierr); 1236 ierr = PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1237 ierr = PetscPrintf(comm, "Parallel Parent Section: \n");CHKERRQ(ierr); 1238 ierr = PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1239 ierr = PetscSFView(parentSF, NULL);CHKERRQ(ierr); 1240 } 1241 ierr = DMPlexSetTree(dmParallel,newParentSection,newParents,newChildIDs);CHKERRQ(ierr); 1242 ierr = PetscSectionDestroy(&newParentSection);CHKERRQ(ierr); 1243 ierr = PetscFree2(newParents,newChildIDs);CHKERRQ(ierr); 1244 ierr = PetscSFDestroy(&parentSF);CHKERRQ(ierr); 1245 } 1246 pmesh->useAnchors = mesh->useAnchors; 1247 PetscFunctionReturn(0); 1248 } 1249 1250 #undef __FUNCT__ 1251 #define __FUNCT__ "DMPlexDistributeSF" 1252 PetscErrorCode DMPlexDistributeSF(DM dm, PetscSF migrationSF, DM dmParallel) 1253 { 1254 DM_Plex *mesh = (DM_Plex*) dm->data; 1255 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1256 PetscMPIInt rank, numProcs; 1257 MPI_Comm comm; 1258 PetscErrorCode ierr; 1259 1260 PetscFunctionBegin; 1261 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1262 PetscValidPointer(dmParallel,7); 1263 1264 /* Create point SF for parallel mesh */ 1265 ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1266 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1267 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1268 ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr); 1269 { 1270 const PetscInt *leaves; 1271 PetscSFNode *remotePoints, *rowners, *lowners; 1272 PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints; 1273 PetscInt pStart, pEnd; 1274 1275 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1276 ierr = PetscSFGetGraph(migrationSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr); 1277 ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr); 1278 for (p=0; p<numRoots; p++) { 1279 rowners[p].rank = -1; 1280 rowners[p].index = -1; 1281 } 1282 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1283 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1284 for (p = 0; p < numLeaves; ++p) { 1285 if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */ 1286 lowners[p].rank = rank; 1287 lowners[p].index = leaves ? leaves[p] : p; 1288 } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */ 1289 lowners[p].rank = -2; 1290 lowners[p].index = -2; 1291 } 1292 } 1293 for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */ 1294 rowners[p].rank = -3; 1295 rowners[p].index = -3; 1296 } 1297 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1298 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1299 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1300 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1301 for (p = 0; p < numLeaves; ++p) { 1302 if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed"); 1303 if (lowners[p].rank != rank) ++numGhostPoints; 1304 } 1305 ierr = PetscMalloc1(numGhostPoints, &ghostPoints);CHKERRQ(ierr); 1306 ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr); 1307 for (p = 0, gp = 0; p < numLeaves; ++p) { 1308 if (lowners[p].rank != rank) { 1309 ghostPoints[gp] = leaves ? leaves[p] : p; 1310 remotePoints[gp].rank = lowners[p].rank; 1311 remotePoints[gp].index = lowners[p].index; 1312 ++gp; 1313 } 1314 } 1315 ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr); 1316 ierr = PetscSFSetGraph((dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 1317 ierr = PetscSFSetFromOptions((dmParallel)->sf);CHKERRQ(ierr); 1318 } 1319 pmesh->useCone = mesh->useCone; 1320 pmesh->useClosure = mesh->useClosure; 1321 ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1322 PetscFunctionReturn(0); 1323 } 1324 1325 #undef __FUNCT__ 1326 #define __FUNCT__ "DMPlexCreatePointSF" 1327 /*@C 1328 DMPlexDerivePointSF - Build a point SF from an SF describing a point migration 1329 1330 Input Parameter: 1331 + dm - The source DMPlex object 1332 . migrationSF - The star forest that describes the parallel point remapping 1333 . ownership - Flag causing a vote to determine point ownership 1334 1335 Output Parameter: 1336 - pointSF - The star forest describing the point overlap in the remapped DM 1337 1338 Level: developer 1339 1340 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1341 @*/ 1342 PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF) 1343 { 1344 PetscMPIInt rank; 1345 PetscInt p, nroots, nleaves, idx, npointLeaves; 1346 PetscInt *pointLocal; 1347 const PetscInt *leaves; 1348 const PetscSFNode *roots; 1349 PetscSFNode *rootNodes, *leafNodes, *pointRemote; 1350 PetscErrorCode ierr; 1351 1352 PetscFunctionBegin; 1353 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1354 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 1355 1356 ierr = PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);CHKERRQ(ierr); 1357 ierr = PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);CHKERRQ(ierr); 1358 if (ownership) { 1359 /* Point ownership vote: Process with highest rank ownes shared points */ 1360 for (p = 0; p < nleaves; ++p) { 1361 /* Either put in a bid or we know we own it */ 1362 leafNodes[p].rank = rank; 1363 leafNodes[p].index = p; 1364 } 1365 for (p = 0; p < nroots; p++) { 1366 /* Root must not participate in the reduction, flag so that MAXLOC does not use */ 1367 rootNodes[p].rank = -3; 1368 rootNodes[p].index = -3; 1369 } 1370 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);CHKERRQ(ierr); 1371 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);CHKERRQ(ierr); 1372 } else { 1373 for (p = 0; p < nroots; p++) { 1374 rootNodes[p].index = -1; 1375 rootNodes[p].rank = rank; 1376 }; 1377 for (p = 0; p < nleaves; p++) { 1378 /* Write new local id into old location */ 1379 if (roots[p].rank == rank) { 1380 rootNodes[roots[p].index].index = leaves[p]; 1381 } 1382 } 1383 } 1384 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1385 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1386 1387 for (npointLeaves = 0, p = 0; p < nleaves; p++) {if (leafNodes[p].rank != rank) npointLeaves++;} 1388 ierr = PetscMalloc1(npointLeaves, &pointLocal);CHKERRQ(ierr); 1389 ierr = PetscMalloc1(npointLeaves, &pointRemote);CHKERRQ(ierr); 1390 for (idx = 0, p = 0; p < nleaves; p++) { 1391 if (leafNodes[p].rank != rank) { 1392 pointLocal[idx] = p; 1393 pointRemote[idx] = leafNodes[p]; 1394 idx++; 1395 } 1396 } 1397 ierr = PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);CHKERRQ(ierr); 1398 ierr = PetscSFSetFromOptions(*pointSF);CHKERRQ(ierr); 1399 ierr = PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1400 ierr = PetscFree2(rootNodes, leafNodes);CHKERRQ(ierr); 1401 PetscFunctionReturn(0); 1402 } 1403 1404 #undef __FUNCT__ 1405 #define __FUNCT__ "DMPlexMigrate" 1406 /*@C 1407 DMPlexMigrate - Migrates internal DM data over the supplied star forest 1408 1409 Input Parameter: 1410 + dm - The source DMPlex object 1411 . sf - The star forest communication context describing the migration pattern 1412 1413 Output Parameter: 1414 - targetDM - The target DMPlex object 1415 1416 Level: intermediate 1417 1418 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1419 @*/ 1420 PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM) 1421 { 1422 MPI_Comm comm; 1423 PetscInt dim, nroots; 1424 PetscSF sfPoint; 1425 ISLocalToGlobalMapping ltogMigration; 1426 ISLocalToGlobalMapping ltogOriginal = NULL; 1427 PetscBool flg; 1428 PetscErrorCode ierr; 1429 1430 PetscFunctionBegin; 1431 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1432 ierr = PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1433 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 1434 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1435 ierr = DMSetDimension(targetDM, dim);CHKERRQ(ierr); 1436 1437 /* Check for a one-to-all distribution pattern */ 1438 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1439 ierr = PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 1440 if (nroots >= 0) { 1441 IS isOriginal; 1442 PetscInt n, size, nleaves; 1443 PetscInt *numbering_orig, *numbering_new; 1444 /* Get the original point numbering */ 1445 ierr = DMPlexCreatePointNumbering(dm, &isOriginal);CHKERRQ(ierr); 1446 ierr = ISLocalToGlobalMappingCreateIS(isOriginal, <ogOriginal);CHKERRQ(ierr); 1447 ierr = ISLocalToGlobalMappingGetSize(ltogOriginal, &size);CHKERRQ(ierr); 1448 ierr = ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1449 /* Convert to positive global numbers */ 1450 for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);} 1451 /* Derive the new local-to-global mapping from the old one */ 1452 ierr = PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1453 ierr = PetscMalloc1(nleaves, &numbering_new);CHKERRQ(ierr); 1454 ierr = PetscSFBcastBegin(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);CHKERRQ(ierr); 1455 ierr = PetscSFBcastEnd(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);CHKERRQ(ierr); 1456 ierr = ISLocalToGlobalMappingCreate(comm, 1, nleaves, (const PetscInt*) numbering_new, PETSC_OWN_POINTER, <ogMigration);CHKERRQ(ierr); 1457 ierr = ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1458 ierr = ISDestroy(&isOriginal);CHKERRQ(ierr); 1459 } else { 1460 /* One-to-all distribution pattern: We can derive LToG from SF */ 1461 ierr = ISLocalToGlobalMappingCreateSF(sf, 0, <ogMigration);CHKERRQ(ierr); 1462 } 1463 ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1464 if (flg) { 1465 ierr = PetscPrintf(comm, "Point renumbering for DM migration:\n");CHKERRQ(ierr); 1466 ierr = ISLocalToGlobalMappingView(ltogMigration, NULL);CHKERRQ(ierr); 1467 } 1468 /* Migrate DM data to target DM */ 1469 ierr = DMPlexDistributeCones(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1470 ierr = DMPlexDistributeCoordinates(dm, sf, targetDM);CHKERRQ(ierr); 1471 ierr = DMPlexDistributeLabels(dm, sf, targetDM);CHKERRQ(ierr); 1472 ierr = DMPlexDistributeSetupHybrid(dm, sf, ltogMigration, targetDM);CHKERRQ(ierr); 1473 ierr = DMPlexDistributeSetupTree(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1474 ierr = ISLocalToGlobalMappingDestroy(<ogOriginal);CHKERRQ(ierr); 1475 ierr = ISLocalToGlobalMappingDestroy(<ogMigration);CHKERRQ(ierr); 1476 ierr = PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1477 PetscFunctionReturn(0); 1478 } 1479 1480 #undef __FUNCT__ 1481 #define __FUNCT__ "DMPlexDistribute" 1482 /*@C 1483 DMPlexDistribute - Distributes the mesh and any associated sections. 1484 1485 Not Collective 1486 1487 Input Parameter: 1488 + dm - The original DMPlex object 1489 - overlap - The overlap of partitions, 0 is the default 1490 1491 Output Parameter: 1492 + sf - The PetscSF used for point distribution 1493 - parallelMesh - The distributed DMPlex object, or NULL 1494 1495 Note: If the mesh was not distributed, the return value is NULL. 1496 1497 The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and 1498 DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function 1499 representation on the mesh. 1500 1501 Level: intermediate 1502 1503 .keywords: mesh, elements 1504 .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure() 1505 @*/ 1506 PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel) 1507 { 1508 MPI_Comm comm; 1509 PetscPartitioner partitioner; 1510 IS cellPart; 1511 PetscSection cellPartSection; 1512 DM dmCoord; 1513 DMLabel lblPartition, lblMigration; 1514 PetscSF sfProcess, sfMigration, sfStratified, sfPoint; 1515 PetscBool flg; 1516 PetscMPIInt rank, numProcs, p; 1517 PetscErrorCode ierr; 1518 1519 PetscFunctionBegin; 1520 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1521 if (sf) PetscValidPointer(sf,4); 1522 PetscValidPointer(dmParallel,5); 1523 1524 ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1525 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1526 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1527 ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr); 1528 1529 *dmParallel = NULL; 1530 if (numProcs == 1) PetscFunctionReturn(0); 1531 1532 /* Create cell partition */ 1533 ierr = PetscLogEventBegin(PETSCPARTITIONER_Partition,dm,0,0,0);CHKERRQ(ierr); 1534 ierr = PetscSectionCreate(comm, &cellPartSection);CHKERRQ(ierr); 1535 ierr = DMPlexGetPartitioner(dm, &partitioner);CHKERRQ(ierr); 1536 ierr = PetscPartitionerPartition(partitioner, dm, cellPartSection, &cellPart);CHKERRQ(ierr); 1537 { 1538 /* Convert partition to DMLabel */ 1539 PetscInt proc, pStart, pEnd, npoints, poffset; 1540 const PetscInt *points; 1541 ierr = DMLabelCreate("Point Partition", &lblPartition);CHKERRQ(ierr); 1542 ierr = ISGetIndices(cellPart, &points);CHKERRQ(ierr); 1543 ierr = PetscSectionGetChart(cellPartSection, &pStart, &pEnd);CHKERRQ(ierr); 1544 for (proc = pStart; proc < pEnd; proc++) { 1545 ierr = PetscSectionGetDof(cellPartSection, proc, &npoints);CHKERRQ(ierr); 1546 ierr = PetscSectionGetOffset(cellPartSection, proc, &poffset);CHKERRQ(ierr); 1547 for (p = poffset; p < poffset+npoints; p++) { 1548 ierr = DMLabelSetValue(lblPartition, points[p], proc);CHKERRQ(ierr); 1549 } 1550 } 1551 ierr = ISRestoreIndices(cellPart, &points);CHKERRQ(ierr); 1552 } 1553 ierr = DMPlexPartitionLabelClosure(dm, lblPartition);CHKERRQ(ierr); 1554 { 1555 /* Build a global process SF */ 1556 PetscSFNode *remoteProc; 1557 ierr = PetscMalloc1(numProcs, &remoteProc);CHKERRQ(ierr); 1558 for (p = 0; p < numProcs; ++p) { 1559 remoteProc[p].rank = p; 1560 remoteProc[p].index = rank; 1561 } 1562 ierr = PetscSFCreate(comm, &sfProcess);CHKERRQ(ierr); 1563 ierr = PetscObjectSetName((PetscObject) sfProcess, "Process SF");CHKERRQ(ierr); 1564 ierr = PetscSFSetGraph(sfProcess, numProcs, numProcs, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);CHKERRQ(ierr); 1565 } 1566 ierr = DMLabelCreate("Point migration", &lblMigration);CHKERRQ(ierr); 1567 ierr = DMPlexPartitionLabelInvert(dm, lblPartition, sfProcess, lblMigration);CHKERRQ(ierr); 1568 ierr = DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);CHKERRQ(ierr); 1569 /* Stratify the SF in case we are migrating an already parallel plex */ 1570 ierr = DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);CHKERRQ(ierr); 1571 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1572 sfMigration = sfStratified; 1573 ierr = PetscLogEventEnd(PETSCPARTITIONER_Partition,dm,0,0,0);CHKERRQ(ierr); 1574 ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1575 if (flg) { 1576 ierr = DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1577 ierr = PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1578 } 1579 1580 /* Create non-overlapping parallel DM and migrate internal data */ 1581 ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr); 1582 ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr); 1583 ierr = DMPlexMigrate(dm, sfMigration, *dmParallel);CHKERRQ(ierr); 1584 1585 /* Build the point SF without overlap */ 1586 ierr = DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);CHKERRQ(ierr); 1587 ierr = DMSetPointSF(*dmParallel, sfPoint);CHKERRQ(ierr); 1588 ierr = DMGetCoordinateDM(*dmParallel, &dmCoord);CHKERRQ(ierr); 1589 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1590 if (flg) {ierr = PetscSFView(sfPoint, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);} 1591 1592 if (overlap > 0) { 1593 DM dmOverlap; 1594 PetscInt nroots, nleaves; 1595 PetscSFNode *newRemote; 1596 const PetscSFNode *oldRemote; 1597 PetscSF sfOverlap, sfOverlapPoint; 1598 /* Add the partition overlap to the distributed DM */ 1599 ierr = DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);CHKERRQ(ierr); 1600 ierr = DMDestroy(dmParallel);CHKERRQ(ierr); 1601 *dmParallel = dmOverlap; 1602 if (flg) { 1603 ierr = PetscPrintf(comm, "Overlap Migration SF:\n");CHKERRQ(ierr); 1604 ierr = PetscSFView(sfOverlap, NULL);CHKERRQ(ierr); 1605 } 1606 1607 /* Re-map the migration SF to establish the full migration pattern */ 1608 ierr = PetscSFGetGraph(sfMigration, &nroots, NULL, NULL, &oldRemote);CHKERRQ(ierr); 1609 ierr = PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1610 ierr = PetscMalloc1(nleaves, &newRemote);CHKERRQ(ierr); 1611 ierr = PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1612 ierr = PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1613 ierr = PetscSFCreate(comm, &sfOverlapPoint);CHKERRQ(ierr); 1614 ierr = PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1615 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1616 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1617 sfMigration = sfOverlapPoint; 1618 } 1619 /* Cleanup Partition */ 1620 ierr = PetscSFDestroy(&sfProcess);CHKERRQ(ierr); 1621 ierr = DMLabelDestroy(&lblPartition);CHKERRQ(ierr); 1622 ierr = DMLabelDestroy(&lblMigration);CHKERRQ(ierr); 1623 ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr); 1624 ierr = ISDestroy(&cellPart);CHKERRQ(ierr); 1625 /* Copy BC */ 1626 ierr = DMPlexCopyBoundary(dm, *dmParallel);CHKERRQ(ierr); 1627 /* Create sfNatural */ 1628 if (dm->useNatural) { 1629 PetscSection section; 1630 1631 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1632 ierr = DMPlexCreateGlobalToNaturalSF(*dmParallel, section, sfMigration, &(*dmParallel)->sfNatural);CHKERRQ(ierr); 1633 } 1634 /* Cleanup */ 1635 if (sf) {*sf = sfMigration;} 1636 else {ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr);} 1637 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1638 ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1639 PetscFunctionReturn(0); 1640 } 1641 1642 #undef __FUNCT__ 1643 #define __FUNCT__ "DMPlexDistributeOverlap" 1644 /*@C 1645 DMPlexDistribute - Add partition overlap to a distributed non-overlapping DM. 1646 1647 Not Collective 1648 1649 Input Parameter: 1650 + dm - The non-overlapping distrbuted DMPlex object 1651 - overlap - The overlap of partitions, 0 is the default 1652 1653 Output Parameter: 1654 + sf - The PetscSF used for point distribution 1655 - dmOverlap - The overlapping distributed DMPlex object, or NULL 1656 1657 Note: If the mesh was not distributed, the return value is NULL. 1658 1659 The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and 1660 DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function 1661 representation on the mesh. 1662 1663 Level: intermediate 1664 1665 .keywords: mesh, elements 1666 .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure() 1667 @*/ 1668 PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap) 1669 { 1670 MPI_Comm comm; 1671 PetscMPIInt rank; 1672 PetscSection rootSection, leafSection; 1673 IS rootrank, leafrank; 1674 DM dmCoord; 1675 DMLabel lblOverlap; 1676 PetscSF sfOverlap, sfStratified, sfPoint; 1677 PetscErrorCode ierr; 1678 1679 PetscFunctionBegin; 1680 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1681 if (sf) PetscValidPointer(sf, 3); 1682 PetscValidPointer(dmOverlap, 4); 1683 1684 ierr = PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1685 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1686 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1687 1688 /* Compute point overlap with neighbouring processes on the distributed DM */ 1689 ierr = PetscLogEventBegin(PETSCPARTITIONER_Partition,dm,0,0,0);CHKERRQ(ierr); 1690 ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr); 1691 ierr = PetscSectionCreate(comm, &leafSection);CHKERRQ(ierr); 1692 ierr = DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);CHKERRQ(ierr); 1693 ierr = DMPlexCreateOverlap(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);CHKERRQ(ierr); 1694 /* Convert overlap label to stratified migration SF */ 1695 ierr = DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);CHKERRQ(ierr); 1696 ierr = DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);CHKERRQ(ierr); 1697 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1698 sfOverlap = sfStratified; 1699 ierr = PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");CHKERRQ(ierr); 1700 ierr = PetscSFSetFromOptions(sfOverlap);CHKERRQ(ierr); 1701 1702 ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr); 1703 ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr); 1704 ierr = ISDestroy(&rootrank);CHKERRQ(ierr); 1705 ierr = ISDestroy(&leafrank);CHKERRQ(ierr); 1706 ierr = PetscLogEventEnd(PETSCPARTITIONER_Partition,dm,0,0,0);CHKERRQ(ierr); 1707 1708 /* Build the overlapping DM */ 1709 ierr = DMPlexCreate(comm, dmOverlap);CHKERRQ(ierr); 1710 ierr = PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");CHKERRQ(ierr); 1711 ierr = DMPlexMigrate(dm, sfOverlap, *dmOverlap);CHKERRQ(ierr); 1712 /* Build the new point SF */ 1713 ierr = DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1714 ierr = DMSetPointSF(*dmOverlap, sfPoint);CHKERRQ(ierr); 1715 ierr = DMGetCoordinateDM(*dmOverlap, &dmCoord);CHKERRQ(ierr); 1716 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1717 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1718 /* Cleanup overlap partition */ 1719 ierr = DMLabelDestroy(&lblOverlap);CHKERRQ(ierr); 1720 if (sf) *sf = sfOverlap; 1721 else {ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr);} 1722 ierr = PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1723 PetscFunctionReturn(0); 1724 } 1725