1 #include <petsc-private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petscsf.h> 3 4 #undef __FUNCT__ 5 #define __FUNCT__ "DMPlexSetAdjacencyUseCone" 6 /*@ 7 DMPlexSetAdjacencyUseCone - Define adjacency in the mesh using either the cone or the support first 8 9 Input Parameters: 10 + dm - The DM object 11 - useCone - Flag to use the cone first 12 13 Level: intermediate 14 15 Notes: 16 $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE 17 $ FVM: Two points p and q are adjacent if q \in star(cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE 18 $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE 19 20 .seealso: DMPlexGetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexGetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator() 21 @*/ 22 PetscErrorCode DMPlexSetAdjacencyUseCone(DM dm, PetscBool useCone) 23 { 24 DM_Plex *mesh = (DM_Plex *) dm->data; 25 26 PetscFunctionBegin; 27 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 28 mesh->useCone = useCone; 29 PetscFunctionReturn(0); 30 } 31 32 #undef __FUNCT__ 33 #define __FUNCT__ "DMPlexGetAdjacencyUseCone" 34 /*@ 35 DMPlexGetAdjacencyUseCone - Query whether adjacency in the mesh uses the cone or the support first 36 37 Input Parameter: 38 . dm - The DM object 39 40 Output Parameter: 41 . useCone - Flag to use the cone first 42 43 Level: intermediate 44 45 Notes: 46 $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE 47 $ FVM: Two points p and q are adjacent if q \in star(cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE 48 $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE 49 50 .seealso: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexGetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator() 51 @*/ 52 PetscErrorCode DMPlexGetAdjacencyUseCone(DM dm, PetscBool *useCone) 53 { 54 DM_Plex *mesh = (DM_Plex *) dm->data; 55 56 PetscFunctionBegin; 57 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 58 PetscValidIntPointer(useCone, 2); 59 *useCone = mesh->useCone; 60 PetscFunctionReturn(0); 61 } 62 63 #undef __FUNCT__ 64 #define __FUNCT__ "DMPlexSetAdjacencyUseClosure" 65 /*@ 66 DMPlexSetAdjacencyUseClosure - Define adjacency in the mesh using the transitive closure 67 68 Input Parameters: 69 + dm - The DM object 70 - useClosure - Flag to use the closure 71 72 Level: intermediate 73 74 Notes: 75 $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE 76 $ FVM: Two points p and q are adjacent if q \in star(cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE 77 $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE 78 79 .seealso: DMPlexGetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator() 80 @*/ 81 PetscErrorCode DMPlexSetAdjacencyUseClosure(DM dm, PetscBool useClosure) 82 { 83 DM_Plex *mesh = (DM_Plex *) dm->data; 84 85 PetscFunctionBegin; 86 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 87 mesh->useClosure = useClosure; 88 PetscFunctionReturn(0); 89 } 90 91 #undef __FUNCT__ 92 #define __FUNCT__ "DMPlexGetAdjacencyUseClosure" 93 /*@ 94 DMPlexGetAdjacencyUseClosure - Query whether adjacency in the mesh uses the transitive closure 95 96 Input Parameter: 97 . dm - The DM object 98 99 Output Parameter: 100 . useClosure - Flag to use the closure 101 102 Level: intermediate 103 104 Notes: 105 $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE 106 $ FVM: Two points p and q are adjacent if q \in star(cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE 107 $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE 108 109 .seealso: DMPlexSetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator() 110 @*/ 111 PetscErrorCode DMPlexGetAdjacencyUseClosure(DM dm, PetscBool *useClosure) 112 { 113 DM_Plex *mesh = (DM_Plex *) dm->data; 114 115 PetscFunctionBegin; 116 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 117 PetscValidIntPointer(useClosure, 2); 118 *useClosure = mesh->useClosure; 119 PetscFunctionReturn(0); 120 } 121 122 #undef __FUNCT__ 123 #define __FUNCT__ "DMPlexSetAdjacencyUseAnchors" 124 /*@ 125 DMPlexSetAdjacencyUseAnchors - Define adjacency in the mesh using the point-to-point constraints. 126 127 Input Parameters: 128 + dm - The DM object 129 - useAnchors - Flag to use the constraints. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place. 130 131 Level: intermediate 132 133 .seealso: DMPlexGetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors() 134 @*/ 135 PetscErrorCode DMPlexSetAdjacencyUseAnchors(DM dm, PetscBool useAnchors) 136 { 137 DM_Plex *mesh = (DM_Plex *) dm->data; 138 139 PetscFunctionBegin; 140 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 141 mesh->useAnchors = useAnchors; 142 PetscFunctionReturn(0); 143 } 144 145 #undef __FUNCT__ 146 #define __FUNCT__ "DMPlexGetAdjacencyUseAnchors" 147 /*@ 148 DMPlexGetAdjacencyUseAnchors - Query whether adjacency in the mesh uses the point-to-point constraints. 149 150 Input Parameter: 151 . dm - The DM object 152 153 Output Parameter: 154 . useAnchors - Flag to use the closure. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place. 155 156 Level: intermediate 157 158 .seealso: DMPlexSetAdjacencyUseAnchors(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors() 159 @*/ 160 PetscErrorCode DMPlexGetAdjacencyUseAnchors(DM dm, PetscBool *useAnchors) 161 { 162 DM_Plex *mesh = (DM_Plex *) dm->data; 163 164 PetscFunctionBegin; 165 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 166 PetscValidIntPointer(useAnchors, 2); 167 *useAnchors = mesh->useAnchors; 168 PetscFunctionReturn(0); 169 } 170 171 #undef __FUNCT__ 172 #define __FUNCT__ "DMPlexGetAdjacency_Cone_Internal" 173 static PetscErrorCode DMPlexGetAdjacency_Cone_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[]) 174 { 175 const PetscInt *cone = NULL; 176 PetscInt numAdj = 0, maxAdjSize = *adjSize, coneSize, c; 177 PetscErrorCode ierr; 178 179 PetscFunctionBeginHot; 180 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 181 ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr); 182 for (c = 0; c < coneSize; ++c) { 183 const PetscInt *support = NULL; 184 PetscInt supportSize, s, q; 185 186 ierr = DMPlexGetSupportSize(dm, cone[c], &supportSize);CHKERRQ(ierr); 187 ierr = DMPlexGetSupport(dm, cone[c], &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 *cone = NULL; 212 PetscInt coneSize, c, q; 213 214 ierr = DMPlexGetConeSize(dm, support[s], &coneSize);CHKERRQ(ierr); 215 ierr = DMPlexGetCone(dm, support[s], &cone);CHKERRQ(ierr); 216 for (c = 0; c < coneSize; ++c) { 217 for (q = 0; q < numAdj || (adj[numAdj++] = cone[c],0); ++q) { 218 if (cone[c] == adj[q]) break; 219 } 220 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 221 } 222 } 223 *adjSize = numAdj; 224 PetscFunctionReturn(0); 225 } 226 227 #undef __FUNCT__ 228 #define __FUNCT__ "DMPlexGetAdjacency_Transitive_Internal" 229 static PetscErrorCode DMPlexGetAdjacency_Transitive_Internal(DM dm, PetscInt p, PetscBool useClosure, PetscInt *adjSize, PetscInt adj[]) 230 { 231 PetscInt *star = NULL; 232 PetscInt numAdj = 0, maxAdjSize = *adjSize, starSize, s; 233 PetscErrorCode ierr; 234 235 PetscFunctionBeginHot; 236 ierr = DMPlexGetTransitiveClosure(dm, p, useClosure, &starSize, &star);CHKERRQ(ierr); 237 for (s = 0; s < starSize*2; s += 2) { 238 const PetscInt *closure = NULL; 239 PetscInt closureSize, c, q; 240 241 ierr = DMPlexGetTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);CHKERRQ(ierr); 242 for (c = 0; c < closureSize*2; c += 2) { 243 for (q = 0; q < numAdj || (adj[numAdj++] = closure[c],0); ++q) { 244 if (closure[c] == adj[q]) break; 245 } 246 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 247 } 248 ierr = DMPlexRestoreTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);CHKERRQ(ierr); 249 } 250 ierr = DMPlexRestoreTransitiveClosure(dm, p, useClosure, &starSize, &star);CHKERRQ(ierr); 251 *adjSize = numAdj; 252 PetscFunctionReturn(0); 253 } 254 255 #undef __FUNCT__ 256 #define __FUNCT__ "DMPlexGetAdjacency_Internal" 257 PetscErrorCode DMPlexGetAdjacency_Internal(DM dm, PetscInt p, PetscBool useCone, PetscBool useTransitiveClosure, PetscBool useAnchors, PetscInt *adjSize, PetscInt *adj[]) 258 { 259 static PetscInt asiz = 0; 260 PetscInt maxAnchors = 1; 261 PetscInt aStart = -1, aEnd = -1; 262 PetscInt maxAdjSize; 263 PetscSection aSec = NULL; 264 IS aIS = NULL; 265 const PetscInt *anchors; 266 PetscErrorCode ierr; 267 268 PetscFunctionBeginHot; 269 if (useAnchors) { 270 ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); 271 if (aSec) { 272 ierr = PetscSectionGetMaxDof(aSec,&maxAnchors);CHKERRQ(ierr); 273 maxAnchors = PetscMax(1,maxAnchors); 274 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 275 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 276 } 277 } 278 if (!*adj) { 279 PetscInt depth, coneSeries, supportSeries, maxC, maxS, pStart, pEnd; 280 281 ierr = DMPlexGetChart(dm, &pStart,&pEnd);CHKERRQ(ierr); 282 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 283 ierr = DMPlexGetMaxSizes(dm, &maxC, &maxS);CHKERRQ(ierr); 284 coneSeries = (maxC > 1) ? ((PetscPowInt(maxC,depth+1)-1)/(maxC-1)) : depth+1; 285 supportSeries = (maxS > 1) ? ((PetscPowInt(maxS,depth+1)-1)/(maxS-1)) : depth+1; 286 asiz = PetscMax(PetscPowInt(maxS,depth)*coneSeries,PetscPowInt(maxC,depth)*supportSeries); 287 asiz *= maxAnchors; 288 asiz = PetscMin(asiz,pEnd-pStart); 289 ierr = PetscMalloc1(asiz,adj);CHKERRQ(ierr); 290 } 291 if (*adjSize < 0) *adjSize = asiz; 292 maxAdjSize = *adjSize; 293 if (useTransitiveClosure) { 294 ierr = DMPlexGetAdjacency_Transitive_Internal(dm, p, useCone, adjSize, *adj);CHKERRQ(ierr); 295 } else if (useCone) { 296 ierr = DMPlexGetAdjacency_Cone_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); 297 } else { 298 ierr = DMPlexGetAdjacency_Support_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); 299 } 300 if (useAnchors && aSec) { 301 PetscInt origSize = *adjSize; 302 PetscInt numAdj = origSize; 303 PetscInt i = 0, j; 304 PetscInt *orig = *adj; 305 306 while (i < origSize) { 307 PetscInt p = orig[i]; 308 PetscInt aDof = 0; 309 310 if (p >= aStart && p < aEnd) { 311 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 312 } 313 if (aDof) { 314 PetscInt aOff; 315 PetscInt s, q; 316 317 for (j = i + 1; j < numAdj; j++) { 318 orig[j - 1] = orig[j]; 319 } 320 origSize--; 321 numAdj--; 322 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 323 for (s = 0; s < aDof; ++s) { 324 for (q = 0; q < numAdj || (orig[numAdj++] = anchors[aOff+s],0); ++q) { 325 if (anchors[aOff+s] == orig[q]) break; 326 } 327 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 328 } 329 } 330 else { 331 i++; 332 } 333 } 334 *adjSize = numAdj; 335 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 336 } 337 PetscFunctionReturn(0); 338 } 339 340 #undef __FUNCT__ 341 #define __FUNCT__ "DMPlexGetAdjacency" 342 /*@ 343 DMPlexGetAdjacency - Return all points adjacent to the given point 344 345 Input Parameters: 346 + dm - The DM object 347 . p - The point 348 . adjSize - The maximum size of adj if it is non-NULL, or PETSC_DETERMINE 349 - adj - Either NULL so that the array is allocated, or an existing array with size adjSize 350 351 Output Parameters: 352 + adjSize - The number of adjacent points 353 - adj - The adjacent points 354 355 Level: advanced 356 357 Notes: The user must PetscFree the adj array if it was not passed in. 358 359 .seealso: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexDistribute(), DMCreateMatrix(), DMPlexPreallocateOperator() 360 @*/ 361 PetscErrorCode DMPlexGetAdjacency(DM dm, PetscInt p, PetscInt *adjSize, PetscInt *adj[]) 362 { 363 DM_Plex *mesh = (DM_Plex *) dm->data; 364 PetscErrorCode ierr; 365 366 PetscFunctionBeginHot; 367 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 368 PetscValidPointer(adjSize,3); 369 PetscValidPointer(adj,4); 370 ierr = DMPlexGetAdjacency_Internal(dm, p, mesh->useCone, mesh->useClosure, mesh->useAnchors, adjSize, adj);CHKERRQ(ierr); 371 PetscFunctionReturn(0); 372 } 373 #undef __FUNCT__ 374 #define __FUNCT__ "DMPlexCreateTwoSidedProcessSF" 375 /*@ 376 DMPlexCreateTwoSidedProcessSF - Create an SF which just has process connectivity 377 378 Collective on DM 379 380 Input Parameters: 381 + dm - The DM 382 - sfPoint - The PetscSF which encodes point connectivity 383 384 Output Parameters: 385 + processRanks - A list of process neighbors, or NULL 386 - sfProcess - An SF encoding the two-sided process connectivity, or NULL 387 388 Level: developer 389 390 .seealso: PetscSFCreate(), DMPlexCreateProcessSF() 391 @*/ 392 PetscErrorCode DMPlexCreateTwoSidedProcessSF(DM dm, PetscSF sfPoint, PetscSection rootRankSection, IS rootRanks, PetscSection leafRankSection, IS leafRanks, IS *processRanks, PetscSF *sfProcess) 393 { 394 const PetscSFNode *remotePoints; 395 PetscInt *localPointsNew; 396 PetscSFNode *remotePointsNew; 397 const PetscInt *nranks; 398 PetscInt *ranksNew; 399 PetscBT neighbors; 400 PetscInt pStart, pEnd, p, numLeaves, l, numNeighbors, n; 401 PetscMPIInt numProcs, proc, rank; 402 PetscErrorCode ierr; 403 404 PetscFunctionBegin; 405 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 406 PetscValidHeaderSpecific(sfPoint, PETSCSF_CLASSID, 2); 407 if (processRanks) {PetscValidPointer(processRanks, 3);} 408 if (sfProcess) {PetscValidPointer(sfProcess, 4);} 409 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &numProcs);CHKERRQ(ierr); 410 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 411 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, NULL, &remotePoints);CHKERRQ(ierr); 412 ierr = PetscBTCreate(numProcs, &neighbors);CHKERRQ(ierr); 413 ierr = PetscBTMemzero(numProcs, neighbors);CHKERRQ(ierr); 414 /* Compute root-to-leaf process connectivity */ 415 ierr = PetscSectionGetChart(rootRankSection, &pStart, &pEnd);CHKERRQ(ierr); 416 ierr = ISGetIndices(rootRanks, &nranks);CHKERRQ(ierr); 417 for (p = pStart; p < pEnd; ++p) { 418 PetscInt ndof, noff, n; 419 420 ierr = PetscSectionGetDof(rootRankSection, p, &ndof);CHKERRQ(ierr); 421 ierr = PetscSectionGetOffset(rootRankSection, p, &noff);CHKERRQ(ierr); 422 for (n = 0; n < ndof; ++n) {ierr = PetscBTSet(neighbors, nranks[noff+n]);} 423 } 424 ierr = ISRestoreIndices(rootRanks, &nranks);CHKERRQ(ierr); 425 /* Compute leaf-to-neighbor process connectivity */ 426 ierr = PetscSectionGetChart(leafRankSection, &pStart, &pEnd);CHKERRQ(ierr); 427 ierr = ISGetIndices(leafRanks, &nranks);CHKERRQ(ierr); 428 for (p = pStart; p < pEnd; ++p) { 429 PetscInt ndof, noff, n; 430 431 ierr = PetscSectionGetDof(leafRankSection, p, &ndof);CHKERRQ(ierr); 432 ierr = PetscSectionGetOffset(leafRankSection, p, &noff);CHKERRQ(ierr); 433 for (n = 0; n < ndof; ++n) {ierr = PetscBTSet(neighbors, nranks[noff+n]);} 434 } 435 ierr = ISRestoreIndices(leafRanks, &nranks);CHKERRQ(ierr); 436 /* Compute leaf-to-root process connectivity */ 437 for (l = 0; l < numLeaves; ++l) {PetscBTSet(neighbors, remotePoints[l].rank);} 438 /* Calculate edges */ 439 PetscBTClear(neighbors, rank); 440 for(proc = 0, numNeighbors = 0; proc < numProcs; ++proc) {if (PetscBTLookup(neighbors, proc)) ++numNeighbors;} 441 ierr = PetscMalloc1(numNeighbors, &ranksNew);CHKERRQ(ierr); 442 ierr = PetscMalloc1(numNeighbors, &localPointsNew);CHKERRQ(ierr); 443 ierr = PetscMalloc1(numNeighbors, &remotePointsNew);CHKERRQ(ierr); 444 for(proc = 0, n = 0; proc < numProcs; ++proc) { 445 if (PetscBTLookup(neighbors, proc)) { 446 ranksNew[n] = proc; 447 localPointsNew[n] = proc; 448 remotePointsNew[n].index = rank; 449 remotePointsNew[n].rank = proc; 450 ++n; 451 } 452 } 453 ierr = PetscBTDestroy(&neighbors);CHKERRQ(ierr); 454 if (processRanks) {ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), numNeighbors, ranksNew, PETSC_OWN_POINTER, processRanks);CHKERRQ(ierr);} 455 else {ierr = PetscFree(ranksNew);CHKERRQ(ierr);} 456 if (sfProcess) { 457 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfProcess);CHKERRQ(ierr); 458 ierr = PetscObjectSetName((PetscObject) *sfProcess, "Two-Sided Process SF");CHKERRQ(ierr); 459 ierr = PetscSFSetFromOptions(*sfProcess);CHKERRQ(ierr); 460 ierr = PetscSFSetGraph(*sfProcess, numProcs, numNeighbors, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);CHKERRQ(ierr); 461 } 462 PetscFunctionReturn(0); 463 } 464 465 #undef __FUNCT__ 466 #define __FUNCT__ "DMPlexDistributeOwnership" 467 /*@ 468 DMPlexDistributeOwnership - Compute owner information for shared points. This basically gets two-sided for an SF. 469 470 Collective on DM 471 472 Input Parameter: 473 . dm - The DM 474 475 Output Parameters: 476 + rootSection - The number of leaves for a given root point 477 . rootrank - The rank of each edge into the root point 478 . leafSection - The number of processes sharing a given leaf point 479 - leafrank - The rank of each process sharing a leaf point 480 481 Level: developer 482 483 .seealso: DMPlexCreateOverlap() 484 @*/ 485 PetscErrorCode DMPlexDistributeOwnership(DM dm, PetscSection rootSection, IS *rootrank, PetscSection leafSection, IS *leafrank) 486 { 487 MPI_Comm comm; 488 PetscSF sfPoint; 489 const PetscInt *rootdegree; 490 PetscInt *myrank, *remoterank; 491 PetscInt pStart, pEnd, p, nedges; 492 PetscMPIInt rank; 493 PetscErrorCode ierr; 494 495 PetscFunctionBegin; 496 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 497 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 498 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 499 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 500 /* Compute number of leaves for each root */ 501 ierr = PetscObjectSetName((PetscObject) rootSection, "Root Section");CHKERRQ(ierr); 502 ierr = PetscSectionSetChart(rootSection, pStart, pEnd);CHKERRQ(ierr); 503 ierr = PetscSFComputeDegreeBegin(sfPoint, &rootdegree);CHKERRQ(ierr); 504 ierr = PetscSFComputeDegreeEnd(sfPoint, &rootdegree);CHKERRQ(ierr); 505 for (p = pStart; p < pEnd; ++p) {ierr = PetscSectionSetDof(rootSection, p, rootdegree[p-pStart]);CHKERRQ(ierr);} 506 ierr = PetscSectionSetUp(rootSection);CHKERRQ(ierr); 507 /* Gather rank of each leaf to root */ 508 ierr = PetscSectionGetStorageSize(rootSection, &nedges);CHKERRQ(ierr); 509 ierr = PetscMalloc1(pEnd-pStart, &myrank);CHKERRQ(ierr); 510 ierr = PetscMalloc1(nedges, &remoterank);CHKERRQ(ierr); 511 for (p = 0; p < pEnd-pStart; ++p) myrank[p] = rank; 512 ierr = PetscSFGatherBegin(sfPoint, MPIU_INT, myrank, remoterank);CHKERRQ(ierr); 513 ierr = PetscSFGatherEnd(sfPoint, MPIU_INT, myrank, remoterank);CHKERRQ(ierr); 514 ierr = PetscFree(myrank);CHKERRQ(ierr); 515 ierr = ISCreateGeneral(comm, nedges, remoterank, PETSC_OWN_POINTER, rootrank);CHKERRQ(ierr); 516 /* Distribute remote ranks to leaves */ 517 ierr = PetscObjectSetName((PetscObject) leafSection, "Leaf Section");CHKERRQ(ierr); 518 ierr = DMPlexDistributeFieldIS(dm, sfPoint, rootSection, *rootrank, leafSection, leafrank);CHKERRQ(ierr); 519 PetscFunctionReturn(0); 520 } 521 522 #undef __FUNCT__ 523 #define __FUNCT__ "DMPlexCreateOverlap" 524 /*@C 525 DMPlexCreateOverlap - Compute owner information for shared points. This basically gets two-sided for an SF. 526 527 Collective on DM 528 529 Input Parameters: 530 + dm - The DM 531 . rootSection - The number of leaves for a given root point 532 . rootrank - The rank of each edge into the root point 533 . leafSection - The number of processes sharing a given leaf point 534 - leafrank - The rank of each process sharing a leaf point 535 536 Output Parameters: 537 + ovRootSection - The number of new overlap points for each neighboring process 538 . ovRootPoints - The new overlap points for each neighboring process 539 . ovLeafSection - The number of new overlap points from each neighboring process 540 - ovLeafPoints - The new overlap points from each neighboring process 541 542 Level: developer 543 544 .seealso: DMPlexDistributeOwnership() 545 @*/ 546 PetscErrorCode DMPlexCreateOverlap(DM dm, PetscSection rootSection, IS rootrank, PetscSection leafSection, IS leafrank, PetscSection ovRootSection, PetscSFNode **ovRootPoints, PetscSection ovLeafSection, PetscSFNode **ovLeafPoints) 547 { 548 DMLabel ovAdjByRank; /* A DMLabel containing all points adjacent to shared points, separated by rank (value in label) */ 549 PetscSF sfPoint, sfProc; 550 IS valueIS; 551 const PetscSFNode *remote; 552 const PetscInt *local; 553 const PetscInt *nrank, *rrank, *neighbors; 554 PetscInt *adj = NULL; 555 PetscInt pStart, pEnd, p, sStart, sEnd, nleaves, l, numNeighbors, n, ovSize; 556 PetscMPIInt rank, numProcs; 557 PetscErrorCode ierr; 558 559 PetscFunctionBegin; 560 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &numProcs);CHKERRQ(ierr); 561 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 562 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 563 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 564 ierr = PetscSectionGetChart(leafSection, &sStart, &sEnd);CHKERRQ(ierr); 565 ierr = PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);CHKERRQ(ierr); 566 ierr = DMLabelCreate("Overlap adjacency", &ovAdjByRank);CHKERRQ(ierr); 567 /* Handle leaves: shared with the root point */ 568 for (l = 0; l < nleaves; ++l) { 569 PetscInt adjSize = PETSC_DETERMINE, a; 570 571 ierr = DMPlexGetAdjacency(dm, local[l], &adjSize, &adj);CHKERRQ(ierr); 572 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remote[l].rank);CHKERRQ(ierr);} 573 } 574 ierr = ISGetIndices(rootrank, &rrank);CHKERRQ(ierr); 575 ierr = ISGetIndices(leafrank, &nrank);CHKERRQ(ierr); 576 /* Handle roots */ 577 for (p = pStart; p < pEnd; ++p) { 578 PetscInt adjSize = PETSC_DETERMINE, neighbors = 0, noff, n, a; 579 580 if ((p >= sStart) && (p < sEnd)) { 581 /* Some leaves share a root with other leaves on different processes */ 582 ierr = PetscSectionGetDof(leafSection, p, &neighbors);CHKERRQ(ierr); 583 if (neighbors) { 584 ierr = PetscSectionGetOffset(leafSection, p, &noff);CHKERRQ(ierr); 585 ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj);CHKERRQ(ierr); 586 for (n = 0; n < neighbors; ++n) { 587 const PetscInt remoteRank = nrank[noff+n]; 588 589 if (remoteRank == rank) continue; 590 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);CHKERRQ(ierr);} 591 } 592 } 593 } 594 /* Roots are shared with leaves */ 595 ierr = PetscSectionGetDof(rootSection, p, &neighbors);CHKERRQ(ierr); 596 if (!neighbors) continue; 597 ierr = PetscSectionGetOffset(rootSection, p, &noff);CHKERRQ(ierr); 598 ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj);CHKERRQ(ierr); 599 for (n = 0; n < neighbors; ++n) { 600 const PetscInt remoteRank = rrank[noff+n]; 601 602 if (remoteRank == rank) continue; 603 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);CHKERRQ(ierr);} 604 } 605 } 606 ierr = PetscFree(adj);CHKERRQ(ierr); 607 ierr = ISRestoreIndices(rootrank, &rrank);CHKERRQ(ierr); 608 ierr = ISRestoreIndices(leafrank, &nrank);CHKERRQ(ierr); 609 { 610 ierr = PetscViewerASCIISynchronizedAllow(PETSC_VIEWER_STDOUT_WORLD, PETSC_TRUE);CHKERRQ(ierr); 611 ierr = DMLabelView(ovAdjByRank, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 612 } 613 /* Convert to (point, rank) and use actual owners */ 614 ierr = PetscSectionSetChart(ovRootSection, 0, numProcs);CHKERRQ(ierr); 615 ierr = DMLabelGetValueIS(ovAdjByRank, &valueIS);CHKERRQ(ierr); 616 ierr = ISGetLocalSize(valueIS, &numNeighbors);CHKERRQ(ierr); 617 ierr = ISGetIndices(valueIS, &neighbors);CHKERRQ(ierr); 618 for (n = 0; n < numNeighbors; ++n) { 619 PetscInt numPoints; 620 621 ierr = DMLabelGetStratumSize(ovAdjByRank, neighbors[n], &numPoints);CHKERRQ(ierr); 622 ierr = PetscSectionAddDof(ovRootSection, neighbors[n], numPoints);CHKERRQ(ierr); 623 } 624 ierr = PetscSectionSetUp(ovRootSection);CHKERRQ(ierr); 625 ierr = PetscSectionGetStorageSize(ovRootSection, &ovSize);CHKERRQ(ierr); 626 ierr = PetscMalloc1(ovSize, ovRootPoints);CHKERRQ(ierr); 627 ierr = PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);CHKERRQ(ierr); 628 for (n = 0; n < numNeighbors; ++n) { 629 IS pointIS; 630 const PetscInt *points; 631 PetscInt off, numPoints, p; 632 633 ierr = PetscSectionGetOffset(ovRootSection, neighbors[n], &off);CHKERRQ(ierr); 634 ierr = DMLabelGetStratumIS(ovAdjByRank, neighbors[n], &pointIS);CHKERRQ(ierr); 635 ierr = ISGetLocalSize(pointIS, &numPoints);CHKERRQ(ierr); 636 ierr = ISGetIndices(pointIS, &points);CHKERRQ(ierr); 637 for (p = 0; p < numPoints; ++p) { 638 ierr = PetscFindInt(points[p], nleaves, local, &l);CHKERRQ(ierr); 639 if (l >= 0) {(*ovRootPoints)[off+p] = remote[l];} 640 else {(*ovRootPoints)[off+p].index = points[p]; (*ovRootPoints)[off+p].rank = rank;} 641 } 642 ierr = ISRestoreIndices(pointIS, &points);CHKERRQ(ierr); 643 ierr = ISDestroy(&pointIS);CHKERRQ(ierr); 644 } 645 ierr = ISRestoreIndices(valueIS, &neighbors);CHKERRQ(ierr); 646 ierr = ISDestroy(&valueIS);CHKERRQ(ierr); 647 ierr = DMLabelDestroy(&ovAdjByRank);CHKERRQ(ierr); 648 /* Make process SF */ 649 ierr = DMPlexCreateTwoSidedProcessSF(dm, sfPoint, rootSection, rootrank, leafSection, leafrank, NULL, &sfProc);CHKERRQ(ierr); 650 { 651 ierr = PetscSFView(sfProc, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 652 } 653 /* Communicate overlap */ 654 ierr = DMPlexDistributeData(dm, sfProc, ovRootSection, MPIU_2INT, (void *) *ovRootPoints, ovLeafSection, (void **) ovLeafPoints);CHKERRQ(ierr); 655 ierr = PetscSFDestroy(&sfProc);CHKERRQ(ierr); 656 PetscFunctionReturn(0); 657 } 658 659 #undef __FUNCT__ 660 #define __FUNCT__ "DMPlexDistributeField" 661 /*@ 662 DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 663 664 Collective on DM 665 666 Input Parameters: 667 + dm - The DMPlex object 668 . pointSF - The PetscSF describing the communication pattern 669 . originalSection - The PetscSection for existing data layout 670 - originalVec - The existing data 671 672 Output Parameters: 673 + newSection - The PetscSF describing the new data layout 674 - newVec - The new data 675 676 Level: developer 677 678 .seealso: DMPlexDistribute(), DMPlexDistributeFieldIS(), DMPlexDistributeData() 679 @*/ 680 PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec) 681 { 682 PetscSF fieldSF; 683 PetscInt *remoteOffsets, fieldSize; 684 PetscScalar *originalValues, *newValues; 685 PetscErrorCode ierr; 686 687 PetscFunctionBegin; 688 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 689 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 690 691 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 692 ierr = VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);CHKERRQ(ierr); 693 ierr = VecSetType(newVec,dm->vectype);CHKERRQ(ierr); 694 695 ierr = VecGetArray(originalVec, &originalValues);CHKERRQ(ierr); 696 ierr = VecGetArray(newVec, &newValues);CHKERRQ(ierr); 697 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 698 ierr = PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); 699 ierr = PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); 700 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 701 ierr = VecRestoreArray(newVec, &newValues);CHKERRQ(ierr); 702 ierr = VecRestoreArray(originalVec, &originalValues);CHKERRQ(ierr); 703 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 704 PetscFunctionReturn(0); 705 } 706 707 #undef __FUNCT__ 708 #define __FUNCT__ "DMPlexDistributeFieldIS" 709 /*@ 710 DMPlexDistributeFieldIS - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 711 712 Collective on DM 713 714 Input Parameters: 715 + dm - The DMPlex object 716 . pointSF - The PetscSF describing the communication pattern 717 . originalSection - The PetscSection for existing data layout 718 - originalIS - The existing data 719 720 Output Parameters: 721 + newSection - The PetscSF describing the new data layout 722 - newIS - The new data 723 724 Level: developer 725 726 .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexDistributeData() 727 @*/ 728 PetscErrorCode DMPlexDistributeFieldIS(DM dm, PetscSF pointSF, PetscSection originalSection, IS originalIS, PetscSection newSection, IS *newIS) 729 { 730 PetscSF fieldSF; 731 PetscInt *newValues, *remoteOffsets, fieldSize; 732 const PetscInt *originalValues; 733 PetscErrorCode ierr; 734 735 PetscFunctionBegin; 736 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 737 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 738 739 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 740 ierr = PetscMalloc(fieldSize * sizeof(PetscInt), &newValues);CHKERRQ(ierr); 741 742 ierr = ISGetIndices(originalIS, &originalValues);CHKERRQ(ierr); 743 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 744 ierr = PetscSFBcastBegin(fieldSF, MPIU_INT, originalValues, newValues);CHKERRQ(ierr); 745 ierr = PetscSFBcastEnd(fieldSF, MPIU_INT, originalValues, newValues);CHKERRQ(ierr); 746 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 747 ierr = ISRestoreIndices(originalIS, &originalValues);CHKERRQ(ierr); 748 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) pointSF), fieldSize, newValues, PETSC_OWN_POINTER, newIS);CHKERRQ(ierr); 749 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 750 PetscFunctionReturn(0); 751 } 752 753 #undef __FUNCT__ 754 #define __FUNCT__ "DMPlexDistributeData" 755 /*@ 756 DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 757 758 Collective on DM 759 760 Input Parameters: 761 + dm - The DMPlex object 762 . pointSF - The PetscSF describing the communication pattern 763 . originalSection - The PetscSection for existing data layout 764 . datatype - The type of data 765 - originalData - The existing data 766 767 Output Parameters: 768 + newSection - The PetscSection describing the new data layout 769 - newData - The new data 770 771 Level: developer 772 773 .seealso: DMPlexDistribute(), DMPlexDistributeField() 774 @*/ 775 PetscErrorCode DMPlexDistributeData(DM dm, PetscSF pointSF, PetscSection originalSection, MPI_Datatype datatype, void *originalData, PetscSection newSection, void **newData) 776 { 777 PetscSF fieldSF; 778 PetscInt *remoteOffsets, fieldSize; 779 PetscMPIInt dataSize; 780 PetscErrorCode ierr; 781 782 PetscFunctionBegin; 783 ierr = PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 784 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 785 786 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 787 ierr = MPI_Type_size(datatype, &dataSize);CHKERRQ(ierr); 788 ierr = PetscMalloc(fieldSize * dataSize, newData);CHKERRQ(ierr); 789 790 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 791 ierr = PetscSFBcastBegin(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr); 792 ierr = PetscSFBcastEnd(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr); 793 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 794 ierr = PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 795 PetscFunctionReturn(0); 796 } 797 798 #undef __FUNCT__ 799 #define __FUNCT__ "DMPlexDistributeCones" 800 PetscErrorCode DMPlexDistributeCones(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel) 801 { 802 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 803 MPI_Comm comm; 804 PetscSF coneSF; 805 PetscSection originalConeSection, newConeSection; 806 PetscInt *remoteOffsets, *cones, *newCones, newConesSize; 807 PetscBool flg; 808 PetscErrorCode ierr; 809 810 PetscFunctionBegin; 811 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 812 PetscValidPointer(dmParallel,4); 813 ierr = PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 814 815 /* Distribute cone section */ 816 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 817 ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr); 818 ierr = DMPlexGetConeSection(dmParallel, &newConeSection);CHKERRQ(ierr); 819 ierr = PetscSFDistributeSection(migrationSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr); 820 ierr = DMSetUp(dmParallel);CHKERRQ(ierr); 821 { 822 PetscInt pStart, pEnd, p; 823 824 ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr); 825 for (p = pStart; p < pEnd; ++p) { 826 PetscInt coneSize; 827 ierr = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr); 828 pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize); 829 } 830 } 831 /* Communicate and renumber cones */ 832 ierr = PetscSFCreateSectionSF(migrationSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr); 833 ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); 834 ierr = DMPlexGetCones(dmParallel, &newCones);CHKERRQ(ierr); 835 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 836 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 837 ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr); 838 ierr = ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);CHKERRQ(ierr); 839 ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr); 840 if (flg) { 841 ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr); 842 ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 843 ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr); 844 ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 845 ierr = PetscSFView(coneSF, NULL);CHKERRQ(ierr); 846 } 847 ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr); 848 ierr = DMPlexGetConeOrientations(dmParallel, &newCones);CHKERRQ(ierr); 849 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 850 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 851 ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr); 852 ierr = PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 853 /* Create supports and stratify sieve */ 854 { 855 PetscInt pStart, pEnd; 856 857 ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 858 ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr); 859 } 860 ierr = DMPlexSymmetrize(dmParallel);CHKERRQ(ierr); 861 ierr = DMPlexStratify(dmParallel);CHKERRQ(ierr); 862 PetscFunctionReturn(0); 863 } 864 865 #undef __FUNCT__ 866 #define __FUNCT__ "DMPlexDistribute" 867 /*@C 868 DMPlexDistribute - Distributes the mesh and any associated sections. 869 870 Not Collective 871 872 Input Parameter: 873 + dm - The original DMPlex object 874 . partitioner - The partitioning package, or NULL for the default 875 - overlap - The overlap of partitions, 0 is the default 876 877 Output Parameter: 878 + sf - The PetscSF used for point distribution 879 - parallelMesh - The distributed DMPlex object, or NULL 880 881 Note: If the mesh was not distributed, the return value is NULL. 882 883 The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and 884 DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function 885 representation on the mesh. 886 887 Level: intermediate 888 889 .keywords: mesh, elements 890 .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure() 891 @*/ 892 PetscErrorCode DMPlexDistribute(DM dm, const char partitioner[], PetscInt overlap, PetscSF *sf, DM *dmParallel) 893 { 894 DM_Plex *mesh = (DM_Plex*) dm->data, *pmesh; 895 MPI_Comm comm; 896 PetscInt dim, numRemoteRanks; 897 IS origCellPart, origPart, cellPart, part; 898 PetscSection origCellPartSection, origPartSection, cellPartSection, partSection; 899 PetscSFNode *remoteRanks; 900 PetscSF partSF, pointSF; 901 ISLocalToGlobalMapping renumbering; 902 PetscBool flg; 903 PetscMPIInt rank, numProcs, p; 904 PetscErrorCode ierr; 905 906 PetscFunctionBegin; 907 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 908 if (sf) PetscValidPointer(sf,4); 909 PetscValidPointer(dmParallel,5); 910 911 ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 912 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 913 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 914 ierr = MPI_Comm_size(comm, &numProcs);CHKERRQ(ierr); 915 916 *dmParallel = NULL; 917 if (numProcs == 1) PetscFunctionReturn(0); 918 919 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 920 /* Create cell partition - We need to rewrite to use IS, use the MatPartition stuff */ 921 ierr = PetscLogEventBegin(PETSCPARTITIONER_Partition,dm,0,0,0);CHKERRQ(ierr); 922 if (overlap > 1) SETERRQ(comm, PETSC_ERR_SUP, "Overlap > 1 not yet implemented"); 923 ierr = PetscSectionCreate(comm, &cellPartSection);CHKERRQ(ierr); 924 ierr = PetscSectionCreate(comm, &origCellPartSection);CHKERRQ(ierr); 925 ierr = PetscPartitionerPartition(mesh->partitioner, dm, overlap > 0 ? PETSC_TRUE : PETSC_FALSE, cellPartSection, &cellPart, origCellPartSection, &origCellPart);CHKERRQ(ierr); 926 /* Create SF assuming a serial partition for all processes: Could check for IS length here */ 927 if (!rank) numRemoteRanks = numProcs; 928 else numRemoteRanks = 0; 929 ierr = PetscMalloc1(numRemoteRanks, &remoteRanks);CHKERRQ(ierr); 930 for (p = 0; p < numRemoteRanks; ++p) { 931 remoteRanks[p].rank = p; 932 remoteRanks[p].index = 0; 933 } 934 ierr = PetscSFCreate(comm, &partSF);CHKERRQ(ierr); 935 ierr = PetscSFSetGraph(partSF, 1, numRemoteRanks, NULL, PETSC_OWN_POINTER, remoteRanks, PETSC_OWN_POINTER);CHKERRQ(ierr); 936 ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 937 if (flg) { 938 ierr = PetscPrintf(comm, "Cell Partition:\n");CHKERRQ(ierr); 939 ierr = PetscSectionView(cellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 940 ierr = ISView(cellPart, NULL);CHKERRQ(ierr); 941 if (origCellPart) { 942 ierr = PetscPrintf(comm, "Original Cell Partition:\n");CHKERRQ(ierr); 943 ierr = PetscSectionView(origCellPartSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 944 ierr = ISView(origCellPart, NULL);CHKERRQ(ierr); 945 } 946 ierr = PetscSFView(partSF, NULL);CHKERRQ(ierr); 947 } 948 /* Close the partition over the mesh */ 949 ierr = DMPlexCreatePartitionClosure(dm, cellPartSection, cellPart, &partSection, &part);CHKERRQ(ierr); 950 ierr = ISDestroy(&cellPart);CHKERRQ(ierr); 951 ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr); 952 /* Create new mesh */ 953 ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr); 954 ierr = DMSetDimension(*dmParallel, dim);CHKERRQ(ierr); 955 ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr); 956 pmesh = (DM_Plex*) (*dmParallel)->data; 957 /* Distribute sieve points and the global point numbering (replaces creating remote bases) */ 958 ierr = PetscSFConvertPartition(partSF, partSection, part, &renumbering, &pointSF);CHKERRQ(ierr); 959 if (flg) { 960 ierr = PetscPrintf(comm, "Point Partition:\n");CHKERRQ(ierr); 961 ierr = PetscSectionView(partSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 962 ierr = ISView(part, NULL);CHKERRQ(ierr); 963 ierr = PetscSFView(pointSF, NULL);CHKERRQ(ierr); 964 ierr = PetscPrintf(comm, "Point Renumbering after partition:\n");CHKERRQ(ierr); 965 ierr = ISLocalToGlobalMappingView(renumbering, NULL);CHKERRQ(ierr); 966 } 967 ierr = PetscLogEventEnd(PETSCPARTITIONER_Partition,dm,0,0,0);CHKERRQ(ierr); 968 969 ierr = DMPlexDistributeCones(dm, pointSF, renumbering, *dmParallel);CHKERRQ(ierr); 970 971 /* Create point SF for parallel mesh */ 972 ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 973 { 974 const PetscInt *leaves; 975 PetscSFNode *remotePoints, *rowners, *lowners; 976 PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints; 977 PetscInt pStart, pEnd; 978 979 ierr = DMPlexGetChart(*dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 980 ierr = PetscSFGetGraph(pointSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr); 981 ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr); 982 for (p=0; p<numRoots; p++) { 983 rowners[p].rank = -1; 984 rowners[p].index = -1; 985 } 986 if (origCellPart) { 987 /* Make sure points in the original partition are not assigned to other procs */ 988 const PetscInt *origPoints; 989 990 ierr = DMPlexCreatePartitionClosure(dm, origCellPartSection, origCellPart, &origPartSection, &origPart);CHKERRQ(ierr); 991 ierr = ISGetIndices(origPart, &origPoints);CHKERRQ(ierr); 992 for (p = 0; p < numProcs; ++p) { 993 PetscInt dof, off, d; 994 995 ierr = PetscSectionGetDof(origPartSection, p, &dof);CHKERRQ(ierr); 996 ierr = PetscSectionGetOffset(origPartSection, p, &off);CHKERRQ(ierr); 997 for (d = off; d < off+dof; ++d) { 998 rowners[origPoints[d]].rank = p; 999 } 1000 } 1001 ierr = ISRestoreIndices(origPart, &origPoints);CHKERRQ(ierr); 1002 ierr = ISDestroy(&origPart);CHKERRQ(ierr); 1003 ierr = PetscSectionDestroy(&origPartSection);CHKERRQ(ierr); 1004 } 1005 ierr = ISDestroy(&origCellPart);CHKERRQ(ierr); 1006 ierr = PetscSectionDestroy(&origCellPartSection);CHKERRQ(ierr); 1007 1008 ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1009 ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1010 for (p = 0; p < numLeaves; ++p) { 1011 if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */ 1012 lowners[p].rank = rank; 1013 lowners[p].index = leaves ? leaves[p] : p; 1014 } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */ 1015 lowners[p].rank = -2; 1016 lowners[p].index = -2; 1017 } 1018 } 1019 for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */ 1020 rowners[p].rank = -3; 1021 rowners[p].index = -3; 1022 } 1023 ierr = PetscSFReduceBegin(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1024 ierr = PetscSFReduceEnd(pointSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1025 ierr = PetscSFBcastBegin(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1026 ierr = PetscSFBcastEnd(pointSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1027 for (p = 0; p < numLeaves; ++p) { 1028 if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed"); 1029 if (lowners[p].rank != rank) ++numGhostPoints; 1030 } 1031 ierr = PetscMalloc1(numGhostPoints, &ghostPoints);CHKERRQ(ierr); 1032 ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr); 1033 for (p = 0, gp = 0; p < numLeaves; ++p) { 1034 if (lowners[p].rank != rank) { 1035 ghostPoints[gp] = leaves ? leaves[p] : p; 1036 remotePoints[gp].rank = lowners[p].rank; 1037 remotePoints[gp].index = lowners[p].index; 1038 ++gp; 1039 } 1040 } 1041 ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr); 1042 ierr = PetscSFSetGraph((*dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 1043 ierr = PetscSFSetFromOptions((*dmParallel)->sf);CHKERRQ(ierr); 1044 } 1045 pmesh->useCone = mesh->useCone; 1046 pmesh->useClosure = mesh->useClosure; 1047 pmesh->useAnchors = mesh->useAnchors; 1048 ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1049 /* Distribute Coordinates */ 1050 { 1051 PetscSection originalCoordSection, newCoordSection; 1052 Vec originalCoordinates, newCoordinates; 1053 PetscInt bs; 1054 const char *name; 1055 const PetscReal *maxCell, *L; 1056 1057 ierr = DMGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr); 1058 ierr = DMGetCoordinateSection(*dmParallel, &newCoordSection);CHKERRQ(ierr); 1059 ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr); 1060 if (originalCoordinates) { 1061 ierr = VecCreate(comm, &newCoordinates);CHKERRQ(ierr); 1062 ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr); 1063 ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr); 1064 1065 ierr = DMPlexDistributeField(dm, pointSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr); 1066 ierr = DMSetCoordinatesLocal(*dmParallel, newCoordinates);CHKERRQ(ierr); 1067 ierr = VecGetBlockSize(originalCoordinates, &bs);CHKERRQ(ierr); 1068 ierr = VecSetBlockSize(newCoordinates, bs);CHKERRQ(ierr); 1069 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 1070 } 1071 ierr = DMGetPeriodicity(dm, &maxCell, &L);CHKERRQ(ierr); 1072 if (L) {ierr = DMSetPeriodicity(*dmParallel, maxCell, L);CHKERRQ(ierr);} 1073 } 1074 /* Distribute labels */ 1075 ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1076 { 1077 DMLabel next = mesh->labels, newNext = pmesh->labels; 1078 PetscInt numLabels = 0, l; 1079 1080 /* Bcast number of labels */ 1081 while (next) {++numLabels; next = next->next;} 1082 ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1083 next = mesh->labels; 1084 for (l = 0; l < numLabels; ++l) { 1085 DMLabel labelNew; 1086 PetscBool isdepth; 1087 1088 /* Skip "depth" because it is recreated */ 1089 if (!rank) {ierr = PetscStrcmp(next->name, "depth", &isdepth);CHKERRQ(ierr);} 1090 ierr = MPI_Bcast(&isdepth, 1, MPIU_BOOL, 0, comm);CHKERRQ(ierr); 1091 if (isdepth) {if (!rank) next = next->next; continue;} 1092 ierr = DMLabelDistribute(next, partSection, part, renumbering, &labelNew);CHKERRQ(ierr); 1093 /* Insert into list */ 1094 if (newNext) newNext->next = labelNew; 1095 else pmesh->labels = labelNew; 1096 newNext = labelNew; 1097 if (!rank) next = next->next; 1098 } 1099 } 1100 ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1101 /* Setup hybrid structure */ 1102 { 1103 const PetscInt *gpoints; 1104 PetscInt depth, n, d; 1105 1106 for (d = 0; d <= dim; ++d) {pmesh->hybridPointMax[d] = mesh->hybridPointMax[d];} 1107 ierr = MPI_Bcast(pmesh->hybridPointMax, dim+1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1108 ierr = ISLocalToGlobalMappingGetSize(renumbering, &n);CHKERRQ(ierr); 1109 ierr = ISLocalToGlobalMappingGetIndices(renumbering, &gpoints);CHKERRQ(ierr); 1110 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1111 for (d = 0; d <= dim; ++d) { 1112 PetscInt pmax = pmesh->hybridPointMax[d], newmax = 0, pEnd, stratum[2], p; 1113 1114 if (pmax < 0) continue; 1115 ierr = DMPlexGetDepthStratum(dm, d > depth ? depth : d, &stratum[0], &stratum[1]);CHKERRQ(ierr); 1116 ierr = DMPlexGetDepthStratum(*dmParallel, d, NULL, &pEnd);CHKERRQ(ierr); 1117 ierr = MPI_Bcast(stratum, 2, MPIU_INT, 0, comm);CHKERRQ(ierr); 1118 for (p = 0; p < n; ++p) { 1119 const PetscInt point = gpoints[p]; 1120 1121 if ((point >= stratum[0]) && (point < stratum[1]) && (point >= pmax)) ++newmax; 1122 } 1123 if (newmax > 0) pmesh->hybridPointMax[d] = pEnd - newmax; 1124 else pmesh->hybridPointMax[d] = -1; 1125 } 1126 ierr = ISLocalToGlobalMappingRestoreIndices(renumbering, &gpoints);CHKERRQ(ierr); 1127 } 1128 /* Set up tree */ 1129 { 1130 DM refTree; 1131 PetscSection origParentSection, newParentSection; 1132 PetscInt *origParents, *origChildIDs; 1133 1134 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 1135 ierr = DMPlexSetReferenceTree(*dmParallel,refTree);CHKERRQ(ierr); 1136 ierr = DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);CHKERRQ(ierr); 1137 if (origParentSection) { 1138 PetscInt pStart, pEnd; 1139 PetscInt *newParents, *newChildIDs; 1140 PetscInt *remoteOffsetsParents, newParentSize; 1141 PetscSF parentSF; 1142 1143 ierr = DMPlexGetChart(*dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1144 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)*dmParallel),&newParentSection);CHKERRQ(ierr); 1145 ierr = PetscSectionSetChart(newParentSection,pStart,pEnd);CHKERRQ(ierr); 1146 ierr = PetscSFDistributeSection(pointSF, origParentSection, &remoteOffsetsParents, newParentSection);CHKERRQ(ierr); 1147 ierr = PetscSFCreateSectionSF(pointSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);CHKERRQ(ierr); 1148 ierr = PetscSectionGetStorageSize(newParentSection,&newParentSize);CHKERRQ(ierr); 1149 ierr = PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);CHKERRQ(ierr); 1150 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, origParents, newParents);CHKERRQ(ierr); 1151 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, origParents, newParents);CHKERRQ(ierr); 1152 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1153 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1154 ierr = ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);CHKERRQ(ierr); 1155 ierr = PetscOptionsHasName(((PetscObject) dm)->prefix, "-parents_view", &flg);CHKERRQ(ierr); 1156 if (flg) { 1157 ierr = PetscPrintf(comm, "Serial Parent Section: \n");CHKERRQ(ierr); 1158 ierr = PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1159 ierr = PetscPrintf(comm, "Parallel Parent Section: \n");CHKERRQ(ierr); 1160 ierr = PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1161 ierr = PetscSFView(parentSF, NULL);CHKERRQ(ierr); 1162 } 1163 ierr = DMPlexSetTree(*dmParallel,newParentSection,newParents,newChildIDs);CHKERRQ(ierr); 1164 ierr = PetscSectionDestroy(&newParentSection);CHKERRQ(ierr); 1165 ierr = PetscFree2(newParents,newChildIDs);CHKERRQ(ierr); 1166 ierr = PetscSFDestroy(&parentSF);CHKERRQ(ierr); 1167 } 1168 } 1169 /* Cleanup Partition */ 1170 ierr = ISLocalToGlobalMappingDestroy(&renumbering);CHKERRQ(ierr); 1171 ierr = PetscSFDestroy(&partSF);CHKERRQ(ierr); 1172 ierr = PetscSectionDestroy(&partSection);CHKERRQ(ierr); 1173 ierr = ISDestroy(&part);CHKERRQ(ierr); 1174 /* Copy BC */ 1175 ierr = DMPlexCopyBoundary(dm, *dmParallel);CHKERRQ(ierr); 1176 /* Cleanup */ 1177 if (sf) {*sf = pointSF;} 1178 else {ierr = PetscSFDestroy(&pointSF);CHKERRQ(ierr);} 1179 ierr = DMSetFromOptions(*dmParallel);CHKERRQ(ierr); 1180 ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1181 PetscFunctionReturn(0); 1182 } 1183