1 #include <petsc/private/dmpleximpl.h> /*I "petscdmplex.h" I*/ 2 #include <petsc/private/dmlabelimpl.h> /*I "petscdmlabel.h" I*/ 3 4 /*@C 5 DMPlexSetAdjacencyUser - Define adjacency in the mesh using a user-provided callback 6 7 Input Parameters: 8 + dm - The DM object 9 . user - The user callback, may be NULL (to clear the callback) 10 - ctx - context for callback evaluation, may be NULL 11 12 Level: advanced 13 14 Notes: 15 The caller of DMPlexGetAdjacency may need to arrange that a large enough array is available for the adjacency. 16 17 Any setting here overrides other configuration of DMPlex adjacency determination. 18 19 .seealso: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexGetAdjacency(), DMPlexGetAdjacencyUser() 20 @*/ 21 PetscErrorCode DMPlexSetAdjacencyUser(DM dm,PetscErrorCode (*user)(DM,PetscInt,PetscInt*,PetscInt[],void*),void *ctx) 22 { 23 DM_Plex *mesh = (DM_Plex *)dm->data; 24 25 PetscFunctionBegin; 26 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 27 mesh->useradjacency = user; 28 mesh->useradjacencyctx = ctx; 29 PetscFunctionReturn(0); 30 } 31 32 /*@C 33 DMPlexGetAdjacencyUser - get the user-defined adjacency callback 34 35 Input Parameter: 36 . dm - The DM object 37 38 Output Parameters: 39 - user - The user callback 40 - ctx - context for callback evaluation 41 42 Level: advanced 43 44 .seealso: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexGetAdjacency(), DMPlexSetAdjacencyUser() 45 @*/ 46 PetscErrorCode DMPlexGetAdjacencyUser(DM dm, PetscErrorCode (**user)(DM,PetscInt,PetscInt*,PetscInt[],void*), void **ctx) 47 { 48 DM_Plex *mesh = (DM_Plex *)dm->data; 49 50 PetscFunctionBegin; 51 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 52 if (user) *user = mesh->useradjacency; 53 if (ctx) *ctx = mesh->useradjacencyctx; 54 PetscFunctionReturn(0); 55 } 56 57 /*@ 58 DMPlexSetAdjacencyUseCone - Define adjacency in the mesh using either the cone or the support first 59 60 Input Parameters: 61 + dm - The DM object 62 - useCone - Flag to use the cone first 63 64 Level: intermediate 65 66 Notes: 67 $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE 68 $ FVM: Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE 69 $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE 70 71 .seealso: DMPlexGetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexGetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator() 72 @*/ 73 PetscErrorCode DMPlexSetAdjacencyUseCone(DM dm, PetscBool useCone) 74 { 75 PetscDS prob; 76 PetscBool useClosure; 77 PetscInt Nf; 78 PetscErrorCode ierr; 79 80 PetscFunctionBegin; 81 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 82 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 83 if (!Nf) { 84 ierr = PetscDSGetAdjacency(prob, PETSC_DEFAULT, NULL, &useClosure);CHKERRQ(ierr); 85 ierr = PetscDSSetAdjacency(prob, PETSC_DEFAULT, useCone, useClosure);CHKERRQ(ierr); 86 } else { 87 ierr = PetscDSGetAdjacency(prob, 0, NULL, &useClosure);CHKERRQ(ierr); 88 ierr = PetscDSSetAdjacency(prob, 0, useCone, useClosure);CHKERRQ(ierr); 89 } 90 PetscFunctionReturn(0); 91 } 92 93 /*@ 94 DMPlexGetAdjacencyUseCone - Query whether adjacency in the mesh uses the cone or the support first 95 96 Input Parameter: 97 . dm - The DM object 98 99 Output Parameter: 100 . useCone - Flag to use the cone first 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 support(p+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: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexGetAdjacencyUseClosure(), DMPlexDistribute(), DMPlexPreallocateOperator() 110 @*/ 111 PetscErrorCode DMPlexGetAdjacencyUseCone(DM dm, PetscBool *useCone) 112 { 113 PetscDS prob; 114 PetscInt Nf; 115 PetscErrorCode ierr; 116 117 PetscFunctionBegin; 118 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 119 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 120 if (!Nf) { 121 ierr = PetscDSGetAdjacency(prob, PETSC_DEFAULT, useCone, NULL);CHKERRQ(ierr); 122 } else { 123 ierr = PetscDSGetAdjacency(prob, 0, useCone, NULL);CHKERRQ(ierr); 124 } 125 PetscFunctionReturn(0); 126 } 127 128 /*@ 129 DMPlexSetAdjacencyUseClosure - Define adjacency in the mesh using the transitive closure 130 131 Input Parameters: 132 + dm - The DM object 133 - useClosure - Flag to use the closure 134 135 Level: intermediate 136 137 Notes: 138 $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE 139 $ FVM: Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE 140 $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE 141 142 .seealso: DMPlexGetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator() 143 @*/ 144 PetscErrorCode DMPlexSetAdjacencyUseClosure(DM dm, PetscBool useClosure) 145 { 146 PetscDS prob; 147 PetscBool useCone; 148 PetscInt Nf; 149 PetscErrorCode ierr; 150 151 PetscFunctionBegin; 152 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 153 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 154 if (!Nf) { 155 ierr = PetscDSGetAdjacency(prob, PETSC_DEFAULT, &useCone, NULL);CHKERRQ(ierr); 156 ierr = PetscDSSetAdjacency(prob, PETSC_DEFAULT, useCone, useClosure);CHKERRQ(ierr); 157 } else { 158 ierr = PetscDSGetAdjacency(prob, 0, &useCone, NULL);CHKERRQ(ierr); 159 ierr = PetscDSSetAdjacency(prob, 0, useCone, useClosure);CHKERRQ(ierr); 160 } 161 PetscFunctionReturn(0); 162 } 163 164 /*@ 165 DMPlexGetAdjacencyUseClosure - Query whether adjacency in the mesh uses the transitive closure 166 167 Input Parameter: 168 . dm - The DM object 169 170 Output Parameter: 171 . useClosure - Flag to use the closure 172 173 Level: intermediate 174 175 Notes: 176 $ FEM: Two points p and q are adjacent if q \in closure(star(p)), useCone = PETSC_FALSE, useClosure = PETSC_TRUE 177 $ FVM: Two points p and q are adjacent if q \in support(p+cone(p)), useCone = PETSC_TRUE, useClosure = PETSC_FALSE 178 $ FVM++: Two points p and q are adjacent if q \in star(closure(p)), useCone = PETSC_TRUE, useClosure = PETSC_TRUE 179 180 .seealso: DMPlexSetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator() 181 @*/ 182 PetscErrorCode DMPlexGetAdjacencyUseClosure(DM dm, PetscBool *useClosure) 183 { 184 PetscDS prob; 185 PetscInt Nf; 186 PetscErrorCode ierr; 187 188 PetscFunctionBegin; 189 ierr = DMGetDS(dm, &prob);CHKERRQ(ierr); 190 ierr = PetscDSGetNumFields(prob, &Nf);CHKERRQ(ierr); 191 if (!Nf) { 192 ierr = PetscDSGetAdjacency(prob, PETSC_DEFAULT, NULL, useClosure);CHKERRQ(ierr); 193 } else { 194 ierr = PetscDSGetAdjacency(prob, 0, NULL, useClosure);CHKERRQ(ierr); 195 } 196 PetscFunctionReturn(0); 197 } 198 199 /*@ 200 DMPlexSetAdjacencyUseAnchors - Define adjacency in the mesh using the point-to-point constraints. 201 202 Input Parameters: 203 + dm - The DM object 204 - useAnchors - Flag to use the constraints. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place. 205 206 Level: intermediate 207 208 .seealso: DMPlexGetAdjacencyUseClosure(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors() 209 @*/ 210 PetscErrorCode DMPlexSetAdjacencyUseAnchors(DM dm, PetscBool useAnchors) 211 { 212 DM_Plex *mesh = (DM_Plex *) dm->data; 213 214 PetscFunctionBegin; 215 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 216 mesh->useAnchors = useAnchors; 217 PetscFunctionReturn(0); 218 } 219 220 /*@ 221 DMPlexGetAdjacencyUseAnchors - Query whether adjacency in the mesh uses the point-to-point constraints. 222 223 Input Parameter: 224 . dm - The DM object 225 226 Output Parameter: 227 . useAnchors - Flag to use the closure. If PETSC_TRUE, then constrained points are omitted from DMPlexGetAdjacency(), and their anchor points appear in their place. 228 229 Level: intermediate 230 231 .seealso: DMPlexSetAdjacencyUseAnchors(), DMPlexSetAdjacencyUseCone(), DMPlexGetAdjacencyUseCone(), DMPlexDistribute(), DMPlexPreallocateOperator(), DMPlexSetAnchors() 232 @*/ 233 PetscErrorCode DMPlexGetAdjacencyUseAnchors(DM dm, PetscBool *useAnchors) 234 { 235 DM_Plex *mesh = (DM_Plex *) dm->data; 236 237 PetscFunctionBegin; 238 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 239 PetscValidIntPointer(useAnchors, 2); 240 *useAnchors = mesh->useAnchors; 241 PetscFunctionReturn(0); 242 } 243 244 static PetscErrorCode DMPlexGetAdjacency_Cone_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[]) 245 { 246 const PetscInt *cone = NULL; 247 PetscInt numAdj = 0, maxAdjSize = *adjSize, coneSize, c; 248 PetscErrorCode ierr; 249 250 PetscFunctionBeginHot; 251 ierr = DMPlexGetConeSize(dm, p, &coneSize);CHKERRQ(ierr); 252 ierr = DMPlexGetCone(dm, p, &cone);CHKERRQ(ierr); 253 for (c = 0; c <= coneSize; ++c) { 254 const PetscInt point = !c ? p : cone[c-1]; 255 const PetscInt *support = NULL; 256 PetscInt supportSize, s, q; 257 258 ierr = DMPlexGetSupportSize(dm, point, &supportSize);CHKERRQ(ierr); 259 ierr = DMPlexGetSupport(dm, point, &support);CHKERRQ(ierr); 260 for (s = 0; s < supportSize; ++s) { 261 for (q = 0; q < numAdj || ((void)(adj[numAdj++] = support[s]),0); ++q) { 262 if (support[s] == adj[q]) break; 263 } 264 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 265 } 266 } 267 *adjSize = numAdj; 268 PetscFunctionReturn(0); 269 } 270 271 static PetscErrorCode DMPlexGetAdjacency_Support_Internal(DM dm, PetscInt p, PetscInt *adjSize, PetscInt adj[]) 272 { 273 const PetscInt *support = NULL; 274 PetscInt numAdj = 0, maxAdjSize = *adjSize, supportSize, s; 275 PetscErrorCode ierr; 276 277 PetscFunctionBeginHot; 278 ierr = DMPlexGetSupportSize(dm, p, &supportSize);CHKERRQ(ierr); 279 ierr = DMPlexGetSupport(dm, p, &support);CHKERRQ(ierr); 280 for (s = 0; s <= supportSize; ++s) { 281 const PetscInt point = !s ? p : support[s-1]; 282 const PetscInt *cone = NULL; 283 PetscInt coneSize, c, q; 284 285 ierr = DMPlexGetConeSize(dm, point, &coneSize);CHKERRQ(ierr); 286 ierr = DMPlexGetCone(dm, point, &cone);CHKERRQ(ierr); 287 for (c = 0; c < coneSize; ++c) { 288 for (q = 0; q < numAdj || ((void)(adj[numAdj++] = cone[c]),0); ++q) { 289 if (cone[c] == adj[q]) break; 290 } 291 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 292 } 293 } 294 *adjSize = numAdj; 295 PetscFunctionReturn(0); 296 } 297 298 static PetscErrorCode DMPlexGetAdjacency_Transitive_Internal(DM dm, PetscInt p, PetscBool useClosure, PetscInt *adjSize, PetscInt adj[]) 299 { 300 PetscInt *star = NULL; 301 PetscInt numAdj = 0, maxAdjSize = *adjSize, starSize, s; 302 PetscErrorCode ierr; 303 304 PetscFunctionBeginHot; 305 ierr = DMPlexGetTransitiveClosure(dm, p, useClosure, &starSize, &star);CHKERRQ(ierr); 306 for (s = 0; s < starSize*2; s += 2) { 307 const PetscInt *closure = NULL; 308 PetscInt closureSize, c, q; 309 310 ierr = DMPlexGetTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);CHKERRQ(ierr); 311 for (c = 0; c < closureSize*2; c += 2) { 312 for (q = 0; q < numAdj || ((void)(adj[numAdj++] = closure[c]),0); ++q) { 313 if (closure[c] == adj[q]) break; 314 } 315 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 316 } 317 ierr = DMPlexRestoreTransitiveClosure(dm, star[s], (PetscBool)!useClosure, &closureSize, (PetscInt**) &closure);CHKERRQ(ierr); 318 } 319 ierr = DMPlexRestoreTransitiveClosure(dm, p, useClosure, &starSize, &star);CHKERRQ(ierr); 320 *adjSize = numAdj; 321 PetscFunctionReturn(0); 322 } 323 324 PetscErrorCode DMPlexGetAdjacency_Internal(DM dm, PetscInt p, PetscBool useCone, PetscBool useTransitiveClosure, PetscBool useAnchors, PetscInt *adjSize, PetscInt *adj[]) 325 { 326 static PetscInt asiz = 0; 327 PetscInt maxAnchors = 1; 328 PetscInt aStart = -1, aEnd = -1; 329 PetscInt maxAdjSize; 330 PetscSection aSec = NULL; 331 IS aIS = NULL; 332 const PetscInt *anchors; 333 DM_Plex *mesh = (DM_Plex *)dm->data; 334 PetscErrorCode ierr; 335 336 PetscFunctionBeginHot; 337 if (useAnchors) { 338 ierr = DMPlexGetAnchors(dm,&aSec,&aIS);CHKERRQ(ierr); 339 if (aSec) { 340 ierr = PetscSectionGetMaxDof(aSec,&maxAnchors);CHKERRQ(ierr); 341 maxAnchors = PetscMax(1,maxAnchors); 342 ierr = PetscSectionGetChart(aSec,&aStart,&aEnd);CHKERRQ(ierr); 343 ierr = ISGetIndices(aIS,&anchors);CHKERRQ(ierr); 344 } 345 } 346 if (!*adj) { 347 PetscInt depth, coneSeries, supportSeries, maxC, maxS, pStart, pEnd; 348 349 ierr = DMPlexGetChart(dm, &pStart,&pEnd);CHKERRQ(ierr); 350 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 351 ierr = DMPlexGetMaxSizes(dm, &maxC, &maxS);CHKERRQ(ierr); 352 coneSeries = (maxC > 1) ? ((PetscPowInt(maxC,depth+1)-1)/(maxC-1)) : depth+1; 353 supportSeries = (maxS > 1) ? ((PetscPowInt(maxS,depth+1)-1)/(maxS-1)) : depth+1; 354 asiz = PetscMax(PetscPowInt(maxS,depth)*coneSeries,PetscPowInt(maxC,depth)*supportSeries); 355 asiz *= maxAnchors; 356 asiz = PetscMin(asiz,pEnd-pStart); 357 ierr = PetscMalloc1(asiz,adj);CHKERRQ(ierr); 358 } 359 if (*adjSize < 0) *adjSize = asiz; 360 maxAdjSize = *adjSize; 361 if (mesh->useradjacency) { 362 ierr = mesh->useradjacency(dm, p, adjSize, *adj, mesh->useradjacencyctx);CHKERRQ(ierr); 363 } else if (useTransitiveClosure) { 364 ierr = DMPlexGetAdjacency_Transitive_Internal(dm, p, useCone, adjSize, *adj);CHKERRQ(ierr); 365 } else if (useCone) { 366 ierr = DMPlexGetAdjacency_Cone_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); 367 } else { 368 ierr = DMPlexGetAdjacency_Support_Internal(dm, p, adjSize, *adj);CHKERRQ(ierr); 369 } 370 if (useAnchors && aSec) { 371 PetscInt origSize = *adjSize; 372 PetscInt numAdj = origSize; 373 PetscInt i = 0, j; 374 PetscInt *orig = *adj; 375 376 while (i < origSize) { 377 PetscInt p = orig[i]; 378 PetscInt aDof = 0; 379 380 if (p >= aStart && p < aEnd) { 381 ierr = PetscSectionGetDof(aSec,p,&aDof);CHKERRQ(ierr); 382 } 383 if (aDof) { 384 PetscInt aOff; 385 PetscInt s, q; 386 387 for (j = i + 1; j < numAdj; j++) { 388 orig[j - 1] = orig[j]; 389 } 390 origSize--; 391 numAdj--; 392 ierr = PetscSectionGetOffset(aSec,p,&aOff);CHKERRQ(ierr); 393 for (s = 0; s < aDof; ++s) { 394 for (q = 0; q < numAdj || ((void)(orig[numAdj++] = anchors[aOff+s]),0); ++q) { 395 if (anchors[aOff+s] == orig[q]) break; 396 } 397 if (numAdj > maxAdjSize) SETERRQ1(PETSC_COMM_SELF, PETSC_ERR_PLIB, "Invalid mesh exceeded adjacency allocation (%D)", maxAdjSize); 398 } 399 } 400 else { 401 i++; 402 } 403 } 404 *adjSize = numAdj; 405 ierr = ISRestoreIndices(aIS,&anchors);CHKERRQ(ierr); 406 } 407 PetscFunctionReturn(0); 408 } 409 410 /*@ 411 DMPlexGetAdjacency - Return all points adjacent to the given point 412 413 Input Parameters: 414 + dm - The DM object 415 . p - The point 416 . adjSize - The maximum size of adj if it is non-NULL, or PETSC_DETERMINE 417 - adj - Either NULL so that the array is allocated, or an existing array with size adjSize 418 419 Output Parameters: 420 + adjSize - The number of adjacent points 421 - adj - The adjacent points 422 423 Level: advanced 424 425 Notes: 426 The user must PetscFree the adj array if it was not passed in. 427 428 .seealso: DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure(), DMPlexDistribute(), DMCreateMatrix(), DMPlexPreallocateOperator() 429 @*/ 430 PetscErrorCode DMPlexGetAdjacency(DM dm, PetscInt p, PetscInt *adjSize, PetscInt *adj[]) 431 { 432 PetscBool useCone, useClosure, useAnchors; 433 PetscErrorCode ierr; 434 435 PetscFunctionBeginHot; 436 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 437 PetscValidPointer(adjSize,3); 438 PetscValidPointer(adj,4); 439 ierr = DMPlexGetAdjacencyUseCone(dm, &useCone);CHKERRQ(ierr); 440 ierr = DMPlexGetAdjacencyUseClosure(dm, &useClosure);CHKERRQ(ierr); 441 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 442 ierr = DMPlexGetAdjacency_Internal(dm, p, useCone, useClosure, useAnchors, adjSize, adj);CHKERRQ(ierr); 443 PetscFunctionReturn(0); 444 } 445 446 /*@ 447 DMPlexCreateTwoSidedProcessSF - Create an SF which just has process connectivity 448 449 Collective on DM 450 451 Input Parameters: 452 + dm - The DM 453 - sfPoint - The PetscSF which encodes point connectivity 454 455 Output Parameters: 456 + processRanks - A list of process neighbors, or NULL 457 - sfProcess - An SF encoding the two-sided process connectivity, or NULL 458 459 Level: developer 460 461 .seealso: PetscSFCreate(), DMPlexCreateProcessSF() 462 @*/ 463 PetscErrorCode DMPlexCreateTwoSidedProcessSF(DM dm, PetscSF sfPoint, PetscSection rootRankSection, IS rootRanks, PetscSection leafRankSection, IS leafRanks, IS *processRanks, PetscSF *sfProcess) 464 { 465 const PetscSFNode *remotePoints; 466 PetscInt *localPointsNew; 467 PetscSFNode *remotePointsNew; 468 const PetscInt *nranks; 469 PetscInt *ranksNew; 470 PetscBT neighbors; 471 PetscInt pStart, pEnd, p, numLeaves, l, numNeighbors, n; 472 PetscMPIInt size, proc, rank; 473 PetscErrorCode ierr; 474 475 PetscFunctionBegin; 476 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 477 PetscValidHeaderSpecific(sfPoint, PETSCSF_CLASSID, 2); 478 if (processRanks) {PetscValidPointer(processRanks, 3);} 479 if (sfProcess) {PetscValidPointer(sfProcess, 4);} 480 ierr = MPI_Comm_size(PetscObjectComm((PetscObject) dm), &size);CHKERRQ(ierr); 481 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 482 ierr = PetscSFGetGraph(sfPoint, NULL, &numLeaves, NULL, &remotePoints);CHKERRQ(ierr); 483 ierr = PetscBTCreate(size, &neighbors);CHKERRQ(ierr); 484 ierr = PetscBTMemzero(size, neighbors);CHKERRQ(ierr); 485 /* Compute root-to-leaf process connectivity */ 486 ierr = PetscSectionGetChart(rootRankSection, &pStart, &pEnd);CHKERRQ(ierr); 487 ierr = ISGetIndices(rootRanks, &nranks);CHKERRQ(ierr); 488 for (p = pStart; p < pEnd; ++p) { 489 PetscInt ndof, noff, n; 490 491 ierr = PetscSectionGetDof(rootRankSection, p, &ndof);CHKERRQ(ierr); 492 ierr = PetscSectionGetOffset(rootRankSection, p, &noff);CHKERRQ(ierr); 493 for (n = 0; n < ndof; ++n) {ierr = PetscBTSet(neighbors, nranks[noff+n]);CHKERRQ(ierr);} 494 } 495 ierr = ISRestoreIndices(rootRanks, &nranks);CHKERRQ(ierr); 496 /* Compute leaf-to-neighbor process connectivity */ 497 ierr = PetscSectionGetChart(leafRankSection, &pStart, &pEnd);CHKERRQ(ierr); 498 ierr = ISGetIndices(leafRanks, &nranks);CHKERRQ(ierr); 499 for (p = pStart; p < pEnd; ++p) { 500 PetscInt ndof, noff, n; 501 502 ierr = PetscSectionGetDof(leafRankSection, p, &ndof);CHKERRQ(ierr); 503 ierr = PetscSectionGetOffset(leafRankSection, p, &noff);CHKERRQ(ierr); 504 for (n = 0; n < ndof; ++n) {ierr = PetscBTSet(neighbors, nranks[noff+n]);CHKERRQ(ierr);} 505 } 506 ierr = ISRestoreIndices(leafRanks, &nranks);CHKERRQ(ierr); 507 /* Compute leaf-to-root process connectivity */ 508 for (l = 0; l < numLeaves; ++l) {PetscBTSet(neighbors, remotePoints[l].rank);} 509 /* Calculate edges */ 510 PetscBTClear(neighbors, rank); 511 for(proc = 0, numNeighbors = 0; proc < size; ++proc) {if (PetscBTLookup(neighbors, proc)) ++numNeighbors;} 512 ierr = PetscMalloc1(numNeighbors, &ranksNew);CHKERRQ(ierr); 513 ierr = PetscMalloc1(numNeighbors, &localPointsNew);CHKERRQ(ierr); 514 ierr = PetscMalloc1(numNeighbors, &remotePointsNew);CHKERRQ(ierr); 515 for(proc = 0, n = 0; proc < size; ++proc) { 516 if (PetscBTLookup(neighbors, proc)) { 517 ranksNew[n] = proc; 518 localPointsNew[n] = proc; 519 remotePointsNew[n].index = rank; 520 remotePointsNew[n].rank = proc; 521 ++n; 522 } 523 } 524 ierr = PetscBTDestroy(&neighbors);CHKERRQ(ierr); 525 if (processRanks) {ierr = ISCreateGeneral(PetscObjectComm((PetscObject)dm), numNeighbors, ranksNew, PETSC_OWN_POINTER, processRanks);CHKERRQ(ierr);} 526 else {ierr = PetscFree(ranksNew);CHKERRQ(ierr);} 527 if (sfProcess) { 528 ierr = PetscSFCreate(PetscObjectComm((PetscObject)dm), sfProcess);CHKERRQ(ierr); 529 ierr = PetscObjectSetName((PetscObject) *sfProcess, "Two-Sided Process SF");CHKERRQ(ierr); 530 ierr = PetscSFSetFromOptions(*sfProcess);CHKERRQ(ierr); 531 ierr = PetscSFSetGraph(*sfProcess, size, numNeighbors, localPointsNew, PETSC_OWN_POINTER, remotePointsNew, PETSC_OWN_POINTER);CHKERRQ(ierr); 532 } 533 PetscFunctionReturn(0); 534 } 535 536 /*@ 537 DMPlexDistributeOwnership - Compute owner information for shared points. This basically gets two-sided for an SF. 538 539 Collective on DM 540 541 Input Parameter: 542 . dm - The DM 543 544 Output Parameters: 545 + rootSection - The number of leaves for a given root point 546 . rootrank - The rank of each edge into the root point 547 . leafSection - The number of processes sharing a given leaf point 548 - leafrank - The rank of each process sharing a leaf point 549 550 Level: developer 551 552 .seealso: DMPlexCreateOverlap() 553 @*/ 554 PetscErrorCode DMPlexDistributeOwnership(DM dm, PetscSection rootSection, IS *rootrank, PetscSection leafSection, IS *leafrank) 555 { 556 MPI_Comm comm; 557 PetscSF sfPoint; 558 const PetscInt *rootdegree; 559 PetscInt *myrank, *remoterank; 560 PetscInt pStart, pEnd, p, nedges; 561 PetscMPIInt rank; 562 PetscErrorCode ierr; 563 564 PetscFunctionBegin; 565 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 566 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 567 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 568 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 569 /* Compute number of leaves for each root */ 570 ierr = PetscObjectSetName((PetscObject) rootSection, "Root Section");CHKERRQ(ierr); 571 ierr = PetscSectionSetChart(rootSection, pStart, pEnd);CHKERRQ(ierr); 572 ierr = PetscSFComputeDegreeBegin(sfPoint, &rootdegree);CHKERRQ(ierr); 573 ierr = PetscSFComputeDegreeEnd(sfPoint, &rootdegree);CHKERRQ(ierr); 574 for (p = pStart; p < pEnd; ++p) {ierr = PetscSectionSetDof(rootSection, p, rootdegree[p-pStart]);CHKERRQ(ierr);} 575 ierr = PetscSectionSetUp(rootSection);CHKERRQ(ierr); 576 /* Gather rank of each leaf to root */ 577 ierr = PetscSectionGetStorageSize(rootSection, &nedges);CHKERRQ(ierr); 578 ierr = PetscMalloc1(pEnd-pStart, &myrank);CHKERRQ(ierr); 579 ierr = PetscMalloc1(nedges, &remoterank);CHKERRQ(ierr); 580 for (p = 0; p < pEnd-pStart; ++p) myrank[p] = rank; 581 ierr = PetscSFGatherBegin(sfPoint, MPIU_INT, myrank, remoterank);CHKERRQ(ierr); 582 ierr = PetscSFGatherEnd(sfPoint, MPIU_INT, myrank, remoterank);CHKERRQ(ierr); 583 ierr = PetscFree(myrank);CHKERRQ(ierr); 584 ierr = ISCreateGeneral(comm, nedges, remoterank, PETSC_OWN_POINTER, rootrank);CHKERRQ(ierr); 585 /* Distribute remote ranks to leaves */ 586 ierr = PetscObjectSetName((PetscObject) leafSection, "Leaf Section");CHKERRQ(ierr); 587 ierr = DMPlexDistributeFieldIS(dm, sfPoint, rootSection, *rootrank, leafSection, leafrank);CHKERRQ(ierr); 588 PetscFunctionReturn(0); 589 } 590 591 /*@C 592 DMPlexCreateOverlap - Compute owner information for shared points. This basically gets two-sided for an SF. 593 594 Collective on DM 595 596 Input Parameters: 597 + dm - The DM 598 . levels - Number of overlap levels 599 . rootSection - The number of leaves for a given root point 600 . rootrank - The rank of each edge into the root point 601 . leafSection - The number of processes sharing a given leaf point 602 - leafrank - The rank of each process sharing a leaf point 603 604 Output Parameters: 605 + ovLabel - DMLabel containing remote overlap contributions as point/rank pairings 606 607 Level: developer 608 609 .seealso: DMPlexDistributeOwnership(), DMPlexDistribute() 610 @*/ 611 PetscErrorCode DMPlexCreateOverlap(DM dm, PetscInt levels, PetscSection rootSection, IS rootrank, PetscSection leafSection, IS leafrank, DMLabel *ovLabel) 612 { 613 MPI_Comm comm; 614 DMLabel ovAdjByRank; /* A DMLabel containing all points adjacent to shared points, separated by rank (value in label) */ 615 PetscSF sfPoint, sfProc; 616 const PetscSFNode *remote; 617 const PetscInt *local; 618 const PetscInt *nrank, *rrank; 619 PetscInt *adj = NULL; 620 PetscInt pStart, pEnd, p, sStart, sEnd, nleaves, l; 621 PetscMPIInt rank, size; 622 PetscBool useCone, useClosure, flg; 623 PetscErrorCode ierr; 624 625 PetscFunctionBegin; 626 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 627 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 628 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 629 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 630 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 631 ierr = PetscSectionGetChart(leafSection, &sStart, &sEnd);CHKERRQ(ierr); 632 ierr = PetscSFGetGraph(sfPoint, NULL, &nleaves, &local, &remote);CHKERRQ(ierr); 633 ierr = DMLabelCreate("Overlap adjacency", &ovAdjByRank);CHKERRQ(ierr); 634 /* Handle leaves: shared with the root point */ 635 for (l = 0; l < nleaves; ++l) { 636 PetscInt adjSize = PETSC_DETERMINE, a; 637 638 ierr = DMPlexGetAdjacency(dm, local[l], &adjSize, &adj);CHKERRQ(ierr); 639 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remote[l].rank);CHKERRQ(ierr);} 640 } 641 ierr = ISGetIndices(rootrank, &rrank);CHKERRQ(ierr); 642 ierr = ISGetIndices(leafrank, &nrank);CHKERRQ(ierr); 643 /* Handle roots */ 644 for (p = pStart; p < pEnd; ++p) { 645 PetscInt adjSize = PETSC_DETERMINE, neighbors = 0, noff, n, a; 646 647 if ((p >= sStart) && (p < sEnd)) { 648 /* Some leaves share a root with other leaves on different processes */ 649 ierr = PetscSectionGetDof(leafSection, p, &neighbors);CHKERRQ(ierr); 650 if (neighbors) { 651 ierr = PetscSectionGetOffset(leafSection, p, &noff);CHKERRQ(ierr); 652 ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj);CHKERRQ(ierr); 653 for (n = 0; n < neighbors; ++n) { 654 const PetscInt remoteRank = nrank[noff+n]; 655 656 if (remoteRank == rank) continue; 657 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);CHKERRQ(ierr);} 658 } 659 } 660 } 661 /* Roots are shared with leaves */ 662 ierr = PetscSectionGetDof(rootSection, p, &neighbors);CHKERRQ(ierr); 663 if (!neighbors) continue; 664 ierr = PetscSectionGetOffset(rootSection, p, &noff);CHKERRQ(ierr); 665 ierr = DMPlexGetAdjacency(dm, p, &adjSize, &adj);CHKERRQ(ierr); 666 for (n = 0; n < neighbors; ++n) { 667 const PetscInt remoteRank = rrank[noff+n]; 668 669 if (remoteRank == rank) continue; 670 for (a = 0; a < adjSize; ++a) {ierr = DMLabelSetValue(ovAdjByRank, adj[a], remoteRank);CHKERRQ(ierr);} 671 } 672 } 673 ierr = PetscFree(adj);CHKERRQ(ierr); 674 ierr = ISRestoreIndices(rootrank, &rrank);CHKERRQ(ierr); 675 ierr = ISRestoreIndices(leafrank, &nrank);CHKERRQ(ierr); 676 /* Add additional overlap levels */ 677 for (l = 1; l < levels; l++) { 678 /* Propagate point donations over SF to capture remote connections */ 679 ierr = DMPlexPartitionLabelPropagate(dm, ovAdjByRank);CHKERRQ(ierr); 680 /* Add next level of point donations to the label */ 681 ierr = DMPlexPartitionLabelAdjacency(dm, ovAdjByRank);CHKERRQ(ierr); 682 } 683 /* We require the closure in the overlap */ 684 ierr = DMPlexGetAdjacencyUseCone(dm, &useCone);CHKERRQ(ierr); 685 ierr = DMPlexGetAdjacencyUseClosure(dm, &useClosure);CHKERRQ(ierr); 686 if (useCone || !useClosure) { 687 ierr = DMPlexPartitionLabelClosure(dm, ovAdjByRank);CHKERRQ(ierr); 688 } 689 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-overlap_view", &flg);CHKERRQ(ierr); 690 if (flg) { 691 ierr = DMLabelView(ovAdjByRank, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 692 } 693 /* Make global process SF and invert sender to receiver label */ 694 { 695 /* Build a global process SF */ 696 PetscSFNode *remoteProc; 697 ierr = PetscMalloc1(size, &remoteProc);CHKERRQ(ierr); 698 for (p = 0; p < size; ++p) { 699 remoteProc[p].rank = p; 700 remoteProc[p].index = rank; 701 } 702 ierr = PetscSFCreate(comm, &sfProc);CHKERRQ(ierr); 703 ierr = PetscObjectSetName((PetscObject) sfProc, "Process SF");CHKERRQ(ierr); 704 ierr = PetscSFSetGraph(sfProc, size, size, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);CHKERRQ(ierr); 705 } 706 ierr = DMLabelCreate("Overlap label", ovLabel);CHKERRQ(ierr); 707 ierr = DMPlexPartitionLabelInvert(dm, ovAdjByRank, sfProc, *ovLabel);CHKERRQ(ierr); 708 /* Add owned points, except for shared local points */ 709 for (p = pStart; p < pEnd; ++p) {ierr = DMLabelSetValue(*ovLabel, p, rank);CHKERRQ(ierr);} 710 for (l = 0; l < nleaves; ++l) { 711 ierr = DMLabelClearValue(*ovLabel, local[l], rank);CHKERRQ(ierr); 712 ierr = DMLabelSetValue(*ovLabel, remote[l].index, remote[l].rank);CHKERRQ(ierr); 713 } 714 /* Clean up */ 715 ierr = DMLabelDestroy(&ovAdjByRank);CHKERRQ(ierr); 716 ierr = PetscSFDestroy(&sfProc);CHKERRQ(ierr); 717 PetscFunctionReturn(0); 718 } 719 720 /*@C 721 DMPlexCreateOverlapMigrationSF - Create an SF describing the new mesh distribution to make the overlap described by the input SF 722 723 Collective on DM 724 725 Input Parameters: 726 + dm - The DM 727 - overlapSF - The SF mapping ghost points in overlap to owner points on other processes 728 729 Output Parameters: 730 + migrationSF - An SF that maps original points in old locations to points in new locations 731 732 Level: developer 733 734 .seealso: DMPlexCreateOverlap(), DMPlexDistribute() 735 @*/ 736 PetscErrorCode DMPlexCreateOverlapMigrationSF(DM dm, PetscSF overlapSF, PetscSF *migrationSF) 737 { 738 MPI_Comm comm; 739 PetscMPIInt rank, size; 740 PetscInt d, dim, p, pStart, pEnd, nroots, nleaves, newLeaves, point, numSharedPoints; 741 PetscInt *pointDepths, *remoteDepths, *ilocal; 742 PetscInt *depthRecv, *depthShift, *depthIdx; 743 PetscSFNode *iremote; 744 PetscSF pointSF; 745 const PetscInt *sharedLocal; 746 const PetscSFNode *overlapRemote, *sharedRemote; 747 PetscErrorCode ierr; 748 749 PetscFunctionBegin; 750 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 751 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 752 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 753 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 754 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 755 756 /* Before building the migration SF we need to know the new stratum offsets */ 757 ierr = PetscSFGetGraph(overlapSF, &nroots, &nleaves, NULL, &overlapRemote);CHKERRQ(ierr); 758 ierr = PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);CHKERRQ(ierr); 759 for (d=0; d<dim+1; d++) { 760 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 761 for (p=pStart; p<pEnd; p++) pointDepths[p] = d; 762 } 763 for (p=0; p<nleaves; p++) remoteDepths[p] = -1; 764 ierr = PetscSFBcastBegin(overlapSF, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 765 ierr = PetscSFBcastEnd(overlapSF, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 766 767 /* Count recevied points in each stratum and compute the internal strata shift */ 768 ierr = PetscMalloc3(dim+1, &depthRecv, dim+1, &depthShift, dim+1, &depthIdx);CHKERRQ(ierr); 769 for (d=0; d<dim+1; d++) depthRecv[d]=0; 770 for (p=0; p<nleaves; p++) depthRecv[remoteDepths[p]]++; 771 depthShift[dim] = 0; 772 for (d=0; d<dim; d++) depthShift[d] = depthRecv[dim]; 773 for (d=1; d<dim; d++) depthShift[d] += depthRecv[0]; 774 for (d=dim-2; d>0; d--) depthShift[d] += depthRecv[d+1]; 775 for (d=0; d<dim+1; d++) { 776 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 777 depthIdx[d] = pStart + depthShift[d]; 778 } 779 780 /* Form the overlap SF build an SF that describes the full overlap migration SF */ 781 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 782 newLeaves = pEnd - pStart + nleaves; 783 ierr = PetscMalloc1(newLeaves, &ilocal);CHKERRQ(ierr); 784 ierr = PetscMalloc1(newLeaves, &iremote);CHKERRQ(ierr); 785 /* First map local points to themselves */ 786 for (d=0; d<dim+1; d++) { 787 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 788 for (p=pStart; p<pEnd; p++) { 789 point = p + depthShift[d]; 790 ilocal[point] = point; 791 iremote[point].index = p; 792 iremote[point].rank = rank; 793 depthIdx[d]++; 794 } 795 } 796 797 /* Add in the remote roots for currently shared points */ 798 ierr = DMGetPointSF(dm, &pointSF);CHKERRQ(ierr); 799 ierr = PetscSFGetGraph(pointSF, NULL, &numSharedPoints, &sharedLocal, &sharedRemote);CHKERRQ(ierr); 800 for (d=0; d<dim+1; d++) { 801 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 802 for (p=0; p<numSharedPoints; p++) { 803 if (pStart <= sharedLocal[p] && sharedLocal[p] < pEnd) { 804 point = sharedLocal[p] + depthShift[d]; 805 iremote[point].index = sharedRemote[p].index; 806 iremote[point].rank = sharedRemote[p].rank; 807 } 808 } 809 } 810 811 /* Now add the incoming overlap points */ 812 for (p=0; p<nleaves; p++) { 813 point = depthIdx[remoteDepths[p]]; 814 ilocal[point] = point; 815 iremote[point].index = overlapRemote[p].index; 816 iremote[point].rank = overlapRemote[p].rank; 817 depthIdx[remoteDepths[p]]++; 818 } 819 ierr = PetscFree2(pointDepths,remoteDepths);CHKERRQ(ierr); 820 821 ierr = PetscSFCreate(comm, migrationSF);CHKERRQ(ierr); 822 ierr = PetscObjectSetName((PetscObject) *migrationSF, "Overlap Migration SF");CHKERRQ(ierr); 823 ierr = PetscSFSetFromOptions(*migrationSF);CHKERRQ(ierr); 824 ierr = DMPlexGetChart(dm, &pStart, &pEnd);CHKERRQ(ierr); 825 ierr = PetscSFSetGraph(*migrationSF, pEnd-pStart, newLeaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_OWN_POINTER);CHKERRQ(ierr); 826 827 ierr = PetscFree3(depthRecv, depthShift, depthIdx);CHKERRQ(ierr); 828 PetscFunctionReturn(0); 829 } 830 831 /*@ 832 DMPlexStratifyMigrationSF - Rearrange the leaves of a migration sf for stratification. 833 834 Input Parameter: 835 + dm - The DM 836 - sf - A star forest with non-ordered leaves, usually defining a DM point migration 837 838 Output Parameter: 839 . migrationSF - A star forest with added leaf indirection that ensures the resulting DM is stratified 840 841 Level: developer 842 843 .seealso: DMPlexPartitionLabelCreateSF(), DMPlexDistribute(), DMPlexDistributeOverlap() 844 @*/ 845 PetscErrorCode DMPlexStratifyMigrationSF(DM dm, PetscSF sf, PetscSF *migrationSF) 846 { 847 MPI_Comm comm; 848 PetscMPIInt rank, size; 849 PetscInt d, ldepth, depth, p, pStart, pEnd, nroots, nleaves; 850 PetscInt *pointDepths, *remoteDepths, *ilocal; 851 PetscInt *depthRecv, *depthShift, *depthIdx; 852 PetscInt hybEnd[4]; 853 const PetscSFNode *iremote; 854 PetscErrorCode ierr; 855 856 PetscFunctionBegin; 857 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 858 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 859 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 860 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 861 ierr = DMPlexGetDepth(dm, &ldepth);CHKERRQ(ierr); 862 ierr = MPIU_Allreduce(&ldepth, &depth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 863 if ((ldepth >= 0) && (depth != ldepth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", ldepth, depth); 864 865 /* Before building the migration SF we need to know the new stratum offsets */ 866 ierr = PetscSFGetGraph(sf, &nroots, &nleaves, NULL, &iremote);CHKERRQ(ierr); 867 ierr = PetscMalloc2(nroots, &pointDepths, nleaves, &remoteDepths);CHKERRQ(ierr); 868 ierr = DMPlexGetHybridBounds(dm,&hybEnd[depth],&hybEnd[depth-1],&hybEnd[1],&hybEnd[0]);CHKERRQ(ierr); 869 for (d = 0; d < depth+1; ++d) { 870 ierr = DMPlexGetDepthStratum(dm, d, &pStart, &pEnd);CHKERRQ(ierr); 871 for (p = pStart; p < pEnd; ++p) { 872 if (hybEnd[d] >= 0 && p >= hybEnd[d]) { /* put in a separate value for hybrid points */ 873 pointDepths[p] = 2 * d; 874 } else { 875 pointDepths[p] = 2 * d + 1; 876 } 877 } 878 } 879 for (p = 0; p < nleaves; ++p) remoteDepths[p] = -1; 880 ierr = PetscSFBcastBegin(sf, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 881 ierr = PetscSFBcastEnd(sf, MPIU_INT, pointDepths, remoteDepths);CHKERRQ(ierr); 882 /* Count recevied points in each stratum and compute the internal strata shift */ 883 ierr = PetscMalloc3(2*(depth+1), &depthRecv, 2*(depth+1), &depthShift, 2*(depth+1), &depthIdx);CHKERRQ(ierr); 884 for (d = 0; d < 2*(depth+1); ++d) depthRecv[d] = 0; 885 for (p = 0; p < nleaves; ++p) depthRecv[remoteDepths[p]]++; 886 depthShift[2*depth+1] = 0; 887 for (d = 0; d < 2*depth+1; ++d) depthShift[d] = depthRecv[2 * depth + 1]; 888 for (d = 0; d < 2*depth; ++d) depthShift[d] += depthRecv[2 * depth]; 889 depthShift[0] += depthRecv[1]; 890 for (d = 2; d < 2*depth; ++d) depthShift[d] += depthRecv[1]; 891 for (d = 2; d < 2*depth; ++d) depthShift[d] += depthRecv[0]; 892 for (d = 2 * depth-1; d > 2; --d) { 893 PetscInt e; 894 895 for (e = d -1; e > 1; --e) depthShift[e] += depthRecv[d]; 896 } 897 for (d = 0; d < 2*(depth+1); ++d) {depthIdx[d] = 0;} 898 /* Derive a new local permutation based on stratified indices */ 899 ierr = PetscMalloc1(nleaves, &ilocal);CHKERRQ(ierr); 900 for (p = 0; p < nleaves; ++p) { 901 const PetscInt dep = remoteDepths[p]; 902 903 ilocal[p] = depthShift[dep] + depthIdx[dep]; 904 depthIdx[dep]++; 905 } 906 ierr = PetscSFCreate(comm, migrationSF);CHKERRQ(ierr); 907 ierr = PetscObjectSetName((PetscObject) *migrationSF, "Migration SF");CHKERRQ(ierr); 908 ierr = PetscSFSetGraph(*migrationSF, nroots, nleaves, ilocal, PETSC_OWN_POINTER, iremote, PETSC_COPY_VALUES);CHKERRQ(ierr); 909 ierr = PetscFree2(pointDepths,remoteDepths);CHKERRQ(ierr); 910 ierr = PetscFree3(depthRecv, depthShift, depthIdx);CHKERRQ(ierr); 911 PetscFunctionReturn(0); 912 } 913 914 /*@ 915 DMPlexDistributeField - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 916 917 Collective on DM 918 919 Input Parameters: 920 + dm - The DMPlex object 921 . pointSF - The PetscSF describing the communication pattern 922 . originalSection - The PetscSection for existing data layout 923 - originalVec - The existing data 924 925 Output Parameters: 926 + newSection - The PetscSF describing the new data layout 927 - newVec - The new data 928 929 Level: developer 930 931 .seealso: DMPlexDistribute(), DMPlexDistributeFieldIS(), DMPlexDistributeData() 932 @*/ 933 PetscErrorCode DMPlexDistributeField(DM dm, PetscSF pointSF, PetscSection originalSection, Vec originalVec, PetscSection newSection, Vec newVec) 934 { 935 PetscSF fieldSF; 936 PetscInt *remoteOffsets, fieldSize; 937 PetscScalar *originalValues, *newValues; 938 PetscErrorCode ierr; 939 940 PetscFunctionBegin; 941 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 942 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 943 944 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 945 ierr = VecSetSizes(newVec, fieldSize, PETSC_DETERMINE);CHKERRQ(ierr); 946 ierr = VecSetType(newVec,dm->vectype);CHKERRQ(ierr); 947 948 ierr = VecGetArray(originalVec, &originalValues);CHKERRQ(ierr); 949 ierr = VecGetArray(newVec, &newValues);CHKERRQ(ierr); 950 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 951 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 952 ierr = PetscSFBcastBegin(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); 953 ierr = PetscSFBcastEnd(fieldSF, MPIU_SCALAR, originalValues, newValues);CHKERRQ(ierr); 954 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 955 ierr = VecRestoreArray(newVec, &newValues);CHKERRQ(ierr); 956 ierr = VecRestoreArray(originalVec, &originalValues);CHKERRQ(ierr); 957 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 958 PetscFunctionReturn(0); 959 } 960 961 /*@ 962 DMPlexDistributeFieldIS - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 963 964 Collective on DM 965 966 Input Parameters: 967 + dm - The DMPlex object 968 . pointSF - The PetscSF describing the communication pattern 969 . originalSection - The PetscSection for existing data layout 970 - originalIS - The existing data 971 972 Output Parameters: 973 + newSection - The PetscSF describing the new data layout 974 - newIS - The new data 975 976 Level: developer 977 978 .seealso: DMPlexDistribute(), DMPlexDistributeField(), DMPlexDistributeData() 979 @*/ 980 PetscErrorCode DMPlexDistributeFieldIS(DM dm, PetscSF pointSF, PetscSection originalSection, IS originalIS, PetscSection newSection, IS *newIS) 981 { 982 PetscSF fieldSF; 983 PetscInt *newValues, *remoteOffsets, fieldSize; 984 const PetscInt *originalValues; 985 PetscErrorCode ierr; 986 987 PetscFunctionBegin; 988 ierr = PetscLogEventBegin(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 989 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 990 991 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 992 ierr = PetscMalloc1(fieldSize, &newValues);CHKERRQ(ierr); 993 994 ierr = ISGetIndices(originalIS, &originalValues);CHKERRQ(ierr); 995 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 996 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 997 ierr = PetscSFBcastBegin(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);CHKERRQ(ierr); 998 ierr = PetscSFBcastEnd(fieldSF, MPIU_INT, (PetscInt *) originalValues, newValues);CHKERRQ(ierr); 999 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 1000 ierr = ISRestoreIndices(originalIS, &originalValues);CHKERRQ(ierr); 1001 ierr = ISCreateGeneral(PetscObjectComm((PetscObject) pointSF), fieldSize, newValues, PETSC_OWN_POINTER, newIS);CHKERRQ(ierr); 1002 ierr = PetscLogEventEnd(DMPLEX_DistributeField,dm,0,0,0);CHKERRQ(ierr); 1003 PetscFunctionReturn(0); 1004 } 1005 1006 /*@ 1007 DMPlexDistributeData - Distribute field data to match a given PetscSF, usually the SF from mesh distribution 1008 1009 Collective on DM 1010 1011 Input Parameters: 1012 + dm - The DMPlex object 1013 . pointSF - The PetscSF describing the communication pattern 1014 . originalSection - The PetscSection for existing data layout 1015 . datatype - The type of data 1016 - originalData - The existing data 1017 1018 Output Parameters: 1019 + newSection - The PetscSection describing the new data layout 1020 - newData - The new data 1021 1022 Level: developer 1023 1024 .seealso: DMPlexDistribute(), DMPlexDistributeField() 1025 @*/ 1026 PetscErrorCode DMPlexDistributeData(DM dm, PetscSF pointSF, PetscSection originalSection, MPI_Datatype datatype, void *originalData, PetscSection newSection, void **newData) 1027 { 1028 PetscSF fieldSF; 1029 PetscInt *remoteOffsets, fieldSize; 1030 PetscMPIInt dataSize; 1031 PetscErrorCode ierr; 1032 1033 PetscFunctionBegin; 1034 ierr = PetscLogEventBegin(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 1035 ierr = PetscSFDistributeSection(pointSF, originalSection, &remoteOffsets, newSection);CHKERRQ(ierr); 1036 1037 ierr = PetscSectionGetStorageSize(newSection, &fieldSize);CHKERRQ(ierr); 1038 ierr = MPI_Type_size(datatype, &dataSize);CHKERRQ(ierr); 1039 ierr = PetscMalloc(fieldSize * dataSize, newData);CHKERRQ(ierr); 1040 1041 ierr = PetscSFCreateSectionSF(pointSF, originalSection, remoteOffsets, newSection, &fieldSF);CHKERRQ(ierr); 1042 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 1043 ierr = PetscSFBcastBegin(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr); 1044 ierr = PetscSFBcastEnd(fieldSF, datatype, originalData, *newData);CHKERRQ(ierr); 1045 ierr = PetscSFDestroy(&fieldSF);CHKERRQ(ierr); 1046 ierr = PetscLogEventEnd(DMPLEX_DistributeData,dm,0,0,0);CHKERRQ(ierr); 1047 PetscFunctionReturn(0); 1048 } 1049 1050 static PetscErrorCode DMPlexDistributeCones(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel) 1051 { 1052 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1053 MPI_Comm comm; 1054 PetscSF coneSF; 1055 PetscSection originalConeSection, newConeSection; 1056 PetscInt *remoteOffsets, *cones, *globCones, *newCones, newConesSize; 1057 PetscBool flg; 1058 PetscErrorCode ierr; 1059 1060 PetscFunctionBegin; 1061 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1062 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 5); 1063 1064 ierr = PetscLogEventBegin(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 1065 /* Distribute cone section */ 1066 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1067 ierr = DMPlexGetConeSection(dm, &originalConeSection);CHKERRQ(ierr); 1068 ierr = DMPlexGetConeSection(dmParallel, &newConeSection);CHKERRQ(ierr); 1069 ierr = PetscSFDistributeSection(migrationSF, originalConeSection, &remoteOffsets, newConeSection);CHKERRQ(ierr); 1070 ierr = DMSetUp(dmParallel);CHKERRQ(ierr); 1071 { 1072 PetscInt pStart, pEnd, p; 1073 1074 ierr = PetscSectionGetChart(newConeSection, &pStart, &pEnd);CHKERRQ(ierr); 1075 for (p = pStart; p < pEnd; ++p) { 1076 PetscInt coneSize; 1077 ierr = PetscSectionGetDof(newConeSection, p, &coneSize);CHKERRQ(ierr); 1078 pmesh->maxConeSize = PetscMax(pmesh->maxConeSize, coneSize); 1079 } 1080 } 1081 /* Communicate and renumber cones */ 1082 ierr = PetscSFCreateSectionSF(migrationSF, originalConeSection, remoteOffsets, newConeSection, &coneSF);CHKERRQ(ierr); 1083 ierr = PetscFree(remoteOffsets);CHKERRQ(ierr); 1084 ierr = DMPlexGetCones(dm, &cones);CHKERRQ(ierr); 1085 if (original) { 1086 PetscInt numCones; 1087 1088 ierr = PetscSectionGetStorageSize(originalConeSection,&numCones);CHKERRQ(ierr); ierr = PetscMalloc1(numCones,&globCones);CHKERRQ(ierr); 1089 ierr = ISLocalToGlobalMappingApplyBlock(original, numCones, cones, globCones);CHKERRQ(ierr); 1090 } 1091 else { 1092 globCones = cones; 1093 } 1094 ierr = DMPlexGetCones(dmParallel, &newCones);CHKERRQ(ierr); 1095 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, globCones, newCones);CHKERRQ(ierr); 1096 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, globCones, newCones);CHKERRQ(ierr); 1097 if (original) { 1098 ierr = PetscFree(globCones);CHKERRQ(ierr); 1099 } 1100 ierr = PetscSectionGetStorageSize(newConeSection, &newConesSize);CHKERRQ(ierr); 1101 ierr = ISGlobalToLocalMappingApplyBlock(renumbering, IS_GTOLM_MASK, newConesSize, newCones, NULL, newCones);CHKERRQ(ierr); 1102 #if PETSC_USE_DEBUG 1103 { 1104 PetscInt p; 1105 PetscBool valid = PETSC_TRUE; 1106 for (p = 0; p < newConesSize; ++p) { 1107 if (newCones[p] < 0) {valid = PETSC_FALSE; ierr = PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);CHKERRQ(ierr);} 1108 } 1109 if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map"); 1110 } 1111 #endif 1112 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-cones_view", &flg);CHKERRQ(ierr); 1113 if (flg) { 1114 ierr = PetscPrintf(comm, "Serial Cone Section:\n");CHKERRQ(ierr); 1115 ierr = PetscSectionView(originalConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1116 ierr = PetscPrintf(comm, "Parallel Cone Section:\n");CHKERRQ(ierr); 1117 ierr = PetscSectionView(newConeSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1118 ierr = PetscSFView(coneSF, NULL);CHKERRQ(ierr); 1119 } 1120 ierr = DMPlexGetConeOrientations(dm, &cones);CHKERRQ(ierr); 1121 ierr = DMPlexGetConeOrientations(dmParallel, &newCones);CHKERRQ(ierr); 1122 ierr = PetscSFBcastBegin(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 1123 ierr = PetscSFBcastEnd(coneSF, MPIU_INT, cones, newCones);CHKERRQ(ierr); 1124 ierr = PetscSFDestroy(&coneSF);CHKERRQ(ierr); 1125 ierr = PetscLogEventEnd(DMPLEX_DistributeCones,dm,0,0,0);CHKERRQ(ierr); 1126 /* Create supports and stratify DMPlex */ 1127 { 1128 PetscInt pStart, pEnd; 1129 1130 ierr = PetscSectionGetChart(pmesh->coneSection, &pStart, &pEnd);CHKERRQ(ierr); 1131 ierr = PetscSectionSetChart(pmesh->supportSection, pStart, pEnd);CHKERRQ(ierr); 1132 } 1133 ierr = DMPlexSymmetrize(dmParallel);CHKERRQ(ierr); 1134 ierr = DMPlexStratify(dmParallel);CHKERRQ(ierr); 1135 { 1136 PetscBool useCone, useClosure, useAnchors; 1137 1138 ierr = DMPlexGetAdjacencyUseCone(dm, &useCone);CHKERRQ(ierr); 1139 ierr = DMPlexGetAdjacencyUseClosure(dm, &useClosure);CHKERRQ(ierr); 1140 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 1141 ierr = DMPlexSetAdjacencyUseCone(dmParallel, useCone);CHKERRQ(ierr); 1142 ierr = DMPlexSetAdjacencyUseClosure(dmParallel, useClosure);CHKERRQ(ierr); 1143 ierr = DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);CHKERRQ(ierr); 1144 } 1145 PetscFunctionReturn(0); 1146 } 1147 1148 static PetscErrorCode DMPlexDistributeCoordinates(DM dm, PetscSF migrationSF, DM dmParallel) 1149 { 1150 MPI_Comm comm; 1151 PetscSection originalCoordSection, newCoordSection; 1152 Vec originalCoordinates, newCoordinates; 1153 PetscInt bs; 1154 PetscBool isper; 1155 const char *name; 1156 const PetscReal *maxCell, *L; 1157 const DMBoundaryType *bd; 1158 PetscErrorCode ierr; 1159 1160 PetscFunctionBegin; 1161 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1162 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1163 1164 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1165 ierr = DMGetCoordinateSection(dm, &originalCoordSection);CHKERRQ(ierr); 1166 ierr = DMGetCoordinateSection(dmParallel, &newCoordSection);CHKERRQ(ierr); 1167 ierr = DMGetCoordinatesLocal(dm, &originalCoordinates);CHKERRQ(ierr); 1168 if (originalCoordinates) { 1169 ierr = VecCreate(PETSC_COMM_SELF, &newCoordinates);CHKERRQ(ierr); 1170 ierr = PetscObjectGetName((PetscObject) originalCoordinates, &name);CHKERRQ(ierr); 1171 ierr = PetscObjectSetName((PetscObject) newCoordinates, name);CHKERRQ(ierr); 1172 1173 ierr = DMPlexDistributeField(dm, migrationSF, originalCoordSection, originalCoordinates, newCoordSection, newCoordinates);CHKERRQ(ierr); 1174 ierr = DMSetCoordinatesLocal(dmParallel, newCoordinates);CHKERRQ(ierr); 1175 ierr = VecGetBlockSize(originalCoordinates, &bs);CHKERRQ(ierr); 1176 ierr = VecSetBlockSize(newCoordinates, bs);CHKERRQ(ierr); 1177 ierr = VecDestroy(&newCoordinates);CHKERRQ(ierr); 1178 } 1179 ierr = DMGetPeriodicity(dm, &isper, &maxCell, &L, &bd);CHKERRQ(ierr); 1180 ierr = DMSetPeriodicity(dmParallel, isper, maxCell, L, bd);CHKERRQ(ierr); 1181 PetscFunctionReturn(0); 1182 } 1183 1184 /* Here we are assuming that process 0 always has everything */ 1185 static PetscErrorCode DMPlexDistributeLabels(DM dm, PetscSF migrationSF, DM dmParallel) 1186 { 1187 DM_Plex *mesh = (DM_Plex*) dm->data; 1188 MPI_Comm comm; 1189 DMLabel depthLabel; 1190 PetscMPIInt rank; 1191 PetscInt depth, d, numLabels, numLocalLabels, l; 1192 PetscBool hasLabels = PETSC_FALSE, lsendDepth, sendDepth; 1193 PetscObjectState depthState = -1; 1194 PetscErrorCode ierr; 1195 1196 PetscFunctionBegin; 1197 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1198 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1199 1200 ierr = PetscLogEventBegin(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1201 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1202 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1203 1204 /* If the user has changed the depth label, communicate it instead */ 1205 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1206 ierr = DMPlexGetDepthLabel(dm, &depthLabel);CHKERRQ(ierr); 1207 if (depthLabel) {ierr = DMLabelGetState(depthLabel, &depthState);CHKERRQ(ierr);} 1208 lsendDepth = mesh->depthState != depthState ? PETSC_TRUE : PETSC_FALSE; 1209 ierr = MPIU_Allreduce(&lsendDepth, &sendDepth, 1, MPIU_BOOL, MPI_LOR, comm);CHKERRQ(ierr); 1210 if (sendDepth) { 1211 ierr = DMRemoveLabel(dmParallel, "depth", &depthLabel);CHKERRQ(ierr); 1212 ierr = DMLabelDestroy(&depthLabel);CHKERRQ(ierr); 1213 } 1214 /* Everyone must have either the same number of labels, or none */ 1215 ierr = DMGetNumLabels(dm, &numLocalLabels);CHKERRQ(ierr); 1216 numLabels = numLocalLabels; 1217 ierr = MPI_Bcast(&numLabels, 1, MPIU_INT, 0, comm);CHKERRQ(ierr); 1218 if (numLabels == numLocalLabels) hasLabels = PETSC_TRUE; 1219 for (l = numLabels-1; l >= 0; --l) { 1220 DMLabel label = NULL, labelNew = NULL; 1221 PetscBool isDepth, lisOutput = PETSC_TRUE, isOutput; 1222 1223 if (hasLabels) {ierr = DMGetLabelByNum(dm, l, &label);CHKERRQ(ierr);} 1224 /* Skip "depth" because it is recreated */ 1225 if (hasLabels) {ierr = PetscStrcmp(label->name, "depth", &isDepth);CHKERRQ(ierr);} 1226 ierr = MPI_Bcast(&isDepth, 1, MPIU_BOOL, 0, comm);CHKERRQ(ierr); 1227 if (isDepth && !sendDepth) continue; 1228 ierr = DMLabelDistribute(label, migrationSF, &labelNew);CHKERRQ(ierr); 1229 if (isDepth) { 1230 /* Put in any missing strata which can occur if users are managing the depth label themselves */ 1231 PetscInt gdepth; 1232 1233 ierr = MPIU_Allreduce(&depth, &gdepth, 1, MPIU_INT, MPI_MAX, comm);CHKERRQ(ierr); 1234 if ((depth >= 0) && (gdepth != depth)) SETERRQ2(PETSC_COMM_SELF, PETSC_ERR_ARG_WRONG, "Inconsistent Plex depth %d != %d", depth, gdepth); 1235 for (d = 0; d <= gdepth; ++d) { 1236 PetscBool has; 1237 1238 ierr = DMLabelHasStratum(labelNew, d, &has);CHKERRQ(ierr); 1239 if (!has) {ierr = DMLabelAddStratum(labelNew, d);CHKERRQ(ierr);} 1240 } 1241 } 1242 ierr = DMAddLabel(dmParallel, labelNew);CHKERRQ(ierr); 1243 /* Put the output flag in the new label */ 1244 if (hasLabels) {ierr = DMGetLabelOutput(dm, label->name, &lisOutput);CHKERRQ(ierr);} 1245 ierr = MPIU_Allreduce(&lisOutput, &isOutput, 1, MPIU_BOOL, MPI_LAND, comm);CHKERRQ(ierr); 1246 ierr = DMSetLabelOutput(dmParallel, labelNew->name, isOutput);CHKERRQ(ierr); 1247 } 1248 ierr = PetscLogEventEnd(DMPLEX_DistributeLabels,dm,0,0,0);CHKERRQ(ierr); 1249 PetscFunctionReturn(0); 1250 } 1251 1252 static PetscErrorCode DMPlexDistributeSetupHybrid(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping renumbering, DM dmParallel) 1253 { 1254 DM_Plex *mesh = (DM_Plex*) dm->data; 1255 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1256 PetscBool *isHybrid, *isHybridParallel; 1257 PetscInt dim, depth, d; 1258 PetscInt pStart, pEnd, pStartP, pEndP; 1259 PetscErrorCode ierr; 1260 1261 PetscFunctionBegin; 1262 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1263 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1264 1265 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1266 ierr = DMPlexGetDepth(dm, &depth);CHKERRQ(ierr); 1267 ierr = DMPlexGetChart(dm,&pStart,&pEnd);CHKERRQ(ierr); 1268 ierr = DMPlexGetChart(dmParallel,&pStartP,&pEndP);CHKERRQ(ierr); 1269 ierr = PetscCalloc2(pEnd-pStart,&isHybrid,pEndP-pStartP,&isHybridParallel);CHKERRQ(ierr); 1270 for (d = 0; d <= depth; d++) { 1271 PetscInt hybridMax = (depth == 1 && d == 1) ? mesh->hybridPointMax[dim] : mesh->hybridPointMax[d]; 1272 1273 if (hybridMax >= 0) { 1274 PetscInt sStart, sEnd, p; 1275 1276 ierr = DMPlexGetDepthStratum(dm,d,&sStart,&sEnd);CHKERRQ(ierr); 1277 for (p = hybridMax; p < sEnd; p++) isHybrid[p-pStart] = PETSC_TRUE; 1278 } 1279 } 1280 ierr = PetscSFBcastBegin(migrationSF,MPIU_BOOL,isHybrid,isHybridParallel);CHKERRQ(ierr); 1281 ierr = PetscSFBcastEnd(migrationSF,MPIU_BOOL,isHybrid,isHybridParallel);CHKERRQ(ierr); 1282 for (d = 0; d <= dim; d++) pmesh->hybridPointMax[d] = -1; 1283 for (d = 0; d <= depth; d++) { 1284 PetscInt sStart, sEnd, p, dd; 1285 1286 ierr = DMPlexGetDepthStratum(dmParallel,d,&sStart,&sEnd);CHKERRQ(ierr); 1287 dd = (depth == 1 && d == 1) ? dim : d; 1288 for (p = sStart; p < sEnd; p++) { 1289 if (isHybridParallel[p-pStartP]) { 1290 pmesh->hybridPointMax[dd] = p; 1291 break; 1292 } 1293 } 1294 } 1295 ierr = PetscFree2(isHybrid,isHybridParallel);CHKERRQ(ierr); 1296 PetscFunctionReturn(0); 1297 } 1298 1299 static PetscErrorCode DMPlexDistributeSetupTree(DM dm, PetscSF migrationSF, ISLocalToGlobalMapping original, ISLocalToGlobalMapping renumbering, DM dmParallel) 1300 { 1301 DM_Plex *mesh = (DM_Plex*) dm->data; 1302 DM_Plex *pmesh = (DM_Plex*) (dmParallel)->data; 1303 MPI_Comm comm; 1304 DM refTree; 1305 PetscSection origParentSection, newParentSection; 1306 PetscInt *origParents, *origChildIDs; 1307 PetscBool flg; 1308 PetscErrorCode ierr; 1309 1310 PetscFunctionBegin; 1311 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1312 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 5); 1313 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1314 1315 /* Set up tree */ 1316 ierr = DMPlexGetReferenceTree(dm,&refTree);CHKERRQ(ierr); 1317 ierr = DMPlexSetReferenceTree(dmParallel,refTree);CHKERRQ(ierr); 1318 ierr = DMPlexGetTree(dm,&origParentSection,&origParents,&origChildIDs,NULL,NULL);CHKERRQ(ierr); 1319 if (origParentSection) { 1320 PetscInt pStart, pEnd; 1321 PetscInt *newParents, *newChildIDs, *globParents; 1322 PetscInt *remoteOffsetsParents, newParentSize; 1323 PetscSF parentSF; 1324 1325 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1326 ierr = PetscSectionCreate(PetscObjectComm((PetscObject)dmParallel),&newParentSection);CHKERRQ(ierr); 1327 ierr = PetscSectionSetChart(newParentSection,pStart,pEnd);CHKERRQ(ierr); 1328 ierr = PetscSFDistributeSection(migrationSF, origParentSection, &remoteOffsetsParents, newParentSection);CHKERRQ(ierr); 1329 ierr = PetscSFCreateSectionSF(migrationSF, origParentSection, remoteOffsetsParents, newParentSection, &parentSF);CHKERRQ(ierr); 1330 ierr = PetscFree(remoteOffsetsParents);CHKERRQ(ierr); 1331 ierr = PetscSectionGetStorageSize(newParentSection,&newParentSize);CHKERRQ(ierr); 1332 ierr = PetscMalloc2(newParentSize,&newParents,newParentSize,&newChildIDs);CHKERRQ(ierr); 1333 if (original) { 1334 PetscInt numParents; 1335 1336 ierr = PetscSectionGetStorageSize(origParentSection,&numParents);CHKERRQ(ierr); 1337 ierr = PetscMalloc1(numParents,&globParents);CHKERRQ(ierr); 1338 ierr = ISLocalToGlobalMappingApplyBlock(original, numParents, origParents, globParents);CHKERRQ(ierr); 1339 } 1340 else { 1341 globParents = origParents; 1342 } 1343 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, globParents, newParents);CHKERRQ(ierr); 1344 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, globParents, newParents);CHKERRQ(ierr); 1345 if (original) { 1346 ierr = PetscFree(globParents);CHKERRQ(ierr); 1347 } 1348 ierr = PetscSFBcastBegin(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1349 ierr = PetscSFBcastEnd(parentSF, MPIU_INT, origChildIDs, newChildIDs);CHKERRQ(ierr); 1350 ierr = ISGlobalToLocalMappingApplyBlock(renumbering,IS_GTOLM_MASK, newParentSize, newParents, NULL, newParents);CHKERRQ(ierr); 1351 #if PETSC_USE_DEBUG 1352 { 1353 PetscInt p; 1354 PetscBool valid = PETSC_TRUE; 1355 for (p = 0; p < newParentSize; ++p) { 1356 if (newParents[p] < 0) {valid = PETSC_FALSE; ierr = PetscPrintf(PETSC_COMM_SELF, "Point %d not in overlap SF\n", p);CHKERRQ(ierr);} 1357 } 1358 if (!valid) SETERRQ(PETSC_COMM_SELF, PETSC_ERR_ARG_OUTOFRANGE, "Invalid global to local map"); 1359 } 1360 #endif 1361 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-parents_view", &flg);CHKERRQ(ierr); 1362 if (flg) { 1363 ierr = PetscPrintf(comm, "Serial Parent Section: \n");CHKERRQ(ierr); 1364 ierr = PetscSectionView(origParentSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1365 ierr = PetscPrintf(comm, "Parallel Parent Section: \n");CHKERRQ(ierr); 1366 ierr = PetscSectionView(newParentSection, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1367 ierr = PetscSFView(parentSF, NULL);CHKERRQ(ierr); 1368 } 1369 ierr = DMPlexSetTree(dmParallel,newParentSection,newParents,newChildIDs);CHKERRQ(ierr); 1370 ierr = PetscSectionDestroy(&newParentSection);CHKERRQ(ierr); 1371 ierr = PetscFree2(newParents,newChildIDs);CHKERRQ(ierr); 1372 ierr = PetscSFDestroy(&parentSF);CHKERRQ(ierr); 1373 } 1374 pmesh->useAnchors = mesh->useAnchors; 1375 PetscFunctionReturn(0); 1376 } 1377 1378 PETSC_UNUSED static PetscErrorCode DMPlexDistributeSF(DM dm, PetscSF migrationSF, DM dmParallel) 1379 { 1380 PetscMPIInt rank, size; 1381 MPI_Comm comm; 1382 PetscErrorCode ierr; 1383 1384 PetscFunctionBegin; 1385 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1386 PetscValidHeaderSpecific(dmParallel, DM_CLASSID, 3); 1387 1388 /* Create point SF for parallel mesh */ 1389 ierr = PetscLogEventBegin(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1390 ierr = PetscObjectGetComm((PetscObject)dm, &comm);CHKERRQ(ierr); 1391 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1392 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1393 { 1394 const PetscInt *leaves; 1395 PetscSFNode *remotePoints, *rowners, *lowners; 1396 PetscInt numRoots, numLeaves, numGhostPoints = 0, p, gp, *ghostPoints; 1397 PetscInt pStart, pEnd; 1398 1399 ierr = DMPlexGetChart(dmParallel, &pStart, &pEnd);CHKERRQ(ierr); 1400 ierr = PetscSFGetGraph(migrationSF, &numRoots, &numLeaves, &leaves, NULL);CHKERRQ(ierr); 1401 ierr = PetscMalloc2(numRoots,&rowners,numLeaves,&lowners);CHKERRQ(ierr); 1402 for (p=0; p<numRoots; p++) { 1403 rowners[p].rank = -1; 1404 rowners[p].index = -1; 1405 } 1406 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1407 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1408 for (p = 0; p < numLeaves; ++p) { 1409 if (lowners[p].rank < 0 || lowners[p].rank == rank) { /* Either put in a bid or we know we own it */ 1410 lowners[p].rank = rank; 1411 lowners[p].index = leaves ? leaves[p] : p; 1412 } else if (lowners[p].rank >= 0) { /* Point already claimed so flag so that MAXLOC does not listen to us */ 1413 lowners[p].rank = -2; 1414 lowners[p].index = -2; 1415 } 1416 } 1417 for (p=0; p<numRoots; p++) { /* Root must not participate in the rediction, flag so that MAXLOC does not use */ 1418 rowners[p].rank = -3; 1419 rowners[p].index = -3; 1420 } 1421 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1422 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, lowners, rowners, MPI_MAXLOC);CHKERRQ(ierr); 1423 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1424 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rowners, lowners);CHKERRQ(ierr); 1425 for (p = 0; p < numLeaves; ++p) { 1426 if (lowners[p].rank < 0 || lowners[p].index < 0) SETERRQ(PETSC_COMM_SELF,PETSC_ERR_PLIB,"Cell partition corrupt: point not claimed"); 1427 if (lowners[p].rank != rank) ++numGhostPoints; 1428 } 1429 ierr = PetscMalloc1(numGhostPoints, &ghostPoints);CHKERRQ(ierr); 1430 ierr = PetscMalloc1(numGhostPoints, &remotePoints);CHKERRQ(ierr); 1431 for (p = 0, gp = 0; p < numLeaves; ++p) { 1432 if (lowners[p].rank != rank) { 1433 ghostPoints[gp] = leaves ? leaves[p] : p; 1434 remotePoints[gp].rank = lowners[p].rank; 1435 remotePoints[gp].index = lowners[p].index; 1436 ++gp; 1437 } 1438 } 1439 ierr = PetscFree2(rowners,lowners);CHKERRQ(ierr); 1440 ierr = PetscSFSetGraph((dmParallel)->sf, pEnd - pStart, numGhostPoints, ghostPoints, PETSC_OWN_POINTER, remotePoints, PETSC_OWN_POINTER);CHKERRQ(ierr); 1441 ierr = PetscSFSetFromOptions((dmParallel)->sf);CHKERRQ(ierr); 1442 } 1443 { 1444 PetscBool useCone, useClosure, useAnchors; 1445 1446 ierr = DMPlexGetAdjacencyUseCone(dm, &useCone);CHKERRQ(ierr); 1447 ierr = DMPlexGetAdjacencyUseClosure(dm, &useClosure);CHKERRQ(ierr); 1448 ierr = DMPlexGetAdjacencyUseAnchors(dm, &useAnchors);CHKERRQ(ierr); 1449 ierr = DMPlexSetAdjacencyUseCone(dmParallel, useCone);CHKERRQ(ierr); 1450 ierr = DMPlexSetAdjacencyUseClosure(dmParallel, useClosure);CHKERRQ(ierr); 1451 ierr = DMPlexSetAdjacencyUseAnchors(dmParallel, useAnchors);CHKERRQ(ierr); 1452 } 1453 ierr = PetscLogEventEnd(DMPLEX_DistributeSF,dm,0,0,0);CHKERRQ(ierr); 1454 PetscFunctionReturn(0); 1455 } 1456 1457 /*@C 1458 DMPlexDerivePointSF - Build a point SF from an SF describing a point migration 1459 1460 Input Parameter: 1461 + dm - The source DMPlex object 1462 . migrationSF - The star forest that describes the parallel point remapping 1463 . ownership - Flag causing a vote to determine point ownership 1464 1465 Output Parameter: 1466 - pointSF - The star forest describing the point overlap in the remapped DM 1467 1468 Level: developer 1469 1470 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1471 @*/ 1472 PetscErrorCode DMPlexCreatePointSF(DM dm, PetscSF migrationSF, PetscBool ownership, PetscSF *pointSF) 1473 { 1474 PetscMPIInt rank; 1475 PetscInt p, nroots, nleaves, idx, npointLeaves; 1476 PetscInt *pointLocal; 1477 const PetscInt *leaves; 1478 const PetscSFNode *roots; 1479 PetscSFNode *rootNodes, *leafNodes, *pointRemote; 1480 PetscErrorCode ierr; 1481 1482 PetscFunctionBegin; 1483 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1484 ierr = MPI_Comm_rank(PetscObjectComm((PetscObject) dm), &rank);CHKERRQ(ierr); 1485 1486 ierr = PetscSFGetGraph(migrationSF, &nroots, &nleaves, &leaves, &roots);CHKERRQ(ierr); 1487 ierr = PetscMalloc2(nroots, &rootNodes, nleaves, &leafNodes);CHKERRQ(ierr); 1488 if (ownership) { 1489 /* Point ownership vote: Process with highest rank ownes shared points */ 1490 for (p = 0; p < nleaves; ++p) { 1491 /* Either put in a bid or we know we own it */ 1492 leafNodes[p].rank = rank; 1493 leafNodes[p].index = p; 1494 } 1495 for (p = 0; p < nroots; p++) { 1496 /* Root must not participate in the reduction, flag so that MAXLOC does not use */ 1497 rootNodes[p].rank = -3; 1498 rootNodes[p].index = -3; 1499 } 1500 ierr = PetscSFReduceBegin(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);CHKERRQ(ierr); 1501 ierr = PetscSFReduceEnd(migrationSF, MPIU_2INT, leafNodes, rootNodes, MPI_MAXLOC);CHKERRQ(ierr); 1502 } else { 1503 for (p = 0; p < nroots; p++) { 1504 rootNodes[p].index = -1; 1505 rootNodes[p].rank = rank; 1506 }; 1507 for (p = 0; p < nleaves; p++) { 1508 /* Write new local id into old location */ 1509 if (roots[p].rank == rank) { 1510 rootNodes[roots[p].index].index = leaves ? leaves[p] : p; 1511 } 1512 } 1513 } 1514 ierr = PetscSFBcastBegin(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1515 ierr = PetscSFBcastEnd(migrationSF, MPIU_2INT, rootNodes, leafNodes);CHKERRQ(ierr); 1516 1517 for (npointLeaves = 0, p = 0; p < nleaves; p++) {if (leafNodes[p].rank != rank) npointLeaves++;} 1518 ierr = PetscMalloc1(npointLeaves, &pointLocal);CHKERRQ(ierr); 1519 ierr = PetscMalloc1(npointLeaves, &pointRemote);CHKERRQ(ierr); 1520 for (idx = 0, p = 0; p < nleaves; p++) { 1521 if (leafNodes[p].rank != rank) { 1522 pointLocal[idx] = p; 1523 pointRemote[idx] = leafNodes[p]; 1524 idx++; 1525 } 1526 } 1527 ierr = PetscSFCreate(PetscObjectComm((PetscObject) dm), pointSF);CHKERRQ(ierr); 1528 ierr = PetscSFSetFromOptions(*pointSF);CHKERRQ(ierr); 1529 ierr = PetscSFSetGraph(*pointSF, nleaves, npointLeaves, pointLocal, PETSC_OWN_POINTER, pointRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1530 ierr = PetscFree2(rootNodes, leafNodes);CHKERRQ(ierr); 1531 PetscFunctionReturn(0); 1532 } 1533 1534 /*@C 1535 DMPlexMigrate - Migrates internal DM data over the supplied star forest 1536 1537 Input Parameter: 1538 + dm - The source DMPlex object 1539 . sf - The star forest communication context describing the migration pattern 1540 1541 Output Parameter: 1542 - targetDM - The target DMPlex object 1543 1544 Level: intermediate 1545 1546 .seealso: DMPlexDistribute(), DMPlexDistributeOverlap() 1547 @*/ 1548 PetscErrorCode DMPlexMigrate(DM dm, PetscSF sf, DM targetDM) 1549 { 1550 MPI_Comm comm; 1551 PetscInt dim, nroots; 1552 PetscSF sfPoint; 1553 ISLocalToGlobalMapping ltogMigration; 1554 ISLocalToGlobalMapping ltogOriginal = NULL; 1555 PetscBool flg; 1556 PetscErrorCode ierr; 1557 1558 PetscFunctionBegin; 1559 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1560 ierr = PetscLogEventBegin(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1561 ierr = PetscObjectGetComm((PetscObject) dm, &comm);CHKERRQ(ierr); 1562 ierr = DMGetDimension(dm, &dim);CHKERRQ(ierr); 1563 ierr = DMSetDimension(targetDM, dim);CHKERRQ(ierr); 1564 1565 /* Check for a one-to-all distribution pattern */ 1566 ierr = DMGetPointSF(dm, &sfPoint);CHKERRQ(ierr); 1567 ierr = PetscSFGetGraph(sfPoint, &nroots, NULL, NULL, NULL);CHKERRQ(ierr); 1568 if (nroots >= 0) { 1569 IS isOriginal; 1570 PetscInt n, size, nleaves; 1571 PetscInt *numbering_orig, *numbering_new; 1572 /* Get the original point numbering */ 1573 ierr = DMPlexCreatePointNumbering(dm, &isOriginal);CHKERRQ(ierr); 1574 ierr = ISLocalToGlobalMappingCreateIS(isOriginal, <ogOriginal);CHKERRQ(ierr); 1575 ierr = ISLocalToGlobalMappingGetSize(ltogOriginal, &size);CHKERRQ(ierr); 1576 ierr = ISLocalToGlobalMappingGetBlockIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1577 /* Convert to positive global numbers */ 1578 for (n=0; n<size; n++) {if (numbering_orig[n] < 0) numbering_orig[n] = -(numbering_orig[n]+1);} 1579 /* Derive the new local-to-global mapping from the old one */ 1580 ierr = PetscSFGetGraph(sf, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1581 ierr = PetscMalloc1(nleaves, &numbering_new);CHKERRQ(ierr); 1582 ierr = PetscSFBcastBegin(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);CHKERRQ(ierr); 1583 ierr = PetscSFBcastEnd(sf, MPIU_INT, (PetscInt *) numbering_orig, numbering_new);CHKERRQ(ierr); 1584 ierr = ISLocalToGlobalMappingCreate(comm, 1, nleaves, (const PetscInt*) numbering_new, PETSC_OWN_POINTER, <ogMigration);CHKERRQ(ierr); 1585 ierr = ISLocalToGlobalMappingRestoreIndices(ltogOriginal, (const PetscInt**)&numbering_orig);CHKERRQ(ierr); 1586 ierr = ISDestroy(&isOriginal);CHKERRQ(ierr); 1587 } else { 1588 /* One-to-all distribution pattern: We can derive LToG from SF */ 1589 ierr = ISLocalToGlobalMappingCreateSF(sf, 0, <ogMigration);CHKERRQ(ierr); 1590 } 1591 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1592 if (flg) { 1593 ierr = PetscPrintf(comm, "Point renumbering for DM migration:\n");CHKERRQ(ierr); 1594 ierr = ISLocalToGlobalMappingView(ltogMigration, NULL);CHKERRQ(ierr); 1595 } 1596 /* Migrate DM data to target DM */ 1597 ierr = DMPlexDistributeCones(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1598 ierr = DMPlexDistributeLabels(dm, sf, targetDM);CHKERRQ(ierr); 1599 ierr = DMPlexDistributeCoordinates(dm, sf, targetDM);CHKERRQ(ierr); 1600 ierr = DMPlexDistributeSetupHybrid(dm, sf, ltogMigration, targetDM);CHKERRQ(ierr); 1601 ierr = DMPlexDistributeSetupTree(dm, sf, ltogOriginal, ltogMigration, targetDM);CHKERRQ(ierr); 1602 ierr = ISLocalToGlobalMappingDestroy(<ogOriginal);CHKERRQ(ierr); 1603 ierr = ISLocalToGlobalMappingDestroy(<ogMigration);CHKERRQ(ierr); 1604 ierr = PetscLogEventEnd(DMPLEX_Migrate, dm, 0, 0, 0);CHKERRQ(ierr); 1605 PetscFunctionReturn(0); 1606 } 1607 1608 /*@C 1609 DMPlexDistribute - Distributes the mesh and any associated sections. 1610 1611 Not Collective 1612 1613 Input Parameter: 1614 + dm - The original DMPlex object 1615 - overlap - The overlap of partitions, 0 is the default 1616 1617 Output Parameter: 1618 + sf - The PetscSF used for point distribution 1619 - parallelMesh - The distributed DMPlex object, or NULL 1620 1621 Note: If the mesh was not distributed, the return value is NULL. 1622 1623 The user can control the definition of adjacency for the mesh using DMPlexSetAdjacencyUseCone() and 1624 DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function 1625 representation on the mesh. 1626 1627 Level: intermediate 1628 1629 .keywords: mesh, elements 1630 .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure() 1631 @*/ 1632 PetscErrorCode DMPlexDistribute(DM dm, PetscInt overlap, PetscSF *sf, DM *dmParallel) 1633 { 1634 MPI_Comm comm; 1635 PetscPartitioner partitioner; 1636 IS cellPart; 1637 PetscSection cellPartSection; 1638 DM dmCoord; 1639 DMLabel lblPartition, lblMigration; 1640 PetscSF sfProcess, sfMigration, sfStratified, sfPoint; 1641 PetscBool flg; 1642 PetscMPIInt rank, size, p; 1643 PetscErrorCode ierr; 1644 1645 PetscFunctionBegin; 1646 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1647 if (sf) PetscValidPointer(sf,4); 1648 PetscValidPointer(dmParallel,5); 1649 1650 if (sf) *sf = NULL; 1651 *dmParallel = NULL; 1652 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1653 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1654 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1655 if (size == 1) PetscFunctionReturn(0); 1656 1657 ierr = PetscLogEventBegin(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1658 /* Create cell partition */ 1659 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1660 ierr = PetscSectionCreate(comm, &cellPartSection);CHKERRQ(ierr); 1661 ierr = DMPlexGetPartitioner(dm, &partitioner);CHKERRQ(ierr); 1662 ierr = PetscPartitionerPartition(partitioner, dm, cellPartSection, &cellPart);CHKERRQ(ierr); 1663 { 1664 /* Convert partition to DMLabel */ 1665 PetscInt proc, pStart, pEnd, npoints, poffset; 1666 const PetscInt *points; 1667 ierr = DMLabelCreate("Point Partition", &lblPartition);CHKERRQ(ierr); 1668 ierr = ISGetIndices(cellPart, &points);CHKERRQ(ierr); 1669 ierr = PetscSectionGetChart(cellPartSection, &pStart, &pEnd);CHKERRQ(ierr); 1670 for (proc = pStart; proc < pEnd; proc++) { 1671 ierr = PetscSectionGetDof(cellPartSection, proc, &npoints);CHKERRQ(ierr); 1672 ierr = PetscSectionGetOffset(cellPartSection, proc, &poffset);CHKERRQ(ierr); 1673 for (p = poffset; p < poffset+npoints; p++) { 1674 ierr = DMLabelSetValue(lblPartition, points[p], proc);CHKERRQ(ierr); 1675 } 1676 } 1677 ierr = ISRestoreIndices(cellPart, &points);CHKERRQ(ierr); 1678 } 1679 ierr = DMPlexPartitionLabelClosure(dm, lblPartition);CHKERRQ(ierr); 1680 { 1681 /* Build a global process SF */ 1682 PetscSFNode *remoteProc; 1683 ierr = PetscMalloc1(size, &remoteProc);CHKERRQ(ierr); 1684 for (p = 0; p < size; ++p) { 1685 remoteProc[p].rank = p; 1686 remoteProc[p].index = rank; 1687 } 1688 ierr = PetscSFCreate(comm, &sfProcess);CHKERRQ(ierr); 1689 ierr = PetscObjectSetName((PetscObject) sfProcess, "Process SF");CHKERRQ(ierr); 1690 ierr = PetscSFSetGraph(sfProcess, size, size, NULL, PETSC_OWN_POINTER, remoteProc, PETSC_OWN_POINTER);CHKERRQ(ierr); 1691 } 1692 ierr = DMLabelCreate("Point migration", &lblMigration);CHKERRQ(ierr); 1693 ierr = DMPlexPartitionLabelInvert(dm, lblPartition, sfProcess, lblMigration);CHKERRQ(ierr); 1694 ierr = DMPlexPartitionLabelCreateSF(dm, lblMigration, &sfMigration);CHKERRQ(ierr); 1695 /* Stratify the SF in case we are migrating an already parallel plex */ 1696 ierr = DMPlexStratifyMigrationSF(dm, sfMigration, &sfStratified);CHKERRQ(ierr); 1697 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1698 sfMigration = sfStratified; 1699 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1700 ierr = PetscOptionsHasName(((PetscObject) dm)->options,((PetscObject) dm)->prefix, "-partition_view", &flg);CHKERRQ(ierr); 1701 if (flg) { 1702 ierr = DMLabelView(lblPartition, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1703 ierr = PetscSFView(sfMigration, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr); 1704 } 1705 1706 /* Create non-overlapping parallel DM and migrate internal data */ 1707 ierr = DMPlexCreate(comm, dmParallel);CHKERRQ(ierr); 1708 ierr = PetscObjectSetName((PetscObject) *dmParallel, "Parallel Mesh");CHKERRQ(ierr); 1709 ierr = DMPlexMigrate(dm, sfMigration, *dmParallel);CHKERRQ(ierr); 1710 1711 /* Build the point SF without overlap */ 1712 ierr = DMPlexCreatePointSF(*dmParallel, sfMigration, PETSC_TRUE, &sfPoint);CHKERRQ(ierr); 1713 ierr = DMSetPointSF(*dmParallel, sfPoint);CHKERRQ(ierr); 1714 ierr = DMGetCoordinateDM(*dmParallel, &dmCoord);CHKERRQ(ierr); 1715 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1716 if (flg) {ierr = PetscSFView(sfPoint, PETSC_VIEWER_STDOUT_WORLD);CHKERRQ(ierr);} 1717 1718 if (overlap > 0) { 1719 DM dmOverlap; 1720 PetscInt nroots, nleaves; 1721 PetscSFNode *newRemote; 1722 const PetscSFNode *oldRemote; 1723 PetscSF sfOverlap, sfOverlapPoint; 1724 /* Add the partition overlap to the distributed DM */ 1725 ierr = DMPlexDistributeOverlap(*dmParallel, overlap, &sfOverlap, &dmOverlap);CHKERRQ(ierr); 1726 ierr = DMDestroy(dmParallel);CHKERRQ(ierr); 1727 *dmParallel = dmOverlap; 1728 if (flg) { 1729 ierr = PetscPrintf(comm, "Overlap Migration SF:\n");CHKERRQ(ierr); 1730 ierr = PetscSFView(sfOverlap, NULL);CHKERRQ(ierr); 1731 } 1732 1733 /* Re-map the migration SF to establish the full migration pattern */ 1734 ierr = PetscSFGetGraph(sfMigration, &nroots, NULL, NULL, &oldRemote);CHKERRQ(ierr); 1735 ierr = PetscSFGetGraph(sfOverlap, NULL, &nleaves, NULL, NULL);CHKERRQ(ierr); 1736 ierr = PetscMalloc1(nleaves, &newRemote);CHKERRQ(ierr); 1737 ierr = PetscSFBcastBegin(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1738 ierr = PetscSFBcastEnd(sfOverlap, MPIU_2INT, oldRemote, newRemote);CHKERRQ(ierr); 1739 ierr = PetscSFCreate(comm, &sfOverlapPoint);CHKERRQ(ierr); 1740 ierr = PetscSFSetGraph(sfOverlapPoint, nroots, nleaves, NULL, PETSC_OWN_POINTER, newRemote, PETSC_OWN_POINTER);CHKERRQ(ierr); 1741 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1742 ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr); 1743 sfMigration = sfOverlapPoint; 1744 } 1745 /* Cleanup Partition */ 1746 ierr = PetscSFDestroy(&sfProcess);CHKERRQ(ierr); 1747 ierr = DMLabelDestroy(&lblPartition);CHKERRQ(ierr); 1748 ierr = DMLabelDestroy(&lblMigration);CHKERRQ(ierr); 1749 ierr = PetscSectionDestroy(&cellPartSection);CHKERRQ(ierr); 1750 ierr = ISDestroy(&cellPart);CHKERRQ(ierr); 1751 /* Copy BC */ 1752 ierr = DMCopyBoundary(dm, *dmParallel);CHKERRQ(ierr); 1753 /* Create sfNatural */ 1754 if (dm->useNatural) { 1755 PetscSection section; 1756 1757 ierr = DMGetDefaultSection(dm, §ion);CHKERRQ(ierr); 1758 ierr = DMPlexCreateGlobalToNaturalSF(*dmParallel, section, sfMigration, &(*dmParallel)->sfNatural);CHKERRQ(ierr); 1759 ierr = DMSetUseNatural(*dmParallel, PETSC_TRUE);CHKERRQ(ierr); 1760 } 1761 /* Cleanup */ 1762 if (sf) {*sf = sfMigration;} 1763 else {ierr = PetscSFDestroy(&sfMigration);CHKERRQ(ierr);} 1764 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1765 ierr = PetscLogEventEnd(DMPLEX_Distribute,dm,0,0,0);CHKERRQ(ierr); 1766 PetscFunctionReturn(0); 1767 } 1768 1769 /*@C 1770 DMPlexDistributeOverlap - Add partition overlap to a distributed non-overlapping DM. 1771 1772 Not Collective 1773 1774 Input Parameter: 1775 + dm - The non-overlapping distrbuted DMPlex object 1776 - overlap - The overlap of partitions 1777 1778 Output Parameter: 1779 + sf - The PetscSF used for point distribution 1780 - dmOverlap - The overlapping distributed DMPlex object, or NULL 1781 1782 Note: If the mesh was not distributed, the return value is NULL. 1783 1784 The user can control the definition of adjacency for the mesh using DMPlexGetAdjacencyUseCone() and 1785 DMPlexSetAdjacencyUseClosure(). They should choose the combination appropriate for the function 1786 representation on the mesh. 1787 1788 Level: intermediate 1789 1790 .keywords: mesh, elements 1791 .seealso: DMPlexCreate(), DMPlexDistributeByFace(), DMPlexSetAdjacencyUseCone(), DMPlexSetAdjacencyUseClosure() 1792 @*/ 1793 PetscErrorCode DMPlexDistributeOverlap(DM dm, PetscInt overlap, PetscSF *sf, DM *dmOverlap) 1794 { 1795 MPI_Comm comm; 1796 PetscMPIInt size, rank; 1797 PetscSection rootSection, leafSection; 1798 IS rootrank, leafrank; 1799 DM dmCoord; 1800 DMLabel lblOverlap; 1801 PetscSF sfOverlap, sfStratified, sfPoint; 1802 PetscErrorCode ierr; 1803 1804 PetscFunctionBegin; 1805 PetscValidHeaderSpecific(dm, DM_CLASSID, 1); 1806 if (sf) PetscValidPointer(sf, 3); 1807 PetscValidPointer(dmOverlap, 4); 1808 1809 if (sf) *sf = NULL; 1810 *dmOverlap = NULL; 1811 ierr = PetscObjectGetComm((PetscObject)dm,&comm);CHKERRQ(ierr); 1812 ierr = MPI_Comm_size(comm, &size);CHKERRQ(ierr); 1813 ierr = MPI_Comm_rank(comm, &rank);CHKERRQ(ierr); 1814 if (size == 1) PetscFunctionReturn(0); 1815 1816 ierr = PetscLogEventBegin(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1817 /* Compute point overlap with neighbouring processes on the distributed DM */ 1818 ierr = PetscLogEventBegin(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1819 ierr = PetscSectionCreate(comm, &rootSection);CHKERRQ(ierr); 1820 ierr = PetscSectionCreate(comm, &leafSection);CHKERRQ(ierr); 1821 ierr = DMPlexDistributeOwnership(dm, rootSection, &rootrank, leafSection, &leafrank);CHKERRQ(ierr); 1822 ierr = DMPlexCreateOverlap(dm, overlap, rootSection, rootrank, leafSection, leafrank, &lblOverlap);CHKERRQ(ierr); 1823 /* Convert overlap label to stratified migration SF */ 1824 ierr = DMPlexPartitionLabelCreateSF(dm, lblOverlap, &sfOverlap);CHKERRQ(ierr); 1825 ierr = DMPlexStratifyMigrationSF(dm, sfOverlap, &sfStratified);CHKERRQ(ierr); 1826 ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr); 1827 sfOverlap = sfStratified; 1828 ierr = PetscObjectSetName((PetscObject) sfOverlap, "Overlap SF");CHKERRQ(ierr); 1829 ierr = PetscSFSetFromOptions(sfOverlap);CHKERRQ(ierr); 1830 1831 ierr = PetscSectionDestroy(&rootSection);CHKERRQ(ierr); 1832 ierr = PetscSectionDestroy(&leafSection);CHKERRQ(ierr); 1833 ierr = ISDestroy(&rootrank);CHKERRQ(ierr); 1834 ierr = ISDestroy(&leafrank);CHKERRQ(ierr); 1835 ierr = PetscLogEventEnd(DMPLEX_Partition,dm,0,0,0);CHKERRQ(ierr); 1836 1837 /* Build the overlapping DM */ 1838 ierr = DMPlexCreate(comm, dmOverlap);CHKERRQ(ierr); 1839 ierr = PetscObjectSetName((PetscObject) *dmOverlap, "Parallel Mesh");CHKERRQ(ierr); 1840 ierr = DMPlexMigrate(dm, sfOverlap, *dmOverlap);CHKERRQ(ierr); 1841 /* Build the new point SF */ 1842 ierr = DMPlexCreatePointSF(*dmOverlap, sfOverlap, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1843 ierr = DMSetPointSF(*dmOverlap, sfPoint);CHKERRQ(ierr); 1844 ierr = DMGetCoordinateDM(*dmOverlap, &dmCoord);CHKERRQ(ierr); 1845 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1846 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1847 /* Cleanup overlap partition */ 1848 ierr = DMLabelDestroy(&lblOverlap);CHKERRQ(ierr); 1849 if (sf) *sf = sfOverlap; 1850 else {ierr = PetscSFDestroy(&sfOverlap);CHKERRQ(ierr);} 1851 ierr = PetscLogEventEnd(DMPLEX_DistributeOverlap, dm, 0, 0, 0);CHKERRQ(ierr); 1852 PetscFunctionReturn(0); 1853 } 1854 1855 /*@C 1856 DMPlexGetGatherDM - Get a copy of the DMPlex that gathers all points on the 1857 root process of the original's communicator. 1858 1859 Input Parameters: 1860 . dm - the original DMPlex object 1861 1862 Output Parameters: 1863 . gatherMesh - the gathered DM object, or NULL 1864 1865 Level: intermediate 1866 1867 .keywords: mesh 1868 .seealso: DMPlexDistribute(), DMPlexGetRedundantDM() 1869 @*/ 1870 PetscErrorCode DMPlexGetGatherDM(DM dm, DM *gatherMesh) 1871 { 1872 MPI_Comm comm; 1873 PetscMPIInt size; 1874 PetscPartitioner oldPart, gatherPart; 1875 PetscErrorCode ierr; 1876 1877 PetscFunctionBegin; 1878 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1879 PetscValidPointer(gatherMesh,2); 1880 *gatherMesh = NULL; 1881 comm = PetscObjectComm((PetscObject)dm); 1882 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1883 if (size == 1) PetscFunctionReturn(0); 1884 ierr = DMPlexGetPartitioner(dm,&oldPart);CHKERRQ(ierr); 1885 ierr = PetscObjectReference((PetscObject)oldPart);CHKERRQ(ierr); 1886 ierr = PetscPartitionerCreate(comm,&gatherPart);CHKERRQ(ierr); 1887 ierr = PetscPartitionerSetType(gatherPart,PETSCPARTITIONERGATHER);CHKERRQ(ierr); 1888 ierr = DMPlexSetPartitioner(dm,gatherPart);CHKERRQ(ierr); 1889 ierr = DMPlexDistribute(dm,0,NULL,gatherMesh);CHKERRQ(ierr); 1890 ierr = DMPlexSetPartitioner(dm,oldPart);CHKERRQ(ierr); 1891 ierr = PetscPartitionerDestroy(&gatherPart);CHKERRQ(ierr); 1892 ierr = PetscPartitionerDestroy(&oldPart);CHKERRQ(ierr); 1893 PetscFunctionReturn(0); 1894 } 1895 1896 /*@C 1897 DMPlexGetRedundantDM - Get a copy of the DMPlex that is completely copied on each process. 1898 1899 Input Parameters: 1900 . dm - the original DMPlex object 1901 1902 Output Parameters: 1903 . redundantMesh - the redundant DM object, or NULL 1904 1905 Level: intermediate 1906 1907 .keywords: mesh 1908 .seealso: DMPlexDistribute(), DMPlexGetGatherDM() 1909 @*/ 1910 PetscErrorCode DMPlexGetRedundantDM(DM dm, DM *redundantMesh) 1911 { 1912 MPI_Comm comm; 1913 PetscMPIInt size, rank; 1914 PetscInt pStart, pEnd, p; 1915 PetscInt numPoints = -1; 1916 PetscSF migrationSF, sfPoint; 1917 DM gatherDM, dmCoord; 1918 PetscSFNode *points; 1919 PetscErrorCode ierr; 1920 1921 PetscFunctionBegin; 1922 PetscValidHeaderSpecific(dm,DM_CLASSID,1); 1923 PetscValidPointer(redundantMesh,2); 1924 *redundantMesh = NULL; 1925 comm = PetscObjectComm((PetscObject)dm); 1926 ierr = MPI_Comm_size(comm,&size);CHKERRQ(ierr); 1927 if (size == 1) { 1928 ierr = PetscObjectReference((PetscObject) dm);CHKERRQ(ierr); 1929 *redundantMesh = dm; 1930 PetscFunctionReturn(0); 1931 } 1932 ierr = DMPlexGetGatherDM(dm,&gatherDM);CHKERRQ(ierr); 1933 if (!gatherDM) PetscFunctionReturn(0); 1934 ierr = MPI_Comm_rank(comm,&rank);CHKERRQ(ierr); 1935 ierr = DMPlexGetChart(gatherDM,&pStart,&pEnd);CHKERRQ(ierr); 1936 numPoints = pEnd - pStart; 1937 ierr = MPI_Bcast(&numPoints,1,MPIU_INT,0,comm);CHKERRQ(ierr); 1938 ierr = PetscMalloc1(numPoints,&points);CHKERRQ(ierr); 1939 ierr = PetscSFCreate(comm,&migrationSF);CHKERRQ(ierr); 1940 for (p = 0; p < numPoints; p++) { 1941 points[p].index = p; 1942 points[p].rank = 0; 1943 } 1944 ierr = PetscSFSetGraph(migrationSF,pEnd-pStart,numPoints,NULL,PETSC_OWN_POINTER,points,PETSC_OWN_POINTER);CHKERRQ(ierr); 1945 ierr = DMPlexCreate(comm, redundantMesh);CHKERRQ(ierr); 1946 ierr = PetscObjectSetName((PetscObject) *redundantMesh, "Redundant Mesh");CHKERRQ(ierr); 1947 ierr = DMPlexMigrate(gatherDM, migrationSF, *redundantMesh);CHKERRQ(ierr); 1948 ierr = DMPlexCreatePointSF(*redundantMesh, migrationSF, PETSC_FALSE, &sfPoint);CHKERRQ(ierr); 1949 ierr = DMSetPointSF(*redundantMesh, sfPoint);CHKERRQ(ierr); 1950 ierr = DMGetCoordinateDM(*redundantMesh, &dmCoord);CHKERRQ(ierr); 1951 if (dmCoord) {ierr = DMSetPointSF(dmCoord, sfPoint);CHKERRQ(ierr);} 1952 ierr = PetscSFDestroy(&sfPoint);CHKERRQ(ierr); 1953 ierr = PetscSFDestroy(&migrationSF);CHKERRQ(ierr); 1954 ierr = DMDestroy(&gatherDM);CHKERRQ(ierr); 1955 PetscFunctionReturn(0); 1956 } 1957